bbella: Theoretical origin of life (Introduction)

by David Turell @, Saturday, April 20, 2013, 15:30 (4014 days ago)

? before the Earth was formed?-"The two researchers acknowledge their ideas are more of a "thought exercise" than a theory proposal, but at the same time suggest their calculations ought to be taken seriously. They start with the idea of genetic complexity doubling every 376 million years—working backwards, they say, means that life first came about almost 10 billion years ago, which of course predates the creation of Earth itself. Most scientists agree the Earth formed just 4.5 billion years ago. Assuming that Moore's Law does apply to biological complexity, this would suggest that life began somewhere other than on Earth and migrated here."-"This cosmic time scale for the evolution of life has important consequences: life took ca. 5 billion years to reach the complexity of bacteria; the environments in which life originated and evolved to the prokaryote stage may have been quite different from those envisaged on Earth; there was no intelligent life in our universe prior to the origin of Earth, thus Earth could not have been deliberately seeded with life by intelligent aliens; Earth was seeded by panspermia; experimental replication of the origin of life from scratch may have to emulate many cumulative rare events; and the Drake equation for guesstimating the number of civilizations in the universe is likely wrong, as intelligent life has just begun appearing in our universe. Evolution of advanced organisms has accelerated via development of additional information-processing systems: epigenetic memory, primitive mind, multicellular brain, language, books, computers, and Internet".- Read more at: http://phys.org/news/2013-04-law-life-began-earth.html#jCp

bbella: Theoretical origin of life

by David Turell @, Saturday, April 27, 2013, 18:27 (4007 days ago) @ David Turell

? before the Earth was formed?
> 
> "The two researchers acknowledge their ideas are more of a "thought exercise" than a theory proposal, but at the same time suggest their calculations ought to be taken seriously. They start with the idea of genetic complexity doubling every 376 million years—working backwards, they say, means that life first came about almost 10 billion years ago, which of course predates the creation of Earth itself. Most scientists agree the Earth formed just 4.5 billion years ago. Assuming that Moore's Law does apply to biological complexity, this would suggest that life began somewhere other than on Earth and migrated here."-Matt Ridley reviews (WSJ) this discussion. Same old problem: "Does that mean life is common? No. We still don't know if it's very easy or very hard for life to emerge from nonlife even in the right conditions". Ridley avoids the obvious from 60 years of research. Life is extremely hard to get started as a large group of intellects in various labs have shown.-http://online.wsj.com/article/SB10001424127887324874204578438701489800128.html-Panspermia solves nothing. It just removes the origin of life problem to outer space.

Theoretical origin of life

by David Turell @, Thursday, February 13, 2014, 15:33 (3715 days ago) @ David Turell

A new conference to review what we don't know; how to create life from non-life:-"The scientific question about the origin of life is still unanswered: it is still one of the great mystery that science is facing. We all accept the 1924 idea of Oparin, according to which life originated from the inanimate matter through a long series of step of increasing molecular complexity and functionality. The real mile stone came 1953 with Stanley Miller flask experiments, showing that amino acids can be formed under prebiotic conditions from a mixture of gas presumably present in the prebiotic atmosphere. Which conceptual progress have we made since then? It is too much to say that we didn't really make any, if we look at data under really and honest prebiotic conditions?
 Adding that this situation is not due to shortage of means and finances in the field- but to a real lack of difficulty to conceive conceptually how this nonliving-living passage really took place?
 
"This is perhaps a too provocative way to introduce the OQOL workshop which will take place at the IIAS (International Institute for Advanced Studies) of Japan and July 12-13, 2014. In fact, while the larger ISSOL meeting should shed light on the new results and progress, the purpose of the OQOL workshop is to indicate instead the shadowy, un-answered aspects of the field. To what extent is this due to the fact that the perhaps the right questions have not been asked, or pursued experimentally? For example: how to make ordered macromolecular sequences in many identical copies under prebiotic conditions? How do you go from a prebiotic chemical scenario containing only ten basic amino acids to a first form of biochemical metabolism? How do you go from the chemistry of reactions under thermodynamic control (production of the Miller' amino acids) to the chemistry of kinetic control- which necessitates catalysts? Did the hypothesis of the prebiotic RNA-world produce any significant fact for understanding the origin of life?"(my bold)-http://www.lifephys.dis.titech.ac.jp/oqol2014/

Theoretical origin of life

by David Turell @, Thursday, February 20, 2014, 01:20 (3709 days ago) @ David Turell

Why it seems to be a miracle:-http://www.evolutionnews.org/2014/02/can_all_the_num082101.html

Theoretical origin of life

by David Turell @, Tuesday, February 25, 2014, 15:37 (3703 days ago) @ David Turell

Using crystals which have a static organization pattern is not a way to create life. This report is a stretch of someone's imagination. Valid research, poor thinking and reporting:-http://www.sciencedaily.com/releases/2014/02/140224171700.htm

Theoretical origin of life: RNA

by David Turell @, Tuesday, March 04, 2014, 00:16 (3697 days ago) @ David Turell

A good review of all the hopeful approaches: lots of wishful thinking.-http://www.the-scientist.com/?articles.view/articleNo/39252/title/RNA-World-2-0/

Theoretical origin of life: overview

by David Turell @, Tuesday, March 04, 2014, 00:24 (3697 days ago) @ David Turell

More approaches:-http://www.the-scientist.com/?articles.view/articleNo/39192/title/Let-There-Be-Life/-Life got complex very early. How?-"Sitting at the base of the three-domain tree is our last universal common ancestor (LUCA). What researchers can say today about the makeup of LUCA is a direct result of the availability of gene sequences from so many species. Aaron Goldman writes that "LUCA is not [Darwin's] 'primordial form,' but rather a sophisticated cellular organism that, if alive today, would probably be difficult to distinguish from other extant bacteria or archaea.'"

bbella: Theoretical origin of life

by David Turell @, Saturday, February 14, 2015, 18:21 (3349 days ago) @ David Turell

Note this new article re organic forms in space as a possible start to life on Earth.-http://journalofcosmology.com/JOC24/Tok_Pans_Paper_1-3.pdf-“The point of view we have developed so far implies that the essential biochemical
requirements of life exist in very large quantities within the dense interstellar clouds of gas, the so called molecular clouds. This material became deposited within the solar system, first in comet-type bodies, and then in the collisions of such bodies with the Earth. We might think of the Earth as having become infected with life-forming materials"

Theoretical origin of life: nireogen fixation

by David Turell @, Wednesday, February 18, 2015, 22:11 (3345 days ago) @ David Turell

Life must fix nitrogen from the atmosphere to form living matter:-"Past genetic analysis of nitrogen-fixing enzymes, which would have been produced by the microbes, placed their origin at between 2.2 billion and 1.5 billion years ago. Now, scientists looking at some of the planet's oldest rocks have found evidence that life was already practicing nitrogen fixation about 3.2 billion years ago, nearly three-quarters of the way back to the birth of the planet. [Photo Timeline: The Birth of Planet Earth]-"It is fascinating to imagine that this complex metabolic process has been operating on the Earth for over 3 billion years," lead study author Eva Stüeken, a geobiologist at the University of Washington in Seattle, told Live Science."-"Chemical analysis of the rocks suggests that nitrogen was being fixed by the most common of the three kinds of nitrogen-fixing enzymes that exist nowadays — an enzyme that contains the element molybdenum.-"Molybdenum is now abundant because oxygen reacts with rocks to convert molybdenum into a soluble form that can wash into the ocean. However, its source on the ancient, oxygen-poor Earth, is uncertain. The researchers suggested that their findings may be evidence that some early life may have existed as single-celled layers on land. Those microbes would have emitted small amounts of oxygen as a byproduct when they broke down nitrogen, the researchers said. Then, the emitted oxygen would have reacted with any molybdenum in the rock, thus helping to release the element into the water."-
http://www.livescience.com/49850-microbes-on-early-earth.html?cmpid=559085

Theoretical origin of life; new theory

by David Turell @, Saturday, June 14, 2014, 18:56 (3594 days ago) @ David Turell

Using hydrothermal vents and energy exchanged with hydrogen, ATP, CO2, etc.:-http://phys.org/news/2014-06-energetic-life.html

Theoretical origin of life; Koonen's odds against

by David Turell @, Saturday, February 21, 2015, 15:06 (3342 days ago) @ David Turell

&quot;at least one RNA encoding a replicase, ~500 nucleotides (low bound)is required. In the above notation, n = 1800, resulting in E <10-1018-&quot;In other words, even in this toy model that assumes a deliberately inflated rate of RNA production, the probability that a coupled translation-replication emerges by chance in a single O-region is P ^ 10-1018. Obviously, this version of the breakthrough stage can be considered only in the context of a universe with an infinite (or, in the very least, extremely vast) number of O-regions. -&quot;The model considered here is not supposed to be realistic by any account. It only serves to illustrate the difference in the demands on chance for the origin of different versions of the breakthrough system (see Fig. 1) and hence the connections between these versions and different cosmological models of the universe.&quot; -http://www.biologydirect.com/content/2/1/15-Eugene Koonen is a highly respected scientist. He obviously put this in the appendix as a back-of-the-cuff estimate.

Theoretical origin of life; Koonen's odds against

by dhw, Saturday, February 21, 2015, 18:01 (3342 days ago) @ David Turell

DAVID: QUOTE: &quot;...at least one RNA encoding a replicase, ~500 nucleotides (low bound)is required. In the above notation, n = 1800, resulting in E <10-1018&#13;&#10;&quot;In other words, even in this toy model that assumes a deliberately inflated rate of RNA production, the probability that a coupled translation-replication emerges by chance in a single O-region is P ^ 10-1018. Obviously, this version of the breakthrough stage can be considered only in the context of a universe with an infinite (or, in the very least, extremely vast) number of O-regions. &#13;&#10;&quot;The model considered here is not supposed to be realistic by any account. It only serves to illustrate the difference in the demands on chance for the origin of different versions of the breakthrough system (see Fig. 1) and hence the connections between these versions and different cosmological models of the universe.&quot; -http://www.biologydirect.com/content/2/1/15-Eugene Koonen is a highly respected scientist. He obviously put this in the appendix as a back-of-the-cuff estimate.-And I assume you have quoted it as evidence against chance. From my position on the fence, I accept the reasonableness of your argument. However, unless I have badly misunderstood his article, this highly respected scientist appears to adopt the opposite view to yours:-QUOTE: &#147;Recent developments in cosmology radically change the conception of the universe as well as the very notions of &quot;probable&quot; and &quot;possible&quot;. The model of eternal inflation implies that all macroscopic histories permitted by laws of physics are repeated an infinite number of times in the infinite multiverse. In contrast to the traditional cosmological models of a single, finite universe, this worldview provides for the origin of an infinite number of complex systems by chance, even as the probability of complexity emerging in any given region of the multiverse is extremely low. This change in perspective has profound implications for the history of any phenomenon, and life on earth cannot be an exception.&#148;&#13;&#10; &#13;&#10;CONCLUSION: &#147;The plausibility of different models for the origin of life on earth directly depends on the adopted cosmological scenario. In an infinite universe (multiverse), emergence of highly complex systems by chance is inevitable. Therefore, under this cosmology, an entity as complex as a coupled translation-replication system should be considered a viable breakthrough stage for the onset of biological evolution.&#148;&#13;&#10; &#13;&#10;Quote: &#147;A final comment on &quot;irreducible complexity&quot; and &quot;intelligent design&quot;. By showing that highly complex systems, actually, can emerge by chance and, moreover, are inevitable, if extremely rare, in the universe, the present model sidesteps the issue of irreducibility and leaves no room whatsoever for any form of intelligent design.&#148; -NB He does not see the multiverse as a necessary requirement, but only an infinite universe. Add eternal (he does talk of eternal inflation) and we have the same argument that you and I have been discussing: infinity and eternity make anything possible.

Theoretical origin of life; Koonen's odds against

by David Turell @, Saturday, February 21, 2015, 20:03 (3342 days ago) @ dhw

&#13;&#10;> dhw: Quote: &#147;A final comment on &quot;irreducible complexity&quot; and &quot;intelligent design&quot;. By showing that highly complex systems, actually, can emerge by chance and, moreover, are inevitable, if extremely rare, in the universe, the present model sidesteps the issue of irreducibility and leaves no room whatsoever for any form of intelligent design.&#148; &#13;&#10;> &#13;&#10;> NB He does not see the multiverse as a necessary requirement, but only an infinite universe. Add eternal (he does talk of eternal inflation) and we have the same argument that you and I have been discussing: infinity and eternity make anything possible.-He has to state this disclaimer to keep his card as an atheist, materialism scientist. He has not proven at all that these complex systems can develop by chance. He can only theorize they can.

Theoretical origin of life; Koonen's odds against

by dhw, Sunday, February 22, 2015, 17:22 (3341 days ago) @ David Turell

Dhw: Quote: &#147;A final comment on &quot;irreducible complexity&quot; and &quot;intelligent design&quot;. By showing that highly complex systems, actually, can emerge by chance and, moreover, are inevitable, if extremely rare, in the universe, the present model sidesteps the issue of irreducibility and leaves no room whatsoever for any form of intelligent design.&#148;-NB He does not see the multiverse as a necessary requirement, but only an infinite universe. Add eternal [...] and we have the same argument that you and I have been discussing: infinity and eternity make anything possible. -DAVID: He has to state this disclaimer to keep his card as an atheist, materialism scientist. He has not proven at all that these complex systems can develop by chance. He can only theorize they can.-You lauded him as a &#147;highly respected scientist&#148; when cherry-picking his theoretical odds against chance. Why do you say he &quot;has to state this disclaimer&quot;? Might it not be that as a card-carrying atheist he actually believes his arguments as strongly as you believe yours? And you know as well as I do that nobody can prove any of the hypotheses, and everybody including yourself can only theorize.

Theoretical origin of life; Koonen's odds against

by David Turell @, Sunday, February 22, 2015, 18:41 (3341 days ago) @ dhw

DAVID: He has to state this disclaimer to keep his card as an atheist, materialism scientist. He has not proven at all that these complex systems can develop by chance. He can only theorize they can.&#13;&#10;> &#13;&#10;> dhw: You lauded him as a &#147;highly respected scientist&#148; when cherry-picking his theoretical odds against chance. Why do you say he &quot;has to state this disclaimer&quot;? Might it not be that as a card-carrying atheist he actually believes his arguments as strongly as you believe yours? And you know as well as I do that nobody can prove any of the hypotheses, and everybody including yourself can only theorize.-His essay did not require those comments about ID. They are obviously purposeful in an attempt to refute a point of view. He is as guilty as you point out I am in defending a position. Your underlying position of neutrality as an agnostic I think blinds you to purposeful content produced on one side or the other.

Theoretical origin of life; Koonen's odds against

by David Turell @, Sunday, February 22, 2015, 21:41 (3341 days ago) @ dhw

dhw: NB He does not see the multiverse as a necessary requirement, but only an infinite universe. Add eternal [...] and we have the same argument that you and I have been discussing: infinity and eternity make anything possible. -Second Thoughts:-He uses the multiverse. Note:-> dhw:CONCLUSION: &#147;The plausibility of different models for the origin of life on earth directly depends on the adopted cosmological scenario. In an infinite universe (multiverse), emergence of highly complex systems by chance is inevitable. Therefore, under this cosmology, an entity as complex as a coupled translation-replication system should be considered a viable breakthrough stage for the onset of biological evolution.&#148;-I have bolded it so you can see it. He also uses infinity under the unproven concept that infinity solves all issues of chance, when the accepted limits of chance is 10^-150, not infinity.-And then we have another well-known and highly respected Mathematician who wants to throw out infinity, a math concept that goes back to Pythagoras. Infinities get in the way of quantum mechanics math, but by renormalization (erasing them) the results of the formulae fit reality:-http://blogs.discovermagazine.com/crux/2015/02/20/infinity-ruining-physics/-&quot;Let&apos;s face it: Despite their seductive allure, we have no direct observational evidence for either the infinitely big or the infinitely small. We speak of infinite volumes with infinitely many planets, but our observable universe contains only about 1089 objects (mostly photons). If space is a true continuum, then to describe even something as simple as the distance between two points requires an infinite amount of information, specified by a number with infinitely many decimal places. In practice, we physicists have never managed to measure anything to more than about seventeen decimal places. Yet real numbers, with their infinitely many decimals, have infested almost every nook and cranny of physics, from the strengths of electromagnetic fields to the wave functions of quantum mechanics. We describe even a single bit of quantum information (qubit) using two real numbers involving infinitely many decimals.-&quot;Not only do we lack evidence for the infinite but we don&apos;t need the infinite to do physics.&quot;-I think the materialist scientists should get their act together.

Theoretical origin of life; Koonen's odds against

by George Jelliss ⌂ @, Crewe, Sunday, February 22, 2015, 23:56 (3341 days ago) @ David Turell

If this is all by Max Tegmark, as the byline says, it is taking a very different view from his recent book &quot;Our Mathematical Universe&quot; where he espouses the idea of infinite multiverses.-If he is now in favour of throwing infinities out of physics I&apos;m whole-heartedly in support. I&apos;ve been saying this for years.-I suspect the 1089 photons you refer to should be 10^89.-By the way Pythagoras and the other Greek mathematicians didn&apos;t espouse infinity. &#13;&#10;They were very cautious about such claims.

--
GPJ

Theoretical origin of life; Koonen's odds against

by David Turell @, Monday, February 23, 2015, 15:44 (3340 days ago) @ George Jelliss

George: look back to see Koonen&apos;s odds from the entry two days ago: Saturday, February 21, 2015, 15:06 -&quot;at least one RNA encoding a replicase, ~500 nucleotides (low bound)is required. In the above notation, n = 1800, resulting in E <10-1018-&quot;In other words, even in this toy model that assumes a deliberately inflated rate of RNA production, the probability that a coupled translation-replication emerges by chance in a single O-region is P ^ 10-1018. Obviously, this version of the breakthrough stage can be considered only in the context of a universe with an infinite (or, in the very least, extremely vast) number of O-regions. -&quot;The model considered here is not supposed to be realistic by any account. It only serves to illustrate the difference in the demands on chance for the origin of different versions of the breakthrough system (see Fig. 1) and hence the connections between these versions and different cosmological models of the universe.&quot; -http://www.biologydirect.com/content/2/1/15

Theoretical origin of life; Koonen's odds against

by dhw, Monday, February 23, 2015, 22:27 (3340 days ago) @ David Turell

DAVID: He has to state this disclaimer to keep his card as an atheist, materialism scientist. He has not proven at all that these complex systems can develop by chance. He can only theorize they can.&#13;&#10;Dhw: You lauded him as a &#147;highly respected scientist&#148; when cherry-picking his theoretical odds against chance. Might it not be that as a card-carrying atheist he actually believes his arguments as strongly as you believe yours? And you know as well as I do that nobody can prove any of the hypotheses, and everybody including yourself can only theorize.-DAVID: His essay did not require those comments about ID. They are obviously purposeful in a attempt to refute a point of view. He is as guilty as you point out I am in defending a position. Your underlying position of neutrality as an agnostic I think blinds you to purposeful content produced on one side of the other.-Everyone with a fixed point of view makes purposeful comments to further their cause at the expense of other causes. Far from being blind to this, it is what I am constantly fighting against. There is absolutely no scientific or philosophical consensus on any of the major questions we all discuss. If there were, there would be no discussion. And yet over and over again, theists and atheists state their hypotheses as if they were based on incontrovertible facts, and each side cancels the other out. You dismiss the theory of an infinite eternal universe inevitably coming up with life, because Koonan hasn&apos;t proved it and &#147;can only theorize&#148;. You haven&apos;t proved intelligent design and you can only theorize. But perhaps you are blind to the pot and kettle syndrome.-xxxxxxxxxxxxxx -dhw: NB He does not see the multiverse as a necessary requirement, but only an infinite universe. Add eternal [...] and we have the same argument that you and i have been discussing: infinity and eternity make anything possible. &#13;&#10;DAVID: Second Thoughts:&#13;&#10;He uses the multiverse. Note:&#13;&#10;&#147;The plausibility of different models for the origin of life on earth directly depends on the adopted cosmological scenario. In an infinite universe (multiverse), emergence of highly complex systems by chance is inevitable. Therefore, under this cosmology, an entity as complex as a coupled translation-replication system should be considered a viable breakthrough stage for the onset of biological evolution.&#148;-Perhaps the parenthesis is simply a possible alternative, to cover both scenarios. In the conclusion he is quite specific: &#13;&#10;&#147;For the present concept to hold, the only essential assumptions are that the universe is infinite [e.g., any (island) universe under MWO; the multiverse, per se, is not a must] and that the number of macroscopic histories in any finite region of spacetime is finite.&quot;-The argument is simply that infinity and eternity make anything possible. I remain baffled by all the vehement opposition to the two concepts. You believe in eternal first cause energy, which would allow for any number of universes. Koonan&apos;s infinity would offer infinite combinations of energy and matter (which George says are interchangeable) to come up with life and knock a dent in the odds against chance, but George says no to infinity. Of course the chance argument is no reason for believing in infinity, but until someone proves that our universe is finite and/or came from nothing, it will remain as much a hypothesis as an infinite eternal universe or succession of universes.

Theoretical origin of life; Koonen's odds against

by David Turell @, Tuesday, February 24, 2015, 00:55 (3340 days ago) @ dhw

&#13;&#10;> dhw: NB He does not see the multiverse as a necessary requirement, but only an infinite universe. Add eternal [...] and we have the same argument that you and i have been discussing: infinity and eternity make anything possible. &#13;&#10;> &#13;&#10;> dhw: Perhaps the parenthesis is simply a possible alternative, to cover both scenarios. In the conclusion he is quite specific: &#13;&#10;> &#147;For the present concept to hold, the only essential assumptions are that the universe is infinite [e.g., any (island) universe under MWO; the multiverse, per se, is not a must] and that the number of macroscopic histories in any finite region of spacetime is finite.&quot;-The point of the infinite universe vs. multiverse comment he makes is that under current theories it doesn&apos;t matter what term is used. An infinite universe can have many regions that are equivalent to the multiverse concept. The infinite universe and the multiverse can be one and the same. That is what he means. &#13;&#10;> &#13;&#10;> dhw: The argument is simply that infinity and eternity make anything possible. I remain baffled by all the vehement opposition to the two concepts.-It is accepted that odds of 10^-150 rule out chance. That is not infinity. The argument is the same as the orbiting teapot. Just because it is imaginable does not mean it is real.-> dhw: Of course the chance argument is no reason for believing in infinity, but until someone proves that our universe is finite and/or came from nothing, it will remain as much a hypothesis as an infinite eternal universe or succession of universes.-This universe appears to have a beginning and a microwave background that represents it. There is an unproven discussion that beyond the CMB is an infinite universe. Unfortunately, we can never see it. Another hypothesis to mull in the confusion. IF the BB created space and time, there must be a boundary with the void. Unfortunately, we cannot see that boundary because space curves back on itself. I think God created all of this to confuse us or keep us guessing. After all, faith requires faith. He shouldn&apos;t allow science to absolutely prove Himself. He leaves room for faith.

Theoretical origin of life; Koonen's odds against

by dhw, Tuesday, February 24, 2015, 19:30 (3339 days ago) @ David Turell

dhw: The argument is simply that infinity and eternity make anything possible. I remain baffled by all the vehement opposition to the two concepts.-DAVID: It is accepted that odds of 10^-150 rule out chance. That is not infinity. The argument is the same as the orbiting teapot. Just because it is imaginable does not mean it is real.-And just because God is imaginable does not mean he is real. Russell&apos;s teapot was a way of poking fun at the argument that nobody can prove God doesn&apos;t exist. The same applies to all the hypotheses, theistic and atheistic, that are offered to explain the origin of life and the universe. Nobody can prove they&apos;re wrong. Theist pots versus atheist kettles.-dhw: Of course the chance argument is no reason for believing in infinity, but until someone proves that our universe is finite and/or came from nothing, it will remain as much a hypothesis as an infinite eternal universe or succession of universes.&#13;&#10;DAVID: This universe appears to have a beginning and a microwave background that represents it. There is an unproven discussion that beyond the CMB is an infinite universe. Unfortunately, we can never see it. Another hypothesis to mull in the confusion. IF the BB created space and time, there must be a boundary with the void. Unfortunately, we cannot see that boundary because space curves back on itself. I think God created all of this to confuse us or keep us guessing. After all, faith requires faith. He shouldn&apos;t allow science to absolutely prove Himself. He leaves room for faith.-It is certainly confusing. You have sometimes rebuked ne for trying to read your God&apos;s mind (e.g. maybe he created life as an entertainment to relieve his eternal boredom), and so it is gratifying to see you offering your own divine mind-reading interpretation of the confusion. But of course the confusion might be caused by the fact that we are specks of dust that arrived long after the birth of our planet, and for all our technical prowess we cannot observe any of the phenomena we theorize about (birth of the universe, infinity, eternity, origin of life). We are way, way, way out of our depth. But it&apos;s fun to speculate.

Theoretical origin of life; Koonen's odds against

by David Turell @, Wednesday, February 25, 2015, 01:13 (3339 days ago) @ dhw

&#13;&#10;> dhw: It is certainly confusing. ... But of course the confusion might be caused by the fact that we are specks of dust that arrived long after the birth of our planet, and for all our technical prowess we cannot observe any of the phenomena we theorize about (birth of the universe, infinity, eternity, origin of life). We are way, way, way out of our depth. But it&apos;s fun to speculate.-There is speculation but also scientific advances that are spectacular. We can see echoes of the BB in the CMB. We have gotten an age for the BB. We see fine tuning, but don&apos;t know how life started. Yet philosophers like Adler offers proof of God from what has been observed. John Leslie offers a 50/50 statement, paraphrased, it is either God or multiverses, which also might have been provided by God). I don&apos;t think we are out of our depth with the information we have and which is still developing.

Theoretical origin of life; Koonen's odds against

by dhw, Wednesday, February 25, 2015, 18:58 (3338 days ago) @ David Turell

dhw: It is certainly confusing. ... But of course the confusion might be caused by the fact that we are specks of dust that arrived long after the birth of our planet, and for all our technical prowess we cannot observe any of the phenomena we theorize about (birth of the universe, infinity, eternity, origin of life). We are way, way, way out of our depth. But it&apos;s fun to speculate.-DAVID: There is speculation but also scientific advances that are spectacular. We can see echoes of the BB in the CMB. We have gotten an age for the BB. We see fine tuning, but don&apos;t know how life started. Yet philosophers like Adler offers proof of God from what has been observed. John Leslie offers a 50/50 statement, paraphrased, it is either God or multiverses, which also might have been provided by God). I don&apos;t think we are out of our depth with the information we have and which is still developing.-The spectacular scientific advances you have listed include not knowing how life originated, a philosopher&apos;s proof of God, and two unproven and unprovable theories about God and multiverses. Even the BB remains a theory, albeit one that most scientists seem to accept, and the age depends on the reliability of dating methods, which must always be open to question. If the BB took place, no-one knows what caused it, but some folk say nothing caused it, and our spectacular advances include the theory that 95% of the universe consists of dark matter and energy - called &#147;dark&#148; because no-one knows what it is - and quantum theory, which no-one understands anyway.&#13;&#10; &#13;&#10;I am full of admiration for the human spirit that is constantly searching for answers, and there is no doubt that science has advanced spectacularly in some fields. But according to your previous post, &#147;God created all this to confuse us or keep us guessing&#148;, which has to be an acknowledgement that we are confused and are guessing, and if your God knows his stuff, that&apos;s how we will have to remain. So are we out of our depth or aren&apos;t we?

Theoretical origin of life; Koonen's odds against

by David Turell @, Thursday, February 26, 2015, 00:24 (3338 days ago) @ dhw

dhw: ..... If the BB took place, no-one knows what caused it, but some folk say nothing caused it, and our spectacular advances include the theory that 95% of the universe consists of dark matter and energy - called &#147;dark&#148; because no-one knows what it is - and quantum theory, which no-one understands anyway.&#13;&#10;> &#13;&#10;> I am full of admiration for the human spirit that is constantly searching for answers, and there is no doubt that science has advanced spectacularly in some fields. But according to your previous post, &#147;God created all this to confuse us or keep us guessing&#148;, which has to be an acknowledgement that we are confused and are guessing, and if your God knows his stuff, that&apos;s how we will have to remain. So are we out of our depth or aren&apos;t we?-We can only go so far, but we should keep trying

Theoretical origin of life; Chirality

by David Turell @, Thursday, March 12, 2015, 15:22 (3323 days ago) @ David Turell

Molecules of a like kind have an affinity:-&quot;Liu explains that all life molecules are paired as left-handed and right-handed structures. In scientific terms, the phenomenon is called chirality. Nature&apos;s selection of only right-handed sugars and left-handed amino acids upon which to build life might be much simpler than we expected before.-&quot;Liu found that any molecules, if large enough (several nanometers) and with an electrical charge, will seek their own type with which to form large assemblies. This &quot;self-recognition&quot; of left-handed and right-handed molecule pairs is featured in the March 10, 2015 issue of Nature Communications.&quot;-http://www.sciencedaily.com/releases/2015/03/150311185836.htm-Still no explanation how the first molecules originated.

Theoretical origin of life; Chirality

by George Jelliss ⌂ @, Crewe, Thursday, March 12, 2015, 16:22 (3323 days ago) @ David Turell

This article and video is fascinating-http://physicsworld.com/cws/article/news/2015/mar/12/how-to-make-droplets-chase-each-other-and-self-assemble-into-devices-Simple molecules can self-assemble, sort themselves in sequence and mutually align. &#13;&#10;No consciousness involved.

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GPJ

Theoretical origin of life; Chirality

by David Turell @, Thursday, March 12, 2015, 18:12 (3323 days ago) @ George Jelliss

This article and video is fascinating&#13;&#10;> &#13;&#10;> http://physicsworld.com/cws/article/news/2015/mar/12/how-to-make-droplets-chase-each-ot... &#13;&#10;> Simple molecules can self-assemble, sort themselves in sequence and mutually align. &#13;&#10;> No consciousness involved.-Simply amazing. No electric charge involved. No quantum mechanics.

Theoretical origin of life; Using UV light

by David Turell @, Thursday, March 26, 2015, 00:45 (3310 days ago) @ David Turell

The latest plausible scenario. A series of lucky reactions requiring in the early Earth lucky components are all in the right places:-http://www.nature.com/articles/nchem.2202.epdf?referrer_access_token=uLrMKkacdApp_f6-xj_wINRgN0jAjWel9jnR3ZoTv0NIo3js7EMAlL7iCggjrUCBrW4ZYTThpc_6DIsDphT9-A1BfL9NwZH8DLA1qmS-mFJSmY_r7_REqDO0W-NgqQ41BcezUDi2H0ILyguqM67PmKg3u4Zyl0LsPNDFw0rZrhVz744QBMtFCv048nn_WhWK2S1q-v2r7llTu2ClJOfnVKo_Fyd-kMj1793zs4i4lKc%3D&tracking_referrer=news.sciencemag.org-This is carefully controlled intelligently designed chemistry in a laboratory:-&quot;A minimal cell can be thought of as comprising informational, compartment-forming and metabolic subsystems. To imagine the abiotic assembly of such an overall system, however, places great demands on hypothetical prebiotic chemistry. The perceived differences and incompatibilities between these subsystems have led to the widely held assumption that one or other subsystem must have preceded the others. Here we experimentally investigate the validity of this assumption by examining the assembly of various biomolecular building blocks from prebiotically plausible intermediates and one-carbon feedstock molecules. We show that precursors of ribonucleotides, amino acids and lipids can all be derived by the reductive homologation of hydrogen cyanide and some of its derivatives, and thus that all the cellular subsystems could have arisen simultaneously through common chemistry. The key reaction steps are driven by ultraviolet light, use hydrogen sulfide as the reductant and can be accelerated by Cu(I)-Cu(II) photoredox cycling.&quot;-Note the word plausible, a weaker word than possible. (my bold)-Also:-http://news.sciencemag.org/biology/2015/03/researchers-may-have-solved-origin-life-conundrum-&quot;The origin of life on Earth is a set of paradoxes. In order for life to have gotten started, there must have been a genetic molecule&#151;something like DNA or RNA&#151;capable of passing along blueprints for making proteins, the workhorse molecules of life. But modern cells can&apos;t copy DNA and RNA without the help of proteins themselves. To make matters more vexing, none of these molecules can do their jobs without fatty lipids, which provide the membranes that cells need to hold their contents inside. And in yet another chicken-and-egg complication, protein-based enzymes (encoded by genetic molecules) are needed to synthesize lipids.-&quot;Now, researchers say they may have solved these paradoxes. Chemists report today that a pair of simple compounds, which would have been abundant on early Earth, can give rise to a network of simple reactions that produce the three major classes of biomolecules&#151;nucleic acids, amino acids, and lipids&#151;needed for the earliest form of life to get its start. Although the new work does not prove that this is how life started, it may eventually help explain one of the deepest mysteries in modern science.-&quot;&apos;This is a very important paper,&#148; says Jack Szostak, a molecular biologist and origin-of-life researcher at Massachusetts General Hospital in Boston, who was not affiliated with the current research. &#147;It proposes for the first time a scenario by which almost all of the essential building blocks for life could be assembled in one geological setting.&apos;&quot;- Valid criticism:-&quot;The experiments by Patel et al. fill in this gap but at the cost of a serious amount of investigator intervention. To claim that the whole suite of &quot;precursors of ribonucleotides, amino acids and lipids can all be derived by the reductive homologation of hydrogen cyanide and some of its derivatives&quot; rests on how one defines what are plausible early Earth conditions. By admitting that the products vary depending upon reaction conditions and metallic co-ions, the idea of a one-pot synthesis is not viable in this scenario. They also stretch the concept of &quot;plausibility&quot; to new extreme. While it is easy to imagine a series of pools of the appropriate conditions and with the appropriate precursor compounds all feeding into a single pool, it would be wrong to conclude that what we can imagine is science. That begs the question of where is the point when randomness ends and intervention by someone or something is the more likely or probable explanation. The fact that any discussion of this issue was omitted from both the paper and its rave reviews in Science Magazine reveals that the paper was written for true believers and not to convince any skeptics.&quot;-http://www.evolutionnews.org/2015/03/solution_to_an_094611.html

Theoretical origin of life; starting with DNA!

by David Turell @, Tuesday, April 07, 2015, 18:32 (3297 days ago) @ David Turell

Hope springs eternal under lab conditions:-http://www.sciencedaily.com/releases/2015/04/150407095635.htm-&quot;The discovery in the 1980&apos;s of the ability of RNA to chemically alter its own structure by CU-Boulder Nobel laureate and Distinguished Professor Tom Cech and his research team led to the development of the concept of an &quot;RNA world&quot; in which primordial life was a pool of RNA chains capable of synthesizing other chains from simpler molecules available in the environment. While there now is consensus among origin-of-life researchers that RNA chains are too specialized to have been created as a product of random chemical reactions, the new findings suggest a viable alternative, said Clark.-&quot;The new research demonstrates that the spontaneous self-assembly of DNA fragments just a few nanometers in length into ordered liquid crystal phases has the ability to drive the formation of chemical bonds that connect together short DNA chains to form long ones, without the aid of biological mechanisms. Liquid crystals are a form of matter that has properties between those of conventional liquids and those of a solid crystal -- a liquid crystal may flow like a liquid, for example, but its molecules may be oriented more like a crystal.-&quot;&apos;Our observations are suggestive of what may have happened on the early Earth when the first DNA-like molecular fragments appeared,&quot; said Clark.-&quot;For several years the research group has been exploring the hypothesis that the way in which DNA emerged in the early Earth lies in its structural properties and its ability to self-organize. In the pre-RNA world, the spontaneous self-assembly of fragments of nucleic acids (DNA and RNA) may have acted as a template for their chemical joining into polymers, which are substances composed of a large number of repeating units.-&quot;&apos;The new findings show that in the presence of appropriate chemical conditions, the spontaneous self assembly of small DNA fragments into stacks of short duplexes greatly favors their binding into longer polymers, thereby providing a pre-RNA route to the RNA world,&quot; said Clark.&quot;-My bold: surely those conditions were in the right place and time.

Theoretical origin of life; another take

by David Turell @, Friday, April 10, 2015, 14:35 (3294 days ago) @ David Turell

No one knows how, but the RNA theory still offers hope:-http://www.abc.net.au/radionational/programs/scienceshow/in-the-beginning-the-new-science-of-the-origins-of-life/6365468-&quot;According to Lane, the environment that created life would need to be &#145;continuously&apos; producing the building blocks of RNA in &#145;large numbers&apos;. &#145;Any form of replication is doubling,&apos; says Lane. &#145;So you need an environment that will feed you.&apos;-&quot;&#145;This is one of the problems with a soup,&apos; says Lane, referring to Darwin&apos;s 1871 theory that life emerged in a &#145;warm little pond&apos;&#151;a soup of chemicals showered in light and heat. &#145;You simply run out of ingredients very, very quickly&#151;the concentration is too low.&apos;-&quot;Matthew Powner isn&apos;t giving up on Darwin&apos;s soup just yet, though.-&quot;&#145;We are thinking about a scenario where you have pools or shallow bodies of water,&apos; he says.-&quot;According to Powner, placing the origins of life in the depths of the ocean would lose a key piece needed in the creation of RNA: UV light. &#145;Ultraviolet light provides an energy source for certain chemical reactions to take place,&apos; he says. &#145;The importance of ultraviolet light suggests that the chemistry would have taken place near the surface of a body.&apos;-&quot;So the debate rages on. Over the past few decades scientists have edged closer to understanding the origin of life, but there is still some way to go, which is probably why when Robyn Williams asked Lane, &#145;What was there in the beginning, do you think?&apos;, the scientist replied wryly: &#145;Ah, &#147;think&#148;. Yes, we have no idea, is the bottom line.&apos;&quot;

Theoretical origin of life; another take

by David Turell @, Thursday, April 16, 2015, 23:35 (3288 days ago) @ David Turell

Another lab experiment to produce amino acids and other compounds, but with no solution to the problem that the formation of RNA is very problematic without enzymes. The fact the bricks are lying around doesn&apos;t get you a building. Still interesting:-http://www.scientificamerican.com/article/meteorite-chemicals-may-have-started-life-on-earth-and-space/?WT.mc_id=SA_SPC_20150416-&quot;The molecules that kick-started life on primordial Earth could have been made in space and delivered by meteorites, according to researchers in Italy. The group synthesised sugars, amino acids and nucleobases with nothing more than formamide, meteorite material and the power of a simulated solar wind, replicating a process they believe cooked up a prebiotic soup long before life existed on Earth.-&quot;Formamide is a simple organic compound first suggested as a starting material for the formation of prebiotic biomolecules back in 2001. The chemical has been detected in galactic centres and stellar nurseries, as well as comets and satellites. These latest experiments show that formamide, irradiated by the solar wind&#151;simulated here by a proton beam&#151;and in the presence of powdered meteorites, gave rise to amino acids, carboxylic acids, sugars and nucleosides&#151;the building blocks of DNA and RNA.&quot;

Theoretical origin of life; another take

by David Turell @, Monday, April 27, 2015, 20:36 (3277 days ago) @ David Turell

This time a book that proposes deep sea vents, hot and acidy, with a proton pump at the beginning. Amino acids don&apos;t work in that climate, and thre are many other problems the book discusses:-http://www.newscientist.com/article/mg22630180.600-the-vital-question-finding-answers-about-the-origin-of-life.html#.VT6S8GB0y1u-&quot;Lane has been developing a grand vision of where and how life began, and why it evolved in the way it did. What&apos;s more, he thinks the &quot;gene-jocks&quot; will never answer these questions by studying genomes and the like. Instead, we need to focus on what drives life: energy.-&quot;Living cells are powered by a totally unexpected process. The energy from food is used to pump protons across a membrane to build up an electrochemical gradient. This gradient drives the machinery of life, like water from a dam driving a turbine.-&quot;And Lane argues that life has been powered by proton gradients from the very beginning. Forget all those primordial soups or &quot;warm ponds&quot;: only the natural proton gradients found in undersea alkaline hydrothermal vents could have provided the continuous flux of carbon and energy that life requires. These vents may be common on rocky planets so, if this reasoning is correct, simple cells should be too.-&quot;It&apos;s the next step that is tricky. To become more complex, cells need more membrane to provide more energy. But the larger the area of membrane, the harder it is to keep control of the proton gradient - and losing control means death. So cells stayed simple. &quot;There is no innate or universal trajectory towards complex life,&quot; Lane writes.-&quot;Not, at least, until something extraordinary happened: one kind of simple cell somehow started living inside another. Eventually, the first cell turned into the self-contained energy-producing structures we call mitochondria. This Russian-doll arrangement meant cells could get more energy simply by making more mitochondria, allowing them to become much larger and more complex.&quot;-Turning into a mitochondrion is not an easy trick. Where did the DNA come from in the organelle? It is all fun and games.

Theoretical origin of life; another rather wooly take

by David Turell @, Tuesday, April 28, 2015, 02:02 (3277 days ago) @ David Turell

that life may have used fewer amino acids in the beginning (less than the 20 now present) has been around for a long time, but the suppositions here are actually dismissed in the article itself:-&quot;How the code came into being presents a chicken-and-egg problem. The key players in the code &#151; DNA, RNA, amino acids, and proteins &#151; are chemically complicated structures that work together to make proteins. But in modern cells, proteins are used to make the components of the code. So how did a highly structured code emerge?-&quot;Most researchers believe that the code began simply with basic proteins made from a limited alphabet of amino acids. It then grew in complexity over time, as these proteins learned to make more sophisticated molecules. Eventually, it developed into a code capable of creating all the diversity we see today. &#147;It&apos;s long been hypothesized that life&apos;s &#145;standard alphabet&apos; of 20 amino acids evolved from a simpler, earlier alphabet, much as the English alphabet has accumulated extra letters over its history,&#148; said Stephen Freeland, a biologist at the University of Maryland, Baltimore County.&quot;-De novo proteins that evolve are discussed!- https://www.quantamagazine.org/20150416-how-structure-evolved-in-the-primordial-soup/

Theoretical origin of life; from a viroid

by David Turell @, Wednesday, May 06, 2015, 21:16 (3268 days ago) @ David Turell

Nuttier than ever: a viroid did it, but how, since it requires ,living in a living cell?-http://www.huffingtonpost.com/suzan-mazur/a-viroidlike-entity-as-fi_b_7197076.html-&quot;Viruses and viroids are able to direct their own replication in the medium -- the cell -- and during the process of replicating they evolve because replication introduces mutations. Those are the two characteristics of life. To be able to replicate and get copies that occasionally are not identical to the original one. In this way viruses and viroids are able to evolve, and in this respect are similar to cells. . . .-&quot;The crucial thing is that at least some viroids are catalytic RNAs, and in the RNA world everything was catalyzed by RNA. . . . That is why there is quite a strong argument for a viroid-like entity having appeared in the early steps of the emergence of life. &quot;-But they still have to live in an living cell.

Theoretical origin of life; molecules made near heat

by David Turell @, Sunday, May 10, 2015, 23:58 (3264 days ago) @ David Turell

Again, fun and games in the lab setting up conditions that might have occurred near a hot star and formed carbon/nitrogen ring molecules as a start toward RNA/DNA, with lots more processing needed:-&quot;Now, researchers from the U.S. Department of Energy&apos;s Lawrence Berkeley National Lab (Berkeley Lab) and the University of Hawaii at Manoa have shown for the first time that cosmic hot spots, such as those near stars, could be excellent environments for the creation of these nitrogen-containing molecular rings.-&quot;In a new paper in the Astrophysical Journal, the team describes the experiment in which they recreate conditions around carbon-rich, dying stars to find formation pathways of the important molecules.-&quot;&apos;This is the first time anyone&apos;s looked at a hot reaction like this,&quot; says Musahid Ahmed, scientist in the Chemical Sciences Division at Berkeley Lab. It&apos;s not easy for carbon atoms to form rings that contain nitrogen, he says. But this new work demonstrates the possibility of a hot gas phase reaction, what Ahmed calls the &quot;cosmic barbeque-&quot;These experiments provide compelling evidence that the key molecules of quinolone and isoquinoline can be synthesized in these hot environments and then be ejected with the stellar wind to the interstellar medium - the space between stars, says Kaiser.-&quot;&apos;Once ejected in space, in cold molecular clouds, these molecules can then condense on cold interstellar nanoparticles, where they can be processed and functionalized.&quot; Kaiser adds. &quot;These processes might lead to more complex, biorelevant molecules such as nucleobases of crucial importance to DNA and RNA formation.&apos;&quot;-&#13;&#10; Read more at: http://phys.org/news/2015-05-hot-life-chemical-bonds-eventually.html#jCp-And they neatly forgot to mention they all have to be right-handed!

Theoretical origin of life; without water

by David Turell @, Saturday, May 23, 2015, 20:27 (3251 days ago) @ David Turell

One of the major problems in working with the protein molecules of life is that water tends to tear them apart. So starting on dry land!?:-http://www.newscientist.com/article/mg22229650.300-no-more-primal-soup-creating-life-without-water.html?page=1-&quot;For Steven Benner, that is all a fairy tale. &quot;We tend to think that water&apos;s properties are ideal for life, but the opposite is true,&quot; he says. &quot;Water is corrosive.&quot; Benner is a chemist at the Westheimer Institute of Science and Technology in Gainesville, Florida, and for three decades he has been doing pioneering work in synthetic biology, which aims to recreate life&apos;s chemistry in the test tube. And he is no lone voice. As water&apos;s deleterious effects have become more apparent, many researchers are asking: is it time to dry out life&apos;s recipe?-&quot;Life&apos;s molecules don&apos;t just dissolve in water; the electron-rich oxygen of its molecules attacks them, and they begin to fall apart. &quot;In your body right now, the DNA in your cells is losing an amino group many times a second because of the action of water,&quot; says Benner. Living things keep their molecules intact only through clever chemical strategies that perpetually repair the breakages.-&quot;Decades of research have shown that making nucleotides in water is a very tricky business. Individual steps can be made to work, but they don&apos;t all gel together. &quot;We are still at the stage of scraping out the product of step seven, and carefully spooning it into the flask to begin step eight,&quot; says Benner. Fail to spoon in just the right amounts of various molecules at the right time, and the end result is a gunky mess.-***-&quot;But he questions whether dry life arriving on a wet Earth on a Martian meteorite could have assimilated well. Genomic studies show that life on our planet traces back to a collection of cells that survived by sharing the products of their genes, creating a single-celled organism referred to as the last universal common ancestor. &quot;If you dropped a primitive Martian cell into Earth&apos;s oceans, it is highly unlikely that it would have proliferated alone,&quot; he says. Rather, it would take a whole microbial ecosystem arriving, intact, from Mars.-&quot;Or we tweak our story still further. Nicholas Hud, a chemist at the Georgia Institute of Technology in Atlanta, points out that most researchers accept that DNA somehow evolved from RNA, so we should at least consider the possibility that RNA evolved from a different molecule that was stable in water. &quot;When I look at RNA, I see a molecule that is perfect at what it does, but that&apos;s hard to make,&quot; he says - perhaps a telltale sign that natural selection helped shape RNA. &quot;Which is more probable? Life began on Mars, was transported to Earth and picked up where it left off, or life began on Earth, but with a molecule different from RNA?&quot;-&quot;Hud&apos;s thinking could remove the need for Kirschvink&apos;s Martian scenarios and Benner&apos;s chemistry, but would demand a rethink of the underlying assumption that life&apos;s chemical origin lies with RNA. It would seem fitting, though, that the ultimate solution to the water problem, even before life as we know it got started, could lie in the principles of natural selection. Stories about the origins of life begin and end with Darwin.&quot;-What does Darwin really have to do with it? Nothing.

Theoretical origin of life; without water

by Balance_Maintained @, U.S.A., Sunday, May 24, 2015, 08:40 (3251 days ago) @ David Turell

Once upon a time, there was a fairy tale princess that lived in a lake... no wait... on dry land... no.. I mean... Once upon a time, there a Martian princess, who imediately left mars, traveling on the back of a giant space rock, braving and surviving all the perils of space and the fiery explosion of her arrival on earth without any protection, to make a lovely new home on Earth. --The End

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Theoretical origin of life; another theory:

by David Turell @, Tuesday, June 02, 2015, 15:57 (3241 days ago) @ David Turell

this one involves the polarity of amino acids without explaining where they came from or that you can&apos;t polymerize in hot water. Great just-so story:-http://www.sciencedaily.com/releases/2015/06/150601172834.htm-&quot;In the beginning, there were simple chemicals. And they produced amino acids that eventually became the proteins necessary to create single cells. And the single cells became plants and animals. Recent research is revealing how the primordial soup created the amino acid building blocks, and there is widespread scientific consensus on the evolution from the first cell into plants and animals. But it&apos;s still a mystery how the building blocks were first assembled into the proteins that formed the machinery of all cells.-&#13;&#10;&quot;Now, two long-time University of North Carolina scientists -- Richard Wolfenden, PhD, and Charles Carter, PhD -- have shed new light on the transition from building blocks into life some 4 billion years ago.-&quot;&apos;Our work shows that the close linkage between the physical properties of amino acids, the genetic code, and protein folding was likely essential from the beginning, long before large, sophisticated molecules arrived on the scene,&quot; said Carter, professor of biochemistry and biophysics at the UNC School of Medicine. &quot;This close interaction was likely the key factor in the evolution from building blocks to organisms.&quot;-&quot;Their findings, published in companion papers in the Proceedings of the National Academy of Sciences, fly in the face of the problematic &quot;RNA world&quot; theory, which posits that RNA -- the molecule that today plays roles in coding, regulating, and expressing genes -- elevated itself from the primordial soup of amino acids and cosmic chemicals to give rise first to short proteins called peptides and then to single-celled organisms.-Wolfenden and Carter argue that RNA did not work alone; in fact, it was no more likely that RNA catalyzed peptide formation than it was for peptides to catalyze RNA formation.-***-&quot;Proteins must fold in specific ways to function properly. The first PNAS paper, led by Wolfenden, shows that both the polarities of the twenty amino acids (how they distribute between water and oil) and their sizes help explain the complex process of protein folding -- when a chain of connected amino acids arranges itself to form a particular 3-dimensional structure that has a specific biological function.-My comment:Specific biologic function is exactly what is wanted, but life is a mass of those functions cooperating together. Seems the authors lightly skip by that point. Smells of planning to me.-&quot;&apos;Our experiments show how the polarities of amino acids change consistently across a wide range of temperatures in ways that would not disrupt the basic relationships between genetic coding and protein folding,&quot; said Wolfenden, Alumni Distinguished Professor of Biochemistry and Biophysics. This was important to establish because when life was first forming on Earth, temperatures were hot, probably much hotter than they are now or when the first plants and animals were established.-&quot;A series of biochemical experiments with amino acids conducted in Wolfenden&apos;s lab showed that two properties -- the sizes as well as the polarities of amino acids -- were necessary and sufficient to explain how the amino acids behaved in folded proteins and that these relationships also held at the higher temperatures of Earth 4 billion years ago.-&quot;The second PNAS paper, led by Carter, delves into how enzymes called aminoacyl-tRNA synthetases recognized transfer ribonucleic acid, or tRNA. Those enzymes translate the genetic code.&quot;

Theoretical origin of life; another theory:

by David Turell @, Monday, June 08, 2015, 14:31 (3235 days ago) @ David Turell

Another article on the latest theory of how RNAs magically can create information and put amino acids together. It doesn&apos;t explain where the amino acids came from, assuming they are just there, and pointing to cyanide research. It assumes a watery birthplace for life, when amino acids are very hydrophobic.-http://news.yahoo.com/origin-life-story-may-found-missing-123319318.html-&quot;By showing that it&apos;s possible for tRNA to discriminate between molecules, and that the links can work without &quot;help,&quot; Carter thinks he&apos;s found a way for the information storage of chemical structures like tRNA to have arisen &#151; a crucial piece of passing on genetic traits. Combined with the work on amino acids and temperature, it offers insight into how early life might have evolved.-&quot;This work still doesn&apos;t answer the ultimate question of how life began, but it does show a mechanism for the appearance of the genetic codes that pass on inherited traits, which got evolution rolling.&quot;-Note all of this is man-made chemistry, by intelligent design

Theoretical origin of life; 15 questions

by David Turell @, Saturday, June 13, 2015, 15:40 (3230 days ago) @ David Turell

A list of the difficulties in theorizing how life began:-http://www.lifephys.dis.titech.ac.jp/oqol2014/?page_id=180-Below I&apos;ve picked out a few of the questions. In total the article shows how little we really know from 60 years of research.-&quot;All life is based on proteins and nucleic acids, which are ordered sequences of units. Not to be confused with a simple random polymerization or copolymerization. The question &#147;how can we make by prebiotic means ordered sequences of amino acids, or mononucleotides?&#148; is in fact never asked in the modern research on the origin of life.-&quot;Premise: Why is the origin of life still a mystery? Yes, we all in science accept 1924 Oparin&apos;s idea that life on Earth originated from the inanimate matter via a series of chemical steps of increasing molecular complexity and functionality. However, the turning point nonlife-life has never been put into one experimental set up-actually it has never be clarified this from a conceptual point of view either. There are of course several hypotheses, and this plethora of ideas means already that we do not have a convincing one. -&quot; At the early stage of RNA world, RNA molecules should have no functional property. What physical or chemical process mediates the selection of specific RNA? Even when functional RNA enzymes are generated, it still remains a challenge to construct sustained self-replication and metabolic system in which multiple RNA molecules function cooperatively. Once we can construct the precursor of a replication system by a set of RNA molecules, is it possible to emulate another path of evolution in a test tube?-&quot;The genetic code is most essential part for the genetic systems. In the context of the origin of life, a major issue on the genetic code is to understand how the materials relevant to genetic code that can translate the sequence of four bases into a polypeptide. In bacteria and cells, each of ~20 different amino-acyl tRNA synthethase (aa-RS) bind to a particular tRNA with high affinity and also has an specific binding to one of twenty amino acids. The aa-RS produces amino-acyl tRNA (aa-tRNA) that has the triplet of anti-codon in a loop of tRNA and a corresponding amino acid at 3&apos; end. How was a family of aa-tRNAs created without sophisticated enzymes? Although RNA-catalyzed self-aminoacylation and tRNA aminoacylation has been demonstrated experimentally, the possible evolutional pathway of genetic coding system is little understood. Can we find or design simple aa-RS and aa-tRNA from the cocktail of molecules (e.g., amino acid, tRNA(-like) molecule, and ATP), which might be relevant to the origin of translation and genetic code? What features are required as a mechanism that ensures robust translation? (my bold)-&quot;The Premise: The transition from non-living to living systems involves, as a key step, the formation of a self-bounded physical system that contains interacting molecules. In many proposed scenarios, the complexity of such an event is often underestimated, and it is typically taken for granted, starting from the separated components. However, compared to the large amount of work done for understanding the emergence and the evolution of functional molecules and networks (ribozymes, catalytic peptides, simple metabolic cycles, self-replicating molecules, hypercycles and autocatalytic sets, etc.), much less has been done for understanding the physical mechanisms underlying the assembly of primitive cell-like structures. In particular, little attention has been given to go beyond the general and simplistic sentence &#145;&#133; and later became encapsulated in a membrane-based compartment&apos;. (my bold)

Theoretical origin of life; autocatalysis

by David Turell @, Thursday, June 18, 2015, 14:20 (3225 days ago) @ David Turell

Stuart Kauffman reappears in this article. His proposition that autocatalysis can create life still lives and has been expanded upon. Again it is intelligent design in the lab and software simulations in the computer with no direct idea of how to cross over from simple inorganic and organic starting points to self contained self-replication systems which are truly life:-http://www.the-scientist.com/?articles.view/articleNo/43082/title/The-Living-Set/-&quot;As this recent research has shown, autocatalytic sets capture essential aspects of the organization of living organisms, and their high probability of emergence and potential to evolve have important implications for the origin of life. Autocatalytic sets can be studied mathematically and with computer simulations, but they also show up in experimental systems of nucleic acids and in the metabolic network of living organisms. They truly seem to represent a fundamental property of life.&quot;-All well and good as a description of life, but this understanding does not get one to the origin of life, it just describes the result!

Theoretical origin of life; making catalysts

by David Turell @, Friday, June 19, 2015, 00:36 (3225 days ago) @ David Turell

Intelligent design in the lab has found a gene which can help form proto-catalysts:-http://phys.org/news/2015-06-scientists-evidence-key-ingredient-dawn.html-&quot;&apos;We now have more information about how amino acids eventually evolved into complex molecules necessary to create life as we know it,&quot; Carter said. &quot;But perhaps more importantly, we&apos;ve been able to provide a new set of tools that will enable others to approach questions about the origin of life in ways that are scientifically sound and productive.&quot;-&quot;And there are still questions about how all this happened.&#13;&#10; (my bold)-&quot;&apos;This doesn&apos;t yet solve the central chicken and the egg problem,&quot; Carter said. &quot;Even the designed protozyme requires a ribosome to synthesize it (my bold)and lead to protein creation. But what we&apos;ve shown is that blueprints for life actually contained more information than anyone had realized (my italics)because both strands of the ancestral gene were responsible for encoding the two classes of synthetases needed for the creation of proteins.&quot;-&quot;This result unifies what scientists previously considered to be two distinct superfamilies of modern enzymes and greatly simplifies the complex process of forming the diversity of catalysts necessary for life: both catalysts were available at the same times and places before there were cells to package life&apos;s machinery.&quot;-Note that information (in the italics) is required. How is that created by chance?

Theoretical origin of life; making catalysts

by dhw, Friday, June 19, 2015, 16:53 (3224 days ago) @ David Turell

DAVID: Intelligent design in the lab has found a gene which can help form proto-catalysts:-http://phys.org/news/2015-06-scientists-evidence-key-ingredient-dawn.html-QUOTE: &quot;&apos;This doesn&apos;t yet solve the central chicken and the egg problem,&quot; Carter said. &quot;Even the designed protozyme requires a ribosome to synthesize it (my bold)and lead to protein creation. But what we&apos;ve shown is that blueprints for life actually contained more information than anyone had realized (my italics)because both strands of the ancestral gene were responsible for encoding the two classes of synthetases needed for the creation of proteins.&quot;-DAVID: Note that information (in the italics) is required. How is that created by chance?-If you were to ask how all these complexities could have come together by chance, I would nod in agreement. But this constant emphasis on the in-word &#147;information&#148; seems to me to damage your case. Information is present in everything, and the same information would be present in the blueprints of life whether they were formed by chance or not.

Theoretical origin of life; making catalysts

by David Turell @, Friday, June 19, 2015, 18:28 (3224 days ago) @ dhw

&#13;&#10;> DAVID: Note that information (in the italics) is required. How is that created by chance?&#13;&#10;> &#13;&#10;> dhw: If you were to ask how all these complexities could have come together by chance, I would nod in agreement. But this constant emphasis on the in-word &#147;information&#148; seems to me to damage your case. Information is present in everything, and the same information would be present in the blueprints of life whether they were formed by chance or not.- Yes, but the information in a crystal is not the same as the information in a living one-celled organism. Where did that living coded information come from? I know you can&apos;t answer, because you will not accept the logical source, a mind.

Theoretical origin of life; making catalysts

by dhw, Saturday, June 20, 2015, 11:13 (3224 days ago) @ David Turell

DAVID: Note that information (in the italics) is required. How is that created by chance?-Dhw: If you were to ask how all these complexities could have come together by chance, I would nod in agreement. But this constant emphasis on the in-word &#147;information&#148; seems to me to damage your case. Information is present in everything, and the same information would be present in the blueprints of life whether they were formed by chance or not. -DAVID: Yes, but the information in a crystal is not the same as the information in a living one-celled organism. Where did that living coded information come from? I know you can&apos;t answer, because you will not accept the logical source, a mind.-All forms of life and non-life are full of information. I was merely pointing out that the information is there, whether the materials were assembled by chance or not. Where did anything and everything come from? None of us can answer, and a sourceless, living mind full of information is no more logical than sourceless, mindless energy and matter full of information.

Theoretical origin of life; making catalysts

by David Turell @, Saturday, June 20, 2015, 20:42 (3223 days ago) @ dhw

&#13;&#10;> DAVID: Yes, but the information in a crystal is not the same as the information in a living one-celled organism. Where did that living coded information come from? I know you can&apos;t answer, because you will not accept the logical source, a mind.&#13;&#10;> &#13;&#10;> dhw: All forms of life and non-life are full of information. I was merely pointing out that the information is there, whether the materials were assembled by chance or not. Where did anything and everything come from? None of us can answer, and a sourceless, living mind full of information is no more logical than sourceless, mindless energy and matter full of information.-You are simply skirting the question. Living matter is filled with the information that makes organic molecules cooperate to create life. Your answer implies that chance could have created that information. Information is something which cannot come from nothing.

Theoretical origin of life; making catalysts

by dhw, Sunday, June 21, 2015, 12:37 (3222 days ago) @ David Turell

DAVID: Yes, but the information in a crystal is not the same as the information in a living one-celled organism. Where did that living coded information come from? I know you can&apos;t answer, because you will not accept the logical source, a mind.-dhw: All forms of life and non-life are full of information. I was merely pointing out that the information is there, whether the materials were assembled by chance or not. Where did anything and everything come from? None of us can answer, and a sourceless, living mind full of information is no more logical than sourceless, mindless energy and matter full of information.-DAVID: You are simply skirting the question. Living matter is filled with the information that makes organic molecules cooperate to create life. Your answer implies that chance could have created that information. Information is something which cannot come from nothing.-If I say the question cannot be answered, I can hardly be accused of skirting it. We began this discussion with my objection to the vague term &#147;information&#148;, but since you insist on using it, I can only repeat that the same information is present, whether the molecules were assembled by God or by chance. I agree that it cannot come from nothing. The alternative sources appear to be: 1) a sourceless mind, which acquired all the &#147;information&#148; from nowhere except itself, and consciously created and combined the molecules out of its non-molecular eternal energy; 2) mindless eternal energy, which has been creating molecules for ever and ever, and eventually chanced to hit upon a life-giving combination; 3) ever-changing inanimate matter, which has - or developed - a mental aspect that enabled it to experiment and eventually find a way of reproducing itself and evolving. I find all three answers impossible to believe, which is why I remain agnostic.

Theoretical origin of life; making catalysts

by David Turell @, Sunday, June 21, 2015, 14:59 (3222 days ago) @ dhw

dhw: We began this discussion with my objection to the vague term &#147;information&#148;, but since you insist on using it, I can only repeat that the same information is present, whether the molecules were assembled by God or by chance. I agree that it cannot come from nothing.-Thank you. There has to be a source for the information.-> dhw: The alternative sources appear to be: 1) a sourceless mind, which acquired all the &#147;information&#148; from nowhere except itself, and consciously created and combined the molecules out of its non-molecular eternal energy; 2) mindless eternal energy, which has been creating molecules for ever and ever, and eventually chanced to hit upon a life-giving combination; 3) ever-changing inanimate matter, which has - or developed - a mental aspect that enabled it to experiment and eventually find a way of reproducing itself and evolving. I find all three answers impossible to believe, which is why I remain agnostic.-An excellent list. I find 1) reasonable and logical; 2) this admits to eternal energy which is magically present from the beginning, but you have decided to make it mindless. Why not allow it to have a mind? That logically fits everything we know about our reality. 3) is quite a stretch, and again begs the question where did innate matter come from, since you admit something cannot come from nothing?

Theoretical origin of life; making catalysts

by dhw, Monday, June 22, 2015, 12:48 (3221 days ago) @ David Turell

dhw: We began this discussion with my objection to the vague term &#147;information&#148;, but since you insist on using it, I can only repeat that the same information is present, whether the molecules were assembled by God or by chance. I agree that it cannot come from nothing.&#13;&#10;DAVID: Thank you. There has to be a source for the information.&#13;&#10;dhw: The alternative sources appear to be: 1) a sourceless mind, which acquired all the &#147;information&#148; from nowhere except itself, and consciously created and combined the molecules out of its non-molecular eternal energy; 2) mindless eternal energy, which has been creating molecules for ever and ever, and eventually chanced to hit upon a life-giving combination; 3) ever-changing inanimate matter, which has - or developed - a mental aspect that enabled it to experiment and eventually find a way of reproducing itself and evolving. I find all three answers impossible to believe, which is why I remain agnostic.-DAVID: An excellent list. I find 1) reasonable and logical; 2) this admits to eternal energy which is magically present from the beginning, but you have decided to make it mindless. Why not allow it to have a mind? That logically fits everything we know about our reality.-Why is mindless energy magic, but conscious energy reasonable and logical? We do not know the origin of consciousness/minds, but you insist that consciousness (earthly) can only be the result of deliberate invention, and so it is hardly logical to claim that consciousness (heavenly) does not require invention and has simply always existed.&#13;&#10; &#13;&#10;DAVID: 3) is quite a stretch, and again begs the question where did innate [inanimate?] matter come from, since you admit something cannot come from nothing?&#13;&#10;&#13;&#10;You claim that eternal energy consciously transformed itself into matter, and (3) claims that eternal energy transformed itself into matter which had or evolved consciousness. In both cases, matter came from energy. If you can believe in a non-invented form of consciousness (1), you can believe that consciousness evolved naturally without deliberate invention (2 or 3), which also fits everything we know about our reality, and does not require any other form of reality. Alternatively, like me, you can opt not to believe in any of these hypotheses.

Theoretical origin of life; making catalysts

by David Turell @, Monday, June 22, 2015, 14:17 (3221 days ago) @ dhw

&#13;&#10;> dhw: Why is mindless energy magic, but conscious energy reasonable and logical? We do not know the origin of consciousness/minds, but you insist that consciousness (earthly) can only be the result of deliberate invention, and so it is hardly logical to claim that consciousness (heavenly) does not require invention and has simply always existed.-You believe in cause and effect and that something cannot come from nothing. Therefore something always existed. And I firmly believe it required a planning &apos;mind&apos; not amorphous energy to evolve what we have in our reality.&#13;&#10;> &#13;&#10;> DAVID: 3) is quite a stretch, and again begs the question where did innate [inanimate?] matter come from, since you admit something cannot come from nothing?&#13;&#10;> &#13;&#10;> dhw: If you can believe in a non-invented form of consciousness (1), you can believe that consciousness evolved naturally without deliberate invention (2 or 3), which also fits everything we know about our reality, and does not require any other form of reality. Alternatively, like me, you can opt not to believe in any of these hypotheses.-Please do not tell me what I can believe. In my view parts of our reality require invention.

Theoretical origin of life; making catalysts

by dhw, Tuesday, June 23, 2015, 13:16 (3220 days ago) @ David Turell

dhw: If you can believe in a non-invented form of consciousness (1), you can believe that consciousness evolved naturally without deliberate invention (2 or 3), which also fits everything we know about our reality, and does not require any other form of reality. Alternatively, like me, you can opt not to believe in any of these hypotheses.-DAVID: Please do not tell me what I can believe. In my view parts of our reality require invention.-My apologies - that was badly phrased. My point, of course, was that one belief is as unlikely as the other, so the same act of irrational faith is required for each of the hypotheses. It was not meant personally. I agree that parts of our reality require invention. The issue is whether that invention stems from the reality we think we know (and may be able to investigate), or from a totally different form of reality, for the existence of which there is no direct evidence.

Theoretical origin of life; making catalysts

by David Turell @, Tuesday, June 23, 2015, 15:16 (3220 days ago) @ dhw

&#13;&#10;> DAVID: Please do not tell me what I can believe. In my view parts of our reality require invention.&#13;&#10;> &#13;&#10;> dhw: My apologies - that was badly phrased. My point, of course, was that one belief is as unlikely as the other, so the same act of irrational faith is required for each of the hypotheses. It was not meant personally. I agree that parts of our reality require invention. The issue is whether that invention stems from the reality we think we know (and may be able to investigate), or from a totally different form of reality, for the existence of which there is no direct evidence.-Accepted, and I agree with your analysis. But the indirect evidence points to a supernatural source in my view.

Theoretical origin of life; a review of RNA first

by David Turell @, Friday, June 26, 2015, 15:39 (3217 days ago) @ David Turell

This is an apologetic view of using the RNA first theory as still the best available. The author points out all the difficulties, and rules out proteins first theory as better. He titles his article as &quot;the worst theory of the start&quot; of life, except for all the others!-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495036/-&quot;Abstract: The problems associated with the RNA world hypothesis are well known. In the following I discuss some of these difficulties, some of the alternative hypotheses that have been proposed, and some of the problems with these alternative models. From a biosynthetic - as well as, arguably, evolutionary - perspective, DNA is a modified RNA, and so the chicken-and-egg dilemma of &#147;which came first?&#148; boils down to a choice between RNA and protein. This is not just a question of cause and effect, but also one of statistical likelihood, as the chance of two such different types of macromolecule arising simultaneously would appear unlikely. The RNA world hypothesis is an example of a &#145;top down&apos; (or should it be &#145;present back&apos;?) approach to early evolution: how can we simplify modern biological systems to give a plausible evolutionary pathway that preserves continuity of function?

Theoretical origin of life; why RNA world couldn't work

by David Turell @, Friday, June 26, 2015, 20:34 (3217 days ago) @ David Turell

Another review of the theory. It has a chicken and egg problem of what came first. Remember all of the research is intelligently designed in a complex lab:-&#13;&#10;http://www.newscientist.com/article/mg22630273.700-why-rna-world-theory-on-origin-of-life-may-be-wrong-after-all.html#.VY2uhGDbK1s-&quot;Life has a chicken-and-egg problem: enzymes are needed to make nucleic acids - the genetic material - but to build them you need the genetic information contained in nucleic acids. So most researchers assume that the earliest life, long before the evolution of cells, consisted of RNA molecules. These contain genetic information but can also fold into complex shapes, so could serve as enzymes to help make more RNA in their own image - enabling Darwinian evolution on a molecular level.-&quot;At some point, the idea goes, this RNA world ended when life outsourced enzymatic functions to proteins, which are more versatile. The key step in this switch was the evolution of the ribosome, a structure that builds protein molecules from genetic blueprints held in RNA.-&quot;But such a transition would require abandoning the enzymatic functions of RNA and reinventing them in proteins. &quot;That is not a simple model,&quot; says Loren Williams, a biochemist at the Georgia Institute of Technology in Atlanta.-&quot;Williams has further reason to question the RNA world. His detailed study of the ribosome shows that its most ancient part, which is identical in every living thing, acts as an enzyme to link amino acids in a growing protein chain. But this ribosomal core works pretty badly, Williams told the Astrobiology Science Conference in Chicago last week, and so is unlikely to be the product of a long period of evolution by natural selection.-****-&quot;How would this have worked? Nick Hud, also at Georgia Tech, has an idea. Modern proteins and RNA don&apos;t assemble on their own, but Hud has found relatives of each that do, spontaneously forming protein-like molecules up to 14 amino acids long as well as gene-like rows of proto-RNA, he reported at the same conference.-&quot;In Williams&apos;s scenario, these crude proto-proteins and proto-RNA would have happened to form a ribosomal core, which helped accelerate the random assembly of more protein and RNA molecules (see diagram). &quot;This is the origin of life. I think this came before replication,&quot; says Williams.-***-&quot;If Williams is right, RNA has cooperated with proteins from the very beginning. &quot;This marriage between RNA and protein is the most ancient and fundamental part of biology,&quot; he says. If so, those who are trying to build self-replicating RNA molecules in the lab are looking for something that never existed.-&quot;Not everyone agrees with this idea, however. &quot;There are other reasons to expect a complex RNA world,&quot; says Steven Benner at the Foundation for Applied Molecular Evolution in Florida. Many modern protein enzymes, for example, have RNA associated with them that serves no functional role. This implies that they must be relics from a time when RNA was the only thing around, he says.-&quot;Williams is now synthesising what he thinks is the most ancient ribosomal core, free of all its later add-ons, to test whether it really assembles RNA and protein molecules.&quot;

Theoretical origin of life; in meteorites

by David Turell @, Saturday, July 11, 2015, 15:40 (3202 days ago) @ David Turell

Researchers of meteorites keep finding &apos;specimens&apos; they try to pass off as evidence of alien life from afar, but so far all claims are debunked:-http://phys.org/news/2015-07-extraterrestrial-life.html-&quot;As we become more advanced in astronomy, continuously searching and finding lots of potentially habitable extrasolar planets that could harbor alien life, it seems that it&apos;s not a matter of if but when we will find extraterrestrial organisms. However, the real tough problem here is: How we could determine if the alien life has really been found? &quot;The question is not so much &apos;when will we find extraterrestrial life?&apos; But &apos;when will we know we have found extraterrestrial life?&apos;&quot; Terence Kee, the President of the Astrobiology Society of Britain told Phys.org. &quot;My feeling is that we may indeed find signs of life in a few decades, but whether we will be unambiguously able to identify it as &apos;extraterrestrial life&apos; - as opposed to terrestrial contamination or abiotic far-from-equilibrium processes - in such a short time-frame, I&apos;m not so sure.&quot; -&quot;We could also turn to meteorites in the ongoing search for E.T. and hope that these rocks came from a parent body that may have harbored life. If we&apos;re lucky, relics of life are contained within that sample and have not been destroyed. Kee surprisingly admits that luck is really the key condition here.-&quot;&apos;As most of these relics are likely to have been fossilized in some way, we would need to cash in on some more luck so that we can demonstrate sufficient differences between such relics and potential abiotic mechanisms of formation on earth&#151;chemical compositional differences, isotopic ratio&apos;s mineral morphologies or, most valuable perhaps, presence of specific molecules which could only be produced by biogenic processes, etcetera,&quot; he said.-****-&quot;But the last week&apos;s claims also sparked skepticism among other scientists specializing in the search for extraterrestrial life, debunking the newly presented hypothesis. The researchers rejecting the new findings emphasize that complex organics are generated in many places in the solar system through photochemistry and this is evidence for anything other than abiotic chemistry.-&quot;So far, we haven&apos;t found any convincing proof of alien life embedded in meteorites. However, Kee, undeterred by the long-lasting search and continuous skepticism, is looking to the future with hope.&quot;

Theoretical origin of life; an article asks for information

by David Turell @, Saturday, July 18, 2015, 21:07 (3195 days ago) @ David Turell

This article specifically says the start of life requires information and knowledge. The source of that information is the question:-http://aeon.co/magazine/science/constructor-theory-solves-the-riddle-of-life/-&quot;Constructor theory gives the &#145;recipe&apos; an exact characterisation in fundamental physics. It is digitally coded information that can act as a constructor and has resiliency - the capacity, once it is instantiated in physical systems, to remain so instantiated. In constructor theory, that is called knowledge - a term used here without the usual connotation that it is known by someone: it merely denotes this particular kind of information with causal power and resiliency. And an essential part of the explanation of all distinctive properties of living things (and of accurate constructors in general) is that they contain knowledge in that sense.-&quot;Moreover, it is a fundamental idea of constructor theory that any transformation that is not forbidden by the laws of physics can be achieved given the requisite knowledge. There is no third possibility: either the laws of physics forbid it, or it is achievable. This accounts for another aspect of the evolutionary story. Ever better constructors can be produced, without limit, given the relevant knowledge, instantiated in digital recipes.-&quot;Thus the constructor theory of life shows explicitly that natural selection does not need to assume the existence of any initial recipe, containing knowledge, to get started. It shows that, whatever recipes we might find in living things, they do not require ad?hoc, biocentric or mysterious laws of physics in order to come into existence from elementary initial components. They need only the laws of physics to permit the existence of digital information, plus sufficient time and energy, which are non-specific to life. This adds another deep reason why a unification in our understanding of the phenomena of life and physics is possible. Whatever the laws of physics do not forbid us, we can do. Whether or not we will, depends on how much knowledge we create. It is up to us.&quot;

Theoretical origin of life; an article asks for information

by dhw, Sunday, July 19, 2015, 13:38 (3194 days ago) @ David Turell
edited by dhw, Sunday, July 19, 2015, 13:44

DAVID: This article specifically says the start of life requires information and knowledge. The source of that information is the question:-http://aeon.co/magazine/science/constructor-theory-solves-the-riddle-of-life/-The heading of this article is &#147;Life without design&#148;, and the basic argument is contained within this dazzling piece of reasoning: &#147;it is a fundamental idea of constructor theory that any transformation that is not forbidden by the laws of physics can be achieved given the requisite knowledge. There is no third possibility: either the laws of physics forbid it, or it is achievable.&#148;-The riddle of life is thus apparently solved by the fact that if materials have the requisite knowledge to create life and the laws of physics don&apos;t forbid the creation of life, you will get life. It is grossly unfair of David to ask for the source of the requisite knowledge!-With my customary zeal, I am now applying for a grant to Wolfson College, Oxford, where Chiara Marletto is a junior research fellow. I wish to continue my research on my own new Theory of Origins. The basis of this is my discovery that life exists and therefore life is possible. I intend to apply this astonishing insight into all forms of existence, demonstrating that everything that exists exists because its existence is possible, and therefore all kinds of existence are possible so long as they are possible.

Theoretical origin of life; an article asks for information

by David Turell @, Sunday, July 19, 2015, 15:09 (3194 days ago) @ dhw

DAVID: This article specifically says the start of life requires information and knowledge. The source of that information is the question:&#13;&#10;> &#13;&#10;> http://aeon.co/magazine/science/constructor-theory-solves-the-riddle-of-life/&#13;&... &#13;&#10;> Dhw: The riddle of life is thus apparently solved by the fact that if materials have the requisite knowledge to create life and the laws of physics don&apos;t forbid the creation of life, you will get life. It is grossly unfair of David to ask for the source of the requisite knowledge!-A stupid article, but it makes the point. Nothing can happen without information at the start.

Theoretical origin of life; an article asks for information

by Balance_Maintained @, U.S.A., Sunday, July 19, 2015, 23:44 (3194 days ago) @ dhw

I&apos;m looking forward to the book that will surely follow such a groundbreaking and breathtaking research.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Theoretical origin of life; hot puddles

by David Turell @, Monday, July 20, 2015, 17:18 (3193 days ago) @ Balance_Maintained

Amino acids in hot puddles that dry out can create polymerization into polymers. Note only eight essential amino acids ha e been found in meteorites than have hit the Earth, but these scientists spin a just so story:-http://www.sciencedaily.com/releases/2015/07/150720094522.htm-&quot;The research supports the theory that life could have begun on dry land, perhaps even in the desert, where cycles of nighttime cooling and dew formation are followed by daytime heating and evaporation. Just 20 of these day-night, wet-dry cycles were needed to form a complex mixture of polypeptides in the lab. The process also allowed the breakdown and reassembly of the organic materials to form random sequences that could have led to the formation of the polypeptide chains that were needed for life.-&quot;Experimentally, graduate student Sheng-Sheng Yu put the amino and hydroxy acid mixtures through 20 wet-dry cycles to produce molecules that are a mixture of polyesters and peptides, containing as many as 14 units. After just three cycles, and at temperatures as low as 65 degrees Celsius, peptides consisting of two and three units began to form. Postdoctoral fellow Jay Forsythe confirmed the chemical structures using NMR mass spectrometry.-&quot;&apos;We allowed the peptide bonds to form because the ester bonds lowered the energy barrier that needed to be crossed,&quot; Hud added.-&quot;On the early Earth, those cycles could have taken 20 days and nights -- or perhaps much longer if the heating and drying cycles corresponded to seasons of the year.-&quot;Beyond easily forming the polypeptides, the wet-dry process has an additional advantage. It allows compounds like peptides to be regularly broken apart and reformed, creating new structures with randomly-ordered amino acids. This ability to recycle the amino acids not only conserves organic material that may have been in short supply on the early Earth, but also provides the potential for creating more useful combinations.&quot;-My usual comment: Done by intelligent design in a lab.

Theoretical origin of life; a computer model

by David Turell @, Tuesday, July 28, 2015, 18:49 (3185 days ago) @ David Turell

Based on lots of hopeful sentiment about small peptides linking up. Computer models can suggest anything, and this is obviously a model built on chance connections of peptides. How can anything meaningful develop?:-http://www.sciencedaily.com/releases/2015/07/150728110720.htm-&quot;Tkachenko and Maslov have proposed a new model that shows how the earliest self-replicating molecules could have worked. Their model switches between &quot;day&quot; phases, where individual polymers float freely, and &quot;night&quot; phases, where they join together to form longer chains via template-assisted ligation. The phases are driven by cyclic changes in environmental conditions, such as temperature, pH, or salinity, which throw the system out of equilibrium and induce the polymers to either come together or drift apart.-&quot;According to their model, during the night cycles, multiple short polymers bond to longer polymer strands, which act as templates. These longer template strands hold the shorter polymers in close enough proximity to each other that they can ligate to form a longer strand -- a complementary copy of at least part of the template. Over time, the newly synthesized polymers come to dominate, giving rise to an autocatalytic and self-sustaining system of molecules large enough to potentially encode blueprints for life, the model predicts.&quot;-***-Under Tkachenko and Maslov&apos;s model, the move from monomers to polymers is a very sudden one. It&apos;s also hysteretic -- that is, it takes a very certain set of conditions to make the initial leap from monomers to self-replicating polymers, but those stringent requirements are not necessary to maintain a system of self-replicating polymers once one has leapt over the first hurdle.-One limitation of the model that the researchers plan to address in future studies is its assumption that all polymer sequences are equally likely to occur. Transmission of information requires heritable variation in sequence frequencies -- certain combinations of bases code for particular proteins, which have different functions. The next step, then, is to consider a scenario in which some sequences become more common than others, allowing the system to transmit meaningful information-***-Summary: &quot;Recent research by Tkachenko and Maslov, published July 28, 2015 in The Journal of Chemical Physics, suggests that self-replicating molecules such as RNA may have arisen through a process called template-assisted ligation. That is, under certain environmental conditions, small polymers could be driven to bond to longer complementary polymer template strands, holding the short strands in close enough proximity to each other that they could fuse into longer strands. Through cyclic changes in environmental conditions that induce complementary strands to come together and then fall apart repeatedly, a self-sustaining collection of hybridized, self-replicating polymers able to encode the blueprints for life could emerge.&quot;

Theoretical origin of life; organic molecules on comets

by David Turell @, Monday, August 03, 2015, 14:29 (3179 days ago) @ David Turell

Quite a variety:-http://www.sciencedaily.com/releases/2015/07/150730172518.htm-&quot;Twenty-five minutes after Philae&apos;s initial contact with the cometary nucleus, COSAC (Cometary Sampling and Composition experiment) carried out a first chemical analysis in sniffing mode, that is, by examining particles that passively enter the instrument. These particles probably came from the cloud of dust raised by Philae&apos;s first contact with the ground. Sixteen compounds were identified, divided into six classes of organic molecules (alcohols, carbonyls, amines, nitriles, amides and isocyanates). Of these, four were detected for the first time on a comet (methyl isocyanate, acetone, propionaldehyde and acetamide).-&quot;These particles are precursors of molecules important for life (sugars, amino acids, DNA bases, etc). However, the possible presence of these more complex compounds was not unambiguously confirmed in this first analysis. In addition, almost all the compounds detected are potential precursors, products, combinations or by-products of each other, which provides a glimpse of the chemical processes at work in a cometary nucleus, and even in the collapsing solar nebula in the very early Solar System.&quot;

Theoretical origin of life; How to glue RNA to membranes

by David Turell @, Thursday, August 13, 2015, 22:14 (3169 days ago) @ David Turell

All done in the lab by intelligent design. No word about the origin of the peptides, the RNA or the membranes.-http://www.scientificamerican.com/article/origin-of-life-first-cells-may-have-been-glued-together/?WT.mc_id=SA_DD_20150813-&quot;Nobel laureate Jack Szostak and his team at the Massachusetts General Hospital in Boston, US, found that peptides just seven amino acids long or fewer can localise RNA to a basic cell membrane. &#145;This mechanism is really quite simple and has been used in other fields to form RNA complexes with a variety of materials,&apos; says Neha Kamat, the first author of the paper. &#145;The simplicity of our system is what makes this mode of RNA-membrane association seem plausible on a primitive Earth.&apos;-&quot;The authors used small peptides containing both a hydrophobic group that associates with the membrane and a cationic group that electrostatically interacts with the negatively charged phosphate groups of RNA. Kamat explains that such peptides could have been present on the prebiotic Earth and may have helped to bring RNA and membranes together. &#145;The peptides essentially act as a kind of glue to bind membranes and then attract and hold the RNA at the membrane surface,&apos; she says.-&quot;&#145;The first forms of life were likely to be simple cells containing systems of peptides and short strands of a nucleic acid such as RNA,&apos; explains David Deamer, a chemist who works on membrane evolution at the University of California, Santa Cruz, US. &#145;The results provide significant insight into the way that protocellular systems could have spontaneously assembled on the prebiotic Earth 4 billion years ago, an essential first step toward the origin of cellular life.&apos;&quot;-Comment: this all happened by chance?

Theoretical origin of life; How to glue RNA to membranes

by romansh ⌂ @, Thursday, August 13, 2015, 22:16 (3169 days ago) @ David Turell

Just ignore the diatribe at the beginning. -http://www.agnosticsinternational.org/forum/viewtopic.php?f=34&t=1819

Theoretical origin of life; How to glue RNA to membranes

by David Turell @, Thursday, August 13, 2015, 23:48 (3169 days ago) @ romansh

Rom: Just ignore the diatribe at the beginning. &#13;&#10;> &#13;&#10;> http://www.agnosticsinternational.org/forum/viewtopic.php?f=34&t=1819-Thank you for a great entry.-Great music. The biochemical information is correct. I&apos;ve read and quoted Szostak. This is much of his research as part of a just-so story of a series of chance events in just the right order to get to life. The lipid membrane is very important because one cannot polymerize in water. Enzymes are also very important, and the video glosses over how big and complex they always are. Information developed by chance? How? Robert Shapiro, a before his death a few years ago, proposed this type of approach would not work. In his book &quot;Origins&quot; he did agree that sea vents are a possible source of energy, and I agree. I also agree that abiogenesis should be kept separate from evolution until life actually begins, but the two are intimately related in that the from of beginning life dictates what forms ensuing life takes in its genome mechanism, not necessarily in the phenotypes that appear.

Theoretical origin of life; bioelectrical energy

by David Turell @, Friday, August 21, 2015, 19:33 (3161 days ago) @ David Turell

The presence of mitochondria and bioelectrical energy allowed life to become multicellular:-http://www.the-scientist.com/?articles.view/articleNo/43668/title/Opinion--Life-s-X-Factor/-&quot;...there is an evolutionary gulf between the structural complexity of even the most multifaceted prokaryotes (still cyanobacteria, which have genomes of up to 12 megabases (compared with Loki&apos;s meagre five) and standard protists, with genomes ranging up to 100,000 megabases, coding for vastly more complex morphologies.-&quot;In my latest book, The Vital Question, I argue that the answer lies in energy&#151;specifically, the totally unanticipated mechanism of membrane bioenergetics. Essentially all cells rely on electrochemical ion gradients (usually proton gradients) across membranes to drive the synthesis of adenosine triphosphate (ATP). Autotrophs rely on membrane bioenergetics to drive carbon fixation, too. In fact, all carbon and energy metabolism depends on proton gradients across membranes.-***-&quot;Any student of evolution can still see the marks of this constraint on Earth&apos;s myriad life forms. Bacteria and archaea remained morphologically simple, despite their metabolic virtuosity, for a staggering 4 billion years.-***-&quot;So how did eukaryotes escape this energetic stranglehold? Through the rare endosymbiosis that gave rise to mitochondria. The advantage of mitochondria had nothing to do with oxygen, or even compartmentalisation: it was all about genes&#151;loss of them. Mitochondria ultimately lost 99 percent of their genes. Yet they invariably retain a small handful of genes that are necessary to control respiration locally, giving eukaryotes multibacterial power without the overhead.-***-&quot;In The Vital Question, I posit that the basal traits of eukaryotes were forged in the crucible of endosymbiosis between prokaryotes, which drove the evolution of sex, the nucleus, the germline-soma distinction, aging, and death. These ideas might be wrong, but they are testable, and could have considerable explanatory power. I think we&apos;ll only understand why life is the way it is when we bring energy into the equation.&quot;-Comment: Yes sufficient energy is needed, but information is needed also

Theoretical origin of life

by romansh ⌂ @, Thursday, August 13, 2015, 23:22 (3169 days ago) @ David Turell

And if anyone wants to see Jack explain it in his own words.-https://www.youtube.com/watch?v=PqPGOhXoprU#t=14

Theoretical origin of life: the effect of comets

by David Turell @, Wednesday, August 26, 2015, 13:36 (3156 days ago) @ romansh

Comets may arrive and produce short peptides:-http://www.sciencedaily.com/releases/2015/08/150819083326.htm-&quot;They took frozen mixtures of amino acid, water ice and silicate (forsterite) at cryogenic condition (77 K), and used a propellant gun to simulate the shock of a comet impact. After analyzing the post-impact mixture with gas chromatography, they found that some of the amino acids had joined into short peptides of up to 3 units long (tripeptides).-&quot;Based on the experimental data, the researchers were able to estimate that the amount of peptides produced would be around the same as had been thought to be produced by normal terrestrial processes (such as lighting storms or hydration and dehydration cycles).-&quot;According to Haruna Sugahara: &quot;Our experiment showed that the cold conditions of comets at the time of the impacts were key to this synthesis, as the type of peptide formed this way are more likely to evolve to longer peptides.-&quot;This finding indicates that comet impacts almost certainly played an important role in delivering the seeds of life to the early Earth. It also opens the likelihood that we will have seen similar chemical evolution in other extraterrestrial bodies, starting with cometary-derived peptides.-***-&quot;The production of short peptides is the key step in the chemical evolution of complex molecules. Once the process is kick-started, then much less energy is needed to make longer chain peptides in a terrestrial, aquatic environment.&quot;-Comment: Peptides cannot be made in water without enzymes!--***-&quot;Commenting, Professor Mark Burchell (University of Kent, UK) said: &quot;This is a new piece of work which adds significantly to the exciting field of the origin of complex molecules on the Earth. It has long been known that ices under shock can generate and break bonds in complex organics. The detection of amino acids on comet 81P/Wild2 by the NASA Stardust mission in the last decade, and the now regular exciting news from the Rosetta mission to comet 67P/Churyumuv-Gerasimenko indicates that comets are a rich source of materials. Two key parts to this story are how complex molecules are initially generated on comets and then how they survive/evolve when the comet hits a planet like the Earth. Both of these steps can involve shocks which deliver energy to the icy body. For example, Zita Martins and colleagues recently showed how complex organic compounds can be synthesized on icy bodies via shocks. Now, building on earlier work, Dr Sughara and Dr Mimura have shown how amino acids on icy bodies can be turned into short peptide sequences, another key step along the path to life.&apos;&quot;-Comment: OOL research folks are always so hopeful they have found something.

Theoretical origin of life: again hot sea vents

by David Turell @, Saturday, September 05, 2015, 19:17 (3146 days ago) @ David Turell

These vents can certainly form organic compounds:-https://www.newscientist.com/article/dn28074-watery-time-capsule-hints-at-how-life-got-started-on-early-earth/-Her team has previously found a wealth of complex organic molecules in the water.-Now her colleague, Christopher Glein, has performed a raft of calculations to show that all of those molecules could have formed through perfectly feasible abiotic chemical reactions in the conditions found in such ancient hydrothermal vents.-His calculations show the conditions were particularly favourable for the formation of some key chemicals, including glyceraldehyde, one of the precursors of RNA and DNA, and pyruvate, which is important for cell metabolism.-Traditionally, biochemists have considered these molecules to be relatively hard to generate abiotically, says Glein who presented his findings at the Goldschmidt conference in Prague this week. &#147;But that&apos;s assuming they are being synthesised under familiar conditions at Earth&apos;s surface,&#148; he says.-Conditions are very different in the ancient hydrothermal vents, they found. The water there has reacted with the rock through a process called serpentinisation to create an environment poor in oxygen but rich in hydrogen, iron and sulphur. Combined with temperatures of about 100 &#176;C - also found there - many complex organic compounds can easily form.-Comment: Complex organic compounds are not proteins. As I&apos;ve noted before, life needs chains of organic molecules forming proteins by the process of polymerization. This will not happen automatically in water of any temperature without complex enzymes to help the process.

Theoretical origin of life: interview with Stanley Miller

by David Turell @, Wednesday, September 16, 2015, 00:57 (3136 days ago) @ David Turell

Miller of the famous Miller-Urey lightning in a bottle experiment. They got 13 of the 20 essential amino acids in the tarry gunk they created. They used a reducing atmosphere which is now not thought to be correct in the proportions of gases, but he insists the atmosphere must be reducing:-http://www.astrobio.net/news-exclusive/primordial-recipe-spark-and-stir/-&quot;AB: What is your current opinion on the need for a primitive reducing atmosphere for pre-biotic life to take hold 3.5 to 3.8 billion years ago?- &quot;SM: I have not found an alternative to disprove the need for a primitive reducing atmosphere.- &quot;AB: Do you believe that material transported on meteors or comets is insufficient to seed life, if such amino acids were successfully transported intact to the surface of the Earth? -&quot;SM: Meteorite and other exogenous contributions become very important only if the earth had a neutral atmosphere. However, if the only sources of organic compounds under such conditions were the very small number of compounds produced with a CO2 rich atmosphere and delivered from outside, the amount may be too low for the origin of life.-&quot; AB: Since many astrobiologists are currently examining hydrothermal vents, in search of extremophiles, does the prebiotic chemistry actually get decomposed rather than enhanced by the presence of such ocean venting?- &quot;SM: Locating extremophiles is not relevant to the synthesis of organic compounds necessary for life, as the conditions of such ocean venting decomposes rather than enhances prebiotic chemistry. -***-&quot;There are other hurdles in the progression from simple molecules to complex life that are large research topics. Producing amino acids and nucleotides , and getting them to polymerize into proteins and nucleic acids (typically, RNA), are parts of a vast and ongoing &#145;origins&apos; discussion. But RNA is a relatively fragile component (compared to DNA, or other biomolecules), and thus again its first appearance remains subject to the particular local conditions of the early Earth. To stabilize or catalyze the first biomolecules, clay crystals and vesicle reactions may have helped. No one has been able to synthesize RNA without the help of protein catalysts or nucleic acid templates.&quot;-Comment: Startng life is not easy. Note &quot;RNA is fragile&quot;.

Theoretical origin of life: using an enzyme

by David Turell @, Wednesday, September 23, 2015, 20:18 (3128 days ago) @ David Turell

By using a living enzyme scientists can create molecules useful in life, but this in no way tells us how life began:-http://phys.org/news/2015-09-synthesis-method-imitates-molecules-dawn.html-&quot;Researchers from the Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), with support from the Nuclear Magnetic Resonance Service of the Universitat Aut&#242;noma de Barcelona (UAB) have developed a method for synthesising organic molecules very selectively, by assembling simple molecules and using an enzyme from E. coli (FSA: D-fructose-6-phosphate aldolase), which acts as a biocatalyst. -&quot;This is a significant step forward since it replicates the formation of carbohydrates in conditions resembling those that presumably initiated life on the Earth (prebiotic conditions) and because it allows relatively large organic molecules to be obtained very selectively and efficiently. -***-&quot;The enzyme FSA was discovered in 2001 and its physiological function in E. coli is still unknown. It is thought to be an ancestral enzyme, and that it is active before a broad range of compounds. What surprised the researchers is that it is a very malleable enzyme, much more so than others. As a result, with only a small number of genetic mutations in the enzyme, its catalytic capacity can be modulated and increased significantly. This is what allows the enzyme to be carefully adapted in order to synthesise several molecules at will.-&quot;The metabolism of carbohydrates in living organisms is a complex process, forged over millions of years of evolution. It is no easy task to carry out these processes in a flask, whether by assembling the enzymes involved in the process or by manipulating the metabolic pathways of living organisms. Nor is it simple to obtain carbohydrates with conventional chemical methods, which require several stages and the use of organic solvents.&#13;&#10;&quot; (my bold)-Comment: If first life had enzymes, very large molecules, how did they arise? So far in the lab e only get life from life.

Plant life: using an enzyme

by David Turell @, Wednesday, September 23, 2015, 20:27 (3128 days ago) @ David Turell

To fix nitrogen from the air, plants have an enzyme in the roots that does this. An unusual enzyme combining sulfur and iron:-http://phys.org/news/2015-09-world-nitrogen-fixation.html-&quot;The process is called nitrogen fixation, and it occurs in microorganisms on the roots of plants. This is how nature makes its own fertilizers to feed plants, which feed us.-&quot;The enzyme responsible for natural nitrogen fixation is called nitrogenase. Yale chemistry professor Patrick Holland and his team designed a new chemical compound with key properties that help to explain nitrogenase. The findings are described in the Sept. 23 online edition of the journal Nature.-&quot;&apos;Nitrogenase reacts with nitrogen at a cluster of iron and sulfur atoms, which is strange because other iron-sulfur compounds typically don&apos;t react with nitrogen, either in other enzymes or in the thousands of known iron-sulfur compounds synthesized by chemists,&quot; Holland said.&#13;&#10; (my bold)&#13;&#10;&quot;Keeping that in mind, Holland and his team designed a new compound with two distinct properties found in nitrogenase: large shielding groups of atoms that prevented undesired reactions, and a weak iron-sulfur bond that could break easily upon the addition of electrons. The design proved successful because the compound binds nitrogen from the atmosphere, just as nitrogenase does.&quot;-Comment: Enzymes are necessary in all life, and note that this one has unusual activity. How did Darwin evolution find it?

Theoretical origin of life: Miller-Urey redone

by David Turell @, Thursday, October 08, 2015, 14:13 (3113 days ago) @ David Turell

Still with lots of lab manipulation a minor success with E. coli growth. How that helps origin-of-life theories is not obvious:-http://www.realclearscience.com/journal_club/2015/10/05/the_primordial_soup_was_edible_109402.html-&quot;Back in 2005, when I was a first-year microbiology graduate student, I enrolled in a course on bacterial physiology. One of our guest lecturers, Dr. Franklin Harold, was an esteemed researcher in bioenergetics, a field that examines how cells derive and utilize energy. One evening, outside of class, I happened upon Dr. Harold at a seminar, and I asked him a question: &quot;What is your opinion on origin of life research?&quot;-&quot;He responded, &quot;It has been an abject failure.&quot;&#13;&#10; &#13;&#10;&quot;Ten years later, it is still difficult to argue with him. A brief survey of the Wikipedia entry on abiogenesis reveals about 20 different theories and explanations for how non-living matter can evolve into metabolizing lifeforms, ranging from the plausible (RNA World) to the patently ridiculous (panspermia). Put simply, a field with so many different interpretations is wandering lost in the long grass. Any sort of hint at the truth, therefore, is a welcome discovery. Such a hint, albeit a small one, may have been uncovered by new research that has been published in Scientific Reports.-&quot;Their finding definitely supports the notion that the Miller-Urey gunk can support life. But, there are three major caveats:-&quot;First, the researchers still had to add inorganic salts (containing ions such as potassium, magnesium, and calcium) in order for the bacteria to grow. Second, it is debatable whether removing toxic molecules, such as cyanide, is legitimate. Finally, their experiment does nothing to solve the biggest questions of all: How did complex molecules form (e.g., DNA), and how did life evolve?-&quot;The answers to those questions remain as murky as the Miller-Urey goo.&quot;

Theoretical origin of life: lab play

by David Turell @, Thursday, October 08, 2015, 18:32 (3113 days ago) @ David Turell

Of course if one sets up a robot to make proteins in a lab, it will work:-http://phys.org/news/2015-10-chemical-life-began-earth.html-&quot;In a new paper published today (Wednesday 7 October) in the journal Nature Communications, a team from the University of Glasgow&apos;s School of Chemistry describe a new approach to solving a 50-year conundrum in which they used an automated robot system to explore many different random combinations of the building blocks of proteins.-&quot;The team found that peptide compounds of long length and complexity can form in a very simple way by heating and cooling the building blocks as they go through wet and dry cycles.-***-&quot;&apos;The problem is that the origin of life was thought to be so complicated that we are not sure if there was enough time to make such complex molecules or understand themechanisms by which they were produced. -&quot;&apos;Our research aimed to help answer this question by creating a robot capable of creating many different random combinations of conditions, and them focusing in on the promising ones. Very quickly, we found that it was possible to assemble the building blocks just like the way we find them in modern proteins Our chemical search engine is able to search large amounts of chemical space, similar to how systems like Google search the internet. Instead of reading HTML, however, the system performs chemical reactions.&quot;-&quot;The team conclude that small protein fragments can be made much longer and much more easily than previously thought, which could lead to the formation of life-like molecules and machines in the laboratory.-&quot;The team&apos;s robot system allows the researchers to record very precisely how many combinations of chemicals and the outcomes of the reaction, which will help them to calculate the likelihood of producing the first complex molecules essential for life as we know it today.-&quot;Professor Cronin added: &quot;We believe this is a significant finding which could suggest that the beginning of life on Earth was a simpler process than we previously expected. It could also provide valuable support to the idea that the universe is teeming with life, as well as allowing us to &apos;search&apos; for new types of life in the laboratory.&apos;&quot; -&#13;&#10; Comment: As Forrest Gump said, &quot;stupid is as stupid does.&quot; Justifying grant moneys! Adds nothing to the problem.

Theoretical origin of life: a wild new theory

by David Turell @, Friday, October 16, 2015, 21:09 (3105 days ago) @ David Turell

The physics of entropy means life has to happen. Whew!:-http://www.businessinsider.com/groundbreaking-idea-of-lifes-origin-2014-12-&quot;At the heart of England&apos;s idea is the second law of thermodynamics, also known as the law of increasing entropy or the &#147;arrow of time.&#148; Hot things cool down, gas diffuses through air, eggs scramble but never spontaneously unscramble; in short, energy tends to disperse or spread out as time progresses. Entropy is a measure of this tendency, quantifying how dispersed the energy is among the particles in a system, and how diffuse those particles are throughout space. It increases as a simple matter of probability: There are more ways for energy to be spread out than for it to be concentrated.-***-&quot;Using Jarzynski and Crooks&apos; formulation, he derived a generalization of the second law of thermodynamics that holds for systems of particles with certain characteristics: The systems are strongly driven by an external energy source such as an electromagnetic wave, and they can dump heat into a surrounding bath. This class of systems includes all living things. England then determined how such systems tend to evolve over time as they increase their irreversibility. &#147;We can show very simply from the formula that the more likely evolutionary outcomes are going to be the ones that absorbed and dissipated more energy from the environment&apos;s external drives on the way to getting there,&#148; he said. The finding makes intuitive sense: Particles tend to dissipate more energy when they resonate with a driving force, or move in the direction it is pushing them, and they are more likely to move in that direction than any other at any given moment.-&#147;&apos;This means clumps of atoms surrounded by a bath at some temperature, like the atmosphere or the ocean, should tend over time to arrange themselves to resonate better and better with the sources of mechanical, electromagnetic or chemical work in their environments,&#148; England explained.-&quot;Self-Replicating Sphere Clusters: According to new research at Harvard, coating the surfaces of microspheres can cause them to spontaneously assemble into a chosen structure, such as a polytetrahedron (red), which then triggers nearby spheres into forming an identical structure.-&quot;Self-replication (or reproduction, in biological terms), the process that drives the evolution of life on Earth, is one such mechanism by which a system might dissipate an increasing amount of energy over time.-&quot;As England put it, &#147;A great way of dissipating more is to make more copies of yourself.&apos;&quot;-Comment: biological physics is a relatively new field, but I think he is straining too hard. Complex molecules still have to get together and self-organization of such a complexity seems unlikely as an unguided process.

Theoretical origin of life: earlier than thought?

by David Turell @, Tuesday, October 20, 2015, 14:25 (3101 days ago) @ David Turell

New research hints at life starting at 4.1 billion years ago, earlier than the 3.8 byo generally considered the starting point:-http://phys.org/news/2015-10-life-earth-billion-years-agomuch.html-&quot;UCLA geochemists have found evidence that life likely existed on Earth at least 4.1 billion years ago&#151;300 million years earlier than previous research suggested. The discovery indicates that life may have begun shortly after the planet formed 4.54 billion years ago. -***-&quot;The researchers, led by Elizabeth Bell&#151;a postdoctoral scholar in Harrison&apos;s laboratory&#151;studied more than 10,000 zircons originally formed from molten rocks, or magmas, from Western Australia. Zircons are heavy, durable minerals related to the synthetic cubic zirconium used for imitation diamonds. They capture and preserve their immediate environment, meaning they can serve as time capsules.-&quot;The scientists identified 656 zircons containing dark specks that could be revealing and closely analyzed 79 of them with Raman spectroscopy, a technique that shows the molecular and chemical structure of ancient microorganisms in three dimensions.-&quot;Bell and Boehnke, who have pioneered chemical and mineralogical tests to determine the condition of ancient zircons, were searching for carbon, the key component for life.-&quot;One of the 79 zircons contained graphite&#151;pure carbon&#151;in two locations.-&quot;&apos;The first time that the graphite ever got exposed in the last 4.1 billion years is when Beth Ann and Patrick made the measurements this year,&quot; Harrison said.-How confident are they that their zircon represents 4.1 billion-year-old graphite?-&quot;&apos;Very confident,&quot; Harrison said. &quot;There is no better case of a primary inclusion in a mineral ever documented, and nobody has offered a plausible alternative explanation for graphite of non-biological origin into a zircon.&quot;-&quot;The graphite is older than the zircon containing it, the researchers said. They know the zircon is 4.1 billion years old, based on its ratio of uranium to lead; they don&apos;t know how much older the graphite is.-&quot;The research suggests life in the universe could be abundant, Harrison said. On Earth, simple life appears to have formed quickly, but it likely took many millions of years for very simple life to evolve the ability to photosynthesize.-&quot;The carbon contained in the zircon has a characteristic signature&#151;a specific ratio of carbon-12 to carbon-13&#151;that indicates the presence of photosynthetic life.-&quot;&apos;We need to think differently about the early Earth,&quot; Bell said.&quot; -Comment: Graphite is a possible signature of life, but the study needs to be confirmed. Life this quick strongly suggests design

Theoretical origin of life: earlier than thought?

by David Turell @, Wednesday, October 21, 2015, 00:38 (3101 days ago) @ David Turell

Another brief story about this finding:-https://www.washingtonpost.com/news/speaking-of-science/wp/2015/10/20/ancient-crystals-might-rewrite-earths-early-history/?wpmm=1&wpisrc=nl_evening-&quot;The study, published recently in the Proceedings of the National Academy of Sciences, presents evidence in the form of zircon crystals. These minerals (which are related to the cubic zirconium made to mimic diamonds) incorporate and preserve materials from their environment as they form. The tiny crystals are basically indestructible, so they&apos;re left behind as time capsules of sorts as other minerals are lost to time.-&quot;An examination of over 10,000 zircons from the early days of the planet yielded one fleck of crystal with pure carbon in the form of graphite. The zircon was dated as 4.1 billion years old, and analysis of the carbon suggested it could have been formed by organic processes -- by a photosynthetic creature, for example.-&#147;&apos;On Earth today, if you were looking at this carbon, you would say it was biogenic,&#148; lead author Elizabeth Bell, a geochemist at the University of California, told Science. &#147;Of course, that&apos;s more controversial for the Hadean.&#148;-&quot;The study authors suggest that perhaps early Earth was more hospitable than previously thought. Recent studies have indicated as much, showing that there was liquid water even during our eon named for Hades. And if their findings are correct, they point out, and simple life arose almost instantaneously on Earth, then it could mean that simple lifeforms are common throughout the universe.-&quot;But even the researchers involved in the study admit that something other than a photosynthesizing organism could have created this particular cocktail of carbon. It&apos;s an intriguing finding, but it&apos;s far from proof that life definitely existed at that time. To really show that life thrived in the Hadean, they&apos;ll need a lot more than one tiny crystal.&quot;-Comment: Carbon should come from life, but?????

Theoretical origin of life: the effect of comets

by David Turell @, Saturday, October 24, 2015, 23:35 (3097 days ago) @ David Turell

A comet found with two organic compounds:-https://in.news.yahoo.com/unexpected-discovery-comet-contains-alcohol-182309427.html-&quot;Ethyl alcohol and a simple sugar known as glycolaldehyde were detected in Comet Lovejoy, said the study in the journal Science Advances.-&quot;&apos;These complex organic molecules may be part of the rocky material from which planets are formed,&quot; said the study.-&quot;Other organic molecules have previously been discovered in comets, most recently in comet 67P/Churyumov-Gerasimenko, on which the European space agency&apos;s Philae found several organic molecules -- including four never detected before on a comet.-&quot;Since comets contain some of the oldest and most primitive material in the solar system, scientists regard them as time capsules, offering a peek and how it all started 4.6 billion years ago.-&quot;But while the latest study does not end the debate over whether falling comets indeed seeded Earth with the components necessary for life, it does add something to our knowledge, said study co-author Dominique Bockel&#233;e-Morvan, an astrophysicist at the French National Center for Scientific Research.-&quot;&apos;The presence of a major complex organic molecule in comet material is an essential step toward better understanding the conditions that prevailed at the moment when life emerged on our planet,&quot; she told AFP.-&quot;&apos;These observations show a possible explanation for its (life&apos;s) origin on our planet,&quot; she added.-Other hypotheses exist too, including the gas from volcanic eruptions.-&quot;Comet Lovejoy is of particular interest to scientists because &quot;it is one of the most active comets in Earth&apos;s orbital neighborhood,&quot; said the study.&quot;-Comment: Comets can certainly deliver organic compounds to earth, but making them form living matter is a mighty hop, skip and jump.

Theoretical origin of life: review article

by David Turell @, Saturday, November 14, 2015, 00:02 (3077 days ago) @ David Turell

It points out how difficult the problem is:-http://www.theatlantic.com/science/archive/2015/11/inside-a-new-effort-to-discover-lifes-origins/415278/-&quot;To kick off the meeting, I&apos;m going to do the only thing I can reasonably do, which is ask the dumbest scientific questions I can think of: Did life originate more than once 4 billion years ago? Do we know for sure that origins of life events aren&apos;t happening today, on the Earth? If life&apos;s origin was a process that took tens of millions of years, how can we hope to repeat that process in an experiment? And what do we even mean when we say that something is &#147;alive&#148;?-&quot;The truth is that the question of life&apos;s origins is about as vexing a problem as science has ever faced. Ask a hundred random scientists to tell you how they think life originated and you will probably get a hundred slightly different answers. To compound matters, technology keeps opening new doors out of which new questions spill.-***-&quot;Therein lies one of the most frustrating aspects of the study of the origins of life; juicy pieces of the puzzle appear all around us, but we still can&apos;t fit them together successfully. Even defining what life really is represents a challenge. Without a good quantitative measure of &#147;aliveness,&#148; it&apos;s actually difficult to talk about origins. That puts us in danger of falling into the ancient Greek philosophical mosh pit, debating whether or not a flame is alive.(my bold)-***-&quot;Whatever the origins of life were on Earth, it&apos;s hard not to marvel at the curious organisms that came along 4 billion years later with the capacity to worry about such questions. And here, on Japan&apos;s fragile crustal island, for tonight, at least, the mood is optimistic that we might yet crack the puzzle.&quot;-Comment: I&apos;m not so confident.

Theoretical origin of life: review article

by dhw, Saturday, November 14, 2015, 13:56 (3076 days ago) @ David Turell

DAVID: It points out how difficult the problem is:-http://www.theatlantic.com/science/archive/2015/11/inside-a-new-effort-to-discover-life...-QUOTE: &quot;Whatever the origins of life were on Earth, it&apos;s hard not to marvel at the curious organisms that came along 4 billion years later with the capacity to worry about such questions. And here, on Japan&apos;s fragile crustal island, for tonight, at least, the mood is optimistic that we might yet crack the puzzle.&quot;-David&apos;s comment: I&apos;m not so confident.-I share your agnosticism.

Theoretical origin of life: review article

by David Turell @, Saturday, November 14, 2015, 15:20 (3076 days ago) @ dhw

&#13;&#10;> QUOTE: &quot;Whatever the origins of life were on Earth, it&apos;s hard not to marvel at the curious organisms that came along 4 billion years later with the capacity to worry about such questions. And here, on Japan&apos;s fragile crustal island, for tonight, at least, the mood is optimistic that we might yet crack the puzzle.&quot;&#13;&#10;> &#13;&#10;> David&apos;s comment: I&apos;m not so confident.&#13;&#10;> &#13;&#10;> dhw: I share your agnosticism.-So you will never reach an answer? I have mine.

Theoretical origin of life: another wild new theory

by David Turell @, Monday, November 23, 2015, 15:25 (3067 days ago) @ David Turell

In this pipedream genes appear from nowhere, horizontal transfers occur and the whole mess is modeled on computers:-http://phys.org/news/2015-11-species-darwinian-evolution.html-&quot;During the earliest evolution on earth, life probably resembled one big genetic jumble. At some time, presumably around 3.8 to 3.5 billion years before today, the very first biological species appeared - the ancestor of all life forms that developed via Darwinian evolution. Researchers at the Max Planck Institute for Dynamics and Self-Organization in G&#246;ttingen and at Cornell University in the USA have now conceived and modelled a possible scenario by which the first defined species could have emerged from this genetic mix. The researchers proposed that before the dawn of Darwinian evolution, life fluctuated back and forth between a genetically highly mixed and a partially unmixed state. Over time, the less mixed state exhibiting a more clearly defined genetic profile became increasingly stable and eventually generated the very first species.&quot; (my bold)-Comment: And just where did those jumbled genes come from? Too much grant money leads to too many crazy ideas.

Theoretical origin of life: more ruminations

by David Turell @, Saturday, November 28, 2015, 00:31 (3063 days ago) @ David Turell

This article wonders whether the environment when lie began on Earth was so different from now that it creates a problem of duplicating conditions. We do know how to make all the molecules under specific lab conditions, but putting them together organized as life is totally beyond us at this point.:-https://theconversation.com/imagining-strange-new-lifeforms-could-help-us-discover-our-own-origins-44869-But how did the very first cells emerge? Living systems are chemically based and therefore must obey the laws of science. Life appears to be just a series of chemical reactions - and we now understand how these reactions work at the molecular level. So surely this should tell us how life came about?-***-The real problem is in understanding how this &#147;machinery&#148; of chemicals came together to generate life. The watershed where lifeless chemical activity is transformed into organised biological metabolism is extremely difficult to identify and the trigger for this is a key ingredient missing from the &#147;primordial soup&#148;.-The assumption that early life forms must have been similar to what we see today may be preventing us from answering this question. It&apos;s possible that there were many unsuccessful precursors that bore little resemblance to present-day life. There has been speculation that primitive starting points could even have been based around an element other than carbon (the substance at the heart of all life today). Some researchers suggest that life may have originally evolved in liquids other than water. These alternatives are fascinating, but it&apos;s difficult to find a starting point for researching them because they are so unfamiliar.-A key trait that sets life apart from inanimate matter is its reliance on organisation. Molecules must be arranged in a specific way and replicate according to a detailed pattern. But the natural tendency of the whole universe is towards a state of equilibrium, or balance - where everything is spread out and nothing is ordered. Maintaining an ordered structure means life is constantly off-balance and this requires energy, which organisms must extract from their surroundings.-One way that organisms do this it to cause movement of molecules or even sub-atomic particles that can then generate energy for a cell. For example, organisms living in hydrothermal vents on the sea floor get their energy from the transfer of protons through the cell membrane.&#13;&#10;Living systems maintain their &#147;off-balance&#148; state by combining the ability to self-replicate with the ability to extract energy from their surroundings. To discover the origin of life, we need to understand how these properties combined to form a sustainable unit.-Some scientists are adopting a top-down approach, attempting to answer this question by removing bits of a living cell to determine the minimum structure required to sustain life. Others are approaching it from the bottom-up by combining the building blocks in a primitive container to mimic a simple cell.-While both approaches may be enlightening, the precise moment of transition from chemical to life (and vice versa) still evades us. But the lack of discovery is fascinating in itself - it confirms that creating life is difficult and requires conditions that are no longer naturally present on the Earth. A breakthrough in this area would not only tell us the requirements for life, but also the circumstances of its emergence.-Comment: No mention of information. Without it how are all those molecules organized?

Theoretical origin of life: more ruminations

by David Turell @, Tuesday, December 15, 2015, 00:40 (3046 days ago) @ David Turell

This is Cornelius Hunter again. He does not believe in evolution. I&apos;m not sure what he does believe in, but his comments about OOL are right on, and my point that we cannot separate origin from evolution is endorsed by him:-http://darwins-god.blogspot.com/2015/12/biologos-and-science-case-of-ool.html-&quot;Finally, there is the ultimate argument which firewalls OOL off from evolution.-&quot;Finally, as a purely technical matter, the theory of evolution does not propose an explanation to the question of the origin of life at all. The theory of evolution becomes relevant only after life has already begun-&quot; As if sensing a problem, and just in case we were beginning to have doubts, we are told to forget about the whole thing. Forget about all those journals, conferences, textbook claims about the origin of life, popular books and newspaper articles, speeches and blogs. It all has nothing to do with evolution after all.&quot;-Comment: Darwin used this as a crutch, and its been used ever since.

Theoretical origin of life: more ruminations

by dhw, Tuesday, December 15, 2015, 22:23 (3045 days ago) @ David Turell

DAVID: This is Cornelius Hunter again. He does not believe in evolution. I&apos;m not sure what he does believe in, but his comments about OOL are right on, and my point that we cannot separate origin from evolution is endorsed by him:-http://darwins-god.blogspot.com/2015/12/biologos-and-science-case-of-ool.html-QUOTE: &quot;Finally, there is the ultimate argument which firewalls OOL off from evolution&quot;&quot;.&#13;&#10;QUOTE (meant ironically): &quot;Finally, as a purely technical matter, the theory of evolution does not propose an explanation to the question of the origin of life at all. The theory of evolution becomes relevant only after life has already begun.&#148;-Absolutely right, and I would also have to agree that evolution cannot be classed as a fact, even though it has been so widely accepted. However, from this point on, he goes off the rails, as you will see from a different quote: -QUOTE: &#147;Evolutionists believe that the species, life, the Earth and planets, the Sun, the galaxies, yes the entire universe arose by chance events. There is no limit to what evolution can create, but when problems arise, the topic is simply dismissed as extraneous to the theory.&#148;-That is what atheistic evolutionists believe, but the theory of common descent, as opposed to separate creation, has been accepted by millions of believers, including Catholics and my favourite panentheist, David Turell. We both disagree with Darwin&apos;s explanation of the driving force (random mutations), but the above is a deliberate attempt to discredit the WHOLE theory by conflating it with a totally different theory (that of abiogenesis). Yet another shameful distortion.-QUOTE: &quot;As if sensing a problem, and just in case we were beginning to have doubts, we are told to forget about the whole thing. Forget about all those journals, conferences, textbook claims about the origin of life, popular books and newspaper articles, speeches and blogs. It all has nothing to do with evolution after all.&quot;-David&apos;s comment: Darwin used this as a crutch, and its been used ever since.-No he didn&apos;t, and you know he didn&apos;t. He emphasized that his theory was perfectly compatible with religious belief, and so it is, though it is not compatible with the story of Creation told in the Bible. As you and I agreed recently, the problem of the origin of life is crucial to concepts of evolutionary purpose, but that is a separate issue from the question of whether we did or did not descend from earlier forms of life.

Theoretical origin of life: more ruminations

by David Turell @, Wednesday, December 16, 2015, 00:44 (3045 days ago) @ dhw

DAVID: This is Cornelius Hunter again. He does not believe in evolution. I&apos;m not sure what he does believe in, but his comments about OOL are right on, and my point that we cannot separate origin from evolution is endorsed by him:&#13;&#10;> &#13;&#10;> dhw: Absolutely right, and I would also have to agree that evolution cannot be classed as a fact, even though it has been so widely accepted. However, from this point on, he goes off the rails, as you will see from a different quote:-I know the quotes. I warned you I used him only to make the point about the continuum of OOL and evolution of living beings.&#13;&#10; &#13;&#10;> &#13;&#10;> David&apos;s comment: Darwin used this as a crutch, and its been used ever since.&#13;&#10;> &#13;&#10;> dhw: No he didn&apos;t, and you know he didn&apos;t.-You are misinterpreting me. I only brought Hunter into the picture to make the point, as he does, Darwin starts after OOL. I think that is a deliberate act on Darwin&apos;s part, because to me, any rational person has to recognize that the mechanism to evolve is part and parcel of original life, or then why did evolution occur at all, if original life did not contain the ability and had to learn how to evolve after arrival? And if it had to learn, how did that happen?

Theoretical origin of life: more ruminations

by dhw, Wednesday, December 16, 2015, 21:54 (3044 days ago) @ David Turell

David&apos;s comment (re OOL): Darwin used this as a crutch, and its been used ever since.-dhw: No he didn&apos;t, and you know he didn&apos;t.-DAVID: You are misinterpreting me. I only brought Hunter into the picture to make the point, as he does, Darwin starts after OOL. I think that is a deliberate act on Darwin&apos;s part, because to me, any rational person has to recognize that the mechanism to evolve is part and parcel of original life, or then why did evolution occur at all, if original life did not contain the ability and had to learn how to evolve after arrival? And if it had to learn, how did that happen?-Of course the mechanism had to be part and parcel of original life. But the fact that Darwin did not offer a solution to the mystery of the origin of life and the mechanism (and in your view and mine was wrong about random mutations and gradualism) does not make one iota of difference to the theory that all forms of life descended from earlier forms. Atheistic neo-Darwinists are just as guilty as creationist theists of distorting his theory, since all of them try to conflate evolution with abiogenesis in order to suit their agenda. But we have had this discussion before, and I thought you had agreed to avoid such blatant misrepresentation. Back we go: &#13;&#10;DARWIN: &#147;There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one.&#148; &#13;&#10;Does this not satisfy you that Darwin&apos;s theory does not need the crutch of abiogenesis?

Theoretical origin of life: more ruminations

by David Turell @, Thursday, December 17, 2015, 00:48 (3044 days ago) @ dhw

David&apos;s comment (re OOL): Darwin used this as a crutch, and its been used ever since.&#13;&#10;> &#13;&#10;> dhw: No he didn&apos;t, and you know he didn&apos;t.&#13;&#10;> &#13;&#10;> DAVID: You are misinterpreting me. I only brought Hunter into the picture to make the point, as he does, Darwin starts after OOL. I think that is a deliberate act on Darwin&apos;s part, because to me, any rational person has to recognize that the mechanism to evolve is part and parcel of original life, or then why did evolution occur at all, if original life did not contain the ability and had to learn how to evolve after arrival? And if it had to learn, how did that happen?&#13;&#10;> &#13;&#10;> Of course the mechanism had to be part and parcel of original life. But the fact that Darwin did not offer a solution to the mystery of the origin of life and the mechanism (and in your view and mine was wrong about random mutations and gradualism) does not make one iota of difference to the theory that all forms of life descended from earlier forms. Atheistic neo-Darwinists are just as guilty as creationist theists of distorting his theory, since all of them try to conflate evolution with abiogenesis in order to suit their agenda. But we have had this discussion before, and I thought you had agreed to avoid such blatant misrepresentation. Back we go: &#13;&#10;> DARWIN: &#147;There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one.&#148; &#13;&#10;> Does this not satisfy you that Darwin&apos;s theory does not need the crutch of abiogenesis?

Theoretical origin of life: more ruminations

by David Turell @, Thursday, December 17, 2015, 00:53 (3044 days ago) @ David Turell

&#13;&#10;> > dhw: Of course the mechanism had to be part and parcel of original life.-Thank you.-> dhw: But the fact that Darwin did not offer a solution to the mystery of the origin of life and the mechanism .... does not make one iota of difference to the theory that all forms of life descended from earlier forms. -I agree that his theory is primarily about common descent-> dhw: But we have had this discussion before, and I thought you had agreed to avoid such blatant misrepresentation. Back we go: &#13;&#10;> > DARWIN: &#147;There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one.&#148;-It depends upon which edition you see. I&apos;ve read it is in some and not others. Why?&#13;&#10; &#13;&#10;> > dhw: Does this not satisfy you that Darwin&apos;s theory does not need the crutch of abiogenesis?-As you present your understanding I agree.

Theoretical origin of life: more ruminations

by dhw, Thursday, December 17, 2015, 19:09 (3043 days ago) @ David Turell

We have reached agreement on the fact that the theory of common descent does not depend on theories concerning the origin of life and the evolutionary mechanism, and I think (hope) you agree that those theists and atheists who try to conflate the whole theory of evolution with that of abiogenesis are guilty of gross distortion. You have, however, raised an interesting question concerning Darwin&apos;s own attitude:&#13;&#10; &#13;&#10;dhw: But we have had this discussion before, and I thought you had agreed to avoid such blatant misrepresentation. Back we go: &#13;&#10;DARWIN: &#147;There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one.&#148;-DAVID: It depends upon which edition you see. I&apos;ve read it is in some and not others. Why?-It had always shocked me (and still does) that atheists blatantly ignore all Darwin&apos;s references to the Creator, and it was George Jelliss who informed me that these were absent from the first edition, which no doubt some editors still prefer. (The Rev. Charles Kingsley&apos;s ringing endorsement of the theory was presumably also absent, as I expect this would have been a response to the book rather than a privileged early insight into Darwin&apos;s thinking.) We can only speculate, but my guess would be that Darwin was shocked by the hostile reaction from the religious community on the grounds that his theory undermined the Bible. They interpreted this as an attack on religion itself, which it was never meant to be. Hence the additions and the explicit reassurances that he was NOT attacking religion. Why else would he have made such insertions and statements? His theory IS compatible with religious belief. That is why I rail against those from both sides of the fence who deliberately distort the theory to serve their own agenda. Maybe his private writings would tell us more, but I don&apos;t have time to delve.

Theoretical origin of life: more ruminations

by David Turell @, Thursday, December 17, 2015, 19:27 (3043 days ago) @ dhw

dhw: They interpreted this as an attack on religion itself, which it was never meant to be. Hence the additions and the explicit reassurances that he was NOT attacking religion. Why else would he have made such insertions and statements? His theory IS compatible with religious belief. That is why I rail against those from both sides of the fence who deliberately distort the theory to serve their own agenda. Maybe his private writings would tell us more, but I don&apos;t have time to delve.-Every side misuses him. I believe his private writings, letters, etc., indicate he was pretty much agnostic. However all sides must accept that origin and evolution are inextricably linked together. One cannot be explained without the other.

Theoretical origin of life: more ruminations

by dhw, Friday, December 18, 2015, 20:01 (3042 days ago) @ David Turell

dhw: They interpreted this as an attack on religion itself, which it was never meant to be. Hence the additions and the explicit reassurances that he was NOT attacking religion. Why else would he have made such insertions and statements? His theory IS compatible with religious belief. That is why I rail against those from both sides of the fence who deliberately distort the theory to serve their own agenda. Maybe his private writings would tell us more, but I don&apos;t have time to delve.-DAVID: Every side misuses him. I believe his private writings, letters, etc., indicate he was pretty much agnostic. However all sides must accept that origin and evolution are inextricably linked together. One cannot be explained without the other.-I can accept common descent without knowing the origin (as could Darwin), but I agree that we cannot explain how it happened without understanding the original mechanism that allowed for life, reproduction, adaptation and innovation. But even if all the codes were finally cracked, I doubt whether there would be consensus as to how it got there in the first place. Thank you for acknowledging the universal misuse of Darwin. I&apos;m sure you will now pounce on it whenever theists or atheists indulge in such distortions, but if you don&apos;t, I shall! As for Darwin&apos;s position, I have previously quoted statements from his writings which establish that he was an agnostic.

Theoretical origin of life: iron-nickel phosphide

by David Turell @, Saturday, January 02, 2016, 15:41 (3027 days ago) @ dhw

A mineral from meteorites may have provided phosphate on the Earth&apos;s surface for the start of life:-http://www.sciencedaily.com/releases/2015/12/151216105118.htm-In previous work, Pasek and colleagues suggested that the ancient meteorites contained the iron-nickel phosphide mineral &quot;schreibersite,&quot; and that when schreibersite came into contact with Earth&apos;s watery environment a phosphate, a salt, was released that scientists believe could have played a role in the development of &quot;prebiotic&quot; molecules.-In a recent study appearing in Nature Publishing Group&apos;s Scientific Reports, the researchers focused on the properties of schreibersite and conducted experiments with the mineral to better understand how -- in a chemical reaction with the corrosive effects of water called &quot;phosphorylation&quot; -- schreibersite could have provided the phosphate important to the emergence of early biological life.-***-To test their hypothesis, they built an early Earth model environment, an organic-rich aqueous solution in which schreibersite might react and corrode in a way similar to how events may have unfolded in prebiotic chemistry. The model they constructed provided an opportunity to observe the thermodynamics of phosphorylation reactions of a phosphorus-containing synthetic schreibersite, which they created to be structurally identical to its meteorite counterpart. (my bold)-A thorough exploration of the extent of phosphorylation of nucleosides (made of a base and a five carbon sugar) by schreibersite was necessary to evaluate its potential prebiotic importance,&quot; explained Gull, a post-doctoral fellow and visiting researcher at USF. &quot;All of our experiments indicated that a basic pH, rather than acidic pH, was required for the production of phosphorylated products. Although phosphorylation can take place using a variety of phosphate minerals in non-aqueous solution, prebiotic oxidation in water is more likely given the dominance of water across the solar system.&quot;-The prebiotic reaction they duplicated in the laboratory may have been similar to the reactions that ultimately led to the emergence of metabolic molecules, such as adenosine triphosphate (ATP), which is called the &apos;molecule of life&apos; because it is central to energy metabolism in all life.&#13;&#10; (my bold)-Comment: Early Earth did not have an &quot;organic rich&quot; set of oceans. Meteorites do not contain many useful organic compounds, but ATP is the energy engine of all life. The OOL lab folks keep trying to keep getting our tax supported research funds. I would not have funded this one.

Theoretical origin of life: energy at thermal vents

by David Turell @, Monday, January 11, 2016, 19:13 (3018 days ago) @ David Turell

There are many mineral and much energy at thermal vents. The article assumes life might have started there:-https://aeon.co/essays/why-life-is-not-a-thing-but-a-restless-manner-of-being?utm_source=Aeon+Newsletter&utm_campaign=7d4d0e0730-Daily_newsletter_Monday_11th_Jan1_11_2016&utm_medium=email&utm_term=0_411a82e59d-7d4d0e0730-68942561-&quot;But within modern organisms there is another clue to life&apos;s origins, one that is more obscure than DNA but just as universal - the way cells harvest energy by shuffling around electrically charged molecules. This process goes by the mouthful &#145;chemiosmosis&apos;, and was first proposed in 1961 by the eccentric British biochemist Peter Mitchell. Chemiosmosis lacks the coded rigour of DNA, but that primal messiness might be exactly what makes it so revealing.-&quot;Energy, Russell thinks, must have preceded anything resembling DNA or RNA, so the origin of chemiosmosis could help to reveal how the first organisms arose. Chemiosmosis takes place deep in our body&apos;s cells, most of which harbour hundreds or thousands of microscopic structures called mitochondria. The mitochondria extract the chemical energy from food and, with the help of the oxygen we breathe, convert it into a molecule called adenosine triphosphate (ATP). Just as much as DNA, ATP is the molecule of life; it is the currency we spend to grow, move or think. Every second, each of our body&apos;s 40 trillion cells use around 10 million molecules of ATP. We can turn over our entire body weight in this special substance every day.-&quot;The flow of energy across the membranes of the mitochondria occurs through a molecular Rube Goldberg contraption so elaborate it almost defies comprehension. A chain of dozens of proteins, each consisting of thousands of atoms, traps high-energy electrons (derived from food), and passes them down the chain like a bucket brigade. The movement of electrons through the proteins in the chain creates an electrical current, which is used to trap massive numbers of protons between the mitochondrion&apos;s inner and outer membranes. The only escape for the protons is through another remarkable protein called ATP synthase. It is an engineering miracle, a nanomachine complete with a molecular rotor, stator and driveshaft, which, as protons fall through it, spins like a waterwheel - hundreds of times per second - to produce ATP.-***-&quot;In a series of papers dating back to 2003, Russell and Martin teamed up to explore the biological implications of the chemical-garden scenario. In their fleshed-out version of the hypothesis, life began not as a free-roaming creature, feeding off natural organic molecules drifting in the ocean, but as a tenant that made its own food in the mineral compartments of underwater rocks. At first, ocean vents were simply sites of geology, gases and dissolved minerals bubbling up to form rocks. But in the microcompartments of those rocks, something unusual began to happen. The carbon dioxide in the ocean reacted with the hydrogen from the vents. Under typical conditions, this reaction wouldn&apos;t occur, but the minerals in the compartment walls, rich in iron and sulfur, coaxed this reluctant partnership. These reactions created small organic molecules such as acetyl-CoA, one of the most ancient metabolic pathways ever discovered.-***-&quot;Biological information systems - the codes needed for life to reproduce - cannot just spring into existence.-***-&quot;In this view, life&apos;s origin isn&apos;t an origin at all, but just another step in a sequence of events set in motion by the Big Bang.-&quot;Thinking of life in terms of energy challenges the very definition of life. &#145;It&apos;s not what life is,&apos; Russell said. &#145;It&apos;s what life does.&apos; After all, you replace each atom in your body, on average, every few years. In that sense, life isn&apos;t a thing so much as a manner of being, a restless fit of destruction and creation. If it can be defined at all, it is this: life is a self-sustaining, highly organised flux, a natural way that matter and energy express themselves under certain conditions. &quot;-Comment: Note the bolds I made. Mitochondria are very complex. Acetyl CoA is a small enzyme but a very complex molecule. Articles are always hopeful.

Theoretical origin of life: early molecules for life

by David Turell @, Wednesday, February 03, 2016, 19:37 (2995 days ago) @ David Turell

What did the supernovas supply at firsts. A new guess:-http://www.sciencedaily.com/releases/2016/02/160203110820.htm-&quot;How did life begin? This is one of the most fundamental questions scientists puzzle over. To address it, they have to look not just back to the primordial Earth, but out into space. Now, scientists propose in the Journal of the American Chemical Society a new set of cosmic chemical reactions that could have contributed to the formation of life on our planet.-&quot;In the earliest minutes of the universe&apos;s formation, from the energy of the big bang, hydrogen and helium formed. All of the other elements developed later in the hot interiors of new stars through the nucleochemical transformation of hydrogen into carbon, nitrogen, oxygen and others. A few million years later, supernova explosions in these stars flung elements into the surrounding space, forming water and hydrocarbons -- compounds containing carbon and hydrogen such as methane and methanol. How more complex hydrocarbons evolved, including those that would eventually lead to life on Earth, remains an open question. Some astrophysicists propose that they all came from methane, which is composed of one carbon atom and four hydrogen atoms. But George Olah, Surya Prakash and colleagues have a different idea.-&quot;The researchers found that methanol, an abundant derivative of methane and better known on Earth as &quot;wood alcohol,&quot; is more reactive than methane itself. Through experiments and calculations, they demonstrated that methanol can give rise to varied hydrocarbons, their derivatives and products, including their ions (carbocations and carbanions), which have been observed in outer space. The scientists believe that when these hydrocarbons and other products were transported to Earth by asteroids or comets, they continued to evolve in the planet&apos;s unique &quot;goldilocks&quot; conditions -- liquid water, a breathable atmosphere and moderate temperatures -- ultimately leading to life as we know it.&quot;-Comment: A very reasonable guess, especially with our nicely planned planet, as the article notes.

Theoretical origin of life: early molecules for life

by David Turell @, Thursday, February 25, 2016, 00:50 (2974 days ago) @ David Turell

Another review article, which does not advance the theory: - https://www.quantamagazine.org/20160216-how-to-build-life-in-a-pre-darwinian-world/ - &quot;However, scientists have found it surprisingly challenging to create self-replicating RNA in the lab. Researchers have had some success, but the candidate molecules they have manufactured to date can only replicate certain sequences or a certain length of RNA. Moreover, these RNA molecules are themselves quite complicated, raising the question of how they might have formed through chance chemical means. (my bold)&#13;&#10;*** - &quot;At the heart of Hud&apos;s proposal is a chemical means for generating a rich diversity of proto-life. Computer simulations show that certain chemical conditions can produce a varied collection of RNA-like molecules. And the team is currently testing the idea with real molecules in the lab; they hope to publish the results soon. - *** - &quot;Hud&apos;s group is leading the way for a number of researchers who are challenging the traditional RNA-world hypothesis and its reliance on biological rather than chemical evolution. In the traditional model, new molecular machinery was created using biological catalysts, known as enzymes, as is the case in modern cells. In Hud&apos;s proto-life stage, myriad RNA or RNA-like molecules could form and change through purely chemical means. &#147;Chemical evolution could have helped life get started without enzymes,&#148; Hud said. - *** - &quot;Carl Woese, a renowned biologist who gave us the modern tree of life, believed that the Darwinian era was preceded by an early phase of life governed by very different evolutionary forces. Woese thought it would have been nearly impossible for an individual cell to spontaneously come up with everything it needed for life. So he envisioned a rich diversity of molecules engaged in a communal existence. Rather than competing with each other, primitive cells shared the molecular innovations they invented. Together, the pre-Darwinian pool created the components needed for complex life, priming the early Earth for the emergence of the magnificent menagerie we see today. (Woese discovered Archaia) - *** - &quot;In Hud&apos;s vision of a prebiotic world, the primordial RNA soup underwent regular cycles of heating and cooling in a thick, viscous solution. Heat separated the bound pairs of RNA, and the viscous solution kept the separated molecules apart for a while. In the interim, small segments of RNA, just a few letters in length, stuck to each long strand. The small segments eventually got sewn together, forming a new strand of RNA that matched the original long strand. The cycle then began again. - &quot;Over time, a pool of varied RNA-like molecules would have accumulated, some of them capable of simple functions, such as metabolism. And just like that, purely chemical reactions would have produced the molecular diversity needed to create Woese&apos;s pre-Darwinian cornucopia of proto-life. - &quot;Hud&apos;s team has been able to carry out the first stages of the replication process in the laboratory, although they can&apos;t yet glue together the short segments without resorting to biological tools. If they can get over that hurdle, they&apos;ll have created a versatile way of replicating any RNA that pops up. - &#13;&#10;*** - &quot;Despite the powerful evidence, it&apos;s still hard to imagine how the ribosomal core could have been created by chemical evolution. An enzyme that makes more of itself &#151; like the replicator RNA of the RNA-world hypothesis &#151; automatically creates a feedback loop, continually boosting its own production. By contrast, the ribosomal core doesn&apos;t produce more ribosomal cores. It produces random chains of amino acids. It&apos;s unclear how this process would encourage the production of more ribosomes. &#147;Why would making random peptides make that thing better?&#148; Higgs said. (Another complication) - &quot;Hud and his collaborators propose that RNA and proteins evolved in tandem, and those that figured out how to work together survived best. This idea lacks the simplicity of the RNA world, which posits a single molecule capable of both encoding information and catalyzing chemical reactions.&quot; - Comment: More complex, and more wishful thinking. Read it all to sense the frustration.

Theoretical origin of life: ocean temerature

by David Turell @, Monday, February 29, 2016, 16:02 (2969 days ago) @ David Turell

One thought which has some basis in fact is that heat can increase the speed of organic chemical reactions. therefore the proposal that oceans were warmer at the start of life. Not so in this study: - http://phys.org/news/2016-02-ocean-cooler-life-began-earth.html - &quot;A pair of researchers, one with Nelson Mandela Metropolitan University in South Africa and the other with the University of Bergen in Norway, has conducted a study of rocks in South Africa, and has concluded that the ocean was not as cold as other studies have shown during the time period when life is believed to have first appeared on Earth. In their paper published in the journal Sciences Advances, Maarten de Wit and Harald Furnes describe their research results and why they now believe that our planet may have existed in the Goldilocks Zone for the entire time that life has existed on our planet. - *** - &quot;In this new study, the research pair suggest that estimate was in error because it did not take into account the possibility that the rocks were near hydrothermal vents, where the water is always warmer than the rest of the ocean. - &quot;To get a better idea of the true early water temperature, the researchers studied other nearby rocks of the same age that had been formed from ocean sediments, which meant they could not have resided near a vent. Those rocks, the team reports, contained gypsum, which in modern times grows only in cold deep sea water. Also, they noted that tiny grains of iron present in the rock at the time of its formation revealed that it had come about at low latitudes, very near the equator. Taken together, the evidence suggests, the researchers claim, that it was likely both the oceans and atmosphere were similar to conditions today, and that suggests that our planet may have resided in the Goldilocks zone (not too hot or too cold to support life) for the entire duration of the existence of life on Earth. They further suggest that their findings will lay to rest the common assumption that the only possibility of life coming to exist on Earth occurred during a time when the oceans were much warmer than today.&quot; - Comment: The key issue is amount of time of organic molecular reactions, and this requires complex enzymes not a little heat.

Theoretical origin of life: ocean vents

by David Turell @, Monday, March 07, 2016, 15:26 (2962 days ago) @ David Turell

This article works with thermal vents and chimneys at the ocean floor. The part that is not consistent with real discovery is that the scientists add complex protein compounds to show that if they appeared they could polymerize. How did &apos;they&apos; appear?- http://phys.org/news/2016-03-life-blocks-replicated-deep-sea.html-&quot;The kind of nucleotides making up RNA are known as ribonucleotides, since they are made with the sugar ribose. The scientists found that unmodified ribonuclotides could form strings of two nucleotides. In addition, ribonucleotides &quot;activated&quot; with a compound known as imidazole&#151;a molecule created during chemical reactions that synthesize nucleotides&#151;could form RNA strings or polymers up to four ribonucleotides long.-&quot;&apos;In order to observe significant RNA polymerization on the time scale of laboratory experiments, it is generally necessary to activate the nucleotides,&quot; McGown said. &quot;Imidazole is commonly used for nucleotide activation in these types of experiments.&quot;-&quot;The scientists found that not only was the chemical composition of the chimneys important when it came to forming RNA, but the physical structure of the chimneys was key too. When the researchers mixed iron, sulfur and silicon solutions into their simulated oceans, instead of slowly injecting them into the seawater to form chimneys, the resulting blend could not trigger RNA formation.-&quot;&apos;The chimneys, and not just their constituents, are responsible for the polymerization,&quot; McGown said.-These experiments for the first time demonstrate that RNAs can form in alkaline hydrothermal chimneys, albeit synthetic ones.-&quot;&apos;Our goal from the start of our RNA polymerization research has been to place the RNA polymerization experiments as closely as possible in the context of the most likely early Earth environments,&quot; McGown said. &quot;Most previous RNA polymerization research has focused on surface environments, and the exploration of deep-ocean hydrothermal vents could yield exciting new possibilities for the emergence of an RNA world.&quot;-&quot;One concern about these findings is that the experiments were performed at room temperature. Hydrothermal vents are much hotter, and such temperatures could destroy RNA. (my bold)-Comment: Oh, the heat, the natural spoiler for the game. Too much money chasing too few ideas!

Origin of life: warm pond encapsolated theory

by David Turell @, Saturday, March 19, 2016, 00:43 (2951 days ago) @ David Turell

An optimistic idea involving encapsulation with a lipid envelop in warm ponds: - &quot;For the past 40 years, David Deamer has been obsessed with membranes. Specifically, he is fascinated by cell membranes, the fatty envelopes that encase our cells. They may seem unremarkable, but Deamer, a biochemist at the University of California, Santa Cruz, is convinced that membranes like these sparked the emergence of life. As he envisions it, they corralled the chemicals of the early Earth, serving as an incubator for the reactions that created the first biological molecules. - &quot;One of the great initial challenges in the emergence of life was for simple, common molecules to develop greater complexity. This process resulted, most notably, in the appearance of RNA, long theorized to have been the first biological molecule. RNA is a polymer &#151; a chemical chain made up of repeating subunits &#151; that has proved extremely difficult to make under conditions similar to those on the early Earth. - *** - &quot;Deamer thinks that volcanic landmasses similar to those in Iceland today would have made a hospitable birthplace for his proto-cells. Freshwater pools scattered across steamy hydrothermal fields would be subject to regular rounds of heating and cooling. That cycle could have concentrated the necessary ingredients &#151; including both lipids and the building blocks for RNA &#151; and provided the energy needed to stitch those building blocks into biological polymers. Deamer is now trying to re-create these conditions in the lab. His goal is to synthesize RNA and DNA polymers. - *** - &quot;Life resists a simple abstract definition. When I try to define life, I put together a set of a dozen properties that don&apos;t fit anything not alive. A few of them are simple: reproduction, evolution, and metabolism. - *** - &quot;DNA is the center of all life, but it can&apos;t be considered alive even though it has all the information required to make a living thing. DNA cannot reproduce by itself. Put DNA in a test tube with water, and it just slowly breaks into different pieces. So right away, you see the limitation of thinking about single molecules as being alive. - &quot;To get a bit of what we call growth, you have to add the subunits of DNA, an enzyme to replicate the DNA, and energy to power the reaction. Now we have molecules that can reproduce themselves if they have certain ingredients. Are they alive yet? The answer is still no, because sooner or later the subunits are used up and reproduction comes to a screeching halt. So how do we get to a system that&apos;s really alive? That&apos;s what we and others are trying to do. The only way we can think of is to put DNA into a membranous compartment. - *** - &quot;Organic compounds accumulated in the pools, washed there by precipitation that rained down on the volcanic landmasses. The pools went through wetting and drying cycles, forming a concentrated film of organic compounds on the rocks like the ring in a bathtub. Within that film, interesting things can happen. Lipids can self-assemble into membrane-like structures, and the subunits of RNA or other polymers join together to create long chains. - *** - &quot;To get the thing to replicate would be a big deal. To do that, we need a ribozyme that makes our polymerization reaction go faster. But we have a long way to go before we can find that kind of ribozyme. - &quot;We&apos;ll probably be able to make lab life, but I&apos;m not sure we can claim that&apos;s how life began. The life we&apos;re trying to synthesize is going to be a very technical life, based in a lab with clean reagents and so forth. I&apos;m not sure we can call that the origin of life until it becomes a self-growing system, until we put that system in an outside environment and watch it grow. - &quot;Although we will never know with certainty how life did begin, it seems eminently possible that we will understand how life can begin on any habitable planet.&quot; - Comment: Supreme optimism, and where will all those organic compounds come from? Meteorites have delivered only 8 of the 20 needed amino acids.

Origin of life: cold oceans?

by David Turell @, Saturday, March 19, 2016, 05:03 (2951 days ago) @ David Turell

The current theory that the Earth was very warm at the time of the origin of life is now disputed. New study says it was cold:-https://www.sciencedaily.com/releases/2016/03/160317144620.htm-&quot;Many researchers believe that Earth&apos;s early oceans were very hot, reaching 80&#176; Celsius, and that life originated in these conditions. New findings may prove the opposite to be true. Harald Furnes, Professor Emeritus at the Department of Earth Science, has analysed volcanic and sedimentary rocks in the Barberton Greenstone Belt, South Africa. The volcanic rocks were deposited at depths of 2 to 4 kilometres.-&quot;We have found evidence that the climate 3.5 billion years ago was a cold environment,&quot; says Furnes.-&quot;Along with Professor Maarten de Wit from Nelson Mandela Metropolitan University, South Africa, Furnes has published the results in the journal Science Advances.-&quot;The rocks analysed by Furnes and de Wit were formed at latitudes comparable with that of the Canary Islands. Some of the sedimentary rocks associated with the volcanic rocks, show a remarkable resemblance to those known from more recent ice ages.-&quot;&apos;This may indicate that Earth, 3.5 billion years ago, experienced an extensive, perhaps global, ice age,&quot; Furnes says.-&quot;Past ocean temperatures are measured by analysing the relations between oxygen isotopes in rocks known as &quot;chert,&quot; a rock composed of pure silicium-oxide. These South African rocks have been exposed to high temperatures. Even so, this is related to hydrothermal activity, or springs of extremely hot water, pumped from the ocean bed.-&quot;Additionally, the researchers found more proof indicating that these rocks had been exposed to cold water. By examining finely grained sedimentary rocks (originally a claylike mud), that exists along with the deep-submarine volcanic rocks, the researchers found gypsum. Gypsum is produced under high pressure and at very cold temperatures, as in the present deep ocean.-&quot;&apos;In other words, we have found independant lines of evidence that the climate conditions at this time may have been quite similar to the conditions we have today,&quot; says Furnes.&quot;-Comment: More confusion about origin of life. Despite a lower general temperature, life could have started close to volcanic vents as has been proposed.

Origin of life: seven weak possibilities

by David Turell @, Saturday, March 26, 2016, 04:57 (2944 days ago) @ David Turell

Seven of them: - 7: Lightning may have provided the spark needed for life to begin.Electric sparks can generate amino acids and sugars from an atmosphere loaded with water, methane, ammonia and hydrogen, as was shown in the famous Miller-Urey experiment reported in 1953, - Known to have been of no value - 6: The first molecules of life might have met on clay, according to an idea elaborated by organic chemist Alexander Graham Cairns-Smith at the University of Glasgow in Scotland. These surfaces might not only have concentrated these organic compounds together, but also helped organize them into patterns much like our genes do now. - True, but where did the organic compounds come from?&#13;&#10;&#13;&#10;5: The deep-sea vent theory suggests that life may have begun at submarine hydrothermal vents spewing key hydrogen-rich molecules. Their rocky nooks could then have concentrated these molecules together and provided mineral catalysts for critical reactions. Even now, these vents, rich in chemical and thermal energy, sustain vibrant ecosystems. - Same problem, the organic molecules have to be there&#13;&#10; - 4: Ice might have covered the oceans 3 billion years ago, as the sun was about a third less luminous than it is now, scientists say. This layer of ice, possibly hundreds of feet thick, might have protected fragile organic compounds in the water below from ultraviolet light and destruction from cosmic impacts. - Again the molecules. Where are they developed? - 3: The answer may be RNA, which can store information like DNA, serve as an enzyme like proteins, and help create both DNA and proteins. Later DNA and proteins succeeded this &quot;RNA world,&quot; because they are more efficient. - Same old, same old. No proof after 30 years - 2: Instead of developing from complex molecules such as RNA, life might have begun with smaller molecules interacting with each other in cycles of reactions. These might have been contained in simple capsules akin to cell membranes, and over time more complex molecules that performed these reactions better than the smaller ones could have evolved, scenarios dubbed &quot;metabolism-first&quot; models, as opposed to the &quot;gene-first&quot; model of the &quot;RNA world&quot; hypothesis. - Another unproven theory /i] - 1:Perhaps life did not begin on Earth at all, but was brought here from elsewhere in space, a notion known as panspermia. - Just places the question of origin elsewhere

Theoretical origin of life: using metals

by David Turell @, Thursday, March 31, 2016, 06:30 (2939 days ago) @ David Turell

Metal ions are part of lots of life&apos;s organic molecules. This article referring to these metals as the &apos;metalome&apos; infers that life started because of them. Of course the organic hydrocarbons and other polymerizing molecules are not given a source. No reference as to where they came from:-http://nautil.us/issue/34/adaptation/the-classic-metal-behind-the-origins-of-life-&quot;Consider the history of iron, one of the metals of the metallome. The early ocean was dominated by iron atoms that were doubly positive charged ions (Fe2+). They were highly soluble in water, and therefore available as a &#147;nutrient&#148; that could be used for essential catalytic functions by oceanic life, like single-cell cyanobacteria.-&quot;The iron was useful in more ways than one. These early lifeforms consumed carbon dioxide and sunlight to produce complex organic hydrocarbon molecules, and, as a byproduct, oxygen. Unfortunately, this oxygen was toxic to them. This is where the iron ions again came in handy: They scavenged toxic oxygen exhaled by the cyanobacteria into ocean water through an electron exchange process that produced triply charged iron atoms (Fe3+), and chemical species containing oxygen. -***-&quot;The metallome didn&apos;t just help early life to perform its basic functions&#151;it also helped it adapt to a changing Earth. Around 2 billion years ago, the Earth experienced a Great Oxidation Event (GOE). The photosynthetic bacteria population grew enough to produce oceanic oxygen at a level high enough for it to escape into the atmosphere.-&quot;This was a pivotal event: The composition of the atmosphere changed dramatically as oxygen levels rose to near-modern levels. These high levels in turn increased the rate at which soluble Fe2+ was oxidized to insoluble Fe3+, but it also increased the rate at which ocean insoluble metallic sulfide salts (metals bound to sulfur) were oxidized to produce soluble sulfate salts (metals bound to sulfur and oxygen). As bio-available iron levels decreased, the availability of copper, zinc, and molybdenum all increased, as their salts became soluble.-***-&quot;The composition of the atmosphere changed dramatically as oxygen levels rose to near-modern levels. These high levels in turn increased the rate at which soluble Fe2+ was oxidized to insoluble Fe3+, but it also increased the rate at which ocean insoluble metallic sulfide salts (metals bound to sulfur) were oxidized to produce soluble sulfate salts (metals bound to sulfur and oxygen). As bio-available iron levels decreased, the availability of copper, zinc, and molybdenum all increased, as their salts became soluble.-&quot;This led to a host of changes in cellular chemistry. Where oceanic life had used tungsten as an oxygen atom transfer catalyst, it began to use molybdenum, which is actually a more efficient catalyst, but had been trapped in an insoluble form. The GOE also reduced oceanic iron concentrations, by transforming soluble iron (Fe2+) to insoluble iron oxide (Fe2O3). So cells adapted by putting an organic molecule coating on the surface of its iron ions, preventing them from being hydrated by water and precipitating out of the ocean as an oxide rock. -***-&quot;The energy required to drive cyclic chemical reactions that are self-replicating&#151;what we might call &#147;life&#148;&#151;could come from reactions of the metallic elements. Our search for extraterrestrial life shouldn&apos;t be restricted to a search for remnants of complex organic molecules. There&apos;s another clear target, with a rather appropriately sci-fi ring to it: Heavy metals in space.&quot;-Comment: To be fair, the author is correct that metal/oxygen reactions and other metal reactions can provide energy for life and still do with metal eating bacteria, but it is the title of the article that should be changed to &quot;After life appeared, these metals helped&quot;.

Theoretical origin of life: Harold Morowitz dead

by David Turell @, Tuesday, April 05, 2016, 15:12 (2933 days ago) @ David Turell

Famous biophysicist who calculated that the chance origin of life had odds of 10^ 100,000,000,000! And believed it occurred naturally:-http://www.the-scientist.com/?articles.view/articleNo/45724/title/Accomplished-Biophysicist-Dies/&utm_campaign=NEWSLETTER_TS_The-Scientist-Daily_2016&utm_source=hs_email&utm_medium=email&utm_content=28059011&_hsenc=p2ANqtz-8CX2YlvMCfEAzEvOVcmZGDxnl10IgEe5BqmHoO4IsN2Dm3sSgq0QOuRsEz-1xSHrnbeD4lMl6JP20XJasai84oPbfhqg&_hsmi=28059012/-&quot;Biophysicist Harold Morowitz, best known for his work on thermodynamics in biology and the origins of life, died in Falls Church, Virginia, last month (March 22). He was 88.-&quot;The Clarence Robinson professor of biology and natural philosophy at George Mason University since 1988, Morowitz engaged in a range of research topics, from the chemistry of brine shrimp eggs to a cycling theory of flow that has been nominated as a candidate for the fourth law of thermodynamics. He authored more than 15 books aimed at students and a general audience.-***&#13;&#10;&quot;A longtime consultant to NASA and a member of the scientific advisory committee for Biosphere 2 (the largest-ever enclosed ecosystem), Morowitz was a strong advocate for a theory of emergence of life from chemical and physical principles. In the 1983 McLean v. Arkansas case over teaching creationism in schools, he provided an expert opinion, testifying in front of the court that the creationist view of life&apos;s origins has no basis in science.-&#147;&apos;Harold Morowitz is one of the world&apos;s seminal thinkers about the origin of life within the context of the physics of our universe,&#148; James Olds of the National Science Foundation told The New York Times. &#147;Insomuch as we have stars with elements that go through life and death cycles of their own, Harold would say those physics and chemistry inevitably produce life.&apos;&#148;-Comment: His &apos;odds&apos; are often quoted by ID&apos;ers and creationists, and yet it seems he was an atheist.

Theoretical origin of life: more ruminations

by David Turell @, Saturday, February 01, 2020, 15:21 (1536 days ago) @ dhw

Putting a living cell together:

https://uncommondescent.com/intelligent-design/researchers-homogenous-rna-could-emerge-...

"How do they get the GCAT-based code in the DNA?
How do they get the promoters and enhancers setup?
How do they get the histone proteins in the chromatin ?
How do they get the epigenetic markers setup?
How do they get the DNA replication machinery?
How do they get the transcription factors?
How do they get the transcription machinery?
How do they get the translation machinery?
How do they get the organelles?
How do they get the membranes?"

Comment: Much too complex for a beginning due to chance. GCAT is a reference to the four bases

Theoretical origin of life: the effect of comets again

by David Turell @, Friday, April 08, 2016, 15:49 (2930 days ago) @ David Turell

A laboratory simulation of a comet has shown that ribose might just arrive on Earth that way. Is this GIGO?:-https://www.sciencedaily.com/releases/2016/04/160407155617.htm-&quot;Researchers have for the first time shown that ribose, a sugar that is one of the building blocks of genetic material in living organisms, may have formed in cometary ices. To obtain this result, scientists at the Institut de Chimie de Nice (CNRS/Universit&#233; Nice Sophia Antipolis) carried out a highly detailed analysis of an artificial comet created by their colleagues at the Institut d&apos;Astrophysique Spatiale (CNRS/Universit&#233; Paris-Sud). Along with other teams[1], including one at the SOLEIL synchrotron, they propose the first realistic scenario for the formation of this key compound, which had never been detected in meteorites or cometary ices until now. -***-&quot; As a first step, an artificial comet was produced at the Institut d&apos;Astrophysique Spatiale. By placing a representative mixture of water (H2O), methanol (CH3OH) and ammonia (NH3) in a high vacuum chamber at -- 200 &#176;C, the astrophysicists simulated the formation of dust grains coated with ice, the raw material of comets. This material was irradiated with UV, as in the molecular clouds where these grains form. The sample was then warmed to room temperature, as in comets when they approach the Sun. Its composition was analyzed at the Institut de Chimie de Nice, optimizing an extremely sensitive and accurate method (multidimensional gas chromatography coupled with time-of-flight mass spectrometry). Several sugars were detected, including ribose. Their diversity and relative abundances suggest that they were formed from formaldehyde (a molecule found in space and on comets that forms in large quantities from methanol and water).-&quot;Although the existence of ribose in real comets remains to be confirmed, this discovery completes the list of the molecular building blocks of life that can be formed in interstellar ice. It also lends further support to the theory that comets are the source of the organic molecules that made life possible on Earth, and perhaps elsewhere in the Universe.&quot;-Comment: A man-made comet controlled by intelligent design of humans. Just because ribose is lying around on earth doesn&apos;t mean it would join forces with some scattered amino acids to form life. Maybe they all gathered at a thermal vent and got cooked together?

Theoretical origin of life: the effect of comets again

by David Turell @, Sunday, April 10, 2016, 03:18 (2929 days ago) @ David Turell

It is possible that comets can make RNA according to lab work here on Earth:-https://www.newscientist.com/article/2083425-missing-building-block-of-life-could-be-made-on-ice-in-space/-&quot;The search for life in space just got a little sweeter. In the early solar system, ice grains hit by sunlight may have formed sugar molecules on their surfaces, according to a new experiment. Those sugars include ribose: the backbone of RNA, which is implicated in the origin of life.-&quot;All known life makes at least some use of RNA as a genetic material, and as the &#147;R&#148; in RNA, ribose holds up the compounds that encode genetic messages. But it&apos;s been hard to understand how ribose could be made in the absence of living organisms, to be part of a precursor for life.-***-&quot;But sugars like ribose are hard to come by, since they often stick together in a way that makes them impossible to extract. &#147;Sugars like to react with each other,&#148; says Cornelia Meinert at the University of Nice Sophia Antipolis in France. &#147;In the end, everything is brown like caramel.&#148; &#13;&#10; &#13;&#10;&quot;Now Meinert&apos;s team was able to produce ribose by shining ultraviolet light on a frozen blend of water, methanol and ammonia. This mixture represents our solar system in its infancy, before tiny grains of dust and ice collapsed into planets.-&#147;&apos;It&apos;s another example of how the universe seems to be hardwired to produce a lot of the kinds of compounds you would like to be around if you want to get life going,&#148; says Scott Sandford of NASA Ames Research Center in California. Sandford&apos;s own team is reporting similar results in a paper now in press, he says. 9my bold-***-&quot;Whether sugars are made on real interstellar ice grains is still an open question. Because these grains are preserved if they gently settle on small bodies far from the sun, checking the surfaces of comets or meteorites may help resolve the issue. ESA&apos;s Rosetta mission and radio astronomers have picked up simple sugars on comets before, but they may struggle to find something complex like ribose, Meinert thinks.-&quot;Finding these sugars on comets would tell us that amino acids, molecules in cell membranes and ribose could all have been made in space, then dropped on Earth just in time for the genesis of life.- &quot;We&apos;re far from understanding what happened next, though. &#147;Just because now you have all the molecules doesn&apos;t mean you have life,&#148; Meinert says. (my bold)-&quot;Still, it doesn&apos;t hurt. &#147;If you think of all these little molecules we&apos;re making as Lego blocks, and life as a kind of very complex, organised Lego castle, the fact that Lego blocks are falling out of the sky can&apos;t be a bad thing,&#148; Sandford says.&quot;-Comment: The first bolded comment suggests more evidence of fine tuning. The second bold is a very logical hedging statement. Did the start of life have help from &apos;?&apos;

Theoretical origin of life: easy lab manipulations

by David Turell @, Monday, April 25, 2016, 17:50 (2913 days ago) @ David Turell

Here we go again. come up with some proteins, not known to be on early Earth, do some lab playing and we get RNA-like molecules, not RNA itself, but close enough to imagine whatever:-https://www.sciencedaily.com/releases/2016/04/160425095115.htm-&quot;Using two molecules known as barbituric acid and melamine, the researchers formed proto-nucleotides so strongly resembling two of RNA&apos;s nucleotides that it is tempting to speculate that they are indeed their ancestors.-&quot;The two ingredients would have been readily abundant for reactions on a prebiotic Earth, Hud said. &quot;And they would have been well suited for primitive information coding,&quot; he added.-&quot;Because of the resemblances and properties, some scientists already have speculated on an ancestral role for melamine and barbituric acid.-***-&quot;To claim ancestry, we would have to show a mechanism by which these nucleotides we made in the lab could turn into the existing nucleotides in RNA,&quot; said Ram Krishnamurthy, Hud&apos;s collaborator from the Scripps Research Institute in La Jolla, California. &quot;It&apos;s a complex path that we&apos;d have to at least design on paper, and we&apos;re not there.&quot;-***-&quot;First, they occurred quickly and the resulting nucleotides spontaneously paired with each other in water, forming hydrogen bonds like the Watson-Crick base pairs that create the &quot;ladder-rung&quot; pattern inside RNA and DNA helixes.-&quot;Then the monomers formed long, supramolecular assemblages that look like strands of RNA when viewed with a high resolution microscope.-&quot;There has been no reported chemical reaction so far that has produced existing components of RNA under commonplace circumstances that spontaneously form Crick-Watson pairs in water.-***-&quot;There was one small caveat.-&quot;&apos;The reaction does not work as well if barbituric acid and melamine are present in the same solution before reacting with ribose because their strong attraction for each other can cause them to precipitate,&quot; Hud said. So, the scientists completed the reaction involving barbituric acid separately from the one involving melamine.&#13;&#10;&#13;&#10;&quot;But that should not have proven prohibitive on prebiotic Earth. Barbituric acid and melamine nucleotides could have been formed in separate locations, even in the same pond. And they could have very well been plentiful.-(Comment: Very hopeful. How did they get together?):-&quot;If melamine and barbituric acid formed their respective nucleotides (C-BMP for barbituric acid and MMP for melamine) in separate puddles on the early Earth, then rain could have easily washed the components together, where they would have rapidly assembled into what could have been a precursor to proto-RNA.-&quot;&apos;The question is: Can these self-assemblies make the transition into what makes up life today,&quot; Krishnamurthy said.-(Comment: saved by rain)-&quot;The chemical reactions that produce the barbituric acid and melamine nucleotides don&apos;t require the use of enzymes and extreme parameters like high heat and pressure. Reminiscent of click chemistry, they could contribute to safe, cost-effective and abundant industrial production.&quot;-Comment: final &apos;save&apos;, no enzymes needed! Intelligent design magic.

Theoretical origin of life:in meteorite & comet crators:

by David Turell @, Wednesday, May 04, 2016, 20:14 (2904 days ago) @ David Turell

Another new theory about the environment in a crator:-http://phys.org/news/2016-05-comet-cratersliteral-pots-life-earth.html-&quot;In a paper just published in the journal Geochimica et Cosmochimica Acta, the team proposes that large meteorite and comet impacts into the sea created structures that provided conditions favourable for life. Water then interacted with impact-heated rock to enable synthesis of complex organic molecules, and the enclosed crater itself was a microhabitat within which life could flourish.-&quot;It has long been suggested that the meteoritic and cometary material that bombarded the early Earth delivered the raw materials - complex organic molecules, such as glycine, ?-alanine, ?-amino-n-butyric acid, and water - and the energy that was required for synthesis. The Trinity group&apos;s work has provided the new hypothesis that impact craters were ideal environments to facilitate the reactions that saw the first &apos;seeds of life&apos; take root.-***-&quot;&apos;Previous studies investigating the origin of life have focused on synthesis in hydrothermal environments. Today these are found at mid-ocean ridges - hallmark features of plate tectonics, which likely did not exist on the early Earth. By contrast, the findings of this new study suggest that extensive hydrothermal systems operated in an enclosed impact crater at Sudbury, Ontario, Canada.&quot;-***-&quot;The first thing that became evident was that the crater was filled with seawater at an early stage, and remained sub-marine throughout deposition. Importantly, the water in the basin was isolated from the open ocean for long enough to deposit more than 1.5 km of volcanic rock and sediment. The lower fill is made up of rocks that formed when the water entered the crater whose floor was covered by hot impact melt. Fuel-coolant reactions deposited volcanic rocks and promoted hydrothermal activity. Above these deposits, reduced carbon starts to appear within the basin fill and the volcanic products become more basaltic.-&quot;Previously the puzzling presence of carbon in these rocks was explained by washing in from outside the crater basin. However, the new data show that it was microbial life within the crater basin that was responsible for the build-up of carbon and also for the depletion in vital nutrients, such as sulphate.-&quot;&apos;There is clear evidence for exhaustion of molybdenum in the water column, and this strongly indicates a closed environment, shut off from the surrounding ocean,&quot; added Edel O&apos;Sullivan.-&quot;Only after the crater walls eventually collapsed did the study show replenishment of nutrients from the surrounding sea. These sub-marine, isolated impact basins, which experienced basaltic volcanism and were equipped with their own hydrothermal systems, thus present a new pathway to synthesis and concentration of the stepping stones to life.&quot;-Comment: The environment might be inviting but the next step to life is still extraordinarily enormous.

Theoretical origin of life: more easy lab stuff

by David Turell @, Friday, May 13, 2016, 01:08 (2896 days ago) @ David Turell

Another hopeful lab approach to making replicating RNA by chance:-https://www.newscientist.com/article/2088006-building-blocks-of-lifes-first-self-replicator-recreated-in-lab/-&quot;RNA, or something very like it, has long been a strong candidate as the first self-replicating molecule in the origin of life. This is because it can both catalyse chemical reactions and carry genetic information.-&quot;But chemists first needed to explain how a large, complex molecule like RNA could form spontaneously to begin the process. They had done so for some, but not all, components of the RNA molecule.-&quot;The biggest sticking point was that until now, no one had identified a plausible way to generate the two purine nucleosides, adenosine and guanosine - A and G in the genetic code.-***-&quot;Previous efforts made the parts of a nucleoside separately and then linked them together - a stepwise process that generally yields a useless mess of many possible configurations.-&quot;Instead, Carell&apos;s team started with even simpler precursors and let the whole process unfold at once, under mildly acidic conditions that mimicked early Earth. Their approach worked, producing high yields of adenosine. Guanosine can then easily be made from this.-Better yet, Carell&apos;s starting points - formic acid and molecules called aminopyrimidines - or their precursors have been found on comets, and thus were probably available at the origin of life.-&#147;We now have a pathway that would allow us to use simple molecules that were likely present on the early Earth,&#148; says Carell. The next step is to link the bases into a full-length RNA strand, he says.-&quot;Carell&apos;s discovery removes one of the key stumbling blocks to RNA-based scenarios of the origin of life, whether they involve RNA alone or in concert with primitive proteins, says Nicholas Hud, a chemist at the Georgia Institute of Technology in Atlanta.-&quot;&apos;Moreover, Carell&apos;s chemical reaction should work equally well with more primitive, RNA-like molecules, making it an excellent candidate for the prebiotic world, says Hud.&quot;-Comment: Note this only provides half the code letters of RNA. The usual euphoric description.

Theoretical origin of life: constructor theory

by David Turell @, Saturday, May 21, 2016, 20:45 (2887 days ago) @ David Turell

This weird essay makes one assumption after another and finally decides that constructor theory can explain how life initially appeared: - https://aeon.co/essays/how-constructor-theory-solves-the-riddle-of-life?utm_source=Aeon... - &quot;the theory of evolution by variation and natural selection - Charles Darwin&apos;s momentous leap - shows how those stupendously intricate mechanisms can come about without one. Yet the task of showing how life itself can arise without design is surprisingly vexed. ( me: that is the part he wisely left out) - *** - &quot;all living things rely on a rather peculiar contrivance: the living cell. Cells can self-reproduce, manufacturing new instances of themselves in a process involving, at its heart, the faithful replication of the genetic information contained in the cell&apos;s DNA. We find this capacity nowhere in the rest of nature. - *** - &quot;the laws of physics contain no built-in facility for accurate transformations; nor, in particular, for biological adaptations that can bring such transformations about. They are no-design, in this special sense. Thus the problem with living things, expressed within physics, is that they are highly adapted to effect all sorts of transformations to high accuracy, whereas the laws of physics aren&apos;t. ( me: there are folks looking at the physics of life) - *** - &quot;Biological replication and self?reproduction are in fact such stupendously well?orchestrated physical transformations that one must explain how they are possible under the simple, no?design laws of physics such as ours. - *** - &quot;In constructor theory, physical laws are formulated only in terms of which tasks are possible (with arbitrarily high accuracy, reliability, and repeatability), and which are impossible, and why - as opposed to what happens, and what does not happen, given dynamical laws and initial conditions. A task is impossible if there is a law of physics that forbids it. Otherwise, it is possible - which means that a constructor for that task - an object that causes the task to occur and retains the ability to cause it again - can be approximated arbitrarily well in reality. (me: what a huge assumption!) - *** - &quot;Constructor theory ..is digitally coded information that can act as a constructor and has resiliency - the capacity, once it is instantiated in physical systems, to remain so instantiated. In constructor theory, that is called knowledge - a term used here without the usual connotation that it is known by someone: it merely denotes this particular kind of information with causal power and resiliency. (me: recognition of the need for information at the basis) - ***&#13;&#10;&quot;The early history of evolution is, in constructor-theoretic terms, a lengthy, highly inaccurate, non-purposive construction that eventually produced knowledge-bearing recipes out of elementary things containing none. These elementary things are simple chemicals such as short RNA strands, (me: and where did RNA, which is not simple, come from?) - *** - &quot;the constructor theory of life shows explicitly that natural selection does not need to assume the existence of any initial recipe, containing knowledge, to get started. It shows that, whatever recipes we might find in living things, they do not require ad?hoc, biocentric or mysterious laws of physics in order to come into existence from elementary initial components. They need only the laws of physics to permit the existence of digital information, plus sufficient time and energy, which are non-specific to life. This adds another deep reason why a unification in our understanding of the phenomena of life and physics is possible.&quot; - Comment. Hogwash, but atheistic hope springs eternally that inorganic chemicals can magically become organic life. Are the constructor laws built-in? And where do the laws of nature come from. At least she recognizes the need for information, which she has arise magically. The commentaries all agree with me.

Theoretical origin of life: constructor theory

by dhw, Sunday, May 22, 2016, 18:08 (2886 days ago) @ David Turell

DAVID: This weird essay makes one assumption after another and finally decides that constructor theory can explain how life initially appeared: - https://aeon.co/essays/how-constructor-theory-solves-the-riddle-of-life?utm_source=Aeon... - QUOTE: &quot;Moreover, it is a fundamental idea of constructor theory that any transformation that is not forbidden by the laws of physics can be achieved given the requisite knowledge. There is no third possibility: either the laws of physics forbid it, or it is achievable. This accounts for another aspect of the evolutionary story. Ever better constructors can be produced, without limit, given the relevant knowledge, instantiated in digital recipes.&quot; - David&apos;s comment: Hogwash, but atheistic hope springs eternally that inorganic chemicals can magically become organic life. Are the constructor laws built-in? And where do the laws of nature come from. At least she recognizes the need for information, which she has arisen magically. The commentaries all agree with me.&#13;&#10; - And so do I. The quote sums it all up. What is possible is possible, what is not possible is not possible, and all the possibles can be achieved if we know how to achieve them. Why stick at physics? Doesn&apos;t the same apply to any branch of knowledge and behaviour you can think of? What is biologically, chemically, sportively, politically, economically, artistically, socially possible is possible if we know how to achieve it. But if it is not possible, it is impossible. And apparently that explains everything.

Theoretical origin of life: constructor theory

by David Turell @, Sunday, May 22, 2016, 22:06 (2886 days ago) @ dhw

&#13;&#10;> dhw: And so do I. The quote sums it all up. But if it is not possible, it is impossible. And apparently that explains everything. - Note this is post-doctoral fellow writing this drivel. This is the state of science today!

Theoretical origin of life: warming solar flares

by David Turell @, Tuesday, May 24, 2016, 21:07 (2884 days ago) @ David Turell

Four billion years ago the sun&apos;s heat output was only 70% of the present, yet water was liquid on Earth, when it seems everything should have been frozen solid. The answer may be a more actively flaring sun:-https://www.newscientist.com/article/2089524-cranky-young-sun-could-have-kickstarted-life-on-earth/-&quot;Giant flare-ups from the young sun might have kept early Earth warm - and any life nicely fertilised. By splitting inert nitrogen molecules in the atmosphere, charged particles from the sun could have sparked chemical reactions that heated the planet and could be the precursor for life.-&quot;This suggestion is the latest attempt to solve a famous paradox known as the &#147;faint young sun&#148; problem. About 4 billion years ago, the sun was only 70 per cent as bright as it is today, which should have made the Earth a frozen snowball. But geological evidence shows that ancient Earth was warm enough for liquid water. The same holds true for Mars.-***-&quot;The Earth&apos;s magnetic field usually protects it from assaults by the sun, but Airapetian&apos;s models showed that these energetic solar particles could easily punch through the magnetic field at the poles.-&#147;&apos;One night it occurred to me, wow, these particles now have a great pathway to get to the atmosphere,&#148; he says. There they could do something useful: destroy molecular nitrogen. -&quot;Nitrogen is an essential component for life on Earth, but the young Earth probably only had its molecular form, N2, which is useless for life. Solar particles from flares could split these molecules apart, allowing nitrogen to take more biologically useful configurations. Nitrous oxide, a more potent greenhouse gas than carbon dioxide, could have kept the climate cosy, for example.-&quot;As a bonus, similar reactions would have also made hydrogen cyanide, which can further react to form organic molecules like amino acids.-&quot;It&apos;s a compelling suggestion, says James Kasting of Penn State University, but it needs to be confirmed with more sophisticated atmospheric models. Kasting thinks that ultraviolet light from the sun might have destroyed nitrous oxide before it could mix into the atmosphere.-&#147;It would take a convoluted mechanism to produce that high up in the atmosphere and then get enough of it into the lower atmosphere to produce a good greenhouse effect,&#148; he says.-&quot;Airapetian hopes to address that charge and others with a forthcoming paper that shows particles from flares can penetrate almost to the surface, where rain could carry the chemical products they make the rest of the way down. Another pending work will apply the same process to explain liquid water on early Mars, he says.&quot;-Comment: Interesting theory, since life began about 3.8 billion years ago and there had to be liquid water. Nitrogen ions are an integral part of most organic molecules of life.

Theoretical origin of life: warming solar flares; stupid

by David Turell @, Friday, May 27, 2016, 22:14 (2881 days ago) @ David Turell

Here is a scientist&apos;s answer to the last article on solar flares. it won&apos;t work and the issue raises a problem in the origin of life debate: life requires fixed nitrogen. Nitrogen gas was on Earth but only as part of the atmosphere as a gas, not on the surface. Protein molecules MUST have nitrogen ions as part of amino acids. Cyanobacteria and legumes fix gaseous nitrogen into the soil or in the ocean. Fixed nitrogen is made by life, so how did life start? Here a space scientist&apos;s take:-http://www.uncommondescent.com/origin-of-life/cranky-young-sun-kickstarted-life-no/-&quot;But what this article does reveal-like so many Darwinian &#147;breakthroughs&#148;-is that nitrogen is a real problem for Origin-of-life (OOL). Every protein and nucleobase has nitrogen in it, which needs to be &#147;fixed&#148; or chemically bound for life to start, because fixed nitrogen is unstable. That is because the N2 gas that fills our atmosphere (&#147;unfixed&#148;) is so extremely stable, as organic matter decomposes in our garden, it loses nitrogen to the atmosphere, which never comes back. That&apos;s why coal has no nitrogen content. Other than fresh organic stuff, (or mined organic stuff such as guano) farmers have to put (fixed) nitrogen back in the soil as &#147;nitrates&#148;, a popular version being &#147;ammonium nitrate&#148;, which is now made synthetically using the Nobel-prize winning &#147;Haber-Bosch&#148; high-temperature catalyst process.-&quot;So what OOL needs, in addition to energy sources, entropy barriers, miscible membranes, hot-springs etc, is some way to get fixed nitrogen in the environment as well. This article wants to tie it into solar flares and thence to a young sun to make OOL on Earth more likely. In contrast, Miller-Urey argued for lightning, which is indeed, far more efficient than solar protons. This fellow is either cheerleading for Darwin, or advertising his (overly-simplistic) 2-D computer modeling codes (having done some 3-D magnetosphere models ~20 years ago.) But that&apos;s the way this&#13;&#10; game is played-no matter how insignificant your result, if you want the media to notice your press release, claim it either supports Darwin or global warming or both.-Comment: Lightning does produce some fixed nitrogen as was done in the Miller-Urey lightning-in-an-bottle experiment, but just a little. Life is required. Another reason, of which I was not really aware, for OOL theories. As for his coal comment, remember coal comes from decomposed plants. Nitrogen really makes for a chicken/egg problem.

Theoretical origin of life: delivery of parts by comet

by David Turell @, Saturday, May 28, 2016, 01:17 (2881 days ago) @ David Turell

Glycine, an essential amino acid, has been found in the atmosphere around a comet. Now, with eternal hope, a paper proposes that comets delivered the ingredients for life to Earth:-http://phys.org/news/2016-05-comet-glycine-key-recipe-life.html-&quot;Glycine, an organic compound contained in proteins, was found in the cloud around Comet 67P/Churyumov-Gerasimenko by the European Space Agency&apos;s probe, Rosetta, said the study in the journal Science Advances.-&quot;The discovery was made using an instrument on the probe, called the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) mass spectrometer. -&quot;This is the first unambiguous detection of glycine in the thin atmosphere of a comet,&quot; said lead author Kathrin Altwegg, principal investigator of the ROSINA instrument at the Center of Space and Habitability of the University of Bern.-&quot;In addition to the simple amino acid glycine, the instrument also found phosphorus. The two are key components of DNA and cell membranes.-***-&quot;&apos;Demonstrating that comets are reservoirs of primitive material in the Solar System, and vessels that could have transported these vital ingredients to Earth, is one of the key goals of the Rosetta mission, and we are delighted with this result.&quot;-&quot;Scientists have long debated the question of whether comets and asteroids brought the components of life to Earth by smashing into oceans on our planet.-&quot;More than one hundred molecules have been detected on comets and in their dust and gas clouds, including many amino acids.-***-&quot;However, the latest finding shows &quot;they certainly had the potential to deliver life&apos;s ingredients,&quot; said a statement by the University of Bern.&quot; -Comment: Just because the ingredients are sitting on the kitchen counter, it doesn&apos;t mean the recipe gets cooked.

Theoretical origin of life: life on carbon planets

by David Turell @, Tuesday, June 07, 2016, 20:24 (2870 days ago) @ David Turell

Theorized as in the early universe, made of carbon without much metal present; a pipe dream following too much grant money:-http://phys.org/news/2016-06-universe-life-born-carbon-planets.html-&quot;Our Earth consists of silicate rocks and an iron core with a thin veneer of water and life. But the first potentially habitable worlds to form might have been very different. New research suggests that planet formation in the early universe might have created carbon planets consisting of graphite, carbides, and diamond. Astronomers might find these diamond worlds by searching a rare class of stars.&#13;&#10; &#13;&#10;&quot;&apos;This work shows that even stars with a tiny fraction of the carbon in our solar system can host planets,&quot; says lead author and Harvard University graduate student Natalie Mashian.-&quot;&apos;We have good reason to believe that alien life will be carbon-based, like life on Earth, so this also bodes well for the possibility of life in the early universe,&quot; she adds.-&quot;The primordial universe consisted mostly of hydrogen and helium, and lacked chemical elements like carbon and oxygen necessary for life as we know it. Only after the first stars exploded as supernovae and seeded the second generation did planet formation and life become possible.-&quot;Mashian and her PhD thesis advisor Avi Loeb (Harvard-Smithsonian Center for Astrophysics) examined a particular class of old stars known as carbon-enhanced metal-poor stars, or CEMP stars. These anemic stars contain only one hundred-thousandth as much iron as our Sun, meaning they formed before interstellar space had been widely seeded with heavy elements.-&quot;These stars are fossils from the young universe,&quot; explains Loeb. &quot;By studying them, we can look at how planets, and possibly life in the universe, got started.&quot;-&quot;Although lacking in iron and other heavy elements compared to our Sun, CEMP stars have more carbon than would be expected given their age. This relative abundance would influence planet formation as fluffy carbon dust grains clump together to form tar-black worlds.-&quot;From a distance, these carbon planets would be difficult to tell apart from more Earth-like worlds. Their masses and physical sizes would be similar. Astronomers would have to examine their atmospheres for signs of their true nature. Gases like carbon monoxide and methane would envelop these unusual worlds.-&quot;Mashian and Loeb argue that a dedicated search for planets around CEMP stars can be done using the transit technique. &quot;This is a practical method for finding out how early planets may have formed in the infant universe,&quot; says Loeb.-&quot;&apos;We&apos;ll never know if they exist unless we look,&quot; adds Mashian.&apos;-&#13;&#10;Comment: What is wrong with this study? Besides no oxygen to fuel carbon-based life (the authors&apos; reasonable assumption), just that without iron to make a magnetic shield what will protect this early life from the nasty radiation from the planet&apos;s star? Phew!

Theoretical origin of life: current dead end

by David Turell @, Thursday, June 09, 2016, 23:19 (2868 days ago) @ David Turell

I&apos;ve shown over and over that the attempts to figure out the start of life have all been dead ends. Starting with advanced forms like RNA doesn&apos;t seem to offer any road to success. Now a Science article which I cannot get, making the same point is reviewed elsewhere:-http://www.evolutionnews.org/2016/06/origin-of-life_1102900.html-Direct article quote:-&quot;How can matter transition from the nonliving to the living state? The answer is essential for understanding the origin of life on Earth and for identifying promising targets in the search for life on other planets. Most studies have focused on the likely chemistry of RNA, protein, lipid, or metabolic &quot;worlds&quot; and autocatalytic sets, including attempts to make life in the lab. But these efforts may be too narrowly focused on the biochemistry of life as we know it today. A radical rethink is necessary, one that explores not just plausible chemical scenarios but also new physical processes and driving forces. Such investigations could lead to a physical understanding not only of the origin of life but also of life itself, as well as to new tools for designing artificial biology. [Emphasis added]-&quot;In one fell swoop, Cronin and Walker have cast doubt on essentially the whole history of origin-of-life research. Whether from Oparin, Miller, Orgel, Benner, Hud, Russell, Cairns-Smith, Wachtershauser, Shapiro, or maybe even &quot;warm little pond&quot; Darwin himself -- it&apos;s all inadequate and probably misguided. Otherwise, why would a &quot;radical rethink&quot; be necessary? -***-&quot;Such thinking is flawed for a number of reasons, some of which we can glean from the paper and summarize here:-&#149;Dilution and entropy: &quot;Left unattended, sophisticated chemistry becomes more dilute and disordered.&quot;-&#149;Oversimplification: &quot;A quick route to complexity and enrichment that could lead to the development of evolvable units seems to be required to avoid this serious issue.&quot;-&#149;Ends without means: &quot;Yet, most research efforts have focused on detailing precise chemical mechanisms for producing high yields of individual bio-inspired products, without addressing the processes necessary to form increasingly complex molecules and networks.&quot;-&#149;Improbability: &quot;The molecular constituents of simple networks are more likely to arise by chance than the highly evolved molecules of extant life.&quot;-&#149;Begging the question: &quot;how did evolution begin if the complex machinery for evolution was not in place?&quot;-***-&quot;A concept of information relevant to biological organization may be essential to identifying these networked processes. Adami and LaBar have described life at a basic level as &quot;information that copies itself&quot;. Given that life not only copies information but also uses information to construct itself, we might instead describe the start of life as &quot;simple machines that can construct slightly more complicated machines.&quot; Focusing on information in this way moves the narrative even further from a chemistry-specific mode than focusing on networks alone but may perhaps provide our best shot at uncovering universal laws of life that work not just for biological systems with known chemistry but also for putative artificial and alien life. For example, Walker et al. have recently shown that information-theoretic measures distinguish biological networks from random ones,&quot; (my bold0-Comment: I&apos;m not surprised at the reappraisal. Note the bolded area that emphasizes information at the basis of life. I couldn&apos;t reproduce a vast amount of the long article. It is worth a review.

Theoretical origin of life: possible early enzymes

by David Turell @, Saturday, June 11, 2016, 23:20 (2866 days ago) @ David Turell

This a theoretical computer study which produced a complex enzyme from very early bacteria 3.5 billion years ago. How is such complexity developed so quickly?: - https://www.newscientist.com/article/2093257-ancient-enzyme-resurrected-from-the-ancest... - &quot;The ancestor of all bacteria may have had sophisticated enzymes 3.4 billion years ago - just 600 million years after the origin of life on Earth. - *** - &quot;The discovery comes as a surprise since we had assumed they didn&apos;t evolve until much later - perhaps even for another billion years. - &quot;Modern enzymes fit the molecules they react with like a lock to a key. They normally only work for one reaction, but they perform that one job very well. &#13;&#10; &#13;&#10;&quot;In contrast, the earliest enzymes were &#147;sloppy&#148;, says Michael Harms of the University of Oregon - they didn&apos;t have a lock and key relationship with their molecules. - &quot;To find out when modern enzymes arose, Reinhard Sterner at the University of Regensburg and his colleagues reconstructed a four-part enzyme as it would have looked before modern bacteria and archaea groups split. - &quot;Called tryptophan synthase, the enzyme aids the creation of an amino acid crucial to bacteria, archaea, plants and fungi. - &quot;First they analysed the gene that codes for the enzyme in modern bacteria and archaea, before feeding the sequences into a computer program that searched for similarities between them. - &quot;They then ran thousands of simulations of what the ancient DNA sequence the modern genes came from might have been. - &quot;The program landed on a sequence that was the most probable based on how the major groups of bacteria branched off from each other. The team inserted this resurrected gene into modern E. coli cells, which churned out an enzyme that behaved much like the modern versions. - &quot;This implies bacteria lost their sloppy proteins earlier than we expected, Harms says. A recent study, for example, claimed that simpler enzymes stuck around for another billion years or more. - &#147;It stands counter to what a lot of people would have predicted,&#148; says Harm. &#147;It challenges some received wisdom in the field.&#148; - &quot;Since no DNA remains from billions of years ago, reconstruction experiments like this are the only way to study ancient genes. - *** - &quot;When treated with heat, the reconstructed bacterial enzyme managed to keep its structure until about 70&#176;C. This suggests it was probably part of a microbe that lived in scalding-hot water, Groussin says. &#147;You can infer with strong confidence that the organism lived in a hot environment,&#148; he says. - &quot;This confirms other scientists&apos; hypotheses about the first bacteria living in hot water, Groussin says. - &quot;While the first living cells probably lived in lukewarm habitats, things changed when more complex bacteria began evolving. It&apos;s possible that asteroid bombardments caused Earth&apos;s surface to sizzle during this phase of evolution, meaning that the species that survived had heat-resistant hardware.&quot; - Comment: I still think evolution is driven, never by chance.

Theoretical origin of life: possible early enzymes

by David Turell @, Wednesday, February 14, 2018, 21:21 (2253 days ago) @ David Turell

This essay covers the relative impossibility of the chance discovery of new enzymes, early or late in evolution due to their size and complexity:

https://evolutionnews.org/2018/02/why-darwinism-cant-accomplish-innovation-or-explain-o...

"When one wants to modify an enzyme for a new function, as Matti Leisola explains in Chapter 10 of his new book Heretic, there are two ways to go about it.
First, one can use what is called directed evolution. The term is a bit misleading — it’s similar to evolution, in that it involves generating millions of random mutations in the gene being studied (not a single gene, but millions of copies of that gene), and then selecting for the desired function by putting the mutated genes into bacteria and asking the resulting proteins to perform the new function.

"But it’s not at all like real Darwinian evolution, in that the experimenter determines what the overall goal is (evolution has no goal) and makes a plan for how to achieve it. The experimenter determines the rate of mutation, and causes all those mutations to take place in one population of bacteria, all at once, and the screening is designed by the experimenter as well, to sort through all those millions of mutations for the desired, designed change.
Second, one can use rational design, which as the name suggests is an attempt to shift the protein’s function by studying how it works, and making modifications to the protein’s sequence. The investigator hopes these changes will make the desired functional change.

"Discerning which changes will work takes a great deal of knowledge about that particular enzyme’s chemistry, as well as its three-dimensional structure. But even with all that knowledge, there is no guarantee that a particular change will work as planned. Much trial and error is involved, because enzyme structure and function are quite complex.

***

"First, folded functional proteins are extremely rare in sequence space. This has been shown by several labs, by measuring the mutational sensitivity of different enzymes, and using that to estimate what fraction of all possible sequences might be able to carry out each enzyme’s function. Second, there is evidence that shows that getting a completely new protein from an existing one “is unlikely to occur by evolution through a route of folded intermediate sequences.” Further, even an enzyme with similar structure but no shared chemistry with another enzyme cannot be converted to carry out the function of that seemingly related enzyme.

***

"It is possible to engineer a new pathway into organisms, that is if one chooses an organism that can tolerate the changes introduced. The metabolism as a whole can be thrown out of balance if a new activity is introduced without the proper care. Matti describes how his lab successfully created a strain of yeast that was able to produce xylitol, for which they received a patent. But it required two new enzymes to be introduced, and much labor and planning on the part of the scientists. Evolution does not have the ability to plan. It has no foresight.

"It is also true that occasionally a spontaneous mutation will occur that will confer a new ability on an organism. One example was when Aerobacter aerogenes developed the ability to use xylitol as a carbon source. It turned out this was not the development of a new enzyme ability, but rather the breaking of a regulatory element, which resulted in the constitutive turning on of an enzyme already in existence. Similarly, in Lenski’s lab E. coli developed the ability to use citrate as a carbon source as the result of a DNA rearrangement. That also proved to be the turning on of a gene that was normally shut off. Finally, the development of the enzyme nylonase proved not to be the result of a frameshift, producing a whole new enzyme, but of two point mutations introduced into an existing enzyme, which improved its ability to digest nylon byproducts. Do these count as innovations? Not if by innovation you mean making something new, that did not exist before. The reconfiguring of existing things by breaking regulatory elements or rearranging DNA or changing substrate preferences does not constitute innovation, at least the kind of innovation needed to explain the diversity of enzymes that exist. No new enzymes were made.

"We didn’t get here from the proverbial warm little pond by not making new things. A lot of new things were required, including 1221 new protein folds (at least as of now in SCOP). That’s 2008 superfamilies of proteins, or 4851 families. Where did they come from? According to Dan Tawfik at the Weizmann Institute, “What we lack is a hypothesis for the earlier stages, where you don’t have this spectrum of enzymatic activities, active sites and folds from which selection can identify starting points. Evolution has this catch-22: Nothing evolves unless it already exists.” In other words, according to Tawfik, the origin of proteins is “something like close to a miracle.'”

Comment: Enzymes are a major part of the origin of life miracle, as this essay shows. Early life had to use enzymes because the natural combination of protein molecules is extremely sluggish without enzymatic help. Living organisms live only if their reactions are instantaneous. The origin of life is a miracle by God.

Theoretical origin of life: more ruminations

by David Turell @, Saturday, March 24, 2018, 14:13 (2215 days ago) @ David Turell

Another thoughtful but empty of conclusions article:

https://www.astrobio.net/alien-life/early-life-evolutionary-power-survive-radical-chang...

"Life on Earth could have originated in cold conditions near the surface, before spreading to warmer environments, according to research that analyzes the possible gene sequences belonging to the earliest life.

"All life on Earth today originates from two distinct developments in our planet’s biological history. These are the emergence of the first life forms billions of years ago, and the subsequent evolution of the last universal common ancestor (LUCA) of all extant organisms.

"Whatever they were at the time, these two extinct species – the first life and LUCA – likely occupied radically different environments, suggesting that early life had to undergo a series of evolutionary changes of which traces may still be detectable in organisms alive today.

“'Encountering such environmental variability early on may be necessary to build up the level of complexity needed for LUCA to have the evolutionary potential to continue to diversify and colonize nearly every habitat on Earth over four billion years,” Greg Fournier, an evolutionary biologist at MIT, tells Astrobiology Magazine.

***

"Ultraviolet light can damage RNA, but it may have also triggered chemical reactions that helped create key building blocks of life. At the time of life’s origins, approximately 4.4 billion years ago, the Sun gave off more ultraviolet rays than it does now. The scientists suggested that life first emerged near Earth’s surface under some form of radiation shield, such as water, ice cover, sediment or other barriers, and had access to unshielded environments that could generate key biomolecules.

"Temperatures on Earth may have also been relatively cold at that time, given the Sun’s cooler youth, enough for significant ocean-ice to form. It is easier for amino acids (the building blocks of proteins) and long RNA molecules to assemble in cooler temperatures. Moreover, icy surfaces and slush could have concentrated biomolecules together to assist the emergence of life.

"In contrast, the last universal common ancestor – the microbial species from which all life that exists today came from – may have lived in moderate temperatures, perhaps at least four billion years ago. Scientists can surmise what LUCA was like by looking at what genes organisms on Earth today have in common, analyzing how these genes changed over the course of evolution, and deducing what the ancestral versions of these genes might have been like. The DNA sequences making LUCA’s 600 or so genes and the amino acids making up its proteins are usually most stable in moderate temperatures, the researchers said.

“'Building on the work of many others, we suggest that life dispersed into and adapted to new environments very early in its history,” says study co-author Marjorie Cantine, a geobiologist at MIT.

***

"The researchers suggested that since life apparently originated in a very different environment than the one in which LUCA lived, early organisms likely evolved to survive radical changes in their surroundings. Such dramatic shifts may have included the Late Heavy Bombardment during which swarms of asteroids and comets collided with Earth and the rest of the inner Solar System; the formation of continental crust; and the widespread emergence of liquid water on Earth’s surface.

"A key early adaptation likely included cellularity — that is, collecting everything about themselves within a cellular membrane. Cellularity would have been critical to organisms dispersing away from their original settings and diversifying into new environments.

"Assuming that early life adapted to survive in a checkerboard of many different kinds of environments, “the complex ecological relationships between different species may have been a part of life on Earth since very near its beginning, and LUCA is only one example of the life that may have been extant at that time,” says Fournier.

“'Perhaps a rapid establishment of complex environmental and ecological relationships was even necessary for early life to persist,” adds Cantine.

"The picture painted by Cantine and Fournier of the early evolution of life on Earth is just one plausible scenario. “Our interpretation, like others, relies on a limited [genetic] record and is one contribution to a lively debate,” says Cantine."

Comment: The only takeaway is that life started early in the history of the Earth under harsh conditions, as if it was designed or mandated to appear. Of course it was!

Theoretical origin of life: a new chemical approach

by David Turell @, Monday, April 09, 2018, 20:09 (2199 days ago) @ David Turell

Using volcanic products that had to be present on Earth:

https://www.sciencedaily.com/releases/2018/04/180409103833.htm

"Around 4 billion years ago, Earth was an inhospitable place, devoid of oxygen, bursting with volcanic eruptions, and bombarded by asteroids, with no signs of life in even the simplest forms. But somewhere amid this chaotic period, the chemistry of the Earth turned in life's favor, giving rise, however improbably, to the planet's very first organisms.

"The researchers found that a class of molecules called sulfidic anions may have been abundant in Earth's lakes and rivers. They calculate that, around 3.9 billion years ago, erupting volcanoes emitted huge quantities of sulfur dioxide into the atmosphere, which eventually settled and dissolved in water as sulfidic anions -- specifically, sulfites and bisulfites. These molecules likely had a chance to accumulate in shallow waters such as lakes and rivers.

***

"Preliminary work by Ranjan and his collaborators suggest that sulfidic anions would have sped up the chemical reactions required to convert very simple prebiotic molecules into RNA, a genetic building block of life.

***

"In 2015, chemists from Cambridge University, led by John Sutherland, who is a co-author on the current study, discovered a way to synthesize the precursors to RNA using just hydrogen cyanide, hydrogen sulfide, and ultraviolet light -- all ingredients that are thought to have been available on early Earth, before the appearance of the first life forms.

"From a chemistry point of view, the researchers' case was convincing: The chemical reactions they carried out in the laboratory overcame longstanding chemical challenges, to successfully yield the genetic building blocks to life. But from a planetary science standpoint, it was unclear whether such ingredients would have been sufficiently abundant to jumpstart the first living organisms.

"For instance, comets may have had to rain down continuously to bring enough hydrogen cyanide to Earth's surface. Meanwhile, hydrogen sulfide, which would have been released in huge amounts by volcanic eruptions, would have mostly stayed in the atmosphere, as the molecule is relatively insoluble in water, and therefore would not have had regular opportunities to interact with hydrogen cyanide.

***

"They took away from that [talk] that, on early Earth, you don't have much oxygen, but you do have sulfur dioxide from volcanism," Ranjan recalls. "As a consequence, you should have sulfites. And they said, 'Can you tell us how much of this molecule there would have been?' And that's what we set out to constrain."

"To do so, he started with a volcanism model developed previously by Sara Seager, MIT's Class of 1941 Professor of Planetary Sciences, and her former graduate student Renyu Hu.

"'They did a study where they asked, 'Suppose you take the Earth and just crank up the amount of volcanism on it. What concentrations of gases do you get in the atmosphere?'" Ranjan says.

***

"Ultimately, he found that, while volcanic eruptions would have spewed huge quantities of both sulfur dioxide and hydrogen sulfide into the atmosphere, it was the former that dissolved more easily in shallow waters, producing large concentrations of sulfidic anions, in the form of sulfites and bisulfites.

***

"Early experiments led by Ranjan's colleagues suggest that sulfites and bisulfites may have indeed encouraged biomolecules to form. The team carried out chemical reactions to synthesize ribonucleotides with sulfites and bisulfites, versus with hydrosulfide, and found the former were able to produce ribonucleotides and related molecules 10 times faster than the latter, and at higher yields. More work is needed to confirm whether sulfidic anions were indeed early ingredients in brewing up the first life forms, but there is now little doubt that these molecules were part of the prebiotic milieu."

Comment: hope springs eternal. Design work in the lab isn't uncontrolled experiments like this. Life's appearance is miraculous. RNA is a specific type of molecule out of many possible molecular forms appearing by chance. The start of life requires design.

Theoretical origin of life: from nuclear geysers

by David Turell @, Saturday, April 21, 2018, 18:50 (2187 days ago) @ David Turell

An interesting new concept on dry land:

https://cosmosmagazine.com/biology/nuclear-geyser-may-be-origin-of-life

"Life may not have originated in the primordial soup of an ancient pond, according to scientists, but rather in a “nuclear geyser” powered by an ancient uranium deposit.

"Shigenori Maruyama of Tokyo Institute of Technology says the idea came from what chemists know about crucial compounds in our own bodies.

"Many of these compounds – including DNA and proteins - are polymers formed from chains of smaller building blocks.

"Each of these molecules serves a different purpose in the body, but something they all have in common, says Nicholas Hud, a chemist from Georgia Institute of Technology, Atlanta, is that a molecule of water is released when each new building block is added.

“'There is a theme here,” he said last week at a NASA-sponsored symposium on the early solar system and the origins of life. To a chemist, this suggests that these biopolymers must have originated under relatively dry conditions.

"Otherwise, Hud says, the presence of water would have forced the reactions to run backwards, breaking chains apart. But, there’s a problem: most scientists assume life started in water.

"The solution to this paradox, according to Hud, comes from realizing that water comes and goes. The major chemicals of life, and presumably life itself, may have formed in an environment that was alternately wet and dry. “It could be seasonal,” he says. “It could be tides. It could be aerosols that go up [into the air] and come back down.”

"Some prebiotic chemical reactions occur easily at moderate temperatures, but others, says Robert Pascal, a physical organic chemist from the University of Montpellier, France, require a more concentrated source of energy. This energy may have come from the sun, which in the early solar system was considerably more active than today. But another source is radiation.
Which brings us back to nuclear geysers.

"Some prebiotic chemical reactions occur easily at moderate temperatures, but others, says Robert Pascal, a physical organic chemist from the University of Montpellier, France, require a more concentrated source of energy. This energy may have come from the sun, which in the early solar system was considerably more active than today. But another source is radiation.
Which brings us back to nuclear geysers.

"Based on analyses similar to Hud’s and Pascal’s, Maruyama has identified nine requirements for the birthplace of life. One place where all can occur at once, Maruyama says, is in the plumbing of a nuclear geyser.

"This would not only produce heat to power the geyser, but produce radiation strong enough to break the recalcitrant molecular bonds of water, nitrogen, and carbon dioxide, all of which must be cleaved in order to produce critical prebiotic compounds. Periodic eruptions of the geyser would also produce alternating wet and dry cycles, and water draining from the surface would bring back dissolved gases from the atmosphere. The rocks lining the geyser’s subterranean channels would provide a source of minerals such as potassium and calcium.

“'This is the place I recommend [for the origin of life],” Maruyama says.

"Once life originated, he says, it would have been spewed onto the surface and from there into the oceans. From there, it spread to every known habitable niche on the modern Earth."

Comment: This idea comes from carefully thought-out reasoning. It is not the stuff of designs in a lab. I still view life as a miracle, but I would think of this idea as placing the origin of life in a place that might have eased the job for God to accomplish it.

Theoretical origin of life: another replicating lab RNA

by David Turell @, Wednesday, May 16, 2018, 01:47 (2163 days ago) @ David Turell

Hope springs eternal in lab work. With lots of adjustments they found another replicating RNA which is a little different from ones in the past:

https://phys.org/news/2018-05-scientists-primordial-life-earth-replicated.html

"The scientists from the Medical Research Council (MRC) Laboratory of Molecular Biology say the new RNA utilises a system of genetic replication unlike any known to naturally occur on Earth today.

***

"Previously, scientists had developed ribozymes that could replicate straight strands of RNA, but if the RNA was folded it blocked the ribozyme from copying it. Since ribozymes themselves are folded RNAs, their own replication is blocked.

"Now, in a paper published today in the journal eLife, the scientists have resolved this paradox by engineering the first ribozyme that is able to replicate folded RNAs, including itself.

"Normally when copying RNA, an enzyme would add single bases (C, G, A or U) one at a time, but the new ribozyme uses three bases joined together, as a 'triplet' (e.g. GAU). These triplet building blocks enable the ribozyme to copy folded RNA, because the triplets bind to the RNA much more strongly and cause it to unravel—so the new ribozyme can copy its own folded RNA strands.

"The scientists say that the 'primordial soup' could have contained a mixture of bases in many lengths—one, two, three, four or more bases joined together—but they found that using strings of bases longer than a triplet made copying the RNA less accurate.

"Dr. Philipp Holliger, from the MRC Laboratory of Molecular Biology and senior author on the paper, said: "We found a solution to the RNA replication paradox by re-thinking how to approach the problem—we stopped trying to mimic existing biology and designed a completely new synthetic strategy. It is exciting that our RNA can now synthesise itself.

"'These triplets of bases seem to represent a sweet spot, where we get a nice opening up of the folded RNA structures, but accuracy is still high. Notably, although triplets are not used in present-day biology for replication, protein synthesis by the ribosome—an ancient RNA machine thought to be a relic of early RNA-based life—proceeds using a triplet code.

"'However, this is only a first step because our ribozyme still needs a lot of help from us to do replication. We provided a pure system, so the next step is to integrate this into the more complex substrate mixtures mimicking the primordial soup—this likely was a diverse chemical environment also containing a range of simple peptides and lipids that could have interacted with the RNA." (my bold)

"The experiments were conducted in ice at -7°C, because the researchers had previously discovered that freezing concentrates the RNA molecules in a liquid brine in tiny gaps between the ice crystals. This also is beneficial for the RNA enzymes, which are more stable and function better at cold temperatures." (my bold)

Comment: More fun and games in the lab. Everything occurs at frozen temperatures with lots of lab help as my bolded areas point out. The Earth was theoretically very hot at the beginning and had to cool down for life to start. And where did the amino acid triplets come from on a rocky inorganic Earth where most organic material appeared only after life started?

Theoretical origin of life; Chirality of space molecules

by David Turell @, Tuesday, June 14, 2016, 20:59 (2863 days ago) @ David Turell

A molecule has been identified in space with chirality, which means left or right handed configuration. In this case the handedness is not identified, but the article waxes excitedly about the relationship to origin of life. to remind everyone, amino acids in life are all left handed, and the DNA and RNA sugar molecules, ribose, are all right handed:-https://www.sciencedaily.com/releases/2016/06/160614142127.htm-&quot;Scientists applaud the first detection of a &quot;handed&quot; molecule, (propylene oxide) in interstellar space. It was detected, primarily with the NSF&apos;s Green Bank Telescope, near the center of our Galaxy in Sagittarius (Sgr) B2, a massive star-forming region. Propylene oxide is one of a class of so-called &quot;chiral&quot; molecules -- molecules that have an identical chemical composition, but right- and left-handed versions. Chiral molecules are essential for life and their discovery in deep space may help scientists understand why life on Earth relies on a certain handedness to perform key biological functions.&quot; -Comment: No one has any idea why handedness is so specific in life, and this fonding won&apos;t help explain it. Studies on living matter might.-&quot;&quot;This is the first molecule detected in interstellar space that has the property of chirality, making it a pioneering leap forward in our understanding of how prebiotic molecules are made in the Universe and the effects they may have on the origins of life,&quot; said Brett McGuire, a chemist&quot; -Comment: Not true. Amino acids have handedness and are found on meteorites from space.-&quot;Complex organic molecules form in interstellar clouds like Sgr B2 in several ways. The most basic pathway is through gas-phase chemistry, in which particles collide and merge to produce ever more complex molecules. Once organic compounds as large as methanol (CH3OH) are produced, however, this process becomes much less efficient.-&quot;To form more complex molecules, like propylene oxide, astronomers believe thin mantles of ice on dust grains help link small molecules into longer and larger structures. These molecules can then evaporate from the surface of the grains and further react in the gas of the surrounding cloud.-&quot;To date, more than 180 molecules have been detected in space. Each molecule, as it naturally tumbles and vibrates in the near vacuum of the interstellar medium, gives off a distinctive signature, a series of telltale spikes that appear in the radio spectrum. Larger and more complex molecules have a correspondingly more complex signature, making them harder to detect.&quot;-Comment: Just because some of life&apos;s molecules exist in space, it doesn&apos;t mean they will spontaneously assemble on Earth&apos;s surface.-&quot;&apos;Meteorites in our Solar System contain chiral molecules that predate the Earth itself, and chiral molecules have recently been discovered in comets,&quot; noted Carroll. &quot;Such small bodies may be what pushed life to the handedness we see today.&quot;-&quot;&apos;By discovering a chiral molecule in space, we finally have a way to study where and how these molecules form before they find their way into meteorites and comets, and to understand the role they play in the origins of homochirality and life,&quot; McGuire said.&apos;-Comment: The amino acids in meteorites are 53% left handed and 47% right handed according to recent reports. In life 100% left. Not much help there. Hope springs eternal that God is not required.

Theoretical origin of life; Chirality of space molecules

by David Turell @, Thursday, August 18, 2016, 00:13 (2799 days ago) @ David Turell

A molecule has been identified in space with chirality, which means left or right handed configuration. In this case the handedness is not identified, but the article waxes excitedly about the relationship to origin of life. to remind everyone, amino acids in life are all left handed, and the DNA and RNA sugar molecules, ribose, are all right handed:&#13;&#10;> &#13;&#10;> https://www.sciencedaily.com/releases/2016/06/160614142127.htm&#13;&#10;> &#13;&#10;> &quot;Scientists applaud the first detection of a &quot;handed&quot; molecule, (propylene oxide) in interstellar space. It was detected, primarily with the NSF&apos;s Green Bank Telescope, near the center of our Galaxy in Sagittarius (Sgr) B2, a massive star-forming region. Propylene oxide is one of a class of so-called &quot;chiral&quot; molecules -- molecules that have an identical chemical composition, but right- and left-handed versions. Chiral molecules are essential for life and their discovery in deep space may help scientists understand why life on Earth relies on a certain handedness to perform key biological functions.&quot; &#13;&#10;> &#13;&#10;> Comment: No one has any idea why handedness is so specific in life, and this fonding won&apos;t help explain it. Studies on living matter might.&#13;&#10;> &#13;&#10;> &quot;&quot;This is the first molecule detected in interstellar space that has the property of chirality, making it a pioneering leap forward in our understanding of how prebiotic molecules are made in the Universe and the effects they may have on the origins of life,&quot; said Brett McGuire, a chemist&quot; &#13;&#10;> &#13;&#10;> Comment: Not true. Amino acids have handedness and are found on meteorites from space.&#13;&#10;> &#13;&#10;> &quot;Complex organic molecules form in interstellar clouds like Sgr B2 in several ways. The most basic pathway is through gas-phase chemistry, in which particles collide and merge to produce ever more complex molecules. Once organic compounds as large as methanol (CH3OH) are produced, however, this process becomes much less efficient.&#13;&#10;> &#13;&#10;> &quot;To form more complex molecules, like propylene oxide, astronomers believe thin mantles of ice on dust grains help link small molecules into longer and larger structures. These molecules can then evaporate from the surface of the grains and further react in the gas of the surrounding cloud.&#13;&#10;> &#13;&#10;> &quot;To date, more than 180 molecules have been detected in space. Each molecule, as it naturally tumbles and vibrates in the near vacuum of the interstellar medium, gives off a distinctive signature, a series of telltale spikes that appear in the radio spectrum. Larger and more complex molecules have a correspondingly more complex signature, making them harder to detect.&quot;&#13;&#10;> &#13;&#10;> Comment: Just because some of life&apos;s molecules exist in space, it doesn&apos;t mean they will spontaneously assemble on Earth&apos;s surface.&#13;&#10;> &#13;&#10;> &quot;&apos;Meteorites in our Solar System contain chiral molecules that predate the Earth itself, and chiral molecules have recently been discovered in comets,&quot; noted Carroll. &quot;Such small bodies may be what pushed life to the handedness we see today.&quot;&#13;&#10;> &#13;&#10;> &quot;&apos;By discovering a chiral molecule in space, we finally have a way to study where and how these molecules form before they find their way into meteorites and comets, and to understand the role they play in the origins of homochirality and life,&quot; McGuire said.&apos;&#13;&#10;> &#13;&#10;> Comment: The amino acids in meteorites are 53% left handed and 47% right handed according to recent reports. In life 100% left. Not much help there. Hope springs eternal that God is not required.-Another take on the same discovery:-http://www.scientificamerican.com/article/astrochemists-detect-chiral-molecules-in-interstellar-space-for-the-first-time/?WT.mc_id=SA_DD_20160817-&quot;Life seems to prefer molecules of a single chemical handedness, however. All DNA, for example, twists clockwise like the threads on a right-handed screw. Nearly all amino acids, meanwhile, are left-handed. Why one or the other? &#147;It&apos;s pretty well established that once an excess [of one chirality] is present, life is going to go with it,&#148; says Brett McGuire, an astrochemist at the National Radio Astronomy Observatory in Charlottesville, Va.&quot;-Comment: this comment is wild speculation, not supported by the general literature re&apos; chirality. Uncontrolled a reaction makes roughly right and left molecules equally:-&quot;Others are skeptical. Arizona State University biochemist Sandra Pizzarello, who has studied chiral molecules in meteorites, says connecting the observations to DNA chirality could be difficult. &#147;We are still left wondering what happens&#148; on the long path between molecular clouds and the origins of life, she says.&quot;

Theoretical origin of life; ealiest possibly found

by David Turell @, Wednesday, August 31, 2016, 22:53 (2785 days ago) @ David Turell

Greenland has the oldest rock on Earth. Previously fossil stromatolites were found in Australia at 3.5 byo. Now similar fossils may have been found in Greenland at 3.7 byo:-https://www.washingtonpost.com/news/speaking-of-science/wp/2016/08/31/3-7-billion-year-old-fossils-may-be-the-oldest-signs-of-life-on-earth/?wpisrc=nl_evening&wpmm=1-&quot;It&apos;s a stunning announcement in a scientific field that is always contentious. But if confirmed, this would push the established fossil record more than 200 million years deeper into the Earth&apos;s early history, and provide support for the view that life appeared very soon after the Earth formed and may be commonplace throughout the universe.-&quot;A team of Australian geologists announced their discovery in a paper titled &#147;Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures,&#148; published Wednesday in Nature.-&quot;They made their find in July 2012 while doing field research in Isua, a region of Greenland so remote that they had to travel there by helicopter. The site is known for having the oldest rocks on Earth, in what is known as the Isua supracrustal belt.-&quot;They examined the outcropping and immediately saw something intriguing: conical structures, just one to four centimeters (less than two inches) high. They look like fossilized microbial mats &#151; basically, pillows of slime &#151; known as stromatolites, which are formed today by bacterial communities living in shallow water.-&#147;&apos;We all said, &apos;This is amazing. These look like stromatolites,&apos; &quot; Nutman told The Washington Post.-&quot;Subsequent laboratory analysis established that the formation is 3.7 billion years old, and turned up additional chemical signatures consistent with a biological origin for the conical structures, Nutman said. The scientists determined the age of the rocks through radiometric dating, measuring the abundance of elements created by the steady decay of uranium.-***-&quot;They might really be biological but it&apos;s hard to absolutely refute the possibility that they formed by localized mineral precipitation from seawater. If we found these on Mars, would we plant a flag and declare that we had found life on Mars? I think not, but we would definitely get very excited and continue looking around for more information,&quot; she said.-&#147;&apos;We expect there will be some robust debate. That&apos;s what science is all about. There will be people surely who will put forward alternative hypotheses. But we think we&apos;ve covered all those alternatives,&quot; Nutman said.-&quot;The Australians&apos; claim of Greenland stromatolites is &quot;plausible and likely correct,&quot; said J. William Schopf, a pioneering paleobiologist at the University of California at Los Angeles who was not involved in the discovery.-***-&quot;The Australian researchers do not contend that these stromatolites represent the first examples of life on the planet. Rather, these would have to be the descendants of the earlier life forms. Microbes capable of performing photosynthesis and forming communities are relatively sophisticated organisms. They presumably had less-sophisticated ancestors that lived more than 4 billion years ago, the Nature paper states.-&#147;&apos;Stromatolites are really complex, so you have to have a lot of evolution from when life started to when stromatolites appeared in the fossil record. So life either had to start earlier, or evolution is more rapid than you might expect,&quot; said Sara Walker, an astrobiologist at Arizona State University who was not involved in the new study.-&quot;Earth, along with the other planets in our solar system, formed about 4.5 billion years ago from a cloud of dust and gas swirling around the embryonic sun. For hundreds of millions of years, ours was a harsh, molten world, heavily bombarded by debris.&quot;-Comment: An Earth 4.5 billion years old has somewhat complex single celled life at 3.7 byo. Life started quickly here. Startling. Can it be by chance?

Theoretical origin of life; most important stages

by David Turell @, Friday, September 02, 2016, 00:36 (2784 days ago) @ David Turell

This article lists key stages in the development of life on Earth:-https://www.washingtonpost.com/news/achenblog/wp/2016/09/01/the-4-biggest-milestones-in-the-history-of-life-on-earth/?wpisrc=nl_popns&wpmm=1-&quot;The first and most obvious milestone was the origin of life. The details of that remain murky. Since life began, Earth has been transmogrified through cataclysmic events. The evidence of life&apos;s origin was eroded, or vanished in the recycling of the surface through plate tectonics. The only thing left are grains of zircon and other minerals that may have signatures of molecules that hint of the presence of life.-***-&quot;Once life got rolling, the Next Big Thing was photosynthesis, says J. William Schopf, a legendary paleobiologist at the University of California at Los Angeles. Photosynthesis, he told us, enabled organisms to create their own food from solar energy and at the same time transform the biosphere by emitting oxygen. For roughly half the Earth&apos;s history, oxygen couldn&apos;t linger in the atmosphere because it kept interacting with other gases and surface elements. But gradually the oxygen &#147;sinks&#148; filled up and oxygen, created by living things, became a major constituent of the air. That, in turn, enabled the emergence of life that could use oxygen metabolically, which supercharged the complexity of Earthlife.-&quot;The next big moment, Schopf said, was the appearance of sexual reproduction roughly a billion years ago. Until then, life merely cloned itself. Sexual reproduction is a technique for mixing genetic material rapidly in novel arrangements. That accelerated evolution, Schopf said. Soon enough we had multicellular organisms, followed by the Cambrian Explosion, 542 million years ago, in which all manner of hard-shelled creatures with elaborate body types evolved quickly.-***-&quot;Then he amended his short list of things that matter: &#147;I guess I would put intelligence in there as the fourth big thing that happened.&#148;-***-&quot;With only one example of life - the stuff we see on Earth - we don&apos;t really have a good, universally accepted definition of life. NASA some years ago defined life as &#147;a self-sustaining chemical system capable of Darwinian evolution.&#148; Not bad, but technically a single rabbit hopping around your garden is not alive, because by itself it can&apos;t reproduce.-&#147;&apos;I don&apos;t think anyone has a definition of life that is universally agreed upon. The best we can do is describe some attributes of life - and then someone will poke holes in that,&#148; says Pamela Conrad, an astrobiologist at NASA. &#147;We know pretty well what non-life is, so we can rule out the other stuff. The leftovers is life.&apos;&#148;-Comment: I think he pinned down the very big steps. What is surprising is the use of oxygen. It is nasty stuff: think of the dangers of giant fires; note that we try to moderate the damage by eating anti-oxidants. We don&apos;t use oxygen directly. Energy in cells is from conversion of ADP to ATP and back again, because the phosphate bonds are energy rich.

Theoretical origin of life; ealiest possibly found

by David Turell @, Saturday, September 03, 2016, 15:07 (2782 days ago) @ David Turell

Another comment on this earliest life offering the opinion that life is likely to start quickly and easily. This is a startling view unless one accepts the idea that God is involved:-http://www.the-scientist.com/?articles.view/articleNo/46946/title/Ancient-Fossils-May-Change-Earth-s-Biological-Origin-Story/-&quot;Fossils recently discovered in Greenland contain evidence of the earliest known life on earth&#151;dating to 3.7 billion years ago (bya), claim researchers who have been studying the finds. The minute, sedimentary remains, called stromatolites, of microbial colonies that grew on an ancient shoreline are described by a team of Australian researchers -&quot;The fossils corroborate previous evidence from genetic molecular clocks that places the origin of life somewhere around 4 bya, the study&apos;s authors note. However, the finding should be interpreted with caution, since &#147;structures that look similar to stromatolites can form without the action of living organisms&#148; and the study is &#147;limited by the information available in the tiny outcrop,&#148; Allwood observes.-&quot;To the untrained eye, the remarkable fossils don&apos;t look like much. They consist of small, cone-shaped disturbances in metamorphic rock, which according to chemical and geological evidence were created by mats of microorganisms living in shallow seawater pools. As the primitive microorganisms grew over each other as if inhabiting ramshackle tenements, they left telltale sediment deposits that researchers can now identify and date. The team of scientists discovered the fossils in southwest Greenland, in rock newly exposed by melting snow.-&#147;&apos;Earth&apos;s surface 3.7 billion years ago was a tumultuous place, bombarded by asteroids and still in its formative stages,&#148; Allwood writes. &#147;If life could find a foothold here, and leave such an imprint that vestiges exist even though only a minuscule sliver of metamorphic rock is all that remains from that time, then life is not a fussy, reluctant and unlikely thing. Give life half an opportunity and it&apos;ll run with it.&apos;&#148; (my bold)-Comment: Start of life exuberant? An opinion from Science magazine. A case for God.

Theoretical origin of life; from clays, an old idea

by David Turell @, Tuesday, September 06, 2016, 00:29 (2780 days ago) @ David Turell

This thought is 50 years old and never found traction in the science world, the use of clay crystals to help bring DNA together. As the attempts at any glimpse of usefulness found nothing the idea went nowhere:-http://www.bbc.com/earth/story/20160823-the-idea-that-life-began-as-clay-crystals-is-50-years-old-&quot;At a later stage, Cairns-Smith reasoned, biological molecules like DNA began to associate with the crystals. This helped the replication process. Eventually, a &quot;genetic takeover&quot; happened: the biological molecules developed the ability to replicate by themselves, and left the crystals behind.-&quot;Cairns-Smith set all this out in a paper published in 1966, half a century ago.-&quot;His ideas are elegant, but there is a big problem: they have proved almost impossible to test. In 50 years there have only been a handful of experiments exploring Cairns-Smith&apos;s ideas.-***-&quot;There may never be hard evidence for Cairns-Smith&apos;s ideas. &quot;If this were to be a huge scientific enterprise, if there were huge technology behind it, there would be enough resources to really push the experiments,&quot; says Braun. &quot;But it&apos;s really just a very small community, and this is a little bit too far out.&quot;-&quot;However, the lack of evidence will not be Cairns-Smith&apos;s real legacy. The specific scenario he envisaged may well be completely wrong. But in terms of inspiring people to look at the question of life&apos;s origin in new ways, his work has punched well above its weight.&quot;-Comment: This article discusses the failures of tis approach:-https://en.wikipedia.org/wiki/Abiogenesis#Clay_hypothesis-Robert Shapiro in his book, Origins, 1986, discusses clays as a substrate on which simple organic molecules could form.-Origin of life is still a total mystery, and looks miraculous

Theoretical origin of life; earliest possibly found

by David Turell @, Friday, September 09, 2016, 01:56 (2777 days ago) @ David Turell

Another comment:-http://www.evolutionnews.org/2016/09/greenland_fossi103110.html-&quot;From the New York Times:-&quot;Geologists have discovered in Greenland evidence for ancient life in rocks that are 3.7 billion years old. The find, if confirmed, would make these fossils the oldest on Earth and may change scientific understanding of the origins of life.-&quot;Experts are likely to debate whether the structures described in the new report were formed biologically or through natural processes. If biological, the great age of the fossils complicates the task of reconstructing the evolution of life from the chemicals naturally present on the early Earth. It leaves comparatively little time for evolution to have occurred and puts the process close to a time when Earth was being bombarded by destructive asteroids. [Emphasis added.]-&quot;The microbial mats from the Isua Greenstone Belt involved creatures already &quot;fairly evolved.&quot;-&quot;Several different species of microbes are involved in stromatolite creation. The Isua structures, if indeed stromatolites, would represent fairly evolved organisms.-&quot;If life on Earth did not begin until after the Late Heavy Bombardment, then it had a mere 100 million years in which to evolve to the quite advanced stage seen in the new fossils.-&quot;If so, Dr. [Abigail] Allwood wrote, then &quot;life is not a fussy, reluctant and unlikely thing.&quot; It will emerge whenever there&apos;s an opportunity.-&quot;But the argument that life seems to have evolved very early and quickly, so therefore is inherently likely, can be turned around, Dr. [Gerald] Joyce said. &quot;You could ask why, if life were such a probable event, we don&apos;t have evidence of multiple origins,&quot; he said.-&quot;In fact, with trivial variations, there is only one genetic code for all known forms of life, pointing to a single origin.-***-&quot;If some unguided chemical and biological evolutionary model must be assumed as explaining the origins of life, then something is wrong. Life springs up easily. It must, &quot;whenever there&apos;s an opportunity.&quot; If so, it should have happened repeatedly on earth -- why not? -- leaving evidence in the form of multiple genetic codes. But there is no such evidence.-***-&quot;For evolutionists, it&apos;s a dilemma without an apparent solution.-***-&quot;Whether the origin of life, of complex animals, or of homo sapiens with our gift of speech, wonderful things have a funny way of &quot;slipping suddenly into being,&quot; in Michael Denton&apos;s phrase.-&quot;Remember, this is all apart from the devilish difficulties for theories of unguided origins. Innovations don&apos;t &quot;evolve.&quot; They spring into existence, we find again and again, with an alarming abruptness. As if by design.&quot;-Comment: My thoughts exactly. Common descent, one form of DNA through out. One origin! As soon as it could! Miracle is the best possibility. From God.

TTheoretical origin of life; lab manufaacture of amyloid

by David Turell @, Monday, September 12, 2016, 18:33 (2773 days ago) @ David Turell

Another intelligent design in a lab, supplying four amino acids and a volcanic gas and playing with them:-http://phys.org/news/2016-09-protein-like-primordial-soup.html-&quot;However, ETH Professor Roland Riek and his senior scientist Jason Greenwald have a compelling idea: these primordial lifelike structures could well have been proteinaceous aggregates, or amyloids. The latest results of their laboratory research now lend weight to their hypothesis.-&quot;The scientists performed an experiment to demonstrate that it is remarkably easy for such amyloid structures to assemble spontaneously from building blocks that existed on the prebiotic Earth, and under reaction conditions that also seem plausible for the primeval era. The scientists used four simple amino acids as starting materials: glycine, alanine, aspartate and valine. In addition, they used carbonyl sulphide as a catalyst for the reaction. This volcanic gas is also likely to have existed in the atmosphere billions of years ago.-(Comment: All these amino acids have to be left handed. Not a natural event. How did these specific amino acids get to exist on an rocky Earth?)-&quot;In the laboratory experiment, the amino acid molecules spontaneously assembled, with the help the carbonyl sulphide, into short chains (peptides) comprising between 5 and 14 building blocks. These chains in turn arranged themselves in parallel into amyloid structures known as beta sheets. In the experiment, these sheet structures took the form of fibres and typically comprised thousands of adjoining peptide chains which the scientists were able to identify using an electron microscope.-(Comment: Amyloid is not a very active protein, and seen as part of Alzheimer&apos;s pathology)-&quot;To make sure the amino acid molecules formed into sufficiently long peptide chains, the scientists had to use a clever trick. &quot;Simply mixing amino acids with carbonyl sulphide in a test tube only produces very short peptide chains which do not assemble into a sheet structure&quot;, Greenwald explains. The scientists therefore slowly dripped amino acid molecules activated with carbonyl sulphide into a test tube in a procedure lasting several hours. &quot;It is conceivable that an equally slow process - possibly taking several years - with a steady flow of new chemical compounds may well have taken place in the Earth&apos;s primeval history&quot;, says Greenwald.-(Comment: pipedream) -&quot;Scientists have already proposed amyloids as candidates for the very first lifelike structures on Earth, as even simple amyloids are capable of performing certain chemical functions. Last year, for example, Professor Riek and his team discovered amyloid structures able to split esters.-(Comment: Where did the esters come from on rocky Earth? They create perfumes and other smelly products.)-&quot;The ETH scientists stress, however, that there is still an important piece of the puzzle missing from their argument in support of the &quot;amyloid hypothesis&quot;: Are amyloids also capable of self-replication, just like RNA molecules? This is conceivable, claim Riek and Greenwald, but there is still no experimental evidence to support it. The professor and his team are working on it.-&quot;Even so, the researchers already describe their hypothesis as being much more plausible than the decades-old scientific assumption that the precursors of life were made up solely of RNA molecules. The scientists&apos; main contention: RNA molecules with a biological function are comparatively large and complex. &quot;They are so big that it would have been difficult for them to form spontaneously. Even with far simpler structures, amyloids exhibit certain chemical functions&quot;, says Greenwald. On top of that, the building blocks of RNA are more complex than those of amyloids and proteins. Furthermore, the latter are more stable even under harsh environmental conditions. &quot;All this makes it plausible that the first functional molecules were amyloids&quot;, concludes Professor Riek. &quot;-Comment: Good point about RNA complexity. Otherwise too much grant money chasing too few valid studies.

Theoretical origin of life; Timing of Earth formation

by David Turell @, Wednesday, September 14, 2016, 20:19 (2771 days ago) @ David Turell

How quickly life appeared on Earth is a critical factor. The current theory of a heavy bombardment of the proto-Earth is that it was severe, hot, and lasted until 3.9 or 4.0 billion years ago. If life popped up at 3.8 billion years ago, that sure is quick. If the formation of Earth was of a milder form perhaps the allowable time for life to appear is longer than 200,000 million years: -https://www.newscientist.com/article/2105823-asteroid-assault-on-early-planets-was-more-like-a-gentle-massage/-&quot;A proposed period of intense asteroid and comet strikes on the inner solar system might be a fiction. Simulations suggest that the purported spike in impacts about 3.9 billion years ago could merely be an artefact of limited samples.-&#147;It&apos;s been an overly simplistic interpretation of complicated data that leads to this illusion,&#148; says Mark Harrison at the University of California, Los Angeles.-&quot;Our solar system coalesced from a giant cloud of gas and dust around 4.6 billion years ago. Colossal planetesimals and other fragments were constantly colliding during this era, leading to dramatic wallops such as the impact between the early Earth and a Mars-sized object that may have spawned the moon.-&quot;After a few hundred million years, these first enormous chunks cleared out and impacts became rarer. But approximately 3.9 billion years ago, during a period known as the Late Heavy Bombardment, a second deluge of asteroids and comets seemed to rain down on the inner solar system. Some suggest this was a lucky break for Earth: that bombardment could have brought the first water and even prebiotic molecules to the infant planet.&#13;&#10; &#13;&#10;&quot;One of the strongest pieces of evidence for this upheaval is that rocks Apollo astronauts brought back from the moon all seem to cluster around this particular date, suggesting the lunar surface experienced a cataclysmic battering. The dating methods looked at a potassium isotope with a half-life of approximately 1.25 billion years, which decays to argon gas. Should a nearby impact heat up the lunar rocks, they will release some argon gas. The leftover argon then theoretically gives an estimate of the last time the rock was hit.-&quot;Harrison and Boehnke created a model divvying up the moon&apos;s surface into 1000 regions. They simulated what it would look like if a decreasing number of asteroids and comets battered this area over time, and found they could produce an illusory uptick at 3.9 billion years. Rather than a sudden deluge of meteorites, the moon might have experienced a slow, steady rain of rocks until the solar system cleared out.-&quot;Though it&apos;s been a bedrock assumption in planetary science for decades, other indications seem to be moving away from the Late Heavy Bombardment theory. Harrison points out that it originated with the Apollo samples, which come from only 4 per cent of the moon&apos;s surface. Subsequent lunar meteorites found on Earth - blown off from random parts of the moon - don&apos;t show a spike around 3.9 billion years, but rather have a wide range of ages.-&quot;Geologic samples from the Earth suggest it was a comparatively pleasant place too, with liquid water, plate tectonics, and perhaps even early life. &#147;How can one line of evidence say this was a hellish horrible time period and this other that says maybe it was quite nice?&#148; asks Boehnke.-&#13;&#10;&#147;&apos;The problem is that your rock might not just be getting hit once, but multiple times,&#148; says Patrick Boehnke, also at UCLA.-&quot;Each subsequent outgassing would make the rocks appear younger and younger. Because all of the moon&apos;s surface formed at roughly the same time, perhaps 4.3 or 4.4 billion years ago, multiple impacts could drive down the surface rocks&apos; ages to the same value, providing an imaginary spike.&quot;-Comment: However long life took to appear it was really quite short. Still a probable miracle.

Theoretical origin of life; 4.2 billion years ago?

by David Turell @, Tuesday, September 27, 2016, 04:46 (2759 days ago) @ David Turell

Finding of Carbon-12 isotope in zircons raises the possibility:-http://3tags.org/article/was-earth-born-with-life-already-on-it-&quot;After all, it&apos;s not like you can just go back in time and look at what was present then; the only evidence we have is the little bits and pieces that survive from back then, and almost all of what survives has changed over that time.-***-&quot;But in the decades since, we realized something: even though the fossils themselves may no longer be discernible to us today, the remnants of organic matter leave a particular signature in the form of carbon. You may be used to &#147;carbon dating&#148; in the form of measuring the carbon-14 to carbon-12 ratio in organisms, since both forms of carbon are absorbed into organic matter, with carbon-14 being created in the upper atmosphere by cosmic rays and decaying with a half-life of around 5,700 years. As long as you&apos;re alive, you breathe in and ingest both forms of carbon; when you decompose, the carbon-14 decays and isn&apos;t replaced by any new carbon-14. Hence, if you can measure the carbon-14 to carbon-12 ratio (carbon dating), you can know roughly, with an error of a few thousand years, how long ago a particular organism died.-***-&quot;But there&apos;s another form of carbon we don&apos;t talk about in the same breath: carbon-13, which, like carbon-12, is stable, and which is about 1.1% as abundant as the other forms of carbon.-&quot;Living organisms?&#151;?as far as we&apos;ve been able to biologically observe?&#151;?seem to prefer to uptake carbon-12 to carbon-13, due to metabolic enzymes reacting with carbon-12 more efficiently. If you find an ancient source of carbon and it&apos;s enhanced with carbon-12 as opposed to carbon-13, that&apos;s a good indicator that it&apos;s the remnants of an organic life-form. By looking for graphite, a form of pure carbon, deposited in otherwise highly metamorphosed rocks (things like zircons), we&apos;ve been able to push back well beyond that 1-2 billion year barrier, and had placed the emergence of Earth-life all the way back to 3.8 billion years ago, or just some 750 million years after Earth formed. But as of 2015, we&apos;ve done even better.-***-&quot;By finding graphite deposits in zircons that are 4.1 billion years old, graphite deposits that show this carbon-12 enhancement, we now have evidence that life on Earth goes back at least 90% of Earth&apos;s history, and possibly even longer! After all, finding the remnants of organic matter in a certain location means the organic matter is at least as old as the location it&apos;s buried in, but it could still be even older. This is so early that it might make you think that perhaps this life didn&apos;t originate here on Earth, but that Earth was born with life. And this could really, truly be the case.-***-&quot;When meteorites land on Earth, like the Murchison meteorite, shown below, we can analyze what&apos;s present inside. Yes, we find all sorts of interesting organic molecules, but what&apos;s perhaps most interesting is the amino acid content. While there are only about 20 amino acids that play a role in life processes here on Earth, there are nearly 100 unique amino acids found in this meteorite, a strong indication that the ingredients for life are ubiquitous throughout the Universe. We even find amino acids on the Moon, indicating that whatever brought these ingredients to Earth did so before the formation of the Moon, less than 100 million years into the age of our Solar System! (He forgets, or ignores, only eight amino acids were in the 20 essential for life group, and handedness was both right and left, not just left s in life)-***-&quot;Well, if the ingredients are there, why couldn&apos;t some primitive form of life be there as well? If all life on Earth has a universal common ancestor, couldn&apos;t it be that there are many forms of ultra-primitive life in the Universe, and the type that came to Earth that was best adapted to the early Earth&apos;s environment was the type that thrived, evolved, reproduced, and out-competed all the others? We don&apos;t have enough evidence to favor this hypothesis over any other, but if we continue to push this limit back earlier and earlier: 4.3 billion years, 4.4 billion years, 4.45 billion years&#133; it&apos;s going to be harder and harder to argue that this life didn&apos;t come to Earth already alive in some sense.&quot;-Comment: He is pushing the old idea of panspermia. Still doesn&apos;t settle the issue of the origin of life.

Theoretical origin of life;RNA & DNA developd in tandem?

by David Turell @, Thursday, September 29, 2016, 05:21 (2757 days ago) @ David Turell

Another wild idea assuming RNA and DNA developed, but how did that happen:-&quot;The study questions the &quot;RNA world&quot; hypothesis, a theory for how RNA molecules evolved to create proteins and DNA. Instead, the new research offers evidence for a world where RNA and DNA evolved simultaneously.&#13;&#10;&quot;Even if you believe in a RNA-only world, you have to believe in something that existed with RNA to help it move forward,&quot; said Ramanarayanan Krishnamurthy, associate professor of chemistry at TSRI and senior author of the new study. &quot;Why not think of RNA and DNA rising together, rather than trying to convert RNA to DNA by means of some fantastic chemistry at a prebiotic stage?&quot;-***-&quot;Researchers have explored the RNA world hypothesis for more than 30 years. The idea behind this theory is that a series of chemical reactions led to the formation of self-replicating RNA molecules. RNA then evolved to create proteins and enzymes that resembled early versions of what makes up life today. Eventually, these enzymes helped RNA produce DNA, which led to complex organisms.-&quot;On the surface, RNA and DNA molecules look similar, with DNA forming a ladder-like structure (with nucleobase pairs as the rungs and sugar molecule backbones as the sides) and RNA forming what looks like just one side of a ladder.-&quot;If the RNA world theory is accurate, some researchers believe there would have been many cases where RNA nucleotides were mixed with DNA backbones, creating &quot;heterogeneous&quot; strands. If stable, these blended &quot;chimeras&quot; would have been an intermediate step in the transition to DNA.-&quot;However, the new study shows a significant loss of stability when RNA and DNA share the same backbone. The chimeras do not stay together as well as pure RNA or pure DNA, which would compromise their ability to hold genetic information and replicate.&#13;&#10;&quot;We were surprised to see a very deep drop in what we would call the &apos;thermal stability,&apos;&quot; said Krishnamurthy....This instability appeared to be due to a difference in the DNA sugar molecule structure versus the RNA sugar molecule.-***-&quot;Because of this instability, chimeras in the RNA world would have likely died off in favor of more stable RNA molecules. This reflects what scientists see in cells today: If RNA nucleobases mistakenly join a DNA strand, sophisticated enzymes will rush to fix the mistake. Evolution has led to a system that favors more stable, &quot;homogeneous&quot; molecules.-&quot;These sophisticated enzymes were probably not around at the time of RNA and DNA&apos;s early evolution, so these substitutions may have had a crippling effect on the molecules&apos; ability to replicate and function. &quot;The transition from RNA to DNA would not have been easy without mechanisms to keep them separate,&quot; said Krishnamurthy. (comment: Complex enzymes are always needed, how were they found on early Earth with sparce amino acids?)-&quot;This realization led the scientists to consider an alternate theory: RNA and DNA may have arisen in tandem.-***-&quot;If the two evolved at the same time, DNA could have established its own homogeneous system early on. RNA could have still evolved to produce DNA, but that may have occurred after it first met DNA and got to know its raw materials.&#13;&#10;Krishnamurthy added that scientists will never know exactly how life began (barring the invention of a time machine).&quot;-Comment: Even origin of life has just-so stories.

Theoretical origin of life; high viscosity goo?

by David Turell @, Monday, October 10, 2016, 19:57 (2745 days ago) @ David Turell

Starting with some RNA or DNA goo seems to help them continue to develop. Pie in the sky. Where did the RNA/DNA come from? -https://www.sciencedaily.com/releases/2016/10/161010120136.htm-&quot;A little goo will do to get RNA and DNA to progress toward self-replication. Could some abundant ingredient have helped the precursors of genes become life molecules? Another indicator that little drama may have been necessary in chemical evolution. -***-&quot;Earliest life was based on RNA, or a similar polymer, according to a hypothesis called the RNA World. In that scenario, on the evolutionary timeline, the self-replication of RNA strands long enough to be potential genes would roughly mark the doorstep to life.-&quot;Those long nucleotide chains may have been mixed together in puddles with shorter nucleotide chains. Heat from the sun would have made long strands detach from their helix structures, giving short ones a chance to match up with them, and become their copies. But there&apos;s a problem.-&quot;In water alone, when cooling sets in, the long chains snap back into their helix structure so rapidly that there&apos;s no time for the matching process with the shorter chains. That snapping shut, which happens in both RNA and DNA, is called &quot;strand inhibition,&quot; and in living cells, enzymes solve the problem of keeping the long chains apart while gene strands duplicate.-***-&quot;He and G&#225;llego&apos;s use of a naturally occurring gene, rather than a specifically engineered sequence, shows that viscosity could have been a very general solution to promote copying of nucleic acids with mixed length and sequences.&#13;&#10;To facilitate quick, clear outcomes, the Georgia Tech researchers used purified short nucleotide chains and applied them in ratios that favored productive reactions. But they had started out with messier, less pure ingredients, and the experience was worthwhile.-***-&quot;The viscous solvent was glycholine, a mixture of glycerol and choline chloride. It was not likely present on pre-biotic Earth, but other viscous solvents likely were.&#13;&#10;Also, after the short strands matched up to each long one, the researchers did apply an enzyme to join the aligned short pieces into a long chain, in a biochemical process called ligation. (my bold)-&quot;The enzymes would not have been present on a prebiotic Earth, and although there are chemical procedure for ligating RNA, &quot;no one has developed a chemistry so robust yet that it could replace the enzyme,&quot; Grover said.&quot;-Comment: Again intelligent design in a lab, starting with RNA or DNA, adding a goo and an enzyme. Viscous goo may have been present in sea bottoms where life probably started, but RNA/DNA and enzymes did not exist. Not an explanation for start of life.

Theoretical origin of life; lab work cannot reproduce

by David Turell @, Thursday, October 27, 2016, 05:01 (2729 days ago) @ David Turell

Using pure starting points with careful lab controls humans cannot produce RNA or anything like it:

http://inference-review.com/article/two-experiments-in-abiogenesis

"This advance by Carell and his team relied on the use of pre-formylated purines and pyrimidines; this made possible their coupling with commercially purchased homochiral ribose. The authors did mention the problems raised by the oxidative instability of aminopyrimidines. There is no reason to suppose that nature could have commanded these exquisite laboratory skills. Often seven major products, and many more minor products, were formed in these reactions, where the combined yield of the anomeric nucleosides could be as high as 60%. When starting with racemic glyceraldehydes and glycoaldehyde, rather than purified homochiral ribose, the yields of the racemic nucleosides dropped to less than 1%, and that 1% contained as many as 16 different isomers. No attempt was made to extract the trace, which was likely less than 0.1%, of targeted nucleosides from the other >99.9% of the gross reaction mixtures.

"This work underscores the difficulties in obtaining even trace amounts of a single desired nucleoside. To make matters worse, it was obtained along with an unusable mixture of products. Impurities are not innocuous. They retard subsequent reactions, first by consuming precious starting materials, and then by consuming the reaction’s final product. The synthesis was complicated, no matter the advanced chemical methods, no matter the purified starting materials, no matter the oxygen-free containment systems, and no matter the most sophisticated laboratories.

***

"This reaction provides only ribose traces in unusable mixtures. Carell and his coworkers assumed ribose as a given. They also used purified aminopyrimidines, relying on research that generated them from small molecules, such as guanidine and hydrogen cyanide. The published protocols on which they reply report equally troubling mixtures of products. No overall bookkeeping standards are maintained from one published work to another. The shortcomings of past generations are subsumed in current work without ever being acknowledged.

Comment: In a highly sophisticated article written in advanced biochemicalese LeTour is saying you can't get there from here, even if you cheat by starting with exactly purified reagents at the start, not likely to b on early ?Eath when life started.

“'It is assumed,” Carell and his colleagues remark, “that life originated from a simple set of small molecules.” His work dispels any such illusions. Reckless general claims are a characteristic of the field. In describing the RNA-world hypothesis, Carrell and his colleagues argue that it would be easy to go from molecules to nucleosides, then to informational polymers, and finally to self-replicating systems. This is to assume, without evidence, that in prebiotic chemistry great oaks follow naturally from small acorns. Views such as this are acceptable in today’s scientific journals.

***

"Hud and his group used a rich characterization suite and their chemical data analyses are superbly done. Had they confined themselves to supramolecular assembly of chiral conjoiners, their article would be a worthwhile contribution to the literature. But, it is a stretch to suggest that these proto-RNA structures—the MMP and BMP hexads—could have been the ancestral forms of canonical structures. Their article leaves the reader wondering. Are they suggesting that the recurring strings of hydrogen-bonded BMP-MMP in some way served as a template for RNA? Can there be anything meaningfully encoded in an alphabet-restricted regularly patterned hexad? Simple regular patterns cannot encode complex function.

"Or are Hud and his colleagues suggesting that something transformed self-assembled BA and melamine into the canonical four bases? There is no conceivable prebiotic synthetic transformation that makes this plausible.

"This cannot be what the authors are suggesting."

Comment: In a highly sophisticated article written in advanced biochemicalese, Tour is saying you can't get there from here, even if you cheat by starting with exactly purified reagents at the start, not likely to be on early Earth when life started, as shown in very sophisticated biochemical labs.

Theoretical origin of life; an optimistic history of researc

by David Turell @, Friday, November 04, 2016, 14:42 (2720 days ago) @ David Turell

This is can extremely long accurate history of the research in origin of life. It is optimistically cast as if 'they' are getting close. No way! What doesn't work is well understood. what dos cerate life is not understood:

http://www.bbc.com/earth/story/20161026-the-secret-of-how-life-on-earth-began

"The strength of Miller-Urey is to show that you can go from a simple atmosphere and produce lots of biological molecules," says John Sutherland of the Laboratory of Molecular Biology in Cambridge, UK.

"The details turned out to be wrong, since later studies showed that the early Earth's atmosphere had a different mix of gases. But that is almost beside the point.

***

"Writing in Nature in 1986, Gilbert proposed that life began in the "RNA World".
The first stage of evolution, Gilbert argued, consisted of "RNA molecules performing the catalytic activities necessary to assemble themselves from a nucleotide soup".

***

"An alternative approach has been put forward by Gerald Joyce and Tracey Lincoln of the Scripps Research Institute in La Jolla, California. In 2009 they created an RNA enzyme that replicates itself indirectly.

"Their enzyme joins together two short pieces of RNA to create a second enzyme. This then joins together another two RNA pieces to recreate the original enzyme.

"This simple cycle could be continued indefinitely, given the raw materials. But the enzymes only worked if they were given the correct RNA strands, which Joyce and Lincoln had to make. ( my bold)

***

"But no self-replicating RNA had been found, and nobody could figure out how RNA formed in the primordial soup. The alternative nucleic acids might solve the latter problem, but there was no evidence they ever existed in nature. That was less good.
The obvious conclusion was that the RNA World, neat as it was, could not be the whole truth.

***

"Once life had harnessed the chemical energy of the vent water, Russell and Martin say, it started making molecules like RNA. Eventually it created its own membrane and became a true cell, and escaped from the porous rock into the open water.

"This story is now regarded as one of the leading hypotheses for the origin of life.

***

"So Sutherland has set out to find a "Goldilocks chemistry": one that is not so messy that it becomes useless, but also not so simple that it is limited in what it can do. Get the mixture just complicated enough and all the components of life might form at once, then come together.

"In other words, four billion years ago there was a pond on the Earth. It sat there for years until the mix of chemicals was just right. Then, perhaps within minutes,
the first cell came into existence.

***

"There might even be room for the alternatives to RNA that have been cooked up in labs, like the TNA and PNA we met in Chapter Three. We do not know if any of them ever existed on Earth, but if they did the first organisms may well have used them alongside RNA.

"This was not an RNA World: it was a "Hodge-Podge World".

"The lesson from these studies is that making the first cell might not have been as hard as it once seemed. Yes, cells are intricate machines. But it turns out that they still work, albeit not quite as well, when they are flung together slapdash from whatever is to hand.

***

"In nature, many enzymes have a metal atom at their core. This is often the "active" part of the enzyme, with the rest of the molecule essentially a support structure. The first life cannot have had these complex enzymes, so instead it probably used "naked" metals as catalysts.

***

"Some of the people alive today will become the first in history who can honestly say they know where they came from. They will know what their ultimate ancestor was like and where it lived."

Comment: the optimistic last paragraph is not consistent with the accurate history given. The enzymes needed have not been found, and no on knows what natural enzymes were available 3.8 billion years ago. My bolds indicate all this research is intelligent design in labs. Very long article. I've only touched the surface.

Theoretical origin of life; early RNA problems

by David Turell @, Wednesday, November 09, 2016, 18:59 (2715 days ago) @ David Turell

Lab research finds first appearing RNA might try different methods with false results:

https://www.sciencedaily.com/releases/2016/11/161102085329.htm

"When a short piece of RNA (green) binds a nucleotide analogue (PZG, pink), three different binding modes are observed, suggesting canonical Watson-Crick is not the only possible mode of RNA self-recognition.

"It's the ultimate chicken-or-egg conundrum: What was the "mother" molecule that led to the formation of life? And how did it replicate itself? One prominent school of thought proposes that RNA is the answer to the first question. Now, in ACS Central Science, researchers in this camp demonstrate RNA has more flexibility in how it recognizes itself than previously believed. The finding might change how we picture the first chemical steps towards replication and life.

"Today, plants, animals and other organisms reproduce by making copies of their DNA with the help of enzymes and then passing the copies onto the next generation. This is possible because genetic material is made of building blocks -- or bases A, T, U, G and C -- that pair up in a specific way. A pairs with T (or U in RNA), and G pairs with C. This rule is called Watson-Crick base pairing, named after the scientists who were credited with solving DNA's structure. But before life as we know it existed, some molecule had to replicate without any help at all. RNA is a likely suspect for this go-it-alone first status because it is simultaneously capable of specific base-pairing like DNA, and catalyzing reactions, like an enzyme. Thus, Jack Szostak and colleagues wanted to investigate how RNA matches up with free nucleotides to see whether its base-pairing methods would allow RNA to copy itself without any outside aid.

"They monitored how an analogue of a free nucleotide interacted with a short piece of RNA using the classic method of X-ray crystallography -- the same technique used more than fifty years ago in the original discovery of DNA's 3-D structure. In addition to forming the expected canonical Watson-Crick pairs, the RNA bonded with the analogue in other less frequently observed ways. Under prebiotic conditions, these unexpected non-Watson-Crick pairings might have caused dead-ends to replication. Thus, the results suggest that the first steps toward life required more trial and error than previously thought."

Comment: Early origin of life research is plagued with problems. Starting life is not easy, and miraculous.

Theoretical origin of life; Lack of code bases

by David Turell @, Thursday, November 10, 2016, 20:45 (2714 days ago) @ David Turell

What might arrive from space by comet or meteorite to supply the base code for RNA and then DNA. Not everything:

https://blogs.scientificamerican.com/guest-blog/did-the-seeds-of-life-come-from-space/?...

"To investigate whether our own nucleobases could have been delivered to Earth inside meteorites, Pearce started by examining the organic content found in meteorite falls.
Nucleobases come in five flavours: guanine (G), adenine (A), cytosine (C), thymine (T) and uracil (U). Pearce confirmed three of these were commonly listed in the meteoritic record, but there was no hint of cytosine or thymine. Intriguingly, these missing members are the complementary pairs to the discovered nucleobases, with guanine pairing with cytosine (G-C) and adenine pairing with thymine (A-T) in DNA.

***

"Using comet composition as a starting point for their model, the scientists calculated the expected yields of the five nucleobases that make up our genetic code.
What they discovered was that while four of the nucleobases formed in measurable amounts, the elusive cytosine was missing. In truth, cytosine was created. However, it rapidly decayed within a few years to produce the more commonly found uracil nucleobase and ammonia. This meant the chances of finding cytosine in meteorite samples were practically zero.

"'It's not that we simply haven't found any cytosine in meteorites,” Pearce exclaimed. “It seems that it can't be found!"

"While this closed the case on the missing cytosine, the other absent nucleobase, thymine, seemed to be produced in detectable abundances. So why is it never seen?
It turns out that thymine decomposes in the presence of hydrogen peroxide; the same chemical in bleach and disinfectant. Hydrogen peroxide has been spotted in comets, making it a potential culprit for destroying any thymine that was formed.

"These models explain the presence of only three nucleobases in the meteorite samples, but they leave a clear conundrum: if our genetic code needs five nucleobases, where did the missing two partners come from?

"These models explain the presence of only three nucleobases in the meteorite samples, but they leave a clear conundrum: if our genetic code needs five nucleobases, where did the missing two partners come from?

"It is a question that still lacks a satisfactory answer. It is possible that these life seeds began on Earth, although this presents a number of tricky problems. Our early atmosphere was inhospitable for creating organic molecules, while our oceans run the risk of also producing only three nucleobases. A promising option is that the sun’s ultraviolet rays triggered the formation the organics on dust grains within our Solar System, which were then captured by the Earth’s pull.

“'This is a big question!” Pearce concludes. “And at the moment, we don’t know the answer.'”

Comment: Some truth about the problem for those who think life occurred naturally. It was rocky Earth that had no organic molecules at first and needed specific ones to start life. Still looks miraculous.

Theoretical origin of life; requires intellect

by David Turell @, Saturday, December 03, 2016, 20:16 (2691 days ago) @ David Turell

A Russian scientist/priest presents his viewpoint. This is an excerpt from a very long essay:

http://www.uncommondescent.com/informatics/ud-guest-post-dr-eugen-s-on-the-second-law-o...

"To create life, from the point of view of systems theory and information theory, it was necessary to organize the complex {code+protocol+translator}, – the whole of it and at once, – simply because code without its complementary translator is useless rubbish and, likewise, a translator without code a meaningless pile of junk. Furthermore, a protocol is a set of rules i.e. a non-physical thing, a logical correspondence of material entities that have no physical or chemical attraction or bias of any sort to one another. How could that arise by purely physicalistic means?! Total nonsense!

"No physical fluctuation of macrostate – of entropy, density, pressure, temperature – can achieve it. The first ever living organism already was not reducible to its constituents. A gradual path for its own assembly starting at a spontaneous fluctuation of state is non-existent if this world. It is a myth. Nature only permits the creation of information processing systems being itself indifferent to information processing; indifferent in the same sense as a spherical mass is at equilibrium on a horizontal plane without friction.

"If we take a look at how life is organized, we shall see that its organization is purposefully directed to counteract entropic increases. Death is the unavoidable end of this wrestling as far as an individual living organism is concerned. Before dying though an organism passes on life to the next generation which is organized in the same way. «The fight against the second law» is realized as replication. Although every new organism and even the replication mechanism itself are subject to degradation over time (the latter at a much slower rate than the former), the heart of life, so to speak, is in replication!

***

"Nothing of the sort can be observed in inanimate nature as a complex. Various individual elements of this complex are observed, such is crystal growth/replication for instance. However, for a crystal to grow information translation and codes are not necessary. Crystals grow mechanically, as matrix bulk-copying of layers upon layers of lattice, in line with the minimum total potential energy principle. In contrast, the genetic code cannot be explained solely by this principle since the essence of translation is in the processing of tokens that only evoke physical effects without determining what these effects should be! Tokens impose boundary conditions on the system dynamics.

"As a matter of fact, biosemiotics as a discipline that describes sign processing in biological systems, views a token, not a gene, as a unit of life. According to biosemiotics (cf. here and here), life is physics coupled with specific symbolic boundary conditions, which includes organized behaviour for working with symbolic memory.This is where our materialist interlocutors are in error or decidedly playing word games.

"Some of them, who are educated enough to appreciate the predicament for their worldview, find nothing better than questioning the objectivity of information as a scientifically detectable phenomenon. That is understandable: if you think of this, they have no other option. Playing the fool is a lot more comfortable than having to acknowledge the obvious i.e. that life has intelligent origin!

"So, non-living matter is missing the important ingredient that is key for the organization of life: it is absolutely void of any information translation. That must be the emphasis in our discussions with naturalists. Unfortunately, from the point of view of mere thermodynamics, life is indistinguishable from non-life: in both there are physical interactions of particles; in both non-living and living systems energy is spent and entropy tends to maximum. After all, both life and non-life use the same chemical elements from the same periodical system."

Comment: This is his conclusion after a long article discussing entropy and how life answers that process. Look at his figures for more explanation.

Theoretical origin of life; requires intellect

by dhw, Sunday, December 04, 2016, 12:32 (2690 days ago) @ David Turell

QUOTE: "So, non-living matter is missing the important ingredient that is key for the organization of life: it is absolutely void of any information translation. That must be the emphasis in our discussions with naturalists. Unfortunately, from the point of view of mere thermodynamics, life is indistinguishable from non-life: in both there are physical interactions of particles; in both non-living and living systems energy is spent and entropy tends to maximum. After all, both life and non-life use the same chemical elements from the same periodical system."

David’s comment: This is his conclusion after a long article discussing entropy and how life answers that process. [...]

Phew! Thank you for editing this. There has to be a distinction between living matter and non-living matter, but it is difficult to pinpoint. I’d say replication with differences is one factor. I would presume sentience is another. Some of us would say the ability to process information and regulate behaviour accordingly is another (perhaps that’s what he means by “information translation”). As evidence for God’s existence, I must say I much prefer your complexity approach to the convoluted one you have summarized.

Theoretical origin of life; requires intellect

by David Turell @, Sunday, December 04, 2016, 15:34 (2690 days ago) @ dhw


David’s comment: This is his conclusion after a long article discussing entropy and how life answers that process. [...]

dhw: There has to be a distinction between living matter and non-living matter, but it is difficult to pinpoint. I’d say replication with differences is one factor. I would presume sentience is another. Some of us would say the ability to process information and regulate behaviour accordingly is another (perhaps that’s what he means by “information translation”). As evidence for God’s existence, I must say I much prefer your complexity approach to the convoluted one you have summarized.

I would edit your statement: there is an obvious difference between life and non-life, but an exact definition of what is life is not yet decided. It is obvious that life's processes depend upon using information implanted within life. Thank you for your appreciation of the complexity argument. But his approach to 'origin of life' is a major part of my argument. Origin is not explained by any research and is as strong an argument for God as is complexity of life.

Theoretical origin of life; requires intellect

by dhw, Monday, December 05, 2016, 13:54 (2689 days ago) @ David Turell

David’s comment: This is his conclusion after a long article discussing entropy and how life answers that process. [...]

dhw: There has to be a distinction between living matter and non-living matter, but it is difficult to pinpoint. I’d say replication with differences is one factor. I would presume sentience is another. Some of us would say the ability to process information and regulate behaviour accordingly is another (perhaps that’s what he means by “information translation”). As evidence for God’s existence, I must say I much prefer your complexity approach to the convoluted one you have summarized.

DAVID: I would edit your statement: there is an obvious difference between life and non-life, but an exact definition of what is life is not yet decided. It is obvious that life's processes depend upon using information implanted within life. Thank you for your appreciation of the complexity argument. But his approach to 'origin of life' is a major part of my argument. Origin is not explained by any research and is as strong an argument for God as is complexity of life.

I would not separate origin from complexity. The author pointed out the problem of defining the difference between life and non-life, so I was trying to pinpoint relevant factors. The three abilities I listed are the products of the complexities, and in analysing the machinery that makes them possible, you put the strongest case for design against chance, which = origin. But you would have understood a lot more of the article than I did, and I am in no position to criticize it. I was just trying to add something useful, and my final remark was “in passing”.

Theoretical origin of life; requires intellect

by David Turell @, Monday, December 05, 2016, 15:19 (2689 days ago) @ dhw


dhw: I would not separate origin from complexity. The author pointed out the problem of defining the difference between life and non-life, so I was trying to pinpoint relevant factors. The three abilities I listed are the products of the complexities, and in analysing the machinery that makes them possible, you put the strongest case for design against chance, which = origin. But you would have understood a lot more of the article than I did, and I am in no position to criticize it. I was just trying to add something useful, and my final remark was “in passing”.

What is significant is that original life had to be highly complex from its beginning when it could replicate, and the complexity then generated was complexity many times over that we still are far from fully appreciating.

Theoretical origin of life; 4.1 billion years ago?

by David Turell @, Saturday, January 14, 2017, 00:39 (2650 days ago) @ David Turell

Claimed to be that early because of graphite (carbon) found in zircons!

http://www.dailygalaxy.com/my_weblog/2017/01/life-on-earth-may-have-started-almost-inst...

"UCLA geochemists have found evidence that life likely existed on Earth at least 4.1 billion years ago — 300 million years earlier than previous research suggested. The discovery indicates that life may have begun shortly after the planet formed 4.54 billion years ago.

The new research suggests that life existed prior to the massive bombardment of the inner solar system that formed the moon’s large craters 3.9 billion years ago.

“If all life on Earth died during this bombardment, which some scientists have argued, then life must have restarted quickly,” said Patrick Boehnke, a co-author of the research and a graduate student in Harrison’s laboratory.

"Scientists had long believed the Earth was dry and desolate during that time period. Harrison’s research — including a 2008 study in Nature he co-authored with Craig Manning, a professor of geology and geochemistry at UCLA, and former UCLA graduate student Michelle Hopkins — is proving otherwise.

"The researchers, led by Elizabeth Bell — a postdoctoral scholar in Harrison’s laboratory — studied more than 10,000 zircons originally formed from molten rocks, or magmas, from Western Australia. Zircons are heavy, durable minerals related to the synthetic cubic zirconium used for imitation diamonds. They capture and preserve their immediate environment, meaning they can serve as time capsules.

"The scientists identified 656 zircons containing dark specks that could be revealing and closely analyzed 79 of them with Raman spectroscopy, a technique that shows the molecular and chemical structure of ancient microorganisms in three dimensions.

***

"One of the 79 zircons contained graphite — pure carbon — in two locations.
“The first time that the graphite ever got exposed in the last 4.1 billion years is when Beth Ann and Patrick made the measurements this year,” Harrison said.

"How confident are they that their zircon represents 4.1 billion-year-old graphite?

“'Very confident,” Harrison said. “There is no better case of a primary inclusion in a mineral ever documented, and nobody has offered a plausible alternative explanation for graphite of non-biological origin into a zircon.”

"The graphite is older than the zircon containing it, the researchers said. They know the zircon is 4.1 billion years old, based on its ratio of uranium to lead; they don’t know how much older the graphite is.

"The carbon contained in the zircon has a characteristic signature — a specific ratio of carbon-12 to carbon-13 — that indicates the presence of photosynthetic life.

"We need to think differently about the early Earth,” Bell said."

Comment: If the Earth is 4.5 billion years old as theorized, life appeared in 0.4 billion years after Earth formation. That seems very quick, even if conditions on Earth were more hospitable than currently believed because of the massive bombardment at 3.9 billion years ago. Miraculously quick?

Theoretical origin of life; an honest assessment

by David Turell @, Saturday, January 14, 2017, 15:09 (2649 days ago) @ David Turell

This philosophic research scientist admits we may never figure out the origin of life:

https://www.sciencedaily.com/releases/2017/01/170112083719.htm

"Life is a process that originated 3.5 billion years ago. It emerged when the basic components of the cells that we know today, in other words, inanimate chemical molecules, gradually joined, merged, assembled themselves and interacted. At a given moment they became alive, or what amounts to the same thing, they turned into autonomous systems. As the years passed they gradually evolved until achieving their current complexity and diversity.

"'Basically, these studies are looking for the 'molecule of life', in other words, they set out to establish which was the most important molecule in making this milestone happen," said Kepa Ruiz-Mirazo, researcher in the Biophysics Unit and of the UPV/EHU's Department of Logic and Philosophy of Science. However, bearing in mind that "life involves activity among a huge variety of molecules and components, a change of approach has been taking place in recent years and research that takes into account various molecules at the same time is gaining strength,"

"Our group has expertise in research into membranes that are created in prebiotic environments, in other words, in the study of the dynamics that fatty acids, the precursors of current lipids, may have had. The Montpellier group for its part specialises in the synthesis of the first peptides. So when the knowledge of each group is put together, and when we experimentally blended the fatty acids and the amino acids, we could see that there was a strong synergy between them."

"As they were able to see, the catalysis of the reaction took place when the fatty acids formed compartments. As they are in an aqueous medium, and due to the hydrophobic nature of lipids, they tend to join with each other and form closed compartments; in other words, they take on the function of a membrane; "at that time the membranes obviously weren't biological but chemical ones," explained Ruiz-Mirazo. In their experiments they were able to see that the conditions offered by these membranes are favourable for amino acids. "The Montpellier group had the prebiotic reactions of the formation of dipeptides very well characterised, so they were able to see that this reaction took place more efficiently in the presence of fatty acids," he added.

"Besides demonstrating the synergy between fatty acids and amino acids, Ruiz-Mirazo believes it is very important to have conducted the study using basic chemical components, in other words, molecular precursors. "Life emerged out of these basic molecules; therefore, to study its origin we cannot start from the complex phospholipids that are found in today's membranes. We have demonstrated the formation of the first coming together and formation of chains on the basis of molecular precursors. Or to put it another way, we have demonstrated that it is possible to achieve diversity and complexity in biology by starting from chemistry."

"Ruiz-Mirazo is working in another two spheres so in the end he is studying the origin of life from three pillars or perspectives: "firstly, we have the experimental field; another is based on theoretical models and computational simulations, which we use to analyse the results obtained in the experiments, and the third is a little broader, because we are studying from the philosophical viewpoint what life is, the influence that the conception held about life exerts on the experimental field, since each conception leads you to carry out a specific type of experiment," he explained. "These three methodologies mutually feed each other: an idea that may emerge in the philosophical analysis leads you to carry out a new simulation, and the results of the simulations mark out the path for designing the experiments. Or the other way round. Most likely we will never manage to find the answer to how life began, but we are working on it: all of us living beings on Earth have the same origin and we want to know how it happened.'"

Comment: My bolded statement shows his honest assessment of where his research might not lead. He is trying to start from the bottom up with lipids and amino acids, but that really isn't the start of the process. He isn't answering the real question: where did the lipids and amino acids come from on a rocky planet? As he shows, life is the result of many very complex molecules coming cooperatively together. At some point what we call life then appears. Still miraculous.

Theoretical origin of life; from dividing droplets

by David Turell @, Friday, January 20, 2017, 21:11 (2643 days ago) @ David Turell

It is fine thatt one can make dividing droplets, but how about the machinery inside?

https://www.quantamagazine.org/20170119-active-droplets-cell-division/?utm_source=Quant...

"The scientists studied the physics of “chemically active” droplets, which cycle chemicals in and out of the surrounding fluid, and discovered that these droplets tend to grow to cell size and divide, just like cells. This “active droplet” behavior differs from the passive and more familiar tendencies of oil droplets in water, which glom together into bigger and bigger droplets without ever dividing.

"If chemically active droplets can grow to a set size and divide of their own accord, then “it makes it more plausible that there could have been spontaneous emergence of life from nonliving soup,” said Frank Jülicher, a biophysicist in Dresden and a co-author of the new paper.

***

"David Deamer, a biochemist at the University of California, Santa Cruz, and a longtime champion of the membrane-first hypothesis, argues that while the newfound mechanism of droplet division is interesting, its relevance to the origin of life remains to be seen. The mechanism is a far cry, he noted, from the complicated, multistep process by which modern cells divide.

***

"Tang’s lab synthesizes artificial cells made of polymers, lipids and proteins that resemble biochemical molecules. Over the next few months, she and her team will look for division of liquid droplets made of polymers that are physically similar to the proteins in P granules and centrosomes. The next step, which will be made in collaboration with Hyman’s lab, is to try to observe centrosomes or other biological droplets dividing, and to determine if they utilize the mechanism identified in the paper by Zwicker and colleagues. “That would be a big deal,” said Giomi, the Leiden biophysicist.

"When Deamer, the membrane-first proponent, read the new paper, he recalled having once observed something like the predicted behavior in hydrocarbon droplets he had extracted from a meteorite. When he illuminated the droplets in near-ultraviolet light, they began moving and dividing. (He sent footage of the phenomenon to Jülicher.) Nonetheless, Deamer isn’t convinced of the effect’s significance. “There is no obvious way for the mechanism of division they reported to evolve into the complex process by which living cells actually divide,” he said.

***

"The luckiest part of the whole process, in Jülicher’s opinion, was not that droplets turned into cells, but that the first droplet — our globule ancestor — formed to begin with. Droplets require a lot of chemical material to spontaneously arise or “nucleate,” and it’s unclear how so many of the right complex macromolecules could have accumulated in the primordial soup to make it happen. But then again, Jülicher said, there was a lot of soup, and it was stewing for eons.

“'It’s a very rare event. You have to wait a long time for it to happen,” he said. “And once it happens, then the next things happen more easily, and more systematically.'”

Comment: Hope springs eternal. to much grant money chasing too few good ideas. I am with Deamer. So droplets can be made to subdivide, but hw do they get filled with the right reactive molecules? Nuts!

Theoretical origin of life; requires intellect

by David Turell @, Thursday, June 22, 2017, 01:59 (2491 days ago) @ David Turell

Another article pointing out that a cell is irreducibly complex and life must have started with cells designed completely:

https://evolutionnews.org/2017/06/the-origin-of-life-self-organization-and-information/

" the simplest cell required machinery, such as some ancient equivalent to ATP synthase or chloroplasts, to process basic chemicals or sunlight. It also needed proteins with the proper information contained in their amino acid sequences to fold into other essential cellular structures, such as portals in the cell membrane. And, it needed proteins with the proper sequences to fold into enzymes to drive the metabolism. A key role of the enzymes is to link reactions moving toward lower free energy (e.g. ATP → ADP + P) to reactions, such as combining amino acids into long chains, which go uphill. The energy from the former can then be used to drive the latter, since the net change in free energy is negative. The free-energy barrier is thus overcome.

"However, the energy-processing machinery and information-rich proteins were still not enough. Proteins eventually break down, and they cannot self-replicate. Additional machinery was also needed to constantly produce new protein replacements. Also, the proteins’ sequence information had to have been stored in DNA using some genetic code, where each amino acid was represented by a series of three nucleotides know as a codon in the same way English letters are represented in Morse Code by dots and dashes. However, no identifiable physical connection exists between individual amino acids and their respective codons. In particular, no amino acid (e.g., valine) is much more strongly attracted to any particular codon (e.g., GTT) than to any other.  Without such a physical connection, no purely materialistic process could plausibly explain how amino acid sequences were encoded into DNA. Therefore, the same information in proteins and in DNA must have been encoded separately.

"In addition, the information in DNA is decoded back into proteins through the use of ribosomes, tRNAs, and special enzymes called aminoacyl tRNA sythetases (aaRS). The aaRSs bind the correct amino acids to the correct tRNAs associated with the correct codons, so these enzymes contain the decoding key in their 3D structures. All life uses this same process, so the first cell almost certainly functioned similarly. However, no possible connection could exist between the encoding and the decoding processes, since the aaRSs’ structures are a result of their amino acid sequences, which happen to be part of the information encoded in the DNA. Therefore, the decoding had to have developed independently of the encoding, but they had to use the same code. And, they had to originate at the same time, since each is useless without the other. (my bold)

"All of these facts indicate that the code and the sequence information in proteins/DNA preexisted the original cell. And, the only place that they could exist outside of a physical medium is in a mind, which points to design."

Comment: DNA is a code that contains information to create and run the process of life. My bolded section creates a question of what came first, chicken or egg. Obviously both all at once. Not by chance.

Theoretical origin of life; requires intellect

by David Turell @, Thursday, June 29, 2017, 20:54 (2483 days ago) @ David Turell

Another commentary on the need for intelligence:

https://evolutionnews.org/2017/06/origin-of-life-and-information-some-common-myths/

"These problems simply highlight one of the challenges for the RNA world hypothesis and for any materialistic explanation for the genetic code. A viable theory would have to explain for both the encoding and decoding several steps:

"Amino acids and nucleotides would have to be created in abundance and then brought together. They would have to originate in separate locations, since the conditions needed for their synthesis are quite different, and cross-reactions would have prevented the creation of either.

"The amino acids and nucleotides would have to form into long chains. These chains would have then needed to replicate by a selective process biased toward sequences which performed some useful biological function. The challenge is that any selective process would have only selected for the efficiency of replication, which has no connection to any life-permitting activity.

"A functional protein or RNA strand would have to unfold to allow for its sequence to be translated. And, such functional sequences would have to separate themselves from other useless chains. An enormous number of chains would have to exist for a useful sequence to have had any chance of forming.

"Individual codons would have to be so strongly attracted to their corresponding amino acids, that they would attach to them for an extended period of time.

"Some enzyme-like molecules would have to come along and then polymerize the nucleotides into strands of RNA or the amino acids into proteins.

"All useful products would have to migrate to some safe location until they could be encapsulated into a cellular membrane. A viable membrane would have to be selectively semipermeable, so it would allow the right molecules to enter and waste products to leave.

"Neither Yarus nor any other researcher has even come close to properly addressing any of these issues in a purely materialistic framework. Nor will they, for any realistic scenario requires intelligent agency to properly coordinate all of these fantastically improbable steps."

Comment: Origin of life remains a miracle

Theoretical origin of life; there is no theory

by David Turell @, Monday, July 10, 2017, 23:18 (2472 days ago) @ David Turell

Statements from many scientists on why no one has a clue:

https://www.questia.com/magazine/1G1-488605102/science-s-confusion-concerning-the-origi...

"Here are just a few statements on the origin of life:

* :James Tour, professor of chemistry at Rice University, 2016: "[There is] collective cluelessness. ... Those who say this is well worked out, they know nothing, nothing about chemical synthesis.... Those who think that scientists understand the details of life's origin are wholly uninformed. Nobody understands. ... When will the scientific community confess to the world that they are clueless on life's origin, that the emperor has no clothes?"

* "Eugene Koonin, microbiologist, 2011: "The origin of life field is a failure."

* "Lee Hartwell, Nobel Prize winner in Medicine, 2011: "With respect to the origin of life, I find the more we learn about cells the more complex they seem; they are just incredibly complex things, and to go from what we can see today and try to reason where it came from, I think is really impossible."

* "Paul Davies, theoretical physicist at Arizona State University, 2010: "How [did life begin]? We haven't a clue."

* Franklin Harold, molecular biologist, at Colorado State University, 2001: "The origin of life appears to me as incomprehensible as ever, a matter for wonder but not for explication."

* "Hubert Yockey, physicist and renowned information theorist, 1981: "Since science does not have the faintest idea how life on Earth originated ... it would only be honest to confess this to other scientists, to grantors, and to the public at large."

Suffice it to say that not only has science not progressed in this area since Charles Darwin published his famous 1859 treatise, "On the Origin of Species," but, on the contrary, it has slid backwards by many orders of magnitude.

***

"As biochemist Klaus Dose wrote: "Experimentation on the origin of life ... has led to a better perception of the immensity of the problem of the origin of life on Earth rather than to its solution." Researchers Carl Woese and Gunter Wachtershauser concur: "While we do not have a solution, we now have an inkling of the magnitude of the problem."

"Why are researchers having such difficulties discovering a naturalistic origin of life? "Certainly," says Koonin, "this is not due to a lack of experimental and theoretical effort, but to the extraordinary intrinsic difficulty and complexity of the problem. A succession of exceedingly unlikely steps is essential for the origin of life.... These make the final outcome seem almost like a miracle."

"In other words, discovering how unguided naturalistic forces could assemble a living cell--a molecular machine that is more sophisticated and functionally complex than anything human technology ever has produced--is a problem of nightmarish proportions."

Comment: Looks like a miracle to me.

Theoretical origin of life; UV and sulfer/iron

by David Turell @, Tuesday, July 18, 2017, 15:18 (2464 days ago) @ David Turell

Another lab experiment with assumptions of organic compounds present:

http://www.sciencemag.org/news/2017/07/how-sunlight-might-have-jump-started-life-earth

"Life on Earth is a paradox—to function, all organisms need energy. But to harness that energy, living creatures rely on enzymes that have evolved over billions of years to make possible everything from respiration to photosynthesis to DNA repair. So what came first, the enzyme or the organism? A new study suggests that the iron-and-sulfur clusters at the heart of many life-critical enzymes could have been floating around Earth’s primordial seas some 4 billion years ago, produced by nothing more than primitive biomolecules, iron salts, and a previously unknown ingredient—ultraviolet (UV) light.

***

"Most research into life’s origins has focused on how organic building blocks, like amino acids and nucleic acids, arose and assembled themselves into proteins and RNA. Less studied is the genesis of iron-sulfur clusters, the active core in enzymes that drive almost every aspect of cellular chemistry. Genetic analysis suggests they’ve been around at least since the time of our last common ancestor. “I’ve never seen an organism that doesn’t depend on them,” says Sheref Mansy, a biochemist at the University of Trento in Italy who led the new work.

"But modern metabolic reactions are carefully calibrated inside living cells, in the presence of oxygen. Neither condition would have existed on Earth without life.

"To find out whether iron-sulfur clusters were a core ingredient for life from the start—or whether the first organisms got along fine without them—Mansy and his team recreated the conditions of early Earth in their lab. University of Trento biochemist Claudia Bonfio removed oxygen and mixed together a brew of iron and glutathione, a sulfur-containing peptide likely present in the prebiotic chemical soup. When the iron was in an oxidation state that predominated on early Earth, iron (II), nothing happened. But when Bonfio flicked on the lights, a transformation took place. (my bold)

“'After a few minutes you could start to see the formation of iron-sulfur clusters,” she says. In the presence of UV light, the solution went from violet to red, indicating that the iron and sulfur were reacting. “And if you waited longer,” she says, “more complex clusters formed that gave the solution a brown color.” The light was simultaneously freeing sulfur atoms from the peptides and oxidizing the iron—turning it into a form, iron (III), that could readily interact with the sulfur, the team reports this week in Nature Chemistry.

"The team then tested more than 30 other potential compounds under different conditions, and found that the reactions also worked with simpler sulfur-containing molecules. Some of them even worked inside fatty acid vesicles, a laboratory stand-in for protocells. In most cases, the process was “strikingly similar” to the way iron-sulfur clusters synthesize in modern living cells, the authors write.

"It makes sense, says Mansy, that sunlight would play a role in early iron-sulfur synthesis. That’s because Earth lacked an ozone layer to protect it from UV light—which was far more intense 4 billion years ago than it is now. What’s more, lakes all over young Earth would have hosted mineral-rich stews similar to those in the experiment.

***

"But Mansy himself is cautious about the new work’s significance. Showing that something can happen in the lab is different from saying that it did happen, he emphasizes. “This reaction only becomes truly important if we can show that there is some kind of selective advantage to the network of chemicals involved.” If that’s the case, it could begin to explain how nonliving chemistry generated reactions that eventually evolved into living systems. But discovering the exact sequence of events that gave life its spark may be forever lost behind time’s horizon, Hazen warns. “Like so many chemical experiments pitched as ‘origins of life’ contributions, [this] is more suggestive than definitive.'”

Comment: Once again, it must be noted that it is a giant jump from this experiment to life. Enzymes are huge organic molecules that run the processes of life. Iron/sulfer is a tiny but necessary part of those molecules. Glutathione is added, which is guesswork, but also a giant step to other organic compounds is required. The above paragraph is on point.

Theoretical origin of life; in hot puddles on land

by David Turell @, Thursday, July 20, 2017, 21:59 (2462 days ago) @ David Turell

A study of Western Australia stromatolites from 3.5 billion years ago:

https://www.sciencedaily.com/releases/2017/07/170718142900.htm

"what Djokic discovered amid the strangling heat and blood-red rocks of the region was evidence that the stromatolites had not formed in salt water but instead in conditions more like the hot springs of Yellowstone.

"The discovery pushed back the time for the emergence of microbial life on land by 580 million years and also bolstered a paradigm-shifting hypothesis laid out by UC Santa Cruz astrobiologists David Deamer and Bruce Damer: that life began, not in the sea, but on land.

***

"In Deamer's vision, ancient Earth consisted of a huge ocean spotted with volcanic land masses. Rain would fall on the land, creating pools of fresh water that would be heated by geothermal energy and then cooled by runoff. Some of the key building blocks of life, created during the formation of our solar system, would have fallen to Earth and gathered in these pools, becoming concentrated enough to form more complex organic compounds.

"The edges of the pools would go through periods of wetting and drying as water levels rose and fell. During these periods of wet and dry, lipid membranes would first help stitch together the organic compounds called polymers and then form compartments that encapsulated different sets of these polymers. The membranes would act like incubators for the functions of life.

"Deamer and his team believe the first life emerged from the natural production of vast numbers of such membrane-encased "protocells."

"While there is still debate about whether life began on land or in the sea, the discovery of ancient microbial fossils in a place like the Pilbara shows that these geothermal areas -- full of energy and rich in the minerals necessary for life -- harbored living microorganisms far earlier than believed.

"For Damer, the new "end-to-end hypothesis" of how life began on land offers something else: that the origin of life was not just a simple story of individual, competing cells. Rather that a plausible new vision of life's start could be a communal unit of protocells that survived and evolved through collaboration and sharing of innovation rather than strict competition."

Comment: how innovation happened is not explained. But it certainly shows how early life appeared on Earth.

Theoretical origin of life;England's physics theory

by David Turell @, Wednesday, July 26, 2017, 20:49 (2456 days ago) @ David Turell

this article covers his strange approach to physical chemistry to get life automatically:

https://www.quantamagazine.org/first-support-for-a-physics-theory-of-life-20170726/

"The biophysicist Jeremy England made waves in 2013 with a new theory that cast the origin of life as an inevitable outcome of thermodynamics. His equations suggested that under certain conditions, groups of atoms will naturally restructure themselves so as to burn more and more energy, facilitating the incessant dispersal of energy and the rise of “entropy” or disorder in the universe. England said this restructuring effect, which he calls dissipation-driven adaptation, fosters the growth of complex structures, including living things. The existence of life is no mystery or lucky break, he told Quanta in 2014, but rather follows from general physical principles and “should be as unsurprising as rocks rolling downhill.”

***

"The simulation involved a soup of 25 chemicals that react with one another in myriad ways. Energy sources in the soup’s environment facilitate or “force” some of these chemical reactions, just as sunlight triggers the production of ozone in the atmosphere and the chemical fuel ATP drives processes in the cell. Starting with random initial chemical concentrations, reaction rates and “forcing landscapes” — rules that dictate which reactions get a boost from outside forces and by how much — the simulated chemical reaction network evolves until it reaches its final, steady state, or “fixed point.”

***

"But even if the fine-tuned fixed points can be observed in settings that are increasingly evocative of life and its putative beginnings, some researchers see England’s overarching thesis as “necessary but not sufficient” to explain life, as Walker put it, because it cannot account for what many see as the true hallmark of biological systems: their information-processing capacity. From simple chemotaxis (the ability of bacteria to move toward nutrient concentrations or away from poisons) to human communication, life-forms take in and respond to information about their environment. (my bold)

***

"Understanding what distinguishes life, she added, “requires some explicit notion of information that takes it beyond the non-equilibrium dissipative structures-type process.” In her view, the ability to respond to information is key: “We need chemical reaction networks that can get up and walk away from the environment where they originated.” (my bold)

"Gunawardena noted that aside from the thermodynamic properties and information-processing abilities of life-forms, they also store and pass down genetic information about themselves to their progeny. The origin of life, Gunawardena said, “is not just emergence of structure, it’s the emergence of a particular kind of dynamics, which is Darwinian. It’s the emergence of structures that reproduce. And the ability for the properties of those objects to influence their reproductive rates. Once you have those two conditions, you’re basically in a situation where Darwinian evolution kicks in, and to biologists, that’s what it’s all about.'”

Comment: England is a fuzzy-headed genius I guess from comments about him. Life is more than physical chemistry. Note my bolds: Life requires information to begin. It must be capable of processing it, copying it and passing it to descendants.

Theoretical origin of life;England's physics theory

by dhw, Thursday, July 27, 2017, 10:49 (2456 days ago) @ David Turell

QUOTE: […] the true hallmark of biological systems: their information-processing capacity. From simple chemotaxis (the ability of bacteria to move toward nutrient concentrations or away from poisons) to human communication, life-forms take in and respond to information about their environment. (David’s bold)[/i]

DAVID’s comment : Life is more than physical chemistry. Note my bolds: Life requires information to begin. It must be capable of processing it, copying it and passing it to descendants.

Information is always present in physical chemistry and in everything else that you can think of, organic and inorganic. The point is not that “life requires information to begin” but that life requires an information-processing capacity (your bold and mine), and the true hallmark of all biological systems is the capacity for processing, copying, passing and using information, communicating, cooperating, decision-making etc., which some of us would call intelligence.

Theoretical origin of life;England's physics theory

by David Turell @, Thursday, July 27, 2017, 15:30 (2455 days ago) @ dhw

QUOTE: […] the true hallmark of biological systems: their information-processing capacity. From simple chemotaxis (the ability of bacteria to move toward nutrient concentrations or away from poisons) to human communication, life-forms take in and respond to information about their environment. (David’s bold)[/i]

DAVID’s comment : Life is more than physical chemistry. Note my bolds: Life requires information to begin. It must be capable of processing it, copying it and passing it to descendants.

dhw: Information is always present in physical chemistry and in everything else that you can think of, organic and inorganic. The point is not that “life requires information to begin” but that life requires an information-processing capacity (your bold and mine), and the true hallmark of all biological systems is the capacity for processing, copying, passing and using information, communicating, cooperating, decision-making etc., which some of us would call intelligence.

A process which automatically decodes the instructions in DNA gives the appearance of intelligence. I propose that original life was both given information and the ability to act upon it automatically.

Theoretical origin of life;England's physics theory

by dhw, Friday, July 28, 2017, 11:34 (2454 days ago) @ David Turell

QUOTE: […] the true hallmark of biological systems: their information-processing capacity. From simple chemotaxis (the ability of bacteria to move toward nutrient concentrations or away from poisons) to human communication, life-forms take in and respond to information about their environment. (David’s bold)[/i]

DAVID’s comment : Life is more than physical chemistry. Note my bolds: Life requires information to begin. It must be capable of processing it, copying it and passing it to descendants. (dhw's bold)

dhw: Information is always present in physical chemistry and in everything else that you can think of, organic and inorganic. The point is not that “life requires information to begin” but that life requires an information-processing capacity (your bold and mine), and the true hallmark of all biological systems is the capacity for processing, copying, passing and using information, communicating, cooperating, decision-making etc., which some of us would call intelligence.

DAVID: A process which automatically decodes the instructions in DNA gives the appearance of intelligence. I propose that original life was both given information and the ability to act upon it automatically.

I was pointing out that your statement “life requires information to begin” missed out the all-important point that even you had put in bold: namely, the ability to process information. We both know one another’s proposals, and I still await your definition of intelligence.-

DAVID's comment: (under "Information: applied to matter creates life") Information which can be used by the proteins of life somehow creates active life. Since Schrodinger's book there is still no answer as to how this happens. The proteins are material but the mechanism of life itself is an immaterial process.

Information is present in everything but creates nothing. It is a particular USE of information that creates things.

Theoretical origin of life;England's physics theory

by David Turell @, Friday, July 28, 2017, 18:40 (2454 days ago) @ dhw


dhw: I was pointing out that your statement “life requires information to begin” missed out the all-important point that even you had put in bold: namely, the ability to process information. We both know one another’s proposals, and I still await your definition of intelligence.-

I'm sure it is close to yours. Intelligence is the ability to learn information and have experiences from which to learn and use that information in daily life and to formulate new thoughts and ideas. It is also to learn about others as in military intelligence. It is also to interpret information and place it in action.


DAVID's comment: (under "Information: applied to matter creates life") Information which can be used by the proteins of life somehow creates active life. Since Schrodinger's book there is still no answer as to how this happens. The proteins are material but the mechanism of life itself is an immaterial process.

dhw: Information is present in everything but creates nothing. It is a particular USE of information that creates things.

Yes, intelligent use.

Theoretical origin of life;England's physics theory

by dhw, Saturday, July 29, 2017, 08:37 (2454 days ago) @ David Turell

dhw: I was pointing out that your statement “life requires information to begin” missed out the all-important point that even you had put in bold: namely, the ability to process information. We both know one another’s proposals, and I still await your definition of intelligence.-

DAVID: I'm sure it is close to yours. Intelligence is the ability to learn information and have experiences from which to learn and use that information in daily life and to formulate new thoughts and ideas. It is also to learn about others as in military intelligence. It is also to interpret information and place it in action.

DAVID's comment: (under "Information: applied to matter creates life") Information which can be used by the proteins of life somehow creates active life. Since Schrodinger's book there is still no answer as to how this happens. The proteins are material but the mechanism of life itself is an immaterial process.

dhw: Information is present in everything but creates nothing. It is a particular USE of information that creates things.

David: Yes, intelligent use.

Thank you. We are indeed in agreement, and so we should avoid concepts such as “intelligent information” (information has no ability of its own), and we should always distinguish between information and the use of information. There are two statements here which illustrate the point.
Life requires information to begin”. Everything living and non-living contains information, so why single out life? I think what you really mean is that life requires the intelligent processing of information to begin. “Information which can be used by the proteins of life somehow creates active life” is misleading, as it implies that information itself is creative. It isn’t. You might rephrase it: “The proteins of life somehow use information in such a way that life is created.” I am not putting forward a particular argument here, but simply trying to avoid future distortions of meaning which we have sometimes come across in your own posts and in articles you have quoted. From your own theistic standpoint, I’d have thought the distinction was essential, since some authors like to suggest that information itself is an active force.You would surely argue that it’s not information that creates life, but intelligent use of information.

Theoretical origin of life;England's physics theory

by David Turell @, Saturday, July 29, 2017, 14:45 (2453 days ago) @ dhw

dhw: I was pointing out that your statement “life requires information to begin” missed out the all-important point that even you had put in bold: namely, the ability to process information. We both know one another’s proposals, and I still await your definition of intelligence.-

DAVID: I'm sure it is close to yours. Intelligence is the ability to learn information and have experiences from which to learn and use that information in daily life and to formulate new thoughts and ideas. It is also to learn about others as in military intelligence. It is also to interpret information and place it in action.

DAVID's comment: (under "Information: applied to matter creates life") Information which can be used by the proteins of life somehow creates active life. Since Schrodinger's book there is still no answer as to how this happens. The proteins are material but the mechanism of life itself is an immaterial process.

dhw: Information is present in everything but creates nothing. It is a particular USE of information that creates things.

David: Yes, intelligent use.

dhw: Thank you. We are indeed in agreement, and so we should avoid concepts such as “intelligent information” (information has no ability of its own), and we should always distinguish between information and the use of information. There are two statements here which illustrate the point.
Life requires information to begin”. Everything living and non-living contains information, so why single out life? I think what you really mean is that life requires the intelligent processing of information to begin. “Information which can be used by the proteins of life somehow creates active life” is misleading, as it implies that information itself is creative. It isn’t. You might rephrase it: “The proteins of life somehow use information in such a way that life is created.” I am not putting forward a particular argument here, but simply trying to avoid future distortions of meaning which we have sometimes come across in your own posts and in articles you have quoted. From your own theistic standpoint, I’d have thought the distinction was essential, since some authors like to suggest that information itself is an active force.You would surely argue that it’s not information that creates life, but intelligent use of information.

I absolutely agree. You are always the consummate editor of the English language as I remember in our tussles over the book wording.

Theoretical origin of life;England's physics theory

by dhw, Sunday, July 30, 2017, 10:59 (2453 days ago) @ David Turell

Dhw: I am not putting forward a particular argument here, but simply trying to avoid future distortions of meaning which we have sometimes come across in your own posts and in articles you have quoted. From your own theistic standpoint, I’d have thought the distinction was essential, since some authors like to suggest that information itself is an active force.You would surely argue that it’s not information that creates life, but intelligent use of information.

DAVID: I absolutely agree. You are always the consummate editor of the English language as I remember in our tussles over the book wording.

Thank you. Our tussles over your book and on this forum were and are a privilege and a pleasure. Language is the only tool we have for formulating our ideas, and I think that many disagreements – not just those between you and me – boil down to unclear definitions.

Theoretical origin of life;England's physics theory

by David Turell @, Sunday, July 30, 2017, 18:44 (2452 days ago) @ dhw

Dhw: I am not putting forward a particular argument here, but simply trying to avoid future distortions of meaning which we have sometimes come across in your own posts and in articles you have quoted. From your own theistic standpoint, I’d have thought the distinction was essential, since some authors like to suggest that information itself is an active force.You would surely argue that it’s not information that creates life, but intelligent use of information.

DAVID: I absolutely agree. You are always the consummate editor of the English language as I remember in our tussles over the book wording.

dhw: Thank you. Our tussles over your book and on this forum were and are a privilege and a pleasure. Language is the only tool we have for formulating our ideas, and I think that many disagreements – not just those between you and me – boil down to unclear definitions.

Exactly, and it applies to the misuse of 'natural selection', which passively receives whatever evolves and therefore does not drive evolution as is often implied.

Theoretical origin of life;England's physics theory

by dhw, Monday, July 31, 2017, 08:27 (2452 days ago) @ David Turell

dhw: I am not putting forward a particular argument here, but simply trying to avoid future distortions of meaning which we have sometimes come across in your own posts and in articles you have quoted. From your own theistic standpoint, I’d have thought the distinction was essential, since some authors like to suggest that information itself is an active force.You would surely argue that it’s not information that creates life, but intelligent use of information.

DAVID: I absolutely agree. You are always the consummate editor of the English language as I remember in our tussles over the book wording.

dhw: Thank you. Our tussles over your book and on this forum were and are a privilege and a pleasure. Language is the only tool we have for formulating our ideas, and I think that many disagreements – not just those between you and me – boil down to unclear definitions.

DAVID: Exactly, and it applies to the misuse of 'natural selection', which passively receives whatever evolves and therefore does not drive evolution as is often implied.

I agree completely, and have made the same point myself many times over. Indeed you can extend such misuse to Darwinism in general, with atheists claiming that it supports atheism (it doesn’t), and theists claiming that any single flaw somehow invalidates the whole theory (it doesn’t). You might say that prejudice engenders its own form of natural selection!

Theoretical origin of life; zircon evidence

by David Turell @, Monday, September 11, 2017, 21:23 (2409 days ago) @ David Turell

There is a suggestion from zircon evidence that life may be more than four billion years old:

https://cosmosmagazine.com/geoscience/zircons-how-tiny-crystals-open-a-window-into-the-...

"In nature, zirconium forms another type of crystal called zircons. To geophysicists, these are the true gems, because they provide vital time capsules from the Earth’s deepest past.

"Chemically, zircons are nothing fancy. They are tiny lumps of zirconium silicate (ZrSiO4) that are ubiquitous in volcanic rocks. But they’re typically only 0.1 mm to 0.3 mm across, making them hard to spot without a magnifying glass. Not exactly the type of thing most of us would notice, let alone care about.

"We have no rocks that are older than 4 billion years,” says John Valley, a geochemist at the University of Wisconsin, Madison. (The Earth itself is 4.543 billion years old.) “[Zircons] are what we study if we want to analyze things that formed that far back.”

"But they have two important traits.

"One is that they are incredibly durable. The rocks in which they initially formed may weather away, but the zircons survive as tiny grains of sand that may later be incorporated into the next generation of rocks.

***

"Their other trait is that they aren’t pure zirconium silicate. They contain trace amounts of other elements, most importantly uranium, trapped within them as they crystalize. Over the eons, that uranium slowly decays to lead. By comparing the amounts of uranium and lead, scientists can determine the date at which the crystal formed.

***

"Another element, oxygen (the “O” in ZrSiO4), helps tell the conditions under which each zircon formed. That’s because oxygen has two well-known stable isotopes, 16O and 18O, either of which can be incorporated into the crystal as it grows.

"Typically, these come from water (H2O), which can contain either 16O or 18O (or a more rare stable isotope called 17O). All these forms of water are chemically identical, but 18O-containing water is about ten percent heavier than 16O-containing water. That causes the two types of water to (very slightly) separate — and to do so by different amounts under different conditions.

"Geologists once thought the early Earth was far too hot for its surface to be anything but an ocean of magma, let alone to have liquid water. In fact, the earliest period in the Earth’s history, from its formation to 4 billion years ago, is called the Hadean because it was widely believed to resemble hell, or Hades. That meant zircons from the Hadean period should have oxygen isotope ratios comparable to that of water molecules in the Earth’s mantle. But geologists studying the Jack Hills region of Western Australia, which has yielded the oldest zircons ever found, have been unearthing zircons from as far back as 4.375 billion years ago whose oxygen isotope ratios show they may have formed from magma that incorporated liquid water.

"Other zircon research has suggested that life too may date back a lot further than we once thought. This research involves the ratio of non-radioactive carbon isotopes (12C and 13C) in tiny diamonds incorporated in the zircon structure. These diamonds have carbon isotope signatures suggesting the carbon from which they were formed may have included organic material from living organisms.

“'This implies that there was life in the Hadean,” says Craig O’Neill, a geodynamicist at Macquarie University."

Comment: Amazing. Could life have appeared just 200 million years after the Earth began formation? If true, certainly not a natural event.

Theoretical origin of life; zircon evidence

by David Turell @, Tuesday, June 05, 2018, 23:18 (2142 days ago) @ David Turell

More evidence of an early crust on Earth to allow the early formation of life:

https://www.sciencedaily.com/releases/2018/06/180605154122.htm

"The early Earth might have been habitable much earlier than thought, according to new research from a group led by University of Chicago scientists.

"Counting strontium atoms in rocks from northern Canada, they found evidence that the Earth's continental crust could have formed hundreds of millions of years earlier than previously thought. Continental crust is richer in essential minerals than younger volcanic rock, which would have made it significantly friendlier to supporting life.

"'Our evidence, which squares with emerging evidence including rocks in western Australia, suggests that the early Earth was capable of forming continental crust within 350 million years of the formation of the solar system," said Patrick Boehnke, the T.C. Chamberlin Postdoctoral Fellow in the Department of Geophysical Sciences and the first author on the paper. "This alters the classic view, that the crust was hot, dry and hellish for more than half a billion years after it formed."

***

"Luckily for scientists, some of these "younger" minerals (still about 3.9 billion years old) are zircons -- very hard, weather-resistant minerals somewhat similar to diamonds. "Zircons are a geologist's favorite because these are the only record of the first three to four hundred million years of Earth. Diamonds aren't forever -- zircons are," Boehnke said.

"Plus, the zircons themselves can be dated. "They're like labeled time capsules," said Prof. Andrew Davis, chair of the Department of Geophysical Sciences and a coauthor on the study.
Scientists usually look at the different variants of elements, called isotopes, to tell a story about these rocks. They wanted to use strontium, which offers clues to how much silica was around at the time it formed. The only problem is that these flecks are absolutely tiny -- about five microns across, the diameter of a strand of spider silk -- and you have to count the strontium atoms one by one.

"This was a task for a unique instrument that came online last year: the CHicago Instrument for Laser Ionization, or CHILI. This detector uses lasers that can be tuned to selectively pick out and ionize strontium. When they used CHILI to count strontium isotopes in rocks from Nuvvuagittuq, Canada, they found the isotope ratio suggested plenty of silica was present when it formed.

"This is important because the makeup of the crust directly affects the atmosphere, the composition of seawater, and nutrients available to any budding life hoping to thrive on planet Earth. It also may imply there were fewer meteorites than thought pummeling the Earth at this time, which would have made it hard for continental crust to form.

"'Having continental crust that early changes the picture of early Earth in a number of ways," said Davis, who is also a professor with the Enrico Fermi Institute. "Now we need a way for the geologic processes that make the continents to happen much faster; you probably need water and magma that's about 600 degrees Fahrenheit less hot.'"

Comment: We know life appeared on Earth at least 3.8 billion years ago, bu tit seems to have offered an opportunity much earlier, at about 4.2 billion years ago.

Theoretical origin of life; possibly on Mars

by David Turell @, Friday, June 08, 2018, 00:44 (2140 days ago) @ David Turell

There is new organic compound evidence from Mars:

http://blogs.discovermagazine.com/d-brief/2018/06/07/curiosity-rover-finds-organics-hid...

"In a much-hyped press conference held on Thursday, NASA announced its Curiosity rover had uncovered new evidence of methane — a potential sign of life — as well as signs of organic compounds buried in ancient mudstone.

"The space agency did not say it had found evidence of alien life. However, these new results are still tantalizing.

***

"In the first paper, a team analyzed three Mars years worth (55 Earth months) of atmospheric data from Curiosity. In that time, the rover caught methane levels spiking as the seasons changed, growing several times stronger at the height of summer in the northern hemisphere.

"Based on the chemical make-up, the scientists suspect this methane was heated up and released from sub-surface reservoirs where it was likely trapped in permafrost. They suspect large amount of the gas may be frozen in such underground reservoirs. But its exact origin remains a mystery.

"The other study, led by NASA biogeochemist Jennifer Eigenbrode, examined drill samples of three-billion year old mudstones that Curiosity collected from two different sites in Gale Crater. The rover dropped these samples into an onboard laboratory and cooked them in order to analyze the gasses they threw out.

"According to Eigenbrode’s team, the rocks released organic molecules much like those found in organic-rich rocks on Earth. And intriguingly, these molecules seem to have broken off of bigger and more complex molecules — the kinds found in coal and shale on Earth.

"This is far from the first time Mars researchers have claimed to find methane. Curiosity itself made headlines in recent years after seeing faint methane signals. But scientists have been chasing this gas for decades.

***

"All this means that, on Earth, methane is a sign of life. That’s given astronomers good reason to see methane as a potential signal of microbes on Mars.

Like Earth, it also has methane-destroying conditions. The Red Planet’s atmosphere is almost completely made of carbon dioxide. And even the ultraviolet light that penetrates Mars’ weak atmosphere could destroy it.

"So, any methane we do see must have been released into the atmosphere very recently.
But life isn’t the only process that makes methane. We know that because it’s abundant on Uranus and Neptune. And there’s enough of the stuff to create bizarre landscapes on the surfaces of Pluto and Titan. And even on Earth, a small amount of methane is made in specific sorts of volcanic reactions, even if it doesn’t stick around long.

"But Mars has no active volcanoes. And it doesn’t have ways of replenishing methane like those outer solar system worlds."

Comment: In an earlier time Mars could have had life. But did Mars have a floating crust with plate tectonics which is a requirement? Exciting, but?

Theoretical origin of life; stop the hype!

by David Turell @, Tuesday, June 19, 2018, 20:03 (2128 days ago) @ David Turell

This thoughtful article asks for reasonable thought and expectations:

https://www.the-scientist.com/?articles.view/articleNo/54863/title/Opinion--Constrain-S...

"There are almost daily reports (and rather excited press releases) of how some scientific observations argue for the plausibility of life on other planets, in other solar systems, or in other galaxies, when in fact, what has been found is one or another organic molecule, or hints of organic material, in meteorites and comets. Rarely is the fact that we have yet to find life anywhere but here on Earth mentioned explicitly.

***

“'Defining life is notoriously difficult; its very diversity resists the confines of any compact definition,” the real problem is that the diversity of life, as we know it, is superficial and something of an illusion—we know of only one type of life, one original organism, and all of the subsequent organisms derived from it by various evolutionary processes. Moreover, we cannot examine this “last universal common ancestor” or LUCA, although there is no scientific doubt that A) it existed, B) it used DNA to store information, C) information was expressed in the form of RNAs, many of which, in turn, encoded polypeptides/proteins, D) it was bounded by a lipid membrane, and F) it can be characterized as a nonequilibrium reaction system, one that has been running continuously for billions of years and whose descendants are present in every living cell since.

LUCA was pretty complex, with the machinery to maintain its nonequilibrium state, a specific nucleotide-to-polypeptide coding scheme, and the ability to carry out DNA replication, transcription factor–regulated RNA synthesis, and ribosome-mediated, RNA-directed polypeptide synthesis. We might go a little further, and speculate that LUCA arose in a special environmental niche, and given its membrane-nature, likely an iso-osmotic one.

"what came before and the exact steps leading to LUCA are unknowable. Moreover, the billions of years that have elapsed since LUCA’s origin and the active nature of evolutionary processes that result in new genes “popping out” of the noise and becoming essential in organisms from fruit flies to humans, combined with the reality of structural or functional convergences, the growing recognition of small and alternative open reading frames that encode functionally different proteins, and the ubiquity of various forms of horizontal gene transfer, means that historic details and their evolutionary drivers are often obscure.

"All pre-LUCA models are based on plausible chemistry, an idea pioneered by the Miller/Urey experiment in 1959 that found that passing electrical current through what the scientists presumed was a likely early terrestrial atmosphere led to the generation of a complex array of organic molecules, including precursors of molecules found in modern organisms. More-recent studies have begun to refine these hypothetical scenarios, defining environments for the synthesis of raw materials, and then more-complex proteins, RNAs, and lipids. These molecules came together in some presumably stable or stably oscillating environment to generate pre-LUCA systems, whether based on “RNA world” type replicators, such as ribozymes—RNA molecules with both enzymatic activity and the ability to replicate themselves—or metabolic (nonequilibrium chemical reaction) systems, leading to membrane-bounded systems. All this not withstanding, until non-LUCA-derived forms of life are discovered, it does not serve the integrity of science as a source of dependable knowledge to speculate on what came before LUCA much beyond that."

Comment: Which is why I show the silly hyper-hyped reporting about minor findings in a highly controlled lab experiments. The start of life still looks like a miracle.

Theoretical origin of life; stop the hype!

by dhw, Wednesday, June 20, 2018, 13:16 (2127 days ago) @ David Turell

QUOTE: “All this not withstanding, until non-LUCA-derived forms of life are discovered, it does not serve the integrity of science as a source of dependable knowledge to speculate on what came before LUCA much beyond that."

DAVID’s comment: Which is why I show the silly hyper-hyped reporting about minor findings in a highly controlled lab experiments. The start of life still looks like a miracle.

If the theory of common descent is true, nothing came before LUCA or (according to Darwin) a few LUCAs, i.e. life originated in a few different forms. Your comment about controlled lab experiments echoes part of the conclusion to my “brief guide”, and I agree with you that whatever the cause, life looks like a miracle!

Thank you for all the other articles you posted yesterday. I don’t feel the need to comment on them, but they are none the less appreciated!

Theoretical origin of life; zircon evidence; another article

by David Turell @, Friday, July 06, 2018, 19:35 (2111 days ago) @ David Turell

A discussion of the findings that may push the origin of life back before four billion years ago:

https://www.quantamagazine.org/fossil-discoveries-challenge-ideas-about-earths-start-20...

"Last month, researchers lobbed another salvo in the decades-long debate about the nature of these forms. They are indeed fossil life, and they date to 3.465 billion years ago, according to John Valley, a geochemist at the University of Wisconsin. If Valley and his team are right, the fossils imply that life diversified remarkably early in the planet’s tumultuous youth.

"The fossils add to a wave of discoveries that point to a new story of ancient Earth. In the past year, separate teams of researchers have dug up, pulverized and laser-blasted pieces of rock that may contain life dating to 3.7, 3.95 and maybe even 4.28 billion years ago. All of these microfossils — or the chemical evidence associated with them — are hotly debated. But they all cast doubt on the traditional tale.

"As that story goes, in the half-billion years after it formed, Earth was hellish and hot.

***

"But this story is increasingly under fire. Many geologists now think Earth may have been tepid and watery from the outset. The oldest rocks in the record suggest parts of the planet’s crust had cooled and solidified by 4.4 billion years ago. Oxygen in those ancient rocks suggest the planet had water as far back as 4.3 billion years ago. And instead of an epochal, final bombardment, meteorite strikes might have slowly tapered off as the solar system settled into its current configuration.

***

"Taken together, the latest evidence from the ancient Earth and from the moon is painting a picture of a very different Hadean Earth: a stoutly solid, temperate, meteorite-clear and watery world, an Eden from the very beginning.

***

"In March 2017, Dominic Papineau, a geochemist at University College London, and his student Matthew Dodd described tubelike fossils in an outcrop in Quebec that dates to the basement of Earth’s history. The formation, called the Nuvvuagittuq (noo-voo-wog-it-tuck) Greenstone Belt, is a fragment of Earth’s primitive ocean floor. The fossils, about half the width of a human hair and just half a millimeter long, were buried within. They are made from an iron oxide called hematite and may be fossilized cities built by microbial communities up to 4.28 billion years ago, Dodd said.

***

“'I was taught when I was young that it would take billions and billions of years for life to form. But I have not been able to find any basis for those sorts of statements,” said Valley. “I think it’s quite possible that life emerged within a few million years of when conditions became habitable. From the point of view of a microbe, a million years is a really long time, yet that’s a blink of an eye in geologic time.”

“'There is no reason life could not have emerged at 4.3 billion years ago,” he added. “There is no reason.”

"If there was no mass sterilization at 3.9 billion years ago, or if a few massive asteroid strikes confined the destruction to a single hemisphere, then Earth’s oldest ancestors may have been here from the haziest days of the planet’s own birth. And that, in turn, makes the notion of life elsewhere in the cosmos seem less implausible. Life might be able to withstand horrendous conditions much more readily than we thought. It might not need much time at all to take hold. It might arise early and often and may pepper the universe yet. Its endless forms, from tubemaking microbes to hunkering slime, may be too small or simple to communicate the way life does on Earth — but they would be no less real and no less alive."

Comment: I've skipped over the repeated zircon evidence. This article shows life was inevitable. On purpose?

Theoretical origin of life; ealiest possibly found

by David Turell @, Wednesday, May 10, 2017, 00:56 (2534 days ago) @ David Turell

More evidence of early life from Australia:

https://phys.org/news/2017-05-oldest-evidence-life-billion-year-old-australian.html

"Fossil evidence of early life has been discovered by UNSW scientists in 3.48 billion year old hot spring deposits in the Pilbara of Western Australia - pushing back by 3 billion years the earliest known existence of inhabited terrestrial hot springs on Earth.

"Previously, the world's oldest evidence for microbial life on land came from 2.7- 2.9 billion year old deposits in South Africa containing organic matter-rich ancient soils.

"'Our exciting findings don't just extend back the record of life living in hot springs by 3 billion years, they indicate that life was inhabiting the land much earlier than previously thought, by up to about 580 million years," says study first author, UNSW PhD candidate, Tara Djokic.

***

"The researchers studied exceptionally well-preserved deposits which are approximately 3.5 billion year old in the ancient Dresser Formation in the Pilbara Craton of Western Australia

"They interpreted the deposits were formed on land, not in the ocean, by identifying the presence of geyserite - a mineral deposit formed from near boiling-temperature, silica-rich, fluids that is only found in a terrestrial hot spring environment. Previously, the oldest known geyserite had been identified from rocks about 400 million years old.


"Within the Pilbara hotspring deposits, the researchers also discovered stromatolites - layered rock structures created by communities of ancient microbes. And there were other signs of early life in the deposits as well, including fossilised micro-stromatolites, microbial palisade texture and well preserved bubbles that are inferred to have been trapped in a sticky substance (microbial) to preserve the bubble shape.

"'This shows a diverse variety of life existed in fresh water, on land, very early in Earth's history," says Professor Van Kranendonk, Director of the Australian Centre for Astrobiology and head of the UNSW school of Biological, Earth and Environmental Sciences."

Comment: I think it is still more likely that life began in the oceans than on land. One reason is the concentration of salt in our blood is the same as the salt concentration in sea water

Theoretical origin of life; Chirality used by nature

by David Turell @, Thursday, February 16, 2017, 01:30 (2617 days ago) @ David Turell

An organic chemist tries to explain the use of chirality in nature. All amino acids in life are left handed. DNA and RNA twist right handed:

http://inference-review.com/article/chiral-induced-spin-selectivity

"Chirality is ubiquitous in biological molecules. Aside from water, glycine, and acetic acid (among others), the majority of such molecules are chiral. The polymers of chiral molecules, such as the polysaccharides, polypeptides, and polynucleotides, are composed of chiral molecules. Such structures take on new shapes, including helices and spiral clefts, that are themselves chiral.

***

"Chemists now know that chiral molecules act as electron spin filters, permitting the one-way passage of electrons of one spin in preference to electrons of the other spin. Selective transmission probabilities can be a hundred times larger in a chiral molecule than in a non-chiral molecule. For an electron of the proper spin, chiral molecules show far less backscattering of the electron; this in turn greatly reduces the heat released from the molecule during the electron’s passage. Lower heat affords any biological system an advantage.

"Scientists have often wondered why living creatures do not overheat while undertaking normal biochemical functions. The existence of exceedingly efficient biochemical routes is something like an a priori deduction. Kwabena Boahen estimated that a microelectronics processor functioning with the capacity of a human brain would need at least ten megawatts to operate. This is equivalent to the output of a small hydroelectric power plant. The human brain needs only about ten watts.

***

:Might CISS help to explain biology’s secret to efficiency?

***

"CISS reveals that more is going on, and it is not subtle in its influence. The attractive interactions between molecules of matched chirality can be higher by as much as one electron volt over their mirror images. This strongly favors enantioselection. Preferred chiral interaction is due to neighboring spin-spin interactions; the electrostatic potentials upon which they depend can interact at near the speed of light.

"Is this how nature accomplishes its ultra-high degree of precision in enantioselective synthesis? Namaan et al. suggest that this is so.

"The overall yield of biochemical processes in which CISS figures is often in excess of 99.99%. Astounding! In the laboratory, if the chemist achieves an eighty percent chemical yield after thorough optimization, he is usually satisfied. By controlling the spin on reactive chemical intermediates, CISS processes influence the course of chemical reactions so that they shovel their yields to one product instead of another. Reversing the spin interactions generates a different product.

"There are other mysteries in nature. Consider the electronic transfers that routinely occur in photosynthesis and respiration. In the laboratory, electron transfer distances are often on the order of 0.5 nanometers or less. Biological systems routinely transfer electrons over distances of the tens of nanometers. Chiral molecules may act as nanoscale conduits for the 100-fold enhanced transmission of these electrons, provided that the spin on the electron is matched to the particular chiral molecule through which it passes.

"There are still other mysteries. Consider how a repair-enzyme senses that there is damage to the DNA chain from a distance of tens of nanometers. How? It may well be by the transmission of electrons through the chiral DNA conduit. Is the plethora of molecule-molecular recognition events impacted by CISS?

"Probably."

Comment: Simple biochemistry results in 50/50 right and left handed products. This experienced chemist can achieve 80% one type with enhanced processes. Nature prefers 99%. We are given this in Nature which results in great efficiency in living processes. Luck or design? Without this starting point in biochemistry life would not have happened.

Theoretical origin of life; lab fun and games

by David Turell @, Thursday, February 16, 2017, 22:33 (2616 days ago) @ David Turell

They are still playing games in the laboratory, creating new DNA hairpin-shaped molecules that can replicate to some degree:

https://www.sciencedaily.com/releases/2017/02/170216103846.htm

"Nucleic acid molecules are made up of subunits called nucleotides, which differ in their so-called bases. The bases found in RNA are referred to as A, C, G and U (DNA uses T in place of U). These bases fall into two complementary pairs, whose members specifically interact, A with T (or U) and G with C. This complementarity is what accounts for the stability of the DNA double helix, and enables single strands of RNA to fold into complex shapes.

"Life is thought to have emerged from a process of chemical evolution in which nucleic acid sequences could be selectively replicated. Thus, in prebiotic systems certain molecular "species" that carried information were reproduced at the expense of others. In biological systems, such selectivity is normally mediated by so-called primers -- strands of nucleic acid that pair (as described above) with part of the molecule to be replicated, to form a short double helix. The primer provides a starting point for the extension of the double-stranded region to form a new daughter strand. Moreover, this process can be reconstructed in the test-tube.

***

"For their experiments, they chose a single-stranded DNA sequence that adopts a so-called hairpin structure. In these molecules, the base sequences at either end are complementary to each other, as are short stretches of sequence within the rest of the molecule. This distribution of complementary sequences causes such a strand to fold into a hairpin-like conformation.

"Thanks to the pairing rules outlined above, replication of a single strand of DNA produces a second strand whose sequence differs from that of the first. Each strand of a non-hairpin structure therefore needs its own primer for replication. But with hairpins, one primer suffices to prime synthesis of both the original and its complementary strand. "This means that hairpins are relatively simple replicators," Georg Urtel points out. The downside is that the hairpin structure makes primer binding more difficult, and this in turn limits their replication rate. Molecular species that are devoid of hairpin structures don't have this problem.

"In subsequent experiments the researchers discovered that two simple hairpin species could cooperate to give rise to a much more efficient replicator, which requires two primers for its amplification. The two hairpin species selected each required a different primer, but their sequences were in part identical. The switch to cooperative replication occurs when replication of one of the hairpins stalls. "As a rule, replication processes in nature are never perfect," says Dieter Braun. "Such a premature halt is not something that one needs to design into the system. It happens stochastically and we make use of it in our experiments." The partially replicated hairpin can, however, bind to a molecule of the second species, and serves as a primer that can be further elongated. Moreover, the resulting product no longer forms a hairpin. In other words, it represents a new molecular species.

"Such so-called 'crossbreeds' need two primers for their replication, but can nevertheless be replicated significantly faster than either of their hairpin progenitors For further experiments showed that, upon serial dilution of the population, the hairpin DNAs soon become extinct. However, the sequence information they contained survives in the crossbreeds and can be replicated further.
The converse experiment confirmed that information is indeed conserved: If crossbreeds are supplied with only one primer, the corresponding progenitor hairpin species can still be replicated by the kind of switching process mentioned above.

"But, in the absence of the second primer, the crossbreed dies out. "Thus, the crossbreeding process not only provides for the transition from 'simple and slow' replicators to more rapid replicators, it also makes it possible for the system to adapt to the prevailing conditions," Urtel explains. "It also suggests how early replicators could have cooperated with each other under prebiotic conditions prior to the origin of living systems.'"

Comment: This all happened by design in a lab, with specialized molecular shapes of RNA/DNA. Sounds great, but there is no way to know if this happened naturally in a prebiotic Earth that lacked organic compounds. Long RNA/DNA was not produced. But some information was carried.

Theoretical origin of life; fossils fron 3.8 byo?

by David Turell @, Wednesday, March 01, 2017, 22:39 (2603 days ago) @ David Turell

The latest finding in Canada:

https://www.washingtonpost.com/news/speaking-of-science/wp/2017/03/01/newfound-3-77-bil...

"The straw-shaped “microfossils,” narrower than the width of a human hair and invisible to the naked eye, are believed to come from ancient microbes, according to a new study in the journal Nature. Scientists debate the age of the specimens, but the authors' youngest estimate — 3.77 billion years — would make these fossils the oldest ever found.

"Claims of ancient fossils are always contentious. Rocks as old as the ones in the new study rarely survive the weathering, erosion, subduction and deformation of our geologically active Earth. Any signs of life in the rocks that do survive are difficult to distinguish, let alone prove. Other researchers in the field expressed skepticism about whether the structures were really fossils, and whether the rocks that contain them are as old as the study authors say.

***

"The microfossils were discovered in rocks from the Nuvvuagittuq (nuh-vu-ah-gi-took) belt in northeastern Canada. This strip of iron-rich jasper now cuts across the eastern shore of Hudson Bay, but it was once a hydrothermal vent on the ocean floor. Billions of years ago, Dodd and his colleagues say, ancient microbes flourished around those vents, taking advantage of their chaotic chemistry to generate fuel.

***

"The optical observations revealed complex fossil structures encased in hematite, a mineral that would have formed as iron in the seawater interacted with the microbe's decaying organic matter. John Slack, a co-author and emeritus scientist at the U.S. Geological Survey who studies jaspers from ancient hydrothermal vents, said the fossils look just like the ones he sees in younger rocks, and around modern-day vents.

"The Raman analysis, which measures the vibrations of atoms as they are struck by a laser to figure out what molecules a material contains, showed that the rocks contain carbonate, apatite and magnetite — minerals that often form in the presence of organic matter.

"Graphite in the rocks also contained telltale signs of life. The mineral disproportionately contained the isotope carbon-12, a form of the atom in which the nucleus has six protons and six neutrons. This form of carbon is preferred for biological processes and is considered an isotopic signature of life.

“'We can think of alternative explanations for each of these singular observations,” said Dodd, “but why all of these features occur together can really only be explained by one thing, which is a biological interpretation.”

***

"'It’s a very exciting set of observations carefully made,” Williford wrote in an email. "… They may indeed have found something truly remarkable.”

"Findings like these are subject to intense scrutiny because they have potentially far-reaching implications for the study of early organisms on Earth and other planets. The oldest universally accepted evidence of life on Earth is dated to about 3.4 billion to 3.5 billion years ago. The new paper proposes pushing that date back by nearly 300 million years."

Comment: I have presented one other finding at the 4 byo period (2017-01-14,00:39). What is amazing is the Earth did not become hospitable for life, it is thought, until about 4 byo. If that is true and these findings are true, life appeared very quickly. More suggestive evidence that God did it.

Theoretical origin of life; without phosphate

by David Turell @, Friday, March 03, 2017, 14:35 (2601 days ago) @ David Turell

It is clear one of the problems at the time life started that phosphates were not in an available form, yet life today requires chemically active phosphates for structure of DNA as one example, and for energy supply as in ATP:

https://cosmosmagazine.com/chemistry/life-without-phosphate-mystery-solved?utm_source=T...

"Phosphate is essential to all modern life forms. From providing the backbone in DNA, to driving the cell’s energy currency in the form of the nucleotide adenosine triphosphate (ATP), phosphate is a key biological building block.

"The chemical is so heavily involved in metabolism, the chemical reactions of life, that it is difficult to imagine life existing without it.

"Yet, scientists believe that there was little phosphate readily available in the prebiotic soup in which life began.

"It is a chicken-and-egg conundrum. The earth’s phosphate is largely locked up in stable minerals, and life forms such as bacteria must use complex enzymes to extract it in a useful form. But how could these enzymes evolve, without using phosphate?

"To address this, the researchers used a theoretical approach known as “systems biology” to explore a phosphate-free metabolism.

***

"The team led by Daniel Segrè began by assembling a large database of all known biochemical reactions from the earth’s entire biosphere.

"Next, they removed all chemicals and reactions from their set which contained phosphate, or phosphorous in any form.

"Then, starting with a “seed” set of eight chemicals that are thought to have been accessible to early life, they used computer simulations to began to look at how these simple molecules might react together to form new metabolites.

"As new chemicals emerged from these reactions, the set grew larger, to include a connected network of 315 reactions and 260 metabolites – including 10 of the 20 amino acids which are used by modern cells to build proteins, as well as several ingredients by which cells metabolise sugars (a process known as the tricarboxylic acid (TCA) or Krebs cycle).

"This new network of phosphate-free reactions was found to be rich in iron-sulfur clusters, supporting the idea that these readily available compounds could have been integral for the beginnings of life – the so-called “iron sulfur world hypothesis”.

"The team also found that a type of sulfur-based compound called thioesters might have filled in some of the roles that phosphate plays in modern biochemistry.

"When a sulfur-containing chemical called pantheteine was included in the set, along with a phosphate-free mechanism for electron transfer, the number of metabolites in the set exploded to include uracil and ribose, some of the key ingredients in RNA.

"Before our study, other researchers had proposed a sulfur-based early biochemistry, with hints that phosphate may not have been necessary until later,” noted lead author Segrè. “What was missing until now was data-driven evidence that these early processes, rather than scattered reactions, could have constituted a highly connected and relatively rich primitive metabolic network.”

"This work, without providing direct experimental evidence, could potentially answer one of biology’s biggest mysteries. This phosphate-free biochemical blueprint allows us to imagine the missing link between the simple molecules of the pre-biotic earth and the phosphate-hungry organisms which populate our world today."

Comment: All theory and computer simulations involved with no hard evidence, just the ifs ands and buts in the article. It finds missing organic molecules, but notes no source of energy cycle which is necessary to run the show. Robert Shapiro discussed that hard problem in a Sci. Am. article many years ago.

Theoretical origin of life; mimicking the Krebs cycle

by David Turell @, Monday, March 13, 2017, 17:41 (2591 days ago) @ David Turell

A part of the ubiquitous mechanism in life supplying energy is the Krebs cycle, a circular arrangement of organic molecules. This lab experiment using many thousand trials finds a sulpher based mimic as a theoretical start of life. It is just fun and games for chance to do this. It is also touted to be enzyme-free which makes it easier to form:

https://phys.org/news/2017-03-enzyme-free-krebs-key-life-earth.html

"The researchers have demonstrated a network of chemical reactions in the lab which mimic the important Krebs cycle present in living organisms today. In a study published in the journal Nature Ecology and Evolution, they say it could explain an important step in how life developed on Earth.

***

"The research group from the Francis Crick Institute and the University of Cambridge say their demonstration offers an answer. They have shown an enzyme-free metabolic pathway that mirrors the Krebs cycle. It is sparked by particles called sulphate radicals under conditions similar to those on Earth four billion years ago.

***

"The scientists used simple carbon compounds which are involved at various points in the Krebs cycle (such compounds have recently been found in a meteorite by NASA scientists) and mixed them with iron and sulphur-containing chemicals that would be found in sediments in the early oceans.

"We took components representative of the sediments present on Earth billions of years ago." says Dr Ralser, "As salts that would have been present in the sediments did not trigger many reactions, we mostly concentrated on metal ions and sulphate species. These are also known to be important in the modern cell's Krebs cycle.

""We conducted a huge screen involving thousands of measurements then systematically worked through them. At the end we found a condition that may have enabled the Krebs cycle to emerge. It relies on sulphate radicals and previously nobody had thought about them." (my bold)

"An alternative hypothesis for the origin of life suggests that RNA - a molecule similar to DNA that can maintain genetic information but is more transient and more reactive - can explain the first steps towards life. This is known as the RNA-world hypothesis.

"Dr Ralser says: "There is a huge scientific debate about whether the first steps towards life were driven by metabolism or genetics."

"He argues that the presence of RNA molecules cannot easily explain the origin of metabolism, as RNA is made from products of metabolism. And that his group's results support the theory that environmental chemistry enabled metabolism to begin.

"'People have tried to work on a non-enzymatic Krebs cycle for years, but most have thought about it theoretically or philosophically. Few have done systematic physical experiments like those we report here. A non-enzymatic catalyst for the Krebs cycle exists and we have found it," concludes Dr Ralser."


Comment: More fun and games in the lab resulting in intelligent design of a system that is unlikely to form by chance. See my bolded area.

Theoretical origin of life; mimicking the Krebs cycle

by David Turell @, Sunday, March 26, 2017, 05:24 (2579 days ago) @ David Turell

Another take on this exploitation of the Krebs cycle:

https://www.newscientist.com/article/2124375-metabolism-may-be-older-than-life-itself-a...

"Metabolism describes the fiendishly complex network of reactions that enable organisms to generate energy and the molecules they need to survive, grow and reproduce.

"So an alternative explanation is that the Krebs cycle existed from the outset, and early life forms simply adopted it and developed enzymes to make it more efficient.
However, modern enzymes that catalyse this cycle all use very different mechanisms to do so. The idea that the type of simple, inorganic molecule that might have existed naturally in the early oceans could catalyse such a diverse set of reactions was once dismissed by RNA-world proponents as an “appeal to magic”.

"Ralser has shifted his focus to the Krebs cycle. Unlike with glucose, the chemicals involved at various points of the Krebs cycle have been identified on meteorites and in laboratory recreations of Earth’s early oceans – so we know they were around.

“'We may not be able to solve where glucose comes from so easily,” says Ralser. “But if we can provide proof that the Krebs cycle could originate from a single, non-enzymatic catalyst, then we would have a very strong case that what we say about the origins of metabolism is true.”

"So his team took chemicals involved in the Krebs cycle and exposed them to chemicals that would have been present in early ocean sediments. Nothing happened, until they introduced a compound called peroxydisulphate, a source of highly reactive agents called sulphate radicals. ( my bold)

"This triggered a sequence of 24 chemical reactions that were very similar – although not identical – to those seen in the Krebs cycle today.

“'The most surprising thing is that again a single molecule acts as the catalyst for all of the reactions we discovered,” says Ralser. “The simplicity of it is super-exciting because it gives you a plausible feeling about how it could have all started.”

"Sulphate radicals would had been found in abundance near hydrothermal vents, which have been suggested as possible locations at which life started, or near to sulphur-rich sediments.

"Ralser believes that these hardwired chemical reactions provided a template upon which the evolutionary machinery could build once it came into being.
Unfinished cycle

"However, the enzyme-free Krebs cycle that Ralser observed isn’t the complete biochemical cycle as it operates in modern cells. That may have come later, after enzymes evolved.

"Furthermore, the sulphate-driven cycle has so far only been shown to run in one direction (the oxidative one). In some species, the Krebs cycle can also run in reverse and help to incorporate CO2 into the building of new carbohydrates. Some think it may therefore have been involved in early carbon fixation, in which case you’d expect to see the cycle spontaneously turning in this direction too.

“'This is a neat paper and the findings are striking and careful,” says Nick Lane, an evolutionary biochemist at University College London. “But this is strictly the oxidative Krebs cycle, which is certainly not ancient. It probably became oxidative after the rise of molecular oxygen in the atmosphere.

“'Before that, there was a reductive Krebs cycle, which fixed CO2 using H2, and which is still found in some ancient bacteria,” says Lane. “They are not simulating the reductive Krebs cycle at all.”

"What’s more, even if all three fundamental metabolic pathways – the Krebs cycle, pentose phosphate pathway and glycolysis – can proceed in the absence of enzymes, there’s still the question of how life’s other components came into being.

“With the metabolic pathway alone, you have a very good starting point for life, but it is not life, just a chemical-reaction network,” says Ralser. “You also need things like membranes to contain the reactions, and the genetic machinery that enables inheritance.

“"How do you bring these elements together in one environment and in non-extreme conditions, and make them work?” he asks. “This is still a big challenge.'”

comment: Again fun and games in a human lab using planning intelligence to design outcomes. Did nature know about peroxydisulphate found by humans to create a pseudo reaction like the Krebs cycle? A planning mind is needed to create life on Earth.

Theoretical origin of life; perhaps UV light helped

by David Turell @, Saturday, April 01, 2017, 01:05 (2573 days ago) @ David Turell

Making some organic molecules when starting with organic molecules in the lab treated with UV light is more lab fun and games:

https://phys.org/news/2017-03-sun-uv-life.html

"Before life began, radiation from the Sun was the primary source of energy on our planet, just as it is today. In this oxygen-poor, prebiotic world, solar energy may have provided the jolt to transform simple organic molecules into more complex ones, which were used as the building blocks of biology and life.

"A new paper by two University of Colorado at Boulder authors considers how this might have happened through a review of existing literature on the topic.

***

"The lack of oxygen in the early atmosphere means that more high-energy ultraviolet radiation from the Sun would have reached the surface of the prebiotic Earth than today, where it is filtered by ozone. Even though this component of sunlight can be destructive to certain biomolecules, the energy provided could still be useful to early life chemistry, Rapf said. "Even if you destroy a molecule, it is broken into smaller, very reactive chunks that readily undergo additional reactions, recombining to form larger high-energy molecules."

"In particular, the researchers were intrigued by a group of oxygen-laden acids called oxoacids. An example is pyruvic acid, which is at the center of key metabolic pathways in life today. When dissolved in water and illuminated with ultraviolet light, pyruvic acid is known to react to make larger molecules, with higher yields under the oxygen-limited conditions that would be found on the early Earth.

"Pyruvic acid is only one of a class of molecules that react in the same way to form these larger species. Another molecule in this class, 2-oxooctanoic acid, is particularly interesting because it is an example of a simple lipid. 2-oxooctanoic acid was likely "prebiotically relevant," Rapf added, meaning it could be useful to the chemistry that eventually led to life.

"In an earlier study on 2-oxooctanoic acid, Rapf and Vaida found that exposing it to light forms a more complex molecule, dihexyltartaric acid. This is noteworthy because the new molecule has two alkyl chains, meaning it more closely resembles the lipids that are in modern cells, which also have two tails. This light-driven process, discovered in the Vaida lab, is one of only a few ways to make double-tailed lipids from simple, single-tailed molecules under prebiotic conditions.

"'We're using sunlight as a way of building bigger molecules, but in order to be useful to the development of biology any molecules you build have to be stable enough to exist in the environment," added Rapf.

"In the case of 2-oxooctanoic acid, the product, dihexyltartaric acid, does not absorb the same UV light and therefore, is protected from undergoing further photochemistry (chemical reactions as a result of sunlight). These double-tailed lipids also spontaneously assemble into membrane-enclosed compartments, resembling simple protocells that are necessary to the evolution of life. The researchers are hunting for other molecules that could be activated by starlight and generate biologically-relevant compounds in a broader astrobiological context."

Comment: The is intelligent design by scientists in their lab. They don't even know that the molecules they start with were available on Earth about four billion years ago before life began.

Theoretical origin of life; using plasmas and electricity

by David Turell @, Sunday, April 23, 2017, 20:18 (2550 days ago) @ David Turell

A more modern approach to the early Miller Urey experiment produces all the RNA bases needed for life:

https://phys.org/news/2017-04-rna-nucleobases-simulated-primordial-earth.html

In 1952, chemists Stanley Miller and Harold Urey conducted a famous experimental simulation of the conditions thought to prevail on early Earth in order to determine possible pathways to the creation of life. The Miller-Urey experiment used water (H2O), methane (CH4), ammonia (NH3) and hydrogen (H2) sealed inside a glass flask. They introduced water vapor from a separate flask while firing electrical sparks between electrodes to simulate lightning.

***

the experiment has been criticized over the years because the gas mixture Miller and Urey used was considered to be too reducing, and because the production of only amino acids was of limited

***

Their experimental setup was similar to the original experiment, using a simple reducing mixture of NH3 + CO and H2O. In addition to electric discharge in water vapor, they also subjected the solution to powerful laser discharges to simulate the plasmas resulting from asteroid impact shock waves. The results of the experiment demonstrated that all RNA nucleobases were synthesized, strongly supporting the emergence of biologically relevant chemicals in a reducing atmosphere.

In their paper, the authors write, "As the most important finding, discharge treatment of NH3 + CO + H2O led to the formation of a significant amount of formamide and hydrogen cyanide (HCN)." This result is key, as formamide has been experimentally shown to create guanine, an RNA nucleobase, at high temperatures under ultraviolet light.

"Additionally," the authors write, "we detected all of the RNA canonical nucleobases—uracil, cytosine, adenine and guanine—together with urea and the simplest amino acid, glycine… these findings support the idea that a NH3 + CO + H2O atmosphere can substitute for pure formamide and act as a starting environment not only for the formation of amino acids, but also of RNA nucleobases."

The researchers also demonstrated that any nucleic acid base can be decomposed to a reducing gaseous atmosphere by electric discharges in the presence of water, and these gases can react in turn to produce all the RNA nucleobases. They also note that their results do not preclude other scenarios, but demonstrate that multiple pathways to the production of RNA nucleobases are possible.

Comment: This laboratory designed result shows the bases for RNA could have been created on Earth. However, the next step is not easy. Creating a complex carbon molecule that is RNA itself is also very difficult by chance.

Theoretical origin of life; James Tour again

by David Turell @, Saturday, August 05, 2017, 21:24 (2446 days ago) @ David Turell

He is a synthetic biochemist who knows how difficult it is to make any organic chemistry molecule. He has been quoted before:

http://inference-review.com/article/an-open-letter-to-my-colleagues

"Synthetic constraints must be taken into account when considering the prebiotic preparation of the four classes of compounds needed for life: the amino acids, the nucleotides, the saccharides, and the lipids.1 The next level beyond synthesis involves the components needed for the construction of nanosystems, which are then assembled into a microsystem. Composed of many nanosystems, the cell is nature’s fundamental microsystem. If the first cells were relatively simple, they still required at least 256 protein-coding genes. This requirement is as close to an absolute as we find in synthetic chemistry. A bacterium which encodes 1,354 proteins contains one of the smallest genomes currently known.

***

"coding information is essential. DNA and RNA are the primary informational carriers of the cell. No matter the medium life might have adopted at the very beginning, its information had to come from somewhere. A string of nucleotides does not inherently encode anything.

***

"Researchers have identified thousands of different lipid structures in modern cell membranes. These include glycerolipids, sphingolipids, sterols, prenols, saccharolipids, and polyketides. When making synthetic vesicles—synthetic lipid bilayer membranes—mixtures of lipids can destabilize the system.

"Lipid bilayers surround subcellular organelles, such as nuclei and mitochondria, which are themselves nanosystems and microsystems. Each of these has their own lipid composition.

"Lipids have a non-symmetric distribution. The outer and inner faces of the lipid bilayer are chemically inequivalent and cannot be interchanged.

"The lipids are just the beginning. Protein–lipid complexes are the required passive transport sites and active pumps for the passage of ions and molecules through bilayer membranes, often with high specificity. Some allow passage for substrates into the compartment, and others their exit. The complexity increases further because all lipid bilayers have vast numbers of polysaccharide (sugar) appendages, known as glycans, and the sugars are no joke. These are important for nanosystem and microsystem regulation. The inherent complexity of these saccharides is daunting. Six repeat units of the saccharide D-pyranose can form more than one trillion different hexasaccharides through branching (constitutional) and glycosidic (stereochemical) diversity.

"Polysaccharides are the most abundant organic molecules on the planet. Their importance is reflected in the fact that they are produced by and are essential to all natural systems. Every cell membrane is coated with a complex array of polysaccharides, and all cell-to-cell interactions take place through saccharide participation on the lipid bilayer membrane surface. Eliminating any class of saccharides from an organism results in its death, and every cellular dysfunction involves saccharides.

***

"very little is known about glycan diversification during evolution. Over three billion years of evolution has failed to generate any kind of living cell that is not covered with a dense and complex array of glycans.

"What is more, Vlatka Zoldoš, Tomislav Horvat, and Gordan Lauc observed: “A peculiarity of glycan moieties of glycoproteins is that they are not synthesized using a direct genetic template. Instead, they result from the activity of several hundreds of enzymes organized in complex pathways.” (my bold)

***

"Polysaccharides carry more potential information than any other macromolecule, including DNA and RNA. For this reason, lipid-associated polysaccharides are proving enigmatic.

"Cellular and organelle bilayers, which were once thought of as simple vesicles, are anything but. They are highly functional gatekeepers. By virtue of their glycans, lipid bilayers become enormous banks of stored, readable, and re-writable information.

***

"Many of the molecular structures needed for life are not thermodynamically favored by their syntheses. Formed by the formose reaction, the saccharides undergo further condensation under the very reaction conditions in which they form. The result is polymeric material, not to mention its stereo-randomness at every stereogenic center, therefore doubly useless.Time is the enemy. The reaction must be stopped soon after the desired product is formed.

***

"We synthetic chemists should state the obvious. The appearance of life on earth is a mystery. We are nowhere near solving this problem. The proposals offered thus far to explain life’s origin make no scientific sense.

***

"The laws of physics and chemistry’s Periodic Table are universal, suggesting that life based upon amino acids, nucleotides, saccharides and lipids is an anomaly. Life should not exist anywhere in our universe. Life should not even exist on the surface of the earth."

Comment: With his background struggling in the lab to synthesize, his point just above is valid. He is describing what is in the simplest of bacteria. Note my bold about glycoproteins being generated by a series of enzymes, not genes. Evolution did not find that system by chance.

Theoretical origin of life; James Tour again III

by David Turell @, Sunday, February 10, 2019, 00:48 (1893 days ago) @ David Turell

Another set of comments about the organic chemistry involved in th origin of life:

https://uncommondescent.com/intelligent-design/researchers-life-didnt-just-hang-on-but-...

An Open Letter to My Colleagues – James Tour – 2017

"Excerpt: We synthetic chemists should state the obvious. The appearance of life on earth is a mystery. We are nowhere near solving this problem. The proposals offered thus far to explain life’s origin make no scientific sense.

"Beyond our planet, all the others that have been probed are lifeless, a result in accord with our chemical expectations. The laws of physics and chemistry’s Periodic Table are universal, suggesting that life based upon amino acids, nucleotides, saccharides and lipids is an anomaly. Life should not exist anywhere in our universe. Life should not even exist on the surface of the earth.

“'We have no idea how the molecules that compose living systems could have been devised such that they would work in concert to fulfill biology’s functions. We have no idea how the basic set of molecules, carbohydrates, nucleic acids, lipids, and proteins, were made and how they could have coupled into the proper sequences, and then transformed into the ordered assemblies until there was the construction of a complex biological system, and eventually to that first cell.

"Nobody has any idea how this was done when using our commonly understood mechanisms of chemical science. Those that say they understand are generally wholly uninformed regarding chemical synthesis. Those that say “Oh, this is well worked out,” they know nothing, nothing about chemical synthesis – Nothing!


"Further cluelessness – From a synthetic chemical perspective, neither I nor any of my colleagues can fathom a prebiotic molecular route to construction of a complex system. We cannot figure out the prebiotic routes to the basic building blocks of life: carbohydrates, nucleic acids, lipids, and proteins. Chemists are collectively bewildered. Hence I say that no chemist understands prebiotic synthesis of the requisite building blocks let alone their assembly into a complex system.

"That’s how clueless we are. I’ve asked all of my colleagues – National Academy members, Nobel Prize winners -I sit with them in offices; nobody understands this. So if your professors say it’s all worked out, your teachers say it’s all worked out, they don’t know what they’re talking about. It is not worked out. You cannot just refer this to somebody else; they don’t know what they’re talking about.'”

James Tour – one of the top ten leading chemists in the world.

Comment: None needed

Theoretical origin of life; Chirality needed by nature

by David Turell @, Saturday, August 05, 2017, 22:46 (2446 days ago) @ David Turell

Chiral molecules guide electrons' spin and transfer under tight control. These quantum effects are required for efficiency. The latest studies show why left and right handed molecules are needed and used exclusively by living organisms:

http://inference-review.com/article/spin-in-quantum-biology#footnote-6

"Electrons have two intrinsic properties, charge and spin. The first is widely known, the second, less appreciated. The spin of an electron is a purely quantum mechanical property; it specifies the electron’s intrinsic angular momentum. ... While classical electrostatics does not allow two electrons to occupy the same region of space in a stable system, it is possible in quantum mechanics as long as their spins are different. This principle guides the organization of electrons in atoms, as well as in the chemical bonds between them.

***

"Here we discuss recent discoveries pointing to the importance of spin in biological systems, such as its role in long-range electron transfer, in reactions that involve multiple electrons, and in biorecognition. All these phenomena arise from chiral-induced spin selectivity (CISS), which links electron transfer through chiral molecules to a specific spin state of the electron. When electrons are transferred through chiral molecules, one spin state of the electron is preferred.

"Chirality is the name for the particular kind of symmetry that arises when one object is the mirror image of the other. An example is the human hand. Mirror images require no internal symmetries. Our two hands are called enantiomers of one another. Chiral molecules are referred to as being a right-handed enantiomer or a left-handed enantiomer.

***

"The components from which proteins are made—the amino acids—are enantiomerically pure in all organisms, and this purity is preserved with extremely high fidelity. Such enantiomeric selectivity is very difficult to achieve artificially in the laboratory. Moreover, the enantiopurity of drug medications is known to be essential to their efficacy. And without it, side effects are common and sometimes deadly.

***

"The CISS effect provides a possible answer. When electrons move elastically through chiral molecules, their spin and linear momentum are coupled; they cannot be reflected back without also flipping their spin, an improbable event in organic molecules. An electron should be able to propagate farther through a chiral molecule than through an achiral analog. This feature enhances the efficiency of electron transfer through chiral proteins.

"It is important to appreciate that molecules in a biological environment undergo significant thermal fluctuations. Nuclear and electronic motions vary and electron transfer thus occurs under the influence of an electronic potential that fluctuates. Under such conditions, backscattering could be significant if the CISS effect did not constrain the process.The use of chiral molecules as bridges for electron transfer could provide symmetry constraints that enhance electron transfer efficiency. Indeed, recent experiments reveal that spin plays a role in electron transfer through peptides, proteins, and DNA.5 For example, the electrons transferred through Photosystem I are spin-polarized.

"Many biochemical processes, such as oxygen formation in photosynthesis and respiration, require the transfer of multiple electrons.

***

"Spin polarization, which in chiral molecules accompanies charge polarization, is another way quantum mechanics affects biology. The coupling of the spin of an electron to its motion in chiral molecules and the resulting CISS have significant effects, even at physiological temperatures. For biomolecules, the effects are wide ranging, from the efficient transfer of electrons over relatively long distances, to enhanced selectivity of oxidation reactions, to the efficiency of enantioselective biorecognition."

Comment: These new finding explain why chirality is necessary. It is to control electron transfer in life's processes. As James Tour expresses in previous entries about synthesizing handedness in the laboratory, maintaining pure handedness of one type is very difficult. Nature does it very easily. Not by chance.

Theoretical origin of life; possible primordial soup

by David Turell @, Monday, September 04, 2017, 22:40 (2416 days ago) @ David Turell

More fun and games in the lab:

https://phys.org/news/2017-09-primordial-soup-hearty-pre-protein-stew.html

"Ancestors of the first protein molecules, which are key components of all cells, could have been bountiful on pre-life Earth, according to a new study led by researchers at the Georgia Institute of Technology, who formed hundreds of possible precursor molecules in the lab. Then they meticulously analyzed the molecules with latest technology and new algorithms.

"They found that the molecules, called depsipeptides, formed quickly and abundantly under conditions that would have been common on prebiotic Earth, and with ingredients that would have likely been plentiful.

"And some of the depsipeptides evolved into new varieties in just a few days, an ability that, eons ago, could have accelerated the birth of long molecules, called peptides, that make up proteins.

***

"But complex molecules of life likely did not arise in one dramatic step that produced final products. That's the hypothesis that drives the research of Fernández and his colleagues at the NSF/NASA Center for Chemical Evolution, headquartered at Georgia Tech and based on close collaboration with the Scripps Research Institute.

"Instead, multiple easier chemical steps produced plentiful in-between products that were useful in subsequent reactions that eventually led to the first biopolymers. The depsipeptides produced in this latest study could have served as such a chemical stepping stone.

***

"To understand depsipeptides and the significance of the researchers' results, it's helpful to start by looking at peptides, which are chains of amino acids. When the chains get really long they are called polypeptides, and then proteins.

"Living cells have machinery that reads instructions in DNA on how to link up amino acids in a specific order to build very specific peptides and proteins that have functions in a living cell. For a protein to have function in a cell, its polypeptide chains have to clump up like sticky yarn to form useful shapes.

"Before cells and DNA existed on an Earth devoid of life, for polypeptides to form, amino acids had to somehow jostle together in puddles or on the banks of rivers or lakes to form chains. But peptide bonds can be tough to form, especially long chains of them.

"Other bonds, called ester bonds, form more easily, and they can link up amino acids with very similar molecules called hydroxy acids. Hydroxy acids are so much like amino acids that they can, in some cases, function as their stand-in doubles.

"The researchers mixed three amino acids with three hydroxy acids in a water solution and they formed depsipeptides, chains of amino acids and hydroxy acids held together by intermittent ester and peptide bonds. The hydroxy acids acted as an enabler to put the chains together that would have otherwise been difficult to form.

"The primordial soup may have lapped its depsipeptides onto rocks, where they dried out in the sun, then rain or dew dissolved them back into the soup, and that happened over and over. The researchers mimicked this cycle in the lab and watched as the depsipeptide chains further developed.

***

"Since ester bonds break more easily, in the experiment, the chains tended to come apart more at the hydroxy acids and hold together between the amino acids, which were connected by the stronger peptide bonds. As a result, chains could re-form and link up more and more amino acids with each other into sturdier peptides.

"In a kind of square-dance, the stand-in hydroxy acids often left their amino acid partners in the chain, and new amino acids latched onto the chain in their place, where they held on tight. In fact, a number of the depsipeptides ended up being composed almost completely of amino acids and had only remnants of hydroxy acids.

"'Now we know how peptides can form easily," Fernández said. "Next, we want to find out what's needed to get to the level of a functional protein.'" ( my bold)

Comment: These lab studies are designs that might fit what happened on Earth. My bold indicates that what they produced are far from functional proteins needed for first life. They assume amino acids were present of the correct chirality (all left handed). As usual no proof of how life might have started.

Theoretical origin of life; horizontal gene transfer

by David Turell @, Monday, September 11, 2017, 22:33 (2409 days ago) @ David Turell

A suggestion that HGT played a major role:

https://www.quantamagazine.org/seeing-emergent-physics-behind-evolution-20170831/

"The Last Universal Common Ancestor is dated to be about 3.8 billion years ago. The earth is 4.6 billion years old. Life went from zero to essentially the complexity of the modern cell in less than a billion years. In fact, probably a lot less: Since then, relatively little has happened in terms of the evolution of cellular architecture. So evolution was slow for the last 3.5 billion years, but very fast initially. Why did life evolve so fast?

"[The late biophysicist] Carl Woese and I felt that it was because it evolved in a different way. The way life evolves in the present era is through vertical descent: You give your genes to your children, they give their genes to your grandchildren, and so on. Horizontal gene transfer gives genes to an organism that’s not related to you. It happens today in bacteria and other organisms, with genes that aren’t really so essential to the structure of the cell.

***

"Life could only have evolved as rapidly and optimally as it did if we assume this early network effect, rather than a [family] tree. We discovered about 10 years ago that this was the case with the genetic code, the rules that tell the cell which amino acids to use to make protein. Every organism on the planet has the same genetic code, with very minor perturbations. In the 1960s Carl was the first to have the idea that the genetic code we have is about as good as it could possibly be for minimizing errors. Even if you get the wrong amino acid — through a mutation, or because the cell’s translational machinery made a mistake — the genetic code specifies an amino acid that’s probably similar to the one you should have gotten. In that way, you’ve still got a chance that the protein you make will function, so the organism won’t die. David Haig [at Harvard University] and Laurence Hurst [at the University of Bath] were the first to show that this idea could be made quantitative through Monte Carlo simulation — they looked for which genetic code is most resilient against these kinds of errors. And the answer is: the one that we have. It’s really amazing, and not as well known as it should be.

"Later, Carl and I, together with Kalin Vetsigian [at the University of Wisconsin-Madison], did a digital life simulation of communities of organisms with many synthetic, hypothetical genetic codes. We made computer virus models that mimicked living systems: They had a genome, expressed proteins, could replicate, experienced selection, and their fitness was a function of the proteins that they had. We found that it was not just their genomes that evolved. Their genetic code evolved, too. If you just have vertical evolution [between generations], the genetic code never becomes unique or optimal. But if you have this collective network effect, then the genetic code evolves rapidly and to a unique, optimal state, as we observe today.

"So those findings, and the questions about how life could get this error-minimizing genetic code so quickly, suggest that we should see signatures of horizontal gene transfer earlier than the Last Universal Common Ancestor, for example. Sure enough, some of the enzymes that are associated with the cell’s translation machineries and gene expression show strong evidence of early horizontal gene transfers.

"Tommaso Biancalani [now at the Massachusetts Institute of Technology] and I discovered in the last year or so — and our paper on this has been accepted for publication — that life automatically shuts off the horizontal gene transfer once it has evolved enough complexity. When we simulate it, it basically shuts itself off on its own. It’s still trying to do horizontal gene transfer, but almost nothing sticks. Then the only evolutionary mechanism that dominates is vertical evolution, which was always present. We’re now trying to do experiments to see whether all the core cellular machinery has gone through this transition from horizontal to vertical transmission."

Comment: this theory doesn't tell us how life started, but it gives us a reason to explain how different forms of bacteria advanced so early and so rapidly. It also suggests why more advanced forms of life do not use horizontal gene transfer as bacteria still do. It also fits the research on zircons suggesting a very early origin of life presented today.

Theoretical origin of life; horizontal gene transfer

by dhw, Tuesday, September 12, 2017, 12:08 (2408 days ago) @ David Turell

DAVID: A suggestion that HGT played a major role:

https://www.quantamagazine.org/seeing-emergent-physics-behind-evolution-20170831/

QUOTE: "The Last Universal Common Ancestor is dated to be about 3.8 billion years ago. The earth is 4.6 billion years old. Life went from zero to essentially the complexity of the modern cell in less than a billion years. In fact, probably a lot less: Since then, relatively little has happened in terms of the evolution of cellular architecture. So evolution was slow for the last 3.5 billion years, but very fast initially. Why did life evolve so fast?
"[The late biophysicist] Carl Woese and I felt that it was because it evolved in a different way. The way life evolves in the present era is through vertical descent: You give your genes to your children, they give their genes to your grandchildren, and so on. Horizontal gene transfer gives genes to an organism that’s not related to you. It happens today in bacteria and other organisms, with genes that aren’t really so essential to the structure of the cell.

I don’t think he’s trying to explain the origin of life at all – just the reason for evolution slowing down. It all makes perfect sense, and fits in with Margulis’s emphasis on cooperation as the key to evolution. Cells cooperated and merged to produce innovations, and initially the potential was enormous. But there has to be a limit somewhere, so the process slows down as the limit approaches. Of course we have no idea what that limit is, and for all we know, life might look very different a thousand million years from now. We are clearly going through a period of stasis. Great article! Thank you.

Theoretical origin of life; horizontal gene transfer

by David Turell @, Tuesday, September 12, 2017, 15:42 (2408 days ago) @ dhw

DAVID: A suggestion that HGT played a major role:

https://www.quantamagazine.org/seeing-emergent-physics-behind-evolution-20170831/

QUOTE: "The Last Universal Common Ancestor is dated to be about 3.8 billion years ago. The earth is 4.6 billion years old. Life went from zero to essentially the complexity of the modern cell in less than a billion years. In fact, probably a lot less: Since then, relatively little has happened in terms of the evolution of cellular architecture. So evolution was slow for the last 3.5 billion years, but very fast initially. Why did life evolve so fast?
"[The late biophysicist] Carl Woese and I felt that it was because it evolved in a different way. The way life evolves in the present era is through vertical descent: You give your genes to your children, they give their genes to your grandchildren, and so on. Horizontal gene transfer gives genes to an organism that’s not related to you. It happens today in bacteria and other organisms, with genes that aren’t really so essential to the structure of the cell.

I don’t think he’s trying to explain the origin of life at all – just the reason for evolution slowing down. It all makes perfect sense, and fits in with Margulis’s emphasis on cooperation as the key to evolution. Cells cooperated and merged to produce innovations, and initially the potential was enormous. But there has to be a limit somewhere, so the process slows down as the limit approaches. Of course we have no idea what that limit is, and for all we know, life might look very different a thousand million years from now. We are clearly going through a period of stasis. Great article! Thank you.

You are welcome. I know he did not describe OOL. My comment: "Comment: this theory doesn't tell us how life started, but it gives us a reason to explain how different forms of bacteria advanced so early and so rapidly. It also suggests why more advanced forms of life do not use horizontal gene transfer as bacteria still do. It also fits the research on zircons suggesting a very early origin of life presented today." The zircon work is fascinating. Possible earlier life than imagined!

Theoretical origin of life; more lab fun

by David Turell @, Wednesday, September 20, 2017, 00:58 (2401 days ago) @ David Turell

The article says it takes a 40 base RNA to replicate. Somehow or other it fell together on early rocky Earth:

https://phys.org/news/2017-09-complex-life-evolved-chance-coupling.html


"In this world, billions of years ago, nothing existed that we would recognise today as living. The world contained only lifeless molecules that formed spontaneously through the natural chemical and physical processes on Earth.

"However, the moment that small molecules connected and formed larger molecules with the ability to replicate themselves, life started to evolve.

"'Life was a chance event, there is no doubt about that," says Dr Pierre Durand from the Evolution of Complexity Laboratory in the Evolutionary Studies Institute at Wits University, who led a project to find out how exactly these molecules linked up with each other. Their results are published today in the journal Royal Society Open Science, in a paper entitled "Molecular trade-offs in RNA ligases affected the modular emergence of complex ribozymes at the origin of life".

"Very simple ribonucleic acid (RNA) molecules (compounds similar to Deoxyribonucleic acid(DNA)) can join other RNA molecules to themselves though a chemical reaction called ligation. The random joining together of different pieces or RNA could give rise to a group of molecules able to produce copies of themselves and so kick start the process of life.
 
"While the process that eventually led to the evolution of life took place over a long period of time, and involved a number of steps, Wits PhD student Nisha Dhar and Durand have uncovered how one of these crucial steps may have occurred. (my bold)

"They have demonstrated how small non-living molecules may have given rise to larger molecules that were capable of reproducing themselves. This path to self-replicating molecules was a key event for life to take hold. 

"'Something needed to happen for these small molecules to interact and form longer, more complex molecules and that happened completely by chance," says Durand."

Comment: A declarative statement that life had to be accidental, yet my bold shows the truth. The certainty of atheism. Same old lab story that manufactured molecules must have happened by chance.

Theoretical origin of life; more lab fun

by dhw, Wednesday, September 20, 2017, 13:51 (2400 days ago) @ David Turell

QUOTE: "'Something needed to happen for these small molecules to interact and form longer, more complex molecules and that happened completely by chance," says Durand."

DAVID’s comment: A declarative statement that life had to be accidental, yet my bold shows the truth. The certainty of atheism. Same old lab story that manufactured molecules must have happened by chance.

I agree with you completely. It’s on a par with declarative statements like “God did/wanted/wants this/that.” One longs for the voice of reason that says: “We don’t know, but here are some hypotheses…” Or even: “We don’t know, but I choose to blinker myself and believe in this particular hypothesis, despite the absence of proof.”

Theoretical origin of life; more lab fun

by David Turell @, Wednesday, September 20, 2017, 14:52 (2400 days ago) @ dhw

QUOTE: "'Something needed to happen for these small molecules to interact and form longer, more complex molecules and that happened completely by chance," says Durand."

DAVID’s comment: A declarative statement that life had to be accidental, yet my bold shows the truth. The certainty of atheism. Same old lab story that manufactured molecules must have happened by chance.

dhw: I agree with you completely. It’s on a par with declarative statements like “God did/wanted/wants this/that.” One longs for the voice of reason that says: “We don’t know, but here are some hypotheses…” Or even: “We don’t know, but I choose to blinker myself and believe in this particular hypothesis, despite the absence of proof.”

The problem is too much government grant money taken from my taxes to support atheistic scientists.

Theoretical origin of life; new earliest?

by David Turell @, Wednesday, September 27, 2017, 21:39 (2393 days ago) @ David Turell

Graphite that seems to come from living matter is found in rock dated at 3.95 byo:

https://phys.org/news/2017-09-life-earth-date-bn-years.html

"Rudimentary life may have existed on Earth 3.95 billion years ago, a time when our infant planet was being bombarded by comets and had hardly any oxygen, researchers said Wednesday.

"A team presented what they say is the oldest-known fossil evidence for life on the Blue Planet—grains of graphite, a form of carbon, wedged into ancient sedimentary rocks in Labrador, Canada.

"The previous most ancient life traces were reported in March, from a site in Quebec estimated at between 3.8 billion and 4.3 billion years old, though an author of the new study called that dating process "highly controversial."

"'This is the oldest evidence," Tsuyoshi Komiya of The University of Tokyo insisted in an email exchange with AFP.

"Our samples are also the oldest supracrustal rocks preserved on Earth"—a type similar to the formation which contained the Quebec samples.

"Fossil evidence for early organisms is scarce, and rocks that remain from that period are often poorly preserved.

"A key difficulty for scientists on a quest to find the oldest life on Earth is proving that organic remains were produced by living organisms rather than geological processes.

"This field of study is aimed not only at pinpointing the start of life on our planet, but also to shed light on the possibility of life having existed—or still existing—on other planets such as Mars.

"For the new study, Komiya and a team studied graphite, a form of carbon used in pencil lead, in rocks at Saglek Block in Labrador, Canada.

"They measured its isotope composition, the signature of chemical elements, and concluded the graphite was "biogenic"—meaning it was produced by living organisms.

"The identity of the organisms, or what they looked like, remains a mystery.
"We will analyse other isotopes such as nitrogen, sulphur and iron of the organic matter and accompanied minerals to identify the kinds of organisms," said Komiya of the next step.

"'In addition, we can estimate the environment" in which the organisms lived by analysing the chemical composition of the rock itself.

"If the findings are accurate, it means life took hold on Earth just a geological second after its formation some 4.5 billion years ago.

"Before the Quebec fossils, which were also described in Nature, the oldest traces of life were found in Greenland's ice cap and dated to 3.7 billion years ago."

Comment: the theory about Earth formation is that it was formed by bombardment of asteroids and other bodies that were very hot, had melted in the past, and this didn't lessen until 4 byo. That life started immediately afterward suggests that it was driven by design. Plate tectonics which manage the carbon cycle controls required by life are thought to begin at 3.5 byo. Again suggesting a planned design.

Theoretical origin of life; new earliest?

by David Turell @, Friday, September 29, 2017, 14:49 (2391 days ago) @ David Turell

Another article comments:

http://www.the-scientist.com/?articles.view/articleNo/50530/title/In-Canada--Signs-of-L...

"In northeastern Canada, scientists have discovered what they believe are signs that bacterial life existed there 3.95 billions years ago—millions of years before the first fossils appeared in the geological record—according to a study published yesterday (September 27) in Nature.

"Living organisms prefer the most common carbon isotope, 12C, to the rarer, heavier 13C for building their cells. Once decomposed, those 12C-rich organisms contribute to the 12C enrichment of their environment. Finding a sample, such as a mineral, enriched in 12C, therefore, can indicate that living organisms were present in the environment when that sample was formed. Study authors Yuji Sano and Tsuyoshi Komiya from the University of Tokyo found graphite enriched with 12C embedded within 3.95-billion-year-old rocks in Labrador.

"This newly investigated graphite adds new evidence to the start of life on our 4.54-billion-year-old planet. As The Atlantic reports, the complexity of the oldest known fossils, dated to 3.7 billion years ago and found in southwest Greenland, indicates that life had arisen well before they formed.

"Scientists have dated other graphite samples in the Greenland region, known as the Isua Belt, and in hydrothermal vents off the coast of Quebec to 3.8 billion years old or older. One study from 2015 detected graphite thought to be 4.1 billion years old—older than the graphite from the present study—within a gemstone in Western Australia.

"All of these dating studies, The Atlantic notes, are somewhat controversial. In the latest study, the graphite’s purported age comes from the fact that it was lodged in 3.95-billion-year-old rock. But that rock is metamorphic, meaning it has been heated and warped over the years. To rule out the possibility that the graphite was younger but somehow made its way into the older rock, the researchers analyzed the graphite’s crystal structure. They found that the arrangement of graphite grains suggested it had undergone the same heating and warping as the surrounding rock and was likely just as old, according to The Atlantic.

"Another source of controversy is that carbon ratios can vary for reasons unrelated to life. The researchers did not find fossils of the organisms that may have enriched this graphite with 12C, but they suspect that the responsible life forms were microbes.

“'The organisms inhabited an open ocean,” study author Komiya tells Reuters.

“'For the moment, it looks very convincing,” Daniele Pinti, a geochemist at the University of Quebec at Montreal, tells CBC News.

“'The emerging picture from the ancient-rock record is that life was everywhere,” Vickie Bennett from Australian National University, tells The Atlantic. “As far back as the rock record extends—that is, as far back as we can look for direct evidence of early life, we are finding it. Earth has been a biotic, life-sustaining planet since close to its beginning.'” (my bold)

Comment: My bold certainly supports the idea that God saw to it that the Earth could nourish life from near its very beginning.

Theoretical origin of life; new earliest?

by dhw, Saturday, September 30, 2017, 13:16 (2390 days ago) @ David Turell

QUOTE: “'The emerging picture from the ancient-rock record is that life was everywhere,” Vickie Bennett from Australian National University, tells The Atlantic. “As far back as the rock record extends—that is, as far back as we can look for direct evidence of early life, we are finding it. Earth has been a biotic, life-sustaining planet since close to its beginning.[/b]'” (David's bold)

DAVID's comment: My bold certainly supports the idea that God saw to it that the Earth could nourish life from near its very beginning.

Your bold does no such thing! It merely supports the idea that Earth has been a biotic, life-sustaining planet since close to its beginning!

Theoretical origin of life; new earliest?

by David Turell @, Saturday, September 30, 2017, 14:57 (2390 days ago) @ dhw

QUOTE: “'The emerging picture from the ancient-rock record is that life was everywhere,” Vickie Bennett from Australian National University, tells The Atlantic. “As far back as the rock record extends—that is, as far back as we can look for direct evidence of early life, we are finding it. Earth has been a biotic, life-sustaining planet since close to its beginning.[/b]'” (David's bold)

DAVID's comment: My bold certainly supports the idea that God saw to it that the Earth could nourish life from near its very beginning.

dhw: Your bold does no such thing! It merely supports the idea that Earth has been a biotic, life-sustaining planet since close to its beginning!

When you add up all the unusual characteristics of the Earth, compared to other planets, wse are very special. It is easy to see God's work.

Theoretical origin of life; new earliest?

by dhw, Sunday, October 01, 2017, 13:33 (2389 days ago) @ David Turell

QUOTE: “'The emerging picture from the ancient-rock record is that life was everywhere,” Vickie Bennett from Australian National University, tells The Atlantic. “As far back as the rock record extends—that is, as far back as we can look for direct evidence of early life, we are finding it. Earth has been a biotic, life-sustaining planet since close to its beginning.'” (David's bold)

DAVID's comment: My bold certainly supports the idea that God saw to it that the Earth could nourish life from near its very beginning.

dhw: Your bold does no such thing! It merely supports the idea that Earth has been a biotic, life-sustaining planet since close to its beginning!

DAVID: When you add up all the unusual characteristics of the Earth, compared to other planets, we are very special. It is easy to see God's work.

I agree that our planet and all forms of life are very special, but the article is not about all the unusual characteristics, and it says nothing about God’s work. It only suggests that “life was everywhere” and it began earlier than was originally thought. Your comment is no more linked to the article than an atheist saying that “life was everywhere” and may have started earlier than we thought, which supports the idea that chance did it. One should not pretend that a purely scientific observation offers support for either theism or atheism. For all you know, the researchers themselves might be atheists!

Theoretical origin of life; new earliest?

by David Turell @, Sunday, October 01, 2017, 14:19 (2389 days ago) @ dhw


DAVID's comment: My bold certainly supports the idea that God saw to it that the Earth could nourish life from near its very beginning.

dhw: Your bold does no such thing! It merely supports the idea that Earth has been a biotic, life-sustaining planet since close to its beginning!

DAVID: When you add up all the unusual characteristics of the Earth, compared to other planets, we are very special. It is easy to see God's work.

dhw: I agree that our planet and all forms of life are very special, but the article is not about all the unusual characteristics, and it says nothing about God’s work. It only suggests that “life was everywhere” and it began earlier than was originally thought. Your comment is no more linked to the article than an atheist saying that “life was everywhere” and may have started earlier than we thought, which supports the idea that chance did it. One should not pretend that a purely scientific observation offers support for either theism or atheism. For all you know, the researchers themselves might be atheists!

My comment is my thought, not that of the authors as you imply. Have you forgotten that I have the right to interpret scientific findings as I wish?

Theoretical origin of life; new earliest?

by dhw, Monday, October 02, 2017, 13:26 (2388 days ago) @ David Turell

DAVID's comment: My bold certainly supports the idea that God saw to it that the Earth could nourish life from near its very beginning.

dhw: I agree that our planet and all forms of life are very special, but the article is not about all the unusual characteristics, and it says nothing about God’s work. It only suggests that “life was everywhere” and it began earlier than was originally thought. Your comment is no more linked to the article than an atheist saying that “life was everywhere” and may have started earlier than we thought, which supports the idea that chance did it. One should not pretend that a purely scientific observation offers support for either theism or atheism. For all you know, the researchers themselves might be atheists!

DAVID: My comment is my thought, not that of the authors as you imply. Have you forgotten that I have the right to interpret scientific findings as I wish?

Of course you have that right. But if you quote another author and claim that the author’s statement (which you even put in bold) “certainly supports” your own hypothesis, you are misleading your reader. I know you don’t mean it that way, but it is a technique that leads to misrepresentation, as when both theists and atheists claim that Darwinism supports atheism, even though Darwin himself categorically denied that this was so. There can be no justification for claiming that a personal belief is “supported” by someone else’s statement, when the statement offers no such support.

Theoretical origin of life; new earliest?

by David Turell @, Monday, October 02, 2017, 15:25 (2388 days ago) @ dhw

DAVID's comment: My bold certainly supports the idea that God saw to it that the Earth could nourish life from near its very beginning.

dhw: I agree that our planet and all forms of life are very special, but the article is not about all the unusual characteristics, and it says nothing about God’s work. It only suggests that “life was everywhere” and it began earlier than was originally thought. Your comment is no more linked to the article than an atheist saying that “life was everywhere” and may have started earlier than we thought, which supports the idea that chance did it. One should not pretend that a purely scientific observation offers support for either theism or atheism. For all you know, the researchers themselves might be atheists!

DAVID: My comment is my thought, not that of the authors as you imply. Have you forgotten that I have the right to interpret scientific findings as I wish?

dhw: Of course you have that right. But if you quote another author and claim that the author’s statement (which you even put in bold) “certainly supports” your own hypothesis, you are misleading your reader. I know you don’t mean it that way, but it is a technique that leads to misrepresentation, as when both theists and atheists claim that Darwinism supports atheism, even though Darwin himself categorically denied that this was so. There can be no justification for claiming that a personal belief is “supported” by someone else’s statement, when the statement offers no such support.

You miss the point that I have the right to interpret an author's statement as supporting my point of view if I clearly state that is what I am doing. It is my interpretation of his statement. Of course Darwinism supports atheism, whether he meant so or not. Why do you defend him?

Theoretical origin of life; never in water

by David Turell @, Monday, October 02, 2017, 21:48 (2388 days ago) @ David Turell

Water destroys polymerization, so how did life start?

https://www.astrobio.net/news-exclusive/water-can-corrosive-life-alternative-solvents/

"Life on early Earth seems to have begun with a paradox: while life needs water as a solvent, the essential chemical backbones of early life-forming molecules fall apart in water. Our universal solvent, it turns out, can be extremely corrosive.

"Some have pointed to this paradox as a sign that life, or the precursor of life, originated elsewhere and was delivered here via comets or meteorites. Others have looked for solvents that could have the necessary qualities of water without that bond-breaking corrosiveness.

"In recent years the solvent often put forward as the eligible alternative to water is formamide, a clear and moderately irritating liquid consisting of hydrogen, carbon, nitrogen and oxygen. Unlike water, it does not break down the long-chain molecules needed to form the nucleic acids and proteins that make up life’s key initial instruction manual, RNA. Meanwhile it also converts via other useful reactions into key compounds needed to make nucleic acids in the first place.

"Although formamide is common in star-forming regions of space, scientists have struggled to find pathways for it to be prevalent, or even locally concentrated, on early Earth. In fact, it is hardly present on Earth today except as a synthetic chemical for companies.

"New research presented by Zachary Adam, an earth scientist at Harvard University, and Masashi Aono, a complex systems scientist at Earth-Life Science Institute (ELSI) at Tokyo Institute of Technology, has produced formamide by way of a surprising and reproducible pathway: bombardment with radioactive particles.

"The two and their colleagues exposed water and a mixture of two chemicals known to have existed on early Earth (hydrogen cyanide and aqueous acetonitrile) to the high-energy particles emitted from a cylinder of cobalt-60, an artificially produced radioactive isotope commonly used in cancer therapy. The result, they report, was the production of substantial amounts of formamide more quickly than earlier attempts by researchers using theoretical models and in laboratory settings.

"It remains unclear whether early Earth had enough radioactive material in the right places to produce the chemical reactions that led to the formation of formamide. And even if the conditions were right, scientists cannot yet conclude that formamide played an important role in the origin of life.

"Still, the new research furthers the evidence of the possible role of alternative solvents and presents a differing picture of the basis of life. Furthermore, it is suggestive of processes that might be at work on other exoplanets as well – where solvents other than water could, with energy supplied by radioactive sources, provide the necessary setting for simple compounds to be transformed into far more complex building blocks.

***

"Adam and Aono remain agnostic about where the formamide-producing radioactive particles came from. But they are convinced that it is entirely possible that such reactions took place and helped produce an environment where each of the backbone precursors of RNA could readily be found in close quarters.

"Current scientific thinking about how formamide appeared on Earth focuses on limited arrival via asteroid impacts or through the concentration of the chemical in evaporated water-formamide mixtures in desert-like conditions. Adam acknowledges that the prevailing scientific consensus points to low amounts of formamide on early Earth.

“'We are not trying to argue to the contrary,” he said, “but we are trying to say that it may not matter.”

"If you have a unique place (or places) on the Earth creating significant amounts of formamide over a long period of time through radiolysis, then an opportunity exists for the onset of some unique chemistry that can support the production of essential precursor compounds for life, Adam said.

“'So, the argument then shifts to— how likely was it that this unique place existed? We only need one special location on the entire planet to meet these circumstances,” he said.
After that, the system set into motion would have the ability to bring together the chemical building blocks of life."

Comment: This study shows how difficult the origin of life is as a subject. Water is a major problem. Putting together all of the factors present in this study to start life doesn't tell us where the energy comes from for life to continue and spread from this one imaginary special spot. Chance can't work to start life, but that is what this study asks.

Theoretical origin of life; new earliest? More comment

by David Turell @, Monday, October 02, 2017, 23:21 (2388 days ago) @ David Turell

Even though there are new arguments against the early life interpretation, it appears most likely that life began earlier than thought until recently:

https://www.newscientist.com/article/2149168-life-may-have-begun-millions-of-years-earl...

"Ben Pearce of McMaster University in Hamilton, Ontario, Canada, and colleagues simulated conditions on early Earth to find out how readily the key molecules of life could have formed. They focused on “warm little ponds” on land, which are one of the suspected sites of the origin of life – the other being deep-sea vents.

"Pearce tackled the formation of RNA, a close cousin of DNA that is widely thought to have been the basis for the first life. Many of the building blocks of RNA are found in asteroids and meteoroids, so Pearce calculated how much could have been delivered to Earth by impacting rocks – of which there were plenty during Earth’s first billion years – and then how much could have accumulated in ponds, given the molecules’ fragility and tendency to leech away.

"He concluded that RNA could have formed within a handful of years of major impacts, implying that life could have formed very early in Earth’s history.

"There are two problems with this argument, says John Sutherland of the MRC Laboratory of Molecular Biology in Cambridge, UK.

"One is that organic compounds carried in meteorites would not necessarily survive the impact. “Large impactors that would have delivered the most organic material, collide with such energy that their organic cargo is atomised,” says Sutherland. (my bold)

" The other problem is that Pearce simulated the wrong chemical process, Sutherland says. Pearce assumed that the first step in making RNA is linking together smaller molecules called nucleobases and ribose, but this “was experimentally shown not to work ages ago”, says Sutherland. In 2009 Sutherland demonstrated an alternative way of making RNA from simpler building blocks. “These authors are still assuming the old model,” he says.

"A second study, published last Wednesday, claims to have identified the oldest firm evidence of life – dating back 3.95 billion years. That is only half a billion years after the Earth formed. Reliable fossils of microorganisms have been dated to roughly 3.5 billion years ago, but the evidence for older life has been less clear.

"Tsuyoshi Komiya of the University of Tokyo, Japan, and colleagues studied graphite found in ancient rocks in northern Labrador, Canada. Graphite is a crystalline form of carbon used to make pencil leads. It contains two forms of carbon: carbon-12 and carbon-13. The samples Komiya looked at had relatively little carbon-13. This, the team claims, is evidence that life was present. And not just any life: organisms that were taking in carbon from their surroundings and using it as raw material to make new organic compounds.

"This result is surprising for several reasons. First, at this time, Earth was being bombarded by large rocks from space, which would have battered the young planet’s surface. If life was present, it must have been impressively resilient.

"But only if Komiya’s study is correct. His only evidence for the existence of life is the unusual ratio of carbon isotopes, and this may not be definitive. “There are many ways in which abiotic processes can produce such an imbalance, so to conclude that it is evidence for life is simply not justified,” says Sutherland.

"Sutherland says a set of chemical reactions known as the Fischer-Tropsch process could be responsible. This process makes organic compounds from hydrogen and carbon monoxide, and show a similar bias towards carbon-12. It is known to occur naturally, for instance in meteorites.

"Komiya’s team assumed these reactions were not responsible for their results, on the grounds that there cannot have been hydrogen in Earth’s atmosphere. But Sutherland says there could well have been. If there was water and carbon monoxide in the air, and hot iron from meteorite impacts to act as a catalyst, “hydrogen can easily be generated”.

"Nevertheless, evidence is mounting that life was present earlier than 3.5 billion years ago. For instance, in 2016 fossilised stromatolites – layered mounds made by microbes living in sediments – were controversially claimed to have been found in 3.7-billion-year-old rocks. Then in March 2017, researchers described apparent fossilised microbes from rocks that were 3.77 to 4.28 billion years old. That claim also divided opinion."

Comment: No question life appeared very early under severe early Earth conditions. Not by chance, as there were so many problems to overcome. Note my bold about meteorites destroying any organic cargo. It must be God at work.

Theoretical origin of life; new earliest?

by dhw, Tuesday, October 03, 2017, 13:25 (2387 days ago) @ David Turell

dhw: […] if you quote another author and claim that the author’s statement (which you even put in bold) “certainly supports” your own hypothesis, you are misleading your reader. I know you don’t mean it that way, but it is a technique that leads to misrepresentation, as when both theists and atheists claim that Darwinism supports atheism, even though Darwin himself categorically denied that this was so. There can be no justification for claiming that a personal belief is “supported” by someone else’s statement, when the statement offers no such support.

DAVID: You miss the point that I have the right to interpret an author's statement as supporting my point of view if I clearly state that is what I am doing. It is my interpretation of his statement. Of course Darwinism supports atheism, whether he meant so or not. Why do you defend him?

Here is the statement you put in bold: ‘Earth has been a biotic, life-sustaining planet since close to its beginning.'
Here is your comment: "My bold certainly supports the idea that God saw to it that the Earth could nourish life from near its very beginning."

Where have you clearly stated that you are interpreting the statement, and how does the statement clearly support the hypothesis that God did it? As for Darwinism, no it does not support atheism. Even the church can accommodate evolution into its doctrines, and so do you. We both reject random mutations and gradualism, but that does not stop either of us from formulating evolutionary hypotheses that include God. Atheists like to twist Darwin’s theory to suit their own agenda, just as you have done with the statement you claim gives support to your theism. However, I don’t want you to take this as an attack on your integrity, which is beyond question. I am simply pointing out that all of us should be careful not to disguise our opinions as scientific facts, especially when quoting others who might even disagree with those opinions. You know what a stickler I am for accurate expression.

Theoretical origin of life; new earliest?

by David Turell @, Tuesday, October 03, 2017, 14:15 (2387 days ago) @ dhw

dhw: […] if you quote another author and claim that the author’s statement (which you even put in bold) “certainly supports” your own hypothesis, you are misleading your reader. I know you don’t mean it that way, but it is a technique that leads to misrepresentation, as when both theists and atheists claim that Darwinism supports atheism, even though Darwin himself categorically denied that this was so. There can be no justification for claiming that a personal belief is “supported” by someone else’s statement, when the statement offers no such support.

DAVID: You miss the point that I have the right to interpret an author's statement as supporting my point of view if I clearly state that is what I am doing. It is my interpretation of his statement. Of course Darwinism supports atheism, whether he meant so or not. Why do you defend him?

Here is the statement you put in bold: ‘Earth has been a biotic, life-sustaining planet since close to its beginning.'
Here is your comment: "My bold certainly supports the idea that God saw to it that the Earth could nourish life from near its very beginning."

dhw: Where have you clearly stated that you are interpreting the statement, and how does the statement clearly support the hypothesis that God did it? As for Darwinism, no it does not support atheism. Even the church can accommodate evolution into its doctrines, and so do you. We both reject random mutations and gradualism, but that does not stop either of us from formulating evolutionary hypotheses that include God. Atheists like to twist Darwin’s theory to suit their own agenda, just as you have done with the statement you claim gives support to your theism. However, I don’t want you to take this as an attack on your integrity, which is beyond question. I am simply pointing out that all of us should be careful not to disguise our opinions as scientific facts, especially when quoting others who might even disagree with those opinions. You know what a stickler I am for accurate expression.

First, we both have integrity in this discussion, but you should be clearly aware that I use this forum to present science all the time that demonstrates the complexity of living biology as a form of propaganda that design is required, to convince others that my belief is correct. As for Darwin, he proposed a chance evolutionary process which dismisses God out of hand. The issue is 'chance' or 'randomness' at the root of evolution not the process itself. My comment above covered that point.

Theoretical origin of life; new earliest?

by dhw, Wednesday, October 04, 2017, 14:09 (2386 days ago) @ David Turell

dhw: [...] I don’t want you to take this as an attack on your integrity, which is beyond question. I am simply pointing out that all of us should be careful not to disguise our opinions as scientific facts, especially when quoting others who might even disagree with those opinions. You know what a stickler I am for accurate expression.

DAVID: First, we both have integrity in this discussion, but you should be clearly aware that I use this forum to present science all the time that demonstrates the complexity of living biology as a form of propaganda that design is required, to convince others that my belief is correct.

And I for one am not only immensely grateful for the way in which you keep us informed of all the new developments, but also accept the complexity argument as a powerful case for the existence of a designer. That is why I cannot embrace atheism, but I have also made clear many times why I cannot embrace theism either. My objection here was simply to your claim that the author’s neutral statement supported your view that God did it.

DAVID: As for Darwin, he proposed a chance evolutionary process which dismisses God out of hand. The issue is 'chance' or 'randomness' at the root of evolution not the process itself. My comment above covered that point.

Darwin never dismisses God out of hand. He was so anxious to avoid having his theory misinterpreted that in later editions he frequently refers to the Creator, and emphasizes that his theory is NOT atheistic. I have frequently quoted these passages, and will do so yet again if you want me to. We both disagree with his hypothesis concerning random mutations and gradualism, but the reason why you find that hypothesis atheistic is that it does not conform to your insistence that God controlled every innovation, lifestyle and natural wonder in order to keep life going until he produced the human brain. The idea that chance governed the COURSE (as opposed to the genesis) of evolution could simply mean that was how your God designed it. Opposition to your hypothesis does not automatically mean that the opponent "dismisses God out of hand".

Theoretical origin of life; new earliest?

by David Turell @, Wednesday, October 04, 2017, 19:01 (2386 days ago) @ dhw

DAVID: As for Darwin, he proposed a chance evolutionary process which dismisses God out of hand. The issue is 'chance' or 'randomness' at the root of evolution not the process itself. My comment above covered that point.

dhw: Darwin never dismisses God out of hand. He was so anxious to avoid having his theory misinterpreted that in later editions he frequently refers to the Creator, and emphasizes that his theory is NOT atheistic. I have frequently quoted these passages, and will do so yet again if you want me to. We both disagree with his hypothesis concerning random mutations and gradualism, but the reason why you find that hypothesis atheistic is that it does not conform to your insistence that God controlled every innovation, lifestyle and natural wonder in order to keep life going until he produced the human brain. The idea that chance governed the COURSE (as opposed to the genesis) of evolution could simply mean that was how your God designed it. Opposition to your hypothesis does not automatically mean that the opponent "dismisses God out of hand".

You have recognized Darwin did not mention a creator in his first edition. He was forced to do so later because of the reaction to his theory. This is the commentary from many reviewers. The atheists use of Darwin is not due to my reaction in accepting god.. I'm simply reporting how they use Darwin. And I see how that use conforms to his theory. I understand your theory that God might have allowed chance. I just can't believe that if He bothered to do all the creating, He would then give up control over the course of events. But the possibility of chance allows for atheism; that is obvious.

Theoretical origin of life; new earliest?

by dhw, Thursday, October 05, 2017, 13:28 (2385 days ago) @ David Turell

DAVID: As for Darwin, he proposed a chance evolutionary process which dismisses God out of hand. The issue is 'chance' or 'randomness' at the root of evolution not the process itself. My comment above covered that point.

dhw: Darwin never dismisses God out of hand. He was so anxious to avoid having his theory misinterpreted that in later editions he frequently refers to the Creator, and emphasizes that his theory is NOT atheistic. I have frequently quoted these passages, and will do so yet again if you want me to. We both disagree with his hypothesis concerning random mutations and gradualism, but the reason why you find that hypothesis atheistic is that it does not conform to your insistence that God controlled every innovation, lifestyle and natural wonder in order to keep life going until he produced the human brain. The idea that chance governed the COURSE (as opposed to the genesis) of evolution could simply mean that was how your God designed it. Opposition to your hypothesis does not automatically mean that the opponent "dismisses God out of hand".

DAVID: You have recognized Darwin did not mention a creator in his first edition. He was forced to do so later because of the reaction to his theory. This is the commentary from many reviewers.

Nevertheless, he only argues that random mutations are the means by which evolution progresses, which does not “dismiss God out of hand”. It only dismisses your contention that God controls everything.

DAVID: The atheists use of Darwin is not due to my reaction in accepting god. I'm simply reporting how they use Darwin. And I see how that use conforms to his theory.

Of course they use his theory to suit their agenda. But the theory itself does not “dismiss God out of hand”.

DAVID: I understand your theory that God might have allowed chance. I just can't believe that if He bothered to do all the creating, He would then give up control over the course of events. But the possibility of chance allows for atheism; that is obvious.

Indeed it does, just as it allows for theism – but the fact that you can’t believe your God would create a spectacle whose unpredictability would add to the interest and wonderment does not mean the theory “dismisses God out of hand”. It simply means God's methods and motives do not conform to your interpretation of them.

Theoretical origin of life; new earliest?

by David Turell @, Thursday, October 05, 2017, 15:05 (2385 days ago) @ dhw


DAVID: I understand your theory that God might have allowed chance. I just can't believe that if He bothered to do all the creating, He would then give up control over the course of events. But the possibility of chance allows for atheism; that is obvious.

dhw: Indeed it does, just as it allows for theism – but the fact that you can’t believe your God would create a spectacle whose unpredictability would add to the interest and wonderment does not mean the theory “dismisses God out of hand”. It simply means God's methods and motives do not conform to your interpretation of them.

Your interpretation of God does not fit mine. I firmly believe chance is never involved. See comments in Evolution and humans today.

Theoretical origin of life; new earliest?

by dhw, Friday, October 06, 2017, 13:36 (2384 days ago) @ David Turell

DAVID: I understand your theory that God might have allowed chance. I just can't believe that if He bothered to do all the creating, He would then give up control over the course of events. But the possibility of chance allows for atheism; that is obvious.

dhw: Indeed it does, just as it allows for theism – but the fact that you can’t believe your God would create a spectacle whose unpredictability would add to the interest and wonderment does not mean the theory “dismisses God out of hand”. It simply means God's methods and motives do not conform to your interpretation of them.

DAVID: Your interpretation of God does not fit mine. I firmly believe chance is never involved. See comments in Evolution and humans today.

You had said that Darwin’s theory “dismisses God out of hand”. It doesn’t. Even the hypothesis of random mutations, which you and I reject, does not dismiss God out of hand, as Darwin himself makes very clear. Your firm belief that your God designed absolutely everything, and left nothing to chance (I wonder if this now includes every environmental change), is of course your prerogative, but it does not mean that whoever disagrees with your interpretation of God “dismisses God out of hand”.

Theoretical origin of life; new earliest?

by David Turell @, Friday, October 06, 2017, 21:31 (2384 days ago) @ dhw

DAVID: I understand your theory that God might have allowed chance. I just can't believe that if He bothered to do all the creating, He would then give up control over the course of events. But the possibility of chance allows for atheism; that is obvious.

dhw: Indeed it does, just as it allows for theism – but the fact that you can’t believe your God would create a spectacle whose unpredictability would add to the interest and wonderment does not mean the theory “dismisses God out of hand”. It simply means God's methods and motives do not conform to your interpretation of them.

DAVID: Your interpretation of God does not fit mine. I firmly believe chance is never involved. See comments in Evolution and humans today.

dhw: You had said that Darwin’s theory “dismisses God out of hand”. It doesn’t. Even the hypothesis of random mutations, which you and I reject, does not dismiss God out of hand, as Darwin himself makes very clear. Your firm belief that your God designed absolutely everything, and left nothing to chance (I wonder if this now includes every environmental change), is of course your prerogative, but it does not mean that whoever disagrees with your interpretation of God “dismisses God out of hand”.

Gradual change by chance mutations is still evolution by chance. That is why atheism sticks to a Darwin style evolutionary process. Pure Darwinism supports atheism, no matter how Darwin himself felt as he reacted to criticism.

Theoretical origin of life; new earliest?

by dhw, Saturday, October 07, 2017, 10:22 (2384 days ago) @ David Turell

dhw: You had said that Darwin’s theory “dismisses God out of hand”. It doesn’t. Even the hypothesis of random mutations, which you and I reject, does not dismiss God out of hand, as Darwin himself makes very clear. Your firm belief that your God designed absolutely everything, and left nothing to chance (I wonder if this now includes every environmental change), is of course your prerogative, but it does not mean that whoever disagrees with your interpretation of God “dismisses God out of hand”.

DAVID: Gradual change by chance mutations is still evolution by chance.

But it does not explain how life and the mechanisms for chance mutations came into existence, and that was not Darwin’s focus: “How a nerve comes to be sensitive to light, hardly concerns us more than how life itself first originated.” (Difficulties on Theory)

DAVID: That is why atheism sticks to a Darwin style evolutionary process. Pure Darwinism supports atheism, no matter how Darwin himself felt as he reacted to criticism.

What do you mean by “pure Darwinism”? Of course atheists twist the theory to support their atheism. Now find me one single passage in The Origin of Species or anywhere else in which Darwin – the prime exponent of “pure Darwinism” – dismisses God out of hand. (Elsewhere he does attack religious dogma, but then so do you and lots of other theists and agnostics.)

Theoretical origin of life; new earliest?

by David Turell @, Saturday, October 07, 2017, 14:32 (2383 days ago) @ dhw

dhw: You had said that Darwin’s theory “dismisses God out of hand”. It doesn’t. Even the hypothesis of random mutations, which you and I reject, does not dismiss God out of hand, as Darwin himself makes very clear. Your firm belief that your God designed absolutely everything, and left nothing to chance (I wonder if this now includes every environmental change), is of course your prerogative, but it does not mean that whoever disagrees with your interpretation of God “dismisses God out of hand”.

DAVID: Gradual change by chance mutations is still evolution by chance.

dhw: But it does not explain how life and the mechanisms for chance mutations came into existence, and that was not Darwin’s focus: “How a nerve comes to be sensitive to light, hardly concerns us more than how life itself first originated.” (Difficulties on Theory)

It is unusual for you to tie origin of life into Darwin! God did it dos not solve Darwin's problem.


DAVID: That is why atheism sticks to a Darwin style evolutionary process. Pure Darwinism supports atheism, no matter how Darwin himself felt as he reacted to criticism.

dhw: What do you mean by “pure Darwinism”? Of course atheists twist the theory to support their atheism. Now find me one single passage in The Origin of Species or anywhere else in which Darwin – the prime exponent of “pure Darwinism” – dismisses God out of hand. (Elsewhere he does attack religious dogma, but then so do you and lots of other theists and agnostics.)

You miss the point. Darwinism is how Darwin is interpreted by atheists to use him. His theory opens the door. Of course Darwin cannot defend himself.

Theoretical origin of life; new earliest?

by dhw, Sunday, October 08, 2017, 13:23 (2382 days ago) @ David Turell

dhw: You had said that Darwin’s theory “dismisses God out of hand”. It doesn’t. […]

DAVID: Gradual change by chance mutations is still evolution by chance.

dhw: But it does not explain how life and the mechanisms for chance mutations came into existence, and that was not Darwin’s focus: “How a nerve comes to be sensitive to light, hardly concerns us more than how life itself first originated.” (Difficulties on Theory)

DAVID: It is unusual for you to tie origin of life into Darwin! God did it does not solve Darwin's problem.

What problem are you referring to? The problem Darwin set out to solve was how all the different life forms came into being (most people at the time believed in separate creation) – i.e. Chapter Two in life’s history. In Origin of Species he explicitly did NOT set out to explain Chapter One – i.e. how the first form(s) of life and the mechanisms for evolution originated. His theory of evolution is as open to theism as it is to atheism. See below.

DAVID: That is why atheism sticks to a Darwin style evolutionary process. Pure Darwinism supports atheism, no matter how Darwin himself felt as he reacted to criticism.

dhw: What do you mean by “pure Darwinism”? Of course atheists twist the theory to support their atheism. Now find me one single passage in The Origin of Species or anywhere else in which Darwin – the prime exponent of “pure Darwinism” – dismisses God out of hand. (Elsewhere he does attack religious dogma, but then so do you and lots of other theists and agnostics.)

DAVID: You miss the point. Darwinism is how Darwin is interpreted by atheists to use him. His theory opens the door. Of course Darwin cannot defend himself.

The theory of common descent as opposed to separate creation is interpreted by theists, including yourself and the Pope, as perfectly compatible with the existence of God. The question of the origin of life and of the mechanisms of evolution remains unanswered, but God could have devised a system of random mutations (Darwin) just as easily as a computer programme (you) or an autonomous inventive mechanism (me). Darwinism IS no more “how Darwinism is interpreted” by theists/atheists than your God IS how he is interpreted by atheists, Christians, Hindus, Muslims, and panentheists. Most of reality (and in God’s case, possibly non-reality) is open to a thousand different interpretations. That does not mean reality IS how it is interpreted by every different interpreter.

And finally, to remind you of the starting point of this particular discussion: there is absolutely no justification for saying that Darwin’s theory “dismisses God out of hand”. Come on, be fair to Darwin for a change!

Theoretical origin of life; new earliest?

by David Turell @, Monday, October 09, 2017, 14:39 (2381 days ago) @ dhw


DAVID: You miss the point. Darwinism is how Darwin is interpreted by atheists to use him. His theory opens the door. Of course Darwin cannot defend himself.

dhw: The theory of common descent as opposed to separate creation is interpreted by theists, including yourself and the Pope, as perfectly compatible with the existence of God. The question of the origin of life and of the mechanisms of evolution remains unanswered, but God could have devised a system of random mutations (Darwin) just as easily as a computer programme (you) or an autonomous inventive mechanism (me). Darwinism IS no more “how Darwinism is interpreted” by theists/atheists than your God IS how he is interpreted by atheists, Christians, Hindus, Muslims, and panentheists. Most of reality (and in God’s case, possibly non-reality) is open to a thousand different interpretations. That does not mean reality IS how it is interpreted by every different interpreter.

And finally, to remind you of the starting point of this particular discussion: there is absolutely no justification for saying that Darwin’s theory “dismisses God out of hand”. Come on, be fair to Darwin for a change!

Come on. Darwin is interpreted as a chance mechanism. Atheists use it to support their point of view. That is my point of view about Darwin. I'm not unfair to him. What I accept from him is common descent, nothing more.

Theoretical origin of life; new earliest?

by dhw, Tuesday, October 10, 2017, 13:54 (2380 days ago) @ David Turell

dhw: And finally, to remind you of the starting point of this particular discussion: there is absolutely no justification for saying that Darwin’s theory “dismisses God out of hand”. Come on, be fair to Darwin for a change!

DAVID: Come on. Darwin is interpreted as a chance mechanism. Atheists use it to support their point of view. That is my point of view about Darwin. I'm not unfair to him. What I accept from him is common descent, nothing more.

DARWIN: “I see no good reason why the views given in this volume should shock the religious feelings of anyone.”

DARWIN: “a celebrated author and divine* has written to me that ‘he has gradually learnt to see that it is just as noble a conception of the Deity to believe that He created a few original forms capable of self-development into other and needful forms, as to believe that He required a fresh act of creation to supply the voids caused by the action of His laws.’

*This was Charles Kingsley, author of The Water Babies, with the beautifully named Mrs Do-As-You-Would-Be-Done-By. (Please note "capable of self-development" as well.)

DARWIN: To my mind it accords better with what we know of the laws impressed on matter by the Creator, that the production and extinction of the past and present inhabitants of the world should have been due to secondary causes, like those determining the birth and death of the individual.’

DARWIN: There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one.

DAVID TURELL: Darwin’s theory “dismisses God out of hand”.

There are different speculations as to why Darwin incorporated such passages into later editions of Origin (towards the end of his life he said he had never been an atheist, but regarded himself as an agnostic), but I fail to see how anyone can interpret them as meaning that his theory dismisses God out of hand. It is atheistic interpreters who dismiss God out of hand. There are plenty of theists who accept his theory as perfectly compatible with belief in God, and share the view expressed in the third of these quotations.

Theoretical origin of life; new earliest?

by David Turell @, Tuesday, October 10, 2017, 14:32 (2380 days ago) @ dhw

dhw: And finally, to remind you of the starting point of this particular discussion: there is absolutely no justification for saying that Darwin’s theory “dismisses God out of hand”. Come on, be fair to Darwin for a change!

DAVID: Come on. Darwin is interpreted as a chance mechanism. Atheists use it to support their point of view. That is my point of view about Darwin. I'm not unfair to him. What I accept from him is common descent, nothing more.

DARWIN: “I see no good reason why the views given in this volume should shock the religious feelings of anyone.”

DARWIN: “a celebrated author and divine* has written to me that ‘he has gradually learnt to see that it is just as noble a conception of the Deity to believe that He created a few original forms capable of self-development into other and needful forms, as to believe that He required a fresh act of creation to supply the voids caused by the action of His laws.’

*This was Charles Kingsley, author of The Water Babies, with the beautifully named Mrs Do-As-You-Would-Be-Done-By. (Please note "capable of self-development" as well.)

DARWIN: To my mind it accords better with what we know of the laws impressed on matter by the Creator, that the production and extinction of the past and present inhabitants of the world should have been due to secondary causes, like those determining the birth and death of the individual.’

DARWIN: There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one.

DAVID TURELL: Darwin’s theory “dismisses God out of hand”.

dhw: There are different speculations as to why Darwin incorporated such passages into later editions of Origin (towards the end of his life he said he had never been an atheist, but regarded himself as an agnostic), but I fail to see how anyone can interpret them as meaning that his theory dismisses God out of hand. It is atheistic interpreters who dismiss God out of hand. There are plenty of theists who accept his theory as perfectly compatible with belief in God, and share the view expressed in the third of these quotations.

I don't know why you struggle. I'll accept Darwin as agnostic. What Darwin thought in his later writings does not change what atheists make of Darwin's theory. Yes, there are theistic Darwinists. My comments relate to atheists and the way current Darwinism comes across.

Theoretical origin of life; new earliest?

by dhw, Wednesday, October 11, 2017, 13:33 (2379 days ago) @ David Turell

DAVID: I don't know why you struggle. I'll accept Darwin as agnostic. What Darwin thought in his later writings does not change what atheists make of Darwin's theory. Yes, there are theistic Darwinists. My comments relate to atheists and the way current Darwinism comes across.

This discussion concerns your comment that Darwin’s theory “dismisses God out of hand.” It doesn’t. That is the only point of disagreement.

Theoretical origin of life; new earliest?

by David Turell @, Wednesday, October 11, 2017, 14:42 (2379 days ago) @ dhw

DAVID: I don't know why you struggle. I'll accept Darwin as agnostic. What Darwin thought in his later writings does not change what atheists make of Darwin's theory. Yes, there are theistic Darwinists. My comments relate to atheists and the way current Darwinism comes across.

dhw: This discussion concerns your comment that Darwin’s theory “dismisses God out of hand.” It doesn’t. That is the only point of disagreement.

My statement:"As for Darwin, he proposed a chance evolutionary process which dismisses God out of hand." I'll stand by it. Chance rules out God.

Theoretical origin of life; new earliest?

by dhw, Thursday, October 12, 2017, 13:48 (2378 days ago) @ David Turell

DAVID: I don't know why you struggle. I'll accept Darwin as agnostic. What Darwin thought in his later writings does not change what atheists make of Darwin's theory. Yes, there are theistic Darwinists. My comments relate to atheists and the way current Darwinism comes across.

dhw: This discussion concerns your comment that Darwin’s theory “dismisses God out of hand.” It doesn’t. That is the only point of disagreement.

DAVID: My statement:"As for Darwin, he proposed a chance evolutionary process which dismisses God out of hand." I'll stand by it. Chance rules out God.

Not if the author explicitly allows for the possibility that God created the mechanism for the evolutionary process! Yet again, you are assuming that anyone who disagrees with your hypothesis of a divine 3.8-billion-year-old computer programme to control the whole of evolution (plus dabbles) is an atheist! It is chance origin of life that would dismiss God out of hand, not random mutations. Darwin's theory concerns Chapter Two of life, not Chapter One.

Theoretical origin of life; new earliest?

by David Turell @, Thursday, October 12, 2017, 14:23 (2378 days ago) @ dhw

DAVID: I don't know why you struggle. I'll accept Darwin as agnostic. What Darwin thought in his later writings does not change what atheists make of Darwin's theory. Yes, there are theistic Darwinists. My comments relate to atheists and the way current Darwinism comes across.

dhw: This discussion concerns your comment that Darwin’s theory “dismisses God out of hand.” It doesn’t. That is the only point of disagreement.

DAVID: My statement:"As for Darwin, he proposed a chance evolutionary process which dismisses God out of hand." I'll stand by it. Chance rules out God.

dhw: Not if the author explicitly allows for the possibility that God created the mechanism for the evolutionary process! Yet again, you are assuming that anyone who disagrees with your hypothesis of a divine 3.8-billion-year-old computer programme to control the whole of evolution (plus dabbles) is an atheist! It is chance origin of life that would dismiss God out of hand, not random mutations. Darwin's theory concerns Chapter Two of life, not Chapter One.

I'm simply observing the way atheists use Darwin. And you forgot my point that origin of life and evolution are a continuum. Darwin's life popped up in some warm pond, and he implied chance!

Theoretical origin of life; new earliest?

by dhw, Friday, October 13, 2017, 10:44 (2378 days ago) @ David Turell

DAVID: My statement:"As for Darwin, he proposed a chance evolutionary process which dismisses God out of hand." I'll stand by it. Chance rules out God.
dhw: Not if the author explicitly allows for the possibility that God created the mechanism for the evolutionary process! Yet again, you are assuming that anyone who disagrees with your hypothesis of a divine 3.8-billion-year-old computer programme to control the whole of evolution (plus dabbles) is an atheist! It is chance origin of life that would dismiss God out of hand, not random mutations. Darwin's theory concerns Chapter Two of life, not Chapter One.
DAVID: I'm simply observing the way atheists use Darwin.

Then please say it is atheists who dismiss God out of hand, not Darwin’s proposal of random mutations that dismisses God out of hand. It doesn’t.

DAVID: And you forgot my point that origin of life and evolution are a continuum. Darwin's life popped up in some warm pond, and he implied chance!

There is a continuum between the origin of life and Darwin’s random mutations or your 3.8-billion-year computer programme or my autonomous inventive mechanism (cellular intelligence). The agnostic Darwin never committed himself to an atheistic theory concerning the origin of life. Here is the warm pond reference:

Did life evolve in a `warm little pond'? - Scientific ...
https://blogs.scientificamerican.com/thoughtomics/did-life-evolve...

"But if (and oh what a big if) we could conceive in some warm little pond with all sorts of ammonia and phosphoric salts, light, heat, electricity etcetera present, that a protein compound was chemically formed, ready to undergo still more complex changes, at the present day such matter wd be instantly devoured, or absorbed, which would not have been the case before living creatures were formed [..] " Darwin, Letter to Joseph Hooker (1871)

A “big if”. And does it not occur to you that if God did create life, he would have had to assemble all the ingredients in a suitable location on Earth?
Darwin avoided publishing any theory about the origin, but if you are really interested in his vacillating views, here is an article with all the information you could wish for.
Charles Darwin and the Origin of Life - PubMed Central …
www.ncbi.nlm.nih.gov › Journal List › Springer Open Choice

(I'm afraid I can't get a direct link with this, but if you google it yourself, you'll be able to find the article. No doubt it's my usual technical incompetence. Sorry!)

In 1837 Darwin expressed the view that spontaneous generation was “not improbable”. That is the nearest he gets to “implying chance”. However, he became increasingly sceptical. Here is an extract from a letter he wrote to the Athenaeum in 1863:

"Your reviewer believes that certain lowly organized animals have been generated spontaneously—that is, without pre-existing parents—during each geological period in slimy ooze. A mass of mud with matter decaying and undergoing complex chemical changes is a fine hiding-place for obscurity of ideas. But let us face the problem boldly. He who believes that organic beings have been produced during each geological period from dead matter must believe that the first being thus arose. There must have been a time when inorganic elements alone existed on our planet: let any assumptions be made, such as that the reeking atmosphere was charged with carbonic acid, nitrogenized compounds, phosphorus, &c. Now is there a fact, or a shadow of a fact, supporting the belief that these elements, without the presence of any organic compounds, and acted on only by known forces, could produce a living creature? At present it is to us a result absolutely inconceivable."

QUOTE: He was to maintain the same attitude for many years to come, as shown by the letter mailed on March 28, 1882, near the end of his life, to George Charles Wallich (de Beer 1959). In it Darwin wrote that,
«My dear Sir,
You expressed quite correctly my views where you say that I had intentionally left the question of the Origin of Life uncanvassed as being altogether ultra vires in the present state of our knowledge, & that I dealt only with the manner of succession. I have met with no evidence that seems in the least trustworthy, in favour of the so-called Spontaneous generation.”

I do wish that you and other anti-Darwinians would read what the agnostic Darwin wrote instead of blithely following one another.
xxxxxx
QUOTE (re “blind cave fish”):"Shuker is suspicious of some efforts to promote the idea of an “extended evolutionary synthesis”. He thinks some people are trying sneak religious ideas back into evolutionary theory." (DAVID’s bold)

DAVID’s comment: Once again we see the battle between atheistic Neo-Darwin defenders and those who champion epigenetics as a definitive adaptive mechanism that might represent religious ideas. This applies directly to our discussion about Darwinists and atheism. Random mutation and natural selection for them obviously denies God.

I am not disputing that atheists use evolutionary theory to support their atheism. Once more: I am disputing your claim that Darwin’s theory of random mutations and natural selection “dismisses God out of hand”. It is the atheistic interpretation that dismisses God out of hand. Since you appear to agree, I suggest we leave it at that.

Theoretical origin of life; new earliest?

by David Turell @, Friday, October 13, 2017, 15:31 (2377 days ago) @ dhw
edited by David Turell, Friday, October 13, 2017, 15:38

dhw: There is a continuum between the origin of life and Darwin’s random mutations or your 3.8-billion-year computer programme or my autonomous inventive mechanism (cellular intelligence). The agnostic Darwin never committed himself to an atheistic theory concerning the origin of life. Here is the warm pond reference:

Did life evolve in a `warm little pond'? - Scientific ...
https://blogs.scientificamerican.com/thoughtomics/did-life-evolve...

"But if (and oh what a big if) we could conceive in some warm little pond with all sorts of ammonia and phosphoric salts, light, heat, electricity etcetera present, that a protein compound was chemically formed, ready to undergo still more complex changes, at the present day such matter wd be instantly devoured, or absorbed, which would not have been the case before living creatures were formed [..] " Darwin, Letter to Joseph Hooker (1871)

I've read this letter before.


dhw: A “big if”. And does it not occur to you that if God did create life, he would have had to assemble all the ingredients in a suitable location on Earth?

Recent commentary suggests multiple spots, which really makes good sense.

xxxxxx
QUOTE (re “blind cave fish”):"Shuker is suspicious of some efforts to promote the idea of an “extended evolutionary synthesis”. He thinks some people are trying sneak religious ideas back into evolutionary theory." (DAVID’s bold)

DAVID’s comment: Once again we see the battle between atheistic Neo-Darwin defenders and those who champion epigenetics as a definitive adaptive mechanism that might represent religious ideas. This applies directly to our discussion about Darwinists and atheism. Random mutation and natural selection for them obviously denies God.

dhw: I am not disputing that atheists use evolutionary theory to support their atheism. Once more: I am disputing your claim that Darwin’s theory of random mutations and natural selection “dismisses God out of hand”. It is the atheistic interpretation that dismisses God out of hand. Since you appear to agree, I suggest we leave it at that.

Thank you for your review of Darwin and your view of him. We shall leave it at that since we interpret him in different ways. By the way I was able to review the article you had trouble getting, by Googling the title of the article you presented.

Theoretical origin of life; RNA world won't work

by David Turell @, Thursday, November 02, 2017, 22:40 (2357 days ago) @ David Turell

The latest papers suggest a different approach, saying RNA first doesn't work:

https://www.sciencedaily.com/releases/2017/11/171101160756.htm

"Life on Earth originated in an intimate partnership between the nucleic acids (genetic instructions for all organisms) and small proteins called peptides, according to two new papers from biochemists and biologists at the University of North Carolina at Chapel Hill and the University of Auckland. Their "peptide-RNA" hypothesis contradicts the widely-held "RNA-world" hypothesis, which states that life originated from nucleic acids and only later evolved to include proteins.

"The new papers -- one in Molecular Biology and Evolution, the other in Biosystems -- show how recent experimental studies of two enzyme superfamilies surmount the tough theoretical questions about how complex life emerged on Earth more than four billion years ago.

***

"The special attributes of the ancestral versions of these enzyme superfamlies, and the self-reinforcing feedback system they would have formed with the first genes and proteins, would have kick-started early biology and driven the first life forms toward greater diversity and complexity, the researchers said.

***

"The special attributes of the ancestral versions of these enzyme superfamlies, and the self-reinforcing feedback system they would have formed with the first genes and proteins, would have kick-started early biology and driven the first life forms toward greater diversity and complexity, the researchers said.

"Each of them recognizes one of the 20 amino acids that serve as the building blocks of proteins. (Proteins, considered the machines of life, catalyze and synchronize the chemical reactions inside cells.) In modern organisms, an aaRS effectively links its assigned amino acid to an RNA string containing three nucleotides complementary to a similar string in the transcribed gene. The aaRSs thus play a central role in converting genes into proteins, a process called translation that is essential for all life forms.

***

"'These interdependent peptides and the nucleic acids encoding them would have been able to assist each other's molecular self-organization despite the continual random disruptions that beset all molecular processes," Carter said. "We believe that this is what gave rise to a peptide-RNA world early in Earth's history," Carter said.

***

"Carter and Wills developed two additional reasons why a pure RNA biology of any significance was unlikely to have predated a peptide-RNA biology. One reason is catalysis -- the acceleration of chemical reactions involving other molecules.
Catalysis is a key feature of biology that RNA cannot perform with much versatility. In particular, RNA enzymes cannot readily adjust their activities to temperature changes likely to have happened as the earth cooled, and so cannot perform the very broad range of catalytic accelerations that would have been necessary to synchronize the biochemistry of early cell-based life forms. Only peptide or protein enzymes have that kind of catalytic versatility, Carter said.

"Secondly, Wills has shown that impossible obstacles would have blocked any transition from a pure-RNA world to a protein-RNA world and onward toward life.

"'Such a rise from RNA to cell-based life would have required an out-of-the-blue appearance of an aaRS-like protein that worked even better than its adapted RNA counterpart," Carter said. "That extremely unlikely event would have needed to happen not just once but multiple times -- once for every amino acid in the existing gene-protein code. It just doesn't make sense."

"Thus, because the new Carter-Wills theory actually addresses real problems of the origin of life that are concealed by the expediency of the RNA-world hypothesis, it is actually a far simpler account of how things probably happened just before life on Earth rose from the primordial soup."

Comment: Of course, life just popped up in the soup. This article is an important criticism of the RBNA world thesis, but it skips the key problem. How does life start on a rocky planet with no organic molecules that are naturally present. Not all the needed ones are shown to arrive from out space on meteorites.

Theoretical origin of life; subterranean extremophiles

by David Turell @, Friday, November 24, 2017, 19:08 (2335 days ago) @ David Turell

Life, however weird is everywhere. Life seems to appear on Earth easily. why? the Earth is made for it!:

https://aeon.co/essays/deep-beneath-the-earths-surface-life-is-weird-and-wonderful?utm_...

"The deep Earth supports an entire biosphere, largely cut off from the surface world, and is still only beginning to be explored and understood.

"The amount of water in the subsurface is considerable. Globally, the freshwater reservoir in the subsurface is estimated to be up to 100 times as great as all the available fresh water in the rivers, lakes and swamps combined. This water, ranging in ages from seven years to 2 billion years, is being intensely studied by researchers because it defines the location and scope of deep life. We know now that the deep terrestrial subsurface is home to one quintillion simple (prokaryotic) cells. That is two to 20 times as many cells as live in all the open ocean. By some estimates, the deep biosphere could contain up to one third of Earth’s entire biomass.

***

"Within this hellish environment, though, are crucial ingredients for nurturing life. Underground water reacts with minerals in the continental crust, and the longer the water has been trapped down there, the more time there has been for the results of those reactions to accumulate along the flow path. The slow reactions between water and rock dissolve minerals into the water, and break up some of the water molecules, producing molecular hydrogen. This hydrogen is an important fuel for microorganisms in the deep subsurface.

***

"Old-water ecosystems are dominated by hydrogen-utilising microorganisms such as sulphate-reducing bacteria and methane-producing archaea. Those methane-producing archaea, or methanogens, are microbes that visually resemble bacteria but are so structurally and genetically distinct that they belong to a completely separate domain of life. Sulfate-reducing bacteria and methanogens are among the life forms that appeared earlier in the evolutionary history. In contrast, young-water ecosystems are dominated by metabolically diverse and versatile bacteria of the phylum proteobacteria.

***

"Subsurface microorganisms are estimated to be extraordinarily long-lived. In our studies, they show a turnover time as slow as 1,000 years, meaning that they divide only once every few thousand years. To put it in perspective, the common gut bacterium E.coli divides once every 20 minutes. One of the long-standing questions is, how do the deep microbes achieve such a slow-motion lifestyle?

***

"Our studies of the proteobacteria-dominated communities (collected from several sites 1 to 3 km below land surface) show that they share a high degree of similarity with each other, as determined by a genetic marker known as the 16S ribosomal RNA. However, the same functional traits are carried out by different taxa. This variation cannot be explained by physical separation of the sites, nor by each location’s unique physico-chemical features – normally the most ecologically influential factors for such segregation. Neither depth nor water-residence time appear to be a significant contributor to differences, either. Future investigations on the origins of subsurface microorganisms, along with their evolution and movement over the geological history, will aid our understanding of the biogeography, or living landscape, of the subsurface. (my bold)

***

"The molecular data, together with isotope geochemistry and thermodynamic modelling, presented a unified story that the most successful group down there is the betaproteobacteria, a class of proteobacteria that obtain energy through a coupling of nitrate reduction and sulphur oxidation in order to fix carbon dioxide for cellular growth. The demand for nitrate among deep microbes was unexpected;... More interesting, we deduce that deep microbial groups have established strong, paired metabolic partnerships, or syntrophic relationships, which helps the organisms overcome the challenges of extracting the limited energy that originated from rocks. Rather than competing directly with each other, these microbes establish a win-win collaboration. (my bold)

***

"The commonality of species on the surface and subsurface posed a consistent research challenge. At all times, we had to make extensive analysis to be sure that any specimen found was not the result of contamination of the mines where we were executing our research.

***

"And our journey into the inner life of the Earth is just beginning. We are interested in determining whether species from the deep subsurface truly are as isolated as they seem, and if the migrations go in both directions. It is possible that some subsurface organisms reappear on the surface via hot springs."

Comment: Note the cooperative behaviour of these strange organisms. Not Darwinian at all. Life blooms easily on Earth with God's control. Perhaps life started in this weird area.

Theoretical origin of life; subterranean extremophiles

by dhw, Saturday, November 25, 2017, 09:12 (2335 days ago) @ David Turell

QUOTE: Rather than competing directly with each other, these microbes establish a win-win collaboration. (David’s bold)

DAVID’s comment: Note the cooperative behaviour of these strange organisms. Not Darwinian at all. Life blooms easily on Earth with God's control. Perhaps life started in this weird area.

Yet again, thank you for all this amazing new information. Once more we have confirmation of Lynn Margulis’s then revolutionary thinking in identifying cooperation as a key element of evolutionary development. She also believed in cellular intelligence.

Yes, life obviously blooms easily on Earth, but even if God exists, I have no idea why you think all these different life forms are evidence of control. Looks to me as if they’re just happily going about their business like the rest of us!

Theoretical origin of life; subterranean extremophiles

by David Turell @, Saturday, November 25, 2017, 15:12 (2334 days ago) @ dhw

QUOTE: Rather than competing directly with each other, these microbes establish a win-win collaboration. (David’s bold)

DAVID’s comment: Note the cooperative behaviour of these strange organisms. Not Darwinian at all. Life blooms easily on Earth with God's control. Perhaps life started in this weird area.

dhw: Yet again, thank you for all this amazing new information. Once more we have confirmation of Lynn Margulis’s then revolutionary thinking in identifying cooperation as a key element of evolutionary development. She also believed in cellular intelligence.

Yes, life obviously blooms easily on Earth, but even if God exists, I have no idea why you think all these different life forms are evidence of control. Looks to me as if they’re just happily going about their business like the rest of us!

I've bolded your sentence above to point out that the reason life blooms easily is because the God you deny made it that way. Remember the research we've done finds it very hard to figure out how to start life, yet 'it blooms easily' in your words.

Theoretical origin of life; subterranean extremophiles

by dhw, Sunday, November 26, 2017, 13:06 (2333 days ago) @ David Turell

DAVID’s comment: Note the cooperative behaviour of these strange organisms. Not Darwinian at all. Life blooms easily on Earth with God's control. Perhaps life started in this weird area. (dhw’s bold)
[…]

dhw: Yes, life obviously blooms easily on Earth, but even if God exists, I have no idea why you think all these different life forms are evidence of control. Looks to me as if they’re just happily going about their business like the rest of us! (David’s bold)

DAVID: I've bolded your sentence above to point out that the reason life blooms easily is because the God you deny made it that way. Remember the research we've done finds it very hard to figure out how to start life, yet 'it blooms easily' in your words.

‘Life blooms easily’ were your words (bolded above), but you seem to have forgotten what you meant. I presumed it was a reference to life’s astonishing fecundity and variety, not its origin. I do not deny God – I am an agnostic, not an atheist. And my comment concerned evidence of control, not the origin of life. If it weren’t for those three errors, there might have been a point somewhere.

Theoretical origin of life; subterranean extremophiles

by David Turell @, Sunday, November 26, 2017, 15:41 (2333 days ago) @ dhw

DAVID’s comment: Note the cooperative behaviour of these strange organisms. Not Darwinian at all. Life blooms easily on Earth with God's control. Perhaps life started in this weird area. (dhw’s bold)
[…]

dhw: Yes, life obviously blooms easily on Earth, but even if God exists, I have no idea why you think all these different life forms are evidence of control. Looks to me as if they’re just happily going about their business like the rest of us! (David’s bold)

DAVID: I've bolded your sentence above to point out that the reason life blooms easily is because the God you deny made it that way. Remember the research we've done finds it very hard to figure out how to start life, yet 'it blooms easily' in your words.

dhw: ‘Life blooms easily’ were your words (bolded above), but you seem to have forgotten what you meant. I presumed it was a reference to life’s astonishing fecundity and variety, not its origin. I do not deny God – I am an agnostic, not an atheist. And my comment concerned evidence of control, not the origin of life. If it weren’t for those three errors, there might have been a point somewhere.

Your points are well taken, but it is still obvious that life appeared quickly and easily on Earth, a point that should startle you. Was it a natural event? I doubt it. Do you?

Theoretical origin of life; subterranean extremophiles

by dhw, Monday, November 27, 2017, 13:52 (2332 days ago) @ David Turell

DAVID’s comment: Note the cooperative behaviour of these strange organisms. Not Darwinian at all. Life blooms easily on Earth with God's control. Perhaps life started in this weird area. (dhw’s bold)
[…]
dhw: Yes, life obviously blooms easily on Earth, but even if God exists, I have no idea why you think all these different life forms are evidence of control. Looks to me as if they’re just happily going about their business like the rest of us! (David’s bold)

DAVID: I've bolded your sentence above to point out that the reason life blooms easily is because the God you deny made it that way. Remember the research we've done finds it very hard to figure out how to start life, yet 'it blooms easily' in your words.

dhw: ‘Life blooms easily’ were your words (bolded above), but you seem to have forgotten what you meant. I presumed it was a reference to life’s astonishing fecundity and variety, not its origin. I do not deny God – I am an agnostic, not an atheist. And my comment concerned evidence of control, not the origin of life. If it weren’t for those three errors, there might have been a point somewhere.

DAVID: Your points are well taken, but it is still obvious that life appeared quickly and easily on Earth, a point that should startle you. Was it a natural event? I doubt it. Do you?

Neither you nor I have the slightest idea how quickly and easily it began, or what the criteria are for speed and ease. Of course life is a startling and wondrous event. Was it natural (Reblak’s hypothesis) or designed by a God (your hypothesis)? You and I have spent nearly ten years discussing the question, and we still don’t know the answer, though you think you do.

Theoretical origin of life; subterranean extremophiles

by David Turell @, Monday, November 27, 2017, 15:06 (2332 days ago) @ dhw


DAVID: Your points are well taken, but it is still obvious that life appeared quickly and easily on Earth, a point that should startle you. Was it a natural event? I doubt it. Do you?

dhw: Neither you nor I have the slightest idea how quickly and easily it began, or what the criteria are for speed and ease. Of course life is a startling and wondrous event. Was it natural (Reblak’s hypothesis) or designed by a God (your hypothesis)? You and I have spent nearly ten years discussing the question, and we still don’t know the answer, though you think you do.

The fact that life appeared at 3.8 billion years ago, only 200 million years after the bombardment stopped speaks to quickly and easily. And it grows in every hostile environment we study, again easily!

Theoretical origin of life; subterranean extremophiles

by David Turell @, Monday, October 01, 2018, 21:48 (2024 days ago) @ David Turell

A review article about how varied they are, and the strange types of energy they use:

https://www.the-scientist.com/features/life-thrives-within-the-earths-crust-64805?utm_c...

"These expeditions are just one part of a rapidly expanding field of research focused on documenting microbial and even eukaryotic life dwelling hundreds of meters deep in the Earth’s crust—the vast sheath of rock encasing the planet’s mantle. Researchers are now exploring this living underworld, or deep biosphere, not only in the ancient, slow-changing continental crust beneath our feet, but in the thinner, more dynamic oceanic crust under the seafloor.

***

"To date, studies of crustal sites all over the world—both oceanic and continental—have documented all sorts of organisms getting by in environments that, until recently, were deemed inhospitable, with some theoretical estimates now suggesting life might survive at least 10 kilometers into the crust. And the deep biosphere doesn’t just comprise bacteria and archaea, as once thought; researchers now know that the subsurface contains various fungal species, and even the occasional animal. Following the 2011 discovery of nematode worms in a South African gold mine, an intensive two-year survey turned up members of four invertebrate phyla—flatworms, rotifers, segmented worms, and arthropods—living 1.4 kilometers below the Earth’s surface.

***

"A key area of research now is understanding how such life survives. Devoid of sunlight, “these systems are typically energy-poor,” says Sherwood Lollar. Compared to surface communities, microbes in the deep biosphere are thought to be relatively slow-growing and sparsely distributed, she adds. While surface soil may contain in excess of 10 billion microbes per gram, oceanic crust usually contains around 10,000 cells per gram, and continental crust—where water is unsurprisingly in shorter supply—holds fewer than 1,000 cells per gram.

***

"When geomicrobiologist Lotta Purkamo of the University of St Andrews and her colleagues characterized the ecosystem of a 600-meter-deep borehole in northern Finland, for example, they found evidence of metabolic pathways based on reducing or oxidizing sulfate, nitrate, methane, ammonia, and iron, as well as fixation reactions involving carbon.

Additionally, thanks to metatranscriptomic analyses, “we’re learning that these organisms have a lot of potential metabolisms that they could be expressing,” says Huber, who recently carried out this sort of assay on the Axial Seamount community.12 “But depending on the conditions and the geological setting, just a small subset of those genes are being used.” Such results hint at flexible and opportunistic lifestyles, she adds, where microbes make use of whatever they can, whenever they can.

***

"Researchers are far from agreeing on the extent of this underworld—one 1990s paper controversially suggested that deep life constituted 50 percent of the Earth’s current biomass, though most estimates are now below 15 percent. Before the rise of land plants around 400 million years ago, though, deep biomass could have outweighed life on the surface by an order of magnitude, according to calculations published this summer by McMahon and the University of Aberdeen’s John Parnell.

***

“'When we think about how life on Earth has changed over time, and how it’s interacted with the chemistry of rocks, sediments, groundwater, oceans, atmosphere, we shouldn’t be thinking just about charismatic animals and plants,” says McMahon. “We should be thinking about this huge quantity of microorganisms, most of which are living on the surfaces of mineral grains and interacting with them.'”

Comment: This type of research makes it seem that given the right planet, life is easy to begin in many different ways on many different substrates.

Theoretical origin of life; subterranean extremophiles

by Balance_Maintained @, U.S.A., Tuesday, October 02, 2018, 00:53 (2024 days ago) @ David Turell

A review article about how varied they are, and the strange types of energy they use:

https://www.the-scientist.com/features/life-thrives-within-the-earths-crust-64805?utm_c...

"These expeditions are just one part of a rapidly expanding field of research focused on documenting microbial and even eukaryotic life dwelling hundreds of meters deep in the Earth’s crust—the vast sheath of rock encasing the planet’s mantle. Researchers are now exploring this living underworld, or deep biosphere, not only in the ancient, slow-changing continental crust beneath our feet, but in the thinner, more dynamic oceanic crust under the seafloor.

***

"To date, studies of crustal sites all over the world—both oceanic and continental—have documented all sorts of organisms getting by in environments that, until recently, were deemed inhospitable, with some theoretical estimates now suggesting life might survive at least 10 kilometers into the crust. And the deep biosphere doesn’t just comprise bacteria and archaea, as once thought; researchers now know that the subsurface contains various fungal species, and even the occasional animal. Following the 2011 discovery of nematode worms in a South African gold mine, an intensive two-year survey turned up members of four invertebrate phyla—flatworms, rotifers, segmented worms, and arthropods—living 1.4 kilometers below the Earth’s surface.

***

"A key area of research now is understanding how such life survives. Devoid of sunlight, “these systems are typically energy-poor,” says Sherwood Lollar. Compared to surface communities, microbes in the deep biosphere are thought to be relatively slow-growing and sparsely distributed, she adds. While surface soil may contain in excess of 10 billion microbes per gram, oceanic crust usually contains around 10,000 cells per gram, and continental crust—where water is unsurprisingly in shorter supply—holds fewer than 1,000 cells per gram.

***

"When geomicrobiologist Lotta Purkamo of the University of St Andrews and her colleagues characterized the ecosystem of a 600-meter-deep borehole in northern Finland, for example, they found evidence of metabolic pathways based on reducing or oxidizing sulfate, nitrate, methane, ammonia, and iron, as well as fixation reactions involving carbon.(Bold Mine)

Additionally, thanks to metatranscriptomic analyses, “we’re learning that these organisms have a lot of potential metabolisms that they could be expressing,” says Huber, who recently carried out this sort of assay on the Axial Seamount community.12 “But depending on the conditions and the geological setting, just a small subset of those genes are being used.” Such results hint at flexible and opportunistic lifestyles, she adds, where microbes make use of whatever they can, whenever they can.

***

"Researchers are far from agreeing on the extent of this underworld—one 1990s paper controversially suggested that deep life constituted 50 percent of the Earth’s current biomass, though most estimates are now below 15 percent. Before the rise of land plants around 400 million years ago, though, deep biomass could have outweighed life on the surface by an order of magnitude, according to calculations published this summer by McMahon and the University of Aberdeen’s John Parnell.

***

“'When we think about how life on Earth has changed over time, and how it’s interacted with the chemistry of rocks, sediments, groundwater, oceans, atmosphere, we shouldn’t be thinking just about charismatic animals and plants,” says McMahon. “We should be thinking about this huge quantity of microorganisms, most of which are living on the surfaces of mineral grains and interacting with them.'”

Comment: This type of research makes it seem that given the right planet, life is easy to begin in many different ways on many different substrates.

Terraforming bacteria. Unsurprising as it fits with my speculation that early microbes were designed to terraform the planet.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Theoretical origin of life; subterranean extremophiles

by David Turell @, Tuesday, October 02, 2018, 01:03 (2024 days ago) @ Balance_Maintained

David: A review article about how varied they are, and the strange types of energy they use:

https://www.the-scientist.com/features/life-thrives-within-the-earths-crust-64805?utm_c...

"These expeditions are just one part of a rapidly expanding field of research focused on documenting microbial and even eukaryotic life dwelling hundreds of meters deep in the Earth’s crust—the vast sheath of rock encasing the planet’s mantle. Researchers are now exploring this living underworld, or deep biosphere, not only in the ancient, slow-changing continental crust beneath our feet, but in the thinner, more dynamic oceanic crust under the seafloor.

***

"To date, studies of crustal sites all over the world—both oceanic and continental—have documented all sorts of organisms getting by in environments that, until recently, were deemed inhospitable, with some theoretical estimates now suggesting life might survive at least 10 kilometers into the crust. And the deep biosphere doesn’t just comprise bacteria and archaea, as once thought; researchers now know that the subsurface contains various fungal species, and even the occasional animal. Following the 2011 discovery of nematode worms in a South African gold mine, an intensive two-year survey turned up members of four invertebrate phyla—flatworms, rotifers, segmented worms, and arthropods—living 1.4 kilometers below the Earth’s surface.

***

"A key area of research now is understanding how such life survives. Devoid of sunlight, “these systems are typically energy-poor,” says Sherwood Lollar. Compared to surface communities, microbes in the deep biosphere are thought to be relatively slow-growing and sparsely distributed, she adds. While surface soil may contain in excess of 10 billion microbes per gram, oceanic crust usually contains around 10,000 cells per gram, and continental crust—where water is unsurprisingly in shorter supply—holds fewer than 1,000 cells per gram.

***

"When geomicrobiologist Lotta Purkamo of the University of St Andrews and her colleagues characterized the ecosystem of a 600-meter-deep borehole in northern Finland, for example, they found evidence of metabolic pathways based on reducing or oxidizing sulfate, nitrate, methane, ammonia, and iron, as well as fixation reactions involving carbon.(Bold Mine)

Additionally, thanks to metatranscriptomic analyses, “we’re learning that these organisms have a lot of potential metabolisms that they could be expressing,” says Huber, who recently carried out this sort of assay on the Axial Seamount community.12 “But depending on the conditions and the geological setting, just a small subset of those genes are being used.” Such results hint at flexible and opportunistic lifestyles, she adds, where microbes make use of whatever they can, whenever they can.

***

"Researchers are far from agreeing on the extent of this underworld—one 1990s paper controversially suggested that deep life constituted 50 percent of the Earth’s current biomass, though most estimates are now below 15 percent. Before the rise of land plants around 400 million years ago, though, deep biomass could have outweighed life on the surface by an order of magnitude, according to calculations published this summer by McMahon and the University of Aberdeen’s John Parnell.

***

“'When we think about how life on Earth has changed over time, and how it’s interacted with the chemistry of rocks, sediments, groundwater, oceans, atmosphere, we shouldn’t be thinking just about charismatic animals and plants,” says McMahon. “We should be thinking about this huge quantity of microorganisms, most of which are living on the surfaces of mineral grains and interacting with them.'”

Comment: This type of research makes it seem that given the right planet, life is easy to begin in many different ways on many different substrates.


Tony: Terraforming bacteria. Unsurprising as it fits with my speculation that early microbes were designed to terraform the planet.

It certainly does, as it seems life can handle any conditions

Theoretical origin of life; subterranean extremophiles

by dhw, Tuesday, October 02, 2018, 13:30 (2023 days ago) @ David Turell

“'When we think about how life on Earth has changed over time, and how it’s interacted with the chemistry of rocks, sediments, groundwater, oceans, atmosphere, we shouldn’t be thinking just about charismatic animals and plants,” says McMahon. “We should be thinking about this huge quantity of microorganisms, most of which are living on the surfaces of mineral grains and interacting with them.'”

DAVID’s comment: This type of research makes it seem that given the right planet, life is easy to begin in many different ways on many different substrates.

An easy beginning, given the right conditions, is indeed a favourite assumption among atheists. They may be right. They may be wrong.

Theoretical origin of life; subterranean extremophiles

by David Turell @, Saturday, October 13, 2018, 15:06 (2012 days ago) @ dhw

Very slow living cells described:

https://www.newscientist.com/article/dn21823-buried-microbes-exist-at-limit-between-lif...

"Everything happens slowly in the North Pacific gyre, one of the five largest ocean gyres in the world. Sand and mud washing off the continents rarely finds its way there, so the seafloor accumulates sediment at a sluggish rate. The clay just 30 metres below the seafloor was deposited 86 million years ago, almost 20 million years before Tyrannosaurus rex graced the Earth.

"That clay contains so little energy in the form of nutrients that it should be incapable of supporting a living community. Microbes have been found in other, only slightly more energy-rich communities below the seafloor, though.

"In a bid to hone in on the lower energy limits for life, Hans Røy at Aarhus University in Denmark probed the clays below the North Pacific gyre. Under the microscope, he found a community made up of bacteria and single-celled organisms called archaea in vanishingly small numbers.

“'There are only 1000 tiny cells in 1 cubic centimetre of sediment, so finding just one is literally like hunting for a needle in a haystack.”

"The microbes rely on oxygen, carbon and other nutrients in their deep environment to live, but Røy’s team found that carbon is so limited that the cells respire oxygen 10,000 times slower than bacteria in lab-grown cultures.

"Røy thinks the microbial community is so sparse, and the metabolic rates so low, that the nutrient levels probably represent the bare minimum required to keep cellular enzymes and DNA working. “It looks like we have reached the absolute lower limit for the metabolism of cells,” he says.

"Yuki Morono at the Japan Agency for Marine-Earth Science and Technology in Nankoku, Japan, recently studied similar low-energy microbial communities below the Pacific seafloor near Japan. Under a microscope, he says, the microbes show few signs of life. “They appear to be dead by our time scale.”

"But when Morono’s team treated the cells to what he calls a “luxury meal” of glucose and other nutrients, most of them incorporated some food – suggesting that they are, in fact, alive. “Their lives are just very slow compared with ours,” he says.

"Because of their remarkably slow metabolic rates, individual cells may have extremely long life spans, says Røy. The cells Morono’s team examined looked intact, yet it would take each of them hundreds or thousands of years to generate enough energy to go through cell division and produce daughter cells. That means some of Morono’s cells could be thousands of years old.

"Røy says his cells could be older still. Elsewhere on Earth, life is primarily concerned with building up enough energy to fuel reproduction. In extremely energy-poor communities, though, reproduction makes less sense because it creates new rivals that also need to feed. “If you can just barely meet your energy requirement, then it is suicide to divide into two,” he says. He thinks it makes more sense for the cells to use the energy they gather to repair cellular molecules that have been damaged over centuries of use instead of fuelling cell division."

Comment: Apparently living a slow form of life. An other example of the extreme limits of the
environment that will support life. Consideration dichotomy: if life is as complex s it seems, and if origin of life on a barren planet seems so improbable, why is life popping up in every seemingly inhospitable spot? Is it so hard to imagine it is guided?

Theoretical origin of life; aged subterranean extremophiles

by David Turell @, Friday, January 25, 2019, 00:59 (1909 days ago) @ dhw

They can exist without light, without water, without oxygen, and may metabolize carbo

https://blogs.scientificamerican.com/artful-amoeba/inside-earth-microbes-approach-immor...

"Last month, the Deep Carbon Observatory announced an astounding fact: the mass of the microbes living beneath Earth’s surface amounts to 15 to 23 billion tons of carbon, a sum some 245 to 385 times greater than the carbon mass of all humans. That’s amazing. It wasn’t so long ago we weren’t even sure life at depth was possible.

"But buried in the press release was a detail I found much more surprising and interesting than the mass of subterranean life: its age.

***
"Back in the late 1920s, a scientist named Charles Lipman, a professor at the University of California, Berkeley, began to suspect there were bacteria in rocks. Not fossil bacteria. Alive bacteria.

"Lipman did not believe that the bacteria he coaxed from coal were alive in the sense that the bacteria in your gut are alive. Rather, he believed that during the process of forming coal, the bacteria had dried up and entered suspended animation.

***

“'It is my view that here and there scattered through the masses of the coal measures an occasional spore or some similarly resistant resting stage of a microorganism has survived the vicissitudes of time and circumstance and retained its living character, its power to develop into a vegetative form, and its power to multiply when conditions are rendered propitious for it.”

"This dessicated condition we now call anhydrobiosis, and it is in such a state that organisms like water bears can withstand the vacuum of space and bombardment with radiation.

***

"A 2017 paper in the Proceedings of the National Academy of Science found low densities of bacteria (although “low” is still 50-2,000 cells per cubic centimeter) in 5 to 30 million-year-old coal and shale beds located two kilometers beneath the floor of the Pacific Ocean off the coast of Japan.

"They were still actively, if extremely slowly, living. Their generation times ranged from months to over 100 years. But this estimate was likely low, the authors conceded. The generation time of E. coli in the lab: 15 to 20 minutes.

***

'Evidence is also accumulating that such nutrient-deprived, superannuated bacteria are not “microbial zombies”. On the contrary, numerous studies have found that when deep subsurface microbes are placed in more moderate environments, they quickly revive.

"Taken together, these findings aren’t as ludicrous as they may seem when you also consider that microbes buried deep beneath Earth’s surface are protected from cosmic radiation – a frequent killer of the preternaturally aged – by thick overburdens of water, sediment, and/or rock (Muons, the form in which cosmic radiation reaches Earth’s surface, can only penetrate tens of meters into rock). Such radiation steadily mutates the DNA of organisms living on Earth’s surface.

***

"To sum up, Earth’s crust appears to be simply lousy with idling, ancient bacteria parked in power-save mode, ready at nearly a moment’s notice to throw the gearshift into drive. But what a life! Eons spent entombed in a dark, airless, silent matrix, barely eating, barely breathing, barely moving, barely living. But not dead. Not dead.

"If Charles Lipman was right, there are also bacterial cells inside our planet that began life 50 million years before dinosaurs evolved that could begin dividing again tomorrow. That … is breathtaking."

Comment: Wow!! What this means is that the process of life is exceedingly tough and can last though any type of trial. If they date back to before dinosaurs (250 myo) they were alive deep in the Earth at 300 myo!

Theoretical origin of life; aged subterranean extremophiles

by dhw, Friday, January 25, 2019, 10:42 (1908 days ago) @ David Turell

DAVID: Wow!! What this means is that the process of life is exceedingly tough and can last though any type of trial. If they date back to before dinosaurs (250 myo) they were alive deep in the Earth at 300 myo!

Thank you for this. I can only echo your “wow!” But I thought bacteria dated back approx. 3.5 billion years, which is an even bigger wow!

Theoretical origin of life; aged subterranean extremophiles

by David Turell @, Friday, January 25, 2019, 13:43 (1908 days ago) @ dhw

DAVID: Wow!! What this means is that the process of life is exceedingly tough and can last though any type of trial. If they date back to before dinosaurs (250 myo) they were alive deep in the Earth at 300 myo!

dhw:Thank you for this. I can only echo your “wow!” But I thought bacteria dated back approx. 3.5 billion years, which is an even bigger wow!

You are comparing origin of life to a survival issue under very extreme conditions.

Theoretical origin of life; aged subterranean extremophiles

by dhw, Saturday, January 26, 2019, 13:26 (1907 days ago) @ David Turell

DAVID: Wow!! What this means is that the process of life is exceedingly tough and can last though any type of trial. If they date back to before dinosaurs (250 myo) they were alive deep in the Earth at 300 myo!

dhw:Thank you for this. I can only echo your “wow!” But I thought bacteria dated back approx. 3.5 billion years, which is an even bigger wow!

DAVID: You are comparing origin of life to a survival issue under very extreme conditions.

Sorry, I didn’t mean to start a discussion! But I would have thought our friends the bacteria would have survived very extreme conditions long before 300 million years ago!

Theoretical origin of life; aged subterranean extremophiles

by David Turell @, Saturday, January 26, 2019, 14:40 (1907 days ago) @ dhw

DAVID: Wow!! What this means is that the process of life is exceedingly tough and can last though any type of trial. If they date back to before dinosaurs (250 myo) they were alive deep in the Earth at 300 myo!

dhw:Thank you for this. I can only echo your “wow!” But I thought bacteria dated back approx. 3.5 billion years, which is an even bigger wow!

DAVID: You are comparing origin of life to a survival issue under very extreme conditions.

dhw: Sorry, I didn’t mean to start a discussion! But I would have thought our friends the bacteria would have survived very extreme conditions long before 300 million years ago!

Of course bacteria survived extremes long before that. This is just the latest example that has been found. Origin of life most likely started in extreme condition on early Earth.

Theoretical origin of life; more directed lab work

by David Turell @, Sunday, January 27, 2019, 23:07 (1906 days ago) @ David Turell
edited by David Turell, Sunday, January 27, 2019, 23:19

The usual fake news. By manipulating proteins in the lab they get something that resembles RNA:

https://www.sciencedaily.com/releases/2019/01/190124095112.htm

"The study's resulting polymers were not RNA but could be have been an important intermediate step in the early evolution of RNA. For building blocks, the researchers used base molecules referred to as "proto-nucleobases," highly suspected to be precursors of nucleobases, main components that transport genetic code in today's RNA.

***

"One main suspected proto-nucleobase in this experiment -- and in previous experiments on the possible the evolution of RNA -- was triaminopyrimidine (TAP). Cyanuric acid (CA) was another. The researchers highly suspect TAP and CA were parts of a proto-RNA.

"The chemical bonds that hold together assemblies of the two suspected proto-nucleobases were surprisingly strong but non-covalent, which is akin to connecting two magnets. In RNA the main bonds holding together modern nucleobases are covalent bonds, akin to welding, and enzymes make those bonds in cells today.

***

"The researchers added two more experiments to test how strongly their RNA-like assemblies preferred making one-handed helices.
First, they introduced a smidgeon of compounds similar to TAP and CA, but which had L or D chirality, to nudge the spiraling direction. The whole batch conformed to the chirality of the respective additive, resulting in assemblies twisting in a unified direction as helices do in RNA and DNA today.

***

"Second, they put the sugar compound ribose-5-phosphate together with TAP to more closely emulate the current building blocks of RNA. The ribose fell into place, and the resulting assembly spiraled in a direction dictated by the ribose chirality.

"This molecule easily formed an RNA-like assembly that was surprisingly stable, even though the pieces were only held together by non-covalent bonds," Karunakaran said.

***

"The research also expands a growing body of evidence supporting an unconventional hypothesis by the Center for Chemical Evolution, which dispenses with the need for a narrative that rare cataclysms and unlikely ingredients were necessary to produce life's early building blocks.

"Instead, most biomolecules likely arose in several gradual steps, on quiet, rain-swept dirt flats or lakeshore rocks lapped by waves. Precursor molecules with the right reactivity enabled those steps readily and produced abundant materials for further evolutionary steps."

Comment: This is all directed by human thought. Where did all these exact proteins come from on a rocky Earth? Fun and games and unrealistic expectations whbich support research grants.

Theoretical origin of life; aged subterranean extremophiles

by David Turell @, Thursday, May 09, 2019, 19:22 (1804 days ago) @ David Turell

How massive they are in comparison to all of us on the surface:

https://stillnessinthestorm.com/2018/12/scientists-reveal-a-massive-biosphere-of-life-h...

"An incredibly vast “dark biosphere” of subterranean lifeforms scientists are hardly beginning to comprehend and observe exists deep within the Earth, as a recent study explored.

"Where they say life theoretically shouldn’t even exist, the oldest and deepest organisms on the planet thrive, apparently just still surviving buried deep within the lost layers of our planet. In this recently released research, scientists have taken some measurements of the microbial world’s “dark matter” in a way that has reportedly never before been seen.

***

"...now thanks to a technique they call ultra-deep sampling, scientists now know that bacteria can be found basically everywhere, as deep as one can go, “albeit the sampling has obviously reached only an infinitesimally tiny part of the deep biosphere,”Lloyd said.

***

"This research was the work of a huge number of people, 1,000 scientists, and it was a 10 year long collaboration. A preview of the results from it was provided to us recently, as Lloyd and peers with the Deep Carbon Observatory (DCO) estimated the deep biosphere to occupy a volume of between 0.48 and 0.55 billion cubic miles, or 2 to 2.3 billion cubic kilometers.

"The deep biosphere then is defined as the zone of life deep underneath Earth’s surface. The estimated volume of the deep biosphere is incredibly massive, almost twice the volume of all the oceans in the world, and deep within the oceans is yet another enormous natural environment that is mostly unexplored by people.

"Now here’s where it gets insane: the mass of all lifeforms, microbes, all those creatures deep in the surface of the Earth in the deep biosphere, is estimated to be between 245 and 385 times greater than the equivalent mass of all human beings on Earth. In other words, right beneath our feet for miles beneath us, there is a larger mass of bacteria than the mass of all people on the planet.

"This is a population totaling around 15 to 23 billion tons of carbon mass, microbes all over the planet deep within the cold, dark Earth.

***

"The deep biosphere bacteria are estimated to compose 70 percent of all bacteria and archaea on Earth. Two distinct forms of microbes, archaea and bacteria, dominate this region of the planet.

***

"Yet another extremely interesting detail was provided by Lloyd, the aforementioned scientist. She explained that the lifeforms weren’t just unusual because of their habitat, but they have extremely long lifespans, with incredibly slow and long life cycles lasting for “near-geologic timescales.”

"With no sunlight, they “subsist” on “meager amounts of chemical energy” harvested from the rocks around them. Lloyd explained that some of the organisms can live for millennia, living for thousands of years, metabolically active but in stasis, using less energy than scientists believed could even support life."

Comment: Another story about these deep life forms to remind us the Earth supports all sorts of life, and life is very tough and tenacious. It is as if life is 'required' to be here.

Theoretical origin of life; aged subterranean extremophiles

by dhw, Friday, May 10, 2019, 11:50 (1803 days ago) @ David Turell

https://stillnessinthestorm.com/2018/12/scientists-reveal-a-massive-biosphere-of-life-h...

QUOTE: "An incredibly vast “dark biosphere” of subterranean lifeforms scientists are hardly beginning to comprehend and observe exists deep within the Earth, as a recent study explored.
"Where they say life theoretically shouldn’t even exist, the oldest and deepest organisms on the planet thrive, apparently just still surviving buried deep within the lost layers of our planet. In this recently released research, scientists have taken some measurements of the microbial world’s “dark matter” in a way that has reportedly never before been seen.

Thank you for this amazing article. I wonder if there might not be similar life forms hidden away on other apparently inhospitable planets. They would obviously not be detectable by instruments currently at our disposal, but eventually we shall find out either way, and it will certainly raise lots of questions for our descendants. I fear that by then you and I will not be around to discuss them!

Theoretical origin of life; aged subterranean extremophiles

by David Turell @, Friday, May 10, 2019, 16:10 (1803 days ago) @ dhw

https://stillnessinthestorm.com/2018/12/scientists-reveal-a-massive-biosphere-of-life-h...

QUOTE: "An incredibly vast “dark biosphere” of subterranean lifeforms scientists are hardly beginning to comprehend and observe exists deep within the Earth, as a recent study explored.
"Where they say life theoretically shouldn’t even exist, the oldest and deepest organisms on the planet thrive, apparently just still surviving buried deep within the lost layers of our planet. In this recently released research, scientists have taken some measurements of the microbial world’s “dark matter” in a way that has reportedly never before been seen.

dhw: Thank you for this amazing article. I wonder if there might not be similar life forms hidden away on other apparently inhospitable planets. They would obviously not be detectable by instruments currently at our disposal, but eventually we shall find out either way, and it will certainly raise lots of questions for our descendants. I fear that by then you and I will not be around to discuss them!

More to the point, the demonstrated very early arrival of life on the surface, less than a billion years after Earth's formation, seems to indicate an imperative for Earth to be life's home.

Theoretical origin of life; aged subterranean extremophiles

by David Turell @, Saturday, May 15, 2021, 19:25 (1067 days ago) @ David Turell

A new study:

https://aeon.co/essays/deep-beneath-the-earths-surface-life-is-weird-and-wonderful?utm_...

The deep Earth supports an entire biosphere, largely cut off from the surface world, and is still only beginning to be explored and understood.

***

"We know now that the deep terrestrial subsurface is home to one quintillion simple (prokaryotic) cells. That is two to 20 times as many cells as live in all the open ocean. By some estimates, the deep biosphere could contain up to one third of Earth’s entire biomass.

***

"Cold is not a problem down there, however. Quite the opposite: rainwater that percolates kilometres deep into the crust along fractures and faults between rocks can reach temperatures of 60°C (140°F) or higher. The further down you go from the surface, the closer you are to the mantle. Heat rising from the inner Earth is what warms the fissure water. Additionally, the water is under high pressure, contains very little or no oxygen, and is bombarded by radiation from natural radioactive elements in the rocks.

"Within this hellish environment, though, are crucial ingredients for nurturing life. Underground water reacts with minerals in the continental crust, and the longer the water has been trapped down there, the more time there has been for the results of those reactions to accumulate along the flow path. The slow reactions between water and rock dissolve minerals into the water, and break up some of the water molecules, producing molecular hydrogen. This hydrogen is an important fuel for microorganisms in the deep subsurface.

***

"Old-water ecosystems are dominated by hydrogen-utilising microorganisms such as sulphate-reducing bacteria and methane-producing archaea. Those methane-producing archaea, or methanogens, are microbes that visually resemble bacteria but are so structurally and genetically distinct that they belong to a completely separate domain of life. Sulfate-reducing bacteria and methanogens are among the life forms that appeared earlier in the evolutionary history. In contrast, young-water ecosystems are dominated by metabolically diverse and versatile bacteria of the phylum proteobacteria.

***

"Subsurface microorganisms are estimated to be extraordinarily long-lived. In our studies, they show a turnover time as slow as 1,000 years, meaning that they divide only once every few thousand years. To put it in perspective, the common gut bacterium E.coli divides once every 20 minutes. One of the long-standing questions is, how do the deep microbes achieve such a slow-motion lifestyle?

"It is not easy to make a living in the subsurface because the biochemical reactions to harness energy from minerals and geological gases – a set of processes known as chemotrophy – are not as efficient as photosynthesis, the process that green plants use to capture energy from photons of sunlight on the surface. Some subsurface microorganisms can form stress-resistant spores and remain inactive in order to withstand extreme subsurface conditions; otherwise, microorganisms have to invest at least a certain amount of energy, which varies from one taxa (evolutionary population) to another, to maintain the integrity and functionality of the cells.

***

"The molecular data, together with isotope geochemistry and thermodynamic modelling, presented a unified story that the most successful group down there is the betaproteobacteria, a class of proteobacteria that obtain energy through a coupling of nitrate reduction and sulphur oxidation in order to fix carbon dioxide for cellular growth. The demand for nitrate among deep microbes was unexpected; it had gone unnoticed prior to our study because the measured nitrate concentrations in the subsurface water samples were tiny. More interesting, we deduce that deep microbial groups have established strong, paired metabolic partnerships, or syntrophic relationships, which helps the organisms overcome the challenges of extracting the limited energy that originated from rocks.

***

"humans need 21 per cent oxygen in our atmosphere to be able to breathe. Nematodes can make do indefinitely with only 0.5 per cent oxygen, and many species can survive extended periods with less or no oxygen at all. (my bold)

***

"Finally, we recognise that we have probably explored only a tiny fraction of the deep biosphere, and might not yet have encountered its most significant inhabitants. It stands to reason that, if cosmopolitan species from the surface can survive in the deep subsurface, isolated from their surface brethren, then over a long period of time some organisms might have adapted to even more extreme conditions deeper in the subsurface. It could be that the real treasure trove of new and weird life forms still awaits discovery far beneath our feet."

Comment: Note my bold. Oxygen is only needed by complex life forms. Living forms can be anywhere.

Theoretical origin of life; RNA world won't work

by David Turell @, Sunday, January 21, 2018, 14:36 (2277 days ago) @ David Turell

Another comment on this article I presented in early November. An RNA world cannot be the origin of life:

http://darwins-god.blogspot.com/2018/01/about-that-rna-world-hypothesis.html

"Given its widespread popularity and acceptance you might not have realized that the so-called RNA-World hypothesis suffers from some dramatic problems. At the top of the list is the rather awkward fact that there is, err, no evidence for it. While skeptics have pointed this out for years, we now see evolutionists coming clean on this inconvenient truth as well. To wit, here is how Peter Wills and Charles Carter open their recent BioSystems paper:

"The RNA World is a widely-embraced hypothetical stage of molecular evolution, devoid of protein enzymes, in which all functional catalysts were ribozymes. Only one fact concerning the RNA World can be established by direct observation: if it ever existed, it ended without leaving any unambiguous trace of itself.

***

"No organisms have ever been discovered that demonstrate the RNA World hypothesis in action. Nor have scientists ever constructed any such organisms in their laboratories. This is not too surprising because no one has even produced anything remotely close to a detailed design of how such organisms could function.

"Wills and Carter also point out negative evidences such as catalysis (RNA enzymes lack the ability to function over a wide range of temperatures) and the “impossible obstacles” to the hypothetical yet necessary transition from the RNA World to something resembling today’s extant cells. As Carter explains:

"Such a rise from RNA to cell-based life would have required an out-of-the-blue appearance of an aaRS [aminoacyl-tRNA synthetase]-like protein that worked even better than its adapted RNA counterpart. That extremely unlikely event would have needed to happen not just once but multiple times—once for every amino acid in the existing gene-protein code. It just doesn’t make sense.

"Indeed, it just doesn’t make sense. And yet in spite of these obvious problems, the RNA World has been a textbook staple, presented as a plausible and likely example of how early life evolved."

Comment: This article is a reiteration of the influence of Darwin-based scientists who just can't give up on their beliefs that Darwin theory provides a mechanism to explain evolution. It doesn't.

Original paper abstract:

http://www.sciencedirect.com/science/article/pii/S0303264717302332

ifferential equations for error-prone information transfer (template replication, transcription or translation) are developed in order to consider, within the theory of autocatalysis, the advent of coded protein synthesis. Variations of these equations furnish a basis for comparing the plausibility of contrasting scenarios for the emergence of specific tRNA aminoacylation, ultimately by enzymes, and the relationship of this process with the origin of the universal system of molecular biological information processing embodied in the Central Dogma. The hypothetical RNA World does not furnish an adequate basis for explaining how this system came into being, but principles of self-organisation that transcend Darwinian natural selection furnish an unexpectedly robust basis for a rapid, concerted transition to genetic coding from a peptide·RNA world.

Comment: How the peptides appeared on an inorganic Earth is unexplained. Darwin scientists never give up.

Theoretical origin of life; new earliest?

by David Turell @, Thursday, December 21, 2017, 00:09 (2309 days ago) @ David Turell

A review article of the latest findings. If life started as early as proposed it seems that it was mandated to start:

https://www.livescience.com/61232-oldest-known-fossils.html?utm_source=ls-newsletter&am...

"Although the fossils were estimated to be about 3.5 billion years old, the diversity of microbes in the group suggested that life probably emerged on Earth even earlier than that, the study authors reported.

"But not everyone may agree that these fossils represent the oldest life on Earth. Some experts have indicated that there are other samples that could be even older than the Australian microfossils, while other researchers have cast doubt on whether these sediments house traces of life at all, suggesting that chemical markers thought to represent biological evidence were the result of geothermal activity.

***

"But microbe fossils, though neither structurally complex nor large, are unrivaled when it comes to age. The first life on Earth was microbial, and fossils from this time offer a tantalizing glimpse of the forms from which all creatures — living and extinct — evolved over billions of years.

"In recent years, other studies have reported microfossils holding evidence of ancient microbial life, such as tiny hematite tubes embedded in iron-rich volcanic rock in Quebec, which may have housed microbes that lived between 3.77 billion and 4.29 billion years ago. Another study described cone-like structures detected in rocks in southwestern Greenland, which could represent sediments surrounding fossilized microbial colonies that lived 3.7 billion years ago.

"Both of those discoveries indicate possible evidence of life that would be older than the microbes evaluated in the new study. However, the new investigation is the first to examine and describe individual, fossilized microbes, finding "both the morphology and geochemical signature of life" in samples that are this old, study co-author John W. Valley, a professor of geoscience at the University of Wisconsin-Madison, told Live Science in an email.

***

"After they scanned the fossils, they isolated and compared carbon isotopes — forms of carbon with the same number of protons but different numbers of neutrons. They found that the ratios of two particular isotopes "are characteristic of biology and metabolic function," Valley said in the statement.

***

"The study authors further identified the microbes as a diverse group, which included some microbes that were methane producers, some that would have consumed methane and others that would have relied on the sun to produce energy.

"The differentiation between these microbes was especially noteworthy, because it suggests that life had already been on Earth long enough for it to begin to diversify and specialize, the study authors reported. While it's impossible to say when life made its first appearance on the planet, these microbes hint that very primitive microbial life could have emerged even in Earth's infancy.

"'We have no direct evidence that life existed 4.3 billion years ago but there is no reason why it couldn't have," Valley said in the statement."

Comment: the Earth formed about 4.5-6 bilion years ago. It was hot and bombarded by space rocks (planetismals), and then life popped up right away! Only if guided by God.

Theoretical origin of life; new earliest proof

by David Turell @, Thursday, December 21, 2017, 14:44 (2308 days ago) @ David Turell

A comment by Paul Davies on 3.5 billion year old microfossils that are proven to be life, using carbon isotopes:

https://cosmosmagazine.com/biology/microscopic-blobs-confirmed-as-earliest-known-microbes

Life has existed on planet Earth for most of its 4.5 billion-year history, but pinning down the oldest traces has been a major challenge. Scientists have long been drawn to the Pilbara region of Western Australia where rocks nearly 3.5 billion years old contain tantalizing evidence for ancient microbes.

In 1982, a team led by William Schopf of UCLA collected samples containing microscopic filaments reminiscent of bacteria, but because no organic material had survived, the interpretation depended largely on shape, leaving plenty of scope for disagreement. Were these features really the remnants of ancient life forms, or just mineral marks in a rock? Now new evidence confirms that the tiny structures are indeed fossilized microbes.

Schopf and his collaborators at UCLA, together with John Valley of the University of Wisconsin in Madison, focused on isotopes of carbon – the life-giving element. Most atoms of carbon have six protons and six neutrons in their nuclei, so they are labelled C12. But about one per cent of carbon is the heavier isotope C13, with six protons and seven neutrons.

C12 and C13 are chemically identical, but because C12 is slightly lighter it reacts faster and so tends to be slightly overabundant in living organisms – and in their fossilised remains. Detecting such an excess is one way that scientists infer signs of ancient life.
Unfortunately, a skewed carbon isotope ratio is not a smoking gun; non-biological processes can produce similar effects. In the case of the Pilbara rocks, other strands of evidence support the claim for a biological origin. Layered mounds of rock known as stromatolites are abundant there, suggesting that communities of microbes were flourishing 3.5 billion years ago.

he new work lays to rest the controversy over the putative microfossils. Advances in technology have permitted the researchers to measure the carbon isotope ratios of individual microscopic blobs using an instrument known as a secondary ion mass spectrometer. Although all of the 11 features analysed display excess C12, the degree of excess varied depending on the actual shapes. This finding accords with the expectation that different species of ancient microbes would have had different metabolisms.

For example, some microbes use photosynthesis, getting energy from the sun. Others produce methane, and yet others consume methane. Schopf’s group identified representatives of all three, across five different taxonomic groups. The key point is that non-biological processes would not have concentrated C12 with a systematic difference depending on the shapes of the features.

Comment: If one viewed the specialization of Earth as a means to produce life this early appearance demonstrates life was written into the plan from the very beginning. God is action is the only conclusion.

Theoretical origin of life; RNA plus peptides

by David Turell @, Saturday, December 23, 2017, 00:17 (2307 days ago) @ David Turell

I have no idea where these complex molecules first came from, but part of the point of the review article is RNA by itself is an inadequate start:

https://www.quantamagazine.org/the-end-of-the-rna-world-is-near-biochemists-argue-20171...

"Recent papers published in Biosystems and Molecular Biology and Evolution delineated why the RNA world hypothesis does not provide a sufficient foundation for the evolutionary events that followed. Instead, said Charles Carter, a structural biologist at the University of North Carolina, Chapel Hill, who co-authored the papers, the model represents “an expedient proposal.” “There’s no way that a single polymer could carry out all of the necessary processes we now characterize as part of life,” he added.

"And that single polymer certainly couldn’t be RNA, according to his team’s studies. The main objection to the molecule concerns catalysis: Some research has shown that for life to take hold, the mystery polymer would have had to coordinate the rates of chemical reactions that could differ in speed by as much as 20 orders of magnitude. Even if RNA could somehow do this in the prebiotic world, its capabilities as a catalyst would have been adapted to the searing temperatures — around 100 degrees Celsius — that abounded on early Earth. Once the planet started to cool, Carter claims, RNA wouldn’t have been able to evolve and keep up the work of synchronization. Before long, the symphony of chemical reactions would have fallen into disarray.

"Perhaps most importantly, an RNA-only world could not explain the emergence of the genetic code, which nearly all living organisms today use to translate genetic information into proteins. The code takes each of the 64 possible three-nucleotide RNA sequences and maps them to one of the 20 amino acids used to build proteins. Finding a set of rules robust enough to do that would take far too long with RNA alone, said Peter Wills, Carter’s co-author at the University of Auckland in New Zealand — if the RNA world could even reach that point, which he deemed highly unlikely. In Wills’ view, RNA might have been able to catalyze its own formation, making it “chemically reflexive,” but it lacked what he called “computational reflexivity.”

***

"Nature had to find a different route, a better shortcut to the genetic code. Carter and Wills think they’ve uncovered that shortcut. It depends on a tight feedback loop — one that would not have developed from RNA alone but instead from a peptide-RNA complex.

***

"At the center of their theory are 20 “loading” molecules called aminoacyl-tRNA synthetases. These catalytic enzymes allow RNA to bond with specific amino acids in keeping with the rules of the genetic code. “In a sense, the genetic code is ‘written’ in the specificity of the active sites” of those enzymes, said Jannie Hofmeyr, a biochemist at Stellenbosch University in South Africa, who was not involved in the study.

***

"To answer these questions, theories abound that move far beyond the RNA world. In fact, some scientists take an approach precisely opposite to that of Carter and Wills: They think instead that the earliest stages of life did not need to begin with anything resembling the kind of chemistry seen today. Doron Lancet, a genomics researcher at the Weizmann Institute of Science in Israel, posits an alternative theory that rests on assemblies of lipids that catalyze the entrance and exit of various molecules. Information is carried not by genetic sequences, but rather by the lipid composition of such assemblies."

Comment: I've ignored much of their fantastical proposition. It is easy to have reasonable fun and games with proposed specialized organic molecules, but how did these complex organic molecules sudenly appear on a hot and rocky mainly inorganic Earth? They see the RNA difficulties and that is what I wanted to present. Life is a miracle unil proven otherwise.

Theoretical origin of life; citric acid cycle

by David Turell @, Tuesday, January 09, 2018, 15:40 (2289 days ago) @ David Turell

More fun and games. A biologic chemical cycle is just one of many, many components of a living organism. These authors are ecstatic over one tiny aspect of what life must have:

http://www.scripps.edu/news/press/2018/20180108krishnamurthy.html

"For the new study, Krishnamurthy and his coauthors, who are all members of the National Science Foundation/National Aeronautics and Space Administration Center for Chemical Evolution, focused on a series of chemical reactions that make up what researchers refer to as the citric acid cycle.

"Every aerobic organism, from flamingoes to fungi, relies on the citric acid cycle to release stored energy in cells. In previous studies, researchers imagined early life using the same molecules for the citric acid cycle as life uses today. The problem with that approach, Krishnamurthy explains, is that these biological molecules are fragile and the chemical reactions used in the cycle would not have existed in the first billion years of Earth—the ingredients simply didn’t exist yet.

"Leaders of the new study started with the chemical reactions first. They wrote the recipe and then determined which molecules present on early Earth could have worked as ingredients.
The new study outlines how two non-biological cycles—called the HKG cycle and the malonate cycle—could have come together to kick-start a crude version of the citric acid cycle. The two cycles use reactions that perform the same fundamental chemistry of a-ketoacids and b-ketoacids as in the citric acid cycle. These shared reactions include aldol additions, which bring new source molecules into the cycles, as well as beta and oxidative decarboxylations, which release the molecules as carbon dioxide (CO2).

"As they ran these reactions, the researchers found they could produce amino acids in addition to CO2, which are also the end products of the citric acid cycle. The researchers think that as biological molecules like enzymes became available, they could have led to the replacement of non-biological molecules in these fundamental reactions to make them more elaborate and efficient. (my bold)

“'The chemistry could have stayed the same over time, it was just the nature of the molecules that changed,” says Krishnamurthy. “The molecules evolved to be more complicated over time based on what biology needed.” (my bold)

“'Modern metabolism has a precursor, a template, that was non-biological,” adds Greg Springsteen, PhD, first author of the new study and associate professor of chemistry at Furman University.

"Making these reactions even more plausible is the fact that at the center of these reactions is a molecule called glyoxylate, which studies show could have been available on early Earth and is part of the citric acid cycle today (called the “Glyoxylate shunt or cycle”).

"Krishnamurthy says more research needs to be done to see how these chemical reactions could have become as sustainable as the citric acid cycle is today."

Comment: The authors' statements bolded by me are patently stupid. Molecules think and evolve?

Theoretical origin of life; new earliest even earlier?

by David Turell @, Thursday, January 25, 2018, 14:35 (2273 days ago) @ David Turell

A review of all the findings about the possible earliest forms. It is apparent life didn't take long to start:

https://www.quantamagazine.org/fossil-discoveries-challenge-ideas-about-earths-start-20...

"From a seam in one of these hills, a jumble of ancient, orange-Creamsicle rock spills forth: a deposit called the Apex Chert. Within this rock, viewable only through a microscope, there are tiny tubes. Some look like petroglyphs depicting a tornado; others resemble flattened worms. They are among the most controversial rock samples ever collected on this planet, and they might represent some of the oldest forms of life ever found.

"Last month, researchers lobbed another salvo in the decades-long debate about the nature of these forms. They are indeed fossil life, and they date to 3.465 billion years ago, according to John Valley, a geochemist at the University of Wisconsin. If Valley and his team are right, the fossils imply that life diversified remarkably early in the planet’s tumultuous youth.

"The fossils add to a wave of discoveries that point to a new story of ancient Earth. In the past year, separate teams of researchers have dug up, pulverized and laser-blasted pieces of rock that may contain life dating to 3.7, 3.95 and maybe even 4.28 billion years ago. All of these microfossils — or the chemical evidence associated with them — are hotly debated. But they all cast doubt on the traditional tale.

***

"Many geologists now think Earth may have been tepid and watery from the outset. The oldest rocks in the record suggest parts of the planet’s crust had cooled and solidified by 4.4 billion years ago. Oxygen in those ancient rocks suggest the planet had water as far back as 4.3 billion years ago. And instead of an epochal, final bombardment, meteorite strikes might have slowly tapered off as the solar system settled into its current configuration.

“'Things were actually looking a lot more like the modern world, in some respects, early on. There was water, potentially some stable crust. It’s not completely out of the question that there would have been a habitable world and life of some kind,” said Elizabeth Bell, a geochemist at the University of California, Los Angeles.

***

"Today, the oldest evidence for possible life — which many scientists doubt or outright reject — is at least 3.77 billion years old and may be a stunningly ancient 4.28 billion years old.

"In March 2017, Dominic Papineau, a geochemist at University College London, and his student Matthew Dodd described tubelike fossils in an outcrop in Quebec that dates to the basement of Earth’s history. The formation, called the Nuvvuagittuq (noo-voo-wog-it-tuck) Greenstone Belt, is a fragment of Earth’s primitive ocean floor. The fossils, about half the width of a human hair and just half a millimeter long, were buried within. They are made from an iron oxide called hematite and may be fossilized cities built by microbial communities up to 4.28 billion years ago, Dodd said.

***

"Then in September 2017, researchers in Japan published an examination of graphite flakes from a 3.95-billion-year-old sedimentary rock called the Saglek Block in Labrador, Canada. Yuji Sano and Tsuyoshi Komiya of the University of Tokyo argued their graphite’s carbon-isotope ratio indicates it, too, was made by life. But the graphite flakes were not accompanied by any feature that looked like a fossil; what’s more, the history of the surrounding rock is murky, suggesting the carbon may be younger than it appears.

"Farther to the east, in southwestern Greenland, another team had also found evidence of ancient life. In August 2016, Allen Nutman of the University of Wollongong in Australia and colleagues reported finding stromatolites, fossil remains of microbes, from 3.7 billion years ago.

***

"In research published in 2015, Bell and her coauthors presented evidence for graphite embedded within a tiny, 4.1-billion-year-old zircon crystal from the same Jack Hills. The graphite’s blend of carbon isotopes hints at biological origins, although the finding is — once again — hotly debated.

“'Are there other explanations than life? Yeah, there are,” Bell said. “But this is what I would consider the most secure evidence for some sort of fossil or biogenic structure.'”

Comment: A very hospitably designed Earth had life pop up easily. The evidence points to God at work.

Theoretical origin of life;original protein building blocks?

by David Turell @, Sunday, January 28, 2018, 00:54 (2271 days ago) @ David Turell

Computer analysis of living proteins has found four basic protein building blocks aht may have been at the origin of life:

http://www.latimes.com/science/sciencenow/la-sci-sn-legos-of-life-20180122-story.html

"By "smashing" proteins and looking at the broken bits, scientists at Rutgers University say they've discovered four basic building blocks that can be stacked like Legos to build all kinds of different proteins.

***

"Many scientists think that some of the earliest forms of life would have hung out where natural electric currents exist — at the bottom of the sea floor, for example, where hydrothermal vents spew material into the ocean.

"Ancient microbes would have needed special proteins to take advantage of those energy sources. These metal-bearing "metalloproteins" would have been able to carry and move electrons around in specific ways. But what exactly did such proteins look like, some 4 billion years ago?

"It's hard to judge by what's in modern-day microbes because their proteins are pretty complex, Nanda said. He pointed to proteins like nitrogenase, an essential enzyme that takes nitrogen and makes ammonia, which is then used to make DNA and amino acids.

"You couldn't imagine that complex nanomachine just emerging out of the primordial soup and just coming into existence," Nanda said. "There had to have been simpler intermediates. But the challenge is we don't have any fossil record of what proteins look like. All we have is the modern proteins, and we have to somehow infer what the simpler proteins may have looked like." (my bold)

***

"the scientists were able to pick out four useful pieces — modules made up of around 60 to 100 amino acids. Each one can carry electrons or carry out reactions but uses different metals (such as copper, iron, nickel or manganese) or puts those metals in different configurations.

"The scientists think the oldest of the four is the one with a cube-shaped cluster of four irons and four sulfurs. That's because this subunit would be very handy for harvesting energy around hydrothermal vents, which are known to host life-like chemical reactions even when living things aren't around. That kind of chemistry could have made it much easier for microbes with the right kinds of electron-shuttling proteins to thrive, the thinking goes.

***

"'We really are only looking at a very small subset of proteins, the ones that are involved in electron transfer," Nanda said.

These smash-and-search methods could be used to find shared building blocks within other groups of proteins beyond the electron-transfer group, he added.

"The scientists also want to chop up those four subunits of 60 to 100 amino acids and find even smaller, simpler essential pieces within them, he said. The simpler the unit, the closer it might be to those primordial proteins."

Comment: Note my bold. How did giant enzyme molecules get created? And where did all the amino acids come from. Only some which can be functional are known to arrive by meteorites. Life still looks miraculous.

Theoretical origin of life; earliest land life

by David Turell @, Tuesday, July 24, 2018, 17:49 (2093 days ago) @ David Turell

The earliest organic molecule signatures of possible life come from rocks that were marine in origin, not land, and have dated back to 3.8 billion years ago. Now a possible terrestrial life is found at 3.2 billion years ago:

https://www.the-scientist.com/news-opinion/oldest-evidence-of-terrestrial-life-on-a-you...

"The earliest signs of life on a young Earth, around 3.5 billion years ago, have generally come from the ocean in the form of fossilized microbes within ancient rock. Now, scientists working in the Barberton Greenstone Belt in South Africa—where some of the oldest rocks on Earth are preserved—find evidence of terrestrial microbial life that they estimate is about 3.22 billion years old. The results, published today (July 23) in Nature Geosciences, represent the oldest signs of land-based life on our planet yet discovered.

“'This work represents the oldest and least unambiguous work that we have so far that life existed on land already 3.2 billion years ago,”

***

"For the current study, Homann and his colleagues focused on ancient sedimentary rocks, known as the Moodies Group, in the Barberton Greenstone Belt that were shown by geologists earlier to be approximately 3.22 billion years old. There, the team uncovered what are known as fossilized microbial mats—composed mainly of the imprints of bacteria and archaea and are among the earliest preserved forms of life. While living on the early Earth, these microbial community mats became interlayered and packed together with sedimentary rock made of rounded stones of different sizes that geologists call a conglomerate.

***

"The researchers then analyzed both the organic carbon and nitrogen isotopes within these fossilized terrestrial microbial mats and compared the profiles to isotopes extracted from nearby fossilized marine microbial mats. Both the carbon and nitrogen isotope values from the terrestrial and marine samples were unique from one another, suggesting that there were differences in the metabolism of microbes in the ocean compared to those on land.

“'Already at 3.2 billion years ago, we see evidence of differences in mat-forming microbial communities suggesting that some were likely better adapted for life in the ocean versus on land,” says Homann."

Comment: This just adds to the evidence that life started very early on the newly formed Earth.

Theoretical origin of life; earliest land life

by dhw, Wednesday, July 25, 2018, 13:02 (2092 days ago) @ David Turell

QUOTE: “'Already at 3.2 billion years ago, we see evidence of differences in mat-forming microbial communities suggesting that some were likely better adapted for life in the ocean versus on land,” says Homann."

DAVID: This just adds to the evidence that life started very early on the newly formed Earth.

It also adds to the evidence that the earliest forms of life were possessed of a mechanism that enabled them to adapt to different environments. Note the term “communities”. All multicellular adaptations and innovations require intelligent cooperation between cells. That may be a sign that the intelligence actually comes from the cells.

Theoretical origin of life; earliest land life

by David Turell @, Wednesday, July 25, 2018, 18:23 (2092 days ago) @ dhw

QUOTE: “'Already at 3.2 billion years ago, we see evidence of differences in mat-forming microbial communities suggesting that some were likely better adapted for life in the ocean versus on land,” says Homann."

DAVID: This just adds to the evidence that life started very early on the newly formed Earth.

dhw: It also adds to the evidence that the earliest forms of life were possessed of a mechanism that enabled them to adapt to different environments. Note the term “communities”. All multicellular adaptations and innovations require intelligent cooperation between cells. That may be a sign that the intelligence actually comes from the cells.

Or the originator of life implanted intelligent instructions for adaptations, which are not speciation.

Theoretical origin of life; more lab play

by David Turell @, Wednesday, July 25, 2018, 21:42 (2092 days ago) @ David Turell

this time the lab work proposes lots of fatty substances were on Earth to fascilitate the joining together of organic compounds:

https://phys.org/news/2018-07-century-old-life-significant-substantiation.html

"In 1924, Russian biochemist Alexander Oparin claimed that life on Earth developed through gradual chemical changes of organic molecules, in the "primordial soup" which likely existed on Earth four billion years ago. In his view, the complex combination of lifeless molecules, joining forces within small oily droplets, could assume life faculties—self-replication, selection and evolution. These ideas were received with considerable doubt, still pertaining today.

"Thirty years later, when DNA structure was deciphered, it was realized that this molecule is capable of self-replication, seemingly solving the enigma of life's origin without resort to Oparin's droplets. But critics argued that life requires not only replicators, but also enzyme catalysts to control­ metabolism. Another 30 years passed before the discovery that RNA, key component in information transfer from DNA to proteins, can also be an enzyme. This is how the concept of "RNA World" was born, whereby life began when the primordial soup gave birth to a ribozyme, which can both replicate and control metabolism.

"Despite this doubts lingered, because a replicating ribosome is a highly complex molecule, with negligible probability of spontaneous appearance in the soup. This led to an alternative concept—mutually catalytic networks, affording the copying of entire molecular ensembles.

"This idea echoes Oparin's evolving complex combination of simple molecules, each with high likelihood of appearance in the soup. What remained was to generate a detailed chemical model that will help support such a narrative.

"Prof. Doron Lancet and colleagues at the Weizmann Institute of Science, Dept. of Molecular Genetics came up with such a model. First, it was necessary to identify the appropriate type of molecules, that can accrete together and effectively form networks of mutual interactions, in line with Oparin's droplets. Lancet proposed lipids, oily compounds that spontaneously form the aggregated membranes enclosing all living cells. Lipid bubbles (vesicles) can grow and split much like living cells. This is how Lancet generated the concept "Lipid World" two decades ago.

***

"Based on the computer model they developed, the scientists demonstrated that specific lipid compositions, called "composomes", can undergo compositional mutations, be subject to natural selection in response to environmental changes, and even undergo Darwinian selection. Prof. Lancet comments that such an information system, which is based on compositions and not on the sequence of chemical "letters" as in DNA, is reminiscent of the realm of epigenetics, where traits are inherited independent of the DNA sequence. This lends credence to the scientists' assumption that life could emerge before the advent of DNA and RNA. In their article they in fact delineate a chemical path that lead to the appearance of genetic material in the framework of the oily droplets.

"Lancet's "Lipid World" concept is contingent upon the question of whether there were sufficient oil-like "water hating" molecules in the primordial soup. Here too, the scientists describe a comprehensive literature search, according to which there is a high probability for such molecules to be present on early Earth."

Comment: As usual full of hope with no real substance to the hope that lipids were all over the Earth at the beginning of first life or even in some lucky spots. I don't know that meteorites showed lipids when analyzed. The Murchison meteorite did not.

Theoretical origin of life; earliest land life

by Balance_Maintained @, U.S.A., Wednesday, July 25, 2018, 22:47 (2092 days ago) @ dhw

And God said, “Let there be a vault between the waters to separate water from water.” 7 So God made the vault and separated the water under the vault from the water above it. And it was so. 8 God called the vault “sky.” And there was evening, and there was morning—the second day.


Carbon Dioxide rich clouded atmosphere, likely full of volcanic ash and debris as early earth tectonics occured.


9 And God said, “Let the water under the sky be gathered to one place, and let dry ground appear.” And it was so. 10 God called the dry ground “land,” and the gathered waters he called “seas.” And God saw that it was good.

End of early tectonic shifting, or possibly the crash that created the moon depending on which theory you like, and settling of the oceans.

11 Then God said, “Let the land produce vegetation: seed-bearing plants and trees on the land that bear fruit with seed in it, according to their various kinds.” And it was so. 12 The land produced vegetation: plants bearing seed according to their kinds and trees bearing fruit with seed in it according to their kinds. And God saw that it was good. 13 And there was evening, and there was morning—the third day.

Introduction of plantlife. Note the fact that the earth is still wrapped in a carbon rich atmosphere which would have caused early plant life to bloom very quickly, causing a tremendous increase in O2 levels and paving the way for early animal life.

14 And God said, “Let there be lights in the vault of the sky to separate the day from the night, and let them serve as signs to mark sacred times, and days and years, 15 and let them be lights in the vault of the sky to give light on the earth.” And it was so. 16 God made two great lights—the greater light to govern the day and the lesser light to govern the night. He also made the stars. 17 God set them in the vault of the sky to give light on the earth, 18 to govern the day and the night, and to separate light from darkness. And God saw that it was good. 19 And there was evening, and there was morning—the fourth day.

Here is the settling of earths orbit, the clearing of the gas cloud to reveal the sun and moon. It is also possible that it would have taken this long for light from the stars to reach earth in a stable configuration.

The creation of animal life comes after, first the fish, birds, and great lizards. Then livestock and wild animals (assuming insects as well, here) though, they could have been in the previous epoch.


Now, I am not implying 6 literal days or anything, but merely pointing out that the bible doesn't specify whether he created each species or not, but it DOES specify that things were created at seperate times, which implies the prototypes were introduced when the time was right in terms of Earth's development.

Even if you don't believe the biblical narrative, you do have to wonder how they could write an accounting so damn close to what we have discovered. It should not be possible by our accounting of history.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Theoretical origin of life; earliest land life

by David Turell @, Thursday, July 26, 2018, 01:22 (2092 days ago) @ Balance_Maintained

Tony: Now, I am not implying 6 literal days or anything, but merely pointing out that the bible doesn't specify whether he created each species or not, but it DOES specify that things were created at seperate times, which implies the prototypes were introduced when the time was right in terms of Earth's development.

Even if you don't believe the biblical narrative, you do have to wonder how they could write an accounting so damn close to what we have discovered. It should not be possible by our accounting of history.

You might be surprised how the Bible can be interpreted by ancient Jewish seers; this is taken from my book and quoted from 'Genesis and the Big Bang' by Gerald Schroeder:

“At the briefest instant following creation all the matter of the universe was concentrated in a very small place, no larger than a grain of mustard [the ‘grain of mustard’ was an ancient colloquialism for the tiniest imaginable speck of space]. The matter at this time was so thin, so intangible, that it did not have real substance. It did have, however, a potential to gain substance and form and to become tangible matter. From the initial concentration of this intangible substance in its minute location, the substance expanded, expanding the universe as it did so. As the expansion progressed, a change in the substance occurred. This initially thin noncorporeal substance took on tangible aspects of matter as we know it. From this initial act of creation, from this ethereally thin pseudosubstance, everything that has existed, or ever will exist, was, is, and will be formed.” This quote is from Nahmanides, written in the 13th century in Commentary on the Torah, Genesis 1:1!! He was a Biblical scholar and commentator, and also a mystic, an early member of a branch of Judaism called the Kabbalah. I am sure you are as astounded as I am that a 700-year old description of the Big Bang is so accurate."

Theoretical origin of life; earliest land life

by dhw, Thursday, July 26, 2018, 13:07 (2091 days ago) @ Balance_Maintained

And God said, “Let there be a vault between the waters to separate water from water.” 7 So God made the vault and separated the water under the vault from the water above it. And it was so. 8 God called the vault “sky.” And there was evening, and there was morning—the second day.

TONY: Carbon Dioxide rich clouded atmosphere, likely full of volcanic ash and debris as early earth tectonics occured.

The author sees the water and the sky, and he says God did it. He doesn’t mention carbon dioxide, volcanic ash, debris or tectonics.

9 And God said, “Let the water under the sky be gathered to one place, and let dry ground appear.” And it was so. 10 God called the dry ground “land,” and the gathered waters he called “seas.” And God saw that it was good.

TONY: End of early tectonic shifting, or possibly the crash that created the moon depending on which theory you like, and settling of the oceans.

The author sees land and sea, and he says God did it. He doesn’t mention tectonic shifting or any other theory. And the author sees vegetation, and animals, and the stars, and the sun and the moon and day and night, and he says God did it. Nobody is denying that sky, water, plants, animals, stars etc. exist, and the only explanation the bible gives is that God did it. Then we humans come along and try to explain the science behind what God did. David’s example of the mustard seed would be a good one (a) if you believed in the big bang theory of a universe springing from some sort of nothing, and (b) if you believed that “In the beginning God created the heaven and the earth” means that in the beginning there was a small place no larger than a grain of mustard.

TONY: Now, I am not implying 6 literal days or anything, but merely pointing out that the bible doesn't specify whether he created each species or not, but it DOES specify that things were created at seperate times, which implies the prototypes were introduced when the time was right in terms of Earth's development.

If separate creation is not specified, then I don’t know what all the fuss was about when Darwin argued for common descent. Species appearing at different times is no problem for a theory which argues that all species descended from earlier forms of life, and it stands to reason that they would only have appeared when conditions were right for them to appear.

TONY: Even if you don't believe the biblical narrative, you do have to wonder how they could write an accounting so damn close to what we have discovered. It should not be possible by our accounting of history.

It’s you who wrote the account of what we have discovered. The author wrote that what he saw was created by God.

Theoretical origin of life; earliest land life on Africa

by David Turell @, Tuesday, July 31, 2018, 05:56 (2087 days ago) @ dhw

About 3.2 million year old mats:

https://www.livescience.com/63199-oldest-life-on-land.html?utm_source=lsa-newsletter&am...

"About 3.22 billion years ago, slimy layers of microbes coated pebbles in what was perhaps an ancient riverbed. Those ancient microbial mats, preserved for eons and only recently discovered in South Africa, may be the oldest fossil evidence of life on land, according to a new study.

"The ancient evidence of terrestrial life is about a half billion years older than the previous record holder — fossilized remains of microbes found decades ago in South Africa and Australia, said Stefan Lalonde, a geochemist from the European Institute for Marine Studies in France and a co-author of the new study, published July 23 in the journal Nature Geoscience.

"Geological evidence has hinted that life existed in the oceans as far back as 3.8 billion years ago. But signs of terrestrial life have been rarer — possibly because most of the planet might have been under water until 3 billion years ago.

***

"The researchers, led by Martin Homann, a sedimentologist at the European Institute for Marine Studies, discovered the fossilized microbes on the side of a rocky cliff in the Barberton Makhonjwa Mountains of eastern South Africa, home to some of the world's oldest geological features. The fossils are part of a chunk of rock called the Moodies Group, which represents one of the world's oldest shorelines, Lalonde said.

"The microbes are extremely well-preserved, he said, showing thick sheets that blanket pebbles, a sign that the critters lived on an ancient riverbed — a terrestrial environment — rather than a sandy beach. Ripple-like features suggest that water flowed in one direction in this area, further evidence that the microbes lived along a river or, perhaps, an alluvial fan. That's a geological feature formed when runoff flows outward in the shape of a fan.

"'This is essentially Earth's oldest riverbed," Lalonde told Live Science. "And it's already containing life."

"Unlike other evidence of land-based life, such as fossilized structures built by bacteria, the newfound fossils are of the preserved microbes themselves. The layered fossils formed when a layer of sediment covered a sheet of microbes, only later to have another blanket of microbes grow on top. Over time, layers of microbes and sediment stacked on top of each other like primordial lasagna and became preserved. Because these are directly preserved microbes, the fossils even contain organic matter, such as carbon and nitrogen atoms that once were part of the organisms.

"An analysis of the type of nitrogen atoms present in the fossils suggests that the ancient microbes thrived by consuming nitrate, or a nitrogen atom bonded to three oxygen atoms, Lalonde said. When these microbes lived, during the Archean eon (which lasted from 4 billion to 2.5 billion years ago), Earth's atmosphere wasn't filled with oxygen as it is now. But a nitrate-based metabolism is the most energy-efficient type of metabolism after an oxygen-based one — which is what humans, for example, use. Nitrate would've given the microbes plenty of energy, Lalonde said."

Comment: More evidence that life appeared quickly.

Theoretical origin of life; earliest land life 3.4 byo?

by David Turell @, Thursday, August 16, 2018, 23:43 (2070 days ago) @ David Turell

With biological traces as proof:

https://phys.org/news/2018-08-microfossils-possibly-world-oldest-biological.html

"Scientists have confirmed that the 3.4 billion year old Strelley Pool microfossils had chemical characteristics similar to modern bacteria. This all but confirms their biological origin and ranks them amongst the world's oldest microfossils.

"A team of scientists, led by Dr. Julien Alleon (IMPMC, Paris, France; and MIT, Cambridge, MA, USA) have been able to show that the chemical residuals from ancient microfossils match those of younger bacterial fossils, and so are likely to have been laid down by early life forms.

"They compared the results of synchrotron-based X-ray absorption spectroscopy analysis of the Strelley Pool microfossils with more recent ones from the Gunflint Formation (1.9 billion years old, found on the shores of Lake Superior, Ontario, Canada) and with modern bacteria.All showed similar absorption features, indicating that the residual chemicals were made from the same building blocks, thereby supporting a biological origin.

"'There are a couple of important points which come out of this work. Firstly, we demonstrate that the elemental and molecular characteristics of these 3.4 Ga microfossils are consistent with biological remains, slightly degraded by fossilization processes. This effectively supports the biological origin of the Strelley Pool microfossils. There are competing claims over which microfossils are actually the world's oldest, this analytical strategy needs to be applied to other ancient samples to help settle the controversy.
Secondly, it is remarkable that these echoes of past life have survived the extreme conditions they have experienced over the last 3.4 billion years: we know from the molecular structure of the microfossils that they have been exposed to temperatures of up to 300 °C for long periods. And yet we are still able to see signs of their original chemistry.

***

"'This is exciting work with the new types of analyses providing compelling evidence that the cherts contain biogenic microfossils. This is in line with other observations for early life from the Strelley Pool rocks, including stromatolites interpreted as microbial mats, and further confirming that the minimum age for life on Earth is 3.4 billion years.

"The techniques used here are not applicable to the older rocks that host the claims for the oldest terrestrial life, as these rocks were exposed to much higher temperatures. These samples include the 3.7 billion year old stromatolites from Isua, Greenland and the 4.1 billion year old Canadian microfossils. However, this work shows how quickly the field is developing and that new capabilities for testing and confirming earlier evidence of life are in reach'".

Comment: 3.8 byo is the earliest discussed, but by any analysis, if the Earth is 4.5 byo, life initiated very early on, which means the conditions for the origin had to be ideal. And where did all the early protein molecules come from? The initial Earth was a rocky hot place, lacking organic molecules which generally have to come from living matter.

Theoretical origin of life; zircons with 4.1 byo evidence:

by David Turell @, Monday, August 20, 2018, 18:14 (2066 days ago) @ David Turell

Zircon research:

http://newsroom.ucla.edu/releases/life-on-earth-likely-started-at-least-4-1-billion-yea...

"The new research suggests that life existed prior to the massive bombardment of the inner solar system that formed the moon’s large craters 3.9 billion years ago.

“'If all life on Earth died during this bombardment, which some scientists have argued, then life must have restarted quickly,” said Patrick Boehnke, a co-author of the research and a graduate student in Harrison’s laboratory.

"Scientists had long believed the Earth was dry and desolate during that time period. Harrison’s research — including a 2008 study in Nature he co-authored with Craig Manning, a professor of geology and geochemistry at UCLA, and former UCLA graduate student Michelle Hopkins — is proving otherwise.

“'The early Earth certainly wasn’t a hellish, dry, boiling planet; we see absolutely no evidence for that,” Harrison said. “The planet was probably much more like it is today than previously thought.”

***

"The scientists identified 656 zircons containing dark specks that could be revealing and closely analyzed 79 of them with Raman spectroscopy, a technique that shows the molecular and chemical structure of ancient microorganisms in three dimensions.

"Bell and Boehnke, who have pioneered chemical and mineralogical tests to determine the condition of ancient zircons, were searching for carbon, the key component for life.

"One of the 79 zircons contained graphite — pure carbon — in two locations.

“'The first time that the graphite ever got exposed in the last 4.1 billion years is when Beth Ann and Patrick made the measurements this year,” Harrison said.

"How confident are they that their zircon represents 4.1 billion-year-old graphite?

“'Very confident,” Harrison said. “There is no better case of a primary inclusion in a mineral ever documented, and nobody has offered a plausible alternative explanation for graphite of non-biological origin into a zircon.”

"The graphite is older than the zircon containing it, the researchers said. They know the zircon is 4.1 billion years old, based on its ratio of uranium to lead; they don’t know how much older the graphite is.

"The research suggests life in the universe could be abundant, Harrison said. On Earth, simple life appears to have formed quickly, but it likely took many millions of years for very simple life to evolve the ability to photosynthesize.

"The carbon contained in the zircon has a characteristic signature — a specific ratio of carbon-12 to carbon-13 — that indicates the presence of photosynthetic life.

“'We need to think differently about the early Earth,” Bell said."

Comment: Earlier and earlier.

Theoretical origin of life; new genetic evidence

by David Turell @, Monday, August 20, 2018, 18:25 (2066 days ago) @ David Turell

Again, before 4 byo:

https://phys.org/news/2018-08-timescale-evolution-life-earth.html

"'The problem with the early fossil record of life is that it is so limited and difficult to interpret—careful reanalysis of the some of the very oldest fossils has shown them to be crystals, not fossils at all."

"Fossil evidence for the early history of life is so fragmented and difficult to evaluate that new discoveries and reinterpretations of known fossils have led to a proliferation of conflicting ideas about the timescale of the early history of life.

"Co-author Professor Philip Donoghue, also from Bristol's School of Earth Sciences, added: "Fossils do not represent the only line of evidence to understand the past. A second record of life exists, preserved in the genomes of all living creatures."

"Co-author Dr. Tom Williams, from Bristol's School of Biological Sciences, said: "Combining fossil and genomic information, we can use an approach called the 'molecular clock' which is loosely based on the idea that the number of differences in the genomes of two living species (say a human and a bacterium) are proportional to the time since they shared a common ancestor."

"By making use of this method the team at Bristol and Mark Puttick from the University of Bath were able to derive a timescale for the history of life on Earth that did not rely on the ever-changing age of the oldest accepted fossil evidence of life.

"Co-author Professor Davide Pisani said: "Using this approach we were able to show that the Last Universal Common Ancestor all cellular life forms, 'LUCA', existed very early in Earth's history, almost 4.5 Billion years ago—not long after Earth was impacted by the planet Theia, the event which sterilised Earth and led to the formation of the Moon.

"'This is significantly earlier than the currently accepted oldest fossil evidence would suggest.

"'Our results indicate that two "primary" lineages of life emerged from LUCA (the Eubacteria and the Archaebacteria), approximately one Billion years after LUCA.

"'This result is testament to the power of genomic information, as it is impossible, based on the available fossil information, to discriminate between the oldest eubacterial and archaebacterial fossil remains."

"The study confirms modern views that the eukaryotes, the lineage to which human life belongs (together with the plants and the fungi, for example), is not a primary lineage of life. Professor Pisani added: "It is rather humbling to think we belong to a lineage that is billions of years younger than life itself.'"

Comment: It makes sense that the earliest cells were the basis for development of future forms, and would not leave fossils behind. Genetic analysis still has to be based on assumptions which might slant the result.

Theoretical origin of life; fun and games in the lab

by David Turell @, Thursday, August 30, 2018, 21:37 (2056 days ago) @ David Turell

Another lab invention that 'might' have been present and work; a very simple organic molecule with sulfur and iron:

https://phys.org/news/2018-08-scientists-protein-life-began.html

"In the late 1980s and early 1990s, the chemist Günter Wächtershäuser postulated that life began on iron- and sulfur-containing rocks in the ocean. Wächtershäuser and others predicted that short peptides would have bound metals and served as catalysts of life-producing chemistry, according to study co-author Vikas Nanda, an associate professor at Rutgers' Robert Wood Johnson Medical School.

"Human DNA consists of genes that code for proteins that are a few hundred to a few thousand amino acids long. These complex proteins—needed to make all living-things function properly—are the result of billions of years of evolution. When life began, proteins were likely much simpler, perhaps just 10 to 20 amino acids long. With computer modeling, Rutgers scientists have been exploring what early peptides may have looked like and their possible chemical functions, according to Nanda.

"The scientists used computers to model a short, 12-amino acid protein and tested it in the laboratory. This peptide has several impressive and important features. It contains only two types of amino acids (rather than the estimated 20 amino acids that synthesize millions of different proteins needed for specific body functions), it is very short and it could have emerged spontaneously on the early Earth in the right conditions. The metal cluster at the core of this peptide resembles the structure and chemistry of iron-sulfur minerals that were abundant in early Earth oceans. The peptide can also charge and discharge electrons repeatedly without falling apart, according to Nanda, a resident faculty member at the Center for Advanced Technology and Medicine.

"'Modern proteins called ferredoxins do this, shuttling electrons around the cell to promote metabolism," said senior author Professor Paul G. Falkowski, who leads Rutgers' Environmental Biophysics and Molecular Ecology Laboratory. "A primordial peptide like the one we studied may have served a similar function in the origins of life.'"

Comment: No one has any idea what existed to start life. All this is, is playing with possibilities.

Theoretical origin of life; fun and games in the lab

by Balance_Maintained @, U.S.A., Friday, August 31, 2018, 04:31 (2056 days ago) @ David Turell

Another lab invention that 'might' have been present and work; a very simple organic molecule with sulfur and iron:

https://phys.org/news/2018-08-scientists-protein-life-began.html

"In the late 1980s and early 1990s, the chemist Günter Wächtershäuser postulated that life began on iron- and sulfur-containing rocks in the ocean. Wächtershäuser and others predicted that short peptides would have bound metals and served as catalysts of life-producing chemistry, according to study co-author Vikas Nanda, an associate professor at Rutgers' Robert Wood Johnson Medical School.

"Human DNA consists of genes that code for proteins that are a few hundred to a few thousand amino acids long. These complex proteins—needed to make all living-things function properly—are the result of billions of years of evolution. When life began, proteins were likely much simpler, perhaps just 10 to 20 amino acids long. With computer modeling, Rutgers scientists have been exploring what early peptides may have looked like and their possible chemical functions, according to Nanda.

"The scientists used computers to model a short, 12-amino acid protein and tested it in the laboratory. This peptide has several impressive and important features. It contains only two types of amino acids (rather than the estimated 20 amino acids that synthesize millions of different proteins needed for specific body functions), it is very short and it could have emerged spontaneously on the early Earth in the right conditions. The metal cluster at the core of this peptide resembles the structure and chemistry of iron-sulfur minerals that were abundant in early Earth oceans. The peptide can also charge and discharge electrons repeatedly without falling apart, according to Nanda, a resident faculty member at the Center for Advanced Technology and Medicine.

"'Modern proteins called ferredoxins do this, shuttling electrons around the cell to promote metabolism," said senior author Professor Paul G. Falkowski, who leads Rutgers' Environmental Biophysics and Molecular Ecology Laboratory. "A primordial peptide like the one we studied may have served a similar function in the origins of life.'"

Comment: No one has any idea what existed to start life. All this is, is playing with possibilities.

It's cool that they are looking for solutions. I just hate that they always try to ignore the idea of a designer. But the problem is still new information.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Theoretical origin of life; fun and games in the lab

by David Turell @, Wednesday, September 12, 2018, 18:41 (2043 days ago) @ Balance_Maintained

Another invented molecule in the lab from proteins that are imagined to exist based on proteins in life today:

https://phys.org/news/2018-09-life.html

"Evolution by Darwinian natural selection is immensely powerful—both in nature and within laboratories. Using 'laboratory evolution', we can take an enzyme which combines random mutations and functional selection, and improve its function by more than 1000 times. You can see evidence of science taking advantage of evolution across the field, from synthesised medications used to prevent the reoccurrence of heart attacks (beta blockers) to the development of tumor-targeting antibody therapeutics.

"However, nothing evolves unless it already exists. When life started more than three billion years ago, what was the spark that created something from randomness? (my bold)

"Researchers from the Monash Biomedicine Discovery Institute (BDI), have identified what they have termed 'Structural Capacitance Elements' in mutated proteins that are associated with many different types of human diseases, in particular a range of cancers.

"Structural Capacitance Elements are localised regions of disorder within proteins, which retain the potential to coalesce into 'micro-structures' following the introduction of a mutation. They act as nucleating seeds, or 'feedstock' for evolution to proceed, providing the basis of an accelerated mechanism of Darwinian evolution by natural selection, supplementing the slow and incremental process of classic Darwinian evolution.

"This discovery has recently been published in the Journal of Molecular Biology. Lead researcher on this paper, Associate Professor Ashley Buckle, explained the significance of this discovery.

"Up until now, the prevailing belief amongst structural biologists has been that mutations that are implicated in disease act by disrupting protein structures—typically referred to as the 'loss-of-structure-function' paradigm. However it has recently been uncovered that more than 40 per cent of proteins have no well-defined structure at all," Associate Professor Buckle said.

"'This prompted us to ask a very different question, and to turn the prevailing belief on its head," he said.

"The research team analysed many of these disease-associated mutations and found that these 'Structural Capacitance Elements' may allow mutations to trigger a 'gain-of-function' by inducing structure where none existed before."

Comment: The key is their statement in bold that proteins have to exist for life to appear and develop. Early Earth was a planet with few if any protein molecules available, so how did life start?

Theoretical origin of life; fun and games in the lab

by dhw, Thursday, September 13, 2018, 11:11 (2043 days ago) @ David Turell

QUOTES: "However, nothing evolves unless it already exists. When life started more than three billion years ago, what was the spark that created something from randomness?" (David’s bold)

"Structural Capacitance Elements are localised regions of disorder within proteins, which retain the potential to coalesce into 'micro-structures' following the introduction of a mutation. They act as nucleating seeds, or 'feedstock' for evolution to proceed, providing the basis of an accelerated mechanism of Darwinian evolution by natural selection, supplementing the slow and incremental process of classic Darwinian evolution."

"The research team analysed many of these disease-associated mutations and found that these 'Structural Capacitance Elements' may allow mutations to trigger a 'gain-of-function' by inducing structure where none existed before."

DAVID’s comment: The key is their statement in bold that proteins have to exist for life to appear and develop. Early Earth was a planet with few if any protein molecules available, so how did life start?

There are two separate mysteries, which they seem to be conflating. One is the origin of life, which they then abandon, and the other is the mechanism that drives evolution. They are clearly championing random mutations for the latter, adding speed to Darwin’s gradualism, but the fact that these “structural capacital elements” allow new structures to be triggered doesn’t explain how or why they actually do it. Randomness certainly doesn’t explain the complexities of new organs.

Theoretical origin of life; fun and games in the lab

by David Turell @, Thursday, September 13, 2018, 15:46 (2042 days ago) @ dhw

QUOTES: "However, nothing evolves unless it already exists. When life started more than three billion years ago, what was the spark that created something from randomness?" (David’s bold)

"Structural Capacitance Elements are localised regions of disorder within proteins, which retain the potential to coalesce into 'micro-structures' following the introduction of a mutation. They act as nucleating seeds, or 'feedstock' for evolution to proceed, providing the basis of an accelerated mechanism of Darwinian evolution by natural selection, supplementing the slow and incremental process of classic Darwinian evolution."

"The research team analysed many of these disease-associated mutations and found that these 'Structural Capacitance Elements' may allow mutations to trigger a 'gain-of-function' by inducing structure where none existed before."

DAVID’s comment: The key is their statement in bold that proteins have to exist for life to appear and develop. Early Earth was a planet with few if any protein molecules available, so how did life start?

dhw: There are two separate mysteries, which they seem to be conflating. One is the origin of life, which they then abandon, and the other is the mechanism that drives evolution. They are clearly championing random mutations for the latter, adding speed to Darwin’s gradualism, but the fact that these “structural capacital elements” allow new structures to be triggered doesn’t explain how or why they actually do it. Randomness certainly doesn’t explain the complexities of new organs.

This is abuse of the grant system. Producing possibilities for a time frame we cannot know, how life started.

Theoretical origin of life; zircons with 4.1 byo evidence:

by David Turell @, Tuesday, October 09, 2018, 15:29 (2016 days ago) @ David Turell

A review article:

https://www.nationalgeographic.com/science/2018/09/news-earth-rocks-sediment-first-life...

"Zircon crystals are almost indestructible; some still around today are nearly 4.4 billion years old. They're like tiny time capsules that retain the chemical fingerprints of this extremely early time. “This is basically our only window into the formative stages of our planet,” says Dustin Trail of the University of Rochester.

"By decoding these chemical clues, scientists are slowly teasing out the environments that fostered the earliest glimmers of life. But exactly what the surface looked like at that time has long remained a mystery. Now, in a new study published in Proceedings of the National Academy of Sciences, Trail and his colleagues pick apart the enigma.

***

"—no physical evidence remains from Earth's first few hundred million years. “The Earth has done a great job erasing some of that information,” Trail says. Our planet is the ultimate recycler. Plate tectonics constantly repurpose old rock into new, and lava flows harden into fresh landscapes.

"Zircon crystals, however, are so tough that they often survive the intense temperatures and pressures of this recycling process, retaining clues about the environments in which they originally formed. Using zircon oxygen isotopes, researchers previously discovered that liquid water covered parts of our planet some 4.3 billion years ago, suggesting the surface cooled just a few hundred million years after our planet’s formation. And just last year, researchers found what they believe might be hints of early life in the form of carbon-rich inclusions in 4.1-billion-year-old zircons.

***

"If we can begin to constrain the types of materials that are around at that time,” Trail says, “that perhaps pushes us one step closer to understanding how biochemical reactions, or prebiotic reactions, may have utilized the crust at that time as a substrate.”

"For answers, Trail and his colleagues turned to silicon and oxygen. Together, these elements make up roughly 75 percent of the rocks on Earth today, he explains. And both have a useful feature: they have more than one type, or isotope.

***

"More than half of the ancient zircons tested reveal early interactions between water and rock, in a range of different environments.

"Some zircons contain the chemical signatures of rocks weathered by water to form clay. Other zircons bear the signatures of dissolved minerals that crystallize to form rocks like chert or banded iron formations in lakes or oceans. Still others have the signature of a process known as serpentinization, so called for its snake-skin-like texture and color. During this process, water reacts with rocks enriched in iron and magnesium, incorporating itself into the mineral structures.

"Most importantly, each of these processes creates a new environmental niche that could foster early biochemical reactions, the glimmers of early life.

“That's a pretty cool result,” says Elizabeth Bell, a geochemist at the University of California, Los Angeles, who was not involved in the work. Many of these processes are largely indistinguishable from oxygen isotopes alone, she notes, calling the use of silicon "really significant.”

"Bell led the 2017 work that identified hints of a biosphere in 4.1-billion-year-old zircons. These latest results bolster her findings and other interpretations of early Earth. “It sort of all comes together in a nice picture,” she says.

"Everything around (and within) us once came from stardust, and the early processes that formed every molecule, mineral, and complex organism of today—from your cell phone to the food you eat to the heart pumping in your chest. And scientists are just beginning to tease out their origins."

Comment: What this means to me is that life could well have started 4.1 billion years ago and based on extremophiles in multiple places and in differing original forms, not just one cell type! Note this article re' Greg Venter:

https://uncommondescent.com/intelligent-design/zircons-are-back-as-a-possible-source-of...

"I hear a lot about the evidence that there seems to be nothing or almost nothing before the cambrian, BUT ALSO I think it is terribly important that it is pointed out that we do not note any lifeforms that show a transition between these phyla – if the main tenant of not just neo-darwinism, but common ancestry to be true, then these lifeforms could not develop independently.

"We should see a LOT of fluidity between these body plans with many, many examples in the fossil record of organisms that show a bridge between these body plans for a common ancestor to be true.

"Greg Venter and many of the greatest secular genomics researchers have stated the tree of life has actually hampered our progress in understanding the development and diversification of life and needs to be “jettisoned” – this is a HUGE shift in thinking. Ventner, to my knowledge, still leans heavily toward the idea that there were many separate ancestors and that they were anything but “common”, which is exactly my point. What he means by anything but common is saying not only are their multiple ancestors, but they are not similar to each other."

Comment: Not a single bush of life but a hedgerow.

Theoretical origin of life; new fun and games in the lab

by David Turell @, Tuesday, October 09, 2018, 22:10 (2016 days ago) @ David Turell

This study uses complex proteins to encapsulate RNA molecules to mimic the way life might have started:

https://phys.org/news/2018-10-life-membraneless-protocells.html

"The RNA world hypothesis assumes that RNA biomolecules were key players during this time as they carry genetic information and act as enzymes. However, one requirement for RNA activity is that there are a certain number of molecules within close enough proximity to one another. This would be possible if RNA was contained within a compartment, such as membraneless microdroplets (coacervates). Researchers at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden and the Max Planck Institute of Biochemistry in Martinsried have shown for the first time that simple RNA is active within membraneless microdroplets, enabling a suitable environment for the beginning of life.

Comment: Definition: coacervate: An aggregate of macromolecules, such as proteins, lipids, and nucleic acids, that form a stable colloid unit with properties that resemble living matter.

***

"In their study, the researchers proved for the first time that RNA is active within such membraneless microdroplets, supporting a previous hypothesis that coacervates act as protocells and could therefore be a precursor of the cell that exists today. The ability of coacervates to accumulate RNA would have helped to overcome the dilution problem of biomolecules and offered a suitable environment for reactions with each other. Furthermore, these membraneless droplets allow free transfer of RNA between the droplets. Dr. Björn Drobot, the first author of this study, explains: "One of the really exciting things is that we have shown that coacervates act as a controlled genetic transfer system, in which shorter RNA pieces can shuttle between droplets while longer pieces are trapped in the hosting microdroplet. In this way, these protocells (coacervates) have the ability to transfer genetic information between other protocells which would have been an important criterion for starting life.'"

Comment: This funded study comes from our taxes. It proves nothing about the origin of life, but supports a theory that requires the Earth was filled with various proteins that somehow happened to get together. Proves nothing to consider as a practical option.

Theoretical origin of life; new fun and games in the lab

by David Turell @, Wednesday, October 31, 2018, 19:35 (1994 days ago) @ David Turell

This time the lab starts with genetically modified life, so it is not about the origin of life so much as how it might evolve:

https://cosmosmagazine.com/biology/gm-micro-organisms-throw-light-on-early-evolution

"Two new synthetic micro-organisms could help reveal how life on the planet evolved, say scientists at Scripps Research Institute in La Jolla, California, US.

"Researchers are hoping a newly engineered bacterium and a genetically modified yeast will allow them to test the theory, developed in the 1960s, that says early life relied on RNA to store information before the evolution of DNA.

"The work could also help explain the development of mitochondria – rod-shaped organelles that synthesise the chemicals that drive cellular metabolism.

"These engineered organisms will allow us to probe two key theories about major milestones in the evolution of living organisms – the transition from the RNA world to the DNA world and the transition from prokaryotes to eukaryotes with mitochondria,” says Peter Schultz , senior author on two linked papers published in the Journal of the American Chemical Society (JACS) and the Proceedings of the National Academy of Sciences (PNAS).

"Prokaryotes, such as bacteria, are unicellular organisms that lack membrane-bound nuclei, mitochondria and other distinct organelles. They are thought to be the earliest forms of life.

“'Access to readily manipulated laboratory models enables us to seek answers to questions about early evolution that were previously intractable,” Schultz explains.
The synthetic bacterium, a strain of E. coli, has a genome that contains up to 50% RNA and uses ribonucleotides to build its DNA, “thus simultaneously representing a new type of synthetic organism and possibly a throwback to billions of years ago”.

“'In science class,” says co-author Angad Mehta, “students learn that DNA leads to RNA which in turn leads to proteins – that's a central dogma of biology – but the RNA world hypothesis turns that on its head.

“'For the RNA world hypothesis to be true, you have to somehow get from RNA to a DNA genome, yet how that might have happened is still a very big question among scientists.”
He adds that the fact that the newly developed E. coli can survive and replicate could support the RNA theory.

"The other microorganism is a yeast strain that uses bacteria that live inside it as its energy source, in a mechanism similar to the way mitochondria function. Mitochondria live inside cells and, among other tasks, supply energy to the cell. They have their own genomes, separate from the organism where they live.

"The researchers are hoping to evolve the bacteria in the yeast, also a strain of E. coli, into “mitochondria-like organelles”, which could help show how mitochondria came into being."

Comment: I doubt that we will learn anything about evolution from a lab designed study, except intelligent design is required, which is all the lab is doing.

Theoretical origin of life; organic molecules on Mars

by David Turell @, Thursday, November 01, 2018, 19:48 (1993 days ago) @ David Turell

Simple forms created by simple reactions, providing nothing that might start life:

https://cosmosmagazine.com/space/martian-organics-arose-on-the-planet-but-not-through-b...

"An electrochemical process resulting from the interaction of particular minerals, sulfides and brine explains the presence of organic compounds found in Martian meteorites, researchers reveal.

"The findings – the results of an extensive microscopic analysis led by Andrew Steele of the Carnegie Institution for Science in Washington DC, US – strongly imply that the compounds are evidence of geophysical processes, not biological ones.

"They also suggest that organic material can be created indigenously on the planet, rather than being deposited by either asteroids or interstellar dust – a finding, Steele and colleagues say, that “has profound implications for our understanding of other Martian phenomena, including the presence of methane in the atmosphere”.

"The researchers explored three Martian meteorites, dubbed Nakhla, Tissint and NWA 1950. Nakhla fell to Earth in Egypt in 1911 and was the first to hint that it might have been exposed to water at some stage. The second landed in Morocco a century later. NWA 1950 was also found in Morocco, in 2001, although exactly where is unknown.

'In particular, they looked at a class of minerals known as spinels found within the three meteorites – including titano-magnetite, magnetite, pyrite, and pyrrhotite – and found evidence that they had very likely interacted with a brine containing carbon-dioxide to produce organic compounds and sulfides.

"The results closely match conclusions drawn from the discovery of organic material in ancient sedimentary rocks in situ on the planet by NASA’s Sample Analysis at Mars (SAM) instrument on board the Curiosity rover.

“These two datasets together represent a mutually confirming analysis of the presence and provenance of organic material in Martian materials conducted using state-of-the-art analysis tools on two planets,” the scientists write in a paper published in the journal Science Advances.

"Steele and colleagues suggest further analysis on more samples will be required to fully confirm their results – and suggest that they could be very important not only in the field planetary geoscience, but also in astrobiology.

"The evidence suggests that the Martian organic compounds had an abiotic – that is, non-biological – origin, and are certainly not proof of life. However, they may indicate the existence of conditions conducive to it.

“'While found here in Martian samples, a similar process would occur wherever igneous rocks encountered brines, and therefore may be a dominant process for the production of organic phases and essential prebiotic molecules and their precursors on early Earth, Europa, and Enceladus,” the researchers conclude."

Comment: This study demonstrates that the early Earth might have had these simple compound but does not answer the question of where did the necessary amino acids required for life come from?

Theoretical origin of life; God of the Gaps doesn't apply

by David Turell @, Sunday, November 11, 2018, 14:46 (1983 days ago) @ David Turell

Moshe Averick again:

https://blogs.timesofisrael.com/god-of-the-gaps-is-there-no-end-to-the-foolishness/

"Dr. Addy Pross, a renowned chemist provides us with the answer to this question in his book What is Life? How Chemistry Becomes Biology. He hypothetically proposes the discovery of a functioning refrigerator, with a solar panel for power, in the middle of a large empty field:

“'But the mystery of how it got there in the middle of the field remains…Now if I told you that no one put the refrigerator there, that it came about spontaneously through natural forces, you would react with total disbelief. How absurd! Impossible!

"Natural forces do not spontaneously assemble refrigerators.

"Nature just doesn’t operate like that. Nature doesn’t spontaneously make highly organized…purposeful entities…Nature pushes systems…toward disorder and chaos, not toward order and function. The simple truth is that the most basic living system, a bacterial cell, is a highly organized…functional system which mimics the operation of the refrigerator, but is orders of magnitude more complex!

"[It] involves the interactions of thousands of different molecules and molecular aggregates…every living cell is effectively a highly organized factory…and here precisely lies the [origin of] life problem. It is not just common sense that tells us that highly organized entities don’t just spontaneously come about. Certain basic laws of physics preach the same sermon – systems tend toward chaos and disorder, not toward order and function…Biology and physics seem contradictory, quite incompatible.”

"In other words, the extraordinary difficulty to which Koonin refers is that an atheist-friendly origin of life would violate the laws of physics and mathematical probability. That is why Koonin added the following comment: “A succession of exceedingly unlikely steps is essential for the Origin of Life…these make the final outcome seem almost like a miracle.”

"So I say to my atheist/materialist friends in general and to Professor Jerry Coyne in particular: Our argument is not based on foolish truisms like God of the Gaps. It is based on common sense, universally observed laws of nature, and fundamental laws of physics and mathematical probability. It is supported by the writings and analysis of world class scientists. If you find that despite everything I have written here you are unable to rationally confront and respond to the points being raised; if you find yourself unable to resist the compulsion to mindlessly chant “God of the Gaps”, I have a great opportunity that I would like to share with you. I know of a mechanical engineer who is determined to build a perpetual motion machine and he’s looking for investors………"

Comment: Just pure logic which dhw loves.

Theoretical origin of life; God of the Gaps doesn't apply

by dhw, Monday, November 12, 2018, 13:00 (1982 days ago) @ David Turell

QUOTE: "So I say to my atheist/materialist friends in general and to Professor Jerry Coyne in particular: Our argument is not based on foolish truisms like God of the Gaps. It is based on common sense, universally observed laws of nature, and fundamental laws of physics and mathematical probability. It is supported by the writings and analysis of world class scientists. If you find that despite everything I have written here you are unable to rationally confront and respond to the points being raised; if you find yourself unable to resist the compulsion to mindlessly chant “God of the Gaps”, I have a great opportunity that I would like to share with you. I know of a mechanical engineer who is determined to build a perpetual motion machine and he’s looking for investors………"

DAVID’s comment: Just pure logic which dhw loves.

Yes, I do, but as is always the case with people who have strong views, this is only one side of the logical argument. Starting point: how did life originate? Theory: by chance. Nope, can’t believe it. Theory: because although life and consciousness must have been designed, there is an unknown, hidden form of life and consciousness, a single mind that did not have to be designed, has simply been there for ever, is capable of creating a universe, knows everything... etc. Nope, can’t believe it.

I am reminded of the conclusion (16. A Mad World) to my “brief guide”:

"Let me, however, conclude with our starting-point of agnosticism, and offer you two alternative forms of madness: 1) countless numbers of people, sums of money, buildings, institutions, wars, miseries, joys, works of art have been devoted to or have sprung from human worship of something that never existed; 2) the designer’s creations are just beginning to understand, after centuries of conscious endeavour, how life functions, but they are still unable to design an organism like themselves that can spring from inanimate matter into living existence, reproduce itself, adapt to a changing environment, invent new mechanisms, and pass on its adaptations and innovations to the organisms it engenders. They believe, however, that if they ever can consciously and deliberately design such an organism, it will prove that they themselves were not designed.

Take your pick."

Theoretical origin of life; God of the Gaps doesn't apply

by David Turell @, Monday, November 12, 2018, 18:43 (1982 days ago) @ dhw

QUOTE: "So I say to my atheist/materialist friends in general and to Professor Jerry Coyne in particular: Our argument is not based on foolish truisms like God of the Gaps. It is based on common sense, universally observed laws of nature, and fundamental laws of physics and mathematical probability. It is supported by the writings and analysis of world class scientists. If you find that despite everything I have written here you are unable to rationally confront and respond to the points being raised; if you find yourself unable to resist the compulsion to mindlessly chant “God of the Gaps”, I have a great opportunity that I would like to share with you. I know of a mechanical engineer who is determined to build a perpetual motion machine and he’s looking for investors………"

DAVID’s comment: Just pure logic which dhw loves.

dhw: Yes, I do, but as is always the case with people who have strong views, this is only one side of the logical argument. Starting point: how did life originate? Theory: by chance. Nope, can’t believe it. Theory: because although life and consciousness must have been designed, there is an unknown, hidden form of life and consciousness, a single mind that did not have to be designed, has simply been there for ever, is capable of creating a universe, knows everything... etc. Nope, can’t believe it.

I am reminded of the conclusion (16. A Mad World) to my “brief guide”:

"Let me, however, conclude with our starting-point of agnosticism, and offer you two alternative forms of madness: 1) countless numbers of people, sums of money, buildings, institutions, wars, miseries, joys, works of art have been devoted to or have sprung from human worship of something that never existed; 2) the designer’s creations are just beginning to understand, after centuries of conscious endeavour, how life functions, but they are still unable to design an organism like themselves that can spring from inanimate matter into living existence, reproduce itself, adapt to a changing environment, invent new mechanisms, and pass on its adaptations and innovations to the organisms it engenders. They believe, however, that if they ever can consciously and deliberately design such an organism, it will prove that they themselves were not designed.

Take your pick."

I would point out that the creation of life by humans, according to current research, involves humans tailoring existing life, and nothing more. The Miller-Urey sparks in the bottle experiment dates to the mid 1950's and we have learned nothing from ensuing research about how life started. It is still we must use life to alter life. I suspect that will never change, as life is too complex to start up a new form of it from scratch by humans.

Theoretical origin of life; Greenland earliest?

by David Turell @, Thursday, November 22, 2018, 00:53 (1973 days ago) @ David Turell

Still debated:

https://www.livescience.com/64115-oldest-fossils-of-life-dispute.html?utm_source=ls-new...

"Scientists will gather in a remote and snowy part of southwestern Greenland next summer to try to determine if rocks from 3.7 billion years ago contain some of the oldest fossils of life on Earth.

"Tiny, triangular structures found in these rocks have been a source of controversy, with some scientists now saying they are not evidence of early life on Earth. The scientists who first reported that they were fossilized evidence of life are defending their claims.

"In a paper published online Oct. 17 in the journal Nature, planetary scientist Abigail Allwood and colleagues, who examined the ancient rocks in Greenland, reported that purely geological processes could explain the triangular rock formations — and that while they might still be formed by microbial life, there was not enough evidence to show definitely that they were.

"Allwood, who works for NASA's Jet Propulsion Laboratory (JPL) in Pasadena, California, is the principal investigator building an instrument called PIXL, based on x-ray fluorescence of rock samples, which will be used by the Mars 2020 rover to search for fossilized evidence of life in Martian rocks.

"Allwood’s team used the PIXL instrument to test rock samples from Greenland and reported that concentrations of titanium, potassium, and carbonate chemicals in the rocks did not show that the triangular structures had been formed by microbial life. [The 7 Most Mars-Like Places on Earth]

"Scientists think that about 3.7 billion years ago, the environment on Mars was very similar to the environment on Earth at that time, and that early forms of life might have evolved at the same time on both planets — although the very cold and dry Martian environment is now thought to be lifeless.

"The Isua Greenstone Belt in southwestern Greenlandis thought by geologists to contain some of the oldest exposed rocks on Earth. Until recently, much of the area was covered by snow — only in the last few years has the snow melted enough for scientists to examine many of the rocks.

"In 2016, geochemist Allen Nutman of Wollongong University in Australia and his colleagues reported in a paper published in the journal Nature that triangular structures seen on the surface of some of the Isua rocks were cross-sections of cone-shaped stromatolites — tiny, fossilized structures built by microbial colonies on the floors of bodies of water.

"Nutman told Live Science in August 2016 that the concentrations of titanium and potassium inside the triangular structures were different than in the rock outside the structures — a possible chemical “biosignature”. His team also reported that the concentrations of carbonate chemicals suggested the microbial colonies were drawing carbonates out of the surrounding seawater.

"Until the discovery in Greenland, the earliest known stromatolites had been found at Strelley Pool in the Pilbara region of Western Australia and dated to about 3.4 billion years ago. Nutman's find, if verified, would push back the earliest evidence for the appearance of life on Earth by about 300,000 years.

"Allwood visited the same rocks in the Isua region of Greenland this summer and took samples for laboratory testing with the PIXL instrument, which will be attached to the rover to carry out X-ray fluorescence analysis on rock on Mars.

"She said that after examining the rocks and studying the geochemistry of the rock samples, she did not believe that the triangular structures were fossilized evidence of very early microbial life: "I think the evidence is very much not in favor of that interpretation," she said.

"As well as finding that the supposedly conical structures actually formed long triangular ridges within the rock, Allwood said that the geochemistry of the structures was the same as in some other patches of weathered rock nearby that did not appear to contain any stromatolites.

***

"Because Allwood and her colleague had analyzed different rock samples than the ones his team had analyzed, they had inevitably found that their observations did not exactly match those of his team. "This is a classic comparing apples and oranges scenario," he wrote.

"Nutman said that his team had found the structures could not be purely geological in origin, and that their shape and geochemistry indicated they were created by "extremely rare stromatolites in the Isua rocks, preserved in a tiny relict of a 3,700-million-year-old shallow sea environment."

***

"The dispute over the Greenland rocks means that the oldest established fossils of life on Earth may again be the stromatolites found at Strelley Pool in Western Australia.

***

"Another recent study has suggested that an outcropping of primitive ocean crust in Quebec in Canada could contain fossils that are even older — between 3.77 billion and 4.29 billion years old — but that study also needs more scientific scrutiny, Allwood said."

Comment: Whatever the exact time for life to appear, it is amazing that it developed so soon after Earth's formation

Theoretical origin of life; a book with a new view

by David Turell @, Friday, November 23, 2018, 23:09 (1971 days ago) @ David Turell

It is written into the laws of the universe:

https://newrepublic.com/article/151988/life-emerge

"In his new book Universe in Creation: A New Understanding of the Big Bang and the Emergence of Life, Roy Gould, an education researcher at the Harvard-Smithsonian Center for Astrophysics, argues that life is neither a miracle nor an aberration, but an inevitability whose emergence is dictated by the laws of nature. He frames his book around a question posed by the physicist John Archibald Wheeler in 1983. “Is the machinery of the universe so set up, and from the very beginning,” Wheeler asked, “that it is guaranteed to produce intelligent life at some long-distant point in its history-to-be?”

Gould answers Wheeler’s hypothetical in the affirmative.

***

"...in the final third of the book, Gould returns to answer Wheeler’s question more directly and persuasively, offering “the chief lines of evidence that life really is written into the universe’s building plan.” He notes, for instance that life appeared very soon after the planet’s birth: there are fossils that are almost 4 billion years old, while the earth has only been around for 4.5 billion years. This rapidity suggests a certain inclination towards life, as does the fact that you can find creatures everywhere on the planet, even in its most inhospitable corners, from the bottom of the oceans to, say, a boiling hot geothermal spring.

"Life’s machinery is remarkably stable: The same basic genetic code exists in all living things and has survived for billions of years. Other evidence for his thesis includes convergent evolution, which happens when two species independently evolve some similar function or organ. For instance, fish have developed electrical organs—which allow them to do fun things, ranging from shocking their prey to navigating their environment—on six or more distinct occasions in evolutionary history, as Gould notes, which suggests a certain predictability; creatures tend to evolve the same kinds of adaptations when they are presented with particular environmental challenges.

"When Gould turns to the origin of life itself, his book leaves somethings to be desired. He largely neglects to discuss competing theories of the origin of life. He favors the predominant theory, RNA World—even though one could argue that theory contradicts his central thesis.

***

"Gould embraces this theory, writing that “an ancient RNA world would make sense … it might have served to jumpstart life.” Yet, as others have argued, the spontaneous emergence of such a highly complex RNA molecule would also have been profoundly improbable. The late Robert Shapiro, professor of chemistry at New York University and author of Origins: A Skeptic’s Guide to the Creation of Life on Earth, has put this eloquently: “The chances for the spontaneous assembly of a[n RNA] replicator,” he wrote in a 2007 article in Scientific American, “can be compared to those of the gorilla composing, in English, a coherent recipe for the preparation of chili con carne.” The unlikeliness of spontaneous RNA replication, then, seems to contradict Gould’s idea that the universe was programmed to produce life. It brings us back to the possibility that yes, life on earth was simply a bizarre, freak occurrence.

"And yet—and here’s where things get interesting—Shapiro actually agreed with Gould’s fundamental thesis. He adhered, however, to an alternative to RNA-world referred to as “metabolism first,” which he thought consistent with this thesis. In this framework, molecules—perhaps fats—aggregated and “self-organized,” as they are apt to do under the laws of nature, forming compartments within which metabolic circuits began to run, well before complex genetic molecules come into being. These early forms of life may not have resembled life at all, but perhaps something intermediate between the living and the non-living. “There’s nothing freaky about life,” Shapiro said in a 2008 talk. “It’s a normal consequence of the laws of the universe.” Gould says nearly the same thing—“life really is written into the behavior of molecules.”

***

"The fascinating thing, however, is that Gould’s thesis may very well prove true. If it turns out that life—even the most rudimentary microbial life—is common to the universe, the case, as Gould suggests, is settled. Given the distances humans would have to travel to verify this, it is not something that can easily be proved. But even if there is or ever has been any sort of simple life on Mars—and this is something that could be ascertained in our lifetime—then Shapiro and Gould, although they embrace different theories of the origins of life, are essentially correct.

"After all, if life emerged independently on two planets in a single solar system, it is nothing unusual. Indeed, that finding alone would be powerful evidence that life has a tendency to emerge, and is presumably widespread throughout the universe. The origins of life would indeed be found in the laws of nature. "

Comment: Comment: It is obvious Gould has not paid close attention to the vast debate on how life originated, and he is a convinced Darwinist. His point that life is built in to the laws of the universe also supports the view that God wrote the laws that way.

Theoretical origin of life; new fun and games in the lab

by David Turell @, Thursday, January 31, 2019, 18:57 (1902 days ago) @ David Turell

More intelligent design in the lab using membraneless globules to contain supplied chemicals which then react in a way mimicking supposed early life:

https://phys.org/news/2019-01-membraneless-protocells-clues-formation-early.html

"Membraneless assemblies of positively- and negatively-charged molecules can bring together RNA molecules in dense liquid droplets, allowing the RNAs to participate in fundamental chemical reactions. These assemblies, called "complex coacervates," also enhance the ability of some RNA molecules themselves to act as enzymes—molecules that drive chemical reactions. They do this by concentrating the RNA enzymes, their substrates, and other molecules required for the reaction. The results of testing and observation of these coacervates provide clues to reconstructing some of the early steps required for the origin of life on Earth in what is referred to as the prebiotic "RNA world."

***

"'RNA—or something similar—has been thought of as a key to solving this dilemma," said Raghav R. Poudyal, Simons Origins of Life Postdoctoral Fellow at Penn State and first author of the paper. "RNA molecules carry genetic information, but they can also function as enzymes to catalyze the chemical reactions needed for early life. This fact has led to the notion that life on Earth went through a stage where RNA played an active role in facilitating chemical reactions—"the RNA World"—where self-replicating RNA molecules both carried the genetic information and performed functions that are now generally carried out by proteins."

"Another common feature of life on Earth is that it is compartmentalized in cells, often with an outer membrane, or in smaller compartments inside cells. These compartments ensure that all the components for the chemical reactions of life are in easy reach, but in the prebiotic world the building blocks for RNA—or the RNA enzymes needed to drive the chemical reactions that could lead to life—would probably have been scarce, floating around in the primordial soup.

***

"'It was previously known that RNA molecules can assemble and elongate in solutions with high concentrations of magnesium," said Poudyal. "Our work shows that coacervates made from certain materials allow this non-enzymatic template-mediated RNA assembly to occur even in the absence of magnesium."

"The coacervates are composed of positively charged molecules called polyamines and negatively charged polymers which cluster together to form membraneless compartments in a solution. Negatively charged RNA molecules are also attracted to the polyamines in the coacervates.

"Within the coacervates the RNA molecules are as much as 4000 times more concentrated than in the surrounding solution. By concentrating the RNA molecules in the coacervates, RNA enzymes are more likely to find their targets to drive chemical reactions.

"'Although all the polyamines we tested were able to participate in formation of RNA-rich droplets, they differed in their ability to support RNA elongation," said Christine Keating, professor of chemistry at Penn State and a senior author on the paper. "These observations help us understand how the chemical environment within different membraneless compartments can impact RNA reactions."

"'Although we can't look back to see the exact steps taken to form the first life on Earth, coacervates like the ones we can create in the laboratory may have helped by facilitating chemical reactions that otherwise would not have been possible," said Poudyal."

Comment: More waste of fund money. The 'RNA world' is formed in human scientific imagination and work like this creates salaries for some science folks, but proves nothing that helps us truly understand how life might have started. But it must have had a containing wall.

Theoretical origin of life; zircons with 4.1 byo evidence:

by dhw, Wednesday, October 10, 2018, 09:24 (2016 days ago) @ David Turell

QUOTE: “Venter, to my knowledge, still leans heavily toward the idea that there were many separate ancestors and that they were anything but “common”, which is exactly my point. What he means by anything but common is saying not only are their multiple ancestors, but they are not similar to each other."

DAVID’s comment: Not a single bush of life but a hedgerow.

Darwin hedged his bets: “There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or one….” Venter, who is an atheist, opts for multiple forms and, presumably, abiogenesis.

Theoretical origin of life; zircons with 4.1 byo evidence:

by David Turell @, Wednesday, October 10, 2018, 15:31 (2015 days ago) @ dhw

As new extremophiles are found, they support the idea that life can handle any condition anywhere:

https://www.nationalgeographic.com/science/2018/10/news-cyanobacteria-photosynthesis-ma...

"In a surprise to scientists, cyanobacteria have been found thriving nearly 2,000 feet below the strange landscape, where sunlight, water, and nutrients are scarce. Researchers previously thought these microbes could survive only while basking in the sun's rays, although they are otherwise a versatile bunch; researchers have found them alive nearly everywhere on Earth.

***

"Cyanobacteria hold an important role in Earth's history: They were responsible for pumping oxygen into the atmosphere, paving the way for life to swim, slither, hop, gallop and fly around the planet. That's why the new study, published today in Proceedings of the National Academy of Sciences, is pushing scientists rethink what can survive deep below our feet—and perhaps even the types of critters we should look for in our search for life on Mars and beyond.

***

"Control samples helped the team determine that the microbes did not come from contamination due to the drilling fluid nor from processing in the lab. And the cyanobacteria were not found in random locations, as you might expect if the samples had been doused in contaminated liquid. Instead, they were congregating along the fractures in the rock, eking out an existence in the tiny pockets of air.

***

"The cyanobacteria don't appear to differ greatly from the same kinds of microbes that thrive at the surface. Metagenomic analysis suggests that they are descendants of rock-dwelling lineages who make their living in tough environments, such as in the desert or within shadowy caves.

"But even in the darkest of caves, cyanobacteria were thought to capture some of the scanty photons that ricochet into the space, using the energy from sunlight to split water and generate electrons during photosynthesis. So how do the subsurface bacteria survive without light?

"These cyanobacteria seem to be largely chowing down on hydrogen gas, as evidenced by the lack of hydrogen wherever there were lots of cyanobacteria in the cores. The gas is a common food source for microbes, particularly those in the subsurface that have few other options.

"The subsurface cyanobacteria, however, seem to be processing and releasing hydrogen electrons using coopted machinery that their surface kin use for photosynthesis. In particular, the microbes seem to be capitalizing on the system's “safety valve,” an electron release mechanism that produces small amounts of energy.

"Microbes on the surface don't really need this extra energy thanks to the abundance of sunlight, relying on the valve only to keep their cells from frying when light is aplenty. But the subsurface cyanobacteria seem to survive in part on the tiny sips of energy that result from the valve releasing pent-up electrons.

“'They don't have to replace much machinery to be able to do this.”

Even so, reusing the photosynthesis system is not necessarily a surprise, says Virginia Edgcomb, a marine and subsurface biosphere microbiologist who also wasn't involved in the study. Microorganisms that live in challenging environments have to be adaptable to survive.

“'It's sort of the 'eggs in a basket' analogy,” she says. “It doesn't make sense to put all your eggs in one basket, because you need to be flexible. You need to be able to use different things as carbon sources, different things as electron acceptors, because chances are your conditions are pretty limiting and unpredictable.'”

Comment: First, this shows life can figure out survival anywhere, but secondly, this is an ideal organism with which life was helped to evolve by progression to oxygen breathing complex forms. God as designer looks very bright in using this bacteria as a ratchet for evolution to progress. Photosynthesis is an extremely complex quantum process key to oxygen production, but can be altered to achieve survival using different energy sources. Only a clever designer could create this.

Theoretical origin of life; logical criticism of studies

by David Turell @, Thursday, January 10, 2019, 00:07 (1924 days ago) @ David Turell

All studies have to supply intelligent designs and intervention. Nothing works from scratch as it would have on early Earth:

https://evolutionnews.org/2019/01/latest-acts-in-the-origin-of-life-circus/

"But one of the most famous candidate molecules, HCN (hydrogen cyanide), often considered a stepping stone to life, is not prebiotically plausible, Benner argues. Why? Because “current theory holds that Earth’s native atmosphere was more oxidizing than the Miller atmosphere.” [Miller-Urey lightning in a bottle]

"Thus, the prebiotic plausibility of HCN, the other molecules, and adenine long ago vanished as Earth-made species, even though literature too voluminous to cite here continues to assume otherwise.

"This creates a paradox. If one premises that life originated via an RNA-First prebiotic process that used adenine as a precursor and that adenine was formed from HCN from a Hadean terran atmosphere, then the premises that view HCN as an impossible product of our early atmosphere force the conclusion that life could not have originated on Earth. An unacceptable conclusion follows by the force of logic from seemingly acceptable premises.

"Organic chemists, if not all experimentalists in the field of prebiotic chemistry, are faced with a similar dilemma. We do our best to perform experiments that we believe re-enact possible steps of prebiotic evolution, but we know that we need to intervene manually to obtain meaningful results. Simply mixing chemicals and watching for a living system to appear from the broth seems unreasonable to me. This approach has never worked, and it is not expected to work, at least not if one is limited to the lifetime of a human, let alone the duration of a funding period or a Ph.D. thesis. So, what is a reasonable level of intervention by the experimentalist in prebiotic chemistry, and what are “plausible prebiotic conditions” in this context?

"Richert identifies numerous sources of intervention in the lab that would never happen in the real world: using pure chemicals from a supplier, breaking up a series of reactions that need to be sequential, using high concentrations of chemicals that would be implausible in nature, eliminating contaminants that would ruin the reaction, inserting enzymes to get steps to run faster, purifying the products of one reaction, then putting the products into another process with a drastic change in conditions for the next stage, and more.

***

" Can Richert rescue OOL from reckless use of human intervention? He agrees with Benner that it is not easy to gauge the plausibility of prebiotic scenarios. He gives several more examples of how the subjective judgment of the investigator can creep in. But “plausibility is important,” he says. “So, perhaps it is time to think about ways out of the ‘Hand of God’ dilemma.”

***

"A final word of caution. Life is a non-equilibrium phenomenon. It requires an energy source that drives its reactions. Assuming that simple heating/cooling cycles could have driven the formation of functional biomacromolecules that were then able to harness the energy emitted by the sun via photosynthesis, seems unrealistic to me. Achieving the level of specificity required to successfully operate a protocell with genetic apparatus, metabolism, and cell division under strongly denaturing conditions is not easy, certainly when it comes to enzyme-free replication relying on the intrinsic specificity of small molecule interactions. So, the periodic addition of a chemical condensing agent may be unavoidable to drive biochemical reactions that are endergonic, even in “minimal intervention” experiments. Without the chemical activation, equilibrium (death) sets in. So, some level of human intervention may always be required for complex, multistep processes. After all, what the dominant activation agent was before enzymes began to use ATP will remain an enigma to many of us for the foreseeable future."

Comment: These comments are from two prominent OOL researchers. They are Steven A. Benner and Clemens Richert. It is going nowhere. But grant money will continue in huge amounts.

Theoretical origin of life; constructor theory sophistry

by David Turell @, Saturday, February 09, 2019, 18:38 (1893 days ago) @ David Turell

It concludes information appears for no reason:

https://aeon.co/essays/how-constructor-theory-solves-the-riddle-of-life?utm_source=Aeon...

"The parent cell contains a recipe – DNA – with all the instructions to construct a new cell (recipe excluded). This means that accurate self‑reproduction can occur only in two steps. Using letter-by-letter replication and error-correction, the parent cell makes a high-fidelity copy of the recipe to be inserted in the new cell; then it constructs the copying mechanism plus the rest of the cell afresh, following the recipe. It was the Hungarian-born physicist John von Neumann who first discovered this logic in the 1940s. He was exploring cellular automata – discrete computational models used, for instance, in Conway’s Game of Life, which rely on unphysical dynamical laws. Constructor theory shows that this is the only possible logic for accurate self-reproduction given any no-design laws. (my bold)

"Constructor theory gives the ‘recipe’ an exact characterisation in fundamental physics. It is digitally coded information that can act as a constructor and has resiliency – the capacity, once it is instantiated in physical systems, to remain so instantiated. In constructor theory, that is called knowledge – a term used here without the usual connotation that it is known by someone: it merely denotes this particular kind of information with causal power and resiliency. And an essential part of the explanation of all distinctive properties of living things (and of accurate constructors in general) is that they contain knowledge in that sense. (my bold)

"Moreover, it is a fundamental idea of constructor theory that any transformation that is not forbidden by the laws of physics can be achieved given the requisite knowledge. There is no third possibility: either the laws of physics forbid it, or it is achievable. This accounts for another aspect of the evolutionary story. Ever better constructors can be produced, without limit, given the relevant knowledge, instantiated in digital recipes. (my bold)

"The early history of evolution is, in constructor-theoretic terms, a lengthy, highly inaccurate, non-purposive construction that eventually produced knowledge-bearing recipes out of elementary things containing none. These elementary things are simple chemicals such as short RNA strands, which can perform only low-fidelity replication, and so do not bear the appearance of design, and are therefore allowed to exist in a pre-biotic environment governed by no-design laws.


"Thus the constructor theory of life shows explicitly that natural selection does not need to assume the existence of any initial recipe, containing knowledge, to get started. It shows that, whatever recipes we might find in living things, they do not require ad‑hoc, biocentric or mysterious laws of physics in order to come into existence from elementary initial components. They need only the laws of physics to permit the existence of digital information, plus sufficient time and energy, which are non-specific to life. This adds another deep reason why a unification in our understanding of the phenomena of life and physics is possible. Whatever the laws of physics do not forbid us, we can do. Whether or not we will, depends on how much knowledge we create. It is up to us."

Comment: Note the bolds. It is never stated where the knowledge or information comes from or how it is created. It is simply assumed to appear.

Theoretical origin of life; lipid containers

by David Turell @, Sunday, March 03, 2019, 01:40 (1872 days ago) @ David Turell

More imagined ways to begin life in lipid capsules into which RNA's suddenly and mysteriously entered:

https://phys.org/news/2019-03-scientists-surfaces-early-life-earth.html

"On early earth, a series of spontaneous events needed to happen in order for life as we know it to begin. One of those phenomena is the formation of compartments enclosed by lipid membranes.

"New research by Irep Gözen, Elif Koksal, and colleagues at the University of Oslo reveals, for the first time, how these vesicles can self-assemble on surfaces without external input. The team discovered the most straight-forward and plausible explanation so far with the simplest assumptions.

'
"The formation of lipid tubes and the emergence of thousands of vesicles was happening spontaneously when we left lipids on a silicon dioxide surface."

"The lipids in their experiment were similar to those in bacteria membranes and have water-loving heads and water-avoiding tails. Because of these water-preferring properties, they spontaneously organize with their tails facing inward and their heads facing out. On the silicon dioxide surface, the lipids became sheets, with layers of these organized lipids. Due to the stickiness of the surface, at some points the two layers separate, and the top layer bulges out, creating tubes and then round balls as they gain more lipids. The entire process is fully autonomous. A gentle flow from the movement of liquid can then cause these vesicles to detach from the surface creating protocells, like those believed to be a stepping-stone to the origin of life.

"It is conceivable that something similar happened on early earth. Silicone dioxide, or silica, is one of the most abundant minerals on the earth's surface. Fatty molecules could have easily existed in the previological era, as confirmed by the results of their successful synthesis performed in possible primitive Earth conditions, together with their traces found in fossils and meteorites. Intriguingly, silicon dioxide was recently detected on Mars by the Curiosity Rover. ( my bold)

"Another puzzle in life's beginnings is how genetic material got inside of protocells. It is not known whether the compartments formed around the already-existing lengthy genetic chains such as RNA, or if the small building blocks somehow found their way inside these tiny bubbles and made the chains inside. Gözen and colleagues added a light-emitting organic molecule similar in size to nucleotides, the genetic building blocks, to the surrounding of the bubbles. Such molecules which were too big to diffuse through the wall of the bubble, could get inside without compromising the protocells. They speculate it gets through transient defects or pores in the protocell wall."

Comment: Another hyperbolic article, filled with wishful assumptions about origin of life.

Theoretical origin of life; inosine is the latest hope

by David Turell @, Monday, March 04, 2019, 21:05 (1870 days ago) @ David Turell

More hyperbole from one of the commenting scientists:

https://www.the-scientist.com/the-literature/primordial-rna-may-have-contained-inosine-...

"Proponents of the RNA world theory argue that life on Earth originated from a mixture of self-replicating, information-storing molecules. But while researchers have discovered ways that RNA’s pyrimidine nucleosides, uridine and cytidine, could have formed in primordial conditions, they’ve had less success with the purine nucleosides adenosine and guanosine, casting the theory into doubt.

"Biologist Jack Szostak’s lab at Harvard Medical School recently set out to test a new hypothesis: that compounds called 8-oxo-purines could have acted as substitutes for modern purines in primordial RNA. His team used an adenosine derivative, inosine, as a control.

"Under early-Earth conditions, 8-oxo-purines turned out to perform poorly—RNA molecules containing them copied slowly and with low accuracy. But inosine, unexpectedly, served as an excellent guanosine substitute. “We were really surprised to see that actually inosine works almost as well as guanosine, and in some cases, slightly better,” says Szostak. While it’s impossible to confirm that inosine really was a component of primordial RNA, “we’re pretty convinced that it could have happened this way.”

'By removing the need for a plausible chemical pathway to generate guanosine under early-Earth conditions, the paper “goes a long way to suggesting a solution to a long-standing problem,” says John Sutherland, a chemist at the MRC Laboratory of Molecular Biology at the University of Cambridge who was not involved in the work but, like Szostak, is part of the Simons Collaboration on the Origins of Life. (my bold)

"Researchers now need only to find out how adenosine could have formed in order to complete the story of how primordial RNA might have come together. “The value of this work is not just in what [Szostak’s group] does next,” says Sutherland, “but what it suggests other people should do next as well.'” (my bold)

Comment: My bolds show the hyperbole from unrealistically hopeful Sutherland, When life started the Earth had bits and pieces of potential proteins, so how did inosine miraculously appear? Wait for the next lab design.

Theoretical origin of life; based on calculus and chance

by David Turell @, Friday, March 15, 2019, 19:00 (1859 days ago) @ David Turell

The working of the genome is analyzed and 'discovery' and magical self-organization of a mass of unexplained suddenly appearing proteins on a rocky planet is proposed to start life:

https://www.biorxiv.org/content/biorxiv/early/2017/05/22/140657.full.pdf

"Concluding remarks
" The direct evolution of a coupled world of genetic information and encoded functional proteins in real-¬‐world molecular biology is far more plausible than any scenario in which there was an initial RNA World of ribozymes sophisticated enough to operate a genetic code. The preservation of encoded information processing during the historically necessary transition of any such system to the ancestral aaRS enzymes of molecular biology appears to be impossible, rendering the notion of an RNA Coding World scientifically superfluous. While this conclusion is grounded in an understanding of exactly how the dynamical architecture of molecular biology can solve the computational chicken-¬‐egg paradox of code evolution, it leaves a host of problems concerning the evolution of the complex apparatus of translation unresolved. On the other hand, recognition of the role of reflexivity in driving the intrinsic self-¬‐organisation of molecular biological coding has stimulated a deeper enquiry into the relationships between structural determinants of the aaRS coding apparatus (Carter and Wills, 2017). The formal requirement for reflexive information that encodes assignment catalysts according to the rules of the code they execute is grounded in a more elementary, physical reflexivity. Instantiation of the computational requirement of reflexivity in the dynamic processes of real-¬‐world molecular interactions demanded of nature that it fall upon, or we might say “discover”, a self-¬‐amplifying set of nanoscopic “rules” for the construction of the pattern that we recognize as “coding relationships” between the sequences of two types of macromolecular polymers. However, nature is innately oblivious to such abstractions: the matching of amino acids to codons is achieved by folded aaRS structures that are, at least according to quantum mechanical demands, “accidentally” produced through the computationally controlled placement of amino acids with different physical properties in specific positions of variants of two basic protein folds, labeled “Class I” and “Class II”. Even this simplest of distinctions had to be a discovery of itself, a “bootblock” that could be built upon and elaborated into the improbably refined system of the universal genetic code through the hierarchical nesting of variant codon-¬‐amino acid pairings. This evolution was continuously driven by newly distinguishable structural elements of folded proteins being able to distinguish more accurately between amino acids and corresponding tRNA sequence motifs, at each point precisely instantiating a “difference that makes a difference”, which Bateson (1972) defined as the elementary unit of naturally functional information. Although the basic steps taken by nature cannot yet be outlined, we are nonetheless approaching the point where aaRS phylogenetics studies can take us closer to that goal. Furthermore, we can now understand how the self-¬‐organised state of coding can be approached “from below”, rather than thinking of it as existing on the verge of a catastrophic fall over a cliff of errors: an incremental improvement in the accuracy of translation will produce replicase molecules that are more faithfully produced from the gene encoding them, probably leading to an incremental improvement in information copying, in turn providing for the selection of narrower genetic quasispecies, an incrementally better encoding of the protein functionalities on which the system relies, including accurate translation. The vicious circle can wind up rapidly from below as a self-¬‐amplifying process, rather than winding down the cliff from above, the push-¬‐pull tension stably maintaining the system near a tipping point, where, all else being equal, informational replication and translation remain impedance matched--that is,until the system falls into a new vortex of possibilities.”

Comment: Yes, a new vortex of possibilities. Under this bright cloud of smoke-screen verbiage all depends upon chance and magical self-organization from suddenly appearing proteins. Read skeptically.

Note this admission from the abstract:

" The hypothetical RNA World does not furnish an adequate basis for explaining how this system came into being, but principles of self-organisation that transcend Darwinian natural selection furnish an unexpectedly robust basis for a rapid, concerted transition to genetic coding from a peptide·RNA world."

Theoretical origin of life; based on Darwin 's warm ponds

by David Turell @, Saturday, April 13, 2019, 23:51 (1830 days ago) @ David Turell

A study tries on the availability of nitrogen:

https://phys.org/news/2019-04-earliest-life-arisen-ponds-oceans.html

"Researchers report that shallow bodies of water, on the order of 10 centimeters deep, could have held high concentrations of what many scientists believe to be a key ingredient for jump-starting life on Earth: nitrogen.

"In shallow ponds, nitrogen, in the form of nitrogenous oxides, would have had a good chance of accumulating enough to react with other compounds and give rise to the first living organisms. In much deeper oceans, nitrogen would have had a harder time establishing a significant, life-catalyzing presence, the researchers say.

"'Our overall message is, if you think the origin of life required fixed nitrogen, as many people do, then it's tough to have the origin of life happen in the ocean," says lead author Sukrit Ranjan,

***

"If primitive life indeed sprang from a key reaction involving nitrogen, there are two ways in which scientists believe this could have happened. The first hypothesis involves the deep ocean, where nitrogen, in the form of nitrogenous oxides, could have reacted with carbon dioxide bubbling forth from hydrothermal vents, to form life's first molecular building blocks.

"The second nitrogen-based hypothesis for the origin of life involves RNA—ribonucleic acid, a molecule that today helps encode our genetic information. In its primitive form, RNA was likely a free-floating molecule. When in contact with nitrogenous oxides, some scientists believe, RNA could have been chemically induced to form the first molecular chains of life. This process of RNA formation could have occurred in either the oceans or in shallow lakes and ponds.

"Nitrogenous oxides were likely deposited in bodies of water, including oceans and ponds, as remnants of the breakdown of nitrogen in Earth's atmosphere. Atmospheric nitrogen consists of two nitrogen molecules, linked via a strong triple bond, that can only be broken by an extremely energetic event—namely, lightning.

***

"Scientists believe that there could have been enough lightning crackling through the early atmosphere to produce an abundance of nitrogenous oxides to fuel the origin of life in the ocean. Ranjan says scientists have assumed that this supply of lightning-generated nitrogenous oxides was relatively stable once the compounds entered the oceans.

"However, in this new study, he identifies two significant "sinks," or effects that could have destroyed a significant portion of nitrogenous oxides, particularly in the oceans. He and his colleagues looked through the scientific literature and found that nitrogenous oxides in water can be broken down via interactions with the sun's ultraviolet light, and also with dissolved iron sloughed off from primitive oceanic rocks.

"Ranjan says both ultraviolet light and dissolved iron could have destroyed a significant portion of nitrogenous oxides in the ocean, sending the compounds back into the atmosphere as gaseous nitrogen.

"In the ocean, ultraviolet light and dissolved iron would have made nitrogenous oxides far less available for synthesizing living organisms. In shallow ponds, however, life would have had a better chance to take hold. That's mainly because ponds have much less volume over which compounds can be diluted. As a result, nitrogenous oxides would have built up to much higher concentrations in ponds. Any "sinks," such as UV light and dissolved iron, would have had less of an effect on the compound's overall concentrations.

"Ranjan says the more shallow the pond, the greater the chance nitrogenous oxides would have had to interact with other molecules, and particularly RNA, to catalyze the first living organisms. (my bold)

"'These ponds could have been from 10 to 100 centimeters deep, with a surface area of tens of square meters or larger," Ranjan says. "They would have been similar to Don Juan Pond in Antarctica today, which has a summer seasonal depth of about 10 centimeters."

"That may not seem like a significant body of water, but he says that's precisely the point: In environments any deeper or larger, nitrogenous oxides would simply have been too diluted, precluding any participation in origin-of-life chemistry. Other groups have estimated that, around 3.9 billion years ago, just before the first signs of life appeared on Earth, there may have been about 500 square kilometers of shallow ponds and lakes worldwide.

"'That's utterly tiny, compared to the amount of lake area we have today," Ranjan says.
"However, relative to the amount of surface area prebiotic chemists postulate is required to get life started, it's quite adequate.'"

Comment: Note my bold. Where did the RNA come from? RNA requires carbon, oxygen, hydrogen, nitrogen to come together to be formed. Amino acids are required for RNA to act upon. Where did they come from? RNA is right-handed and amino acids care left-handed. How did that happen?

Theoretical origin of life; lipid containers

by David Turell @, Wednesday, May 01, 2019, 23:57 (1812 days ago) @ David Turell

As cell membranes they will not work to support a living cell:

https://evolutionnews.org/2019/04/with-three-nobel-endorsements-chemist-marcos-eberlin-...

".... the book, which both recounts Dr. Eberlin’s personal experiences and gives his own perspective on the evidence for design in life. He surveys powerful indications at the micro and macro levels — bacteria, plants, birds, and more — that life’s evolution demonstrates not blind groping but intelligent “foresight,” looking from simpler beginnings to the complex biological wonders we know today.

"In case after case, he argues that life purposefully devised “solutions that anticipated problems before they arose,” a sure “hallmark of mind.” The unintelligent Darwinian process lacks the capacity for such engineering but so do other “alternative evolutionary proposals” (neutral evolution, evolutionary developmental biology, natural genetic engineering, a hypothetical multiverse, and other popular proposals).

Selected quote:

"The Cell Membrane
Only intelligent design stands as a theory capable of explaining, for example, the ingenious invention, the cell membrane, that keeps every living cell both sealed against and selectively open to its environment. No cell could live a moment without this remarkable feat of engineering. It must have been present in the first cell. As Eberlin writes:

{"If you were to bid this demanding, multifaceted job out to the most technologically advanced engineering firms in the world, their top engineers might either laugh in your face or run screaming into the night. The requisite technology is far beyond our most advanced human knowledge. And remember, getting two or three things about this membrane job right — or even 99 percent of the job — wouldn’t be enough. It is all or death! A vulnerable cell waiting for improvements from the gradual Darwinian process would promptly be attacked by a myriad of enemies and die, never to reproduce, giving evolution no time at all to finish the job down the road.

"This is the refrain of the book: “It is all or death!” “All or nothing!” Half-solutions are no solutions at all. As just one example, again drawn from his discussion of the cell membrane, “A successful water gate…poses an ‘all or nothing’ challenge for life. Foresee the need for these exquisitely precise water gates and somehow engineer them for just-in-time delivery, or the grand start-up called life quickly goes bust.”

"Scientists, though, habitually overlook the imperative of foresight:

"'Sometimes I come across articles in journals such as Science and Nature theorizing about simple, primordial cell membranes made of “rudimentary” molecules such as fatty acids. But such flights of fancy ignore key chemical details of what’s needed to render cellular life viable. '" (my bold)

Comment: This is the same observation as Behe's Irreducible Complexity. Biological cells and organisms must be completely designed from the beginning to function properly. They cannot be evolved stepwise. Which tells us the whole process runs with purpose. Please take careful note of the bolded last observation about science articles. That is why I constantly remind all that I reserve the right to interpret results. Don't just swallow the author's opinion about his results. I accept those but make my own judgment as to meaning.

Theoretical origin of life; lipid containers

by dhw, Thursday, May 02, 2019, 09:32 (1812 days ago) @ David Turell

QUOTE"'Sometimes I come across articles in journals such as Science and Nature theorizing about simple, primordial cell membranes made of “rudimentary” molecules such as fatty acids. But such flights of fancy ignore key chemical details of what’s needed to render cellular life viable.'" (David’s bold)

DAVID: This is the same observation as Behe's Irreducible Complexity. Biological cells and organisms must be completely designed from the beginning to function properly. They cannot be evolved stepwise. Which tells us the whole process runs with purpose. Please take careful note of the bolded last observation about science articles. That is why I constantly remind all that I reserve the right to interpret results. Don't just swallow the author's opinion about his results. I accept those but make my own judgment as to meaning.

I agree with you and Behe on the logic of the case for design, but I do not “swallow” his or your opinion; I make my own judgement. I do the same when you inform us that your God’s one and only purpose was to specially design H. sapiens (possible), and his chosen method was to specially design billions of other life forms to eat or not eat one another until he specially designed the only thing he wanted to specially design (illogical). Please stop implying that anyone who disagrees with you is just swallowing the opinions of “their” authors. We see the same results, and we make our own judgement as to meaning. As a matter of interest, please tell us now which authors support your conclusion that there is a divine 3.8-billion-year-old computer programme for every single undabbled innovation, life form, bacterial action, econiche, lifestyle and natural wonder in the history of life. Be assured, I will not “swallow” their opinion and will make my own judgement.

Theoretical origin of life; lipid containers

by David Turell @, Thursday, May 02, 2019, 15:10 (1811 days ago) @ dhw

QUOTE"'Sometimes I come across articles in journals such as Science and Nature theorizing about simple, primordial cell membranes made of “rudimentary” molecules such as fatty acids. But such flights of fancy ignore key chemical details of what’s needed to render cellular life viable.'" (David’s bold)

DAVID: This is the same observation as Behe's Irreducible Complexity. Biological cells and organisms must be completely designed from the beginning to function properly. They cannot be evolved stepwise. Which tells us the whole process runs with purpose. Please take careful note of the bolded last observation about science articles. That is why I constantly remind all that I reserve the right to interpret results. Don't just swallow the author's opinion about his results. I accept those but make my own judgment as to meaning.

dhw: I agree with you and Behe on the logic of the case for design, but I do not “swallow” his or your opinion; I make my own judgement. I do the same when you inform us that your God’s one and only purpose was to specially design H. sapiens (possible), and his chosen method was to specially design billions of other life forms to eat or not eat one another until he specially designed the only thing he wanted to specially design (illogical). Please stop implying that anyone who disagrees with you is just swallowing the opinions of “their” authors. We see the same results, and we make our own judgement as to meaning. As a matter of interest, please tell us now which authors support your conclusion that there is a divine 3.8-billion-year-old computer programme for every single undabbled innovation, life form, bacterial action, econiche, lifestyle and natural wonder in the history of life. Be assured, I will not “swallow” their opinion and will make my own judgement.

My theories are my own developed from reading thousands of articles and close to 200 books. Your question about authors who support my thoughts is exactly the issue I am raising. I don't care who concludes what I conclude. Subtracting Darwin bias is easy as the author above relates. Do you develop an idea and then go to the internet to find who might support you?

Theoretical origin of life; lipid containers

by dhw, Friday, May 03, 2019, 12:10 (1810 days ago) @ David Turell

DAVID: My theories are my own developed from reading thousands of articles and close to 200 books. Your question about authors who support my thoughts is exactly the issue I am raising. I don't care who concludes what I conclude. Subtracting Darwin bias is easy as the author above relates. Do you develop an idea and then go to the internet to find who might support you?

You dismiss as “pure speculation” the proposal that the “massively complex genome” which controls “all the evolutionary processes” might be guided by cellular intelligence, and yet you claim that in proposing an undiscovered 3.8-billion-year-old programme for every undabbled bacterial action, evolutionary innovation, econiche, lifestyle and natural wonder in life’s history – all specially designed to enable organisms to eat or not eat one another until your God specially designed the only thing he wanted to design – you ”try to base every theory on the scientific facts”, and you start with “what science shows us as established”. I would like to know what scientific facts and established truths your proposal is based on. You are happy to quote Adler (anthropocentrism) and Behe (design) in support of individual aspects of your hypothesis, and I am happy to quote Margulis, McClintock and Shapiro in support of aspects of mine, but I really don’t know why the other aspects of your proposal should be considered any more scientific or any less speculative than mine. I was merely wondering whether there are ANY scientists who support yours.

Theoretical origin of life; lipid containers

by David Turell @, Friday, May 03, 2019, 19:19 (1810 days ago) @ dhw

DAVID: My theories are my own developed from reading thousands of articles and close to 200 books. Your question about authors who support my thoughts is exactly the issue I am raising. I don't care who concludes what I conclude. Subtracting Darwin bias is easy as the author above relates. Do you develop an idea and then go to the internet to find who might support you?

dhw: You dismiss as “pure speculation” the proposal that the “massively complex genome” which controls “all the evolutionary processes” might be guided by cellular intelligence, and yet you claim that in proposing an undiscovered 3.8-billion-year-old programme for every undabbled bacterial action, evolutionary innovation, econiche, lifestyle and natural wonder in life’s history – all specially designed to enable organisms to eat or not eat one another until your God specially designed the only thing he wanted to design – you ”try to base every theory on the scientific facts”, and you start with “what science shows us as established”. I would like to know what scientific facts and established truths your proposal is based on. You are happy to quote Adler (anthropocentrism) and Behe (design) in support of individual aspects of your hypothesis, and I am happy to quote Margulis, McClintock and Shapiro in support of aspects of mine, but I really don’t know why the other aspects of your proposal should be considered any more scientific or any less speculative than mine. I was merely wondering whether there are ANY scientists who support yours.

I've admitted that my proposals as to how God guides evolution are speculations. From Adler certainly the issue of why humans are here is a major point. Behe is different. He firmly supports the need for a mind to design evolution and for me has totally demolished Darwin except for common descent. As for cellular reactions which I have studied and understand, they all have the regular appearance of automaticity. There is no proof here is intelligence guiding them. Intelligent instructions are all that is required. The only evidence of planning intelligence is in humans. As to your quoting M,M,S, and A, just as I'm quoting opinion that is all either of us has. I've gone beyond reasonable doubt. Have you?

Theoretical origin of life; lipid containers

by dhw, Saturday, May 04, 2019, 13:42 (1809 days ago) @ David Turell

dhw: […] you claim that […] you ”try to base every theory on the scientific facts”, and you start with “what science shows us as established”. I would like to know what scientific facts and established truths your proposal is based on. You are happy to quote Adler (anthropocentrism) and Behe (design) in support of individual aspects of your hypothesis, and I am happy to quote Margulis, McClintock and Shapiro in support of aspects of mine, but I really don’t know why the other aspects of your proposal should be considered any more scientific or any less speculative than mine. I was merely wondering whether there are ANY scientists who support yours.

DAVID: I've admitted that my proposals as to how God guides evolution are speculations. From Adler certainly the issue of why humans are here is a major point. Behe is different. He firmly supports the need for a mind to design evolution and for me has totally demolished Darwin except for common descent.

Yes, your proposal that your God specially designed every evolutionary change, and did so in order that organisms could eat or not eat one another until he specially designed H. sapiens is pure speculation with no basis in science. I know what Adler and Behe propose, and have no quarrel with their logic.

DAVID: As for cellular reactions which I have studied and understand, they all have the regular appearance of automaticity. There is no proof here is intelligence guiding them. Intelligent instructions are all that is required.

You have admitted that they have the “regular appearance” of intelligence (50/50), but of course we do not have the proof – if we did, the hypothesis would be a fact. You have no proof that they are guided by a 3.8-billion-year-old computer programme which you prefer to gloss over as “intelligent instructions”.

DAVID: The only evidence of planning intelligence is in humans.

Even you have admitted that our fellow animals are intelligent. I don’t know why you insist on inserting “planning” but see my post under “Bacterial intelligence”.

DAVID: As to your quoting M,M,S, and A, just as I'm quoting opinion that is all either of us has. I've gone beyond reasonable doubt. Have you?

Yes, we both quote opinions, but reasonable versus unreasonable is pure subjectivity. My subjective view is that your belief in the design argument for God and in the specialness of humans is reasonable, your opinion that cells are automatons is nowhere near beyond reasonable doubt, and your proposal that your God specially designed every life form etc, and did so in order to make them eat or not each other until he specially designed the only thing he wanted to design is unreasonable, especially since you yourself have no idea why he would come up with such a method.

Theoretical origin of life; lipid containers

by David Turell @, Saturday, May 04, 2019, 18:59 (1809 days ago) @ dhw

DAVID: As for cellular reactions which I have studied and understand, they all have the regular appearance of automaticity. There is no proof here is intelligence guiding them. Intelligent instructions are all that is required.

dhw: You have admitted that they have the “regular appearance” of intelligence (50/50), but of course we do not have the proof – if we did, the hypothesis would be a fact. You have no proof that they are guided by a 3.8-billion-year-old computer programme which you prefer to gloss over as “intelligent instructions”.

DAVID: The only evidence of planning intelligence is in humans.

dhw: Even you have admitted that our fellow animals are intelligent. I don’t know why you insist on inserting “planning” but see my post under “Bacterial intelligence”.

Planning for future needs requires a planning mind a concept presented many times.


DAVID: As to your quoting M,M,S, and A, just as I'm quoting opinion that is all either of us has. I've gone beyond reasonable doubt. Have you?

dhw: Yes, we both quote opinions, but reasonable versus unreasonable is pure subjectivity. My subjective view is that your belief in the design argument for God and in the specialness of humans is reasonable, your opinion that cells are automatons is nowhere near beyond reasonable doubt, and your proposal that your God specially designed every life form etc, and did so in order to make them eat or not each other until he specially designed the only thing he wanted to design is unreasonable, especially since you yourself have no idea why he would come up with such a method.

You constantly come back to my simple acceptance of God's choice of method as somehow lacking substance. We see the evolutionary history as evidence of how it was done. What more do you need? I can only think of direct creation or evolution as possibilities. Do you know of a third way?

Theoretical origin of life; organic matter 3.3 byo found

by David Turell @, Friday, May 24, 2019, 20:25 (1789 days ago) @ David Turell

In a layer on Earth, insoluble organic material:

https://www.newscientist.com/article/2204354-organic-matter-from-space-preserved-in-3-3...

"thin layer of 3.3 billion-year-old rock contains unexpected treasure: organic matter that was carried to Earth by meteorites when the planet was still young.
The find supports the idea that organic, meaning carbon-based, chemicals from space supplied some of the raw materials for the first life on Earth. It could also complicate the search for life on other planets.

“'This is the very first time that we have found actual evidence for extraterrestrial carbon in terrestrial rocks,” says Frances Westall of the CNRS Centre"

https://www.researchgate.net/publication/333113746_Extraterrestrial_organic_matter_pres...

"Electron paramagnetic resonance (EPR) analysis of carbonaceous, volcanic, tidal sediments from the 3.33 Ga-old Josefsdal Chert (Kromberg Formation, Barberton Greenstone Belt), documents the presence of two types of insoluble organic matter (IOM): (1) IOM similar to that previously found in Archean cherts from numerous other sedimentary rocks in the world and of purported biogenic origin; (2) anomalous IOM localized in a 2 mm-thick sedimentary horizon. Detailed analysis by continuous-wave-EPR and pulse-EPR reveals that IOM in this layer is similar to the insoluble component of the hydrogenated organic matter in carbonaceous chondrites, suggesting that this narrow sedimentary horizon has preserved organic matter of extraterrestrial origin. This conclusion is supported by the presence in this thin layer of another anomalous EPR signal at g = 3 attributed to Ni-Cr-Al ferrite spinel nanoparticles, which are known to form during atmospheric entry of cosmic objects. From this EPR analysis, it was deduced that the anomalous sedimentary layer originates fromdeposition, in a nearshore environment, of a cloud of tiny dust particles originating from a flux of micrometeorites falling through the oxygen-poor Archean atmosphere."

Comment: This article shows the Earth received organic material from space early on, but this stuff is insoluble, and even if the Earth is very water rich, how does that contribute to forming the proper proteins to start life? Still quite interesting

Theoretical origin of life; more false hope from a lab

by David Turell @, Tuesday, July 02, 2019, 00:04 (1751 days ago) @ David Turell

This headline is totally false based on what was found: "Researchers identify the origins of metabolism":

https://phys.org/news/2019-07-metabolism.html

To answer that question, the researchers reverse-engineered a primordial protein and inserted it into a living bacterium, where it successfully powered the cell's metabolism, growth and reproduction, according to the study in Proceedings of the National Academy of Sciences.

***

The researchers looked at a class of proteins called ferredoxins, which support metabolism in bacteria, plants and animals by moving electricity through cells. These proteins have different, complex forms in today's living things, but researchers speculate they all arose from a much simpler protein that was present in the ancestor of all life.

Similar to the ways biologists compare modern birds and reptiles to draw conclusions about their shared ancestor, the researchers compared ferredoxin molecules that are present in living things and, using computer models, designed ancestral forms that may have existed at an earlier stage in the evolution of life. (my bold)

That research led to their creation of a basic version of the protein—a simple ferredoxin that is able to conduct electricity within a cell and that, over eons of evolution, could have given rise to the many types that exist today.

Then, to prove their model of the ancient protein could actually support life, they inserted it into a living cell. They took the genome of E. coli bacteria, removed the gene it uses to create ferredoxin in nature, and spliced in a gene for their reverse-engineered protein. The modified E. coli colony survived and grew although more slowly than normal.

Study co-author Vikas Nanda, a professor at Rutgers Robert Wood Johnson Medical School and Center for Advanced Biotechnology and Medicine, said the discovery's implications for synthetic biology and bioelectronics come from ferredoxins' role in the circuitry of life.

"These proteins channel electricity as part of a cell's internal circuitry. The ferredoxins that appear in modern life are complex—but we've created a stripped-down version that still supports life.

Comment: Note what was presented and note my bold. This is intelligent design in a lab. Obviously nothing is proven but some interesting possibilities are raised by the analysis performed. A molecule that may have existed proves nothing. The headline is a phony interpretation.

Theoretical origin of life; criticism of the usual hype

by David Turell @, Thursday, July 04, 2019, 19:51 (1748 days ago) @ David Turell

The new lab work always is touted as solving the problem of origin of life:

https://evolutionnews.org/2019/06/astrobiology-searching-for-the-origin-of-life-in-all-...

"Astrobiologists think they may have found where life came from — cyanide in meteorites! From Live Science:

"Cyanide isn’t just the last resort for the captured spies of Hollywood film. It’s also a crucial component of the early chemistry of life. And now, new research finds that cyanide might have ridden to Earth on meteorites.

"Samples of a particular group of primitive meteorites — including a large one that fell near Murchison, Australia, in 1969 — all contain cyanide, bound in a stable configuration with iron and carbon monoxide. These same sorts of structures are found in enzymes called hydrogenases in modern bacteria and archaea, which could suggest that early life either borrowed from meteorites or that early Earth’s geology formed the same kind of cyanide compounds, said study co-author Michael Callahan, an analytical chemist Boise State University.

"You can predict the rest — breathless excitement in the astrobiology community! Perhaps the mystery of life has finally been unraveled!

"Materialist “astrobiology” is a parody of itself. Imagine a computer scientist trying to understand the origin of — that is, reverse-engineer — a software program of unknown provenance. He would be a fool to chemically analyze the computer’s chip or chassis. The origin of the program is in the information encoded in it. He would study the program as a designed artifact, and only by that approach would the scientist be able to understand its origin.

"The same reasoning applies to origin of life research. Life isn’t characterized by cyanide, or even nucleotides or lipids or proteins or the host of substrates in living things. The essence of life is information — the gigabytes of information in the genetic code in DNA, the astonishingly complex molecular machinery of cellular metabolism, the intricate orchestration of the physiology of higher organisms, and the immaterial power of rational thought and free will in man. The material components of living things are merely the substrate in which this elegant information is stored and expressed. And information always originates in a mind.

“'Astrobiologists” who search for life’s origin in cyanide in meteorites or in any material substrate are fools blinded by materialist ideology.

"The origin of life is intelligence — intelligence from a Mind of astonishing power and beauty. To the extent that “astrobiology” ignores this basic scientific truth, it is a pseudoscience, devoted not to the truth about life, but to the protection of the materialist creation myth."

Comment: this essay from the ID community doesn't require much imagination or extrapolation to understand how they support my approach to the origin of life and to evolution by the intelligence of God. dhw constantly demands that I name names of ID folks. This piece is by Michael Egnor, neurosurgeon.

Now read James Tour, world renowned biochemist who makes organic molecules from scratch:

https://evolutionnews.org/2019/07/on-the-origin-of-life-science-uprising-helps-break-a-...

"Professor Tour is a personality to be reckoned with, pouring steely scorn on his colleagues who study, and mislead, about the origin of life.

“'All of these little pictures of molecules coming together to form the first cell are fallacious, are ridiculous,” says Tour. “The origin of life community has not been honest.” Claims by Craig Venter and others are little more than hype. What about claims that material processes at the dawn of life had time on their side? No, the opposite is true. Claims by researchers of having created “proto-cells” are like saying you’ve created a “proto-turkey” by warming some cold cuts, broth, and a few feathers.

"Dr. Axe and Dr. Meyer clarify both the complexity of the object needing to be explained — the first cell — and the delusion of imagining that the “functional, digital information” in DNA could have been authored with no intelligence having played any part in it."

Comment: Tour, Axe, and Meyer should be enough names to silence dhw's demands for names and it should be clear ID is in full support of my theories.

Theoretical origin of life; criticism of the hype from Tour

by David Turell @, Sunday, July 14, 2019, 19:29 (1738 days ago) @ David Turell

James Tour has produced a long critical article against the hype of OOL research, and finds the research itself quite lacking. Very long essay:

https://inference-review.com/article/time-out

"This essay comprises an argument, but it also contains an appeal to the OOL community. The history of science suggests that on occasion what is required for research to flourish is not further research—at least to the extent that further research involves doing the same thing. This is one of those times.

***

"Constructing the molecules necessary for life from their prebiotic precursors represents one goal of OOL research; putting them together, another. Some of synthetic chemistry is pedestrian, and some ingenious. Fundamental questions remain unaddressed. Claims that these structures could be prepared under prebiotic conditions in high enantiomeric purity using inorganic templates, or any presumed templates, have never been realized. The carbohydrates, amino acids, lipids, and other compounds within each of these classes require specific methods in order to control their regiochemistry and stereochemistry. The differences in reaction rates often require chiral systems acting upon chiral molecules. If this were possible under prebiotic conditions, it is odd that it cannot be replicated by synthetic chemists.

"They have, after all, had 67 years to try.

***

"A Harvard researcher seeking a model for the earliest cells has created a system that self-assembles from a chemical soup into cell-like structures that grow, move in response to light, replicate, and exhibit signs of rudimentary evolutionary selection [emphasis added].5
This degree of hyperbole is excessive.6 Nothing in this experiment had growing cell-like structures with replication, or that exhibited aspects of evolutionary selection.

***

"Terminology is one thing, non-sequiturs quite another. “After much trial and error,” the authors write, “one protocell assembles the complicated molecular machinery that enables it to divide into daughter cells. This paves the way for the first living microbial community.” How is the molecular machinery made? They do not say. The mechanisms needed for cellular division are complex, requiring cascades of precisely functioning enzymes. There is nothing between what the authors demonstrate and what they claim to have established, and nothing they propose “paves the way for the first living microbial community.”

***

"Peter Tompa and George Rose have calculated that if one considers only protein combinations in a single yeast cell, the result would be an estimated 1079,000,000,000 combinations.14 The authors understand that this is a very large number, one that precludes “formation of a functional interactome by trial and error complex formation within any meaningful span of time.”

***

"I have discussed these issues with OOL researchers, and I am amazed that they fail to appreciate the magnitude of the problem in building molecules. They see little difficulty in accepting a chemical synthesis where a desired product is mixed with a large array of closely related yet undesired compounds. They seem unaware that separations would be enormously complex, and subsequent reactions unavailing. In a 2018 article for Progress in Biophysics and Molecular Biology, Edward Steele et al. concede the following.

"The transformation of an ensemble of appropriately chosen biological monomers (e.g. amino acids, nucleotides) into a primitive living cell capable of further evolution appears to require overcoming an information hurdle of superastronomical proportions, an event that could not have happened within the time frame of the Earth except, we believe, as a miracle. All laboratory experiments attempting to simulate such an event have so far led to dismal failure. (my bold)

***

"It is time for a temporary time out. Why not admit what we cannot yet explain: the mass transfer of starting materials to the molecules needed for life; the origin of life’s code; the combinatorial complexities present in any living system; and the precise non-regular assembly of cellular components?

"It would be helpful if leading researchers, among them very sophisticated synthetic chemists, were to step back, pause, and join forces. If the origins of life remain a mystery, two goals are within reach: an agreement about the rational standards by which OOL research should be judged, and a candid acknowledgment of the problems that remain to be overcome. A statement of this sort would be reassuring in its candor."

Comment: A superb commentary supporting my presentations of the super-hype re OOL. Note my bold. Life is a miracle event.

Theoretical origin of life; criticism of the hype from Tour

by dhw, Monday, July 15, 2019, 10:27 (1738 days ago) @ David Turell

DAVID: James Tour has produced a long critical article against the hype of OOL research, and finds the research itself quite lacking. Very long essay:

https://inference-review.com/article/time-out

DAVID: A superb commentary supporting my presentations of the super-hype re OOL. Note my bold. Life is a miracle event.

Just to say thank you for this article. It really is superb, and should be recommended reading for all those whose fixed beliefs lead them to embrace chance as the creator of life.

Theoretical origin of life; criticism of the hype from Tour

by David Turell @, Monday, July 15, 2019, 17:51 (1737 days ago) @ dhw

DAVID: James Tour has produced a long critical article against the hype of OOL research, and finds the research itself quite lacking. Very long essay:

https://inference-review.com/article/time-out

DAVID: A superb commentary supporting my presentations of the super-hype re OOL. Note my bold. Life is a miracle event.

dhw: Just to say thank you for this article. It really is superb, and should be recommended reading for all those whose fixed beliefs lead them to embrace chance as the creator of life.

His criticism shows the research of OOL is all at a dead end and is really a misuse of grant monies.

Theoretical origin of life; earliest possible time frame

by David Turell @, Monday, August 12, 2019, 18:02 (1709 days ago) @ David Turell

The Earth appears to be about 4.6 byo. Traces of early life are dated at 3.8 byo. The study says it could have appeared earlier:

https://phys.org/news/2019-08-timeline-earth-cataclysmic.html

"Welcome to the early solar system. Just after the planets formed more than 4.5 billion years ago, our cosmic neighborhood was a chaotic place. Waves of comets, asteroids and even proto-planets streamed toward the inner solar system, with some crashing into Earth on their way.

"Now, a team led by University of Colorado Boulder geologist Stephen Mojzsis has laid out a new timeline for this violent period in our planet's history.

"In a study published today, the researchers homed in on a phenomenon called "giant planet migration." That's the name for a stage in the evolution of the solar system in which the largest planets, for reasons that are still unclear, began to move away from the sun.

"Drawing on records from asteroids and other sources, the group estimated that this solar system-altering event occurred 4.48 billion years ago—much earlier than some scientists had previously proposed.

"The findings, Mojzsis said, could provide scientists with valuable clues around when life might have first emerged on Earth.

"'We know that giant planet migration must have taken place in order to explain the current orbital structure of the outer solar system," said Mojzsis, a professor in the Department of Geological Sciences. "But until this study, nobody knew when it happened."

"It's a debate that, at least in part, comes down to moon rocks collected by Apollo astronauts—many of which seemed to be only 3.9 billion years old, hundreds of millions of years younger than the moon itself.

"To explain those ages, some researchers suggested that our moon, and Earth, were slammed by a surge of comets and asteroids around that time. But not everyone agreed with the theory, Mojzsis said.

***

"'The surfaces of the inner planets have been extensively reworked both by impacts and indigenous events until about 4 billion years ago," said study coauthor Ramon Brasser of the Earth-Life Science Institute in Tokyo. "The same is not true for the asteroids. Their record goes back much further."

"But those records, the team discovered, only went back to about 4.5 billion years ago.
For the researchers, that presented only one possibility: The solar system must have experienced a major bombardment just before that cut-off date. Very large impacts, Mojzsis said, can melt rocks and variably reset their radioactive ages, a bit like shaking an etch-a-sketch.

"Mojzsis explained that this carnage was likely kicked off by the solar system's giant planets, which researchers believe formed much closer together than they are today. Using computer simulations, however, his group demonstrated that those bodies started to creep toward their present locations about 4.48 billion years ago.

"In the process, they scattered the debris in their wake, sending some of it hurtling toward Earth and its then-young moon.

"The findings, Mojzsis added, open up a new window for when life may have evolved on Earth. Based on the team's results, our planet may have been calm enough to support living organisms as early as 4.4 billion years ago."

Comment: Perhaps we will find evidence of life earlier than 3.8 byo. Working backward studies suggest that very early life was highly complex. How did it develop so quickly after the Earth's climate might have allowed it? Suggests strongly it was helped by design.

Theoretical origin of life; proteins stabilize membranes

by David Turell @, Wednesday, August 14, 2019, 19:05 (1707 days ago) @ David Turell

More pie in the sky ignoring Tour's warning essay:

https://www.sciencedaily.com/releases/2019/08/190812155502.htm

"Scientists have discovered that the building blocks of proteins can stabilize cell membranes. This finding may explain how the first cells emerged from the primordial soup billions of years ago: The protein building blocks could have stabilized cell membranes against salt and ions that were present in ancient oceans. In addition, membranes may have been a site for these precursor molecules to co-localize, a potential mechanism to explain what brought together the ingredients for life.

***

"A team of researchers at the University of Washington has solved this puzzle using only molecules that would have been present on the early Earth. Using cell-sized, fluid-filled compartments surrounded by membranes made of fatty acid molecules, the team discovered that amino acids, the building blocks of proteins, can stabilize membranes against magnesium ions. Their results set the stage for the first cells to encode their genetic information in RNA, a molecule related to DNA that requires magnesium for its production, while maintaining the stability of the membrane.

***

"The team hypothesized that amino acids might also stabilize membranes. They used a variety of experimental techniques -- including light microscopy, electron microscopy and spectroscopy -- to test how 10 different amino acids interacted with membranes. Their experiments revealed that certain amino acids bind to membranes and stabilize them. Some amino acids even triggered large structural changes in membranes, such as forming concentric spheres of membranes -- much like layers of an onion.

"'Amino acids were not just protecting vesicles from disruption by magnesium ions, but they also created multilayered vesicles -- like nested membranes," said lead author Caitlin Cornell, a UW doctoral student in the Department of Chemistry.

"The researchers also discovered that amino acids stabilized membranes through changes in concentration. Some scientists have hypothesized that the first cells may have formed within shallow basins that went through cycles of high and low concentrations of amino acids as water evaporated and as new water washed in.

"The new findings that amino acids protect membranes -- as well as prior results showing that RNA building blocks can play a similar role -- indicate that membranes may have been a site for these precursor molecules to co-localize, providing a potential mechanism to explain what brought together the ingredients for life."

comment: A marvelous example of the hype noted by Tour. So proteins can stabilize membranes, ignoring the issue of how did lipid membranes initially form? How did the initial amino acids get to the earth, and only in left-handed form? Space rocks that have landed here contain few of the necessary essential amino acids.

Theoretical origin of life; a review of fake news

by David Turell @, Monday, September 02, 2019, 18:12 (1688 days ago) @ David Turell

An essay that encapsulates all the articles I have presented showing that design in labs proves nothing:

https://evolutionnews.org/2019/08/origin-of-life-public-education-and-religious-neutral...

The problem starts with OOL researchers greatly exaggerating the significance of their results. Then, the popular press amplifies the claims to ridiculous extremes. Finally, science textbook publishers canonize the misinformation by embedding it in official curricula.

This way, the public receives a quasi-religious education in what has been called exclusive humanism, an understanding of reality that denies the existence of any transcendent agent directly acting in the world. Among other consequences, many people are thus robbed of the freedom even to consider belief in a traditional religion.

***

Dr. Tour generated some controversy by stating that the researchers were “lying” to their readers. Tour’s comments were made largely in jest, and he has apologized for his choice of a verb, yet assertions in the articles were indeed demonstrably false.

The origin of life is not a normal scientific theory, for the belief that life formed purely through natural processes represents a sacrosanct secular creation myth. I do not use the term “myth” pejoratively but in the anthropological sense of a story that helps provide a unifying framework for thinking about life. With that in mind, one could argue that Szostak and Sutherland were not speaking as dispassionate scientists, but were instead functioning in their roles as secular faith leaders who were entrusted to propagate cherished creation narratives. Their articles functioned less as scientific works than as sacred literature, so the authors could not be expected to concern themselves too greatly with scientific plausibility.

The popular media have further contributed to the general misunderstanding of the true state of OOL studies by publishing hyperbolic claims,

***

For example, the common statement that an experiment mimics “plausible” conditions on the early Earth actually means that the experiment employs conditions completely unlike anything that could have ever occurred outside an advanced laboratory setting. Meanwhile, people are often referred to as “antiscientific” if they judge the viability of OOL scenarios based upon hard evidence and well established physical processes. In contrast, people are applauded as “scientific” if they uncritically accept OOL theories based on little more than wild speculation.

***

This epic journey from simple chemicals to life certainly captures the imagination, but it is completely detached from reality. Meteorites only contain biological molecules in trace quantities, often just a few parts per million, amidst countless other molecules. The formation of stable vesicles is only possible in highly controlled laboratory conditions, and the prebiotic synthesis of long strands of RNA or even the base nucleotides in significant quantities is completely implausible. Presenting such grossly inaccurate information to students only serves to erode the public trust in our educational and scientific institutions.

Perhaps the greatest violation of trust is how such content infringes on the principle of religious neutrality. Public education is expected to neither advance one religious or philosophical faith nor inhibit another. Yet the belief that life arose through undirected natural processes is the number one hindrance among atheists and agnostics to considering the existence of a Creator.

That belief is based almost entirely on misrepresentations of the scientific literature. In reality, OOL research over the past 65 years has uniformly demonstrated that the transformations of simple molecules into just the most basic components of a cell require dramatic investigator (intelligent) intervention. Teaching students the truth would not inspire such enchanting prebiotic stories, but it would protect the integrity of science education in the public eye.

Comment: Note that this is an ID article. It clearly shows they believe in a Creator of no religious identity, but most of the followers are Christian and don't hide the fact. A number of their members (fellows) are Jewish. My theories simply use their theories. Some agree with my theories about God choosing to evolve humans. Others at not quite as clear.

Theoretical origin of life; another article example

by David Turell @, Tuesday, September 03, 2019, 20:42 (1687 days ago) @ David Turell

The lab produces the wanted result and touts it is possible near stars. How did it get to Earth? Not told:

https://phys.org/news/2019-09-reveals-radical-wrinkle-complex-carbon.html

"A team of scientists has discovered a new possible pathway toward forming carbon structures in space using a specialized chemical exploration technique at the Department of Energy's Lawrence Berkeley National Laboratory

"The team's research has now identified several avenues by which ringed molecules known as polycyclic aromatic hydrocarbons, or PAHs, can form in space. The latest study is a part of an ongoing effort to retrace the chemical steps leading to the formation of complex carbon-containing molecules in deep space.

"PAHs—which also occur on Earth in emissions and soot from the combustion of fossil fuels—could provide clues to the formation of life's chemistry in space as precursors to interstellar nanoparticles. They are estimated to account for about 20 percent of all carbon in our galaxy, and they have the chemical building blocks needed to form 2-D and 3-D carbon structures.

"In the latest study, published in Nature Communications, researchers produced a chain of ringed, carbon-containing molecules by combining two highly reactive chemical species that are called free radicals because they contain unpaired electrons. The study ultimately showed how these chemical processes could lead to the development of carbon-containing graphene-type PAHs and 2-D nanostructures. Graphene is a one-atom-thick layer of carbon atoms.

"Importantly, the study showed a way to connect a five-sided (pentagon-shaped) molecular ring with a six-sided (hexagonal) molecular ring and to also convert five-sided molecular rings to six-sided rings, which is a stepping stone to a broader range of large PAH molecules.

***
The conditions required to produce naphthalene in space are present in the vicinity of carbon-rich stars, the study noted.

***

"'The radicals are short-lived - they react with themselves and react with anything else around them," Ahmed said. "The challenge is, 'How do you generate two radicals at the same time and in the same place, in an extremely hot environment?' We heated them up in the reactor, they collided and formed the compounds, and then we expelled them out of the reactor."

"Kaiser said, "For several decades, radical-radical reactions have been speculated to form aromatic structures in combustion flames and in deep space, but there has not been much evidence to support this hypothesis." He added, "The present experiment clearly provides scientific evidence that reactions between radicals at elevated temperatures do form aromatic molecules such as naphthalene.'"

Comment: the usual hype. Most proteins for life arrived in various meteorites and space rocks and do not show these compounds when analyzed.

Theoretical origin of life; a mix of molecules

by David Turell @, Wednesday, September 18, 2019, 19:36 (1672 days ago) @ David Turell

This foolish article assume a mash-mosh of various molecules miraculously appearing on a rocky Earth devoid of life or much advanced biochemistry:

https://www.the-scientist.com/news-opinion/rna-dna-chimeras-might-have-supported-the-or...

"The work, reported by Scripps Research Institute chemist Ramanarayanan Krishnamurthy and his postdoc Subhendu Bhowmik, came out of research exploring the transition from RNA-based lifeforms—commonly thought to be the first life on the planet—to the DNA-based life that is ubiquitous today. In making chimeric RNA-DNA molecules, Krishnamurthy and colleagues previously found that they have some advantages that might make them better candidates than pure RNA for the first reproducing molecules.

***

"In the newly published study, Krishnamurthy and Bhowmik found that the molecules consisting of both RNA and DNA components formed weaker bonds between the strands, allowing them to easily separate for replication. Then, as new strands formed, they preferentially bonded to like structures, yielding molecules of pure RNA and pure DNA. Similarly, chimeric molecules of RNA and an artificial nucleic acid known as TNA, which researchers speculate may represent a molecule that existed before RNA, were better able to yield nucleic acids composed entirely of RNA or TNA components than when starting with RNA or TNA alone."

Comment. James Tour are you watching this? And just where did these molecules come from on a lifeless Earth? The meteorites (like Murchison) don't contain them.

Theoretical origin of life; stromatolites were live organism

by David Turell @, Wednesday, September 25, 2019, 22:06 (1665 days ago) @ David Turell

Australian stromatolites are shown to be from living animals by the latest techniques:

https://www.newscientist.com/article/2217747-fossilised-microbes-from-3-5-billion-years...

"The Dresser Formation appears to contain layered structures called stromatolites. These are known to form when microbes grow into thin layers, which then become covered in sediment, only for another layer of microbes to form on top, and so forth.

"However, many researchers are not convinced that the rock structures really are stromatolites, arguing that they could have formed without life being present.

"Baumgartner’s team drilled into the rocks to get the best-preserved samples. They found many layers that looked like stromatolites. These contained “exceptionally preserved organic matter”, says Baumgartner, including strands of the sort seen when microbes form slimy layers called biofilms. Multiple chemical analyses indicate that the organic matter came from living organisms.

“'We have found smoking gun evidence for some of the earliest life on Earth,” says Baumgartner. “There are no convincing organic matter or microbial remains older than ours.”
There are plenty of claims of older fossils, or of chemical traces of life, some dating to over 4 billion years ago. But none has found widespread acceptance.

"The organic matter Baumgartner’s team found was mostly trapped inside a mineral called pyrite or fool’s gold, which is based on iron and sulphur.

“'The pyrite is extraordinary,” says Baumgartner. Because the microbes are so well-preserved, it must have formed quickly – perhaps even while they were alive. If that is true, it could reveal their survival strategy. Some modern microbes live off sulphur and produce pyrite as a waste product. The Dresser Formation microbes may have done the same, says Baumgartner.

"Pyrite may even have played a role in the origin of life, if the first life used sulphur as an energy source. This is the basis of the Iron-Sulphur World hypothesis, which was proposed by Günter Wächtershäuser in the late 1980s.

"Baumgartner says it is not clear what sort of environment his stromatolites were orginally formed in. In 2017 his colleague Tara Djokic showed that parts of the Dresser Formation preserve hot springs from on land, but other regions seem to have been shallow seas. Baumgartner suspects the Dresser Formation preserves a coastal region. “From this we can speculate that the origin of life might have been near,” he says.

“'They’ve done a good job,” says Lindsay Hays, Deputy Program Scientist for the NASA Astrobiology program in Washington, DC. “I can’t say this is definitely true or definitely not true,” she cautions, as closer examination of the rocks may reveal alternative explanations.

"However, she says Baumgartner’s evidence is based on multiple techniques, which makes it more reliable. “That has become the standard in this type of work, not to just say ‘we looked at this one line of evidence and it showed what we hoped it would show’, but ‘we looked at multiple lines of evidence and they all line up together’.”

Comment: If it is agreed this is acceptable evidence, then life was certainly on Earth very early, considering that the Earth formed about 4.5 byo and is considered to have been too hot of life at 4 byo. These appear to be organized organisms, advanced beyond what simple early life may have looked like.

Theoretical origin of life; another lab try

by David Turell @, Monday, November 04, 2019, 20:19 (1625 days ago) @ David Turell

With the usual silly result :

https://phys.org/news/2019-11-deep-sea-vents-ideal-conditions.html

By creating protocells in hot, alkaline seawater, a UCL-led research team has added to evidence that the origin of life could have been in deep-sea hydrothermal vents rather than shallow pools.

Previous experiments had failed to foster the formation of protocells—seen as a key stepping stone to the development of cell-based life—in such environments, but the new study, published in Nature Ecology & Evolution, finds that heat and alkalinity might not just be acceptable, but necessary to get life started.

***

Scientists researching the origins of life have made great progress with experiments to recreate the early chemical processes in which basic cell formations would have developed. The creation of protocells has been an important step, as they can be seen as the most basic form of a cell, consisting of just a bilayer membrane around an aqueous solution—a cell with a defined boundary and inner compartment.

Previous experiments to create protocells from naturally-occurring simple molecules—specifically, fatty acids—have succeeded in cool, fresh water, but only under very tightly controlled conditions, whereas the protocells have fallen apart in experiments in hydrothermal vent environments.

The study's first author, Dr. Sean Jordan (UCL Genetics, Evolution & Environment), said he and his colleagues identified a flaw in the previous work: "Other experiments had all used a small number of molecule types, mostly with fatty acids of the same size, whereas in natural environments, you would expect to see a wider array of molecules."

For the current study, the research team tried creating protocells with a mixture of different fatty acids and fatty alcohols that had not previously been used.

The researchers found that molecules with longer carbon chains needed heat in order to form themselves into a vesicle (protocell). An alkaline solution helped the fledgling vesicles keep their electric charge. A saltwater environment also proved helpful, as the fat molecules banded together more tightly in a salty fluid, forming more stable vesicles.

For the first time, the researchers succeeded at creating self-assembling protocells in an environment similar to that of hydrothermal vents. They found that the heat, alkalinity and salt did not impede the protocell formation, but actively favoured it.

"In our experiments, we have created one of the essential components of life under conditions that are more reflective of ancient environments than many other laboratory studies," Dr. Jordan said.

"We still don't know where life first formed, but our study shows that you cannot rule out the possibility of deep-sea hydrothermal vents."

Comment: This is a 'tightly controlled' experiment, like all others. The authors do not describe these molecules found in hot deep sea vents. Ignoring Tour's warning. more fun and games wasting grant money in the lab.

Theoretical origin of life; not materially possible

by David Turell @, Sunday, November 17, 2019, 22:49 (1612 days ago) @ David Turell

There is no way to naturally start life on Earth from a lifeless Earth:

https://stream.org/materialism-cannot-explain-the-origin-of-life-on-earth/

"Natural selection is the core mechanism in the Darwinian model for explaining life. This is the source of the “survival of the fittest” idea with which we are all familiar. Mutations in some organisms provide them with a competitive advantage over others. These more adaptive traits are “selected” and further enhance the propagation of those species.

"This seems to make sense. But it cannot apply to the origin of life. A lifeless Earth would have contained no organisms. There was nothing to mutate so there could not have been any “helpful” mutations. Natural selection had nothing to work with. It may help us understand the diversity of life. But what it cannot do is explain life’s origin. So, evolutionary biologists have been trying for decades to find a way to explain how life got started using only stuff available in the material world.

***

"In 1953, biochemists Stanley Miller and Harold Urey of the University of Chicago, conducted an experiment to demonstrate how life began. Their goal was to show that life could have arisen through purely chemical processes.

***

"Their goal was to confirm Charles Darwin’s speculations about the origin of life. Darwin believed that life arose from a “primordial soup” of pure chemicals in a “warm little pond.”

"On their first attempt, Miller and Urey were able to form some simple amino acids. They believed they had proved that the origin of life on Earth was no longer a mystery. To this day you will still see the staggering success of this experiment touted in science textbooks.

"But it’s not true. Reports of the success of their experiment have been greatly exaggerated.
For starters, it turns out Miller-Urey assumed the wrong initial conditions that existed on the early Earth. Most importantly, they neglected to include oxygen as being part of the early atmosphere.

"As it turns out, oxygen was not only present, it is also required to support life. The problem is that if there is oxygen in the atmosphere, or dissolved in water, it shuts down pre-biotic chemical pathways. But that’s not all. If oxygen is not present, pre-biotic chemistry doesn’t work either. So, whether oxygen is present or absent, it ruins Darwin’s infamous “primordial soup.” Pre-biotic molecules cannot form.

"Explaining the origin of life requires that oxygen be present. But the presence of oxygen also wrecks the process. The oxygen conundrum is that both of these have to be true at the same time.

***

"Cellular life must be able to use the energy it gets from its surroundings. To survive, it has to transform that energy so that it can develop, grow and sustain itself. This is known as metabolism. No matter how simple the life form is, it must also have the ability to copy and reproduce itself. This is what we call replication. This means that the very first life form must also have had these processes in place. And both of these processes had to have arisen simultaneously.

"Along with the replication issue, there is an even more intractable problem. Replication requires proteins which act to copy DNA and use that copy to form a new cell. But without DNA, the cell cannot produce proteins. DNA is the ‘blueprint” used to build an organism. Proteins are the “workers” that follow the blueprint to assemble the cell. And therein lies the problem.

"You can’t create the blueprint (DNA) without the workers.

"But you can’t assemble the workers without the blueprint.

"You need both the blueprint and the workers to be in place right from the beginning.

"But here’s the bottom line. There is no materialistic explanation for the emergence of life from non-life. Wishful thinking and Darwinian “just-so” stories are easy to concoct. But the evidence against them continues to pile up. The more we learn, the more the existence of life seems to depend on the intervention of an intelligent agent. But one thing is certain — materialism cannot explain the origin of life."

Comment: The usual list of problems with finding a reasonable theory for the origin of life on Earth.

Theoretical origin of life; ribose found in meteorites

by David Turell @, Thursday, November 21, 2019, 21:03 (1608 days ago) @ David Turell

Some amino acids and sugars have been found before:

https://www.sciencedaily.com/releases/2019/11/191121095004.htm

"Researchers from Tohoku University, Hokkaido University, JAMSTEC, and NASA Goddard Space Flight Center investigated meteorites and found ribose and other sugars. These sugars possessed distinct carbon-isotope compositions, differing from terrestrial biological sugars, indicating their extraterrestrial origin. The results suggest that the sugars formed in the early solar system and made their way to earth via meteorites.

***

"Amino acids and nucleobases, other vitally important compounds in the building block of life, have been found in meteorites previously. Scientists have known of the existence of sugars in meteorites. However, research to date has largely revealed sugar-related compounds (sugar acids and sugar alcohols) and the simplest sugar (dihydroxy acetone), compounds not considered essential for life.

"Formation of bio-essential sugars, including ribose, on the prebiotic Earth, is considered to have been possible. However, there is no geological evidence of their formation. Furthermore, it is not clear which and how much sugar(s) formed on the prebiotic Earth.

"With the current research evidencing the delivery of bio-essential sugars, it is plausible that extraterrestrial sugar contributed to the formation of primordial RNA on the prebiotic Earth. This, in turn, has the possibility of being a factor in the origin of life.

"'The next step is to investigate the chirality of the sugars in more meteorites and to investigate how much sugars were provided from space and how the extraterrestrial sugar influenced life's homochirality" says the team."

Comment: These sugars are not shown to be same as those in life. Ribose in RNA is right handed, and natural ribose comes both right and left handed forms.

Theoretical origin of life; phosphorus rich lakes

by David Turell @, Saturday, January 04, 2020, 15:47 (1564 days ago) @ David Turell

Most phosphorus is not freely available and is essential to life. Some lakes like Mono Lake in California may be the answer to solve the problem:

https://wattsupwiththat.com/2020/01/02/life-could-have-emerged-from-lakes-with-high-pho...

"Life as we know it requires phosphorus. It’s one of the six main chemical elements of life, it forms the backbone of DNA and RNA molecules, acts as the main currency for energy in all cells and anchors the lipids that separate cells from their surrounding environment.

"But how did a lifeless environment on the early Earth supply this key ingredient?

***

"The problem is that chemical reactions that make the building blocks of living things need a lot of phosphorus, but phosphorus is scarce. A new UW study, published Dec. 30 in the Proceedings of the National Academy of Sciences, finds an answer to this problem in certain types of lakes.

***

"Today these carbonate-rich lakes are biologically rich and support life ranging from microbes to Lake Magadi’s famous flocks of flamingoes. These living things affect the lake chemistry. So researchers did lab experiments with bottles of carbonate-rich water at different chemical compositions to understand how the lakes accumulate phosphorus, and how high phosphorus concentrations could get in a lifeless environment.

"The reason these waters have high phosphorus is their carbonate content. In most lakes, calcium, which is much more abundant on Earth, binds to phosphorus to make solid calcium phosphate minerals, which life can’t access. But in carbonate-rich waters, the carbonate outcompetes phosphate to bind with calcium, leaving some of the phosphate unattached. Lab tests that combined ingredients at different concentrations show that calcium binds to carbonate and leaves the phosphate freely available in the water.

“'It’s a straightforward idea, which is its appeal,” Toner said. “It solves the phosphate problem in an elegant and plausible way.”

***

“'The extremely high phosphate levels in these lakes and ponds would have driven reactions that put phosphorus into the molecular building blocks of RNA, proteins, and fats, all of which were needed to get life going,” said co-author David Catling, a UW professor of Earth & space sciences.

"The carbon dioxide-rich air on the early Earth, some four billion years ago, would have been ideal for creating such lakes and allowing them to reach maximum levels of phosphorus. Carbonate-rich lakes tend to form in atmospheres with high carbon dioxide. Plus, carbon dioxide dissolves in water to create acid conditions that efficiently release phosphorus from rocks.

“'The early Earth was a volcanically active place, so you would have had lots of fresh volcanic rock reacting with carbon dioxide and supplying carbonate and phosphorus to lakes,” Toner said. “The early Earth could have hosted many carbonate-rich lakes, which would have had high enough phosphorus concentrations to get life started.”

"Another recent study by the two authors showed that these types of lakes can also provide abundant cyanide to support the formation of amino acids and nucleotides, the building blocks of proteins, DNA and RNA. Before then researchers had struggled to find a natural environment with enough cyanide to support an origin of life. Cyanide is poisonous to humans, but not to primitive microbes, and is critical for the kind of chemistry that readily makes the building blocks of life."

Comment: The conditions may be perfect, but it still requires the design of the appropriate active protein molecules all coordinating in the dance of life..

Theoretical origin of life; flaws of RNA-World theory

by David Turell @, Saturday, February 15, 2020, 15:09 (1522 days ago) @ David Turell

thoughts from a chemist:

https://www.chemistryworld.com/opinion/flaws-in-the-rna-world/4011172.article

"The hypothesis of an ‘RNA world’ as the font of all life on Earth has been with us now for more than 30 years, the term having been coined by the biologist Wally Gilbert in 1986. You could be forgiven for thinking that it pretty much solves the conundrum of how the replication of DNA could have avoided a chicken-and-egg impasse: DNA replication requires protein enzymes, but proteins must be encoded in DNA. The intermediary RNA breaks that cycle of dependence because it can both encode genetic information and act catalytically like enzymes. Catalytic RNAs, known as ribozymes, play several roles in cells.

"It’s an alluring picture – catalytic RNAs appear by chance on the early Earth as molecular replicators that gradually evolve into complex molecules capable of encoding proteins, metabolic systems and ultimately DNA. But it’s almost certainly wrong. For even an RNA-based replication process needs energy: it can’t shelve metabolism until later. And although relatively simple self-copying ribozymes have been made,1 they typically work only if provided with just the right oligonucleotide components to work on. What’s more, sustained cycles of replication and proliferation require special conditions to ensure that RNA templates can be separated from copies made on them.

"Perhaps the biggest problem is that self-replicating ribozymes are highly complex molecules that seem very unlikely to have randomly polymerised in a prebiotic soup. And the argument that they might have been delivered by molecular evolution merely puts the cart before the horse....It’s nigh impossible to see how anything lifelike could come from it without mechanisms for both concentrating and segregating prebiotic molecules – to give RNA-making ribozymes any hope of copying themselves rather than just churning out junk, for example.

***

"Joyce and his coworkers have now found a ribozyme that holds the potential to copy heritable ‘pre-genetic’ information into RNAs considerably more complex and structured than any seen before.

***

"The best RNA polymerase the researchers obtained this way had a roughly 8% chance of inserting any nucleotide wrongly, and any such error increased the chance that the full chain encoded by the molecule would not be replicated. What’s more, making the original class I ligase was even more error-prone and inefficient – there was a 17% chance of an error on each nucleotide addition, plus a small chance of a spurious extra nucleotide being added at each position.

"These errors would be critical to the prospects of molecular evolution, since there is a threshold error rate above which a replicating molecule loses any Darwinian advantage over the rest of the population – in other words, evolution depends on good enough replication. Fidelity of copying could thus be a problem, hitherto insufficiently recognised, for the appearance of a self-sustaining, evolving RNA-based system: that is, for an RNA world.

"Maybe this obstacle could have been overcome in time. But my hunch is that any prebiotic molecule will have been too inefficient, inaccurate, dilute and noise-ridden to have cleared the hurdle. Rather, we’ll need to look for ways in which noisy, heterogeneous and perhaps compartmentalised molecular collectives could have bootstrapped their way to life. And that, after all, makes complete sense when you recognise that this is precisely what cells still are."

Comment: As Paul Davies noted in his book, a miracle is needed. All the lab work is intelligent design.

Theoretical origin of life; requires information

by David Turell @, Sunday, March 08, 2020, 00:57 (1501 days ago) @ David Turell

A Paul Davies article:

https://royalsocietypublishing.org/doi/full/10.1098/rsif.2012.0869

"Abstract
Although it has been notoriously difficult to pin down precisely what is it that makes life so distinctive and remarkable, there is general agreement that its informational aspect is one key property, perhaps the key property. The unique informational narrative of living systems suggests that life may be characterized by context-dependent causal influences, and, in particular, that top-down (or downward) causation—where higher levels influence and constrain the dynamics of lower levels in organizational hierarchies—may be a major contributor to the hierarchal structure of living systems. Here, we propose that the emergence of life may correspond to a physical transition associated with a shift in the causal structure, where information gains direct and context-dependent causal efficacy over the matter in which it is instantiated. Such a transition may be akin to more traditional physical transitions (e.g. thermodynamic phase transitions), with the crucial distinction that determining which phase (non-life or life) a given system is in requires dynamical information and therefore can only be inferred by identifying causal architecture. We discuss some novel research directions based on this hypothesis, including potential measures of such a transition that may be amenable to laboratory study, and how the proposed mechanism corresponds to the onset of the unique mode of (algorithmic) information processing characteristic of living systems. (my bold)

***

"Although it is notoriously hard to identify precisely what makes life so distinctive and remarkable, there is general agreement that its informational aspect is one key property, and perhaps the key property. The manner in which information flows through and between cells and sub-cellular structures is quite unlike anything else observed in nature. If life is more than just complex chemistry, its unique informational management properties may be the crucial indicator of this distinction. Unfortunately, the way that information operates in biology is not easily characterized. While standard information-theoretic measures, such as Shannon information, have proved useful, biological information has an additional quality which may roughly be called ‘functionality’—or ‘contextuality’—that sets it apart from a collection of mere bits as characterized by its Shannon information content. The information content of DNA, for example, is usually defined by the Shannon (sequential) measure. However, the genome is only a small part of the story. DNA is not a blueprint for an organism:1 no information is actively processed by DNA alone. Rather, DNA is a (mostly) passive repository for transcription of stored data into RNA, some (but by no means all) of which goes on to be translated into proteins. The biologically relevant information stored in DNA therefore has very little to do with its specific chemical nature (beyond the fact that it is a digital linear polymer). The genetic material could just as easily be a different variety of nucleic acid (or a different molecule altogether), as recently experimentally confirmed. It is the functionality of the expressed RNAs and proteins—not the bits—that is biologically
important. (my bold)

***

"The central position of information in biology is not itself especially new or radical. What is often sidestepped, however, is the fact that in biological systems information is not merely a way to label states, but a property of the system. To be explicit, biological information is distinctive because it possesses a type of causal efficacy—it is the information that determines the current state and hence the dynamics (and therefore also the future state(s)). In this paper, we postulate that it is the transition to context-dependent causation—mediated by the onset of information control—that is the key defining characteristic of life."

Comment: Simple. The way life uses the information it has makes life exist from a bunch of active protein molecules all in the same soup. Not by chance.

Theoretical origin of life; latest lab study

by David Turell @, Monday, March 16, 2020, 19:28 (1492 days ago) @ David Turell

An iron containing molecule acting as an early enzyme had to be present:

https://phys.org/news/2020-03-scientists-blocks-life.html

"Rutgers researchers have discovered the origins of the protein structures responsible for metabolism: simple molecules that powered early life on Earth and serve as chemical signals that NASA could use to search for life on other planets.

"Their study, which predicts what the earliest proteins looked like 3.5 billion to 2.5 billion years ago

***

The ENIGMA project seeks to reveal the role of the simplest proteins that catalyzed the earliest stages of life.

"'We think life was built from very small building blocks and emerged like a Lego set to make cells and more complex organisms like us," said senior author Paul G. Falkowski, ENIGMA principal investigator and a distinguished professor at Rutgers University-New Brunswick who leads the Environmental Biophysics and Molecular Ecology Laboratory. "We think we have found the building blocks of life—the Lego set that led, ultimately, to the evolution of cells, animals and plants."

"The Rutgers team focused on two protein "folds" that are likely the first structures in early metabolism. They are a ferredoxin fold that binds iron-sulfur compounds, and a "Rossmann" fold, which binds nucleotides (the building blocks of DNA and RNA). These are two pieces of the puzzle that must fit in the evolution of life.

"Proteins are chains of amino acids and a chain's 3-D path in space is called a fold. Ferredoxins are metals found in modern proteins and shuttle electrons around cells to promote metabolism. Electrons flow through solids, liquids and gases and power living systems, and the same electrical force must be present in any other planetary system with a chance to support life.

"There is evidence the two folds may have shared a common ancestor and, if true, the ancestor may have been the first metabolic enzyme of life."

Comment: Please see the diagram. What they are presenting is an advanced molecule that may well have been present ass a later part of the process. It does not explain why life exists.

Theoretical origin of life; hunting for stromatolites

by David Turell @, Monday, March 30, 2020, 23:46 (1478 days ago) @ David Turell

Then one must locate traces of biological life:

https://www.smithsonianmag.com/science-nature/earth-earliest-life-fossils-stromatolites...

"The search for signs of Earth’s earliest forms of life isn’t quite like looking for dinosaur bones protruding out from desert outcrops. The oldest species on our planet were microscopic, nothing more than itty-bitty specks. Detecting them, and verifying their identity, is a complicated task that often relies not only hunting town tiny remains but also on chemistry and perceiving how those microorganisms modified their environments.

"Picking out the evidence of Earth’s earliest life is more than a needle-in-a-haystack problem. The entire planet is the metaphorical haystack, while the needles are no more than microscopic cells or faint chemical traces. Even when scientists can pin down possible candidates, it’s can be hard to know for sure when something is a signature of ancient life rather than a plain-old geologic phenomenon.

***

"In 2016, a team of researchers from Australia proposed that they had found evidence of stromatolites being formed about 3.7 billion years ago, which would make them a remnant of some of the earliest known organisms. The Earth itself, after all, is only about 4.5 billion years old.

"But other experts weren’t convinced. The fossils preserved only the stromatolite structure, not the organisms that created them, and some researchers argued that the rocks were formed by other geological processes. However, a study published just last year put forth stronger evidence, including geochemical analysis, that suggests some 3.5-billion-year-old stromatolites found at a different site in Australia do record and contain evidence of some of Earth’s oldest microbes.

"The search for the signs of early life, what experts call biosignatures, often focuses on four different lines of evidence, says University of New South Wales astrobiologist Tara Djokic. The first kind of evidence is relatively large and can be seen with the naked eye, such as the stromatolites. Other traces are much harder to find, and that group includes chemical traces of fossils, degraded biological compounds, and fossils of microorganisms themselves.

***

“'Thanks to billions of years of the rock cycle, there are not so many rocks which are even suitable to search in for signs of early life,” Olcott says. Searching for early life requires understanding—and correcting for—the factors that may obscure the truth. “It’s like coming to a crime scene and having to piece together what has happened and who was involved,” Djokic says.

"At present, the starting date for life on Earth is still rough. “There is no specific site that is considered [to be] 100 percent proof of the earliest signs of life on Earth,” Djokic says. One of the oldest, least controversial sites is the 3.4-billion-year-old Strelley Pool Formation in Australia, Olcott notes. Researchers have found stromatolites, microbial mats, chemical signatures indicative of life and more. Older sites hold potential but are controversial. A roughly 3.8-billion-year-old site in Greenland may contain even older traces of life, but this spot is more contentious, Djokic says, because the rocks there have been through the geological ringer and are more difficult to interpret."

Comment: This information has been presented before, but is worth reviewing. What is amazing is how early life might have arrived on an Earth estimated as 4.5 byo. Certainly looks as if the Earth was well-prepared in advance for life to start. As Paul Davies notes, life sure looks like a miracle. I view it as God planning well.

Theoretical origin of life; another odds against paper

by David Turell @, Tuesday, April 28, 2020, 16:34 (1449 days ago) @ David Turell

Like Koonen, (see here: 2015-02-21, 15:06) author using RNA world basis:

https://www.space.com/origin-of-life-rna-universe-model.html

"Totani's study looks at a leading hypothesis for abiogenesis, that life as we know it began in what researchers call an RNA world. This hypothesis suggests that before the evolution of proteins and the double-stranded genetic molecule called DNA, or deoxyribonucleic acid — which today provides the instructions for life on Earth — the world was dominated by similar but less efficient molecules called RNA, or ribonucleic acid.

***

"Although primitive, RNA is made up of many chemicals called monomers that link together to form a polymer. Particularly, RNA is made up of a chain of nitrogen-based molecules called nucleotides. Researchers think that in order for RNA to perform its essential function of copying itself, it needs to be composed of a chain of nucleotides longer than 40 to 60 nucleotides.

***

"Totani's model uses the most conservative method of RNA polymerization, where each monomer is attached randomly one-by-one until a chain of monomers is formed. Scientists have suggested that polymers (each made up of multiple monomers) could attach to each other to speed up the process, but Totani said such a process is "highly speculative and hypothetical."

***

"Scientists think life emerged on Earth around 500 million years after the planet formed. Given that there are an estimated 10 sextillion (10^22) stars in the observable universe, it may seem that the odds of life popping up in the universe should be good. But researchers have found that the random formation of RNA with a length greater than 40 is incredibly unlikely given the number of stars — with habitable planets — in our cosmic neighborhood. There are too few stars with habitable planets in the observable universe for abiogenesis to occur within the timeframe of life emerging on Earth.

***

"It is estimated that the whole universe could contain more than 1 googol (10^100) stars. When Totani factored in this new abundance of stars, he found that the emergence of life was no longer improbable, but very likely.

"This may be good news for the RNA world hypothesis, though it could also mean that the search for life in the universe is a hopeless pursuit.

If life first got its start in RNA, "life on Earth was created by a very rare chance of producing a long RNA polymer," said Totani. "Most likely, Earth is the only planet harboring life in the observable universe. I predict that future observations or explorations of extraterrestrial life will yield no positive results.

***

"Totani's work is far from an answer to one of science's most existential questions but it may guide further research on the origins of life. Whether we are alone in the universe still remains unanswered, but if Totani's numbers tell us anything, you shouldn't bet on it."

Comment: Highly theoretical fun. The first assumption about an RNA world is itself problematic. Further remember my recent comment about DNA/RNA simply supplying ingredients, not all the necessary reactions between controlling protein molecules:

RNA naturally appearing on is own without all the other surrounding layers is poppycock. All of this integration of molecules influencing each other, some 'mastering' each other, cannot naturally be added layer by layer in a chance fashion to end up with life as we know it. This requires precise design by a designer. The existence of a designer cannot be denied no matter how that designer is named or not named. This is the ID position. (Saturday, April 25, 2020, 17:27)

Theoretical origin of life; another odds against paper

by dhw, Wednesday, April 29, 2020, 15:34 (1448 days ago) @ David Turell

DAVID: Highly theoretical fun. The first assumption about an RNA world is itself problematic. Further remember my recent comment about DNA/RNA simply supplying ingredients, not all the necessary reactions between controlling protein molecules.

As you say, lots of fun, and why shouldn’t we all join in? I estimate that there are at least 1.33 googols of stars in the universe, and I predict that a thousand years from now, we shall find some form of primitive life on at least three of them (though nobody will speak English). What’s more, I predict that humans will still be here, and some will claim that the newly discovered forms of life are proof of abiogenesis, and others will claim that they could only have been the products of design by a designer. I am prepared to bet a million dollars on this, and if anyone is willing to join in the game, I will give you the details of the account to which you should send your money.

Theoretical origin of life; another odds against paper

by David Turell @, Wednesday, April 29, 2020, 18:19 (1448 days ago) @ dhw

DAVID: Highly theoretical fun. The first assumption about an RNA world is itself problematic. Further remember my recent comment about DNA/RNA simply supplying ingredients, not all the necessary reactions between controlling protein molecules.

dhw: As you say, lots of fun, and why shouldn’t we all join in? I estimate that there are at least 1.33 googols of stars in the universe, and I predict that a thousand years from now, we shall find some form of primitive life on at least three of them (though nobody will speak English). What’s more, I predict that humans will still be here, and some will claim that the newly discovered forms of life are proof of abiogenesis, and others will claim that they could only have been the products of design by a designer. I am prepared to bet a million dollars on this, and if anyone is willing to join in the game, I will give you the details of the account to which you should send your money.

How about a whole new form of biochemistry not based on carbon? God could start inventing life again since you think He has to run experiments.

Theoretical origin of life;a very critical essay of research

by David Turell @, Thursday, May 07, 2020, 01:33 (1441 days ago) @ David Turell

The cause of the origin of life is totally unknown and a very diffcult nut to crack:

https://inference-review.com/article/hot-wired

"It is a commonplace of criticism that the spontaneous formation of a living system by chance is unlikely. How unlikely? Fred Hoyle put the odds at roughly 1 in 1040,000. These odds he compared to the chance of a tornado plowing through a junkyard and assembling a Boeing 747.31 Hoyle’s tornado has enjoyed an existence all its own.

***

"Nature abhors low odds. This is the simple meaning of the second law of thermodynamics. With Hoyle’s 747 having lumbered down various runways, nearly all origins of life (OOL) researchers came to recognize that the appearance of the first cell could not have been a matter of sheer dumb luck. (my bold)

***

"..the simplest functional cell has both lower entropy and higher energy than its prebiotic precursors, or even its building blocks. The atoms in a cell are arranged in highly specified low-entropy configurations, and they are comprised of high-energy chemical bonds. These are unnatural circumstances. Natural systems never both decrease in entropy and increase in energy—not at the same time.

***

"Physicists and chemists often combine the entropy and energy of a system to form a definition of its free energy. For spontaneous processes, a change in free energy is always negative. Harold Morowitz estimated the probability that a bacterial cell might have originated through thermal fluctuations, and determined that the probability of spontaneously going from low to high, when every other system was spontaneously going from high to low, was on the order of one part in ten to the power of a hundred billion.

***

"the key challenge in OOL research lies in explaining how a system could extract energy from the environment and then direct it toward increasing its internal free-energy non-transiently. England’s experiments do not address this concern, for the energy absorbed is almost immediately dissipated away. (England mentioned, not edited by me as unnecessary)

***

"All cells accomplish the goal of maintaining a high-free-energy state against opposing thermodynamic forces by employing complex molecular machinery and finely tuned chemical networks to convert one form of energy from the environment into high-energy molecules. The energy from the breakdown of these energy-currency molecules is directed toward powering targeted chemical reactions. The energy coupling is accomplished through complex enzymes and other proteins comprised of information-rich amino-acid sequences.

***

"In any OOL scenario, the protocell would have to generate at least this amount in the latter stages just to overcome the thermodynamic drive back toward equilibrium, and even greater amounts would be required for replication. In contrast, a leading proposal for energy production centers on proton gradients in hydrothermal vents. Experimental simulations of vents under ideal conditions only generate small quantities of possible precursors to life’s building blocks, and the corresponding power production density is on the order of 0.001 μW/g. This quantity is considerably greater than what could practically be transferred to any stage of abiogenesis, yet it is still eight orders of magnitude too small even to prevent a protocell from quickly degrading back to simple, low-energy molecules.

***

"Enzymes are essential for energetically favorable reactions since most reactions are too slow to drive cellular operations. Enzymes accelerate the reactions’ turnover rates by factors typically between 10^8 and 10^10,and the increase in many cases is significantly higher. Without enzymes... This is not a plausible scenario. In addition, individual steps in the chemical pathways to synthesize life’s building blocks and then to link them together require multiple, mutually exclusive reaction conditions, so no environment could support more than a few required steps. The enzymes create the necessary nano-environments in their active sites to support their targeted reactions, so a multitude of diverse reactions can be maintained in the same cellular microenvironment simultaneously. They are required both to specify and power the correct set of processes. (my bold)

"A minimally complex free-living cell requires hundreds of tightly regulated enzyme-enabled reactions. If even one enzyme were missing, all metabolic processes would cease, and the system would head irreversibly back toward equilibrium. England’s research does not explain how such a complex, specified system could originate. Both the proteins that constitute an engine’s building blocks and enzymes represent sequences of amino acids that contain large quantities of functional information. The amino acids must be arranged in the right order in the same way the letters in a sentence must be arranged properly to convey its intended meaning. This arrangement is crucial for the chains to fold into the correct three-dimensional structures to properly perform their assigned functions. This information is essential for constructing and maintaining the cell’s structures and processes. Until origins researchers address the central role of information, the origin of life will remain shrouded in mystery."

Comment: Origin of life must be seen as a miracle, as Paul Davies has suggested.

Theoretical origin of life; energy needs of first cell

by David Turell @, Wednesday, May 13, 2020, 21:33 (1434 days ago) @ David Turell

A highly theoretical discussion:

https://evolutionnews.org/2020/05/on-the-origin-of-life-here-is-my-response-to-jeremy-e...

"England rightly states that the fluctuation theorems allow for the possibility that some mechanism could drive matter to both lower entropy and higher energy (higher free energy), thus potentially solving the problem of the origin of life, at least in theory. In contrast, I addressed the likelihood that, given the practical constraints, realistic natural processes on the early earth could generate a minimally complex cell. In that context, England indirectly affirmed the main points of my argument and thus reinforced the conclusion that an undirected origin of life might be possible in principle, but it is completely implausible in practice.

"1) The main points of my argument can be summarized as follows:
Natural processes tend to drive systems toward higher entropy, lower energy, or both. In direct conflict, the origin of life requires a collection of molecules to move toward dramatically lower entropy and higher energy.

"2) The only way to overcome the thermodynamic barriers is for an engine to be present at the very instantiation of life that can convert some available source of energy into a form that can fuel the construction and operations of a cell.

'3) Significant quantities of information must also be present both to steer a highly specific set of interconnected chemical reactions that comprise a minimally viable cell and to direct the generated energy toward powering the otherwise nonspontaneous reactions.

***

"The role of information in the simulation is more subtle and calls for a brief digression into information theory. A key tenet is that information can often be thought of as that which enacts causal control over or reduces the uncertainty in an outcome. In the case of the experiment, the highly specified construction of the simulation entails the implementation of information. The applied information constrains the dynamics (reduces the uncertainty) to effect a specific category of outcomes. It functions equivalently to the information in an enzyme that directs the production of a specific molecule.

***

"These specifications represent applied information that constrains the dynamics in such a way as to produce the desired results. Here again, achieving noteworthy behavior requires an energy converter and the application of information.

***

"The constraints governing an emerging cell present even greater challenges than in the cited experiments for nature to assemble a viable engine. In life, the energy produced must be in the form of high-energy (energy-currency) molecules that could power the chemical reactions undergirding cellular operations. The challenge is that the energy requirement is enormous. As I explained in my article, the minimal power production capacity needed for a nascent cell just to prevent it from degrading into simple chemicals approaches, if scaled, that of a high-performance racing car.

"The most promising candidate for a “natural engine” is proton flows across thermal vents that theoretically could generate high-energy molecules. However, simulations of vents under ideal conditions only produce chemical energy at a rate that is at least eight orders of magnitude too small. And the actual product is formaldehyde in concentrations far too miniscule to contribute to any stage in the genesis of a cell. Such meager results simply highlight the fact that no natural mechanism could realistically generate the required energy to power even the earliest stages of any origin-of-life scenario.

"Moreover, the driven objects in each of the cited experiments are identical, so they all interact uniformly with the applied field. In contrast, the reactions in a cell are quite different. As a result, no single engine could drive more than one or two of them even under ideal conditions. Consequently, a cell requires multiple mechanisms to extract the energy from the energy-currency molecules and direct it toward powering each distinct reaction. I detailed in my article how only a suite of hundreds of enzymes could meet this requirement, which corresponds to at least a million bits of information. England’s response to my article has only reinforced these conclusions." (my bold)

Comment: The takeaway is simple: all the research that looks at one simple aspect of the first cell, like RNA, misses the entire point. A cell is made up of millions specifically placed amino acids, fleets of enzymes to run processes as fast as possible and lacks mitochondria, so the source of lots of energy is a problem for it. And information must be present as shown in my bold, just above.

Theoretical origin of life; available organic molecules

by David Turell @, Sunday, June 14, 2020, 20:07 (1402 days ago) @ David Turell

There are simple organic molecules existing in the universe, but taht explain wh life appeared:

https://phys.org/news/2020-06-ingredients-life-stellar-nurseries-stars.html

Complex organic molecules that could serve as building blocks for life are more ubiquitous than previously thought in cold clouds of gas and dust that give birth to stars and planets, according to astronomers at the University of Arizona Steward Observatory.

These molecules also appear much earlier than conventional wisdom suggested, hundreds of thousands of years before stars actually begin to form, the researchers found. Published in The Astrophysical Journal, the results challenge existing theories that require an environment heated by proto-stars—stars in the making—for complex organic molecules to become observable.

The study is the first to look for the signatures of two complex organic molecules, methanol and acetaldehyde, in a substantial number of prospective star-forming sites, unlike previous observations, which had mostly focused on individual objects. Pre-stellar or starless cores are so-named because while they do not yet contain any stars, they mark regions in space where cold dust and gases coalesce into the seeds that will give rise to stars and possibly planets.

***

"These starless cores we looked at are several hundred thousand years away from the initial formation of a protostar or any planets," said Yancy Shirley, associate professor of astronomy, who co-authored the paper with lead author Samantha Scibelli, a third-year doctoral student in Shirley's research group. "This tells us that the basic organic chemistry needed for life is present in the raw gas prior to the formation of stars and planets."

While scientists have long known about the existence in space of prebiotic molecules—which provide the building blocks necessary for life as we know it—it has been difficult to come up with conclusive answers to where and how they form and the mechanisms by which they end up on the surfaces of any prospective planet. (my bold)

***

These findings challenge traditional theories of how prebiotic molecules form, because they assume a scenario in which the heat from newborn stars provides the necessary environment for organic molecules to form. (my bold)

Comment: These simple molecules are certainly the forerunners of amino acids but as my bold indicate there are huge steps necessary, that the authors note, to create real amino acids on a planet, but more than that only left-handed forms. I doubt we will ever learn how life started spontaneously. Which brings us back to a designer.

Theoretical origin of life;strong objection to natural start

by David Turell @, Wednesday, June 17, 2020, 19:47 (1399 days ago) @ David Turell

The problems are overwhelming:

https://evolutionnews.org/2020/06/origin-stories-rna-dna-and-a-dose-of-imagination/

"one of the challenges facing this RNA/DNA World scenario is that it would have required the abiotic synthesis of building blocks of both DNA and RNA in close proximity and, preferably, under the same geochemical scenario. It is in this area that the researchers seek to make a contribution, demonstrating that certain building blocks of both RNA and DNA can be synthesized with “prebiotically plausible reactions and substrates.”

***

"we might get the impression that in fact “there was a mixed genetic system with RNA and DNA building blocks” under early Earth conditions.

***

"First, there was no “mixed genetic system.” In fact, there wasn’t any kind of functional system, just molecules interacting under the normal tug-and-pull of physics and chemistry. Furthermore, a genetic system requires a special kind of functional capability. It requires not just DNA and RNA, but the information content that ebbs and flows between them. Meaning, a symbolic code, pursuant to which a string of nucleotides in the primordial DNA would be interpreted and translated into another state — the symbolic and the immaterial being coaxed into the concrete and the material. Such a system necessarily involves information processing, with not just bare DNA storage at hand, but also retrieval and translation mechanisms. Such a system arising through unguided natural processes has never been observed, and we have theoretical and practical reasons to conclude it never will be.

***

"Yet from an information-theoretic standpoint, having building blocks for a potential alphabet is unremarkable. I can build an information storage system out of sticks and stones.
There are multiple elephants in this room: What is the functional context of that system? Where does the information come from? How it is retrieved? How is it interpreted and acted upon? What is the overall meaning and purpose of that information? How does it become directed toward a comprehensive, integrated, cohesive end — producing a living organism? The mere existence of molecules that could hypothetically serve as physical carriers of hypothetical symbols as part of a hypothetical primordial alphabet tells us nothing in response to these questions.

***

"Sutherland mentions that the group’s research fulfills a “key precondition for the spontaneous emergence of life on Earth.” What was fulfilled? His point is that many people believe life had to start with both DNA and RNA together, not the traditional RNA World scenario that slowly gave rise to DNA.

"He is right. There are good reasons for thinking life started with both DNA and RNA. That’s both because (as noted above) no one has been able to propose a plausible scenario that would produce DNA from RNA under real-world conditions, and also because the genetic systems we are familiar with in biology indeed include both DNA and RNA.

"Yet the recent research did not demonstrate that such a genetic system can realistically arise by itself. Nor did it bring us closer to demonstrating “the spontaneous emergence of life on Earth.”

"After all, beyond a genetic system, to keep life going on the early Earth another capability is required: self-replication. Many origin-of-life researchers view self-replication as the key goal, relying on the Darwinian process of mutation and natural selection to build the rest of the systems for the first organism. (See, for example, here and here.) Yet as I demonstrate in my engineering analysis in Evolution and Intelligent Design in a Nutshell, self-replication is not the starting point for the origin of life. Instead, it “lies at the end of an extremely complicated, sophisticated, and specified engineering process.”

***

"This impressive work was performed by some of the most capable researchers in this field. The authors deserve recognition for it. Origin-of-life research doesn’t get any better.

"Yet for anyone tempted to think we are on our way to explaining the origin of life in naturalistic terms, what do we really have? Well, we now have building blocks on the early Earth that, potentially, could be used in some later process as part of the production of DNA and RNA. Alternatively, as the authors suggest, perhaps the building blocks could have served as the initial information carrier and then later turned into modern RNA and DNA.

"Either way, these would then need to be carefully strung together into information-rich molecules, based on a symbolic code. That in turn would require multiple machines and interrelated systems to access, interpret, and utilize the information, which would further require a suite of hundreds of genes, components, and systems to survive in a prebiotic environment and self-replicate. None of these steps is plausible by purely natural means. All of them speak to the need for intelligent input.

Comment: this is an answer to a hopeful article like all the ones I present. The so-called positive results are zilch over 70 years. Clearly the research has not established any sort of natural mechanism. Unless one is found, a designer has to be accepted.

Theoretical origin of life; a combined RNA/DNA start

by David Turell @, Monday, June 22, 2020, 22:47 (1394 days ago) @ David Turell

that's the new proposal as usdual based on lab based invented evidence:

https://www.scientificamerican.com/article/the-first-gene-on-earth-may-have-been-a-hybr...


"DNA and RNA, the two major modern forms of genetic code underpinning all of earthly biology, could have coexisted in strict pairings on our planet before life arose here, scientists in England, Scotland and Poland say. Using a hydrogen cyanide–based chemical system intended to mimic conditions in Earth’s early history, the researchers made four bases, the molecular “letters” of the genetic alphabet. Strung together, these bases form gene sequences that cells translate into proteins. But surprisingly, the team found that of the four bases their experiments consistently made, two were in a form found in DNA, whereas the other two were of a kind seen in RNA.

"The study, ... further undermines the so-called RNA world hypothesis. This idea, long one of the most prominent in origins-of-life research, posits that RNA formed the basis of Earth’s biosphere long before DNA and other molecules important to life emerged. Yet to date, scant evidence has been found of chemical pathways to make the RNA-exclusive system that rigid versions of the idea adopt or that could lead to DNA. “People have tended to think of RNA as the parent of DNA,” Sutherland says. “This [paper] suggests that they are molecular siblings.”

"Other scientists who were not involved with the study question the plausibility of the conditions used in this hydrogen cyanide-based route, however. Frances Westall, director of the exobiology group at the French National Center for Scientific Research’s Center for Molecular Biophysics in Orléans, notes that forming the bases requires very specific conditions. Mixtures would need to dry out and be exposed to ultraviolet light—two hurdles most easily surmounted on dry land, which was in short supply during our planet’s ocean-covered early days more than four billion years ago. “These conditions certainly existed on the early Earth,” Westall says. “They would not have been that common because there was not that much exposed landmass.” Although she adds that the study is “clever” and “not completely impossible,” she concludes that “there are other, better hypotheses as to locations for the emergence of life and prebiotic molecules.”

***

"This is a key issue for Nicholas Hud, an origins-of-life researcher at the Georgia Institute of Technology, who was not involved in the study. He calls it an “excellent compilation of organic chemistry research” on water-based nucleoside synthesis. But Hud is not convinced that the paper resolves whether these nucleosides actually arose before living creatures. His own research suggests amino acids could have linked up to carry information and act as a catalyst before RNA. Hud thinks evolution would then have gradually produced the current genetic system over long stretches of geologic time. “If a molecule looks very difficult, from a chemical perspective, to make, yet it functions exquisitely in biology, then it’s probably the case that it has been evolved over time,” he says. For the same reasons, he is also skeptical about the RNA world hypothesis.

"Furthermore, Hud sees the new study’s reliance on rigid incremental steps, each performed in strict order and under carefully controlled conditions, as a significant weakness. If the order of the steps changed or certain products were not isolated, Sutherland and his colleagues would have made much less of the substances they are interested in, Hud says. That caveat reduces the chances of the scenario unfolding in the chaotic environs of the early Earth."

comment: Just more fun and games with intelligent design in a lab and even the researchers very doubtful about each 'new' advance.

Theoretical origin of life; another 'early' protein start

by David Turell @, Tuesday, June 23, 2020, 22:08 (1393 days ago) @ David Turell

Lots more lab experimentation with supposed early molecules:

https://www.sciencedaily.com/releases/2020/06/200622095023.htm

"What did the very first proteins look like -- those that appeared on Earth around 3.7 billion years ago? Prof. Dan Tawfik of the Weizmann Institute of Science and Prof. Norman Metanis of the Hebrew University of Jerusalem have reconstructed protein sequences that may well resemble those ancestors of modern proteins, and their research suggests a way that these primitive proteins could have progressed to forming living cells.

***

"Showing amino acids could, under the right conditions, form without help from enzymes or any other mechanism in a living organism suggested that amino acids were the "egg" that preceded the enzyme "chicken."

***

"...that is all well and good, "but one vital type of amino acid has been missing from that experiment and every experiment that followed in its wake: amino acids like arginine and lysine that carry a positive electric charge." These amino acids are particularly important to modern proteins, as they interact with DNA and RNA, both of which carry net negative charges. RNA is today presumed to be the original molecule that could both carry information and make copies of itself, so contact with positively-charged amino acids would theoretically be necessary for further steps in the development of living cells to occur.

"But there was one positively-charged amino acid that appeared in the Miller-Urey experiments, an amino acid called ornithine that is today found as an intermediate step in arginine production, but is not, itself, used to build proteins. The research team asked: What if ornithine was the missing amino acid in those ancestral proteins? They designed an original experiment to test this hypothesis. (my bold)

***

"The scientists began with a relatively simple protein from a family that binds to DNA and RNA, applying phylogenetic methods to infer the sequence of the ancestral protein. This protein would have been rich in positive charges -- 14 of the 64 amino acids being either arginine or lysine. Next, they created synthetic proteins in which ornithine replaced these as the positive charge carrier.

"The ornithine-based proteins bound to DNA, but weakly. In Metanis' lab, however, the researchers found that simple chemical reactions could convert ornithine to arginine. And these chemical reactions occurred under those conditions assumed to have prevailed on Earth at the time the first proteins would have appeared. As more and more of the ornithine was converted to arginine, the proteins came more and more to resemble modern proteins, and to bind to DNA in a way that was stronger and more selective.

"The scientists also discovered that in the presence of RNA, that the ancient form of the peptide engaged in phase separation (like oil drops in water) -- a step that can then lead to self-assembly and "departmentalization." And this, says Tawfik, suggests that such proteins, together with RNA, could form proto-cells, from which true living cells might have evolved."

Comment: Note my bold. There is no evidence the Miller-Urey experiment produced any true factual results about the long ago period. Again more intelligent design in a lab, nothing more.

Theoretical origin of life; Darwin evolution hope

by David Turell @, Friday, August 07, 2020, 19:47 (1348 days ago) @ David Turell

More fun and games in a lab with intelligent design:

https://phys.org/news/2020-08-life-chemical-evolution-tiny-gulf.html

"Chemical reactions driven by the geological conditions on the early Earth might have led to the prebiotic evolution of self-replicating molecules. Scientists at Ludwig-Maximilians Universitaet (LMU) in Munich now report on a hydrothermal mechanism that could have promoted the process.

"Life is a product of evolution by natural selection. That's the take-home lesson from Charles Darwin's book "The Origin of Species," published over 150 years ago.

***

"One major problem with ribozyme-driven scenario for replication of RNA is that the initial result of the process is a double-stranded RNA. To achieve cyclic replication, the strands must be separated ('melted'), and this requires higher temperatures, which are likely to unfold—and inactivate—the ribozyme. Braun and colleagues have now demonstrated how this can be avoided. "In our experiment, local heating of the reaction chamber creates a steep temperature gradient, which sets up a combination of convection, thermophoresis and Brownian motion," says Braun. Convection stirs the system, while thermophoresis transports molecules along the gradient in a size-dependent manner. The result is a microscopic version of an ocean current like the Gulf Stream. This is essential, as it transports short RNA molecules into warmer regions, while the larger, heat-sensitive ribozyme accumulates in the cooler regions, and is protected from melting. Indeed, the researchers were astonished to discover that the ribozyme molecules aggregated to form larger complexes, which further enhances their concentration in the colder region. In this way, the lifetimes of the labile ribozymes could be significantly extended, in spite of the relatively high temperatures. "That was a complete surprise," says Braun.

"The lengths of the replicated strands obtained are still comparatively limited. The shortest RNA sequences are more efficiently duplicated than the longer, such that the dominant products of replication are reduced to a minimal length. Hence, true Darwinian evolution, which favors synthesis of progressively longer RNA strands, does not occur under these conditions. "However, based on our theoretical calculations, we are confident that further optimization of our temperature traps is feasible," says Braun. A system in which the ribozyme is assembled from shorter RNA strands, which it can replicate separately, is also a possible way forward."

Comment: this is at an insane extension of OOL research, full of intelligent manipulation with the hope that somehow nature can replicate the method naturally.

Theoretical origin of life; early anoxic bacteria

by David Turell @, Friday, August 07, 2020, 20:53 (1348 days ago) @ David Turell

Had a metabolism without oxygen:

"In the first billion years, there was no oxygen on Earth. Life developed in an anoxic environment. Early bacteria probably obtained their energy by breaking down various substances by means of fermentation. However, there also seems to have been a kind of "oxygen-free respiration." This was suggested by studies on primordial microbes that are still found in anoxic habitats today.

***

"...we at some point took a heat-loving bacterium, Thermotoga maritima, which grows at temperatures between 60 and 90°C," explains Dragan Trifunovic, who will shortly complete his doctorate. "Thermotoga also contains Rnf genes, and we hoped that the Rnf enzyme in this bacterium would be a bit more stable. Over the years, we then managed to develop a method for isolating the entire Rnf enzyme from the membrane of these bacteria."

"As the researchers report in their current paper, the enzyme complex functions a bit like a pumped-storage power plant that pumps water into a lake higher up and produces electricity via a turbine from the water flowing back down again.

"Only in the bacterial cell the Rnf enzyme (biochemical name = ferredoxin:NAD-oxidoreductase) transports sodium ions out of the cell's interior via the cell membrane to the outside and in so doing produces an electric field. This electric field is used to drive a cellular "turbine" (ATP synthase): It allows the sodium ions to flow back along the electric field into the cell's interior and in so doing it obtains energy in the form of the cellular energy currency ATP.

"The biochemical proof and the bioenergetic characterization of this primordial Rnf enzyme explains how first forms of life produced the central energy currency ATP. The Rnf enzyme evidently functions so well that it is still contained in many bacteria and some archaea today, in some pathogenic bacteria as well where the role of the Rnf enzyme is still entirely unclear."

Comment: It is important to remember all enzymes aere giant protein molecules with specific areas which force reactions to happen by keeping reactive molecules together. They are so specific they have to be designed.

Theoretical origin of life; early anoxic bacteria

by David Turell @, Wednesday, September 23, 2020, 01:23 (1302 days ago) @ David Turell

Perhaps using arsenic:

https://www.sciencedaily.com/releases/2020/09/200922112236.htm

"Much of life on planet Earth today relies on oxygen to exist, but before oxygen was present on our blue planet, lifeforms likely used arsenic instead.

***

"Theories as to how life's processes functioned in the absence of oxygen have mostly relied on hydrogen, sulfur, or iron as the elements that ferried electrons around to fulfill the metabolic needs of organisms.

"Visscher explains these theories are contested, for example photosynthesis is possible with iron but researchers do not find evidence of that in the fossil record before oxygen appeared some 2.4 billion years ago. Hydrogen is mentioned yet the energetics and competition for hydrogen between different microbes shows it is highly unfeasible.

"Arsenic is another theoretical possibility, and evidence for that was found in 2008. Visscher says the link with arsenic was strengthened in 2014 when he and colleagues found evidence of arsenic-based photosynthesis in deep time. To further support their theory, the researchers needed to find a modern analog to study the biogeochemistry and element cycling.

***

"However, a breakthrough happened when the team discovered an active microbial mat, currently existing in the harsh conditions in Laguna La Brava in the Atacama Desert in Chile.

"The mats have not been studied previously but present an otherworldly set of conditions, like those of early Earth. The mats are in a unique environment which leaves them in a permanent oxygen-free state at high altitude where they are exposed to wild, daily temperature swings, and high UV conditions. The mats serve as powerful and informative tools for truly understanding life in the conditions of early Earth.

"Visscher explains, "We started working in Chile, where I found a blood red river. The red sediments are made up by anoxogenic photosynthetic bacteria. The water is very high in arsenic as well. The water that flows over the mats contains hydrogen sulfide that is volcanic in origin and it flows very rapidly over these mats. There is absolutely no oxygen."

"The team also showed that the mats were making carbonate deposits and creating a new generation of stromatolites. The carbonate materials also showed evidence for arsenic cycling -- that arsenic is serving as a vehicle for electrons -- proving that the microbes are actively metabolizing arsenic much like oxygen in modern systems. Visscher says that these findings, along with the fossil evidence gives a strong indication of what was seen on early earth.

"'Arsenic-based life has been a question in terms of does it have biological role or is it just a toxic compound?" says Visscher. That question appears to be answered, "I have been working with microbial mats for about 35 years or so. This is the only system on Earth where I could find a microbial mat that worked absolutely in the absence of oxygen.'"

Since life dates back to 3.8 bya, it had to exist somehow. This appears to be the how. What is of great interest is that life depends on arsenic, a poison, or oxygen, a dangerous element because it causes unwanted oxidation so easily, i.e., forest fires. So we have to ask, why God would choose this approach? Answer, it must be the best one.

Theoretical origin of life; hostile hot springs

by David Turell @, Thursday, September 24, 2020, 20:02 (1300 days ago) @ David Turell

Another review:

https://www.sciencenews.org/article/life-earth-origins-hostile-hot-springs-microbes

"Microorganisms at hot springs can form communities called microbial mats. Made up of layers of microbes, mats have been found in geothermal areas all over the world, including in Yellowstone National Park, the Garga hot spring in southern Russia and Lassen — home to Bumpass Hell.

"Over time, microbial mats can form into stromatolites, structures of microbes and minerals that have accumulated on top of one another; the layered appearance of a stromatolite reflects the passage of time, like a tree’s growth rings. Researchers found evidence of stromatolites in the Dresser Formation, a 3.5-billion–year-old rock feature in the Western Australia outback, along with evidence of hot spring mineral deposits, describing the findings in 2017

***

"These results, reported in December 2019 in Astrobiology, indicate that complex molecules can form at hot springs, supporting the hypothesis that life on Earth may have developed in such an environment.

***

"In 2017, researchers found fossils in 3.77-billion-year-old rocks from Quebec that originated from the ancient ocean floor and had signs of hydrothermal activity (SN: 4/1/17, p. 6). The researchers claim that the distinct structures resemble those of microbes, suggesting that deep-sea environments may have supported some of the earliest life on Earth.

***

"To Deamer, there are big barriers to putting life’s pieces together near underwater vents: The vastness of the ocean would dilute molecules so they wouldn’t be concentrated enough to drive chemical reactions. Also, there are “no wet-dry cycles underwater.” In his view, repeated evaporation is needed to pull together enough molecules to bump into each other and react to form longer chains. Plus, unlike a hot spring’s freshwater, salty ocean water inhibits the formation of membranes and reactions that link together molecules, he says.

"However, Deamer’s hot springs theory has its critics as well. DNA and RNA strands are composed of alternating phosphate and sugar molecules, but sugars “are profoundly unstable in hot spring environments,” says David Des Marais, an astrobiologist at NASA’s Ames Research Center.

"And it may be too soon to rule out wet-dry cycles underwater. “You can have a little bit of water get stuck in a pore,” says Bill Brazelton, a marine microbiologist at the University of Utah in Salt Lake City. And then, because the serpentinization reaction at a vent uses up water in making other molecules, “you can have these cycles of dehydration inside a rock underneath the ocean.'”

Comment: Still no clear cut theory. Hot springs or hot vents make an interesting proposal. Certainly not anything like lightning in a bottle, which started all of this.

Theoretical origin of life: computer wishful thinking

by David Turell @, Thursday, October 01, 2020, 18:58 (1293 days ago) @ David Turell

Using computer algorithms to find possible roads to life ,but the road from likely organic vital molecules is long and winding:

https://www.chemistryworld.com/news/algorithm-discovers-how-six-simple-molecules-could-...

"An organic synthesis algorithm has mapped out the thousands of reactions that might have converted abiotic compounds into the building blocks of life more than 3.5 billion years ago. Starting off with six simple precursors, the program discovered many known as well as 24 entirely new pathways to prebiotic molecules, and showed how catalytic and self-replicating systems might emerge.

***

"Now, researchers have done just that. A team led by Bartosz Grzybowski and Sara Szymkuć from the Polish Academy of Sciences encoded all 500 known prebiotic reactions and a feedstock of six precursors – water, hydrogen cyanide, ammonia, hydrogen sulphide, nitrogen and methane – into open-use platform Allchemy. The algorithm then used encoded mechanistic chemistry rules to produce a map of their combinations.

***

"Running the program for seven generations, each time combining the generated molecules with what came before, the researchers ended up with almost 35,000 compounds including 50 biotic ones. The program was able to find many prebiotic syntheses previously described in the literature, for example 10 pathways leading to the DNA component adenine. But it also discovered 24 entirely new pathways to biotic compounds – more than 20 of which the team experimentally validated.

***

"One of the reasons computer programs are better at finding these pathways than humans, explains Szymkuć, is that ‘people aren’t accustomed, when designing something, to incorporate a step, which degrades a molecule, and that’s necessary for the cycle.’

"But the vast majority of reaction combinations led to abiotic compounds – molecules that were never incorporated into living systems. Analysis showed that the molecules that became the building blocks of life were more soluble in water and more thermodynamically stable. ‘The chosen ones had a balanced number of hydrogen bond donors and acceptors,’ Grzybowski adds. ‘When you think about it, this makes perfect sense – think about DNA. Nature chose molecules that are more likely to be fitting into a larger architecture, to build these kinds of supramolecular assemblies.’"

Comment: More intelligent design in the lab. What must happen naturally is much more complex.

Theoretical origin of life: possible early beginning

by David Turell @, Monday, October 12, 2020, 19:28 (1282 days ago) @ David Turell

Using two common amino acids and a little heat and early parts of the Krebs (TCA) molecular energy supplying cycle can form naturally:

https://www.quantamagazine.org/new-clues-to-chemical-origins-of-metabolism-at-dawn-of-l...

"A central pillar of all cellular metabolism — and the bane of generations of high school biology students who had to memorize it — is a complex 10-step chemical process variously known as the tricarboxylic acid (TCA) cycle, the citric acid cycle or the Krebs cycle. “The TCA cycle is at the heart of much of modern biology, where it is used both to break down food into energy and to synthesize vital building blocks of proteins,” said Greg Springsteen,

***

"Because the TCA cycle feeds into so many vital processes in even the simplest cells, scientists suspect it was one of the early reactions to establish itself in the prebiotic soup.

***

"They started with just two compounds — glyoxylate and pyruvate, the two smallest alpha-ketoacids, containing only two and three carbon atoms respectively. Alpha-ketoacids drew their attention because of “their stability in water and their propensity to form carbon-carbon bonds, the skeleton of biology,” Springsteen said.

"Astonishingly, they found that the glyoxylate and pyruvate reacted to make a range of compounds that included chemical analogues to all the intermediary products in the TCA cycle except for citric acid. Moreover, these products all formed in water within a single reaction vessel, at temperatures and pH conditions mild enough to be compatible with conditions on Earth.

***

"Krishnamurthy and Springsteen both emphasize that their experiments do not prove that the ancestor of the TCA cycle emerged this way: There are similarities between the reactions and intermediary molecules they created and those in the TCA cycle, but without further evidence, it is more prudent to refer to them as analogs of TCA cycle intermediaries. They did not create a cycle of any kind, just a mixture of molecules that could in principle be organized to act as one.

***

"But if the precursors of cells had those molecules at their disposal, then they might have performed some of the synthetic chemistry useful to life. That first draft of metabolism would almost certainly have been crude and poorly controlled, and it might not have even been organized into a complete cycle. But over time, as proteins also became part of the mix, enzymes could have taken control over some of the reactions, and the real TCA cycle might have started to take shape. " (my bold)

Comment: The bold above shows all the caveats, while pursuing wishful thinking. Where do the required giant enzymes come from? Where the original molecules used in this study present on
Earth at that time? But a good try.

Theoretical origin of life: between mica sheets

by David Turell @, Wednesday, November 04, 2020, 23:23 (1259 days ago) @ David Turell

A strange new but unlikely successful theory:

https://evolutionnews.org/2020/11/barriers-to-an-unguided-origin-of-life-biophysicist-h...

"I previously interacted with physicist Jeremy England in the journal Inference on the thermodynamics of the origin of life (here, here, here). I argued that life’s genesis required the sudden appearance of a fully functional cell with highly efficient molecular engines that generated chemical energy to power cellular processes. In addition, the cell required a significant quantity of information instantiated in such structures as proteins and DNA.

"I then described how researchers have attempted to identify “natural engines” on the early earth that could have provided the required energy. The most plausible scenario is hydrothermal vents converting the energy from proton gradients into chemical energy. Yet, this scenario is crippled by two fatal flaws. First, the amount of power generated could not drive even the earliest stages of any origin-of-life scenario. And, information is still required to direct the energy and matter toward constructing specific molecular structures and driving specific reactions. Without such preexistent information, no amount of supplied chemical energy could enable any but the simplest of biologically relevant processes.

***

"Professor Hansma pioneered the origins model postulating that the motion of mica sheets along the ocean floor could have driven chemical reactions energetically uphill, resulting in higher-energy molecules. In her letter, she challenges my evaluation of the power limitations on “natural engines” by asserting that the mechanical energy of the mica sheets could have provided sufficient energy to sustain some pathway to the first cell. In my response, I demonstrate that mica sheets, like all other proposals, could never provide even the tiniest fraction of the energy that would have been required.

"Hansma also maintains that sets of integrated reactions could have been directed by natural selection to gradually evolve into an autonomous cell. The problem is that nearly all chemical reactions in cells are either energetically unfavorable (i.e., they move in the wrong direction), or they are too slow, without assistance, to ever compete with the countless other reactions that could have occurred. Moreover, before high-accuracy self-replication emerged, all natural processes would have driven a mixture of chemicals toward lower free energy. Consequently, they would have always moved away from life, never toward it.

"In the same vein, Hansma appeals to self-replicating sets of RNAs evolving into forms that could have supported life-relevant chemical reactions. The challenge is that the likelihood of even a single RNA of substantial length ever forming is beyond remote. Even if some local environment hosted an evolving assembly of RNAs, evolution would have favored those chains that specialized in efficient self-replication and thus performed no other life-relevant function. The thermodynamic and information barriers place the belief that solely natural processes could explain the origin of the first cell very nearly into the same category as belief in alchemy or the possibility of a perpetual motion machine."

Comment: Again another wishful theory that strains credulity.

Theoretical origin of life: from early polypeptides

by David Turell @, Thursday, November 12, 2020, 23:13 (1251 days ago) @ David Turell

Another hopeful approach:

https://science.sciencemag.org/content/370/6518/767

"It is unsurprising, however, that nature provides a guide to its own beginnings. In biochemistry, most amino acid polymerization occurs by translation, which requires ribosomes—a massive assembly of proteins and RNA. Building a primordial ribosome under the conditions of a lifeless planet is a hefty and, as of now, unmet challenge. However, microorganisms use biological nonribosomal peptide synthesis for the production of peptide-based natural products. The nonribosomal peptide synthetases that perform this reaction are chemically much simpler than ribosomes.

***

"...most scientists do not believe that cysteine commonly participated in prebiotic chemistry at its earliest stages. Cysteine is often regarded as a late evolutionary addition to the proteinogenic amino acid pool

***

"Devising a plausible prebiotic route to cysteine has proven to be challenging. In biology, cysteine synthesis starts from serine and proceeds through a pyridoxal phosphate cofactor-bound dehydroalanine, an intermediate that has a markedly short lifetime in the absence of the cofactor. Foden et al. proposed how this inherent instability might be overcome by beginning the prebiotic synthesis of cysteine from a nonbiological nitrile analog of the amino acid serine.

***

"The process began with amino nitriles, but under conditions of alternating reducing and oxidizing environments and excess quantities of sulfide. Such step-changes in reaction conditions pose a problem for a realistic early Earth scenario. However, by exploiting the fact that thiols reversibly add to α-amidonitriles, Foden et al. proposed a strategy for catalytic and redox-neutral oligopeptide synthesis proceeding via a thioimidate intermediate in neutral water. The authors subjected acetylated glycinyl nitrile and free glycine to acetylated cysteine (a hypothetical phosphopantetheine precursor) at 60°C in neutral water. Within 24 hours, an acetylated Gly-Gly peptidyl amidine had formed, at a 60% yield, without the need for synthetic activating agents. This reactivity occurred with a variety of thiols and amino acids. Only amino-terminal serine, threonine, and cysteine could be coupled to α-amidonitriles stereoselectively, which might have implications for the origins of biological homochirality. (my bolds)

"Foden et al. highlight the potential of small-molecule organocatalysis and the pivotal role that thiols might have played in the emergence of biochemistry. Could nature have made peptides this way before the advent of enzymes or the ribosome? This exciting question reveals how much we do not know about the rationale behind the shaping of life's biochemical pathways and the chemical structures used as cofactors and metabolites. If life did once use nitrile-based chemistry, it is unclear why it would have shifted to a biochemistry where nitriles are rare. Also, why does life—seemingly so wastefully—use the phosphopantetheine moiety in nonribosomal peptide synthesis, when it might have used a much simpler thiol, such as cysteine? Experimental insights into these questions will illuminate the currently opaque middle ground between reactions that attempt to recreate life's earliest chemistry and the biochemistry we study today." (my bolds)

Comment: The usual wishful thinking as humans try to design a reasonable natural path to origin of life. The first bold in the second paragraph above points out the guesswork about early Earth and what was available to do the job. The second bold reminds us about all amino acids being left-handed and we do not know why, since it should not naturally happen that way. In the final paragraph the first bold how big the problem is and the second bold questions the chemical design of life as being too complex. I would remind everyone the stupid decisions by so-called thinking humans that our appendix is not necessary and our backwards retina is wrong, have all been disproven.

Theoretical origin of life;stromatolite fossil due to virus

by David Turell @, Sunday, February 21, 2021, 22:28 (1150 days ago) @ David Turell

An unproven theory:

https://phys.org/news/2021-02-stromatolitesfossils-earliest-life-earthmay-viruses.html

"'Stromatolites are pervasive in the fossil record and are some of our earliest examples of life on Earth," he says.

"'The microbial mats that created them were predominantly made up of cyanobacteria, which used photosynthesis—like plants do—to turn sunlight into energy, while producing so much oxygen over time they changed the early Earth's atmosphere to make it habitable for complex life.

"'You could say we owe our very existence to these living rocks."

***

"In the paper, the authors postulate that microbial mat transition from soft cells to rock is enhanced by interactions with viruses.

"'We propose viruses may have a direct or indirect impact on microbial metabolisms that govern the transition from microbial mat to stromatolite," he says.

"In the direct impact scenario, viruses infiltrate the nucleus of the cyanobacteria and influence the host metabolism, inserting and removing genes that increase the fitness of the virus and the host at the same time.

"'This, in turn, increases survival of the microbial mat and selects for genes that potentially influence carbonate precipitation—basically the process of microbes pouring the concrete to make their stromatolite apartment blocks," A/Prof. Burns says.

"In the indirect scenario, the scientists talk about a process known as viral lysis, where viruses invade living cells and trigger the disintegration of their membranes and release of contents—effectively bringing about cell death.

"'We think viral lysis may release material that promotes metabolism of organisms which results in mineral precipitation and eventual stromatolite formation."

"Whether viruses cause the microbial mats to harden into stromatolites directly or indirectly, or a combination of both, A/Prof. Burns says more research is needed."

Comment: All theory, no proof, but somehow the giant clumps of cyanobacteria fossilized to allow us to see very early life on Earth.

Theoretical origin of life;more attempts with lab alteration

by David Turell @, Tuesday, March 02, 2021, 19:52 (1141 days ago) @ David Turell

Another foolish attempt using existing tRNA:

https://www.sciencedaily.com/releases/2021/03/210302094102.htm

"A Ludwig-Maximilians-Universitaet (LMU) in Munich team has shown that slight alterations in transfer-RNA molecules (tRNAs) allow them to self-assemble into a functional unit that can replicate information exponentially. tRNAs are key elements in the evolution of early life-forms.

***

"Transfer RNAs act as intermediaries between mRNAs and proteins: they ensure that the amino-acid subunits of which each particular protein consists are put together in the sequence specified by the corresponding mRNA.

"How could such a complex interplay between DNA replication and the translation of mRNAs into proteins have arisen when living systems first evolved on the early Earth? We have here a classical example of the chicken-and-the-egg problem: Proteins are required for transcription of the genetic information, but their synthesis itself depends on transcription.

***

"In their experiments, Braun and his colleagues used a set of reciprocally complementary DNA strands modeled on the characteristic form of modern tRNAs. Each was made up of two 'hairpins' (so called because each strand could partially pair with itself and form an elongated loop structure), separated by an informational sequence in the middle. Eight such strands can interact via complementary base-pairing to form a complex. Depending on the pairing patterns dictated by the central informational regions, this complex was able to encode a 4-digit binary code.

***

"The team was able to show that the system is capable of exponential replication. This is an important finding, as it shows that the replication mechanism is particularly resistant to collapse owing to the accumulation of errors. The fact that the structure of the replicator complex itself resembles that of modern tRNAs suggests that early forms of tRNA could have participated in molecular replication processes, before tRNA molecules assumed their modern role in the translation of messenger RNA sequences into proteins. "This link between replication and translation in an early evolutionary scenario could provide a solution to the chicken-and-the-egg problem," says Alexandra Kühnlein. It could also account for the characteristic form of proto-tRNAs, and elucidate the role of tRNAs before they were co-opted for use in translation."

Comment: Insane research. The group starts with complex DNA molecules and tells us that steps to life could happen this way. Fine, but this is a giant step from no molecules at all to this complex point. A waste of research grant money. After almost 70 years of research no one is any closer to figuring out the first steps, and my sneaking suspicion is we will never know.

Theoretical origin of life; lightning did it

by David Turell @, Tuesday, March 16, 2021, 22:47 (1127 days ago) @ David Turell

New theory reverts to Urey-Miller lightning in a bottle from the 1950's. Old ideas are resurrected:

https://cosmosmagazine.com/earth/earth-sciences/did-lightning-spark-life-on-earth/?utm_...

"The earliest undisputed signs of life show up around 3.5 billion years ago, although researchers have good reason to suspect that the whole affair of living could have got going much earlier. But there’s a small problem: life didn’t have the right ingredients yet.

"The organic molecules that make up the building blocks of life – including sugars, enzymes, protein and DNA – didn’t exist naturally on the very early Earth, and the elements needed to make them (like carbon, nitrogen, hydrogen and oxygen) were bound up in the rocks, atmosphere and early oceans.

"Now, a new study published in Nature Communications suggests that lightning could have “freed” one such element: phosphorous.

“'We propose that under the conditions on early Earth, phosphorus reduction via lightning strikes is a more significant process than previously appreciated,” the authors write in their paper.

"Phosphorous has long been known to be fundamental to all living things, essential to the formation of DNA, cell membranes and more. Today, it enters the planet’s systems through the weathering of rocks over time, but the phosphorous on early Earth was locked up in insoluble minerals.

***

"The team, led by Benjamin Hess from Yale, used computer modelling to estimate that the ancient Earth experienced far more lightning than we do now.

"The Earth today sees about 560 million flashes of lightning per year, while the early Earth saw 1–5 billion flashes, with between 100 million and 1 billion of these striking the ground.

"Over a billion years, those kinds of numbers add up: potentially, a quintillion (a billion billion) strikes could have struck the ground and helped release usable phosphorous.

***

"Their models also suggest that lightning would have been more prevalent on land masses in tropical regions, potentially creating areas of concentrated phosphorous.

“'This work helps us understand how life may have formed on Earth and how it could still be forming on other, Earth-like planets,” says Hess. “It makes lightning strikes a significant pathway toward the origin of life.'”

Comment: The usual pie-in-the-sky hopefulness. Phosphorus is only one tiny part of the complex mass of items/processes required to start life. Ten days ago I entered an article that between 3-4 million years ago the Earth was covered totally by water. ( Wednesday, March 10, 2021, 14:25) So, what did the lightning strike? Not land. All these OOL researchers need to read all the papers produced to get their acts together.

Theoretical origin of life; new earliest?

by David Turell @, Thursday, April 14, 2022, 19:33 (733 days ago) @ David Turell

Current thought based on latest discoveries:

https://www.sciencealert.com/complex-life-may-have-started-on-earth-much-earlier-than-w...

All life on Earth likely emerged from one spark in Earth's early history. Some time later, it diversified, branching off into lineages that helped it survive.

Exactly when these moments occurred has been a point of contention in the scientific community, but new research suggests both steps may have taken place earlier than we previously thought.

The study, led by University College London researchers builds on evidence of diverse microbial life inside a fist-sized piece of rock from Quebec in Canada, dated to around 3.75 billion to 4.28 billion years.

In 2017, the researchers who discovered it speculated that structures in the rock – tiny filaments, knobs, and tubes – had been left by ancient bacteria.

But not everyone was convinced that these structures – which would push the date for the first signs of life on Earth back by at least 300 million years – were biological in origin.

However, after further extensive analysis of the rock, the team discovered an even larger and more complex structure than those which were previously identified. Within the rock was a stem-like structure with parallel branches on one side that are nearly a centimeter long, as well as hundreds of distorted spheres, or ellipsoids, alongside the tubes and filaments.

"This means life could have begun as little as 300 million years after Earth formed. In geological terms, this is quick – about one spin of the Sun around the galaxy," says lead author of the study, geochemist Dominic Papineau from UCL.

***

According to the paper, some of the smaller structures could have conceivably been the product of abiotic reactions, however, the newly identified 'tree-like' stem is most likely biological in origin, as no structure like it, created through chemical reactions alone, has been found before.

In addition to the structures, researchers identified mineralized chemicals in the rock that could have been byproducts of different types of metabolic processes.

The chemicals are consistent with energy-extraction processes in the bacteria that would have involved iron and sulfur; depending on the interpretation of chemical signatures, there could even be hints of a version of photosynthesis.

This finding points to the possibility that the early Earth – only 300 million years after its formation – was inhabited by an array of microbial life.

***

Prior to this discovery, the earliest fossil evidence of life was found in Western Australia, which dates back 3.46 billion years. However, similar contention exists around whether these fossils were biological in origin.

Comment: same old problem, identifying organic molecules that could have come only from life. The structure found is intriguing, but a 'look alike' is not proof. If it is life, happening so early after Earth formed in an horrendous hot situation, only God's actions could have done it.

Theoretical origin of life; Chirality needed by nature

by David Turell @, Saturday, May 23, 2020, 16:00 (1424 days ago) @ David Turell

Chiral molecules guide electrons' spin and transfer under tight control. These quantum effects are required for efficiency. The latest studies show why left and right handed molecules are needed and used exclusively by living organisms:

http://inference-review.com/article/spin-in-quantum-biology#footnote-6


"Chirality is the name for the particular kind of symmetry that arises when one object is the mirror image of the other. An example is the human hand. Mirror images require no internal symmetries. Our two hands are called enantiomers of one another. Chiral molecules are referred to as being a right-handed enantiomer or a left-handed enantiomer.

David: Comment: These new finding explain why chirality is necessary. It is to control electron transfer in life's processes. As James Tour expresses in previous entries about synthesizing handedness in the laboratory, maintaining pure handedness of one type is very difficult. Nature does it very easily. Not by chance.

David: A new discussion about origin of life whether we can discover the natural process that produced initial chirality of amino acids so life could start:

https://uncommondescent.com/intelligent-design/stanford-cosmic-rays-helped-create-chira...

"In their paper, published on May 20 in Astrophysical Journal Letters, the researchers detail their argument in favor of cosmic rays as the origin of homochirality. They also discuss potential experiments to test their hypothesis.

"Rob Sheldon responds:

***

"the chiral interaction between radiation and molecules is at a maximum when they are in resonance–the wavelength of the radiation and the “wavelength” of the helical twist are the same. DNA has a helical twist some 3.5 nm long. This corresponds to a 350 eV photon or soft X-ray energy. Photons of this energy are likely to destroy everything, regardless of resonance. But the muon has a much shorter wavelength, closer to 0.0001 of this length. It can’t be made resonant with chiral molecules no matter how hard you tried.

"Roger, as a typical astrophysicist, leaves everything as a formula and never actually calculates any numbers. Mind you, if the numbers had been favorable, he would have included them in his paper. But when the calculation looked improbable, he didn’t want to waste his effort so he published it as a formula with a plea to experimentalists to search for some effect.

***

"Sabine Hossenfelder has said that particle physicists are “lost in math,” > trained to play with “beautiful” equations rather than actual physics. Here we have a similar example in astrophysics. Roger makes one unsupported assumption after another, leading to an effect so small as to “need amplification.”

"But the field is enamored of the math, not the physics, and that is what Roger delivers in spades.... The Origin-of-Chirality subproblem of Origin-of-Life looks to be as hard a problem as Origin-of-Consciousness, or Origin-of-Language. 150 years after Darwin’s Origin, and we have only multiplied all the origin problems." (my bold)

Comment: Lots of smoke but no fire. Chirality is a major problem in the origin of life research. All the lab studies assume the presence of left-handed amino acids. Why only left-handed molecules is never solved. To solve the problem we must solve all of it. We see nothing in nature. Only design can account for it.

Theoretical origin of life; amino acids from meteorites

by David Turell @, Monday, June 08, 2020, 19:36 (1408 days ago) @ David Turell

Possibly due to crashing into oceans and forming:

https://phys.org/news/2020-06-ancient-asteroid-impacts-ingredients-life.html

"A new study published in Scientific Reports reveals that asteroid impact sites in the ocean may possess a crucial link in explaining the formation of the essential molecules for life. The researchers discovered the emergence of amino acids that serve as the building blocks for proteins—demonstrating the role of meteorites in bringing life's molecules to Earth, and potentially Mars.

"There are two explanations for the origins of life's building molecules: extraterrestrial delivery, such as via meteorites, and endogenous formation. The presence of amino acids and other biomolecules in meteorites points to the former.

"Researchers from Tohoku University,... simulated the reactions involved when a meteorite crashes into the ocean. To do this, they investigated the reactions between carbon dioxide, nitrogen, water, and iron in a laboratory impact facility using a single stage propellant gun. Their simulation revealed the formation of amino acids such as glycine and alanine. These amino acids are direct constituents of proteins, which catalyze many biological reactions.

"The team used carbon dioxide and nitrogen as the carbon and nitrogen sources because these gasses are regarded as the two major components in the atmosphere on the Hadean Earth, which existed more than 4 billion years ago.

"Corresponding author from Tohoku University, Yoshihiro Furukawa, explains, "Making organic molecules form reduced compounds like methane and ammonia are not difficult, but they are regarded as minor components in the atmosphere at that time. The finding of amino acid formation from carbon dioxide and molecular nitrogen demonstrates the importance in making life's building blocks from these ubiquitous compounds."

"The hypothesis that an ocean once existed on Mars also raises interesting avenues for exploration. Carbon dioxide and nitrogen are likely to have been the major constituent gasses of the Martian atmosphere when the ocean existed. Therefore, impact-induced amino acid formation also provides a possible source of life's ingredients on ancient Mars."

Comment: Of course with 70% of our surface as water, this obviously happened. But, as usual the problems are ignored in the hype. So some amino acids were here four million years ago. By itself that does not cause life to appear. And the authors don't mention the problem of life using only left-handed molecules, as they ignored telling us about the chirality produced, which assuredly is both right and left.

Theoretical origin of life; importance of chirality

by David Turell @, Monday, June 08, 2020, 19:50 (1408 days ago) @ David Turell

Comments on the problem from a study on it:

https://www.sciencedaily.com/releases/2020/06/200608104733.htm

"Chirality is found in almost all molecules occurring in nature. "Molecules are spatial arrangements of interconnected atoms. Many molecules, however, have not only one form, but at least two," explains Professor Carsten Tschierske, a chemist at MLU. When these forms are mirror images of each other it is called chirality.

"Both mirror-image forms are produced in equal numbers during normal chemical reactions in the laboratory. "However, things occur differently in nature: carbohydrates, amino acids and nucleic acids only have one dominant form," explains Tschierske. And with good reason: for example, nucleic acids carry information about our DNA. Even the slightest changes to our genetic material can lead to serious diseases. "If each nucleic acid had two forms, the structure of our DNA would be chaotic because there would be too many possible variations. Life as we know it would be impossible," states Tschierske. (my bold)

Comment: The bold indicates the probable reason why life's biology has strict chirality, and had to be designed that way.

Theoretical origin of life; importance of chirality

by David Turell @, Monday, June 29, 2020, 19:33 (1387 days ago) @ David Turell

Chirality is a knife in the heart of theoretical natural chance origin of life theories. This is an attempt to explain it:

https://www.quantamagazine.org/cosmic-rays-may-explain-lifes-bias-for-right-handed-dna-...

"Cosmic Rays May Explain Life’s Bias for Right-Handed DNA

***

"The theory, which appeared in May in The Astrophysical Journal Letters, doesn’t explain every step of how life acquired its current handedness, but it does assert that the shape of terrestrial DNA and RNA is no accident. Our spirals might all trace back to an unexpected influence from cosmic rays.

***

"Physical events typically break right as often as they break left, but cosmic ray particles called pions tap into one of nature’s rare exceptions. When pions decay, the process is governed by the weak force — the only fundamental force with a known mirror asymmetry. Pions slamming into the atmosphere produce showers of particles including electrons and their heavier siblings, muons, all of which are equipped by the weak force with the same chiral magnetic orientation relative to their path. The particles bounce around as they streak through the atmosphere, Globus said, but overall they tend to keep their preferred chirality when they slam into the ground.

***

"With a series of toy models, the researchers calculated that the biased cosmic ray particles were ever-so-slightly more likely to knock an electron loose from a “live” helix than from an “evil” one, an event that theoretically causes mutations.

"The effect would be tiny: Millions if not billions of cosmic ray strikes could be required to yield one additional free electron in a “live” strand, depending on the event’s energy. But if those electrons changed letters in the organisms’ genetic codes, those tweaks may have added up. Over perhaps a million years, Globus suggests, cosmic rays might have accelerated the evolution of our earliest ancestors, letting them out-compete their “evil” rivals. “If you don’t have mutations, you don’t evolve,” she said.

***

"Proof that the handedness of particles really can mutate microbes would strengthen their case that cosmic rays shoved our ancestors off the evolutionary starting block, but it still wouldn’t fully explain the uniform chirality of life on Earth. The theory doesn’t address, for example, how “live” organisms and “evil” organisms managed to materialize from a primordial smoothie containing both right- and left-handed building blocks.

***

"...another unknown process seems to handicap “evil” life. The simple amino acid molecules that form proteins also exist in “live” configurations favored by life and “evil” configurations that are not (although the preferred chirality for “live” amino acids is almost exclusively left-handed). Careful analysis of meteorites by Dworkin and others has found that certain “live” amino acids outnumber “evil” ones by 20% or more, a surplus they may have passed on to Earth. The excess molecules could be the lucky survivors of billions of years of exposure to circularly polarized light, a collection of beams all spiraling in the same direction that, experiments have shown, can destroy one type of amino acid slightly more thoroughly than the other.

"But, like the cosmic rays, the beams of light have a marginal effect. Countless interactions would be needed to leave behind a noticeable imbalance, so some other force may be at work as well. Light would have to pulverize untenably huge quantities of molecules to explain the excesses on its own, Dworkin says.

"Sasselov has encouraged Globus and Blandford to consider whether cosmic rays might join forces with polarized light to shape the amino acids on asteroids. On Earth, the doses of cosmic rays — which he likens to supersonic bullets — that would be needed to make a noticeable chiral difference might prove too lethal, he speculated. “You’re destroying so much of everything,” he said. “You may be left with the [correct] handedness, but essentially you’re shooting yourself in the foot.” (m y bold)

***

“'There is something special about planets like the Earth that protect this kind of chemistry,” Sasselov said." (my bold)

Comment: It all appears to be against the odds. I like it. Each desperate experiment helps prove the need for a designer. The Earth is very special.

Theoretical origin of life; glycine in comets

by David Turell @, Monday, November 16, 2020, 19:47 (1247 days ago) @ David Turell

One of the important amino acids made in space:

https://phys.org/news/2020-11-blocks-life-stars.html

"Comets are the most pristine material in our Solar System and reflect the molecular composition present at the time our Sun and planets were just about to form. The detection of glycine in the coma of comet 67P/Churyumov-Gerasimenko and in samples returned to Earth from the Stardust mission suggests that amino acids, such as glycine, form long before stars. However until recently, it was thought that glycine formation required energy, setting clear constraints to the environment in which it can be formed.

***

"'Dark chemistry refers to chemistry without the need of energetic radiation. In the laboratory we were able to simulate the conditions in dark interstellar clouds where cold dust particles are covered by thin layers of ice and subsequently processed by impacting atoms causing precursor species to fragment and reactive intermediates to recombine."

"The scientists first showed methylamine, the precursor species of glycine that was detected in the coma of the comet 67P, could form. Then, using a unique ultra-high vacuum setup, equipped with a series of atomic beam lines and accurate diagnostic tools, they were able to confirm glycine could also be formed, and that the presence of water ice was essential in this process.

"Further investigation using astrochemical models confirmed the experimental results and allowed the researchers to extrapolate data obtained on a typical laboratory timescale of just one day to interstellar conditions, bridging millions of years. "From this we find that low but substantial amounts of glycine can be formed in space with time," said Professor Herma Cuppen from Radboud University, Nijmegen, who was responsible for some of the modelling studies within the paper.

"'The important conclusion from this work is that molecules that are considered building blocks of life already form at a stage that is well before the start of star and planet formation," said Harold Linnartz, Director of the Laboratory for Astrophysics at Leiden Observatory. "Such an early formation of glycine in the evolution of star-forming regions implies that this amino acid can be formed more ubiquitously in space and is preserved in the bulk of ice before inclusion in comets and planetesimals that make up the material from which ultimately planets are made.'"

Comment: Great news but too optimistic. The comets have to deliver 20 essential amino acids here and they all have to be left-handed to make life as we know it. As usual the authors don't mention the problems, which are major.

Theoretical origin of life: the latest review

by David Turell @, Thursday, December 10, 2020, 20:38 (1223 days ago) @ David Turell

There are lots of worries about water, which can break up polypeptides and DNA:

https://www.nature.com/articles/d41586-020-03461-4?WT.ec_id=NATURE-20201210&utm_sou...


"Although many scientists have long speculated that those pioneering cells arose in the ocean, recent research suggests that the key molecules of life, and its core processes, can form only in places such as Jezero — a relatively shallow body of water fed by streams.

"That’s because several studies suggest that the basic chemicals of life require ultraviolet radiation from sunlight to form, and that the watery environment had to become highly concentrated or even dry out completely at times. In laboratory experiments, Sutherland and other scientists have produced DNA, proteins and other core components of cells by gently heating simple carbon-based chemicals, subjecting them to UV radiation and intermittently drying them out. Chemists have not yet been able to synthesize such a wide range of biological molecules in conditions that mimic seawater.

"The emerging evidence has caused many researchers to abandon the idea that life emerged in the oceans and instead focus on land environments, in places that were alternately wet and dry. The shift is hardly unanimous, but scientists who support the idea of a terrestrial beginning say it offers a solution to a long-recognized paradox: that although water is essential for life, it is also destructive to life’s core components.

"Surface lakes and puddles are highly promising, says David Catling, a planetary scientist at the University of Washington in Seattle. “There’s a lot of work that’s been done in the last 15 years which would support that direction.”

***

"...life’s cornerstone molecules break down in water. This is because proteins, and nucleic acids such as DNA and RNA, are vulnerable at their joints. Proteins are made of chains of amino acids, and nucleic acids are chains of nucleotides. If the chains are placed in water, it attacks the links and eventually breaks them. In carbon chemistry, “water is an enemy to be excluded as rigorously as possible”, wrote the late biochemist Robert Shapiro in his totemic 1986 book Origins, which critiqued the primordial ocean hypothesis.

"This is the water paradox. Today, cells solve it by limiting the free movement of water in their interiors, says synthetic biologist Kate Adamala at the University of Minnesota in Minneapolis. For this reason, popular images of the cytoplasm — the substance inside the cell — are often wrong. “We are taught that cytoplasm is just a bag that holds everything, and everything is swimming around,” she adds. “That’s not true, everything is incredibly scaffolded in cells, and it’s scaffolded in a gel, not a water bag.” (my bold)

***

"...studies have given momentum to the idea that life began on a well-lit surface with a limited amount of water. However, there is still debate over how much water was involved, and what part it played in starting life.

Like Deamer, Frenkel-Pinter argues that wet–dry cycles were crucial. Dry conditions, she says, provided an opportunity for chain molecules such as proteins and RNA to form.

"But simply making RNA and other molecules is not life. A self-sustaining, dynamic system has to form. Frenkel-Pinter suggests that water’s destructiveness could have helped to drive that. Just as prey animals evolved to run faster or secrete toxins to survive predators, the first biological molecules might have evolved to cope with water’s chemical attacks — and even to harness its reactivity for good.

***

"...modern organisms use completely different chemical processes to make substances such as RNA. He argues that these processes must have arisen first, not the substances themselves. “Life, it picks very particular molecules. But you can’t pick them from the bench. You’ve got to make them from scratch and that’s what life does.'”

Comment: The Shapiro who is my hero is Robert. See my bold. His book, Origins is from 1986 and he could easily see the problems in trying to understand the origin of life, about which we are obviously no closer to a reasonable theory. His book is one of the first I read to divorce myself from Darwin. I've not presented the lengthy descriptions of all the current attempts to make an advance, just the obvious frustrations of the reviewing author. This problem is why I think it is a major proof of the need for a designer God.

Theoretical origin of life: RNA world can't work

by David Turell @, Saturday, January 02, 2021, 15:44 (1200 days ago) @ David Turell

Where are the necessary enzymes?:

https://www.popularmechanics.com/science/a35084871/rna-world-hypothesis-origins-of-life...

"Here’s the problem with the RNA-only model (also known as the "RNA world hypothesis"), stated at its most succinct: RNA is too “sticky.”

"That means that, like hydrogen for example, RNA bonds and will not detach from other molecules. In evolutionarily modern times, we know RNA is split from its fresh copies by enzymes, but enzymes arose after RNA. How did the first RNA strands come unstuck without help?

"For primordial molecular strands of DNA and RNA, chimerism takes the form of single strands with evidence of both kinds of genetic information. That means reducing the “stickiness” of RNA alone and creating a path that explains original RNA replication without enzymes. It’s like those popsicles with two sticks: holding the sticks gives you leverage to snap apart the double popsicle.

***

"if RNA managed to unstick itself without enzyme help, that could have implications for the same mRNA that’s in the news in 2020. Enzymes are fragile, researchers say, meaning that in any given supply chain that results in mRNA for consumption, the enzymes are often the weakest link.

"Scientists may be able to model future RNA synthesis on an original, chimeric process that doesn’t require enzymes at all. With fewer moving parts and less vulnerability, that could mean more robust products that can travel further, last longer, and endure a wider variety of conditions—even vaccines."

Comment: The article presents the huge known problem: enzyme molecules are enormous and very specific in shape and content of amino acids. Where did they come from on early Earth?

Theoretical origin of life: RNA world can't work

by David Turell @, Friday, January 15, 2021, 21:57 (1187 days ago) @ David Turell

Cornelius Hunter comments:

https://evolutionnews.org/2021/01/rna-world-repeated-downfalls-repeated-resurrections/

"We’ve long since lost track of how many times the RNA World hypothesis — which states that life originated from an RNA enzyme-genome combination rather than from DNA — failed only to be once again resurrected, but we do know this crazy idea will, for a long time to come, continue to be cited as “good solid” evidence for evolution. This despite new research that gives yet another reason for its failure.

"There are big problems with the idea that life arose from a random assembly of DNA. Aside from the little problem of generating astronomical amounts of crucial information from, err, random mutations, the resulting DNA doesn’t do anything by itself. That is because proteins are needed to extract said information and do something with it.

"So, evolutionists came up with the clever idea of using RNA instead of DNA, since RNA can both store genetic information and also do something with it. Of course, this idea still has that little problem of generating the information in the first place. Oh, also, there is precisely zero evidence of any “RNA World” organisms. Now or ever.

"There is no organism that does this. There is no organism that does anything like this. There is no controlled, laboratory, version of such a thing. There isn’t even a computer simulation of it, at least in any kind of detail.

"Not only does this call the entire idea into question, it also raises another little problem: that if there was this so-called RNA World, then it must have gone away at some point, and neatly transitioned into a DNA world, without leaving a trace. But aside from vague speculation, there is no compelling notion of how this would occur.

***

"Now, this new research points out the rather inconvenient fact that RNA is too sticky:

"But while RNA strands may be good at templating complementary strands, they are not so good at separating from these strands. Modern organisms make enzymes that can force twinned strands of RNA — or DNA — to go their separate ways, thus enabling replication, but it is unclear how this could have been done in a world where enzymes didn’t yet exist.

***

"And while one might have thought that this rather fundamental problem would have disqualified the RNA World hypothesis a long time ago — RNA’s “stickiness” was not just discovered yesterday — it turns out that fundamental problems such as this tend to be openly discussed only when a replacement theory is at the ready.

"And sure enough, since DNA didn’t work, and perhaps now we can finally say that RNA also didn’t work, perhaps the trick is to combine them. Don’t two wrongs make a right? And so it is: the new research indeed proposes that life got going by using fancy chimeric molecular strands that are part DNA and part RNA.

"Well, evolution dodged another bullet. But we think we can at least say that Alexander Oparin’s 1924 prediction that origin-of-life research would be solved “very, very soon” hasn’t quite turned out right."

Comment: The way life evolved won't ever be found by humans is my point. Hunter and I have made the same comments many times.

Theoretical origin of life: Where did carbon come from?

by David Turell @, Sunday, March 07, 2021, 01:33 (1137 days ago) @ David Turell

A rocky planet like Earth should no have had carbon in its beginning. A theory:

https://phys.org/news/2021-03-comet-catalina-comets-carbon-rocky.html

"In early 2016, an icy visitor from the edge of our solar system hurtled past Earth. It briefly became visible to stargazers as Comet Catalina before it slingshotted past the Sun to disappear forevermore out of the solar system.

***

"Using one of its unique infrared instruments, SOFIA was able to pick out a familiar fingerprint within the dusty glow of the comet's tail—carbon.

"Now this one-time visitor to our inner solar system is helping explain more about our own origins as it becomes apparent that comets like Catalina could have been an essential source of carbon on planets like Earth and Mars during the early formation of the solar system.

***

"'Carbon is key to learning about the origins of life," said the paper's lead author, Charles "Chick" Woodward, an astrophysicist and professor in the University of Minnesota Twin Cities Minnesota Institute of Astrophysics. "We're still not sure if Earth could have trapped enough carbon on its own during its formation, so carbon-rich comets could have been an important source delivering this essential element that led to life as we know it."

***

"SOFIA's infrared observations were able to capture the composition of the dust and gas as it evaporated off the comet, forming its tail. The observations showed that Comet Catalina is carbon-rich, suggesting that it formed in the outer regions of the primordial solar system, which held a reservoir of carbon that could have been important for seeding life.

"While carbon is a key ingredient of life, early Earth and other terrestrial planets of the inner solar system were so hot during their formation that elements like carbon were lost or depleted. While the cooler gas giants like Jupiter and Neptune could support carbon in the outer solar system, Jupiter's jumbo size may have gravitationally blocked carbon from mixing back into the inner solar system.

"So how did the inner rocky planets evolve into the carbon-rich worlds that they are today?

"Researchers think that a slight change in Jupiter's orbit allowed small, early precursors of comets to mix carbon from the outer regions into the inner regions, where it was incorporated into planets like Earth and Mars.

"Comet Catalina's carbon-rich composition helps explain how planets that formed in the hot, carbon-poor regions of the early solar system evolved into planets with the life-supporting element.

"'All terrestrial worlds are subject to impacts by comets and other small bodies, which carry carbon and other elements," Woodward said. "We are getting closer to understanding exactly how these impacts on early planets may have catalyzed life.'"

Comment: Carbon for early life is still a big mystery and a part of the struggle understanding life's origin. Research labs simply assume there was lots if carbon around. But, then again, the origin of life researchers make lots of wild assumptions, and the granting funds swallow it whole hog. I view it as something we will never solve, by describing natural events that we prove.

Theoretical origin of life: RNA lab manufactured

by David Turell @, Thursday, March 18, 2021, 20:49 (1125 days ago) @ David Turell

Knowing what is required in an RNA world, this lab Frankensteined together a better mousetrap all by intelligent design:

https://science.sciencemag.org/content/371/6535/1225?utm_campaign=toc_sci-mag_2021-03-1...

"The RNA World Hypothesis posits that at the dawn of evolution, RNA played a key role in the establishment of life. Central to this hypothesis is the existence of an RNA replicase ribozyme capable of copying its own genome using a supply of prebiotically synthesized nucleotide monomers and RNA polymers. Ever since the class I ligase ribozyme was isolated from a high-diversity RNA pool, there has been a sustained effort to produce highly processive polymerase ribozymes. Because the affinity of these polymerases for their RNA templates is weak, with Michaelis constant (KM) values in the millimolar range, the most successful strategies to date have colocalized polymerase ribozymes with their substrates using concentration-enhancing micelles or by anchoring either the RNA template or the RNA primer to be extended to the polymerase ribozyme. These strategies create a high local concentration of primer template with respect to the polymerase but fail to create a truly processive polymerase by virtue of the tethering strategies used to enhance polymerization.

***

"All extant DdRPs, including the bacteriophage polymerases, use a variation of this two-step process. Thus, we selected a ribozyme with a similar mechanism to explore the potential connection between promoter recognition and processivity.

***

"We engineered three changes into this parental ribozyme by appending a PBS to its 5′ end, synthesizing a high-diversity pool containing 1013 sequence variants by inserting random sequence libraries at three distinct sites, and removing sequence from the B6.61 accessory domain known to be redundant.

***

After 25 rounds of selection, a substantial decrease in pool diversity occurred, with the final five rounds of selection being dominated by five major ribozyme polymerase families.

***

"Through in vitro evolution, we have found an RNA polymerase that can search for a promoter by first forming a functional open holopolymerase complex and then in a second step rearrange into a processive elongation form. The correct assembly of this CPCLOSED complex results in a more than one order of magnitude increase in extension, with extension on randomly generated templates being directly comparable to the best RNA polymerase ribozymes isolated to date, which on highly repetitive tethered templates are able to synthesize 75 to 203 nt of sequence."

***

Although many outstanding challenges remain to producing a self-evolving system in the laboratory, including increased polymerization rate, fidelity, and, most importantly, strand displacement, the development of a promoter-dependent RNA polymerase ribozyme with processive clamping ability offers many insights into the dilemmas faced by life in the earliest periods of evolution on this planet. (my bold)

Comment: I have necessarily omitted all the intricate details of how they cobbled this molecule together. The color red segment in the bold shows what they really proved. It takes intelligent design.

Theoretical origin of life: lab manufactured nonsense

by David Turell @, Saturday, March 20, 2021, 21:40 (1123 days ago) @ David Turell

A lab manufactured study to show that death is important for complexity to develop:

https://www.sciencedaily.com/releases/2021/03/210317141453.htm

"Simple systems can reproduce faster than complex ones. So, how can the complexity of life have arisen from simple chemical beginnings? Starting with a simple system of self-replicating fibres, chemists at the University of Groningen have discovered that upon introducing a molecule that attacks the replicators, the more complex structures have an advantage. This system shows the way forward in elucidating how life can originate from lifeless matter.

"The road to answering the question of how life originated is guarded by Spiegelman's monster, named after the American molecular biologist Sol Spiegelman, who some 55 years ago described the tendency of replicators to become smaller when they were allowed to evolve. 'Complexity is a disadvantage during replication, so how did the complexity of life evolve?' asked Sijbren Otto, Professor of Systems Chemistry at the University of Groningen. He previously developed a self-replicating system in which self-replication produces fibres from simple building blocks and, now, he has found a way to beat the monster.


"'To achieve this, we introduced death into our system,' Otto explains. His fibres are made up of stacked rings that are self-assembled from single building blocks. The number of building blocks in a ring can vary, but stacks always contain rings of the same size. Otto and his team tweaked the system in such a way that rings of two different sizes were created, containing either three or six building blocks.

"Under normal circumstances, fibres that are made up of small rings will outgrow the fibres with larger rings. 'However, when we added a compound that breaks up rings inside the fibres, we found that the bigger rings were more resistant. This means that the more complex fibres will dominate, despite the smaller rings replicating faster. Fibres that are made from small rings are more easily "killed." '

"Otto acknowledges that the difference in complexity between the two types of fibres is small.

***

"'All in all, we have now shown that it is possible to beat Spiegelman's monster,' says Otto. 'We did this in a particular way, by introducing chemical destruction, but there may be other routes.

***

"The new system is the first of its kind and opens a route to more complex chemical evolution. 'In order to achieve real Darwinian evolution that leads to new things, we will need more complex systems with more than one building block,' says Otto. The trick will be to design a system that allows for the right amount of variation. 'When you have unlimited variation, the system won't go anywhere, it will just produce small amounts of all kinds of variants.' In contrast, if there is very little variation, nothing really new will appear. (my bold)

Comment: From laughable to ridiculous as I see it. The bolded paragraph shows us how human intelligent design looks for clues as to how life developed on a rocky Earth. But note: these invented molecules have no relationship to the real RNA/DNA molecules we know.

Theoretical origin of life: simple organic molecules in rock

by David Turell @, Wednesday, March 31, 2021, 21:13 (1112 days ago) @ David Turell

A new discovery that ancient rocks hold simple carbon compounds and gasses:

https://www.nature.com/articles/s41467-021-21323-z#Sec9

"It is widely hypothesised that primeval life utilised small organic molecules as sources of carbon and energy. However, the presence of such primordial ingredients in early Earth habitats has not yet been demonstrated. Here we report the existence of indigenous organic molecules and gases in primary fluid inclusions in c. 3.5-billion-year-old barites (Dresser Formation, Pilbara Craton, Western Australia). The compounds identified (e.g., H2S, COS, CS2, CH4, acetic acid, organic (poly-)sulfanes, thiols) may have formed important substrates for purported ancestral sulfur and methanogenic metabolisms. They also include stable building blocks of methyl thioacetate (methanethiol, acetic acid) – a putative key agent in primordial energy metabolism and thus the emergence of life. Delivered by hydrothermal fluids, some of these compounds may have fuelled microbial communities associated with the barite deposits. Our findings demonstrate that early Archaean hydrothermal fluids contained essential primordial ingredients that provided fertile substrates for earliest life on our planet.

***

"As yet, however, such distinctive organic molecules have not been found in rocks that directly testify to the emergence of life on our planet. (my bold)
***

"Here we report on the presence of biologically-relevant primordial organic molecules in primary fluid inclusions trapped in barites of the c. 3.5 billion-year-old Dresser Formation. To explore the full range of volatiles, we combined gas chromatography–mass spectrometry (GC–MS), microthermometry, fluid inclusion petrography, and stable isotope analysis. Our findings reveal an intriguing diversity of organic molecules with known or inferred metabolic relevance and provide a strong clue as to how ancient hydrothermal fluids sustained microbial life ~3.5 billion years ago.

***

"Black barites studied here classify as primary hydrothermal sediments that precipitated from discharging fluids. This interpretation is additionally supported by the facts that (i) the originally sulfidic stromatolite interbeds are still largely intact and show no indications for a progressive replacement by barite and (ii) that the barite does not contain relicts of potential precursor materials. Our observations are therefore consistent with earlier studies that argued for a primary, synsedimentary origin of the Dresser barites analysed herein (i.e. precipitation in surface environments linked to hydrothermal activity)"

Comment: Simple carbon-based molecules do not make the complex molecules such as amino acids necessary for living organisms, but it shows possible molecular substrates to help start life.

Theoretical origin of life: constant hopeful articles

by David Turell @, Monday, May 10, 2021, 21:00 (1072 days ago) @ David Turell

Another one of constant examples:

https://www.sciencenews.org/article/life-chemistry-ingredients-methanol-planet-forming-...

"In the planet-forming disk of gas and dust around a young star, astronomers have detected methanol. The disk is too warm for the methanol to have formed there, so this complex organic molecule probably originated in the interstellar cloud that collapsed to form the star and its disk, researchers report online May 10 in Nature Astronomy. This finding offers evidence that at least some organic matter from interstellar space can seed the disks around newborn stars to provide potential ingredients for life on new planets. (my bold)

“'That’s pretty exciting, because it means that, in principle, all planets forming around any kind of star could have this material,” says Viviana Guzmán, an astrochemist at the Pontifical Catholic University of Chile

"Complex organic molecules have been observed in interstellar clouds of gas and dust (SN: 3/22/21), as well as in planet-forming disks around young stars (SN: 2/18/08). But astronomers didn’t know whether organic material from interstellar space could survive the formation of a protoplanetary disk, or whether organic chemistry had to start from scratch around new stars.

“'When you form a star and its disk, it’s not a very easy, breezy process,” says Alice Booth, an astronomer at Leiden University in the Netherlands. Radiation from the new star and shock waves in the imploding material, she says, “could destroy a lot of the molecules that were originally in your initial cloud.”

***

"Methanol could not have originated in the disk, because this molecule forms when hydrogen interacts with carbon monoxide ice, which freezes below temperatures of about –253° Celsius. The disk around HD 100546 is much warmer than that, heated by a star whose surface is roughly 9,700° C — some 4,000 degrees hotter than the sun. So the disk must have inherited its methanol from the interstellar cloud that forged its central star, the researchers conclude."

Comment: Every time an organic molecule is found in space articles like this appear, rhapsodically trying to promote the thought of how easy it must be for life to appear. We know just the opposite. Note my bold in the first paragraph. Methanol is a very simple molecule, not complex..

Theoretical origin of life: chaperones required

by David Turell @, Monday, May 31, 2021, 15:36 (1051 days ago) @ David Turell

All protein processes in life make mistakes. Chaperones had to exist at the origin of life:

https://www.pnas.org/content/118/21/e2020885118.long

"Across the Tree of Life, life’s phenotypic diversity has been accompanied by a massive expansion of the protein universe. Compared with simple prokaryotes that harbor thousands of proteins, plants and animals harbor hundreds of thousands of proteins that are also longer, multidomain, and comprise a variety of folds and fold combinations, repeated segments, and beta-rich architectures that make them prone to misfolding and aggregation. Surprisingly, the relative representation of core chaperones, those dedicated to maintaining the folding quality of these increasingly complex proteomes, did not change from prokaryotic to mammalian genomes. To reconcile the expanding proteomes, core chaperones have rather increased in cellular abundance and evolved to function cooperatively as a network, combined with their supporting workforce, the cochaperones.

"Abstract
Across the Tree of Life (ToL), the complexity of proteomes varies widely. Our systematic analysis depicts that from the simplest archaea to mammals, the total number of proteins per proteome expanded ∼200-fold. Individual proteins also became larger, and multidomain proteins expanded ∼50-fold. Apart from duplication and divergence of existing proteins, completely new proteins were born. Along the ToL, the number of different folds expanded ∼5-fold and fold combinations ∼20-fold. Proteins prone to misfolding and aggregation, such as repeat and beta-rich proteins, proliferated ∼600-fold and, accordingly, proteins predicted as aggregation-prone became 6-fold more frequent in mammalian compared with bacterial proteomes. To control the quality of these expanding proteomes, core chaperones, ranging from heat shock proteins 20 (HSP20s) that prevent aggregation to HSP60, HSP70, HSP90, and HSP100 acting as adenosine triphosphate (ATP)-fueled unfolding and refolding machines, also evolved. However, these core chaperones were already available in prokaryotes, and they comprise ∼0.3% of all genes from archaea to mammals. This challenge—roughly the same number of core chaperones supporting a massive expansion of proteomes—was met by 1) elevation of messenger RNA (mRNA) and protein abundances of the ancient generalist core chaperones in the cell, and 2) continuous emergence of new substrate-binding and nucleotide-exchange factor cochaperones that function cooperatively with core chaperones as a network.

"All cellular life is thought to have stemmed from the last universal common ancestor (LUCA), that emerged more than 3.6 billion y ago. Two major kingdoms of life diverged from LUCA: bacteria and archaea, which about 2 billion y later merged into the eukaryotes. Since the beginning of biological evolution, life’s volume has increased on a grand scale: The average size of individual cells has increased ∼100-fold from prokaryotes to eukaryotes, the number of cell types has increased ∼200-fold from unicellular eukaryotes to humans, and average body size has increased ∼5,000-fold from the simplest sponges to blue whales.

"This expansion in organismal complexity and variability was accompanied by an expansion in life’s molecular workforce, proteomes in particular, which in turn presented a challenge of reaching and maintaining properly folded and functional proteomes. Most proteins must fold to their native structure in order to function, and their folding is largely imprinted in their primary amino acid sequence. However, many proteins, and especially large multidomain polypeptides, or certain protein types such as all-beta or repeat proteins, tend to misfold and aggregate into inactive species that may also be toxic. Life met this challenge by evolving molecular chaperones that can minimize protein misfolding and aggregation, even under stressful out-of-equilibrium conditions favoring aggregation. Chaperones can be broadly divided into core and cochaperones. Core chaperones can function on their own, and include ATPases heat shock protein 60 (HSP60), HSP70, HSP100, and HSP90 and the adenosine triphosphate (ATP)-independent HSP20. The basal protein holding, unfolding, and refolding activities of the core chaperones are facilitated and modulated by a range of cochaperones such as J-domain proteins. (my bold)

***

"Thus, across the Tree of Life, proteomes have massively expanded, not just by duplication of preexisting proteins but also by the emergence of completely new ones. Eukaryotic proteomes became particularly large and specifically richer in repeat, beta-rich, and aggregation-prone proteins whose folding is inherently challenging. These changes in proteome size and composition intensified the demand for chaperone action. Curiously, however, no new core chaperones emerged in response to this increased demand. Instead, they increased in abundance relative to all other proteins in the cell. Foremost, an entire network of cochaperones had evolved that facilitate the basal core-chaperone activity."

Comment: The design of the origin of life required correcting chaperones and cochaperones from the very beginning. Without arguing about a designer, the design creation had to have had knowledge aforehand of the impending problem a life based on proteins must have. Therefore a mechanism of chaperoning and cochaperoning exists. Natural events do not have foresight. A designer is reqired.

Theoretical origin of life: basic physicochemical restraints

by David Turell @, Monday, June 07, 2021, 17:54 (1044 days ago) @ David Turell

New research is this area defines constraints:

https://phys.org/news/2021-06-basic-physics-chemistry-constrain-cellular.html

"Advances have been made in mapping out the organic molecules that likely existed on the early Earth, and recently candidate prototypic pathways in early cells have been formulated. But how did these candidates' early biochemistry actually function as a system on which subsequent cellular life is based?

"A team of bioengineers at the Novo Nordisk Foundation Center for Biosustainability, DTU, has now defined ten overarching classes of constraints on early metabolic networks dictated by basic chemistry and physics. These constraints concern fundamental aspects of chemical processes, such as thermodynamics, electroneutrality, osmotic pressure, and pH. These are abiotic constraints (called ABCs given their fundamental nature) that all living systems have to abide by.

"The challenge has been to simultaneously reconcile all these complex constraints to define allowable operating conditions for living cells. This problem is a challenge in computational biology, a challenge that the team has resolved, the results having been published in Nature Communications.

"'The computations are challenging because of the nonlinearity of governing equations and nonconvexity of solution spaces, which required special optimization techniques tailored to the geometric structure of the problem," says Dr. Amir Akbari, the lead author of the study.

"'We worked hard on the formulation of the algorithms that eventually gave the solution and thus the conditions under which fundamental biochemical processes can operate."

"The investigators analyzed how these constraints operate on basic energy metabolism in bacteria. The results demonstrated, among other things, the fundamental role of thermodynamic constraints in the evolution of alternative transport systems.

"'The computations are consistent with published metabolomic data," says Bernhard Palsson, CEO and Professor at The Novo Nordisk Foundation Center for Biosustainability at Technical University of Denmark.

"'The study also revealed how basic stress response mechanisms, such as those for osmotic pressure and reactive oxygen species (ROS) have to work and be regulated. Remarkably, the behavior of modern bacteria reflects the computational predictions."

"Overall, this advancement helps to understand systems biology at a fundamental level and how the basis for the process of life shapes possible early evolutionary trajectories. The next step for the scientists is to apply this computational framework to gain insight into candidate abiotic organic chemical processes and the possible forms of initial metabolic networks.

"'These processes have to form homeostatic states that are sufficiently stable to provide the environment for the evolution of more complex cellular functions," says Professor Palsson."

Comment: This is a welcome addition to the usual wishful thinking pie-in-the-sky silly research as though it is is all so simple. It isn't. When this work is completed it will bring realism to future research.

Theoretical origin of life: early living filament fossils

by David Turell @, Friday, July 16, 2021, 21:42 (1005 days ago) @ David Turell

From 3.42 byo:

https://advances.sciencemag.org/content/7/29/eabf3963?utm_campaign=toc_advances_2021-07...

"Abstract
Subsurface habitats on Earth host an extensive extant biosphere and likely provided one of Earth’s earliest microbial habitats. Although the site of life’s emergence continues to be debated, evidence of early life provides insights into its early evolution and metabolic affinity. Here, we present the discovery of exceptionally well-preserved, ~3.42-billion-year-old putative filamentous microfossils that inhabited a paleo-subseafloor hydrothermal vein system of the Barberton greenstone belt in South Africa. The filaments colonized the walls of conduits created by low-temperature hydrothermal fluid. Combined with their morphological and chemical characteristics as investigated over a range of scales, they can be considered the oldest methanogens and/or methanotrophs that thrived in an ultramafic volcanic substrate.

***

"The filaments satisfy the commonly accepted biogenicity, indigenicity, and syngenicity criteria. The studied filaments also differ from known abiotic pseudofossils in the specific combination of their site of occurrence, 3D morphological complexity, kerogenous nature, spectrally observed ultrastructures, and their specific metal-organic signature. Although biomorphs, produced in the absence of any direct biological activity under geochemical conditions that could have existed on early Earth, must be considered when evaluating the biogenicity of putative early trace of life, their features with the various attributes of the filaments described here are currently not known. Possibly the strongest evidence for the biogenicity of the studied filaments is their occurrence in specific associations (single or in clusters) within different parts of the vein microhabitat and in association with biofilms.

"Although cellular fossils of archaeal methanogens and methanotrophs have not yet been reported in the Paleoarchean record and Paleoarchean geochemical evidence (carbon isotopes) for microbially produced methane is limited, methane-utilizing metabolic pathways are commonly recognized as ancient in origin. Despite the demonstrated fossilization potential of Archaea, their fossil record is restricted to the Phanerozoic. Our findings could possibly extend this record back to 3.42 Ga.

***

"In this work, a suite of converging and mutually supportive evidence indicative of biogenicity (morphology and chemical composition) and a favorable ecological setting along with meeting endogenicity and syngenicity criteria was established for filaments in a habitable Archean subsurface ultramafic environment. This discovery of microfossils extends knowledge of the early subsurface fossil record and provides a strong case for the importance of subsurface hydrothermal systems as an abode for early life. These findings provide the oldest direct evidence for subsurface methane-cycling microorganisms, most likely methanogens, consistent with their expected antiquity based on carbon isotope analysis of fluid inclusions and molecular evidence.

Comment: More evidence of an early start to life after Earth formed.

Theoretical origin of life: early living filament fossils

by David Turell @, Monday, July 26, 2021, 19:54 (995 days ago) @ David Turell

From 3.42 byo:

https://advances.sciencemag.org/content/7/29/eabf3963?utm_campaign=toc_advances_2021-07...

More commentary:

https://www.sciencenews.org/article/oldest-archaea-microbe-fossil-fillaments-life-evolu...

"...some researchers aren’t convinced these fossils are the real deal. In silica-rich hydrothermal environments, the ingredients for structures that mimic cells mingle and can form life look-alikes through chemistry, says Julie Cosmidis, a geobiologist at the University of Oxford. “They fossilize better than actual cells, so I think it could very well be what those things are,” she says, pointing out that nickel, common in the early Earth, clings easily to organic matter, whether it’s living or not. “We don’t understand enough [about] the processes that can create false biosignatures,” says Cosmidis, whose lab studies such questions.

"Cavalazzi and her colleagues contend that the different lines of evidence together support the living origin of the microfossils. Papineau also notes that “the evidence is very good,” but adds that it’s “not necessarily rock solid.” Other tests could strengthen the case for the earliest methane-using microbes, he says.

"If the strands are ancient archaea, they’d become the earliest fossil evidence for this domain of life, predating specimens from less than 500 million years ago. And if such microbes evolved so quickly on Earth, within around 1 billion years of the planet’s origin, methane-cyclers may be more common than realized on other planets where liquid water has been around for a while, Papineau says."

Comment: We'll wait for more studies.

Theoretical origin of life: excerpt from Neil Thomas book

by David Turell @, Thursday, August 19, 2021, 00:26 (972 days ago) @ David Turell

It ain't as easy as Dawkins claims:

https://evolutionnews.org/2021/08/myths-monsters-and-lifes-elusive-first-step/

"We might, therefore, do well to pause over the truth status and indeed even the logic of Dawkins’s notion of “entities sufficiently simple to have come into existence by chance,” and establish whether such a notion can be supported by experimental evidence — especially since recent advances in molecular biology show that the humblest bacterium contains more genetic information than the instruction manual for NASA space probes. The very notion of a simple biological entity has become deeply problematical with our increasing knowledge of the molecular world in the last half century, and one might therefore wish to query whether such a thing can exist in nature.

[The Miller-Urey 1953 lightning in a bottle experiment is reviewed]

***

"...the media interest in the Miller-Urey experiment is unsurprising. However, the complete chemical pathway devoutly hoped for by many in the wake of the experiment was not to materialize. In fact, the unlikelihood of such a materialization was underscored in the very same year that the Miller-Urey experiment took place, when Francis Crick and James Watson succeeded in identifying the famous double helix of DNA. Their discovery revealed, among other things, that even if amino acids could somehow be induced to form proteins, there was more to the story. Life also depends on nucleic acids, one of which is deoxyribonucleic acid or DNA, where the vital information needed to replicate and operate any given organism is encoded.

"Proteins and DNA must be able to work together. DNA is both highly complex and highly specific, to the extent that just small differences in its letter sequences can make the difference between a living, thriving animal and a stillborn. Proteins are indispensable, but they do not have the capacity to store and transmit information for their own construction. DNA, on the other hand, can store information but cannot manufacture anything or duplicate itself. It’s a chicken-and-egg situation, so much so that Francis Crick was once moved to comment that the beginnings of life seemed impossible, barring a miracle, since “so many are the conditions which would have to be satisfied to get it going.”

"Finally, it had to be conceded that life was unlikely to form at random from the so-called “prebiotic” substrate on which scientists had previously pinned so much hope. (To this day, biochemists remain ignorant of the modalities of a jump from amino acids to proteins, and the origin of nucleic acids is similarly shrouded in darkness.) To complicate things even further, it is now widely disputed whether the early atmosphere of the Earth postulated by Miller and Urey would have been such as they assumed, and so it may not have supported the formation of the organic compounds they identified. Hence the problem appears now to extend to include the origin of the basic building blocks themselves.

"The hope that life may be somehow “dormant” in chemicals, waiting to be unlocked when the correct combination of chemicals clicks into place, as it were, has clearly suffered a signal reverse."

Comment: so much for origin of life experimentation. An other point made is that the chemicals used in experimental labs are purified, not at all like the natural ones lying about on the early Earth.

Theoretical origin of life: excerpt from Neil Thomas book

by dhw, Thursday, August 19, 2021, 11:57 (971 days ago) @ David Turell

It ain't as easy as Dawkins claims:
https://evolutionnews.org/2021/08/myths-monsters-and-lifes-elusive-first-step/

QUOTE: "We might, therefore, do well to pause over the truth status and indeed even the logic of Dawkins’s notion of “entities sufficiently simple to have come into existence by chance,” and establish whether such a notion can be supported by experimental evidence — especially since recent advances in molecular biology show that the humblest bacterium contains more genetic information than the instruction manual for NASA space probes. The very notion of a simple biological entity has become deeply problematical with our increasing knowledge of the molecular world in the last half century, and one might therefore wish to query whether such a thing can exist in nature.

So far, Mr Thomas seems to have provided us with nothing we haven’t read many times before. Here, purely for your interest, is an extract from a work you may or may not be familiar with: “But how does life get started?” Again he [Dawkins] admits that this “may have been a highly improbable occurrence”. “The origin of life was the chemical event, or series of events, whereby the vital condition for natural selection first came about. The major ingredient was heredity, either DNA or (more probably) something that copies like DNA but less accurately, perhaps the related molecule RNA.” This is an extraordinary simplification. The origin of life must at the very least have had two major ingredients, and they must have sparked into life at precisely the same moment: heredity was one, but what Darwin called the “breath” was the other. DNA is not much use in a lifeless body. By only calling on DNA/RNA, at a stroke Dawkins has halved the degree of the already high improbability. But be reassured: “I shall not be surprised if, within the next few years, chemists report that they have successfully midwifed a new origin of life in the laboratory” (p. 137). That’s OK then. Dawkins thinks that the combined knowledge of the finest brains, working on the findings of generations of earlier fine brains, will soon be able consciously to put together the ingredients and breathe the spark of life into them … which will prove that life came about through unconscious chance. Abiogenesis is the name of the theory that inanimate matter spontaneously assembled itself to create life. And it requires just as much credulity as the genesis theory it seeks to replace.

You will find this in section 5, “Origins”, of the “Brief Guide to the Universe”. Maybe you should read it some time.

Theoretical origin of life: excerpt from Neil Thomas book

by David Turell @, Thursday, August 19, 2021, 15:39 (971 days ago) @ dhw

It ain't as easy as Dawkins claims:
https://evolutionnews.org/2021/08/myths-monsters-and-lifes-elusive-first-step/

QUOTE: "We might, therefore, do well to pause over the truth status and indeed even the logic of Dawkins’s notion of “entities sufficiently simple to have come into existence by chance,” and establish whether such a notion can be supported by experimental evidence — especially since recent advances in molecular biology show that the humblest bacterium contains more genetic information than the instruction manual for NASA space probes. The very notion of a simple biological entity has become deeply problematical with our increasing knowledge of the molecular world in the last half century, and one might therefore wish to query whether such a thing can exist in nature.

dhw: So far, Mr Thomas seems to have provided us with nothing we haven’t read many times before. Here, purely for your interest, is an extract from a work you may or may not be familiar with: “But how does life get started?” Again he [Dawkins] admits that this “may have been a highly improbable occurrence”. “The origin of life was the chemical event, or series of events, whereby the vital condition for natural selection first came about. The major ingredient was heredity, either DNA or (more probably) something that copies like DNA but less accurately, perhaps the related molecule RNA.” This is an extraordinary simplification. The origin of life must at the very least have had two major ingredients, and they must have sparked into life at precisely the same moment: heredity was one, but what Darwin called the “breath” was the other. DNA is not much use in a lifeless body. By only calling on DNA/RNA, at a stroke Dawkins has halved the degree of the already high improbability. But be reassured: “I shall not be surprised if, within the next few years, chemists report that they have successfully midwifed a new origin of life in the laboratory” (p. 137). That’s OK then. Dawkins thinks that the combined knowledge of the finest brains, working on the findings of generations of earlier fine brains, will soon be able consciously to put together the ingredients and breathe the spark of life into them … which will prove that life came about through unconscious chance. Abiogenesis is the name of the theory that inanimate matter spontaneously assembled itself to create life. And it requires just as much credulity as the genesis theory it seeks to replace.

You will find this in section 5, “Origins”, of the “Brief Guide to the Universe”. Maybe you should read it some time.

You have beautifully destroyed Dawkins. Thomas' book is a slog I am still performing since it is an exposition of how erudite he is. It appears he is travelling your path to agnosticism recognizing design,

Theoretical origin of life: pure chemicals cheat

by David Turell @, Saturday, August 21, 2021, 15:32 (969 days ago) @ David Turell

Only impure chemicals could have been present on early Earth:

https://evolutionnews.org/2021/08/tonight-new-long-story-short-video-delivers-a-dose-of...

"Experiments to produce the building blocks of life always begin with unnaturally pure, concentrated reagents. These are purchased from laboratory supply shops and produced through sophisticated, intelligently designed processes. For example, in a 2008 publication, Stanley Miller and his graduate student Jeff Bada reported using a mixture of nitrogen gas and CO2 to produce some amino acids. They described the starting materials this way:

"Medical grade nitrogen gas (purity > 99.99% N2) and industrial grade carbon dioxide (claimed by the manufacturer to contain no more than 10 ppm impurities) were purchased from Airgas.

"Where on a prebiotic Earth could you find gasses with no more than 10-parts-per-million impurity? Airgas, the supplier from which the researchers obtained their materials, was not around at the time. I recognize that the motivation to work with such unnaturally pure reagents was to avoid criticism that the experiment was contaminated. However, after succeeding in producing some amino acids from these ingredients, the team of scientists claimed success and moved on.

"And that’s a problem. In my own research on heart disease, the gap between an initial proof of concept (e.g., success in a petri dish experiment) and the practical, widespread application of a new heart failure therapy can be enormous. If I stopped working after proof of concept, publishing only my initial findings but extrapolating the results to claim sweeping success in curing heart failure, I could rightly be accused of academic fraud. The origin-of-life research community is clearly held to a different standard.

"In chemical reactions, the amount of product produced commonly depends on the concentration of the reagents. This is known as Le Chatelier’s principle. Unnaturally concentrated reagents drive the reaction to produce more product. As origin-of-life researcher Pier Luigi Luisi has said:

"[C]oncentration can indeed be seen as a chemical constraint in the origin of life, since chemistry cannot operate below a certain threshold of concentration.

"On a prebiotic Earth, though, with lower concentrations of reagents and plenty of impurities, Miller and Bada’s reaction may not have produced any appreciable amino acid product at all."

Comment: papers on OOL never mention this. We can view all studies of origin of life as really fraudulent attempts. Discount all exuberant takes.

Theoretical origin of life: basalt glass fantasy

by David Turell @, Saturday, September 04, 2021, 17:38 (955 days ago) @ David Turell

Another lab study:

https://www.nature.com/articles/s41557-021-00772-5

"Abstract
Catalytic nucleic acids, such as ribozymes, are central to a variety of origin-of-life scenarios. Typically, they require elevated magnesium concentrations for folding and activity, but their function can be inhibited by high concentrations of monovalent salts. Here we show that geologically plausible high-sodium, low-magnesium solutions derived from leaching basalt (rock and remelted glass) inhibit ribozyme catalysis, but that this activity can be rescued by selective magnesium up-concentration by heat flow across rock fissures. In contrast to up-concentration by dehydration or freezing, this system is so far from equilibrium that it can actively alter the Mg:Na salt ratio to an extent that enables key ribozyme activities, such as self-replication and RNA extension, in otherwise challenging solution conditions. The principle demonstrated here is applicable to a broad range of salt concentrations and compositions, and, as such, highly relevant to various origin-of-life scenarios."

Clear commentary:

https://www.sciencealert.com/scientists-identify-a-mixture-of-salts-that-could-have-spa...

"New research looking at how the conditions on primordial Earth might have produced life has identified a mixture of salts that, mixed with heat flows from molten rock, could potentially have contributed to the formation of self-replicating biomolecules.

***

"In this case, scientists looked at the mixture of magnesium (Mg) and sodium (Na) as it might have been on Earth in its earliest years: for RNA folding to work, a relatively high concentration of doubly charged magnesium ions and a lower concentration of singly charged sodium is required.

"'Accordingly, the question arises as to which environments on early Earth might have provided suitable salt conditions for such prebiotic processes. One geologically probable process that produces saline environments is the leaching of salts from basalt," the international team of researchers writes in their study.

"'As a primary partial melt of the Earth's mantle, basalt is one of the most abundant rock types to be expected in the Earth's early crust, as well as the crust of other terrestrial planets in our Solar System."

"The team synthesized basaltic glass – which naturally occurs on Earth when melted basalt is rapidly cooled (by contact with ocean water, for instance) – and characterized it in its various forms, including both rock and glass.

***

"Together, convection and thermophoresis increase the number of magnesium ions in the mix, creating conditions where self-replicating RNA can occur, the study shows. The same sort of chemical reactions may have played out on Earth 4 billion years ago.

"This leaching of salts from basalt – found in abundance in Earth's mantle – fits the template for the RNA world hypothesis to work, the research shows. What's more, it widens out the possibilities in terms of salt mixes that may have helped spark life.

"'The principle demonstrated here is applicable to a broad range of salt concentrations and compositions, and, as such, highly relevant to various origin-of-life scenarios," write the researchers in their published paper."

Comment: All this shows is if RNA is already around the salts help it fold. The author of the commentary shows the usual thoughtless hopefulness about these studies. So what made the RNA from those amino acids which just happen to be lying around in just the right structural organization to become RNAs? RNAs must come first!!!

Theoretical origin of life: made in a lab, impossible

by David Turell @, Tuesday, November 16, 2021, 14:56 (882 days ago) @ David Turell

A strong opinion:

https://www.grisda.org/synthesizing-life-in-the-lab?mc_cid=5a79992abf

"Quoting a prominent scientist on this subject: “…life itself can be seen as an emergent property: the molecules that constitute a living cell (DNA, proteins, polysaccharides, lipids, etc.) are not living. The quality “life” arises from the assembly of these non-living elements, duly arranged in space and time.”

"Underlying all efforts in synthetic biology is the fundamentally crucial assumption that it is possible to assemble living matter stepwise from a set of biomolecules. A corollary of this supposition is that, at least in principle, living matter may be disassembled reversibly and reassembled. While such is the nearly universal consensus within the scientific community, as of now, these assumptions have not been verified experimentally.

***

"However, a more cautious reviewer of the subject states: “…it is important to note that minimal life has not yet been achieved in the laboratory. Does this mean that it is in principle not possible? I do not believe so, although as a scientist it is always good to have a bit of doubt (perhaps we missed something important in our theoretical analysis)”

"This communication points to just such an oversight, the underestimation of the essential nature of the “out-of equilibrium” state of living matter.

"All life processes, metabolism, growth, stimulus response and replication are driven by on-going chemical reactions. Every chemical reaction exists in one of two states, non-equilibrium and equilibrium. On-going chemical processes are always in states of non-equilibrium.

"When a chemical reaction, aA + bB ⇌ cC + dD runs its course, equilibrium ensues, where the mass action ratio Γ=[C]cx[D]d/[A]axb becomes the equilibrium constant, Keq. At equilibrium, the change in free energy ∆F=0 and in this state the reaction cannot generate or absorb any energy.

"During chemical reactions there is a net flux of matter from reactants to products or the reverse. However, at equilibrium the flux stops.

"Moreover, the state of equilibrium resists change. As the Le Chatelier’s principle[20] states, if a chemical system at equilibrium experiences a change in concentration, temperature, volume, or partial pressure, then the equilibrium shifts to counteract the imposed change and a new equilibrium is established. Thus, according to this principle, any change from a state of non-equilibrium to equilibrium is irreversible.

"Even though in living cells each reaction is pushed toward equilibrium by an enzyme (so as to forestall the possibility of slower, random non-biological chemical events), if any of the hundreds to thousands of chemical processes could actually reach equilibrium, an irreversible metabolic block would result. Multiple such equilibriums would kill the cell. However, in live cells there are no isolated reactions and the problem of equilibrium is avoided. Rather, chemical events are linked into pathways, so that the products of reactions do not accumulate, but immediately react with another substance.

"The end products of metabolic pathways are either utilized immediately or they are secreted from the cell. Moreover, regulatory systems such as “feedback inhibition” help maintain homeostasis.

***

"Current practitioners of synthetic biology, while recognizing the compulsory “out-of-equilibrium homeostatic state” of living matter, do not appear to appreciate the irreversibility <non-spontaneity?> of the state of equilibrium. Building artificial cells in a modular fashion will inevitably result in the onset of chemical equilibrium within each module. Once equilibrium is reached, the artificial cell, figuratively speaking, “runs into a brick wall”. It is no longer capable of growth or accomplish any net chemical process.

"No technology is known to achieve modular assembly of artificial cells while preserving the non-equilibrium status of each component reaction. While these considerations do not apply to polymerizations, such as RNA or DNA synthesis, as each incremental extension of the polymer is accompanied by the hydrolysis of a high-energy bond rendering these steps essentially irreversible, any other metabolic event is very much subject to termination due to reaching equilibrium. Until the construction of cell-like structures harboring metabolisms in homeostatic non-equilibrium states become reality, the most sophisticated efforts of synthetic biology will come to naught.

"Therefore, more than a century later, our response to Jacques Loeb’s call for the synthesis of living matter is that we are not there yet. We need to find ways to generate steady state non-equilibrium conditions within the artificial cells. These technologies await inventions in the future."

Comment: in our reality only life begets life. This exposition of the complexity of cells should show dhw how the automaticity of life is necedssary.

Theoretical origin of life: Miller-Urey all wrong

by David Turell @, Tuesday, November 23, 2021, 18:09 (875 days ago) @ David Turell

Further repeat studies with new findings:

https://www.realclearscience.com/2021/11/23/what_the_famous_miller-urey_experiment_got_...

"The experiment mixed water and simple gases — methane, ammonia, and hydrogen — and shocked them with artificial lightning within a sealed glass apparatus. Within days, a thick colored substance built up at the bottom of the apparatus. This detritus contained five of the basic molecules common to living creatures. Revising this experiment over the years, Miller claimed to find as many as 11 amino acids. Subsequent work varying the electrical spark, the gases, and the apparatus itself created another dozen or so. After Miller’s death in 2007, the remains of his original experiments were re-examined by his former student. There may have been as many as 20-25 amino acids created even in that primitive original experiment.

"The Miller-Urey experiment is a daring example of testing a complex hypothesis. It is also a lesson in drawing more than the most cautious and limited conclusions from it.

"In the years following the original work, several limitations curbed excitement over its result. The simple amino acids did not combine to form more complex proteins or anything resembling primitive life. Further, the exact composition of the young Earth did not match Miller’s conditions. And small details of the setup appear to have affected the results. A new study published last month in Scientific Reports investigates one of those nagging details. It finds that the precise composition of the apparatus housing the experiment is crucial to amino acid formation.

***

"One of the elements of art in science is to divine which of innumerable complexities matter and which do not. Which variables can be accounted for or understood without testing, and which ones can be cleverly elided by experimental design? This is a borderland between hard science and intuitive art. It is certainly not obvious that glass would play a role in the outcome, but it apparently does.

***

"The authors of the new work performed just such a single-variable test. They ran the entire Miller-Urey experiment multiple times, varying only the presence of silicate glass. The runs performed in as glass vessel produced one set of results, while those using a Teflon apparatus produced another.

"Systematically marching through each potential variable, one at a time, might be called “brute force.” But there is art here too, namely, in deciding which single variable out of many possibilities to test and in what way. In this case, we learned that glass silicates played an important role in the Miller-Urey experiment. Perhaps this means that silicate rock formations on the early Earth were necessary to produce life. Maybe."

Comment: a brilliant experiment for its time, but concludes nothing. The author forgets to note that the amino acids produced were both right and left handed, and proteins for life are left handed.

Theoretical origin of life: a woolly math approach

by David Turell @, Wednesday, November 24, 2021, 19:55 (874 days ago) @ David Turell

A far-out paper assuming heat production guided by inherited information that seems to appear out of nowhere:

https://www.quantamagazine.org/at-the-dawn-of-life-heat-may-have-driven-cell-division-2...

"An elegant ballet of proteins enables modern cells to replicate themselves. During cell division, structural proteins and enzymes coordinate the duplication of DNA, the division of a cell’s cytoplasmic contents, and the cinching of the membrane that cleaves the cell. Getting these processes right is crucial because errors can lead to daughter cells that are abnormal or unviable.

"Billions of years ago, the same challenge must have faced the first self-organizing membranous bundles of chemicals arising spontaneously from inanimate materials. But these protocells almost certainly had to replicate without relying on large proteins. How they did it is a key question for astrobiologists and biochemists studying the origins of life.

“'If you delete all enzymes in the cell, nothing happens. They’re just inert sacks,” said Anna Wang, an astrobiologist at the University of New South Wales in Sydney. “They’re really stable, and that’s kind of the point.”

***

"Attal thinks that that the chemical and physical processes active in early life were probably quite simple, and that thermodynamics alone could therefore have played a significant role in how life began. He said that the kinds of basic equations he has been working on could spell out some of the rules that governed how life first emerged.

***

"For primitive cells to divide themselves without complex protein machinery, the process would have needed a physical or chemical driver. “It’s really about stripping a cell down to its basic functions and thinking, ‘What are the basic physical and chemical principles, and how can we mimic that without proteins?’” Wang said.

***

"What scientists do agree on is that protocells must have had some kind of heritable information they could pass down to daughter cells, a metabolism that carried out chemical reactions, and a lipid membrane isolating the metabolism and heritable information from the randomness in the rest of Earth’s primordial soup. Whereas the outside chemical world was inherently random, the partitioning provided by the lipid membrane could create an area of lower entropy. (my bold)

***

"Attal realized that the energy produced by the primitive cellular metabolism would heat up the lipids on the inside of the membrane more quickly than those on the outside. Thermodynamics would then force the energetic inner lipids to “flip” to the outside, causing the outer membrane layer to expand at the expense of the inner layer. One easy solution to this imbalance would be for the cell to pinch together into two daughter cells. This pinching would occur at the middle of the parent cell, where it was hottest and the lipid movements were most pronounced.

[There follows a large series of objections from others]

"Neither of these issues means that heat didn’t play a role in early cell division, only that Attal’s mathematical model may not be the most accurate, Wang says. Still, Claudia Bonfio, a biochemist at the University of Strasbourg in France, says that the paper adds to the literature on early life because “it’s a nice starting point for experiments. We too often forget that reactions consume and produce heat, which could have an effect on things like fission.'”

Comment: note in the bold the miraculous appearance of necessary parts of the protocell. The obvious objections were quite strong, but note the final paragraph trying to justify this foolishness.

Theoretical origin of life: hydrogen energy

by David Turell @, Wednesday, December 15, 2021, 19:25 (853 days ago) @ David Turell

If there is available energy, the metabolic processes miraculously appear:

https://cosmosmagazine.com/science/biology/what-fuelled-the-origins-of-life/

"Now, researchers at the Heinrich Heine University Düsseldorf (HHU), Germany, say they’ve found the smoking gun. The secret ingredient that fuelled the origins of life is the modern era’s cleanest, greenest energy carrier: hydrogen gas (H2).

***

"The team identified 402 metabolic reactions that have been virtually unchanged since the origins of life some four billion years ago, and which all occur among some of the present day’s simplest life forms – bacteria and archaea. By looking at these extraordinarily well-conserved reactions, PhD researcher and lead author on the study Jessica Wimmer was able to piece together LUCA’s metabolic activity – peering through the veil at the functioning of primordial life billions of years in the past.

***

"To find the source of energy in these primordial metabolic reactions, the team calculated the amount of free energy – also known as Gibbs energy – released in each reaction.

"What they found was startling. LUCA didn’t need UV light, meteorite impacts, volcanic eruptions or radioactivity to spark the earliest earthly metabolism. Instead, the energy for LUCA’s reactions came from its own metabolism. What that means is that LUCA’s metabolic reactions liberated its own energy, and this probably occurred in an environment much like modern-day, submarine hydrothermal vents.

***

"Hydrogen is crucial in these reactions.

“Without hydrogen, nothing happens at all, because hydrogen is required to get carbon from CO2 incorporated into metabolism in the first place,” says Wimmer.

"So the energy needed to ignite that initial spark of life is really quite simple.

“'We need no sunlight, no meteorites, no UV light, just H2 and CO2, plus some ammonia and salts,” Wimmer says."

Comment: the height of stupidity. How did those 402 processes appear at first? By design? By accident? That an element is present doesn't make it the cause. As with oxygen available for the new Cambrian species its presence allows the process, but is not the cause!!

Theoretical origin of life: identifying basic proteins

by David Turell @, Monday, January 17, 2022, 19:40 (820 days ago) @ David Turell

Metal containing proteins are analyzed finding basic building blocks that theoretically were a basic starting group:

https://www.sciencedaily.com/releases/2022/01/220114153440.htm

"The researchers explored how primitive life may have originated on our planet from simple, non-living materials. They asked what properties define life as we know it and concluded that anything alive would have needed to collect and use energy, from sources such as the Sun or hydrothermal vents.

"In molecular terms, this would mean that the ability to shuffle electrons was paramount to life. Since the best elements for electron transfer are metals (think standard electrical wires) and most biological activities are carried out by proteins, the researchers decided to explore the combination of the two -- that is, proteins that bind metals.

"They compared all existing protein structures that bind metals to establish any common features, based on the premise that these shared features were present in ancestral proteins and were diversified and passed down to create the range of proteins we see today.

"Evolution of protein structures entails understanding how new folds arose from previously existing ones, so the researchers designed a computational method that found the vast majority of currently existing metal-binding proteins are somewhat similar regardless of the type of metal they bind to, the organism they come from or the functionality assigned to the protein as a whole. (my bold)

"'We saw that the metal-binding cores of existing proteins are indeed similar even though the proteins themselves may not be," said the study's lead author Yana Bromberg, a professor in the Department of Biochemistry and Microbiology at Rutgers University-New Brunswick. "We also saw that these metal-binding cores are often made up of repeated substructures, kind of like LEGO blocks. Curiously, these blocks were also found in other regions of the proteins, not just metal-binding cores, and in many other proteins that were not considered in our study. Our observation suggests that rearrangements of these little building blocks may have had a single or a small number of common ancestors and given rise to the whole range of proteins and their functions that are currently available -- that is, to life as we know it.'"

Comment: designing basic starting proteins and building from there is a standard design plan for future development. The bold about one step leading to another is what dhw's complaints always seem to skip or minimize. This is a standard article without mentioning God. For me it shows God's planning at the beginning of life.

Theoretical origin of life: started with hydrogen cyanide

by David Turell @, Tuesday, February 01, 2022, 19:10 (805 days ago) @ David Turell

Another wild lab based theory:

https://www.livescience.com/first-life-on-earth-deadly-poisonous-gas?utm_source=SmartBr...

"Those early life-forms were almost certainly very different from modern-day ones. That's because modern-day life-forms require three macromolecules: DNA, RNA and proteins. Very roughly, our DNA stores information, the RNA transmits that information to manufacture proteins, and the proteins do most of the work of keeping life alive — including replicating DNA.

"This system is so interconnected that it's unlikely that it all appeared at once in its modern form. But primitive life still needed to perform the basic functions of life: store information, replicate itself and catalyze other chemical reactions.

"It's possible that RNA alone is capable of doing all three — definitely not as efficiently as the DNA-RNA-protein combo we have today, but it makes for a plausible starting point for life.

"If RNA can get going as a primitive form of life, then Darwinian evolution can take over, enabling more complex and more efficient biochemical processes to emerge. So perhaps to crack the origins of life on Earth, we just need a lot of self-replicating RNA. But where does the self-replicating RNA come from?

***

"...as the meteorites were delivering fresh supplies of hydrogen to Earth's atmosphere, those volcanoes were spewing tremendous amounts of carbon dioxide. Also, the oceans were much warmer than they are today, and they were constantly evaporating into the atmosphere. Lastly, undersea vents were leaking methane.

"As all those molecules built up in the atmosphere, lightning strikes and ultraviolet radiation from the sun provided the energy to shake things up a bit. In this case, those sources provided the energy necessary to form … hydrogen cyanide.

"That's right, hydrogen cyanide. The poisonous gas that can spell certain death for modern-day life may have been the most important molecule in the development of that same life.

***

"They found that during a 100 million year-long period some 4.4 billion years ago, the amount of hydrogen cyanide raining into ponds was enough to create high concentrations of adenine, one of the components of RNA.

***

"Eventually, as meteorites stopped dropping, the hydrogen levels in the atmosphere fell. But by then, enough adenine may have been created to begin the formation of RNA strands, which may have triggered the exploration of self-replication and the beginning stages of life, the researchers explained.

"If it seems like a lot of steps, it's because it is. Even though these early life-forms would be considered highly primitive from the perspective of modern life, self-replicating and catalyzing RNA strands are already extremely complex molecules, and their appearance necessarily includes a lot of precursor reactions.

"No matter what, something special definitely happened on Earth long ago, and it may have started with hydrogen cyanide."

Comment: One 'possible' tiny step and ignoring all the other steps mentioned in the article, the researchers still hope for a magic introduction of life naturally. So they estimated somehow enough hydrogen cyanide to form adenine, just one minor necessary step and the article is ecstatic

Theoretical origin of life: simple peptides are out there

by David Turell @, Tuesday, March 08, 2022, 22:52 (770 days ago) @ David Turell

And as usual we are starting to know how life appeared naturally; Not!:

https://www.quantamagazine.org/peptides-on-stardust-may-have-provided-a-shortcut-to-lif...

"Last month in Nature Astronomy, a group of astrobiologists showed that peptides, the molecular subunits of proteins, can spontaneously form on the solid, frozen particles of cosmic dust drifting through the universe. Those peptides could in theory have traveled inside comets and meteorites to the young Earth — and to other worlds — to become some of the starting materials for life.

***

{"Whether those peptides could have survived their arduous trek from space and contributed meaningfully to the origin of life is very much an open question. Paul Falkowski, a professor at the School of Environmental and Biological Sciences at Rutgers University, said that the chemistry demonstrated in the new paper is “very cool” but “doesn’t yet bridge the phenomenal gap between proto-prebiotic chemistry and the first evidence of life.” He added, “There’s a spark that’s still missing.”

***

"But before cells existed, there wasn’t an easy way to do it on Earth, Krasnokutski said. Without any of the enzymes that biochemistry provides, the production of peptides is an inefficient two-step process that involves first making amino acids and then removing water as the amino acids link up into chains in a process called polymerization. Both steps have a high energy barrier, so they occur only if large amounts of energy are available to help kick-start the reaction.

***

"In their new paper, Krasnokutski and his colleagues showed that these reactions in the gas clouds would likely lead to the condensation of carbon onto cosmic dust particles and the formation of small molecules called aminoketenes. These aminoketenes would spontaneously link up to form a very simple peptide called polyglycine. By skipping the formation of amino acids, reactions could proceed spontaneously, without needing energy from the environment.

***

"The researchers hypothesized that billions of years ago, as cosmic dust stuck together and formed asteroids and comets, simple peptides on the dust could have hitchhiked to Earth in meteorites and other impactors. They might have done the same on countless other worlds, too.

"The delivery of peptides to Earth and other planets “certainly would provide a head start” to forming life, said Daniel Glavin, an astrobiologist at NASA’s Goddard Space Flight Center. But “I think there’s a large jump to go from interstellar ice dust chemistry to life on Earth.”

"First the peptides would have to endure the perils of their journey through the universe, from radiation to water exposure inside asteroids, both of which can fragment the molecules. Then they’d have to survive the impact of hitting a planet. And even if they made it through all that, they would still have to go through a lot of chemical evolution to get large enough to fold into proteins that are useful for biological chemistry, Glavin said.

"Is there evidence that this has happened? Astrobiologists have discovered many small molecules including amino acids inside meteorites, and one study from 2002 discovered that two meteorites held extremely small, simple peptides made from two amino acids. But researchers have yet to discover other convincing evidence for the presence of such peptides and proteins in meteorites or samples returned from asteroids or comets, Glavin said. It’s unclear if the nearly total absence of even relatively small peptides in space rocks means that they don’t exist or if we just haven’t detected them yet.

***

"The researchers are now planning to test whether bigger peptides or different types of peptides can form in molecular clouds. Other chemicals and energetic photons in the interstellar medium might be able to trigger the formation of larger and more complex molecules, Krasnokutski said. Through their unique laboratory window into molecular clouds, they hope to witness peptides getting longer and longer, and one day folding, like natural origami, into beautiful proteins that burst with potential." (my bold)

Comment: note the bold, lots of grant money based on hope, while ignoring the obvious massive problems pointed out with great reason by James Tour.

Theoretical origin of life: more hype for lab coaxed RNA

by David Turell @, Friday, March 18, 2022, 19:38 (760 days ago) @ David Turell

Very fanciful again:

https://www.sciencealert.com/scientists-have-designed-their-own-evolving-rna-soup-for-t...

"Long before Earth had its first budding cells of primordial ooze, it was awash with a churning organic soup that sat on the brink of something profound. (my bold)

***

Their work shows how a molecule that remains crucial to the survival and reproduction of every living thing today can inch its way towards an evolving system if it works as a team.

"'We found that the single RNA species evolved into a complex replication system: a replicator network comprising five types of RNAs with diverse interactions, supporting the plausibility of a long-envisioned evolutionary transition scenario," says evolutionary biologist Ryo Mizuuchi.

***

"RNA has long been a frontrunner in this search. It's ubiquitous throughout the biosphere today, could have been present on ancient Earth as a result of non-biological processes, can preserve a large amount of information, and act as a dynamic physical unit.

"This means it could potentially make structures that can physically build new molecules that can in turn build new structures. If this process is imperfect, some of the 'replicator' structures will do the job faster or more efficiently than others, becoming the dominant form of RNA ... at least, until something even better comes along.

"As alluring as this idea is, we've known for decades that self-constructed units of individual RNA molecules are just too simple and too unstable for such a scenario. Even its deoxygenated sibling, DNA, lacks the grit to hold itself together long enough for natural selection to get off to a flying start. (my bold)

***

"Mizuuchi's team have cracked the right design of RNA molecules to create individual replicator molecules that can operate collectively to not only preserve information and change over time, but to do so in such a way that the solution becomes more complex over successive generations.

'Their experiment used cloned lengths of RNA in water droplets suspended in oil which underwent more than a hundred rounds of replication, with each round being tested and analyzed. (my bold)

"'Honestly, we initially doubted that such diverse RNAs could evolve and coexist," says Mizuuchi.

"'In evolutionary biology, the 'competitive exclusion principle' states that more than one species cannot coexist if they are competing for the same resources. This means that the molecules must establish a way to use different resources one after another for sustained diversification. They are just molecules, so we wondered if it were possible for nonliving chemical species to spontaneously develop such innovation."

"The proof-of-concept demonstrates this is possible, so long as the RNA don't compete with one another for resources, but rely on one another in a sort of host-parasite manner. If even one RNA replicator is removed, the others go extinct.

While we can be more confident that an 'RNA world' scenario is plausible, it falls short of showing this is how life bloomed on Earth billions of years ago. For that we'd need diverse bodies of evidence, from geology to astrophysics, to build a convincing case.

"Nonetheless, it's a solid step forward in our search for chemical models of evolution that are capable of transforming primordial goop into a dazzling array of biodiversity that continues to become more complex to this very day."

Comment: More pie in the sky. The first bold is a complete lie from the science reporter. Early hot Earth had no or very few organic molecules. They had to come from meteorites, and current arrivals are amino acid poor. The rest is lab design coaxing of molecules fragments they chose from analysis of which fragments might work. We're back to intelligent design. I don't blame the lab so much as I detest the reporter's take.

Theoretical origin of life: deep underground

by David Turell @, Thursday, April 14, 2022, 22:33 (733 days ago) @ David Turell

And early in Earth's origin:

https://www.realclearscience.com/blog/2022/04/12/did_life_start_deep_below_earths_surfa...

G"old, an influential Professor of Astronomy at Cornell University who also nurtured interests in biophysics and geophysics, published a paper, "The Deep, Hot Biosphere," in which he proposed that life may have initially began many kilometers below Earth's surface. Writer Will Hunt summarized Gold's basic contention in his 2019 book Underground:

"'Four billion years ago, Gold pointed out, the surface of the Earth was a war zone. It was being inundated with lava from volcanic eruptions, baked under intense UV rays, and pummeled with a barrage of asteroids. It was extremely improbable, Gold argued, that the original delicate reactions of life... could have occurred amidst such tumult. The subsurface, on the other hand, was stable: no weather, no harsh light, no violent seismic activity."

"According to Gold, the subsurface's warmth, coupled with nutrients both present in rocks and rising in fluids from farther below, provided a fertile ground for nascent microbial life. Over many millions of years, some of these microbes, gently baked inside Earth, migrated upwards, seeding the surface with life.

***

"Thankfully, scientists elected a more enlightened approach to Gold's ideas – they undertook ambitious research probing deeper into the Earth than ever before. While these efforts largely debunked Gold's claim that oil and gas were as old as the Earth, they did turn up lots and lots of life!

"'Overwhelming evidence now supports the presence of a deep biosphere ubiquitously distributed on Earth in both terrestrial and marine settings," a team of scientists wrote in a 2017 paper published in the Proceedings of the National Academy of Sciences.

"Microbes have been found as far as 2.8 kilometers underground, munching on a range of minerals for "food" and generally subsisting at a much slower pace compared to life up above. Some are so different from surface microbes that they've garnered a catchy nickname: "intraterrestrials". Crucially, in regards' to Gold's bold hypotheses that deep microbes could have started life and may exist in the interiors of far-flung planets, scientists have found a bacterium that seems to exist totally independent from Earth's surface. Candidatus Desulforudis audaxviator was found under a deep gold mine in South Africa and exists at temperatures as high as 140 degrees Fahrenheit in the absence of organic compounds, light, and oxygen."

Comment: I added the 2017 material prior to this one. This is a 'where' concept, not a woolly lab approach. I find it reasonable under Gods design.

Theoretical origin of life: no God involved

by David Turell @, Saturday, April 16, 2022, 20:06 (731 days ago) @ David Turell

A very complete essay (4,000 words) of the history of the attempt, with a nod to the lab work:

https://aeon.co/essays/physics-and-information-theory-give-a-glimpse-of-lifes-origins?u...

"...even though experimentalists could show that RNA could act like an enzyme, they typically relied on external enzymes to get the process of replication started. Furthermore, many scientists now think that RNA is so unstable that it couldn’t continue to catalyse reactions and evolve in the extreme temperatures of prebiotic Earth.

***

"Challenges to RNA world are but one indication that scientists are far from a consensus about life’s chemical origins. In fact, the lack of consensus seems to be driving scientists to return to hypothetical beginnings and develop radical new hypotheses.

***

"For Dyson...he likened the former to computer hardware and the latter to software – hardware, he argued, must come first, but both are essential to the machine. Recalling Shannon, Dyson said that the origin of life is the origin of an information-processing system.

***

"David Baum, a botanist and experimental biologist at the University of Wisconsin-Madison, emphasises that in order to understand life’s chemical origins we must do justice to the immense complexity of prebiotic chemical systems. As he explains:

"One of the frustrations for the origins of life field is that people often present it as a single problem, but it’s not. It’s a whole series of separate problems. It wasn’t that life suddenly jumped over this transition from random chemistry to systems with genetics and cells and so forth.

***

"It seems possible to Baum that the laws of the Universe necessarily generate life, but the particularities of how chemicals become living systems remain unpredictable. We might say that the early chemistry of life is full of Shannon information – full of surprises.

***

"In accordance with England’s theory, life forms increase in complexity not only because they are subject to Darwinian evolution, but also, more fundamentally, because they must improve at dissipating energy. According to England: ‘Thinking about evolution in the language of physics allows us to identify new ways by which adaptations can emerge that do not necessarily require a Darwinian mechanism.’

***

"Krakauer shares many of Schrödinger’s views. He thinks that there are many forms of life – that Hamlet, for example, is alive, and that computer viruses and cultural networks might rightly be considered life forms, too. He also thinks that we don’t yet understand the principles of life. I asked Krakauer whether he thought that Schrödinger, in these closing reflections, was a mystic or provocateur or something else. He said that Schrödinger was interested in understanding consciousness and that he wasn’t being mystical with his suggestions. As Krakauer explained: ‘Schrödinger was struggling to find the principles that would unify cultural evolution with organic evolution.’ In short, he, too, was seeking broader principles of life.

***

"When we look at the work in origins of life from the time of Darwin on, we see that the field is astonishingly resilient – perhaps not unlike the emergent life systems that it studies. When it hits a dead end, it spontaneously reconceives of itself. The theoretical frameworks that animate its research have adapted Darwin’s thinking in myriad ways, and now they’re moving beyond Darwin into new theoretical frames.

"These frames make us pay attention to life in different ways. When we recognise the universal ways that matter organises and replicates; when we entertain the possibility that the transmission of information across computational and cultural systems can mark the emergence of life; when we turn to the biosphere as a living system, we begin to look for life in places that often seem inanimate. We look for signs of life in the outer planets or in the interstices of rocks and ice; or we see life replicating in the iterative tapestries of culture. We look for ways that life surprises us. It almost seems as though life emerges precisely when our ideas about it begin to conform to the phenomenon that we are attempting to conceive."

Comment: what is obvious is that all of the biological systems in life must work in coordinated concert, that is irreducibly complex and therefore all must be deigned at once to work together in the simplest bacteria. I've left out a few of the theories. Read the essay for completeness.

Theoretical origin of life:all DNA bases found in meteorites

by David Turell @, Tuesday, April 26, 2022, 18:04 (721 days ago) @ David Turell

Recent find:

https://www.sciencenews.org/article/all-of-the-bases-in-dna-and-rna-have-now-been-found...

"Space rocks that fell to Earth within the last century contain the five bases that store information in DNA and RNA, scientists report April 26 in Nature Communications.

"These “nucleobases” — adenine, guanine, cytosine, thymine and uracil — combine with sugars and phosphates to make up the genetic code of all life on Earth. Whether these basic ingredients for life first came from space or instead formed in a warm soup of earthly chemistry is still not known (SN: 9/24/20). But the discovery adds to evidence that suggests life’s precursors originally came from space, the researchers say. (my bold)

"Scientists have detected bits of adenine, guanine and other organic compounds in meteorites since the 1960s (SN: 8/10/11, SN: 12/4/20). Researchers have also seen hints of uracil, but cytosine and thymine remained elusive, until now.

“'We’ve completed the set of all the bases found in DNA and RNA and life on Earth, and they’re present in meteorites,” says astrochemist Daniel Glavin of NASA’s Goddard Space Flight Center in Greenbelt, Md."

Comment: this is not panspermia, life from space. Life requires 20 essential amino acids. Not all of those have been found. The gap from finding bits of the code to forming an actual code of DNA is obviously enormous, but the writer must insert the hopeful statement I have in bold to stick to the narrative of natural chance, and never God.

Theoretical origin of life: abiotic is impossible

by David Turell @, Monday, May 30, 2022, 15:48 (687 days ago) @ David Turell

The objections:

https://reasonandscience.catsboard.com/t2887-chemical-evolution-of-amino-acids-and-prot...


Chemical evolution of amino acids and proteins? Impossible!!

The amino acids would be concentrated all together at one assembly site.
There would be selected twenty, and not more or less amino acids to make proteins.
Only the best suited would have been selected to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets inside proteins
The amino acids were only in homochiral, that is the left-handed configuration. They would be pure, and without contaminating reactants, somehow avoiding the concomitant synthesis of undesired or irrelevant by-products. They would be able to bond and polymerize by non-enzymatic means, without the ribosome. In each trial, the average protein would be 400 amino acid units in length. 1/3 of all proteins once folded require chaperones, other proteins, that help the protein to fold into its proper, functional shape. They were not required for the first protein folds. Somehow, nature knew how to transition from prebiotic synthesis to cell synthesis of amino acids. A minimum of 112 enzymes is required to synthesize the 20 (+2) amino acids used in proteins. (my bold)

Other problems:

How could ammonia (NH3), the precursor for amino acid synthesis, have accumulated on prebiotic earth, if the lifetime of ammonia would be short because of its photochemical dissociation?
How could prebiotic events have delivered organosulfur compounds required in a few amino acids used in life, if in nature sulfur exists only in its most oxidized form (sulfate or SO4), and only some unique groups of procaryotes mediate the reduction of SO4 to its most reduced state (sulfide or H2S)?
How did unguided stochastic coincidence select the right amongst over 500 that occur naturally on earth? All life on Earth uses the same 20 (genetically encoded) amino acids to construct its proteins even though this represents a small subset of the amino acids available in nature.
How did prebiotic events produce the twenty amino acids used in life? Eight proteinogenic amino acids were never abiotically synthesized under prebiotic conditions.
How did a prebiotic synthesis of biological amino acids avoid the concomitant synthesis of undesired or irrelevant by-products?
How did nature "know how could ammonia (NH3), the precursor for amino acid synthesis, have accumulated on prebiotic earth, if the lifetime of ammonia would be short because of its photochemical dissociation?
How could prebiotic events have delivered organosulfur compounds required in a few amino acids used in life, if in nature sulfur exists only in its most oxidized form (sulfate or SO4), and only some unique groups of procaryotes mediate the reduction of SO4 to its most reduced state (sulfide or H2S)?
chlorophyll requires the complex biosynthesis process of 17 enzymes, lined up in the right order, each producing the substrate used by the next enzyme. But chlorophyll has no function unless inserted in the light-harvesting antenna complex used in photosynthesis to capture light and funnel it to the reaction center. (my bold)
But even if that complex, chlorophyll and the LHC would be fully set up, they have no function without all over 30 protein complexes forming photosynthesis, used to make hydrocarbons, essential for all advanced life forms.
Now, let's suppose all this would assemble by a freaky random accident on early earth, there would still be no mechanisms of transition from a prebiotic assembly, to Cell factory synthesis.

**

Truth said: The information barrier is a problem that CANNOT be solved, and puts all abiogenesis explanations into the realm of SCIENCE FICTION. The ONLY reasonable, logical, and sound inference is that an immensly intelligent, powerful, eternal creator, created a universe, suited to host life, and created life in accordance to his eternal purposes. The fact that we do not know how the interface mind/matter works, says nothing about the possibility/impossibility.

Eliminative inductions argue for the truth of a proposition by arguing that competitors to that proposition are false. Provided the proposition, together with its competitors, form a mutually exclusive and exhaustive class, eliminating all the competitors entails that the proposition is true. Since either there is a God, or not, either one or the other is true. As Sherlock Holmes famous dictum says: when you have eliminated the impossible, whatever remains, however not fully comprehensible, but logically possible, must be the truth. Eliminative inductions, in fact, become deductions. (my bold)


Comment: presented to show that a very intimate knowledge of biochemistry is required to demonstrate the real degree of complexity involved in origin of life. Note the last bold. Doyle and I, as fellow physicians, fully recognize how important this principle is.

Theoretical origin of life: basaltic glass to the fore

by David Turell @, Friday, June 10, 2022, 15:52 (676 days ago) @ David Turell

As a ground powder it makes long stands of RNA:

https://www.sciencemagazinedigital.org/sciencemagazine/10_june_2022/MobilePagedArticle....

"...they show how rocks called basaltic glasses help individual RNA letters, known as nucleoside triphosphates, link into strands up to 200 letters long. The glasses would have been abundant in the fire and brimstone of early Earth; they are created when lava is quenched in air or water or when the melted rock created in asteroid strikes cools off rapidly.

"The result has divided top origin-of-life researchers. “This seems to be a wonderful story that finally explains how the nucleoside triphosphates react with each other to give RNA strands,” says Thomas Carell, a chemist at the Ludwig Maximilian University of Munich. But Jack Szostak, an RNA expert at Harvard University, says he won’t believe the result until the research team better characterizes the RNA strands.

***

"RNA also brings headaches. No one has found a set of plausible prebiotic conditions that would cause hundreds of RNA letters—each of them complex molecules—to link into strands long enough to support the complex chemistry needed to ignite evolution.

"Stephen Mojzsis, a geologist now at the Research Centre for Astronomy and Earth Sciences of the Hungarian Academy of Sciences, wondered whether basaltic glasses played a role. They are rich in metals such as magnesium and iron that promote many chemical reactions. And, he says, “Basaltic glass was everywhere on Earth at the time.”

"He sent samples of five different basaltic glasses to the Foundation for Applied Molecular Evolution. There, Elisa Biondi, a molecular biologist, and her colleagues ground each sample into a fine powder, sterilized it, and mixed it with a solution of nucleoside triphosphates. Without a glass powder present, the RNA letters failed to link up. But when mixed with the glass powders, the molecules joined into long strands, some hundreds of letters long, the researchers report last week in Astrobiology. No heat or light was needed. “All we had to do was wait,” Biondi says. Small RNA strands formed after just a day, but strands kept growing for months. “The beauty of this model is its simplicity,” says Jan Špaček, a molecular biologist at Firebird Biomolecular Sciences. “Mix the ingredients, wait for a few days, and detect the RNA.” (my bolds)

"Still, the results leave questions unanswered. One is how the nucleoside triphosphates could have arisen in the first place. Biondi’s colleague Steven Benner says recent research shows how the same basaltic glasses could have promoted the formation and stabilization of the individual RNA letters.

"A bigger issue, Szostak says, is the shape of the RNA strands. In modern cells, enzymes ensure most RNAs grow into linear chains. But RNA can also bind in complex branching patterns. Szostak wants the researchers to report which type of RNA the basaltic glasses created."(my bold)

Comment: all done by supplying all the ingredients, mixing them properly. On early Earth wha magic genie was present to do this? The usual hopeful intellgent design in a lab!

Theoretical origin of life: available amino acids

by David Turell @, Saturday, June 25, 2022, 17:20 (661 days ago) @ David Turell

Without twenty essential amino acids there would be no life. Where are they? All over the universe in asteroids:

https://www.universetoday.com/156245/samples-of-asteroid-ryugu-contain-more-than-20-ami...

"In 2014, the Japan Aerospace Exploration Agency (JAXA) dispatched its Hayabusa2 spacecraft to rendezvous with 162173 Ryugu, a Near-Earth Asteroid (NEA) that periodically passes close to Earth. In 2018, this sample-return mission reached Ryugu and spent the next year and a half studying its surface and obtaining samples from its surface and subsurface. By 2020, these samples made it back to Earth, where scientists began analyzing them in the hopes of learning more about the early history of the Solar System and answering key questions about the origins of life.

"Earlier this year, the first results of the analysis showed that Ryugu is (as expected) rich in carbon, organic molecules, and volatiles (like water) and hinted at the possibility that it was once a comet. Based on a more recent analysis, eight teams of Japanese researchers (including one from JAXA) recently announced that Ryugu carries strains of no less than 20 different amino acids -the building blocks of DNA and life itself! These findings could provide new insight into how life is distributed throughout the cosmos and could mean that it is more common than previously thought.

"This investigation was launched in 2021 by the JAXA and numerous Japanese research institutions, including the University of Tokyo and Hiroshima University. Initially, the analysis found evidence of 10 types of amino acids, but that number has since grown to 20. Since C-type asteroids are composed of material left over from the formation of the Solar System, the study of these ancient bodies could reveal things about its early history. While samples of asteroids have been found on Earth that contained organic molecules, it is uncertain if this was the result of contamination by Earth’s biosphere.

***

"In the case of the Ryugu samples, scientists have been looking to answer a longstanding question: are C-type asteroids responsible for distributing water and the building blocks of life throughout the Solar System via CC meteorites? Per the Nebula Hypothesis, the planets coalesced ca. 4.5 billion years ago from a disk of gas and dust that settled around the newly-born Sun. One theory suggests that after Earth accreted from this disk, the planet’s surface was in a molten state that would have destroyed any amino acids. Gradually, meteorites reintroduced them to Earth after the surface cooled.

"If this theory is correct, life on Earth emerged thanks to organic material that did not originate here but was introduced by asteroids from the outer Solar System (aka. lithopanspermia). Hiroshi Naraoka, a planetary scientist at Kyushu University and the leader of the team, explained at the Lunar and Planetary Science Conference in March:

***

"Hayabusa2 was groundbreaking in that it collected samples of subsurface materials that were not weathered by sunlight or cosmic rays. Kensei Kobayashi, a professor emeritus of astrobiology at Yokohama National University, also explained how these findings have significant implications for astrobiology. “Proving amino acids exist in the subsurface of asteroids increases the likelihood that the compounds arrived on Earth from space,” he said, adding that this is a possible indication of how “life could have been born in more places in the universe than previously thought.”

"Hayabusa2 is one of a handful of existing or proposed sample-return missions dedicated to investigating the origins of life in the Solar System."

Comment: that amino acids are found all over the place doesn't solve the problem of the origin of life. Life uses precisely twenty specific amino acids, all left-handed. Since the article makes no comment about chirality, I assume the amino acids found were equally right and left-handed. How did life start using only left-handed amino acids? How did it choose before alive?

Theoretical origin of life: Asgard archaea and viruses

by David Turell @, Monday, June 27, 2022, 19:40 (659 days ago) @ David Turell

Makes more sense than the usual intelligent design in a lab:

https://phys.org/news/2022-06-virus-discovery-clues-complex-life.html

"There is a well-supported hypothesis that all complex life forms such as humans, starfish and trees—which feature cells with a nucleus and are called eukaryotes—originated when archaea and bacteria merged to form a hybrid organism. Recent research suggests the first eukaryotes are direct descendants of so-called Asgard archaea. The latest research, by Ian Rambo (a former doctoral student at UT Austin) and other members of Brett Baker's lab, sheds light on how viruses, too, might have played a role in this billions-year-old history.

"'This study is opening a door to better resolving the origin of eukaryotes and understanding the role of viruses in the ecology and evolution of Asgard archaea," Rambo said. "There is a hypothesis that viruses may have contributed to the emergence of complex cellular life."

"Rambo is referring to a hotly debated hypothesis called viral eukaryogenesis. It suggests that, in addition to bacteria and archaea, viruses might have contributed some genetic component to the development of eukaryotes. This latest discovery does not settle that debate, but it does offer some interesting clues.

"The newly discovered viruses that infect currently living Asgard archaea do have some features similar to viruses that infect eukaryotes, including the ability to copy their own DNA and hijack protein modification systems of their hosts. The fact that these recovered Asgard viruses display characteristics of both viruses that infect eukaryotes and prokaryotes, which have cells without a nucleus, makes them unique since they are not exactly like those that infect other archaea or complex life forms.

"'The most exciting thing is they are completely new types of viruses that are different from those that we've seen before in archaea and eukaryotes, infecting our microbial relatives," said Baker, associate professor of marine science and integrative biology and corresponding author of the study.

"The Asgard archaea, which probably evolved more than 2 billion years ago and whose descendents are still living, have been discovered in deep sea sediments and hot springs around the world, but so far only one strain has been successfully grown in the lab. To identify them, scientists collect their genetic material from the environment and then piece together their genomes. In this latest study, the researchers scanned the Asgard genomes for repeating DNA regions known as CRISPR arrays, which contain small pieces of viral DNA that can be precisely matched to viruses that previously infected these microbes. These genetic "fingerprints" allowed them to identify these stealthy viral invaders that infect organisms with key roles in the complex origin story of eukaryotes.

"'We are now starting to understand the implication and role that viruses could have had in the eukaryogenesis puzzle," said Valerie De Anda, a research associate at UT Austin and co-author of the study."

Comment: I know this does not explain origin of life but does help us see the probable role of viruses in guiding evolution.

Theoretical origin of life: deep Earth early oxygen supply

by David Turell @, Monday, August 08, 2022, 18:55 (617 days ago) @ David Turell

A new study of heat and rocks:

https://www.sciencedaily.com/releases/2022/08/220808085900.htm

"Scientists have shown the importance of hot temperatures in maximizing hydrogen peroxide generation from rocks during the movement of geological faults, and say it may have influenced the early evolution, and feasibly even origin, of life in hot environments on the early Earth prior to the evolution of photosynthesis.

***

"The pioneering research project, led by Newcastle University's School of Natural and Environmental Sciences and published today in Nature Communications, uncovered a mechanism that can generate hydrogen peroxide from rocks during the movement of geological faults.

"While in high concentrations hydrogen peroxide can be harmful to life, it can also provide a useful source of oxygen to microbes. This additional source of oxygen may have influenced the early evolution, and feasibly even origin, of life in hot environments on the early Earth prior to the evolution of photosynthesis.

"In tectonically active regions, the movement of the Earth's crust not only generates earthquakes but riddles the subsurface with cracks and fractures lined with highly reactive rock surfaces containing many imperfections, or defects. Water can then filter down and react with these defects on the newly fractured rock.

"In the laboratory, Masters student Jordan Stone simulated these conditions by crushing granite, basalt and peridotite -- rock types that would have been present in the early Earth's crust. These were then added to water under well controlled oxygen-free conditions at varying temperatures.

"The experiments demonstrated that substantial amounts of hydrogen peroxide -- and as a result, potentially oxygen -- was only generated at temperatures close to the boiling point of water. Importantly, the temperature of hydrogen peroxide formation overlaps the growth ranges of some of the most heat-loving microbes on Earth called hyperthermophiles, including evolutionary ancient oxygen-using microbes near the root of the Universal Tree of Life.

"Lead author Jordan Stone, who conducted this research as part of his MRes in Environmental Geoscience, said: "While previous research has suggested that small amounts of hydrogen peroxide and other oxidants can be formed by stressing or crushing of rocks in the absence of oxygen, this is the first study to show the vital importance of hot temperatures in maximising hydrogen peroxide generation.'"

Comment: we know the deep Earth contains extremophiles from deep core studies in mines and under the oceans. This adds to the possibilities of how life started beside deep sea hot vents theory

Theoretical origin of life: deep ocean vents extremophiles

by David Turell @, Thursday, August 25, 2022, 23:49 (600 days ago) @ David Turell

Home to strange life:

https://www.sciencealert.com/theres-a-lost-city-deep-in-the-ocean-and-its-a-place-unlik...

"Discovered by scientists in 2000, more than 700 meters (2,300 feet) beneath the surface, the Lost City Hydrothermal Field is the longest-lived venting environment known in the ocean. Nothing else like it has ever been found.

"For at least 120,000 years and maybe longer, the upthrusting mantle in this part of the world has reacted with seawater to puff hydrogen, methane, and other dissolved gases out into the ocean.

"In the cracks and crevices of the field's vents, hydrocarbons feed novel microbial communities even without the presence of oxygen.

"Chimneys spewing gases as hot as 40 °C (104 °F) are home to an abundance of snails and crustaceans. Larger animals such as crabs, shrimp, sea urchins and eels are rare, but still present.

"Despite the extreme nature of the environment, it appears to be teeming with life, and some researchers think it's worth our attention and protection.

"While other hydrothermal fields like this one probably exist elsewhere in the world's oceans, this is the only one remotely operated vehicles have been able to find thus far.

"The hydrocarbons produced by the Lost City's vents were not formed from atmospheric carbon dioxide or sunlight, but by chemical reactions on the deep seafloor.

"Because hydrocarbons are the building blocks of life, this leaves open the possibility that life originated in a habitat just like this one. And not just on our own planet.

***

Unfortunately, scientists aren't the only ones beckoned by that unusual terrain.

"In 2018, it was announced that Poland had won the rights to mine the deep sea around The Lost City. While there are no precious resources to be dredged up in the actual thermal field itself, the destruction of the city's surroundings could have unintended consequences.

"Any plumes or discharges, triggered by the mining, could easily wash over the remarkable habitat, scientists warn.

"Some experts are therefore calling for the Lost City to be listed as a World Heritage site, to protect the natural wonder before it's too late.

"For tens of thousands of years, the Lost City has stood as a testament to the enduring force of life.

"It would be just like us to ruin it."

Comment: Please hands off

Theoretical origin of life: needed chemicals rare

by David Turell @, Saturday, September 03, 2022, 19:53 (591 days ago) @ David Turell

What is found in our universe is extremely low levels of possible precursors:

https://reasons.org/explore/blogs/todays-new-reason-to-believe/have-astronomers-found-l...

"For at least five decades, proponents of a naturalistic origin of life have been searching for evidence of the RNA world hypothesis. The RNA world is a proposed step in the evolution of life on Earth in which self-replicating RNA molecules preceded genetic material and proteins. Life on Earth appeared suddenly about 3.8 billion years ago. However, evidence for organic molecules that could possibly give rise to RNA is lacking on Earth; thus, astrobiologists believe the building blocks of life must reside in interstellar space.

***

"One of chemistry’s great enigmas is that nitriles are key precursor molecules of the nucleobases, which when joined to a ribose and a phosphate molecule comprise the fundamental building blocks of RNA and DNA molecules. RNA molecules together with DNA molecules, proteins, and lipids are the molecules every organism possesses and without which no life-form can possibly survive.

***

"Rivilla’s team detected the following four nitriles: cyanic acid, cyanoallene, propargyl cyanide, and cyanopropyne. They achieved tentative detections of cyanoformaldehyde and glycolonitrile. They did not detect cyanoacetaldehyde. Cyanoallene and propargyl cyanide had been previously detected in the TMC-1 dark molecular cloud, which, at a distance of only 140 light-years is the nearest large molecular interstellar cloud. The simplest oxygen-bearing nitrile, cyanic acid, was also previously detected in another giant molecular cloud at the galactic center.

"The measured abundance levels for the detected nitriles were very low. Even the simplest one, cyanic acid (HOCN), measured rare. Rivilla’s team determined that in G+0.693-0.027 there is only one molecule of cyanic acid for every 6 billion molecules of molecular hydrogen (H2). The three non-oxygen-bearing nitriles detected by Rivilla and his colleagues were measured, in each case, at one molecule for every 6–10 billion H2 molecules.

"The British newspaper, The Telegraph, in the headline of their report on the Rivilla team’s discoveries stated that the “building blocks of life” found by the team “suggests we are not alone.” One of Rivilla’s coauthors, Miguel Requena-Torres, was quoted as saying to Sarah Knapton, science editor for The Telegraph, “We now know that nitriles are among the most abundant chemical families in the universe.” By “chemical families,” Requena-Torres had to be referring to precursor molecules for nucleobases and amino acids. Another coauthor, Izaskun Jiménez-Serra, referring to such precursor molecules, said “There are still key missing molecules.”

"In the conclusion to their paper, Rivilla’s team noted that nitriles are not a direct precursor to either nucleobases or amino acids. The early Earth’s atmosphere would need to have been chemically reducing and must have contained high amounts of ammonia for amidines to possibly form from nitriles. Several amidines are direct precursors for nucleobases and amino acids. However, as we explained and documented in our book Origins of Life, Earth’s early atmosphere was neither reducing nor did it contain more than a trace amount of ammonia.

"What Ravilla’s team found were a few of the hundred-plus molecules that are the “building blocks of the building blocks of the building blocks” of life molecules. They found them at abundance levels far below what is needed for any conceivable naturalistic model for life’s origin. And they found them in an interstellar molecular cloud where the chemical reactions that produce them are counterbalanced by chemical reactions that destroy them.

"Thus, Ravilla’s team’s detections do not, as they claim, provide support for the RNA world hypothesis for the origin of life. Rather, their detections provide additional confirmation for what Fazale Rana and I heard Leslie Orgel, the father of the RNA world hypothesis, say in the opening plenary session message at the 2002 International Society for the Study of the Origin of Life conference, “It would be a miracle if a strand of RNA ever appeared on the primitive Earth.” (my bold)

Comment: the usual hype that solving the origin of life is right around the corner is dismissed by Hugh Ross. We should all listen to Leslie Orgel.

Theoretical origin of life: more lab designs for RNA

by David Turell @, Wednesday, September 14, 2022, 21:58 (580 days ago) @ David Turell

Intelligent design at work in the lab:


https://phys.org/news/2022-09-life-rna-pocket.html

"As to the primordial peptide-bond-making machine, they discovered that it's still present in virtually every cell of all living organisms, from bacteria to plants and animals, including ourselves.

***

"'We discovered a surprising feature in the structure of this protein-making machine," says Dr. Anat Bashan, a senior staff scientist in Yonath's lab in Weizmann's Chemical and Structural Biology Department. "The ribosome is an enormous macromolecule that is not at all symmetrical; at its heart, it contains two semisymmetrical elements joined together to form a pocket."

"Yonath says that they "were particularly struck by the fact that this pocket is found in the ribosomes of all organisms. And this is where all the action takes place—it's where all peptide bonds that create the chain of linked amino acids making up a protein are formed. That's why this basic machinery seems to have persisted unchanged throughout evolution."

"Meet the protoribosome: That's what the scientists call this pocket-like structure. They hypothesized that the protoribosome is the ancestor of all modern ribosomes, an ancient machine dating back to the prelife period. In comparison to the size of the cell, the protoribosome is rather small. It consists of RNA molecules comprising some 120 nucleotides, about 60 for each of its two semisymmetrical components, which accounts for less than 5 percent of the modern ribosome's dimensions: some 4,500 nucleotides in bacteria and nearly 6,000 in humans.

***

"The protoribosome came about when a bunch of RNA nucleotide chains self-assembled into two semisymmetrical walls hooked up to create a pocket. Endless other structures must have accidentally self-assembled around the same time, but the protoribosome survived, "going viral," it seems, because it performed useful functions and, thanks to RNA's intrinsic capabilities, it could self-replicate.

"When two activated amino acids happened to interact with one another within this pocket, they formed a bond, facilitated by the prevailing chemical conditions. Those amino acids may have arisen on Earth or, as some argue, landed with asteroids from outer space, but their origin is irrelevant to our story. What matters is that within the protoribosome, two activated amino acids could bind to each other. Later on, such bond making united many more amino acids, linking them into a chain.

***

"To the team's delight, the synthetic protoribosomes created in the lab rose to the task. "Peptide bond formation is the most vital activity in any cell, and we've shown that it can take place within a protoribosome," Bose says.

"'The proposed protoribosome might be the missing link between an RNA-dominated world—one that may have existed before proteins and DNA appeared—and life that is based on proteins and nucleic acids, as we know it today," Bashan says."

Comment: all protein function is based on the proper series/sequence of amino acids and its special folded shape. Also, they are describing molecules with thousands of amino acids that must be in a correct position to function. This is the usual fairy tale of chance development shown by intelligent design in the lab.

Theoretical origin of life: in droplets of water

by David Turell @, Monday, October 03, 2022, 23:49 (561 days ago) @ David Turell

Carefully studied water droplets in a lab:

https://phys.org/news/2022-10-fountain-life-droplets-secret-ingredient.html

"'This is essentially the chemistry behind the origin of life," said Graham Cooks, the Henry Bohn Hass Distinguished Professor of Analytical Chemistry in Purdue's College of Science."This is the first demonstration that primordial molecules, simple amino acids, spontaneously form peptides, the building blocks of life, in droplets of pure water. This is a dramatic discovery."

***

"For decades scientists have theorized that life on Earth began in the oceans. The chemistry, however, remained an enigma. Raw amino acids—something that meteorites delivered to early Earth daily—can react and latch together to form peptides, the building blocks of proteins and, eventually, life. Puzzlingly, the process requires the loss of a water molecule, which seems highly unlikely in a wet, aqueous or oceanic environment. For life to form, it needed water. But it also needed space away from the water.

"Cooks, an expert in mass spectrometry and early Earth chemistry, and his team have uncovered the answer to the riddle: "Water isn't wet everywhere." On the margins, where the water droplet meets the atmosphere, incredibly rapid reactions can take place, transforming abiotic amino acids into the building blocks of life. Places where sea spray flies into the air and waves pound the land, or where fresh water burbles down a slope, were fertile landscapes for life's potential evolution.

"The chemists have spent more than 10 years using mass spectrometers to study chemical reactions in droplets containing water.

"'The rates of reactions in droplets are anywhere from a hundred to a million times faster than the same chemicals reacting in bulk solution," Cooks said.

"The rates of these reactions make catalysts unnecessary, speeding up the reactions and, in the case of early Earth chemistry, making the evolution of life possible. Understanding how this process works has been the goal of decades of scientific research. The secret of how life arose on Earth can help scientists understand why it happened and inform the search for life on other planets, or even moons.

"Understanding how amino acids built themselves up into proteins and, eventually, life-forms revolutionizes scientists' understanding of chemical synthesis. That same chemistry could now aid synthetic chemists in speeding the reactions critical to discovering and developing new drugs and therapeutic treatments for diseases.

"'If you walk through an academic campus at night, the buildings with the lights on are where synthetic chemists are working," Cooks said. "Their experiments are so slow that they run for days or weeks at a time. This isn't necessary, and using droplet chemistry, we have built an apparatus, which is being used at Purdue now, to speed up the synthesis of novel chemicals and potential new drugs.'"

Comment: this may be a great advance for organic chemists, butn the places where droplets appear natrually are in highly active regions of water movement as the article notes. Not like Darwin's warm pond. Start of life is much more complex than this single finding. Just more hype.

Theoretical origin of life: from meteorites

by David Turell @, Thursday, December 08, 2022, 16:03 (495 days ago) @ David Turell

Same old story known in the Murchison mee=teorite in Australia:

https://www.livescience.com/radioactive-meteorites-seeded-life-on-earth?utm_term=C3CFD6...

"A special type of radioactive meteorite could have seeded life on Earth, a new study found.

Carbonaceous chondrites, a type of radioactive meteorite chock full of water and organic compounds, produce energetic gamma rays that can drive the chemical reactions to synthesize amino acids — the building blocks of life — researchers discovered.

***

"...the researchers mixed ammonia, methanol and formaldehyde into water in quantities similar to those found inside meteorites. Then, to see if the radioactive, gamma-ray producing elements such as aluminum-26 inside the meteorites could generate the heat needed for amino acid synthesis, the researchers irradiated their mixture with gamma rays from an analog isotope called cobalt-60.

"Sure enough, the scientists found that the gamma-ray bombardment caused a spike in the production of amino acids inside the solution. Higher gamma-ray production increased the rate of amino acid synthesis. Additionally, the researchers discovered that the proportions of lab-produced amino acids matched those found in the Murchison meteorite — a 2205-pound (100 kilograms) space rock that landed in Australia in 1969. Further analysis revealed that it would have taken anywhere from 1,000 to 100,000 years to produce the amino acid quantities found inside the Murchison meteorite."

Comment: the usual empty thoughtless hope for a quick start to life. Amino acids just lying around don't simply jump together to make life. The requirements are hopelessly complex

Theoretical origin of life: wet/dry polymerization

by David Turell @, Monday, December 26, 2022, 15:15 (477 days ago) @ David Turell

Man-made experiments:

https://www.sciencealert.com/frequent-dry-spells-could-have-been-essential-for-life-to-...

"Water, for instance, seems like an essential component of life from the very start. Yet the process of growing some of life's most vital components has a frustrating aversion to getting wet.

"'We know amino acids are the building blocks of proteins and proteins are essential for life," says University of Wisconsin–Madison biochemical engineer John Yin.

"'In prebiotic chemistry, it's long been a question of how we could get these things to form bonds and strings in a manner that might eventually lead to a living cell. The question is hard because the particular chemistry involved is one that tends to fail in the presence of water."

***

"Boigenzahn's team combined a selection of amino acids which have proven quite easy to produce naturally. As the building-blocks of proteins – units that can perform the mechanical work of living processes – the resulting structures are a sound bet for playing a major role in early forms of biology.

"Unfortunately, getting those units to link together into longer chains is something of a challenge. In this case, the researchers used the amino acid glycine.

"Then they added trimetaphosphate into their soup, a molecule naturally produced in volcanoes.

"Finally, the soup was spiced with sodium hydroxide (NaOH) to increase its pH.

"Lo and behold, during the first hour of the experiment, glycine coupled up to make a two unit molecule called a dimer. This reaction releases protons that in turn neutralize the pH required for the dimerization to take place, effectively putting the brakes on the whole process.

"As found in previous research, as the solution's pH became more neutral the dimers slowly started to link with each other into slightly longer chains. As the solution dried out, however, the reaction rate increased, possibly due to concentrations of the molecules crowding closer together, the team suspects.

"'What we're showing here is that it doesn't necessarily have to be the same environment throughout all the reactions," says Boigenzahn. "They can occur in different environments, provided that the reactions that are occurring help create an environment that's beneficial for the next steps."

***

"This is not the first clue that the origins of life may have occurred at the edge of wetness either. Earlier this year chemists found free floating amino acids were more reactive at the air-water boundary of tiny droplets. What's more, these reactions happened in normal environmental conditions without the need of other chemicals or radiation.

"There's still a long way to go before understanding all that's involved, but making sense of the processes behind the creation of life could also open the door to new, more powerful chemistry-based technologies.

"Eventually you might create chemical systems that are able to store information, adapt and evolve," says Yin. (my bold)

"'DNA stores information at thousands of times the density of a computer chip can. If we could get systems that do this without necessarily being living cells, then you start to think about all sorts of new functions and processes occurring at the molecular level.'"

Comment: the usual hopeful study guided by mental activity. All steps were planned to avoid known problems. Note my bold. What information is there to be stored? Descriptivev or instructions as in DNA?

Theoretical origin of life: terrible chemistry presented

by David Turell @, Sunday, January 15, 2023, 21:54 (457 days ago) @ David Turell

James Tour plus one to the battle lines:

https://inference-review.com/letter/a-storm-in-a-primordial-teacup

"In a recent review, James Tour wrote that Eddy Jiménez et al., in a study on the chemical origins of life, made “bold claims” about the significance of their work.1 Tour claimed that their experimental approach is “unconscionable” and stated that “rather than leading to any sort of chemical model, the research serves only to underscore how this particular approach is unlikely to yield any clues about how life emerged.”

"Tour does not take exception to the chemistry; rather he is scathing about the ramifications of this study for understanding the origin of life. He picks up on five areas he believes are shortcomings that, furthermore, epitomize many studies on the origin of life:

"The inability of the study to explain the prebiotic source of homochiral precursors such as 2′-deoxyribonucleoside.
The high concentrations used in the laboratory studies—that is to say “how might starting materials become available in sufficiently high yields and undiluted by the oceans.”

"The use of a specific precursor, namely DAP, which according to Tour “has become so ubiquitous in origins of life (OOL) research that it is now simply accepted as being prebiotically relevant.”

"The lack of explanation for how the desired reactions managed to occur without competing compounds, which in this case are other nucleophiles.

"The inability to dispose of unwanted and undesirable chemical products—here, a deleterious 2′, 5′-linkage.

Are Tour’s claims valid, or is he on the verge of insanity?

"If Tour is insane, then I will offer to join him at the asylum check-in. I find exactly the same assumptions at play in my own area of research, namely lipids, and in the potential roles that lipids may have played in the origin of life and in the formation of the first protocell. To illustrate the similarities with the issues raised by Tour, I will briefly consider a study published in 2019 by Luping Liu et al., from the laboratory of Neal Devaraj, entitled “Enzyme-Free Synthesis of Natural Phospholipids in Water.”3 The claims made by Devaraj et al. might actually be stronger than those made by Jiménez, inasmuch as Devaraj states, “This high-yielding non-enzymatic synthesis of natural phospholipids in water … sheds light on the origin and evolution of cellular membranes.” All five of the issues raised by Tour can be seen in this study:

"The authors do not consider chirality.

"The study uses high concentrations of precursors, in the millimolar range, without ever discussing how such high concentrations could have been generated prebiotically.

"The study also uses a specific precursor, in this case an acyl thioester, suggested to be “obtained using prebiotically relevant condensing agents such as dicyandiamid.”

"Competing compounds are barely considered.

"The authors essentially ignore the effect of unwanted chemical reactions that might produce products that would interfere with the required reaction.

"it is the “Results and Discussion” section that gives away the game. I can do no better than quote the authors, who state,

"We further attempted to obtain various diacylphospholipids such as phosphatidylethanolamine, phosphatidylserine and phosphatidylglycerol by oleoylating the corresponding lysophospholipids; however, the reactivity of [the] acylation reagent is insufficient for these lysolipids and no considerable yields of the desired diacylphospholipids were achieved.
In other words, the conditions selected for the enzyme-free synthesis of phospholipids only works with one specific lysolipid precursor. But it gets worse. While the authors did not consider the presumably deleterious role of side-products that would have accumulated during the reactions, the addition of other lipids, such as sodium dodecyl sulfate, almost completely inhibited the acylation reaction even using the one lipid precursor that had worked previously—i.e., lysophosphatidylcholine—such that the yield dropped to less than 10%. Presumably, the inclusion of other lipids or chemical side-products would similarly inhibit the transacylation reaction.

***

"Just as the Jiménez et al. paper seems to be much ado about nothing, I would argue, agreeing with Tour, that many similar articles about the origin of life do not actually explain anything. Admittedly, careful choice of conditions, whether realistic or not for prebiotic scenarios, demonstrates that certain reactions and pathways might conceivably occur. But when considering the kind of issues raised by Tour, and raised herein, it might be more realistic, and humble, to tone down widely publicized claims that researchers understand the chemical reactions and pathways that result in the emergence of life."

Comment: any followers of this website know my feelings that the research is awful and over- hyped. I stand fully with this article. Grant committees need their heads examined.

Theoretical origin of life: organic chemicals in space

by David Turell @, Saturday, January 28, 2023, 19:13 (444 days ago) @ David Turell

A constant barrage of hopeful comments about the origin of life:

https://www.sciencealert.com/jwst-has-found-lifes-elemental-building-blocks-in-the-dept...

"JWST's unparalleled ability to peer into the shrouded hearts of distant clouds has revealed the elements of biochemistry in the coldest and darkest place we've seen them yet.

"In a molecular cloud called Chamaeleon I, located over 500 light-years from Earth, data from the telescope has revealed the presence of frozen carbon, hydrogen, oxygen, nitrogen, and sulfur – elements vital to the formation of atmospheres and molecules such as amino acids, collectively known as CHONS.

"'These elements are important components of prebiotic molecules such as simple amino acids – and thus ingredients of life, so to speak," says astronomer Maria Drozdovskaya of the University of Bern in Germany.

"In addition, an international team of researchers led by astronomer Melissa McClure of Leiden University in the Netherlands has also identified frozen forms of more complex molecules, such as water, methane, ammonia, carbonyl sulfide, and the organic molecule methanol.

"Cold, dense clumps in molecular clouds are where stars and their planets are born. Scientists believe that CHONS and other molecules were present in the molecular cloud that birthed the Sun, some of which were later delivered to Earth via icy comet and asteroid impacts.

"Although the elements and molecules detected in Chamaeleon I are quietly floating about right now, one day, they could be caught up in planet formation, delivering the ingredients necessary for the emergence of life to new baby planets.

"'Our identification of complex organic molecules, like methanol and potentially ethanol, also suggests that the many star and planet systems developing in this particular cloud will inherit molecules in a fairly advanced chemical state," explains astronomer Will Rocha of Leiden Observatory.

"'could mean that the presence of prebiotic molecules in planetary systems is a common result of star formation rather than a unique feature of our own Solar System.'"

Comment: every time these molecules are noted they raise excitement about life. Followers here know those molecules are all over the universe.

Theoretical origin of life: more lab designed work

by David Turell @, Friday, February 10, 2023, 19:12 (431 days ago) @ David Turell

always making the early molecules of life appear easil y:

https://phys.org/news/2023-02-lifea-abiotic-pathway-formation-peptide.html

"'Two scenarios are being discussed for the emergence of life on Earth: On the one hand, the first-time creation of such amino acid chains on Earth, and on the other hand, the influx from space," explains Tilmann Märk from the Department of Ion Physics and Applied Physics. of the University of Innsbruck. "For the latter, such amino acid chains would have to be generated in the very unfavorable and inhospitable conditions in space."

"A team of researchers led by Michel Farizon from the University of Lyon and Tilmann Märk has now made a significant discovery in the field of abiotic peptide chain formation from amino acids for the smallest occurring amino acid, glycine, a molecule that has been observed several times extraterrestrially in recent years.

"A study published in the Journal of Physical Chemistry A, which also made the cover of the journal, shows that small clusters of glycine molecules exhibit polymerization upon energy input. A reaction occurs within a cluster consisting of two glycine molecules. The two amino acids become a dipeptide and a water molecule. The reaction of a dipeptide to a tripeptide within a cluster was also demonstrated by the researchers.

"'Our study sheds light on the less likely unimolecular scenario for the formation of such amino acid chains in the extreme conditions of space," says Michel Farizon. "We were able to show that peptide chain growth occurs through unimolecular reactions in excited cluster ions, without the need for contact with an additional partner such as dust or ice."

"The recent paper provides evidence that the first step toward the origin of life can occur in the highly unlikely conditions of space. "The study is an important milestone on the route to understanding the origins of life. The results will serve as a basis for further research in this field," Michel Farizon and Tilmann Märk are convinced."

Comment: two major problems. The lab must supply all left-handed all amino acids which are m
mixed equqlly with right-handed in space. And the finding of one of the necessary molecules still doesn't tell much about how the mixture was all produded to to make life.

Theoretical origin of life: a plea or less guesswork

by David Turell @, Saturday, February 11, 2023, 20:25 (430 days ago) @ David Turell

Based on studies of early Earth:

https://phys.org/news/2023-02-life.html

"But what was Earth like billions of years ago, and what characteristics may have helped life to form? In a paper published in Science, Trail and Thomas McCollom, a research associate at the University of Colorado Boulder, reveal key information in the quest to find out. The research has important implications not only for discovering the origins of life but also in the search for life on other planets.

***

"Research into life and its origins typically involves a variety of disciplines including genomics, the study of genes and their functions; proteomics, the study of proteins; and an emerging field called metallomics, which explores the important role of metals in performing cellular functions. As life evolved, the need for certain metals changed, but Trail and McCollom wanted to determine what metals may have been available when microbes first appeared billions of years ago.

"'When hypotheses are proposed for different origin-of-life scenarios, scientists have generally assumed all metals were available because there weren't studies that provided geologically robust constraints on metal concentrations of fluids for the earliest times of Earth's history," Trail says.

"To address this shortcoming, Trail and McCollom studied the composition and characteristics of fluids in the lithosphere—the outer layer of Earth that includes the crust and upper mantle—billions of years ago. These lithospheric fluids are key pathways to transport dissolved parts of rocks and minerals between Earth's interior and hydrothermal pools in its exterior where microbial life could have formed. While researchers cannot directly measure the metals that existed billions of years ago, by determining the properties of the fluids, they can infer what metals—and the concentrations of the metals—could feasibly have been transported between Earth's interior and exterior during the time when life emerged on the planet.

***

"The researchers conducted high-pressure, high-temperature experiments and applied these results to early-Earth zircons, a robust type of mineral collected at sites in Western Australia, to determine the oxygen pressure, chlorine content, and temperature of lithospheric fluids billions of years ago. They then input this information into computer models. The models allowed them to simulate the properties of the lithospheric fluids, and, in turn, simulate which metals could have travelled through the fluids to reach hydrothermal pools at Earth's surface.

"The researchers were surprised by what the model simulations indicated. Many origin-of-life researchers, for instance, consider copper a likely component in the chemistry that could have led to life. But Trail and McCollom did not find evidence that copper would have been abundant under the constraints in their analysis.

"One metal they did test that may have been available in high concentrations was manganese. While it is rarely considered in origin-of-life scenarios, today manganese helps the body form bones and assists enzymes in breaking down carbohydrates and cholesterol.

"'Our research shows that metals like manganese may function as important links between the 'solid' Earth and emerging biological systems at Earth's surface," Trail says."

Comment: at last, a solid practical approach to real initial conditions

Theoretical origin of life: a very different approach

by David Turell @, Monday, March 06, 2023, 15:00 (407 days ago) @ David Turell

Ocean hydrothermal vents are absolutely the spot:

https://aeon.co/essays/why-life-is-not-a-thing-but-a-restless-manner-of-being?utm_sourc...

"For decades, most origin-of-life research has focused on how such self-replicating chemistry could have arisen. They largely brushed aside the other key question, how the first living things obtained the energy to grow, reproduce and evolve to greater complexity.

***

"within modern organisms there is another clue to life’s origins, one that is more obscure than DNA but just as universal – the way cells harvest energy by shuffling around electrically charged molecules. This process goes by the mouthful ‘chemiosmosis’, and was first proposed in 1961 by the eccentric British biochemist Peter Mitchell. Chemiosmosis lacks the coded rigour of DNA, but that primal messiness might be exactly what makes it so revealing.

"Energy, Russell thinks, must have preceded anything resembling DNA or RNA, so the origin of chemiosmosis could help to reveal how the first organisms arose. Chemiosmosis takes place deep in our body’s cells, most of which harbour hundreds or thousands of microscopic structures called mitochondria. The mitochondria extract the chemical energy from food and, with the help of the oxygen we breathe, convert it into a molecule called adenosine triphosphate (ATP). Just as much as DNA, ATP is the molecule of life; it is the currency we spend to grow, move or think.

"No replication-focused origin-of-life theory has yet provided good explanation for the parallel origin of the elaborate machinery of chemiosmosis.

***

"From Martin’s perspective , it made perfect sense that chemiosmosis came first, before RNA. ‘When you look at a group of organisms – in this case all life as we know it – and there is a property that is present in all forms, you put this property in the common ancestor. And that common property is harnessing an ion gradient,’ he says.

***

"The expanded chemical garden hypothesis addressed another key question about the origin of life: how molecular building blocks become concentrated enough to react and link up with each other. Russell predicted there would be a temperature gradient across ocean-vent rocks – cool on the outside, warm on the inside. That gradient would have promoted a convective process called thermophoresis, which traps larger organic molecules in the compartments, encouraging the formation of sugars, amino acids, lipids and nucleotides – the building blocks of life. At the intense temperature and pressure of the deep sea, such building blocks inevitably began to link up, forming larger and more intricate molecules.

***

"Over the next 15 years, more data began to pile up in support of life’s origin in a chemical garden. In one major change, most researchers are now convinced that life’s universal ancestor was an autotroph – meaning it made its own food from inorganic matter – just as Russell and Martin had predicted. A 2015 genomic study provided the most convincing evidence to date. An analysis of nearly 40 genes strongly suggested that the most ancient microbes generated methane from carbon dioxide and hydrogen. This analysis dovetails with geological work showing that methane formed by biological processes is the earliest organic compound found in ancient rocks.

***

"...past the half-mile mark on the depth gauge. Suddenly, the vehicle’s lamps illuminated something utterly unexpected: a cluster of otherworldly pinnacles rising from the ocean floor, as tall as 20-storey buildings. Shimmering plumes of heated water billowed from their tops like smoke from chimneys. This strange landscape turned out to host an exotic ecosystem of snails, crabs, worms and shellfish, sustained by microbes that convert raw elements from the inner Earth into life without any help from the Sun. This field of hydrothermal vents, dubbed the Lost City, conformed almost exactly to Russell’s 1983 predictions. His chemical gardens had been found.

***

"Over the next 15 years, more data began to pile up in support of life’s origin in a chemical garden. In one major change, most researchers are now convinced that life’s universal ancestor was an autotroph – meaning it made its own food from inorganic matter – just as Russell and Martin had predicted. A 2015 genomic study provided the most convincing evidence to date. An analysis of nearly 40 genes strongly suggested that the most ancient microbes generated methane from carbon dioxide and hydrogen. This analysis dovetails with geological work showing that methane formed by biological processes is the earliest organic compound found in ancient rocks.

***

"Without energy gradients, even if all the right ingredients are in the right place for an RNA world, life cannot just appear. The implication is that biological information systems – the codes needed for life to reproduce – cannot just spring into existence. ‘The key to the beginning of living systems is to generate this energy storage conformation system, and to use the same energy machine to build the storage of information through DNA and RNA,’ Karsenti explained. ‘I would say energy came first.'’ (my bold)

Comment: An important new view of how to look at the problem. Note the bold. A just-so story of how deeply complex genetic information just falls into place.

Theoretical origin of life: a very different approach

by David Turell @, Monday, March 06, 2023, 16:02 (407 days ago) @ David Turell

Another different approach with evolving amino acid supply:

https://www.sciencealert.com/evolution-could-predate-life-itself-protein-discovery-sugg...

"Together, amino acids form proteins that play many vital roles in organisms. This new study was designed to help establish why a specific group of 20 'canonical' amino acids is used again and again to build proteins when there are so many more of these amino acids to pick from.

"It's thought that these 20 amino acids are made up of 10 'early' ones picked from the atmosphere and meteorite fragments of early Earth, and 10 'later' ones added on top – but what the selection process for the latter 10 involved isn't clear.

"You see the same amino acids in every organism, from humans to bacteria to archaea, and that's because all things on Earth are connected through this tree of life that has an origin, an organism that was the ancestor to all living things," says chemist Stephen Fried, from Johns Hopkins University in Maryland. "We're describing the events that shaped why that ancestor got the amino acids that it did."

"Through a reconstruction of primordial protein synthesis, the researchers showed that ancient organic compounds would have favored the amino acids best at folding proteins, tailoring them for specific functions.

"In other words, a process of evolution or natural selection was underway even at this stage: it wasn't the amino acids that were most readily available that were picked, but the amino acids most suited to a particular job.

"If other amino acids had been selected as part of the core group billions of years ago, the scientists determined that the very building blocks of life would not have been as efficient at doing that life-building.

"'Protein folding was basically allowing us to do evolution before there was even life on our planet," says Fried. "You could have evolution before you had biology, you could have natural selection for the chemicals that are useful for life even before there was DNA."

"Molecules, including proteins, are thought to have started putting together simple organisms some 3.8 billion years ago, so there's a stretch of earlier Earth history that scientists have been very keen to look into.

"The team behind the study suggests that the 10 'later' amino acids, in particular, were selected for their protein-folding capabilities, enabling the replication of DNA and the production of proteins that sparked life into being.

Comment: stringing amino acids together into information-containing polymers is chemically difficult and must involve immaterial input in making the information guiding the process. The limited number of amino acids used in life may well to have been limited by supply, as the article proposes. What is ignored as usual is chirality. Life uses 20 left-handed amino acids only. Naturally formed amino acids are an even fifty-fifty right or left. Why did life make a defninte choice?

Theoretical origin of life: a very different approach

by David Turell @, Friday, March 10, 2023, 19:37 (403 days ago) @ David Turell

A new molecule is suggested:

https://phys.org/news/2023-03-scientists-substance-life-earth.html

"A team of Rutgers scientists dedicated to pinpointing the primordial origins of metabolism—a set of core chemical reactions that first powered life on Earth—has identified part of a protein that could provide scientists clues to detecting planets on the verge of producing life.

***

"Based on laboratory studies, Rutgers scientists say one of the most likely chemical candidates that kickstarted life was a simple peptide with two nickel atoms they are calling "Nickelback" not because it has anything to do with the Canadian rock band, but because its backbone nitrogen atoms bond two critical nickel atoms. A peptide is a constituent of a protein made up of a few elemental building blocks known as amino acids.

"'Scientists believe that sometime between 3.5 and 3.8 billion years ago there was a tipping point, something that kickstarted the change from prebiotic chemistry—molecules before life—to living, biological systems," Nanda said. "We believe the change was sparked by a few small precursor proteins that performed key steps in an ancient metabolic reaction. And we think we've found one of these 'pioneer peptides.'"

***

"When scouring the universe with telescopes and probes for signs of past, present or emerging life, NASA scientists look for specific "biosignatures" known to be harbingers of life. Peptides like nickelback could become the latest biosignature employed by NASA to detect planets on the verge of producing life, Nanda said.

"An original instigating chemical, the researchers reasoned, would need to be simple enough to be able to assemble spontaneously in a prebiotic soup. But it would have to be sufficiently chemically active to possess the potential to take energy from the environment to drive a biochemical process.

"To do so, the researchers adopted a "reductionist" approach: They started by examining existing contemporary proteins known to be associated with metabolic processes. Knowing the proteins were too complex to have emerged early on, they pared them down to their basic structure.

"After sequences of experiments, researchers concluded the best candidate was Nickelback. The peptide is made of 13 amino acids and binds two nickel ions.

"Nickel, they reasoned, was an abundant metal in early oceans. When bound to the peptide, the nickel atoms become potent catalysts, attracting additional protons and electrons and producing hydrogen gas. Hydrogen, the researchers reasoned, was also more abundant on early Earth and would have been a critical source of energy to power metabolism.

"'This is important because, while there are many theories about the origins of life, there are very few actual laboratory tests of these ideas," Nanda said. "This work shows that, not only are simple protein metabolic enzymes possible, but that they are very stable and very active—making them a plausible starting point for life.'"

Comment: the usual blithe acceptance that if some molecules are present, they will simply fall together into a living organism. More intelligent design in a lab, no closer to an answer than before.

Theoretical origin of life: parts of DNA in outer space

by David Turell @, Tuesday, March 21, 2023, 16:53 (392 days ago) @ David Turell

Asteroid Ryugu contained uracil:

https://www.sciencealert.com/scientists-discover-rna-component-buried-in-the-dust-of-an...

"A sample extracted from an asteroid far from Earth has confirmed that RNA nucleobases can be found in space rocks.

"Analysis of dust ferried home from asteroid Ryugu has been found to contain uracil – one of the four nucleobases that make up RNA – in addition to niacin, a form of the vitamin B3, which plays an important role in metabolism.

"This adds to a growing body of evidence that the building blocks for life form in space, and may have been at least partially delivered to Earth by asteroid bombardment early in our planet's history.

***

"As we are increasingly discovering, the building blocks for life out there are plentiful. They've been spotted in planet-forming dust, and in the clouds of star-forming dust that shroud the heart of our galaxy. And they've been found in multiple meteorites that have penetrated Earth's atmosphere and fallen to ground.

***

"The team took the two samples, obtained from different locations on the asteroid, soaked them in hot water, and subjected them to high-performance liquid chromatography coupled with electrospray ionization high-resolution mass spectrometry. This technique, when employed on the Murchison meteorite that fell to Earth in 1969, yielded all five canonical nucleobases.

***

"'We found uracil in the samples in small amounts, in the range of 6–32 parts per billion (ppb), while vitamin B3 was more abundant, in the range of 49–99 ppb," Oba says. "Other biological molecules were found in the sample as well, including a selection of amino acids, amines and carboxylic acids, which are found in proteins and metabolism, respectively.'"

Comment: The report ignores chirality as usual. All amino acids in life are in 3-D lefthanded. Naturally formed amino acids will be 50/50 left and right. Just having amino acids lying around does not tell us how they jumped into forming living organisms.

Theoretical origin of life: the need for nitrogen

by David Turell @, Wednesday, May 10, 2023, 17:29 (342 days ago) @ David Turell

Hard to get in a useable form:

https://www.sciencenews.org/article/volcanic-eruption-nitrogen-lightning-life

"Millions of years ago, giant volcanic eruptions in what’s now Turkey and Peru each deposited millions of metric tons of nitrate on the surrounding land. That nutrient may have come from volcanic lightning, researchers reported April 24 at a meeting of the European Geosciences Union in Vienna.

"The discovery adds evidence to the idea that, early in Earth’s history, volcanoes could have provided some of the materials that made it possible for life to emerge, says volcanologist Erwan Martin of Sorbonne University in Paris.

"Nitrogen is an essential ingredient in biological molecules, such as proteins and DNA. It makes up about 78 percent of the atmosphere. But nitrogen molecules in the air consist of two tightly bound nitrogen atoms. Only when these atoms are separated will they react with other elements and create forms of nitrogen useful to life, such as nitrate.

"Some microbes can tease apart the nitrogen molecules and provide “fixed nitrogen” to plants and fungi. Human chemists can do it too, creating fertilizer. But before life could start, some nonbiological process must have been at play.

"Lightning is the obvious candidate, Martin says. These extremely energetic electric discharges can tear apart nitrogen atoms, which will combine with oxygen to form nitrogen oxides and eventually nitrate.

***

"Even that large amount of lightning creates a relatively small amount of nitrate. But rare, huge eruptions, of the kind that happen only every 100,000 years or so, could create much more. The idea that such events could produce and deposit a lot of nitrate is not new, Martin says, but until now nobody had actually looked at the nitrogen content of volcanic deposits from these eruptions.

"His group sampled outcrops in Turkey and Peru linked to 10 explosive eruptions that happened between 20 million and 1 million years ago. Their locations’ relatively dry climate helps ensure that any nitrate formed long ago, which is soluble in water, would not have all leached out by now.

"The nitrate that the researchers found turns out to contain oxygen atoms with different masses, in a proportion similar to that of the three oxygen atoms that make up each molecule of ozone in the air. This shows that the nitrates were formed in the atmosphere and not by some process on the ground, the team says.

***

"The study’s concept is interesting, says marine chemist Jeffrey Bada of the Scripps Institution of Oceanography in La Jolla, Calif. But he thinks the researchers should have addressed the different composition of the atmosphere at the time that life first came on the scene.

“'In today’s world, lightning on volcanic islands produces copious amounts of nitrogen oxides,” Bada says. “But in the early Earth, when the atmosphere had little oxygen in it, the product would have been probably ammonia.” Like nitrate, ammonia is a form of nitrogen that’s biologically usable.

"But, Martin says, in a volcanic plume, there is a lot of water and other oxygen compounds coming from the magma, which could have supplied some of that oxygen. And in those early days, he says, “maybe it wasn’t nitrate but ammonia — it’s still nitrogen available for life. These are still things that need to be studied.'”

Comment: this story concentrates on necessary ingredients for life. But all the ingredients lying round won't produce life. The mechanism is still totally unknown.

Theoretical origin of life: a study of chirality

by David Turell @, Sunday, May 28, 2023, 20:04 (324 days ago) @ David Turell

All living amino acids are left-handed:

https://www.sciencedaily.com/releases/2023/05/230525141329.htm

"Interestingly, one of the many mysteries surrounding the origin of life as we know it has to do with chirality. It turns out that biological amino acids (AAs) -- the building blocks of proteins -- on Earth appear only in one of their two possible enantiomeric forms, namely the L-form. However, if you synthesize AAs artificially, both L and D forms are produced in equal amounts. This suggests that, at some early point in the past, L-AAs must have come to dominate a hetero-chiral world. This phenomenon is known as "chiral symmetry breaking."

***

"'The idea that homochirality may have originated in space was suggested after AAs were found in the Murchison meteorite that fell in Australia in 1969," explains Dr. Shoji. Curiously enough, in the samples obtained from this meteorite, each of the L-enantiomers was more prevalent than its D-enantiomer counterpart. One popular explanation for this suggests that the asymmetry was induced by ultraviolet circularly polarized light (CPL) in the star-forming regions of our galaxy. Scientists verified that this type of radiation can, indeed, induce asymmetric photochemical reactions that, given enough time, would favor the production of L-AAs over D-AAs. However, the absorption properties of the AA isovaline are opposite to those of the other AAs, meaning that the UV-based explanation alone is either insufficient or incorrect.

"Against this backdrop, Dr. Shoji's team pursued an alternate hypothesis. Instead of far-UV radiation, they hypothesized that the chiral asymmetry was, in fact, induced specifically by the CP Lyman-α (Lyα) emission line, a spectral line of hydrogen atom that permeated the early Milky Way. Moreover, instead of focusing only on photoreactions in AAs, the researchers investigated the possibility of the chiral asymmetry starting in the precursors to the AAs, namely amino propanals (APs) and amino nitriles (ANs).

***

"The results showed that L-enantiomers of ANs are preferentially formed under right-handed CP (R-CP) Lyα irradiation, with their enantiomeric ratios matching those for the corresponding AAs. "Taken together, our findings suggest that ANs underlie the origin of the homochirality," remarks Dr. Shoji. "More specifically, irradiating AN precursors with R-CP Lyα radiation lead to a higher ratio of L-enantiomers. The subsequent predominance of L-AAs is possible via reactions induced by water molecules and heat." (my bold)

"The study thus brings us one step closer to understanding the complex history of our own biochemistry" (my bold)

Comment: The bold above is pure hype. All they had shown is a slight tendency to produce left-handedness under intelligently guided lab reactions. All of life's amino acids are left-handed. Note my bolds. It is not predominance, it is absolute!

Theoretical origin of life: a study of chirality

by David Turell @, Wednesday, June 14, 2023, 22:47 (307 days ago) @ David Turell

A new try to solve the problem of chirality:

https://www.science.org/content/article/breakthrough-could-explain-why-life-molecules-a...

"In 1848, French chemist Louis Pasteur discovered that some molecules essential for life exist in mirror image forms, much like our left and right hands. Today, we know biology chooses just one of these “chiral” forms: DNA, RNA, and their building blocks are all right-handed, whereas amino acids and proteins are all left-handed. Pasteur, who saw hints of this selectivity, or “homochirality,” thought magnetic fields might somehow explain it, but its origin has remained one of biology’s great mysteries. Now, it turns out Pasteur may have been onto something.

"In three new papers, researchers suggest magnetic minerals common on early Earth could have caused key biomolecules to accumulate on their surface in just one mirror image form, setting off a positive feedback that continued to favor the same form. “It’s a real breakthrough,” says Jack Szostak, an origin of life chemist at the University of Chicago who was not involved with the new work. “Homochirality is essential to get biology started, and this is a possible—and I would say very likely—solution.”

"Chemical reactions are typically unbiased, yielding equal amounts of right- and left-handed molecules. But life requires selectivity: Only right-handed DNA, for example, has the correct twist to interact properly with other chiral molecules. To get life, “you’ve got to break the mirror, or you can’t pull it off,” says Gerald Joyce, an origin of life chemist and president of the Salk Institute for Biological Studies.

***

"A glimmer of an amplification mechanism emerged in 2009. Researchers led by Matthew Powner and John Sutherland at the University of Manchester were studying possible origins of RNA, which many researchers think was a central player in the origin of life. They were intrigued by a molecule called ribo-aminooxazoline (RAO), which they discovered could react to form two of RNA’s nucleotide building blocks. RAO is among a rare class of crystals that enforce a single chirality: Once a crystal starts to grow from either right- or left-handed versions of the molecule, only molecules with the same chirality can bind to the structure. Such crystals, if they started with an initial bias, could have caused chiral RAO to build up.

"Now, Sasselov and his colleagues have put these two pieces together. They wondered whether magnetic surfaces might favor a single RAO chiral form. To find out, they turned to magnetite, a magnetic mineral that is common in Earth’s crust. They applied a strong external magnetic field, aligning electron spins in the magnetite and strengthening its magnetism. When they exposed the magnetite surface to a solution containing an equal mix of right- and left-handed RAO molecules, 60% of those that settled on top were of a single handedness. This created a crystalline seed that caused additional like-handed RAOs to bind, eventually forming pure single-handed RAO crystals, the researchers reported last week in Science Advances. When they flipped the field’s orientation and repeated the experiment, crystals with the opposite handedness took shape. “It’s a really cool effect and a way to break the symmetry,” says Powner, now at University College London.

***

"The chiral RAO in turn imposes its handedness on the RNA building blocks it generates, and Sasselov’s team has now shown that the effects cascade to other biological molecules. In a report accepted last week in The Journal of Chemical Physics they show that once an excess of chiral RNA is formed, known chemical reactions could pass on this chiral bias, templating amino acids and proteins with the opposite handedness and ultimately fostering other chiral molecules essential to cell metabolism. “There is no solution out there that solves all the steps out there that this does,” Szostak says.

"The quest that began with Pasteur isn’t quite over, though. One loose end, Sasselov acknowledges, is that RAO has only been shown to lead to the synthesis of two of RNA’s four nucleotides, cytosine and uracil. It isn’t known to produce the other two, adenine and guanine, although Sasselov says there’s a “big push” to search for RAO reactions that could do it. If they can, the mystery of biological handedness might be another step closer to being solved."

Comment: the same old, same old. Totally unnatural work in a laboratory produces a 60% inclination and origin-of-life folks do victory dances. DNA and RNA are right-handed and all amino acids are left-handed. There are two chirality problem in living biochemistry. Why should nature go in both directions? They discovered RAO makes two of the RNA bases. That is intelligent design in a laboratory. Advance in origin-of-life theory? No way.

Theoretical origin of life: a need for new information

by David Turell @, Friday, June 23, 2023, 19:22 (298 days ago) @ David Turell

An ID essay:

https://evolutionnews.org/2023/06/information-and-lifes-origin-a-retrospective-view/

"In conjunction with the understanding that the formation of life from non-life constitutes a rise in specified complexity rather than increasing order, this generalized Second Law raised a theoretical barrier against any natural origin of life scenario.

"The traditional Second Law of Thermodynamics is viewed as an inviolable arbiter of possible outcomes for all physical processes. In particular, any conceivable proposal for a perpetual motion machine can, without analysis, be rejected based on the Second Law. With regard to the origin and development of life, the generalized Second Law states that any “alleged natural explanation…will be untrue in the same way a patent examiner in Washington, DC, knows an alleged invention for a perpetual motion machine is untrue.

"...articles by Hubert Yockey on the application of information theory to the origin of life. Noting that “The information content of amino acid sequences cannot increase until a genetic code with an adaptor function has appeared,” Yockey states,

"Nothing which even vaguely resembles a code exists in the physico-chemical world. One must conclude that no valid scientific explanation of the origin of life exists at present.

"By the mid 1990s, I had read The Mystery of Life’s Origin4, in which the authors distinguish between thermal entropy (related to the distribution of energy in the system), and configurational entropy (related to the distribution of mass — for example, the specific sequence of amino acids comprising a protein). Their analysis of multiple proposals for natural mechanisms to overcome the thermodynamic barrier represented by the high degree of configurational entropy in living systems led them to conclude that all such mechanisms are “clearly inadequate to account for the configurational entropy work of coding.

***

"In the late 1990s, my academic schedule allowed me to pursue other source material on the physics of the generalized Second Law, and I obtained copies of two main textbooks on statistical mechanics referenced by Gange. The author of one of these texts gives a fundamental definition of information that emphasizes the relationship between information and the mind:

"Information is the entity which makes the difference between knowing and not knowing, between being faced with a number of possibilities and between knowing the one that actually prevails.

***

"...Arthur Hobson, affirms that given an initial measurement of a system, predictions of the system at a later time “cannot contain more information (but may contain less information)” than the initial data describing the system.7 This limitation on natural processes, based upon the laws of quantum mechanics, prohibits a system (even the entire universe bounded by the cosmic horizon) from progressing from a state of lower information (pre-life) to a state of higher information (post-life) by any combination of natural forces.

"William Dembski affirms the proscriptions of the generalized Second Law by showing that chance and necessity are insufficient to ratchet up the complex specified information (CSI) content of a closed system over time:

"at natural causes cannot do, however, is originate CSI. This strong proscriptive claim, that natural causes can only transmit CSI but never originate it, I call the Law of Conservation of Information. It is this law that gives definite scientific content to the claim that CSI is intelligently caused.

***

"Have the last twenty years produced any experimental research demonstrating how unguided natural processes can successfully produce the complex, specified arrangements of components inherent in functional biomolecules? Any dearth of success in this field is not for lack of trying, nor is it surprising that scientists have not been able to coax even a single biochemically relevant protein into existence from a mix of ingredients likely to be available on the early Earth.

"A Rice University professor of chemistry, James Tour, who is renowned for his research in synthetic organic chemistry, draws this conclusion regarding any naturalistic origin-of-life scenario:

"…the requisite molecules (lipids, proteins, nucleic acids, and carbohydrates) are so unlikely to have occurred in the states and quantities needed, that we could never have gotten to the point of figuring out the genesis of the requisite code or information.

"Unguided natural processes, according to the generalized Second Law, cannot systematically increase the information content of a closed system over time. Since the origin of life, represented by the formation of a single-cell organism, constitutes just such an increase in information, natural processes are not expected to be the cause. Intelligence is the only recognized source of information, as inherent in living organisms. What we know of the laws of physics supports this conclusion."

Comment: this discussion of the need for information is quite clear and not confusing. I await dhw's thoughts.

Theoretical origin of life: meteorites have all five bases

by David Turell @, Sunday, July 30, 2023, 15:27 (261 days ago) @ David Turell

Latest analysis:

https://www.sciencenews.org/article/all-of-the-bases-in-dna-and-rna-have-now-been-found...

"Space rocks that fell to Earth within the last century contain the five bases that store information in DNA and RNA, scientists report April 26 in Nature Communications.

"These “nucleobases” — adenine, guanine, cytosine, thymine and uracil — combine with sugars and phosphates to make up the genetic code of all life on Earth. Whether these basic ingredients for life first came from space or instead formed in a warm soup of earthly chemistry is still not known. But the discovery adds to evidence that suggests life’s precursors originally came from space, the researchers say.

***

"The researchers think their milder extraction technique, which uses cold water instead of the usual acid, keeps the compounds intact. “We’re finding this extraction approach is very amenable for these fragile nucleobases,” Glavin says. “It’s more like a cold brew, rather than making hot tea.”

"With this technique, Glavin, Oba and their colleagues measured the abundances of the bases and other compounds related to life in four samples from meteorites that fell decades ago in Australia, Kentucky and British Columbia. In all four, the team detected and measured adenine, guanine, cytosine, uracil, thymine, several compounds related to those bases and a few amino acids."

Comment: there are 20 essential amino acids in life, all left-handed. The article, as usual ignores the point. The other caveat is finding some of the ingredients of life's doesn't tell us how the working biochemistry of life was formed.

Theoretical origin of life: homochirality huge problem

by David Turell @, Thursday, August 10, 2023, 16:12 (250 days ago) @ David Turell

All proteins in life are either right or left-handed, and to function are more than 200 units long:

https://evolutionnews.org/2023/08/origin-of-life-the-challenge-of-achieving-homochirali...

"The chemical properties of mirror imaged compounds are equivalent for all practical purposes. The production of these building blocks in a prebiotic world, using very simple compounds as starting material, would therefore be expected to result in a racemic mixture, or 50/50 distribution, of these building blocks. This has already been confirmed from analysis of organic compounds retrieved from an asteroid.

"Producing polymers consisting of only one configuration from this mixture is obligatory if a prebiotic origin of life on Earth is be convincingly explained to the scientific community. Proposing chemical schemes that produce polypeptides (proteins) or RNA using homochiral building blocks is the task at hand. Performing such a feat in solution appears unfeasible, so the prebiotic soup approach has been abandoned by many origin of life (OOL) scientists. A better alternative, widely investigated, is the use of mineral surfaces where adsorption of organic chemicals could theoretically select preferentially one configuration of a pair of chiral molecules.

***

"...many other laboratories undertook similar approaches, testing out different mineral surfaces and a variety of reaction conditions. The highest achievers managed to produce polypeptides up to decamers. It became clear from these studies that the longer the polypeptide produced, the harder it was to retrieve it from the mineral surface, as it was tightly bound via a multitude of chemical bonding forces spread over a long chain of amino acids. Success at making long polypeptides seemingly dooms the polymer to remain fixed to the surface instead of being released into solution as needed by life.

"A major flaw with the studies described above is that they did not attempt to account for how homochiral selectivity could be enforced by this route. Synthesizing polypeptides with a racemic mixture of amino acids offers prebiotic life nothing in terms of functionality. For proteins to assume specific and reproducible structures, a homochiral set of amino acids must be used.

***

"Among the 20 amino acids, only 11 possess at least three functional groups required for appropriate spatial positioning to the mineral interface. The remaining nine have only two, one carboxyl and one amine group. This leaves little room for attaining homochirality for all amino acids as needed to construct proteins.

"To give this laboratory credit, they did mention that alanine, valine, and lysine do not exhibit chiral selection on calcite. The lack of data for most remaining amino acids leads one to believe minerals in general are another dead end for the homochirality problem that OOL protein researchers are trying to solve.

***

"The carbohydrate ribose, required to make RNA, presents a highly problematic situation. Ribose has four chiral centers, unlike amino acids with just one. Therefore, D-ribose found in RNA has seven other chemical partners differing in their spatial arrangement of atoms.

***

"The tighter binding of ribose, by virtue of its hydroxyl groups all pointing to the mineral surface, would permit tighter retention where the other sugars would proceed more rapidly through this chromatographic separation.

"There are several problems with this innovative proposal. Setting up a chromatographic separation does not happen naturally. It requires a specific design where all molecules must enter the chromatographic medium simultaneously. In other words, an external agent is required to carry out this exercise. Assuming that chromatography proceeds as hoped, the last 5-carbon sugar eluting from the chromatographic medium will be D- and L-ribose. There is still a racemic mixture of ribose that must be contended with. Finally, as discussed in my earlier article, appropriately linking a nucleobase and finally phosphate to D-ribose is an extremely difficult task without the use of specifically engineered catalysts, e.g., enzymes. This is highly unlikely to happen in a prebiotic scenario.

"I have addressed here the potential minerals proposed by OOL researchers to abiotically synthesize the first functional biopolymers. Simple principles discounting these proposals can be applied to other comparable scenarios in this area, but that would require a much longer and more technical article. Suffice it to say there are sound counterarguments to the plethora of schemes that OOL researchers devise in trying to account for how life could have emerged abiotically. Critically examining these schemes is the job with which scientists on the other side of the field are tasked."

Comment: to fit here I have omitted much complex organic chemistry discussion. To get around these problems the labs use off-the-shelf purified left or right molecules. OOL researchers never note these problems.

Theoretical origin of life: age of LUCA

by David Turell @, Wednesday, November 22, 2023, 19:25 (146 days ago) @ David Turell

Latest estimates:

https://www.sciencedaily.com/releases/2023/11/231121175308.htm

LUCA, the 'last universal common ancestor' of all living organisms, lived 4.32 to at most 4.52 billion years ago. This is indicated by a study from NIOZ biologists Tara Mahendrarajah and senior author Anja Spang, with collaborating partners from Universities in Bristol, Hungary and Tokyo, that was published today in Nature Communications. What LUCA looked like is unknown, but it must have been a cell with among others ribosomal proteins and an ATP synthase. "These proteins are shared by all bacteria, archaea, and eukaryotes such as plants and animals," Spang said. Using a new molecular dating approach, the researchers were able to more accurately estimate the moment when LUCA split into bacteria and archaea, as well as when eukaryotes emerged.

***

"Archaea are often called ancient bacteria," says Spang. "That would suggest that they stem from an ancestor that is older than the one of today's bacteria. But with this improved dating approach, we see that the ancestor of all current archaea lived between 3.37 and 3.95 billion years ago . This makes the last common ancestor of known archaea younger than the one of all bacteria, which lived between 4.05 and 4.49 billion years back. This suggests that earlier archaea either died out, or they live somewhere hidden on Earth where we have not found them yet," Spang hypothesizes.

The eukaryotes, meaning cells with a nucleus, such as all plants and animals, had their last common ancestor between 1.84 to 1.93 billion years back.

Tara Mahendrarajah explains: "If you imagine all life on earth as a family tree, LUCA is at the base and at some point, the trunk splits into a bacterial and an archaeal branch. But eukaryotes are not a separate branch on this tree of life, but rather a fusion of two branches that came out of the bacterial and the archaeal branches. We have a bit of both in us."

Comment: this is consistent with previous estimates, which means life appeared within 300-400 million years after the Earth formed.

Theoretical origin of life: UV light

by David Turell @, Tuesday, December 12, 2023, 18:15 (126 days ago) @ David Turell

Is UV light important:

https://www.sciencenews.org/article/dwarf-star-light-origin-life

"A look at about 200 ultracool dwarf stars shows that they lack sufficient ultraviolet light intensity to have the potential to jump-start life, researchers report December 1 in the Monthly Notices of the Royal Astronomical Society. That may initially seem to be bad news for finding signs of alien life on distant planets. But the diminutive stars could instead serve as test beds to determine what other conditions can create the chemical foundations of life.

***

For life to exist on a habitable planet, though, it must start somehow. One possibility is that UV starlight provides the energy needed to link together the hydrogen, oxygen, carbon, nitrogen, sulfur and other atoms that make up the compounds that are precursors to life. [I would add phosphorous]

***

"...overall, the UV energy the small stars release is too low to forge the chemicals needed to kick-start life, the team found.

"The dearth of UV light doesn’t necessarily quash hopes of finding life around such stars. “UV is an energy source for prebiotic chemistry that we can measure, and that is why we focused on it,” says Segura, of the National Autonomous University of Mexico in Mexico City. “But there are many other energy sources, like cosmic and stellar particles, and particles, radiation and heat produced by radioactive decay, to name a few.”

"Ultracool stars might be useful to discover whether something other than UV light can get life going. “We should search for life on the planets that have the least [UV] activity, where we can know with confidence that UV-driven prebiotic chemistry cannot happen,” says Paul Rimmer, a University of Cambridge astrophysicist who was not involved in the study. “If we find evidence of life on these [types of] planets, this will show that there are other paths to life.'”

Comment: this wishful article tells us the contribution of UV light to the origin of life is unknown, if at all useful. Biochemical studies never use UV light now. I reviewed the literature on Google. Nothing but sheer speculation. More grasping at straws.

Theoretical origin of life: just one step!!!

by David Turell @, Friday, January 26, 2024, 01:13 (82 days ago) @ David Turell

Another nutty review article with a new twist:

https://www.newscientist.com/article/mg24732940-800-a-radical-new-theory-rewrites-the-s...

"Many ideas have been proposed to explain how life began. Most are based on the assumption that cells are too complex to have formed all at once, so life must have started with just one component that survived and somehow created the others around it. When put into practice in the lab, however, these ideas don’t produce anything particularly lifelike. It is, some researchers are starting to realise, like trying to build a car by making a chassis and hoping wheels and an engine will spontaneously appear.

"The alternative – that life emerged fully formed – seems even more unlikely. Yet perhaps astoundingly, two lines of evidence are converging to suggest that this is exactly what happened. It turns out that all the key molecules of life can form from the same simple carbon-based chemistry. What’s more, they easily combine to make startlingly lifelike “protocells”. As well as explaining how life began, this “everything-first” idea of life’s origins also has implications for where it got started – and the most likely locations for extraterrestrial life, too.

***

"Life can be boiled down to three core systems. First, it has structural integrity: that means each cell has an outer membrane holding it together. Second, life has metabolism, a set of chemical reactions that obtain energy from its surroundings. Finally, life can reproduce using genes, which contain instructions for building cells and are passed on to offspring.

***

"Beyond this, things start to become more complicated. Life’s three core processes are intertwined. Genes carry instructions for making proteins, which means proteins only exist because of genes. But proteins are also essential for maintaining and copying genes, so genes only exist because of proteins. And proteins – made by genes – are crucial for constructing the lipids for membranes. Any hypothesis explaining life’s origin must take account of this. Yet, if we suppose that genes, metabolism and membranes were unlikely to have arisen simultaneously, that means one of them must have come first and “invented” the others.

***

"...biochemists have spent decades struggling to get RNA to self-assemble or copy itself in the lab, and now concede that it needs a lot of help to do either.

***

"In the 1970s, his team discovered that lipids found in cell membranes could be made when two simple chemicals, cyanamide and glycerol, were mixed with water and heated to 65°C. If these lipids were subsequently added to salt water and shaken, they formed spherical blobs with two outer layers of lipids, just like cells. “The simplest function is the self-assembly of membranes. It’s spontaneous,” says Deamer. Nevertheless, he now accepts that this isn’t enough, because lipids can’t carry genes or form enzymes.

"The shortcomings of these simple models of life’s origin have led Deamer and others to explore the seemingly less plausible alternative that all three systems emerged together in a highly simplified form.

***

"In 2001, his team found that formamide could give rise to several components of RNA if it was heated to 160°C in the presence of minerals like limestone. The researchers later discovered that a common type of clay called montmorillonite helps. Formamide can also generate amino acids, the building blocks of proteins. “It produces complex mixtures,” says Di Mauro.

***

"By combining a similar organic compound called cyanamide with other simple chemicals, John Sutherland at the MRC Laboratory of Molecular Biology in Cambridge, UK, has created nucleotides, the building blocks of RNA. The reaction requires ultraviolet light, heating and drying, and wetting with water. Sutherland’s team found that the same starting chemicals can also make the precursors of amino acids and lipids. “All the cellular subsystems could have arisen simultaneously through common chemistry,” he concluded. The key is what Sutherland calls “Goldilocks chemistry”: a mixture with enough variety for complex reactions to occur, but not so much that it becomes a jumbled mess. (my bold)

"Jack Szostak at Harvard Medical School has taken remarkable strides toward revealing how this might have happened. Beginning in 2003, his team built model cells with outer layers of fatty acids surrounding an internal space that could host RNA.

***

"The one system still missing from these protocells is metabolism. This is particularly challenging because it means creating entire sequences of chemical reactions. In modern organisms, these are controlled by battalions of protein enzymes, which can’t have existed when life began. (my bold)

***

"Of course, all this depends on the everything-first idea proving correct. Szostak’s protocells and the new biochemical insights have won over many researchers, but some pieces of the puzzle are still missing. Perhaps the most persuasive argument is that the simpler ideas don’t work. As is the case with many things in life, the beginning was probably more complicated than we had thought."

Comment: Finally, at the end some common sense. Goldilocks is God!!!

Theoretical origin of life: finding early phosphorus

by David Turell @, Saturday, February 03, 2024, 17:28 (73 days ago) @ David Turell

Certain elements are vital for life to begin:

https://www.sciencealert.com/nanoparticles-in-some-of-the-worlds-oldest-rocks-found-to-...

"Encased inside some of the oldest rocks on Earth are previously overlooked nanocrystals that tell a story about how life might have emerged.

"Earth scientists at the University of Western Australia and the University of Cambridge say their findings could explain why phosphorus became a major building block of life and how molecules first clicked together to form primitive RNA at hydrothermal vents on the seafloor.

"They examined 3.5-billion-year-old rocks from the Pilbara region of Western Australia under a transmission electron microscope and found unexpected minerals.

"The Pilbara is renowned for its pristine preservation of the Earth's crust during the Archean era when life was just getting started. The rocks in this area are a time capsule containing insights into prebiotic chemistry.

"From afar, a trained eye might identify the Pilbara's stripy red rock as a mix of very fine quartz (containing silicon and oxygen) and hematite (made of iron and oxygen), a combination known as jaspilite.

"Closer inspection reveals something surprising; hidden nanocrystals with interesting properties. Dispersed throughout the jasper beds are fine particles of greenalite, a mineral containing iron, silicon, and oxygen, which would have been ejected from a nearby hydrothermal vent and precipitated on the seafloor billions of years ago.

***

"Long considered a likely place for life to emerge, hydrothermal vents provide the perfect location for this process to happen. They constantly churn seawater through magma chambers, and spew hot, smoky plumes filled with nutrients back into the ocean.

"'It's a great place for chemical reactions to occur … because they are areas of extreme gradients," says Rasmussen.

"The 3.5-billion-year-old rocks from the Pilbara also contained nanoparticles of fluorapatite (a mineral made of oxygen, calcium, fluorine and phosphorus).

"Scientists have been puzzled over why phosphorus is found in so many biological structures (including DNA, membranes, and lipids) in spite of such low concentrations of the element in the ocean.

"But the presence of the phosphorus-containing mineral fluorapatite in billion-year-old rocks provides a potential explanation: hydrothermal vents might have been an early source of accessible phosphorus.

"The researchers' modeling suggests that the concentration of phosphorus in deep seawater 3.5 billion years ago was likely 10 to 100 times higher than it is today.

"'Why did life select phosphorus for so many essential biochemical processes, including the manufacture of genetic material, when it is so scarce in the ocean today? The answer may be that phosphorus was much more abundant during the origin and early evolution of life," says Rasmussen."

Comment: an important finding since phosphorus is not abundant now.

Theoretical origin of life: finding early nitrogen

by David Turell @, Sunday, February 11, 2024, 16:00 (65 days ago) @ David Turell

Lots here but hard to free:

https://www.sciencealert.com/life-on-earth-may-have-been-born-in-t

"The chaos of lightning crackling through the sky has been speculated to play a key role in freeing elements like phosphorus, making it more accessible to burgeoning life on ancient Earth. [note previous entry]

"Now, scientists have found geological evidence that the lightning discharges associated with volcanic events may have also played a role in nitrogen fixation, making it available for biological processes too.

***

"'For the first time, significant amounts of nitrate have been discovered in volcanic deposits from very large explosive eruptions," writes a team led by geoscientist Adeline Aroskay of Sorbonne University.

"'These findings provide geological support for a unique role played by subaerial explosive eruptions in high energy-demanding processes, which were essential in supplying building blocks for life during its emergence on Earth."

"Somehow, back when Earth was wild and young, processes on our planet transformed a mixture of ingredients into the stuff needed to kickstart life. One of the things life needs is nitrogen, an essential nutrient for building things like proteins, amino acids, and nucleic acids.

"Earth has scads of nitrogen; some 78 percent of the atmosphere is made up of the stuff. But biology can't access it in its atmospheric form of molecular nitrogen, or N2; the nitrogen atoms need to be split apart and fixed to other atoms to form more reactive compounds, such as nitrates or ammonia.

"Now that life exists, biological processes such as those in microbes living in the roots of plants can speed up the process. Human industrial techniques can also pump in nitrogen and pump out compounds like ammonia by the tank load.

"But before there was life, a non-biological process was needed to kickstart nitrogen fixation. And here's where electricity – lightning – comes into play. Electrical discharges can fix nitrogen, as first established in 1784.

***

"Aroskay and her team have found that evidence, in the form of nitrates embedded in ancient volcanic deposits. They collected samples from a number of volcanic deposits from explosive eruptions in Turkey and Peru, which took place between 1.6 and 20 million years ago, and looked specifically for nitrates, which are the end product of the oxidation of nitrogen.

***

"There was no correlation between the age of the deposit and the concentration of nitrates, which means, the researchers believe, that the deposition of the compounds is not a result of gradual processes that occur over long timescales. The nitrates are dumped into the volcanic rock in one fell swoop.

"The concentrations of sulfur and chlorine in the deposits were also consistent with a volcanic origin. Taken together, this suggests that volcanic lightning can fix nitrogen in amounts significant enough to play a role in life's emergence.

"And it could give us a tool to interpret other nitrate deposits around the world. In the Atacama desert, for example, the presence of nitrates was attributed to atmospheric deposition, because it was thought that the ratios of oxygen isotopes weren't possible with volcanic deposition. The team's findings show that these bonds are possible in large explosive events.

***

""We estimate that, on average, about 60 teragrams of nitrogen can be fixed during a large explosive event. Our findings hint at a unique role potentially played by subaerial explosive eruptions in supplying essential ingredients for the emergence of life on Earth.""

Comment: Nitrogen in the atmosphere is rather inert compared to oxygen. The lightning theory led to the Miller-Urey sparks in a bottle study years ago, producing a gunk of organic molecules. How all the molecules came together is still unknown.

Theoretical origin of life: panspermia again

by David Turell @, Sunday, February 18, 2024, 18:59 (58 days ago) @ David Turell

An article with a highly critical conclusion:

https://www.sciencealert.com/life-spreads-across-space-on-tiny-invisible-particles-stud...

New research examines the idea that cosmic dust could be responsible for spreading life throughout the galaxy by panspermia. Life arose elsewhere, and was delivered to the young Earth. This is not a new idea, but in this work, the author calculates how quickly it could happen.

***

No matter how much we ponder and investigate the origins of life, we don't know how it starts. We have an idea about the type of environment that could spawn it, but even that is an idea obscured by billions of years.

"It is clear that the main problem is the origin of life or abiogenesis, the details of which are still unknown to us," Osmanov writes.

But it started somehow. Leaving life's original appearance aside, for now, Osmanov moves on to how it could spread.

***

The idea that life itself could travel through space on comets and asteroids is familiar to many people. When these objects crash into planets, the thinking goes, hitchhiking life is delivered, and if there's a niche it can exploit, it will. But how could simple dust accomplish the same thing?

***

A 2017 paper in the journal Astrobiology showed how hypervelocity space dust can interact with this Earth dust, creating powerful momentum flows. A small fraction of the planetary dust particles can be accelerated enough to escape the planet's gravity.

Once free of its planet's gravity, dust is then at the mercy of stellar radiation pressure.

***

Life would need to be very hardy to survive on a dust grain as it travels through interstellar space. It would have to avoid hazards like radiation and heat. If life itself couldn't do it, maybe complex molecules that lead to life could. If we grant that it's possible, the next question concerns how quickly it could spread.

"It has been shown that, during 5 billion years, the dust grains will reach 105 stellar systems, and by taking the Drake equation into account, it has been shown that the whole galaxy will be full of planetary dust particles," Osmanov explains.

***

"In particular, it has been pointed out that, by means of the solar radiation pressure, small dust grains containing live organisms can travel to the nearest solar system, Alpha Centauri, in nine thousand years," Osmanov writes. Our powerful rockets, like the Space Launch System and the Falcon Heavy, would take over 100,000 years to make the journey.

***

He takes a bold step beyond our current knowledge when he writes, "On the other hand, it is natural to assume that the number of planets with at least primitive life should be enormous." It might be a natural assumption, but there's little evidence that it's true. It's conjecture, stimulating conjecture, but conjecture nonetheless. (my bold)

Working with a statistical approach to the Drake Equation, Osmanov writes that the number of planets that developed life is on "the order of 3×107."

***

It's very interesting work. But the frustrating thing about this entire topic is that we still don't know how life appears or how often it appears. So, all of our thought experiments and calculations, including Osmanov's, have a stubborn nugget of the unknown at the centre.
(my bold)

Osmanov claims that the number of planets with primitive life is enormous. We don't know that. Planets are extraordinarily complex, and there are a bewildering number of variables. Even if there are an enormous number of planets with primitive life, many of them will be more massive than Earth. Will dust particles carrying life or complex organic molecules be able to escape the gravitational grasp of super-Earths, for example?

This research shows how life, or at least its building blocks, could escape from planets and survive the interstellar journey to another world. If it's true, and panspermia can account for life appearing on Earth so soon after it formed and cooled, then it changes our understanding of our origins and even the rest of the Universe.

But we don't know how true it is, and we still don't know how it starts.(my bold)

Comment: finally, a non-sensationalist science writer with as brain. Panspermia is a nutty theory with no real answers. It is no solution to the question of how life started.

Theoretical origin of life: newest Darwinist critique

by David Turell @, Thursday, February 29, 2024, 21:20 (47 days ago) @ David Turell

Not from ID but sounds like it:

https://www.nature.com/articles/d41586-024-00544-4

"There is no consensus about what to look for, or where. Nor is there even agreement on whether all life must be carbon-based — although all known life on Earth is. Did meteorites deliver cells or organic material from outer space? Did life start on Earth in the hot waters of hydrothermal systems on land or in deep seas?

"Observations alone cannot constrain these possibilities. The few geological traces that hint at early life are enigmatic. Is a bacterium-like imprint really a fossil, or some geochemical structure? Is a weak carbon isotope signature on the surface of a mineral a fingerprint of life (which accumulates the lighter carbon-12) or the result of another type of chemical activity?

"Genes are not directly helpful either. Comparing gene sequences in modern organisms allows researchers to reconstruct a ‘tree of life’ going back to some of the earliest cells that have genes. Although the exact genetic make-up of this ancestral population is disputed, by definition it already had genes and proteins and so can tell us little about how they arose.

"None of this precludes understanding the origin of life, but it does make competing hypotheses hard to prove or disprove unambiguously. Combine that with the overarching importance of the question and it’s clear why the field is beset with over-claims and counter-claims, which in turn warp funding, attention and recognition.

"This context has splintered the field. Strongly opposed viewpoints have coexisted for decades over basic questions such as the source of energy and carbon, the need for light and whether selection acts on genes, chemical networks or cells.

"To understand how life might have begun, researchers must stop cherry-picking the most beautiful bits of data or the most apparently convincing isolated steps, and explore the implications of these deep differences in context. Depending on the starting point, each hypothesis has different testable predictions. For example, if life started in a warm pond on land, the succession of steps leading from prebiotic chemistry to cells with genes is surprisingly different from those that must be posited if the first cells emerged in deep-sea hydrothermal vents.

***

"On balance, we would say that prebiotic chemistry starting with cyanide can produce the building blocks of life, but most of the downstream steps predicted by this framework remain problematic.

***

"the hydrothermal scenario offers a promising route to the emergence of genetic information, overcoming Hoyle’s jumbo-jet argument. Patterns in the genetic code suggest direct physical interactions between amino acids and the nucleotides that encode them, especially for those formed most easily by metabolism5. Such associations mean that random RNA sequences could act as templates for non-random peptides that have a function in growing protocells. The first genes wouldn’t have had to encode metabolism, but just enhance flux through a spontaneous protometabolism — for example, by enabling the reaction between H2 and CO2.

"Thus, in short, the two frameworks have different advantages and disadvantages, and it is premature to dismiss either.

***

"If none of these scenarios is ‘wrong’, then there is space in the field to pursue multiple frameworks. No one needs to abandon their favoured positions (yet). But brash claims for a breakthrough on the origin of life are unhelpful noise if they do not come in the context of a wider framework. The problem is ultimately answerable only if the whole question is taken seriously. (my bold)

***

"The origins-of-life field faces the same problems with culture and incentives that afflict all of science — overselling ideas towards publication and funding, too little common ground between competing groups and perhaps too much pride: too strong an attachment to favoured scenarios, and too little willingness to be proved wrong. These incentives are amplified by the difficulty of disproving complex interrelated hypotheses involving different disciplines when there is so little direct evidence — no ‘smoking gun’ to be discovered.

***

"It is too soon to aim for consensus or unity, and the question is too big; the field needs constructive disunity. Embracing multiple rigorous frameworks for the origin of life, as we advocate here, will promote objectivity, cooperation and falsifiability — good science — while still enabling researchers to focus on what they care most about. Without that, science loses its sparkle and creativity, never more important than here. With it, the field might one day get close to an answer."

Comment: has the honest tone of James Tour, but isn't ID. Note my bold, the hype about each new tiny discovery is disgusting. What I have left out are long chemical discussions of each approach.

Theoretical origin of life: problem of chirality solved?

by David Turell @, Friday, March 01, 2024, 16:13 (46 days ago) @ David Turell

The usual over hyped hope:

https://www.sciencemagazinedigital.org/sciencemagazine/library/item/01_march_2024/41767...

"There’s a bias at the heart of life, and its origin is an enduring mystery. Nearly all the amino acid building blocks of proteins today exist in mirror-image forms, like right- and left-handed gloves. But life only uses left-handed ones, even though both forms should have been equally abundant during the planet’s early days and can readily link up in the lab. Something must have tipped the balance toward lefties in the primordial soup and preserved the bias ever since.

"Now, a trio of U.S. researchers proposes a novel explanation. This week in Nature, they report that by monitoring the formation rates of amino acid pairs, called dipeptides, they’ve found multiple mechanisms that ultimately promote dipeptides whose two members share the same handedness.

“'It’s quite convincing,” says Gerald Joyce, a pioneering origin of life chemist and president of the Salk Institute for Biological Studies who was not involved with the study. Researchers next hope to learn whether the same mechanisms skew larger peptides and proteins toward left-handedness—and whether it can explain the opposite bias in RNA and DNA, whose bases have sugars that are inevitably right-handed. If so, the new mechanisms could explain how life itself took on one mirror-image form and not the other.

***

"But as Blackmond and her colleagues looked more deeply, the news got better. In a series of experiments, the Scripps researchers started with skewed proportions of L and D amino acids—for example, 60% Ls and 40% Ds. The L,D and D,L heterochiral dipeptides formed most quickly, and as they did they pulled equal numbers of L and D amino acids out of the mix. Because of the baseline bias, eventually a predominance of Ls remained in the pool of unreacted amino acids, raising the likelihood of forming fully lefthanded dipeptides. “It’s like a domino effect,” Powner says. The first heterochiral reaction eventually encourages more homochirals to form. “And it’s a general process that works with all amino acids,” Powner says. Joyce adds: “It’s just math.” (my bold)

"Follow-up experiments suggested a second bias that amplifies the effect. The team found that heterochiral dipeptides precipitate out of a solution more quickly than homochiral ones, speeding the way to a relative abundance of either homochiral L,L or D,D pairs, depending the starting mix. Just why this precipitation bias occurs isn’t yet clear, Blackmond says. However, Joyce says, together with the other effect, “it beautifully fits the [experimental] data.” Blackmond adds: “The wrong answer turned out to be the right answer to get us to homochirality.”

"For now, this push toward a particular handedness has only been shown with dipeptides. But Blackmond says preliminary work suggests the same biasing process unfolds when the sulfur catalysts stitch short peptides together into longer peptide chains.

"Joyce thinks it’s possible that the same sort of math may also help explain how life’s genetic molecules gained their handedness. “This could happen with all kinds of other things, like RNA,” he says. Perhaps it was just a statistical coin flip that caused an original bias toward building blocks of one handedness to form, Joyce says. “But once that coin flipped it caused other coins to flip.'”

Comment: just the same sort of over-hyped interpretation yesterday's entry complained about. Getting to first base doesn't mean you can reach home plate. Starting with a biased beginning is just a designer trick, not what nature offers which is always 50/50 L/D.

Theoretical origin of life: cosmic dust delivered proteins

by David Turell @, Saturday, March 02, 2024, 15:53 (45 days ago) @ David Turell

To a prebiotic Earth:

https://www.nature.com/articles/s41550-024-02212-z

"Abstract
Earth’s surface is deficient in available forms of many elements considered limiting for prebiotic chemistry. In contrast, many extraterrestrial rocky objects are rich in these same elements. Limiting prebiotic ingredients may, therefore, have been delivered by exogenous material; however, the mechanisms by which exogeneous material may be reliably and non-destructively supplied to a planetary surface remains unclear. Today, the flux of extraterrestrial matter to Earth is dominated by fine-grained cosmic dust. Although this material is rarely discussed in a prebiotic context due to its delivery over a large surface area, concentrated cosmic dust deposits are known to form on Earth today due to the action of sedimentary processes. Here we combine empirical constraints on dust sedimentation with dynamical simulations of dust formation and planetary accretion to show that localized sedimentary deposits of cosmic dust could have accumulated in arid environments on early Earth, in particular glacial settings that today produce cryoconite sediments. Our results challenge the widely held assumption that cosmic dust is incapable of fertilizing prebiotic chemistry. Cosmic dust deposits may have plausibly formed on early Earth and acted to fertilize prebiotic chemistry."

Another view: https://www.universetoday.com/165875/cosmic-dust-could-have-helped-get-life-going-on-ea...

"Life on our planet appeared early in Earth’s history. Surprisingly early, since in its early youth our planet didn’t have much of the chemical ingredients necessary for life to evolve. Since prebiotic chemicals such as sugars and amino acids are known to appear in asteroids and comets, one idea is that Earth was seeded with the building blocks of life by early cometary and asteroid impacts. While this likely played a role, a new study shows that cosmic dust also seeded young Earth, and it may have made all the difference.

"Although we’ve long known that cosmic dust accumulated on early Earth, it’s not been seen as a major source for early life because of how it accumulates. With comet and asteroid impacts, a great deal of prebiotic material is present at the site of the impact. Dust, on the other hand, is scattered across Earth’s surface rather than accumulating locally. However, the authors of this new work noted that cosmic dust can accumulate and be concentrated in sedimentary deposits, and wanted to see how that might play a role in the early appearance of terrestrial life.

"Using estimates of the rate of cosmic dust accumulation in the early period of Earth and computer simulations of how that dust could accumulate in sediment layers over time, the team looked at how concentrated deposits might form. One of the things they noticed was that while cometary impacts could create a local spike in prebiotic material, the amount deposited by cosmic dust was much higher. They also found that the melting and freezing of glacial areas could significantly increase the concentration of chemicals from the dust. For example, for early sub-glacial lakes, the concentration of prebiotic chemistry from dust would have been much higher than that found at impact sites. This means that cosmic dust could have played a much larger role in the appearance of life than impacts.

"There is still much we have to learn about early life on Earth and how life can form from prebiotic chemistry, but it is clear that life on Earth is only possible because of extraterrestrial chemistry. From dust came the building blocks of life, and so we and every living thing on Earth can trace its lineage back to the early chemistry of dust in the solar system."

Comment: it's the same old story, just mix up some proteins and life will magically appear. Now, certainly proteins had to get here for life to happen, but that happening is just a whole 'nother story requiring something supernatural. Just recognize the pile of reqired contingencies.

Theoretical origin of life: more hype about protolife cells

by David Turell @, Sunday, March 03, 2024, 19:05 (44 days ago) @ David Turell

All by hunt and peck lab trials;

https://www.sciencedaily.com/releases/2024/02/240229124507.htm

Now, Scripps Research scientists have discovered one plausible pathway for how protocells may have first formed and chemically progressed to allow for a diversity of functions.

"The findings suggest that a chemical process called phosphorylation (where phosphate groups are added to the molecule) may have occurred earlier than previously expected. This would lead to more structurally complex, double chained protocells capable of harboring chemical reactions and dividing with a diverse range of functionalities. By revealing how protocells formed, scientists can better understand how early evolution could have taken place.

***

"They sought to examine if phosphates may have been involved during the formation of protocells. Phosphates are present in nearly every chemical reaction in the body, so Krishnamurthy suspected they may have been present earlier than previously believed.

***

"The scientists wanted to mimic plausible prebiotic conditions -- the environments that existed prior to the emergence of life. They first identified three likely mixtures of chemicals that could potentially create vesicles, spherical structures of lipids similar to protocells. The chemicals used included fatty acids and glycerol (a common byproduct of soap production that may have existed during early Earth). Next, they observed the reactions of these mixtures and added additional chemicals to create new mixtures. These solutions were cooled and heated on repeat overnight with some shaking to promote chemical reactions.

***

"'The vesicles were able to transition from a fatty acid environment to a phospholipid environment during our experiments, suggesting a similar chemical environment could have existed 4 billion years ago," says first author Sunil Pulletikurti, postdoctoral researcher in Krishnamurthy's lab.

"It turns out that fatty acids and glycerol may have undergone phosphorylation to create that more stable, double chain structure. In particular, glycerol derived fatty acid esters may have led to vesicles with different tolerances to metal ions, temperatures, and pH -- a critical step in diversifying evolution.

"'We've discovered one plausible pathway for how phospholipids could have emerged during this chemical evolutionary process," says Deniz. "It's exciting to uncover how early chemistries may have transitioned to allow for life on Earth. Our findings also hint at a wealth of intriguing physics that may have played key functional roles along the way to modern cells.'"

Comment: intelligent lab folks nurse a desired process along to preconceived success and then cheer the expected result as telling us how life might have started. The usual origin of life garbage, critiqued severely in earlier entries.

Theoretical origin of life: molecules cooked in rock fissure

by David Turell @, Wednesday, April 03, 2024, 19:17 (13 days ago) @ David Turell

Another wild idea since all is at a dead end:

https://www.newscientist.com/article/2425247-lifes-vital-chemistry-may-have-begun-in-ho...

"Chemical reactions key to the origin of life on Earth could have occurred as molecules moved along thermal gradients within networks of thin rock fractures deep underground.

"Such networks, which would have been common on the early Earth, could have provided a kind of natural laboratory in which many of life’s building blocks were concentrated and separated from other organic molecules.

“'It’s very difficult to get a more general environment where you could have these purifications and intermediate steps,” says Christof Mast at the Ludwig Maximilian University of Munich in Germany.

"He and his colleagues created a heat flow chamber about the size of a playing card to model how a mix of organic molecules might behave in such rock fractures. (my bold)
)

"They heated one side of the 170-micrometre-thick chamber to 25°C (77°F) and the other to 40°C (104°F), creating a temperature gradient along which molecules would move in a process called thermophoresis. How sensitive a molecule is to this process depends on its size and electrical charge and how it interacts with the fluid in which it is dissolved.

"In an 18-hour experiment in the heat flow chamber, they found a variety of molecules were concentrated at different parts of the chamber according to their sensitivity to thermophoresis. Among these molecules were many amino acids and the A, T, G and C nucleobases, which are a key component of DNA. This effect was magnified further when they created a network of three interconnected chambers, again with one side of the chamber network at 25°C and the other side at 40°C. The additional chambers further enriched compounds concentrated by the first.

"In a mathematical simulation with 20 interconnected chambers, which might better resemble the complexity of a natural system of fractures, they found the enrichment of different molecules could be amplified yet again. In one chamber, the amino acid glycine reached concentrations around 3000 times higher than that of a different amino acid, isoleucine, despite them entering the network at the same concentration.

The researchers also demonstrated that this process of enrichment could enable a reaction to occur that would otherwise be extremely challenging. They showed that glycine molecules were able to bond to each other as the concentration of a molecule that catalyses the reaction called trimetaphosphate (TMP) increased. TMP is a noteworthy molecule to enrich as it would have been rare on the early Earth, says Mast. “Since [the chambers] are all randomly connected you could implement all sorts of reaction conditions.”

“'It’s extremely interesting to have regions in a crack with different ratios of compounds,” says Evan Spruijt at Radboud University in the Netherlands, who was not involved with the research. “You can create more diversity out of very simple building blocks with this added enrichment.”

"However, he says enrichment in rock fractures is still far from a viable scenario for an origin of life. “In the end, they still need to come together to form anything that resembles a cell or a protocell.” (my bold)

Comment: my bolds point out the fallacy of this study. They supplied all the initial organic molecules. How did they know what organic molecules might have been present and in laboratory concentrations? But their last admission about needing cellar formations tells us they recognize this does not advance the theories about originating life. More waste of grant money.

Theoretical origin of life; hydrothermal vents

by David Turell @, Thursday, June 30, 2016, 18:42 (2847 days ago) @ David Turell

Back to the possibility of hydrothermal vents: - http://nautil.us/issue/37/currents/the-fly-in-the-primordial-soup - &quot;The idea that life began at hydrothermal vents challenges the older, familiar scientific creation story of the &#147;primordial soup.&#148; In a letter to Joseph Hooker in 1871, Charles Darwin fancied that life originated &#147;in some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity etc., present,&#148; in which a &#147;protein compound was chemically formed ready to undergo still more complex changes.&#148; In the 1920s, the Russian scientist Aleksandr Oparin and the British polymath J.B.S. Haldane independently fleshed out models of how life might have arisen this way, out of an ancient ocean with the consistency, Haldane said, of a &#147;hot, dilute soup.&#148; The name stuck. - *** - &quot;The soup has an intuitive appeal: From it you can derive the building blocks of life. But it also has a fatal flaw: No matter what it produces, it&apos;s dead. Lightning bolts may spark biochemical reactions, but the energy quickly dissipates and the system returns to equilibrium. Primordial soup requires evolution to go uphill, thermodynamically, toward increasing order. It&apos;s like one of those &#147;gravity hills&#148; much documented on the Internet, where cars seem to roll uphill. Starting from heat, rocks, and seawater, amino acids and nucleotides self-assembled. They organized themselves into even more ordered molecules such as enzymes and proteins. From them evolution built the first cells, and eventually redwoods and roses, honeybees and apple trees, hyenas and humans. - &quot;But the gravity hills are a trick of perspective. A carpenter&apos;s level would reveal the truth, but you don&apos;t often see one in the &#147;like-magic&#148; gravity hill videos. The laws of physics, in fact, remain intact. So too, say the vent theorists, with the emergence of life.2-5 Evolution only seems to move toward greater order; in the larger scheme, it&apos;s downhill all the way. Vent models posit that given the initial conditions, the emergence of life was not a near-miracle. It was inevitable. - *** - &quot;Russell and his colleague Allan Hall, now an archaeologist at the University of Glasgow, chimed in. You&apos;re right, they told the Millerites: Black smokers are too hot, and acidic, for life to have formed there. Near them, though, they wrote, one ought to find mineral tubes that emit lukewarm, alkaline fluid. They would be ideal sites for the emergence of life. - *** - &quot;Modern hydrothermal vent models suggest an explanation of how that chain was built. The giant battery of an early Lost City drives an engine that makes complex molecules, mainly out of carbon, hydrogen, and oxygen. Iron sulfide, as well as other small molecules found at the vents, act as &#147;coenzymes&#148;&#151;catalytic nanoengines that drive the reactions lying at the heart of all metabolism. The chimneys, in short, have a kind of metabolism, which takes energy from hydrogen, CO2, and other molecules, and uses it to build more complex molecules, mainly out of carbon, hydrogen, and oxygen. The most ancient metabolic pathways in biology recapitulate the chemistry of that early Lost City. - *** - &quot;If Barge and I watched our laboratory model long enough, would it too evolve a metabolic pathway? Enzymes? Genes? Barge is taking the first steps in that direction, though the steps are small. Instead of building a chimney, she deposits iron sulfide and other minerals onto a porous, inert disk. That disk can serve as a membrane between, say, a positively charged fluid and a negatively charged one. Barge measures the voltage and pH differences across the membrane&#151;the flow of electrons and protons. Those currents drive chemical reactions that are fundamental to life. The next step will be to get the chemical reactions to evolve more complex molecules. &#147;You could also set up experiments,&#148; she says, &#147;to test the emerging feedback of organics with minerals.&#148; Simple catalysts could favor reactions whose products were more complex catalysts, which could produce yet more complex catalysts, in a feedback loop leading ultimately&#151;way down the road&#151;to protein and DNA. - &quot;In one of my two worlds, the chimney developed a slender stalk, and then a heavy bulb swelled at the tip. &#147;That one will probably break,&#148; Barge says. It did: a dead end of evolution. But the chimney in the other flask grew a fat, flat base and tapered mountainously into a series of peaks that, if you were a water flea, would seem majestic.&quot; - Comment: In this article, which should be read completely, the author visits a lab which recreates sea vents. No success so far but life stared in the oceans and the vents are a likely spot. At least there are chemicals and heat to begin with. Still the issue of chance or design.

Theoretical origin of life; experts' opinions

by David Turell @, Monday, August 15, 2016, 15:40 (2801 days ago) @ David Turell

Rabbi Moshe Averick has a new article on the subject:-http://www.algemeiner.com/2016/08/10/its-easy-to-be-an-atheist-if-you-ignore-science/# -&quot;Here are just a few well-chosen statements on the Origin of Life:&#13;&#10;?(2016) &#147;[There is] collective cluelessness&#133;those who say this is well worked out, they know nothing, nothing about chemical synthesis&#133;Those who think that scientists understand the details of life&apos;s origin are wholly uninformed. Nobody understands&#133;when will the scientific community confess to the world that they are clueless on life&apos;s origin, that the emperor has no clothes?&#148; James Tour &#151; Professor of Chemistry, Rice University &#13;&#10;?(2011) &#147;The Origin of Life field is a failure.&#148; Eugene Koonin, microbiologist at the National Center for Biotechnology Information&#13;&#10;?(2011) &#147;With respect to the Origin of Life, I find the more we learn about cells, the more complex they seem; they are just incredibly complex things, and to go from what we can see today and try to reason where it came from, I think is really impossible.&#148; Lee Hartwell, Nobel Prize in Medicine, 2001&#13;&#10;?(2001) &#147;The origin of life appears to me as incomprehensible as ever, a matter for wonder but not for explication.&#148; Franklin Harold, Professor Emeritus, Department of Biochemistry and Molecular Biology, Colorado State University&#13;&#10;?(1983) &#147;In short, there is not a shred of objective evidence to support the hypothesis that life began in an organic soup here on earth.&#148; Sir Fred Hoyle, distinguished British astronomer, physicist, mathematician &#13;&#10;?(1981) &#147;Since Science does not have the faintest idea how life on earth originated&#133;it would only be honest to confess this to other scientists, to grantors, and to the public at large.&#148; Hubert Yockey, physicist and renowned information theorist)-***-&quot;As Biochemist Klaus Dose wrote: &#147;Experimentation on the origin of life&#133;has led to a better perception of the immensity of the problem of the origin of life on Earth rather than to its solution.&#148; Researchers Carl Woese and Gunter Wachtershauser concur: &#147;While we do not have a solution, we now have an inkling of the magnitude of the problem.&#148;-atheist microbiologist Eugene Koonin answers this question: &#147;Certainly this is not due to a lack of experimental and theoretical effort, but to the extraordinary intrinsic difficulty and complexity of the problem. A succession of exceedingly unlikely steps is essential for the Origin of Life&#133;these make the final outcome seem almost like a miracle.&#148;-***-&quot;The living cell is best thought of as a supercomputer - an information processing and replicating system of astonishing complexity. DNA is not a special life giving molecule but a genetic data bank that transmits its information using a mathematical code. Most of the workings of the cell are best described as&#133;information, or software. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won&apos;t work because it addresses the problem at the wrong conceptual level. (Dr. Paul Davies,) &#13;&#10;***-&apos;&#147;Abiogenesis [life from non-life] strikes many as virtually miraculous&#133;you might get the impression from what I have written not only that the origin of life is virtually impossible, but that life itself is impossible&#133;So what is the answer? Is life a miracle after all?&#148; (Dr. Paul Davies)&#13;&#10;?&#147;[We have no naturalistic explanation for] the origin of life, which is unknown so far&#133;As long as the origin of life can&apos;t be explained in natural terms, the hypothesis of an instant Divine creation of life cannot objectively be ruled out.&#148; (Dr. Christian DeDuve, Nobel Prize-Medicine, 1974)&#13;&#10;?&#147;There are only two possibilities as to how life arose. One is spontaneous generation arising to evolution; the other is a supernatural creative act of God. There is no third possibility.&#148; (George Wald, Nobel Prize-Medicine, 1967)&#13;&#10;&#147;Although a biologist, I must confess I do not understand how life came about&#133;I consider that life only starts at the level of a functional cell. The most primitive cells may require at least several hundred different specific biological macro-molecules. How such already quite complex structures may have come together remains a mystery to me. The possibility of the existence of a Creator, of God, represents to me a satisfactory solution to this problem.&#148; (Dr. Werner Arber, Nobel Prize-Medicine, 1978)&#13;&#10;?&#147;From my earliest training as a scientist I was very strongly brainwashed to believe that science cannot be consistent with any kind of deliberate creation. That notion has had to be very painfully shed. I am quite uncomfortable in the situation, the state of mind I now find myself in. But there is no logical way out of it; it is just not possible that life could have originated from a chemical accident.&#148; (Chandra Wickramasinghe, mathematician, astronomer, astrobiologist - longtime collaborator of Sir Fred Hoyle)&#13;&#10;?&#147;Indeed, such a theory [Intelligent Design] is so obvious that one wonders why it is not widely accepted as being self-evident. The reasons are psychological rather than scientific.&#148; &#147;A common sense interpretation of the facts suggests that a super intellect has monkeyed with the laws of physics, as well as with chemistry and biology, and that there are no blind forces worth speaking about in nature.&#148; (Sir Fred Hoyle)&quot;-Comment: My thoughts exactly.

Theoretical origin of life; more on hydrothermal vents

by David Turell @, Wednesday, August 17, 2016, 15:31 (2799 days ago) @ David Turell

Another comment on the strong possibility that vents were the start of life:-http://www.realclearscience.com/articles/2016/08/15/life_probably_didnt_start_in_primordial_soup_109722.html-&quot;Laboratory experiments confirm that trace amounts of molecular building blocks that make up proteins and information-storing molecules can indeed be created under these conditions. For many, the primordial soup has become the most plausible environment for the origin of first living cells.-&quot;But life isn&apos;t just about replicating information stored within DNA. All living things have to reproduce in order to survive, but replicating the DNA, assembling new proteins and building cells from scratch require tremendous amounts of energy. At the core of life are the mechanisms of obtaining energy from the environment, storing and continuously channelling it into cells&apos; key metabolic reactions.-&quot;Where this energy comes from and how it gets there can tell us a whole lot about the universal principles governing life&apos;s evolution and origin. Recent studies increasingly suggest that the primordial soup was not the right kind of environment to drive the energetics of the first living cells.-***-&quot;Life could have evolved to exploit any of the countless energy sources available on Earth, from heat or electrical discharges to naturally radioactive ores. Instead, all life forms are driven by proton concentration differences across cells&apos; membranes. This suggests that the earliest living cells harvested energy in a similar way and that life itself arose in an environment in which proton gradients were the most accessible power source.-&quot;Recent studies based on sets of genes that were likely to have been present within the first living cells trace the origin of life back to deep-sea hydrothermal vents. These are porous geological structures produced by chemical reactions between solid rock and water. Alkaline fluids from the Earth&apos;s crust flow up the vent towards the more acidic ocean water, creating natural proton concentration differences remarkably similar to those powering all living cells.-&quot;The studies suggest that in the earliest stages of life&apos;s evolution, chemical reactions in primitive cells were likely driven by these non-biological proton gradients. Cells then later learned how to produce their own gradients and escaped the vents to colonise the rest of the ocean and eventually the planet.-&quot;While proponents of the primordial soup theory argue that electrostatic discharges or the Sun&apos;s ultraviolet radiation drove life&apos;s first chemical reactions, modern life is not powered by any of these volatile energy sources. Instead, at the core of life&apos;s energy production are ion gradients across biological membranes. Nothing even remotely similar could have emerged within the warm ponds of primeval broth on Earth&apos;s surface. In these environments, chemical compounds and charged particles tend to get evenly diluted instead of forming gradients or non-equilibrium states that are so central to life.-&quot;Deep-sea hydrothermal vents represent the only known environment that could have created complex organic molecules with the same kind of energy-harnessing machinery as modern cells. Seeking the origins of life in the primordial soup made sense when little was known about the universal principles of life&apos;s energetics. But as our knowledge expands, it is time to embrace alternative hypotheses that recognise the importance of the energy flux driving the first biochemical reactions. These theories seamlessly bridge the gap between the energetics of living cells and non-living molecules.-Comment: Since all early life is related to oceans, the warm sunny pond idea seems remote. The vents are a very likely spot, as previously noted, but knowing the likely place of the origin of life does not explain how life originated. Still a miracle to me.

Theoretical origin of life; more on hydrothermal vents

by David Turell @, Tuesday, February 26, 2019, 20:06 (1876 days ago) @ David Turell

A lab mimics the vents and gets some proteins:

https://phys.org/news/2019-02-nasa-life-ocean-floor.html

"Scientists have reproduced in the lab how the ingredients for life could have formed deep in the ocean 4 billion years ago. The results of the new study offer clues to how life started on Earth and where else in the cosmos we might find it.

***

" Found around cracks in the seafloor, hydrothermal vents are places where natural chimneys form, releasing fluid heated below Earth's crust. When these chimneys interact with the seawater around them, they create an environment that is in constant flux, which is necessary for life to evolve and change. This dark, warm environment fed by chemical energy from Earth may be the key to how life could form on worlds farther out in our solar system, far from the heat of the Sun.

***

"Barge and Flores used ingredients commonly found in early Earth's ocean in their experiments. They combined water, minerals and the "precursor" molecules pyruvate and ammonia, which are needed to start the formation of amino acids. They tested their hypothesis by heating the solution to 158 degrees Fahrenheit (70 degrees Celsius)—the same temperature found near a hydrothermal vent—and adjusting the pH to mimic the alkaline environment. They also removed the oxygen from the mixture because, unlike today, early Earth had very little oxygen in its ocean. The team additionally used the mineral iron hydroxide, or "green rust," which was abundant on early Earth.

"The green rust reacted with small amounts of oxygen that the team injected into the solution, producing the amino acid alanine and the alpha hydroxy acid lactate. Alpha hydroxy acids are byproducts of amino acid reactions, but some scientists theorize they too could combine to form more complex organic molecules that could lead to life.

"'We've shown that in geological conditions similar to early Earth, and maybe to other planets, we can form amino acids and alpha hydroxy acids from a simple reaction under mild conditions that would have existed on the seafloor," said Barge.

"Barge's creation of amino acids and alpha hydroxy acids in the lab is the culmination of nine years of research into the origins of life. Past studies looked at whether the right ingredients for life are found in hydrothermal vents, and how much energy those vents can generate (enough to power a light bulb). But this new study is the first time her team has watched an environment very similar to a hydrothermal vent drive an organic reaction. Barge and her team will continue to study these reactions in anticipation of finding more ingredients for life and creating more complex molecules. Step by step, she's slowly inching her way up the chain of life."

Comment: It takes very much more than two amino acids to get to RNA. As usual lots of hope in this research.

Theoretical origin of life; more on hydrothermal vents

by David Turell @, Friday, March 13, 2020, 17:22 (1495 days ago) @ David Turell

A new study pushing the theory of hydrothermal vents:

https://www.sciencedaily.com/releases/2020/03/200312101054.htm

"Since the origin of life, metabolic networks provide cells with nutrition and energy. Modern networks require thousands of enzymes that perform catalysis. Such networks must have arisen from simpler precursors. Investigating the metabolism of modern cells, Xavier et al. have identified ancient and conserved autocatalytic networks at the core of microbial metabolism that require only co-factors and metals as catalysts. (my bold)

***

"Living cells are the end product of metabolic networks. Food molecules that enter the cell are converted to central intermediates that are then channeled into the pathways that produce the molecules of which cells are made. These networks typically entail more than 1000 reactions, almost all of which are performed by enzymes (proteins), which are encoded by genes (nucleic acids). The link between genes and proteins is, in turn, the universal genetic code that instructs ribosomes to make proteins according to the information stored in genes. (my bold)

***

"The existence and properties of such autocatalytic sets remained the subject of much speculation and decades of fierce debate until the mathematician Mike Steel from the University of Canterbury in New Zealand and Wim Hordijk, a computer scientist from The Netherlands, both coauthors on the study, found ways of harnessing them in the computer. They found that a particular class of autocatalytic sets called RAFs (for reflexively autocatalytic food generated networks), which are very similar in design to cellular metabolism, have the unexpected property of being downright likely to arise from scratch. "The surprise is that the elements only need to add a tiny amount of catalysis to the system before they start to make more of themselves" says Steel. "This is what physicists call self organization, a kind of holy grail in origin of life research" adds Hordijk.

***

"The two kinds of unicellular organisms at the focus of the study, called acetogens and methanogens, have long been in the sights of microbiologists interested in the origin of life. They have been linked to the last universal common ancestor, LUCA, and to geochemical reactions at hydrothermal vents.

***

"Did life arise at hydrothermal vents? "The closer we look, the more signs keep pointing in that direction" says Xavier, "the idea keeps uncovering findings that converge. These vents were probably the first bioreactors on Earth." The identification of autocatalytic networks as components of modern metabolism takes them off the drawing board and into the real world of microbial life. That they uncover fossils from the earliest stages of chemical evolution was unexpected, and opens up new routes for the study of our deepest evolutionary past, probing the time 4 billion years ago, when life was just starting from a small set of naturally-occurring chemical reactions that took place somewhere, perhaps at a hydrothermal vent."

Comment: Once again a highly theoretical view of how life might have automatically started, ignoring the statement in the study about how complex the actual metabolism any living organisms happens to be. Note the first bold. The second bold notes the primary role of onboard information. Where did the information come from if al of this appeared automatically? Information requires mental activity to create it.

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