LUCA latest (Introduction)

by George Jelliss ⌂ @, Crewe, Monday, July 25, 2016, 22:12 (2803 days ago)

Saw this and thought of you: - http://www.nytimes.com/2016/07/26/science/last-universal-ancestor.html?_r=1 - Latest ideas from genetics on LUCA (last universal common ancestor). 
Seems it probably lived in deep sea vents, rather than a Darwinian pond. 
Still a lot of explanation needed as to how it appeared though.

--
GPJ

LUCA latest

by David Turell @, Monday, July 25, 2016, 23:57 (2803 days ago) @ George Jelliss

George: Saw this and thought of you: 
> 
> http://www.nytimes.com/2016/07/26/science/last-universal-ancestor.html?_r=1
&am... 
> Latest ideas from genetics on LUCA (last universal common ancestor). 
> Seems it probably lived in deep sea vents, rather than a Darwinian pond. 
> Still a lot of explanation needed as to how it appeared though. - Thank you George. A great article. I have published a number of articles on the vents. Certainly a likely spot to start life.

LUCA latest

by dhw, Tuesday, July 26, 2016, 13:24 (2802 days ago) @ David Turell

George: Saw this and thought of you: 
> > 
> > http://www.nytimes.com/2016/07/26/science/last-universal-ancestor.html?_r=1
&am... > 
> > Latest ideas from genetics on LUCA (last universal common ancestor). 
> > Seems it probably lived in deep sea vents, rather than a Darwinian pond. 
> > Still a lot of explanation needed as to how it appeared though.
> 
> DAVID: Thank you George. A great article. I have published a number of articles on the vents. Certainly a likely spot to start life.-My thanks, too. You probably won't have been following our discussion on David's theory that all the information needed for evolution may have been present from the beginning, and innovations are caused by loss of information. In this context, I was struck by the following quote:-"He argues that Luca is very close to the origin of life itself. The organism is missing so many genes necessary for life that it must still have been relying on chemical components from its environment."-I don't know about you, but I find it pretty hard to imagine our poor old LUCA sweltering in his deep sea vent, lacking all those genes, and yet at the same time possessing all the information needed to become an Eskimo living in Alaska.

LUCA latest

by David Turell @, Tuesday, July 26, 2016, 15:08 (2802 days ago) @ dhw

dhw: In this context, I was struck by the following quote:
> 
> "He argues that Luca is very close to the origin of life itself. The organism is missing so many genes necessary for life that it must still have been relying on chemical components from its environment."
> 
> I don't know about you, but I find it pretty hard to imagine our poor old LUCA sweltering in his deep sea vent, lacking all those genes, and yet at the same time possessing all the information needed to become an Eskimo living in Alaska.-Please remember LUCA is a theorized close-to-the-origin animal, based on genome studies and assumptions, not a real discovery. It makes the assumption that evolution went from a few genes to many which is most likely true. From the article:-"Their starting point was the known protein-coding genes of bacteria and archaea. Some six million such genes have accumulated over the last 20 years in DNA databanks as scientists with the new decoding machines have deposited gene sequences from thousands of microbes.-"Genes that do the same thing in a human and a mouse are generally related by common descent from an ancestral gene in the first mammal. So by comparing their sequence of DNA letters, genes can be arranged in evolutionary family trees, a property that enabled Dr. Martin and his colleagues to assign the six million genes to a much smaller number of gene families. Of these, only 355 met their criteria for having probably originated in Luca, the joint ancestor of bacteria and archaea."-Finally, remember that these genes must contain information on how to evolve. All the probably correct genes may not have been chosen.

LUCA latest

by dhw, Wednesday, July 27, 2016, 15:54 (2801 days ago) @ David Turell

dhw: In this context, I was struck by the following quote:
"He argues that Luca is very close to the origin of life itself. The organism is missing so many genes necessary for life that it must still have been relying on chemical components from its environment."
I don't know about you, but I find it pretty hard to imagine our poor old LUCA sweltering in his deep sea vent, lacking all those genes, and yet at the same time possessing all the information needed to become an Eskimo living in Alaska.-DAVID: Please remember LUCA is a theorized close-to-the-origin animal, based on genome studies and assumptions, not a real discovery. It makes the assumption that evolution went from a few genes to many which is most likely true […]
Finally, remember that these genes must contain information on how to evolve. All the probably correct genes may not have been chosen.-Thank you for the reminders. Information on how to evolve is another term for what I call the autonomous inventive mechanism, which would have had to be there from the beginning or there would have been no evolution. But equally evolution could not have taken place without masses and masses of new information for the mechanism to work with. Otherwise, if this LUCA theory is correct, life would have been confined to deep sea vents.

LUCA latest

by David Turell @, Wednesday, July 27, 2016, 17:19 (2801 days ago) @ dhw

dhw: But equally evolution could not have taken place without masses and masses of new information for the mechanism to work with. Otherwise, if this LUCA theory is correct, life would have been confined to deep sea vents. - The vents are a very logical place to start life which obviously occurred in the oceans. The vents have all sorts of minerals available, but not amino acids. The ones possibly arriving by meteorite would have to reach those vents to be helpful!

LUCA latest

by David Turell @, Thursday, April 23, 2020, 05:52 (1436 days ago) @ David Turell

It is all very scrambled and we don't know much, which is really an honest assessment, especially in view of today's entry about the small role DNA really plays:

https://phys.org/news/2020-04-reveals-life-earliest-evolution-complicated.html

"Previous studies have suggested this information can be obtained by comparing the genes present in modern organisms. New research indicates that only limited information can be derived using this approach.

"Biologists classify all living organisms into three major groups they call 'domains.' Two of these domains—the Bacteria and the Archaebacteria—consist of single-celled organisms, while the third—the Eukaryota—includes most of the larger, multicellular organisms we are all familiar with: fungi, plants and animals including ourselves. Of the three domains, the Eukaryota almost certainly evolved the most recently, but questions remain about which of the two single-celled domains arose first in the history of life.

***

"New research from Tokyo Tech and the Max Planck Institute suggests understanding early life may be trickier than previously thought.

***

"Their analyses confirm other work which suggested that only a limited understanding of the lifestyle of the most ancient cells can be derived from DNA comparison. Although this is a disappointing result for evolutionary biologists, it is important to understand what can and cannot be known from the data that scientists are able to gather from modern organisms.
Berkemer and McGlynn's work does supply one silver lining however; while it is clear that we don't know what the first organisms metabolised or where they lived, their work provides insight into how quickly they may have evolved billions of years ago.

***

"Their careful analysis showed that early in life's history, different gene types changed at different rates. This suggests that early mutation rates were much higher than at present and there has been a significant contribution of 'gene jumping' over time which makes a simple interpretation of the early 'family tree' of life misleading. They concluded that previous studies sometimes vastly under-sampled the available data and that the data cannot resolve these questions, but that it does show that early evolution was wildly different from what it is at present.

***

"'A fundamental question in biology is what were the first life forms on Earth. There are two basic ways to try and address this. First, we can use the comparison of gene sequences to try and understand which ones seem most ancient. Second, we can look for evidence biology may have left in the geological record." McGlynn says this work shows that although it is clear there is a fuzzy yet remarkable general outline of a family tree of life in the available DNA sequence data, there has been so much evolutionary change that it is still as of yet impossible to say how the earliest organisms made their living or in what types of environments they lived. This is because the signal is simply too noisy due to this early genetic scrambling. As a result, we are still a long way from understanding what the most primitive organisms on Earth were like or the sorts of environments they lived in.

"This work shows there is a detectable signal of very rapid early evolution, thus, while we may not know exactly what early organisms were like, it seems likely life was mutating and evolving very quickly early on. Nevertheless, McGlynn believes it is still amazing that this limited information can be understood at all, that it still tells us important things about the evolution of life on Earth, and suggests we need to develop new ways of looking at available DNA data to find novel techniques of learning what Earth's earliest life was like."

Comment: Finally some sensible discussion. Early life logically had to be just as complex as living cells today. That somehow earliest life was quite simple really makes no sense, in view of simplest life today which is very complex. DNA studies are not the answer as the y simply show protein sources, not how tiers of protein reactions integrate to have life emerge.

LUCA latest: a bacterium stripped of unessential genes

by David Turell @, Wednesday, July 05, 2023, 16:28 (267 days ago) @ David Turell

And it evolved:

https://phys.org/news/2023-07-artificial-cells-life.html

"Evolutionary biologist Jay T. Lennon's research team has been studying a synthetically constructed minimal cell that has been stripped of all but its essential genes. The team found that the streamlined cell can evolve just as fast as a normal cell—demonstrating the capacity for organisms to adapt, even with an unnatural genome that would seemingly provide little flexibility.

***

"'It appears there's something about life that's really robust," says Lennon. "We can simplify it down to just the bare essentials, but that doesn't stop evolution from going to work."

"For their study, Lennon's team used the synthetic organism, Mycoplasma mycoides JCVI-syn3B—a minimized version of the bacterium M. mycoides commonly found in the guts of goats and similar animals. Over millennia, the parasitic bacterium has naturally lost many of its genes as it evolved to depend on its host for nutrition.

"Researchers at the J. Craig Venter Institute in California took this one step further. In 2016, they eliminated 45% of the 901 genes from the natural M. mycoides genome—reducing it to the smallest set of genes required for autonomous cellular life. At 493 genes, the minimal genome of M. mycoides JCVI-syn3B is the smallest of any known free-living organism. In comparison, many animal and plant genomes contain more than 20,000 genes.

***

"Although M. mycoides JCVI-syn3B could grow and divide in laboratory conditions, Lennon and colleagues wanted to know how a minimal cell would respond to the forces of evolution over time, particularly given the limited raw materials upon which natural selection could operate as well as the uncharacterized input of new mutations.

"'Every single gene in its genome is essential," says Lennon in reference to M. mycoides JCVI-syn3B. "One could hypothesize that there is no wiggle room for mutations, which could constrain its potential to evolve."

"The researchers established that M. mycoides JCVI-syn3B, in fact, has an exceptionally high mutation rate. They then grew it in the lab where it was allowed to evolve freely for 300 days, equivalent to 2,000 bacterial generations or about 40,000 years of human evolution.

"The next step was to set up experiments to determine how the minimal cells that had evolved for 300 days performed in comparison to the original, non-minimal M. mycoides as well as to a strain of minimal cells that hadn't evolved for 300 days. In the comparison tests, the researchers put equal amounts of the strains being assessed together in a test tube. The strain better suited to its environment became the more common strain.

"They found that the non-minimal version of the bacterium easily outcompeted the unevolved minimal version. The minimal bacterium that had evolved for 300 days, however, did much better, effectively recovering all of the fitness that it had lost due to genome streamlining. The researchers identified the genes that changed the most during evolution. Some of these genes were involved in constructing the surface of the cell, while the functions of several others remain unknown.

***

"The research done by Lennon and his team demonstrates the power of natural selection to rapidly optimize fitness in the simplest autonomous organism, with implications for the evolution of cellular complexity. In other words, it shows that life finds a way."

Comment: since this resembles earliest life it indicates that life has a built-in drive for survival.

LUCA latest: a bacterium stripped of unessential genes

by dhw, Thursday, July 06, 2023, 11:56 (266 days ago) @ David Turell

LUCA latest: a bacterium stripped of unessential genes

DAVID: And it evolved:
https://phys.org/news/2023-07-artificial-cells-life.html

QUOTES: "'It appears there's something about life that's really robust," says Lennon. "We can simplify it down to just the bare essentials, but that doesn't stop evolution from going to work."
"The research done by Lennon and his team demonstrates the power of natural selection to rapidly optimize fitness in the simplest autonomous organism, with implications for the evolution of cellular complexity. In other words, it shows that life finds a way."

DAVID: since this resembles earliest life it indicates that life has a built-in drive for survival.

It indicates far, far more than that! It indicates that there is a built–in mechanism which enables cells autonomously to EVOLVE in response to the requirements of the environment. But it’s not the power of natural selection that does this, because natural selection does not create anything – it only determines what does or does not survive. So what IS the power that enables cells to restructure themselves autonomously? I would suggest that James A. Shapiro has the answer: cellular intelligence. How did such a mechanism originate? David Turell suggests it was designed by an unknown, eternal, sourceless mind we call God. No doubt Richard Dawkins would suggest it arose by chance. Panpsychists believe that all spatio-temporal things have some kind of quasi-consciousness. Dhw finds all these theories equally hard to believe, and remains perched on his agnostic fence.

My thanks to David for this extremely important and revealing article, which posits the autonomous ability of cells to conduct their own evolution. Worth a post of its own.

LUCA latest: Shapiro redux

by David Turell @, Thursday, July 06, 2023, 17:59 (266 days ago) @ dhw

A giant new essay by Shapiro:

https://aeon.co/essays/why-did-darwins-20th-century-followers-get-evolution-so-wrong?ut...

This failure to take account of alternative modes of change has been foundational to popular and scientific misconceptions of evolution.

***

During the past century, discoveries that have challenged the gradualist view of evolution have been sidelined, forgotten, and derided. This includes the work of 20th-century geneticists...Their findings were ignored or ridiculed to convey the message that the gradual accumulation of random mutations was the only reasonable explanation for evolution...However, it’s an absence that’s particularly conspicuous because alternatives to random mutation have not been difficult to find.

***

These arguments about symbiotic cell fusions, despite being vigorously championed by the evolutionary biologist Lynn Margulis in later years, did not find a place in evolutionary textbooks until they were confirmed by DNA sequencing at the end of the 20th century. And yet, even though these arguments have now been confirmed,...symbiotic cell fusions have still not been incorporated into mainstream evolutionary theory.

An absence that’s perhaps even harder to explain is why the pioneering work of the cytogeneticist Barbara McClintock, one of the giants of 20th-century genetics, has not been accepted as posing a viable alternative to dominant theories of evolution. McClintock won the Nobel Prize in 1983 for her discovery during the 1940s...of rapid genetic changes in maize plants that were definitely not random – changes found not only in maize but, we now know, across all forms of life. After confirmation by molecular geneticists in the 20th century, discoveries like hers should have inspired a radical rethinking of evolution. Instead, these ideas were accepted only among a small circle of geneticists.

***

McClintock found that unstable loci carried insertions of genetic material that were unlike any previously discovered. She demonstrated that these ‘controlling elements’,...Controlling elements were not fixed at a specific site in the chromosomes and, unexpectedly, were able to move or ‘transpose’ from one place to another in the genome. When they arrived at a new location in the genome, they could alter the expression of nearby genetic material. This discovery revealed an entirely new mechanism of genetic regulation and variability: maize plants were rapidly changing their own genomes through transposable controlling elements (TEs). And moreover, TE changes were nonrandom in two ways. Firstly, the same DNA element could insert repeatedly at new target sites; and, secondly, TE mobility and mutagenic activity was activated by specific organismal stress conditions.

***

The fact that TEs respond to stress indicates that they are regulated biological entities that play a sensory-guided role in survival and reproduction. The notion of controlled biological processes at the core of organic evolution is plainly incompatible with a purely physicalist explanation, such as random mutations plus natural selection.

***

Eukaryotes appeared around 2 billion years ago, and we know from DNA sequencing that this important step in biological evolution included a cell fusion, or ‘symbiogenetic’ event, between a particular kind of aerobic bacterium and a particular kind of anaerobic archaeon. The bacterium was the ancestor of the mitochondria that allow our cells and those of other eukaryotes to efficiently generate energy in the presence of oxygen, known as aerobic metabolism.

***

Horizontal DNA transfer occurs across all taxonomic boundaries... For a horizontal transfer to occur, a DNA sequence has to be extracted from one organism and taken up by another. There are multiple biological mechanisms involved in these horizontal DNA exchanges, including viruses, parasites and the uptake of DNA from the environment.

***

Like horizontal DNA transfer, ‘domain shuffling’ involves inserting extended segments of protein-coding DNA in various locations in the genome. This means that cells can cut and splice their own DNA molecules, a capability that I call ‘natural genetic engineering’.

***

The rapidly expanding catalogue of functions shows that, through ncRNAs, genomes encode biologically functional molecules other than proteins. It is possible that ncRNAs even represent a higher level of biological control than proteins...the discovery of functional ncRNAs in the genome completely undermines arguments for evolution by Dawkins and similar thinkers that rely on random mutation and natural selection.

***

In many cases of hybrid speciation, the novel hybrid genome undergoes a whole genome duplication (WGD), involving the duplication of all chromosomes. WGD does not take place through random mutation but rather by control over cellular reproduction.

***

By turning evolutionary variation from random accidents to biological responses, 21st-century molecular genetics and genomics have revealed that living organisms possess tremendous potential for adaptive genome reconfiguration.

Comment: I have eviscerated a 5.000-word essay. Read it all with pleasure.

LUCA latest: Shapiro redux

by dhw, Friday, July 07, 2023, 13:33 (265 days ago) @ David Turell

Once more my thanks for posting such material. Brilliant essay! It speaks for itself, of course, but it should be mentioned that the two “giants” Shapiro mentions – Margulis and McClintock – were, like himself, firm believers in cellular intelligence. I’ve picked out one quote from your text and two from the complete essay:

cells can cut and splice their own DNA molecules, a capability that I call ‘natural genetic engineering’”.

This autonomy lies at the heart of Shapiro’s whole theory. But he does not tell us how they acquired the ability – he is concerned with the way evolution works, and not with the origin of the mechanisms that make it work. Just like Darwin (whose random mutations he convincingly debunks), he offers a theory which need not offend any religious believer.

In other words, within a small number of generations, descendants of the initial hybrid constitute a newly evolved species with novel adaptive characters and reproductive isolation.

This is a major point in the discussion of the time available for species to evolve. ID-ers like to emphasize how long it would take for random mutations to accumulate into new species. But if we substitute a non-random process by which cells respond to environmental change by engineering their own mutations, it is generations that matter, not years.

Those obligations include reorienting our studies of adaptive variation towards learning how deeply genome change is integrated with biocognitive sensory responses.”

Again, this lies at the heart of his theory: cells are cognitive beings which engineer the “adaptive variations” that lead to speciation.

LUCA latest: Shapiro redux

by David Turell @, Friday, July 07, 2023, 17:33 (265 days ago) @ dhw

dhw: Once more my thanks for posting such material. Brilliant essay! It speaks for itself, of course, but it should be mentioned that the two “giants” Shapiro mentions – Margulis and McClintock – were, like himself, firm believers in cellular intelligence. I’ve picked out one quote from your text and two from the complete essay:

cells can cut and splice their own DNA molecules, a capability that I call ‘natural genetic engineering’”.

This autonomy lies at the heart of Shapiro’s whole theory. But he does not tell us how they acquired the ability – he is concerned with the way evolution works, and not with the origin of the mechanisms that make it work. Just like Darwin (whose random mutations he convincingly debunks), he offers a theory which need not offend any religious believer.

In other words, within a small number of generations, descendants of the initial hybrid constitute a newly evolved species with novel adaptive characters and reproductive isolation.

This is a major point in the discussion of the time available for species to evolve. ID-ers like to emphasize how long it would take for random mutations to accumulate into new species. But if we substitute a non-random process by which cells respond to environmental change by engineering their own mutations, it is generations that matter, not years.

Those obligations include reorienting our studies of adaptive variation towards learning how deeply genome change is integrated with biocognitive sensory responses.”

Again, this lies at the heart of his theory: cells are cognitive beings which engineer the “adaptive variations” that lead to speciation.

Just to remind the reader, all of Shapiro's studies were on the bacterian ability to edit their own DNA. Animals and plants have adaptive abilities, much short of actual speciation. Thanks for adding the new quotes.

LUCA latest: Shapiro redux

by dhw, Saturday, July 08, 2023, 11:43 (264 days ago) @ David Turell

https://aeon.co/essays/why-did-darwins-20th-century-followers-get-evolution-so-wrong?ut...

QUOTE: “cells can cut and splice their own DNA molecules, a capability that I call ‘natural genetic engineering’”.

dhw: This autonomy lies at the heart of Shapiro’s whole theory. But he does not tell us how they acquired the ability – he is concerned with the way evolution works, and not with the origin of the mechanisms that make it work. Just like Darwin (whose random mutations he convincingly debunks), he offers a theory which need not offend any religious believer.

QUOTE: “In other words, within a small number of generations, descendants of the initial hybrid constitute a newly evolved species with novel adaptive characters and reproductive isolation.”

dhw: This is a major point in the discussion of the time available for species to evolve. ID-ers like to emphasize how long it would take for random mutations to accumulate into new species. But if we substitute a non-random process by which cells respond to environmental change by engineering their own mutations, it is generations that matter, not years.

QUOTE:“Those obligations include reorienting our studies of adaptive variation towards learning how deeply genome change is integrated with biocognitive sensory responses.

dhw: Again, this lies at the heart of his theory: cells are cognitive beings which engineer the “adaptive variations” that lead to speciation.

DAVID: Just to remind the reader, all of Shapiro's studies were on the bacterian ability to edit their own DNA. Animals and plants have adaptive abilities, much short of actual speciation. Thanks for adding the new quotes.

Do you honestly think Shapiro knows nothing about other life forms?

LUCA latest: Shapiro redux

by David Turell @, Saturday, July 08, 2023, 17:28 (264 days ago) @ dhw

https://aeon.co/essays/why-did-darwins-20th-century-followers-get-evolution-so-wrong?ut...

QUOTE: “cells can cut and splice their own DNA molecules, a capability that I call ‘natural genetic engineering’”.

dhw: This autonomy lies at the heart of Shapiro’s whole theory. But he does not tell us how they acquired the ability – he is concerned with the way evolution works, and not with the origin of the mechanisms that make it work. Just like Darwin (whose random mutations he convincingly debunks), he offers a theory which need not offend any religious believer.

QUOTE: “In other words, within a small number of generations, descendants of the initial hybrid constitute a newly evolved species with novel adaptive characters and reproductive isolation.”

dhw: This is a major point in the discussion of the time available for species to evolve. ID-ers like to emphasize how long it would take for random mutations to accumulate into new species. But if we substitute a non-random process by which cells respond to environmental change by engineering their own mutations, it is generations that matter, not years.

QUOTE:“Those obligations include reorienting our studies of adaptive variation towards learning how deeply genome change is integrated with biocognitive sensory responses.

dhw: Again, this lies at the heart of his theory: cells are cognitive beings which engineer the “adaptive variations” that lead to speciation.

DAVID: Just to remind the reader, all of Shapiro's studies were on the bacterian ability to edit their own DNA. Animals and plants have adaptive abilities, much short of actual speciation. Thanks for adding the new quotes.

dhw: Do you honestly think Shapiro knows nothing about other life forms?

Of course he does, as we all do. He is trying to tell us theoretically speciation acts that way. You and I view Shapiro very differently while we both appreciate his work.

LUCA latest: Shapiro redux

by dhw, Sunday, July 09, 2023, 10:43 (263 days ago) @ David Turell

DAVID: Just to remind the reader, all of Shapiro's studies were on the bacterian ability to edit their own DNA. Animals and plants have adaptive abilities, much short of actual speciation. [...]

dhw: Do you honestly think Shapiro knows nothing about other life forms?

DAVID: Of course he does, as we all do. He is trying to tell us theoretically speciation acts that way. You and I view Shapiro very differently while we both appreciate his work.

Yes, he has proposed a theory which you have tried to dismiss on the somewhat insulting grounds that he only knows about bacteria. We both know exactly what his theory is, and the difference between us is that I find his theory far more convincing than you do!

LUCA latest: Shapiro redux

by David Turell @, Sunday, July 09, 2023, 15:40 (263 days ago) @ dhw

DAVID: Just to remind the reader, all of Shapiro's studies were on the bacterian ability to edit their own DNA. Animals and plants have adaptive abilities, much short of actual speciation. [...]

dhw: Do you honestly think Shapiro knows nothing about other life forms?

DAVID: Of course he does, as we all do. He is trying to tell us theoretically speciation acts that way. You and I view Shapiro very differently while we both appreciate his work.

dhw: Yes, he has proposed a theory which you have tried to dismiss on the somewhat insulting grounds that he only knows about bacteria. We both know exactly what his theory is, and the difference between us is that I find his theory far more convincing than you do!

Yes, it fits your preconceived bias.

LUCA latest: Shapiro redux

by dhw, Monday, July 10, 2023, 13:17 (262 days ago) @ David Turell

DAVID: Just to remind the reader, all of Shapiro's studies were on the bacterian ability to edit their own DNA. Animals and plants have adaptive abilities, much short of actual speciation. [...]

dhw: Do you honestly think Shapiro knows nothing about other life forms?

DAVID: Of course he does, as we all do. He is trying to tell us theoretically speciation acts that way. You and I view Shapiro very differently while we both appreciate his work.

dhw: Yes, he has proposed a theory which you have tried to dismiss on the somewhat insulting grounds that he only knows about bacteria. We both know exactly what his theory is, and the difference between us is that I find his theory far more convincing than you do!

DAVID: Yes, it fits your preconceived bias.

I had never even heard of Shapiro until you summarized his theory in your excellent book The Atheist Delusion ten years ago. I am now revising my “brief guide” to incorporate it. Thank you so much for introducing me to it. Finding one theory more convincing than another, and explaining why one does so, is nothing like the preconceived bias which insists on a belief even though the believer himself can make no sense of it (see the thread on your theory of evolution).

LUCA latest: Shapiro redux

by David Turell @, Tuesday, July 11, 2023, 04:03 (262 days ago) @ dhw

DAVID: Just to remind the reader, all of Shapiro's studies were on the bacterian ability to edit their own DNA. Animals and plants have adaptive abilities, much short of actual speciation. [...]

dhw: Do you honestly think Shapiro knows nothing about other life forms?

DAVID: Of course he does, as we all do. He is trying to tell us theoretically speciation acts that way. You and I view Shapiro very differently while we both appreciate his work.

dhw: Yes, he has proposed a theory which you have tried to dismiss on the somewhat insulting grounds that he only knows about bacteria. We both know exactly what his theory is, and the difference between us is that I find his theory far more convincing than you do!

DAVID: Yes, it fits your preconceived bias.

dhw: I had never even heard of Shapiro until you summarized his theory in your excellent book The Atheist Delusion ten years ago. I am now revising my “brief guide” to incorporate it. Thank you so much for introducing me to it. Finding one theory more convincing than another, and explaining why one does so, is nothing like the preconceived bias which insists on a belief even though the believer himself can make no sense of it (see the thread on your theory of evolution).

Don't fool yourself. It feels so good to you, you will put it your "brief guide". Preconception is involved.

LUCA latest: Shapiro redux

by dhw, Tuesday, July 11, 2023, 09:04 (261 days ago) @ David Turell

DAVID: Just to remind the reader, all of Shapiro's studies were on the bacterian ability to edit their own DNA. Animals and plants have adaptive abilities, much short of actual speciation. [...]

dhw: Do you honestly think Shapiro knows nothing about other life forms?

DAVID: Of course he does, as we all do. He is trying to tell us theoretically speciation acts that way. You and I view Shapiro very differently while we both appreciate his work.

dhw: Yes, he has proposed a theory which you have tried to dismiss on the somewhat insulting grounds that he only knows about bacteria. We both know exactly what his theory is, and the difference between us is that I find his theory far more convincing than you do!

DAVID: Yes, it fits your preconceived bias.

dhw: I had never even heard of Shapiro until you summarized his theory in your excellent book The Atheist Delusion ten years ago. I am now revising my “brief guide” to incorporate it. Thank you so much for introducing me to it. Finding one theory more convincing than another, and explaining why one does so, is nothing like the preconceived bias which insists on a belief even though the believer himself can make no sense of it (see the thread on your theory of evolution).

DAVID: Don't fool yourself. It feels so good to you, you will put it your "brief guide". Preconception is involved.

Of course nobody would express any kind of belief if they didn’t believe it before they expressed it. Your only objection to Shapiro’s theory seems to be that he did his research on bacteria, which you have now withdrawn. I find his explanation of the vast variety of life forms more convincing (though still unproven) than your own rigid belief that your God deliberately created them all, although 99% had no connection with the only life forms he wanted to create. As you cannot find a single reason why he would use such a method to achieve such a purpose, I would certainly regard your belief as “preconceived bias”. I would regard my support for Shapiro’s theory as a well-reasoned argument, just as I see your support for the theory of intelligent design as a well-reasoned argument. It is only when you cling to an irrational belief - which does not even make sense to you - and reject any alternative and well-reasoned theory, that I would accuse you of preconceived bias.

LUCA latest: Shapiro redux

by David Turell @, Tuesday, July 11, 2023, 18:15 (261 days ago) @ dhw

DAVID: Yes, it fits your preconceived bias.

dhw: I had never even heard of Shapiro until you summarized his theory in your excellent book The Atheist Delusion ten years ago. I am now revising my “brief guide” to incorporate it. Thank you so much for introducing me to it. Finding one theory more convincing than another, and explaining why one does so, is nothing like the preconceived bias which insists on a belief even though the believer himself can make no sense of it (see the thread on your theory of evolution).

DAVID: Don't fool yourself. It feels so good to you, you will put it your "brief guide". Preconception is involved.

dhw: Of course nobody would express any kind of belief if they didn’t believe it before they expressed it. Your only objection to Shapiro’s theory seems to be that he did his research on bacteria, which you have now withdrawn. I find his explanation of the vast variety of life forms more convincing (though still unproven) than your own rigid belief that your God deliberately created them all, although 99% had no connection with the only life forms he wanted to create. As you cannot find a single reason why he would use such a method to achieve such a purpose, I would certainly regard your belief as “preconceived bias”. I would regard my support for Shapiro’s theory as a well-reasoned argument, just as I see your support for the theory of intelligent design as a well-reasoned argument. It is only when you cling to an irrational belief - which does not even make sense to you - and reject any alternative and well-reasoned theory, that I would accuse you of preconceived bias.

I developed my ideas about God from a ground zero agnostic viewpoint. No bias involved. You expressed a need for Shapiro in adapting his ideas. That is evidence for preconceived bias. I have not withdrawn my objection to his theory based on bacteria.

LUCA latest: Shapiro redux

by dhw, Wednesday, July 12, 2023, 12:07 (260 days ago) @ David Turell

(Edited for clarity)

DAVID: Don't fool yourself. It feels so good to you, you will put it your "brief guide". Preconception is involved.

dhw: Of course nobody would express any kind of belief if they didn’t believe it before they expressed it. Your only objection to Shapiro’s theory seems to be that he did his research on bacteria, which you have now withdrawn.

DAVID: I have not withdrawn my objection to his theory based on bacteria.

You reminded the reader that “all of Shapiro’s studies were on the bacterian ability to edit their own DNA.” I asked if you honestly thought he knew nothing about other life forms. You replied: “Of course he does.” I’d have thought this invalidated your objection.

DAVID: I developed my ideas about God from a ground zero agnostic viewpoint. No bias involved.

When you were developing your ideas, I’m sure there was no bias involved. And eventually you came to a definite conclusion. Bias only comes on the scene when a definite conclusion is challenged, flaws appear in the argument that led to the conclusion, but you refuse to consider the flaws even though you can’t find a single explanation for them.

DAVID: You expressed a need for Shapiro in adapting his ideas. That is evidence for preconceived bias.

The basis of agnosticism is acknowledgement of ignorance. As you say, the agnostic starts from “ground zero”. I have considered all the evidence and find the theory of common descent so convincing that I believe it. However, the theory of random mutations as the driving force of change does not convince me. Nor does the theory that God, if he exists, programmed every speciation, natural wonder, strategy, lifestyle etc. 3.8 billion years ago. Nor does the theory that God, if he exists, keeps popping in to perform countless operations or give countless lessons to all life forms whenever they have a problem. However, Shapiro’s theory (which I have not “adapted”) that the driving force is intelligent cells which respond to changing conditions seems to me far more convincing than the other theories I’ve mentioned. It also leaves wide open the question of God’s existence, which I must always take into account, partly because the argument for design is so convincing. That is the point I have reached. You have not offered me a single reason why I should reject Shapiro’s theory, and so I continue to regard it as the most convincing. I don’t know why you consider this to be “preconceived bias”. Meanwhile, you stick rigidly to your own theories in spite of all the flaws which you are unable to explain. Rigid adherence to an irrational belief is a pretty good definition of “preconceived bias”.

LUCA latest: Shapiro redux

by David Turell @, Wednesday, July 12, 2023, 19:23 (260 days ago) @ dhw

(Edited for clarity)

DAVID: Don't fool yourself. It feels so good to you, you will put it your "brief guide". Preconception is involved.

dhw: Of course nobody would express any kind of belief if they didn’t believe it before they expressed it. Your only objection to Shapiro’s theory seems to be that he did his research on bacteria, which you have now withdrawn.

DAVID: I have not withdrawn my objection to his theory based on bacteria.

You reminded the reader that “all of Shapiro’s studies were on the bacterian ability to edit their own DNA.” I asked if you honestly thought he knew nothing about other life forms. You replied: “Of course he does.” I’d have thought this invalidated your objection.

DAVID: I developed my ideas about God from a ground zero agnostic viewpoint. No bias involved.

When you were developing your ideas, I’m sure there was no bias involved. And eventually you came to a definite conclusion. Bias only comes on the scene when a definite conclusion is challenged, flaws appear in the argument that led to the conclusion, but you refuse to consider the flaws even though you can’t find a single explanation for them.

DAVID: You expressed a need for Shapiro in adapting his ideas. That is evidence for preconceived bias.

dhw; The basis of agnosticism is acknowledgement of ignorance. As you say, the agnostic starts from “ground zero”. I have considered all the evidence and find the theory of common descent so convincing that I believe it. However, the theory of random mutations as the driving force of change does not convince me. Nor does the theory that God, if he exists, programmed every speciation, natural wonder, strategy, lifestyle etc. 3.8 billion years ago. Nor does the theory that God, if he exists, keeps popping in to perform countless operations or give countless lessons to all life forms whenever they have a problem. However, Shapiro’s theory (which I have not “adapted”) that the driving force is intelligent cells which respond to changing conditions seems to me far more convincing than the other theories I’ve mentioned. It also leaves wide open the question of God’s existence, which I must always take into account, partly because the argument for design is so convincing. That is the point I have reached. You have not offered me a single reason why I should reject Shapiro’s theory, and so I continue to regard it as the most convincing. I don’t know why you consider this to be “preconceived bias”. Meanwhile, you stick rigidly to your own theories in spite of all the flaws which you are unable to explain. Rigid adherence to an irrational belief is a pretty good definition of “preconceived bias”.

You are convinced of the bolded because it fits your preconception of a necessary force for speciation. You are fully aware of the exquisite designs organisms exhibit. Only a designing mind can achieve that level of design. Cells do not have that degree of mental capacity, even huge committees of them.

LUCA latest: Shapiro redux

by David Turell @, Thursday, July 13, 2023, 01:59 (260 days ago) @ David Turell

Larry Moran's criticism of Shapiro's book, Evolution:


https://sandwalk.blogspot.com/2012/12/james-shapiro-responds-to-my-review-of.html

"I can understand Shapiro's frustration because everyone who knows anything about his subject matter thinks he's way off base. On the other hand, Intelligent Design Creationists are big fans of his writing. I suppose he would have preferred it if Casey Luskin had written the review for NCSE Reports. I don't think that was going to happen.

"Shapiro continues ...
My argument is that molecular research over the past sixty years on DNA change processes has taught us that virtually all genetic variation results from the action of regulated cell biochemistry, including a wide array of cutting, splicing and polymerizing functions that I summarize under the term “natural genetic engineering”. I assert that this realization represents a fundamental shift from the conventional view that genetic change is a random, accidental process.

"Yep, that's true. Shapiro claims that the "old" idea of variation caused mostly by accidental DNA replication errors is wrong. The implication is that of the roughly 100 new mutations in every new born baby, most are due to "natural genetic engineering."

"And when we compare the DNA sequences of genes from different species the results don't actually show mostly neutral changes that have been fixed by random genetic drift but, instead, they show that most of this variation is due to "natural genetic engineering." There's no defense of these implications in his book but I suppose that's simply because he thinks they are self-evident.

***

"Shapiro says,
In his review, Moran tells us “I have to confess that I skipped most of this chapter [that is, Part II, emphasis added]. I know about genome rearrangements and so does everyone else who has read a textbook in the past forty years” Frankly, I am not aware of textbooks that have routinely covered mutator polymerases, diversity-generating retroelements, retrosplicing group II introns, CRISPRs, SINE elements and many other natural genetic engineering systems over the past 40 years.

"I discussed all those topics, except CRISPRs, in my big biochemistry textbook twenty years ago. They have also been covered in the various editions of Genes by Benjamin Lewin, beginning in the mid 1980's. I can't begin to imagine how James Shapiro can claim to be an expert on these things without being aware of what's taught in undergraduate molecular biology classes.

"One of the main points of my critique was that rare events such as genome duplications do occur but that is fully consistent with the role of chance and accident in evolution. Events occurring on million year time scales do not justify a claim that "virtually all genetic variation" is due to "natural genetic engineering."

"Here's how Shapiro responds to that criticism ...

To counter my position, Moran writes,
His main thesis seems to be that such mutations are not random as neo-Darwinism demands. Genome duplication is one example. There may have been two genome duplications in the vertebrate lineage. Both of them occurred in fish.
This is wrong and misleading. There were indeed two genome duplications in the history of teleosts, at key points of phylogenetic diversification, but they were far from unique in vertebrate evolution. I was quite explicitly referring to the pair of duplications that, successively, coincided with the origins of all vertebrates and then of all jawed vertebrates. I think RNCSE readers will agree that these certainly constituted major events in animal evolution.

***

"I raised the same issue with respect to transposon mediated events. Are they common and do they provide evidence for some directed form of evolution ("natural genetic engineering"). Are they evidence against randomness and accident as the main source of variation?

"Shapiro thinks my criticism was misguided ...
Moran continues to depict what I had to say about the evolutionary role of natural genetic engineering as exaggerated:
Another example involves transposons. In the hominid lineage there may be evidence of a few transposon-related genome alterations that turned out to be beneficial and subsequently became fixed in the population. That’s a rate of approximately one every million years or so. (Moran 2012:9.2)
This downplaying of the role of transposons (a class of mobile genetic elements) is quite an ironic assertion. The rate with which “transposon-related genome alterations” are being discovered by parsing genome sequences is truly astonishing. At the end of last year, a group of bioinformaticians published a Nature paper examining the human genome as compared to 29 other aligned vertebrate genomes. They said:
We report … 280,000 non-coding elements exapted from mobile elementsand more than 1,000 primate- and human-accelerated elements. (Lindblad-Toh and others 2011:476)
Perhaps Moran would not have made his tendentious error about the rarity of “transposon related genome alterations” if he had not have skipped so much of the core of my book.

***

"I once asked James Shapiro whether he believes in god(s) and whether his "discovery" of some form of directed evolution has anything to do with that belief. He declined to answer."

Comment: we know the answer. Shapiro was a president of his Temple. Moran is a devoted Darwinist/Atheist who denies the ENCODE removal of junk DNA in his own new book.

LUCA latest: Shapiro redux

by dhw, Thursday, July 13, 2023, 09:27 (259 days ago) @ David Turell

Shapiro’s theory (which I have not “adapted”) that the driving force is intelligent cells which respond to changing conditions seems to me far more convincing than the other theories I’ve mentioned. It also leaves wide open the question of God’s existence, which I must always take into account, partly because the argument for design is so convincing. That is the point I have reached. You have not offered me a single reason why I should reject Shapiro’s theory, and so I continue to regard it as the most convincing. I don’t know why you consider this to be “preconceived bias”. Meanwhile, you stick rigidly to your own theories in spite of all the flaws which you are unable to explain. Rigid adherence to an irrational belief is a pretty good definition of “preconceived bias”.

DAVID: You are convinced of the bolded because it fits your preconception of a necessary force for speciation.

In my search for a convincing cause of speciation, I am indeed convinced that there must be a cause or “necessary force” for speciation. You think it’s your God’s 3.8-billion-year-old programme or ad hoc dabbling, Darwin thinks its random mutations, and Shapiro thinks it’s cellular intelligence.

DAVID: You are fully aware of the exquisite designs organisms exhibit. Only a designing mind can achieve that level of design. Cells do not have that degree of mental capacity, even huge committees of them.

And there you go again, insisting that you know Shapiro is wrong and so, by extension, your theory must be right, in spite of all its logical flaws. Even though it doesn’t make sense to you, you can’t see that this constitutes “preconceived bias”, and you can’t see that your rejection of Shapiro’s theory is based solely on your preconceived bias that cells are not capable of that level of design. NB I am not asking you to believe his theory. I am asking you not to reject it. My view that it is more convincing than the other theories does not constitute a rigid belief, but your “preconceived bias” against it does not provide a single reason for rejecting it.

Larry Moran's criticism of Shapiro's book, Evolution:

https://sandwalk.blogspot.com/2012/12/james-shapiro-responds-to-my-review-of.html

QUOTES: "I can understand Shapiro's frustration because everyone who knows anything about his subject matter thinks he's way off base. On the other hand, Intelligent Design Creationists are big fans of his writing. I suppose he would have preferred it if Casey Luskin had written the review for NCSE Reports. I don't think that was going to happen.

"I once asked James Shapiro whether he believes in god(s) and whether his "discovery" of some form of directed evolution has anything to do with that belief. He declined to answer."

Comment: we know the answer. Shapiro was a president of his Temple. Moran is a devoted Darwinist/Atheist who denies the ENCODE removal of junk DNA in his own new book.”

Shapiro’s theory does not depend on the existence of God! That’s why he objects to it being equated with the ID movement. Moran’s theory depends on his faith in chance, and even you would reject such faith.

*********************************

I may not be able to post any replies for the next two or three days, as the family is gathering for my son’s funeral.

LUCA latest: Shapiro redux

by David Turell @, Thursday, July 13, 2023, 20:39 (259 days ago) @ dhw

dhw: Shapiro’s theory (which I have not “adapted”) that the driving force is intelligent cells which respond to changing conditions seems to me far more convincing than the other theories I’ve mentioned. It also leaves wide open the question of God’s existence, which I must always take into account, partly because the argument for design is so convincing. That is the point I have reached. You have not offered me a single reason why I should reject Shapiro’s theory, and so I continue to regard it as the most convincing. I don’t know why you consider this to be “preconceived bias”. Meanwhile, you stick rigidly to your own theories in spite of all the flaws which you are unable to explain. Rigid adherence to an irrational belief is a pretty good definition of “preconceived bias”.

DAVID: You are convinced of the bolded because it fits your preconception of a necessary force for speciation.

dhw: In my search for a convincing cause of speciation, I am indeed convinced that there must be a cause or “necessary force” for speciation. You think it’s your God’s 3.8-billion-year-old programme or ad hoc dabbling, Darwin thinks its random mutations, and Shapiro thinks it’s cellular intelligence.

DAVID: You are fully aware of the exquisite designs organisms exhibit. Only a designing mind can achieve that level of design. Cells do not have that degree of mental capacity, even huge committees of them.

dhw: And there you go again, insisting that you know Shapiro is wrong and so, by extension, your theory must be right, in spite of all its logical flaws. Even though it doesn’t make sense to you, you can’t see that this constitutes “preconceived bias”, and you can’t see that your rejection of Shapiro’s theory is based solely on your preconceived bias that cells are not capable of that level of design. NB I am not asking you to believe his theory. I am asking you not to reject it. My view that it is more convincing than the other theories does not constitute a rigid belief, but your “preconceived bias” against it does not provide a single reason for rejecting it.

Only God's designing mind is capable of the biochemical complexities of living forms.


Larry Moran's criticism of Shapiro's book, Evolution:

https://sandwalk.blogspot.com/2012/12/james-shapiro-responds-to-my-review-of.html

QUOTES: "I can understand Shapiro's frustration because everyone who knows anything about his subject matter thinks he's way off base. On the other hand, Intelligent Design Creationists are big fans of his writing. I suppose he would have preferred it if Casey Luskin had written the review for NCSE Reports. I don't think that was going to happen.

"I once asked James Shapiro whether he believes in god(s) and whether his "discovery" of some form of directed evolution has anything to do with that belief. He declined to answer."

Comment: we know the answer. Shapiro was a president of his Temple. Moran is a devoted Darwinist/Atheist who denies the ENCODE removal of junk DNA in his own new book.

dhw; Shapiro’s theory does not depend on the existence of God! That’s why he objects to it being equated with the ID movement. Moran’s theory depends on his faith in chance, and even you would reject such faith.

Shapiro as a professional scientist cannot bring god into the picture.


*********************************

dhw; I may not be able to post any replies for the next two or three days, as the family is gathering for my son’s funeral.

We all offer our condolences and look forward to your return.

LUCA latest: Shapiro redux

by dhw, Monday, July 17, 2023, 13:51 (255 days ago) @ David Turell

DAVID: You are fully aware of the exquisite designs organisms exhibit. Only a designing mind can achieve that level of design. Cells do not have that degree of mental capacity, even huge committees of them.

dhw: And there you go again, insisting that you know Shapiro is wrong and so, by extension, your theory must be right, in spite of all its logical flaws. NB I am not asking you to believe his theory. I am asking you not to reject it. My view that it is more convincing than the other theories does not constitute a rigid belief, but your “preconceived bias” against it does not provide a single reason for rejecting it.

DAVID: Only God's designing mind is capable of the biochemical complexities of living forms.

We are not talking about the biochemical complexities, but about the ability to process information, to communicate, to take decisions etc. – all the hallmarks of autonomous intelligence.

Larry Moran's criticism of Shapiro's book, Evolution:

MORAN: "I once asked James Shapiro whether he believes in god(s) and whether his "discovery" of some form of directed evolution has anything to do with that belief. He declined to answer."
MORAN: we know the answer. Shapiro was a president of his Temple. Moran is a devoted Darwinist/Atheist who denies the ENCODE removal of junk DNA in his own new book.

dhw: Shapiro’s theory does not depend on the existence of God! That’s why he objects to it being equated with the ID movement. Moran’s theory depends on his faith in chance, and even you would reject such faith.

DAVID: Shapiro as a professional scientist cannot bring god into the picture.

And there is no reason why he should. He is dealing with evolution, which is Chapter Two in the history of life, not Chapter One, which is the origin of life. Theists and atheists can both use his theory – just as they can both use Darwin’s theory.

LUCA latest: Shapiro redux

by David Turell @, Monday, July 17, 2023, 16:24 (255 days ago) @ dhw

DAVID: Only God's designing mind is capable of the biochemical complexities of living forms.

dhw: We are not talking about the biochemical complexities, but about the ability to process information, to communicate, to take decisions etc. – all the hallmarks of autonomous intelligence.

BUT, it is exactly the biochemical complexities that process the information.


Larry Moran's criticism of Shapiro's book, Evolution:

MORAN: "I once asked James Shapiro whether he believes in god(s) and whether his "discovery" of some form of directed evolution has anything to do with that belief. He declined to answer."
DAVID: we know the answer. Shapiro was a president of his Temple. Moran is a devoted Darwinist/Atheist who denies the ENCODE removal of junk DNA in his own new book.

dhw: Shapiro’s theory does not depend on the existence of God! That’s why he objects to it being equated with the ID movement. Moran’s theory depends on his faith in chance, and even you would reject such faith.

DAVID: Shapiro as a professional scientist cannot bring God into the picture.

dhw: And there is no reason why he should. He is dealing with evolution, which is Chapter Two in the history of life, not Chapter One, which is the origin of life. Theists and atheists can both use his theory – just as they can both use Darwin’s theory.

Whoa! What Shapiro studied was bacteria, which represent the unevolved start of life. They cannot represent the future.

LUCA latest: Shapiro redux

by dhw, Tuesday, July 18, 2023, 11:21 (254 days ago) @ David Turell

DAVID: Only God's designing mind is capable of the biochemical complexities of living forms.

dhw: We are not talking about the biochemical complexities, but about the ability to process information, to communicate, to take decisions etc. – all the hallmarks of autonomous intelligence.

DAVID: BUT, it is exactly the biochemical complexities that process the information.

There speaks a self-professed dualist. But even if you believe that all mental processes stem from biochemical processes, you are still stuck with the fact that living cells process information, communicate, take decisions, solve problems etc., and these activities are hallmarks of autonomous intelligence. If that is true of us humans, whether designed by God or not, and whether biochemical or not, then why can’t it be true of other life forms, including individual cells?

DAVID: Shapiro as a professional scientist cannot bring God into the picture.

dhw: And there is no reason why he should. He is dealing with evolution, which is Chapter Two in the history of life, not Chapter One, which is the origin of life. Theists and atheists can both use his theory – just as they can both use Darwin’s theory.

DAVID: Whoa! What Shapiro studied was bacteria, which represent the unevolved start of life. They cannot represent the future.

How many more times? You have agreed that Shapiro would have known about other life forms, and his conclusions are not based solely on bacterial behaviour, and the theory of cellular intelligence has been embraced by other experts in the field. And this is a complete digression from the subject, which was Moran’s objections.

LUCA latest: Shapiro redux

by David Turell @, Tuesday, July 18, 2023, 13:50 (254 days ago) @ dhw

DAVID: Only God's designing mind is capable of the biochemical complexities of living forms.

dhw: We are not talking about the biochemical complexities, but about the ability to process information, to communicate, to take decisions etc. – all the hallmarks of autonomous intelligence.

DAVID: BUT, it is exactly the biochemical complexities that process the information.

dhw: There speaks a self-professed dualist. But even if you believe that all mental processes stem from biochemical processes, you are still stuck with the fact that living cells process information, communicate, take decisions, solve problems etc., and these activities are hallmarks of autonomous intelligence. If that is true of us humans, whether designed by God or not, and whether biochemical or not, then why can’t it be true of other life forms, including individual cells?

The automaticity of cells is clearly shown in everyday research. Yes, they look intelligent, but they follow very intelligent instructions from God, the designer.


DAVID: Shapiro as a professional scientist cannot bring God into the picture.

dhw: And there is no reason why he should. He is dealing with evolution, which is Chapter Two in the history of life, not Chapter One, which is the origin of life. Theists and atheists can both use his theory – just as they can both use Darwin’s theory.

DAVID: Whoa! What Shapiro studied was bacteria, which represent the unevolved start of life. They cannot represent the future.

dhw: How many more times? You have agreed that Shapiro would have known about other life forms, and his conclusions are not based solely on bacterial behaviour, and the theory of cellular intelligence has been embraced by other experts in the field. And this is a complete digression from the subject, which was Moran’s objections.

Of course Shapiro knew all of the other research. His theory is based on his bacterial works and is an extrapolation into a theory that explains natural evolution asking, if bacteria can edit DNA why can't that explain evolution. But editing elsewhere is not present. End of theory.

LUCA latest: Shapiro redux

by dhw, Wednesday, July 19, 2023, 12:23 (253 days ago) @ David Turell

DAVID: Only God's designing mind is capable of the biochemical complexities of living forms.

dhw: We are not talking about the biochemical complexities, but about the ability to process information, to communicate, to take decisions etc. – all the hallmarks of autonomous intelligence.

DAVID: BUT, it is exactly the biochemical complexities that process the information.

dhw: There speaks a self-professed dualist. But even if you believe that all mental processes stem from biochemical processes, you are still stuck with the fact that living cells process information, communicate, take decisions, solve problems etc., and these activities are hallmarks of autonomous intelligence. If that is true of us humans, whether designed by God or not, and whether biochemical or not, then why can’t it be true of other life forms, including individual cells?

DAVID: The automaticity of cells is clearly shown in everyday research. Yes, they look intelligent, but they follow very intelligent instructions from God, the designer.

Of course cells behave automatically most of the time. If they didn’t, species would not remain species! But every innovation and every response to new threats will require a change in what has previously been automatic! See below on the subject of “editing”.

DAVID: Shapiro as a professional scientist cannot bring God into the picture.

dhw: And there is no reason why he should. He is dealing with evolution, which is Chapter Two in the history of life, not Chapter One, which is the origin of life. Theists and atheists can both use his theory – just as they can both use Darwin’s theory.

DAVID: Whoa! What Shapiro studied was bacteria, which represent the unevolved start of life. They cannot represent the future.

dhw: How many more times? You have agreed that Shapiro would have known about other life forms, and his conclusions are not based solely on bacterial behaviour, and the theory of cellular intelligence has been embraced by other experts in the field. And this is a complete digression from the subject, which was Moran’s objections.

DAVID: Of course Shapiro knew all of the other research. His theory is based on his bacterial works and is an extrapolation into a theory that explains natural evolution asking, if bacteria can edit DNA why can't that explain evolution. But editing elsewhere is not present. End of theory.

Of course editing is present elsewhere! How can evolution have proceeded without it? But you insist that only your God could have preprogrammed the editing 3.8 billion years ago, or popped in over and over and over and over again to do a dabble (even though 99% of his dabbles had no connection with the only dabbles he actually wanted to perform). And you find this absurd theory more convincing than the proposal that he might have designed a mechanism whereby the cells themselves did/do their own editing, or ultimately failed/fail to edit themselves successfully – hence the 99% extinction rate which you prefer to attribute to your God’s messy, cumbersome and inefficient method of design.

LUCA latest: Shapiro redux

by David Turell @, Wednesday, July 19, 2023, 17:28 (253 days ago) @ dhw

DAVID: Whoa! What Shapiro studied was bacteria, which represent the unevolved start of life. They cannot represent the future.

dhw: How many more times? You have agreed that Shapiro would have known about other life forms, and his conclusions are not based solely on bacterial behaviour, and the theory of cellular intelligence has been embraced by other experts in the field. And this is a complete digression from the subject, which was Moran’s objections.

DAVID: Of course Shapiro knew all of the other research. His theory is based on his bacterial works and is an extrapolation into a theory that explains natural evolution asking, if bacteria can edit DNA why can't that explain evolution. But editing elsewhere is not present. End of theory.

dhw: Of course editing is present elsewhere! How can evolution have proceeded without it?

Don't try that. All we know about now is epigenetics for minor adaptations, not speciation!!!

dhw: But you insist that only your God could have preprogrammed the editing 3.8 billion years ago, or popped in over and over and over and over again to do a dabble (even though 99% of his dabbles had no connection with the only dabbles he actually wanted to perform). And you find this absurd theory more convincing than the proposal that he might have designed a mechanism whereby the cells themselves did/do their own editing, or ultimately failed/fail to edit themselves successfully – hence the 99% extinction rate which you prefer to attribute to your God’s messy, cumbersome and inefficient method of design.

Your absurd approach of cell committees producing speciation is a wild theory, based solely on the observation cells act as if intelligent when it all can be explained as automaticity. The intense requirements for design of complex biochemical reactions requires a mind in action, one simple biochemical cells cannot create.

LUCA latest: Shapiro redux

by dhw, Thursday, July 20, 2023, 11:58 (252 days ago) @ David Turell

DAVID: Of course Shapiro knew all of the other research. His theory is based on his bacterial works and is an extrapolation into a theory that explains natural evolution asking, if bacteria can edit DNA why can't that explain evolution. But editing elsewhere is not present. End of theory.

dhw: Of course editing is present elsewhere! How can evolution have proceeded without it?

DAVID: Don't try that. All we know about now is epigenetics for minor adaptations, not speciation!!!

You have completely missed the point. Even if your God was responsible for evolution, he still had to edit DNA, as explained below.

dhw: But you insist that only your God could have preprogrammed the editing 3.8 billion years ago, or popped in over and over and over and over again to do a dabble (even though 99% of his dabbles had no connection with the only dabbles he actually wanted to perform). And you find this absurd theory more convincing than the proposal that he might have designed a mechanism whereby the cells themselves did/do their own editing, or ultimately failed/fail to edit themselves successfully – hence the 99% extinction rate which you prefer to attribute to your God’s messy, cumbersome and inefficient method of design.

DAVID: Your absurd approach of cell committees producing speciation is a wild theory, based solely on the observation cells act as if intelligent when it all can be explained as automaticity.

And there you go again with your built-in prejudice. If cells act as if intelligent, maybe they ARE intelligent! Why do you keep glossing over the absurdity of your own theory, as summarized above, and to which I might add all the courses your God had to give in lifestyles and strategies and navigation and nest-building etc.?

DAVID: The intense requirements for design of complex biochemical reactions requires a mind in action, one simple biochemical cells cannot create.

Biochemical cells are not simple, and their immense complexity is a potent argument for your designer God. Furthermore, you agree that their actions appear to be intelligent, but you simply refuse to contemplate the possibility that your God might actually have endowed them with intelligence. Instead you cling to the alternative theories I have summarized above, and you try to belittle Shapiro because his personal research was based mainly on bacteria.

LUCA latest: Shapiro redux

by David Turell @, Thursday, July 20, 2023, 17:04 (252 days ago) @ dhw

dhw: But you insist that only your God could have preprogrammed the editing 3.8 billion years ago, or popped in over and over and over and over again to do a dabble (even though 99% of his dabbles had no connection with the only dabbles he actually wanted to perform). And you find this absurd theory more convincing than the proposal that he might have designed a mechanism whereby the cells themselves did/do their own editing, or ultimately failed/fail to edit themselves successfully – hence the 99% extinction rate which you prefer to attribute to your God’s messy, cumbersome and inefficient method of design.

DAVID: Your absurd approach of cell committees producing speciation is a wild theory, based solely on the observation cells act as if intelligent when it all can be explained as automaticity.

dhw: And there you go again with your built-in prejudice. If cells act as if intelligent, maybe they ARE intelligent! Why do you keep glossing over the absurdity of your own theory, as summarized above, and to which I might add all the courses your God had to give in lifestyles and strategies and navigation and nest-building etc.?

In order to reduce God's possible functions, you hand it over to the cells He created. Cells are tiny factories producing product over and over, nothing more.


DAVID: The intense requirements for design of complex biochemical reactions requires a mind in action, one simple biochemical cells cannot create.

dhw: Biochemical cells are not simple, and their immense complexity is a potent argument for your designer God. Furthermore, you agree that their actions appear to be intelligent, but you simply refuse to contemplate the possibility that your God might actually have endowed them with intelligence. Instead you cling to the alternative theories I have summarized above, and you try to belittle Shapiro because his personal research was based mainly on bacteria.

I seriously belittle your blown-up interpretation of Shapiro's theory. I introduced you to Shapiro whose work I ADMIRE. But it was limited to bacteria. When you understand bacteria's free-living needs, altering DNA is extremely important. but despite that ability, bacteria are still bacteria. No other more complex organisms cannot edit DNA in a major way, but simple viruses can.

LUCA latest: Shapiro redux

by dhw, Friday, July 21, 2023, 09:10 (251 days ago) @ David Turell

dhw: But you insist that only your God could have preprogrammed the editing 3.8 billion years ago, or popped in over and over and over and over again to do a dabble (even though 99% of his dabbles had no connection with the only dabbles he actually wanted to perform). And you find this absurd theory more convincing than the proposal that he might have designed a mechanism whereby the cells themselves did/do their own editing, or ultimately failed/fail to edit themselves successfully – hence the 99% extinction rate which you prefer to attribute to your God’s messy, cumbersome and inefficient method of design.

DAVID: Your absurd approach of cell committees producing speciation is a wild theory, based solely on the observation cells act as if intelligent when it all can be explained as automaticity.

dhw: And there you go again with your built-in prejudice. If cells act as if intelligent, maybe they ARE intelligent! Why do you keep glossing over the absurdity of your own theory, as summarized above, and to which I might add all the courses your God had to give in lifestyles and strategies and navigation and nest-building etc.?

DAVID: In order to reduce God's possible functions, you hand it over to the cells He created.

You really are desperate to find some way of discrediting Shapiro’s theory, but this plumbs the depths. Why would I want to reduce your God’s possible functions? Your own theories are so absurd that even you can’t understand them. I am looking for explanations that make sense of evolution’s history, always allowing for your God as the possible designer. Shapiro’s theory provides a perfectly logical explanation of the history.

DAVID: Cells are tiny factories producing product over and over, nothing more.

Cells process information, communicate, take decisions etc., all of which you agree appear to indicate intelligence. Maybe they DO indicate intelligence.

DAVID: The intense requirements for design of complex biochemical reactions requires a mind in action, one simple biochemical cells cannot create.

dhw: Biochemical cells are not simple, and their immense complexity is a potent argument for your designer God. Furthermore, you agree that their actions appear to be intelligent, but you simply refuse to contemplate the possibility that your God might actually have endowed them with intelligence. Instead you cling to the alternative theories I have summarized above, and you try to belittle Shapiro because his personal research was based mainly on bacteria.

DAVID: I seriously belittle your blown-up interpretation of Shapiro's theory.

I have repeated the exact wording of his theory as quoted by you in your book The Atheist Delusion. Please stop pretending that I have “blown it up”.

DAVID: I introduced you to Shapiro whose work I ADMIRE. But it was limited to bacteria.

It was not limited to bacteria. Studying other people’s research is also “work”, and you have agreed that “Shapiro knew of all the other research”.

DAVID: When you understand bacteria's free-living needs, altering DNA is extremely important. but despite that ability, bacteria are still bacteria. No other more complex organisms cannot [sic] edit DNA in a major way, but simple viruses can.

Bacteria are still bacteria, but bacteria also evolved into multicellular species, and species remained species for millions of years, but they also evolved into new species. You mean no other organism can edit DNA, but now at least you are qualifying that by “in a major way”. Since nobody knows how speciation takes place, maybe Shapiro is right, and cells/cell communities can edit their DNA in a major as well as a minor way.

LUCA latest: Shapiro redux

by David Turell @, Friday, July 21, 2023, 16:37 (251 days ago) @ dhw

DAVID: In order to reduce God's possible functions, you hand it over to the cells He created.

dhw: You really are desperate to find some way of discrediting Shapiro’s theory, but this plumbs the depths. Why would I want to reduce your God’s possible functions? Your own theories are so absurd that even you can’t understand them. I am looking for explanations that make sense of evolution’s history, always allowing for your God as the possible designer. Shapiro’s theory provides a perfectly logical explanation of the history.

Only if the cells we analyze in current living forms showeed evidence of speciated ability. They don't!!! See below:


DAVID: Cells are tiny factories producing product over and over, nothing more.

dhw: Cells process information, communicate, take decisions etc., all of which you agree appear to indicate intelligence. Maybe they DO indicate intelligence.

Yes, intelligent design with no evidence of speciating ability.


DAVID: The intense requirements for design of complex biochemical reactions requires a mind in action, one simple biochemical cells cannot create.

dhw: Biochemical cells are not simple, and their immense complexity is a potent argument for your designer God. Furthermore, you agree that their actions appear to be intelligent, but you simply refuse to contemplate the possibility that your God might actually have endowed them with intelligence. Instead you cling to the alternative theories I have summarized above, and you try to belittle Shapiro because his personal research was based mainly on bacteria.

DAVID: I seriously belittle your blown-up interpretation of Shapiro's theory.

dhw: I have repeated the exact wording of his theory as quoted by you in your book The Atheist Delusion. Please stop pretending that I have “blown it up”.

I faithfully presented Shapiro as an historical figure in the debate.


DAVID: I introduced you to Shapiro whose work I ADMIRE. But it was limited to bacteria.

dhw: It was not limited to bacteria. Studying other people’s research is also “work”, and you have agreed that “Shapiro knew of all the other research”.

The new facts Shapiro's research produced were all about bacteria, nothing more.


DAVID: When you understand bacteria's free-living needs, altering DNA is extremely important. but despite that ability, bacteria are still bacteria. No other more complex organisms cannot [sic] edit DNA in a major way, but simple viruses can.

dhw: Bacteria are still bacteria, but bacteria also evolved into multicellular species, and species remained species for millions of years, but they also evolved into new species. You mean no other organism can edit DNA, but now at least you are qualifying that by “in a major way”. Since nobody knows how speciation takes place, maybe Shapiro is right, and cells/cell communities can edit their DNA in a major as well as a minor way.

All we see are epigenetic editing, nothing close to speciation. Nothing 'major' in current research.

LUCA latest: Shapiro redux

by dhw, Saturday, July 22, 2023, 12:43 (250 days ago) @ David Turell

DAVID: In order to reduce God's possible functions, you hand it over to the cells He created.

dhw: You really are desperate to find some way of discrediting Shapiro’s theory, but this plumbs the depths. Why would I want to reduce your God’s possible functions? Your own theories are so absurd that even you can’t understand them. I am looking for explanations that make sense of evolution’s history, always allowing for your God as the possible designer. Shapiro’s theory provides a perfectly logical explanation of the history.
And:

dhw: Cells process information, communicate, take decisions etc., all of which you agree appear to indicate intelligence. Maybe they DO indicate intelligence.

DAVID: Only if the cells we analyze in current living forms showed evidence of speciated ability. They don't!!!
And:
DAVID: intelligent design with no evidence of speciating ability.
And:
All we see are epigenetic editing, nothing close to speciation. Nothing 'major' in current research.

It’s a theory! Nobody knows how speciation happens! But if we know that “minor” autonomous editing does occur, why should we discount the possibility that “major” autonomous editing could also have occurred when conditions required it? Meanwhile, what evidence has been found to prove the theoretical existence of a divine, 3.8-billion-year old programme for every innovation, lifestyle, strategy, natural wonder in the history of evolution. What evidence is there for an unknown, sourceless mind named God theoretically intervening to specially design every innovation etc. in the history of evolution (99% of which are/were irrelevant to what you say was his one and only purpose)?

DAVID: The intense requirements for design of complex biochemical reactions requires a mind in action, one simple biochemical cells cannot create.

dhw: Biochemical cells are not simple, and their immense complexity is a potent argument for your designer God. Furthermore, you agree that their actions appear to be intelligent, but you simply refuse to contemplate the possibility that your God might actually have endowed them with intelligence. Instead you cling to the alternative theories I have summarized above, and you try to belittle Shapiro because he did not personally do all the research that underlies his theory.

DAVID: I seriously belittle your blown-up interpretation of Shapiro’s theory.

dhw: I have repeated the exact wording of his theory as quoted by you in your book The Atheist Delusion. Please stop pretending that I have “blown it up”.

DAVID: I faithfully presented Shapiro as an historical figure in the debate.

You faithfully quoted his exact summary of his theory, e.g. “evolutionary novelty arises from the production of new cell and multicellular structures as a result of cellular self-modification and cell fusions.” Stop pretending that I have “blown it up”.

DAVID: I introduced you to Shapiro whose work I ADMIRE. But it was limited to bacteria.

dhw: It was not limited to bacteria. Studying other people’s research is also “work”, and you have agreed that “Shapiro knew of all the other research”.

DAVID: The new facts Shapiro's research produced were all about bacteria, nothing more.

You have agreed that he would have researched work on other organisms before reaching his general conclusions. Stop pretending that his theory is only based on bacteria.

LUCA latest: Shapiro redux

by David Turell @, Saturday, July 22, 2023, 18:30 (250 days ago) @ dhw

DAVID: All we see are epigenetic editing, nothing close to speciation. Nothing 'major' in current research.

dhw: It’s a theory! Nobody knows how speciation happens! But if we know that “minor” autonomous editing does occur, why should we discount the possibility that “major” autonomous editing could also have occurred when conditions required it?

"Major autonomous editing...when conditions required it" is what happened, but that 'why' does not tell us 'how' it happened.

dhw; Meanwhile, what evidence has been found to prove the theoretical existence of a divine, 3.8-billion-year old programme for every innovation, lifestyle, strategy, natural wonder in the history of evolution. What evidence is there for an unknown, sourceless mind named God theoretically intervening to specially design every innovation etc. in the history of evolution (99% of which are/were irrelevant to what you say was his one and only purpose)?

The evidence you recognize is complex design of living forms.


DAVID: The intense requirements for design of complex biochemical reactions requires a mind in action, one simple biochemical cells cannot create.

dhw: Biochemical cells are not simple, and their immense complexity is a potent argument for your designer God. Furthermore, you agree that their actions appear to be intelligent, but you simply refuse to contemplate the possibility that your God might actually have endowed them with intelligence. Instead you cling to the alternative theories I have summarized above, and you try to belittle Shapiro because he did not personally do all the research that underlies his theory.

DAVID: I seriously belittle your blown-up interpretation of Shapiro’s theory.

dhw: I have repeated the exact wording of his theory as quoted by you in your book The Atheist Delusion. Please stop pretending that I have “blown it up”.

DAVID: I faithfully presented Shapiro as an historical figure in the debate.

dhw: You faithfully quoted his exact summary of his theory, e.g. “evolutionary novelty arises from the production of new cell and multicellular structures as a result of cellular self-modification and cell fusions.” Stop pretending that I have “blown it up”.

What you have blown up is that cells have the intelligence to create irreducible complexity in likving forms.


DAVID: I introduced you to Shapiro whose work I ADMIRE. But it was limited to bacteria.

dhw: It was not limited to bacteria. Studying other people’s research is also “work”, and you have agreed that “Shapiro knew of all the other research”.

DAVID: The new facts Shapiro's research produced were all about bacteria, nothing more.

dhw: You have agreed that he would have researched work on other organisms before reaching his general conclusions. Stop pretending that his theory is only based on bacteria.

Not true. It is your invention. What I agreed to is Shapiro was fully aware of other studies and research.

LUCA latest: Shapiro redux

by dhw, Sunday, July 23, 2023, 13:07 (249 days ago) @ David Turell

DAVID: All we see are epigenetic editing, nothing close to speciation. Nothing 'major' in current research.

dhw: It’s a theory! Nobody knows how speciation happens! But if we know that “minor” autonomous editing does occur, why should we discount the possibility that “major” autonomous editing could also have occurred when conditions required it?

DAVID: "Major autonomous editing...when conditions required it" is what happened, but that 'why' does not tell us 'how' it happened.

Agreed. Thank you for repeating my bold. How does that come to mean we must discount the possibility that intelligent cells could have been the agents of major as well as known minor editing.

dhw: Meanwhile, what evidence has been found to prove the theoretical existence of a divine, 3.8-billion-year old programme for every innovation, lifestyle, strategy, natural wonder in the history of evolution. What evidence is there for an unknown, sourceless mind named God theoretically intervening to specially design every innovation etc. in the history of evolution (99% of which are/were irrelevant to what you say was his one and only purpose)?

DAVID: The evidence you recognize is complex design of living forms.

Hence the theory of intelligent cells doing their own designing, as opposed to your God’s 3.8-billion-year-old programme and/or his non-stop (and 99% irrelevant) dabbling.

DAVID: I faithfully presented Shapiro as an historical figure in the debate.

dhw: You faithfully quoted his exact summary of his theory, e.g. “evolutionary novelty arises from the production of new cell and multicellular structures as a result of cellular self-modification and cell fusions.” Stop pretending that I have “blown it up”.

DAVID: What you have blown up is that cells have the intelligence to create irreducible complexity in living forms.

I have never mentioned the “irreducible complexity” of anything. I have repeated word for word Shapiro’s theory, and added that it is perfectly possible that your God designed the original cells and their intelligence. Please stop dodging the issues and inventing arguments I have never used.

dhw: You have agreed that he would have researched work on other organisms before reaching his general conclusions.Stop pretending that his theory is only based on bacteria.

DAVID: Not true. It is your invention. What I agreed to is Shapiro was fully aware of other studies and research.

What is my invention? You agree to my bold, then you say it is not true, and then you repeat my bold!

LUCA latest: Shapiro redux

by David Turell @, Sunday, July 23, 2023, 17:23 (249 days ago) @ dhw

DAVID: All we see are epigenetic editing, nothing close to speciation. Nothing 'major' in current research.

dhw: It’s a theory! Nobody knows how speciation happens! But if we know that “minor” autonomous editing does occur, why should we discount the possibility that “major” autonomous editing could also have occurred when conditions required it?

DAVID: "Major autonomous editing...when conditions required it" is what happened, but that 'why' does not tell us 'how' it happened.

dhw: Agreed. Thank you for repeating my bold. How does that come to mean we must discount the possibility that intelligent cells could have been the agents of major as well as known minor editing.

It is still happening in bacteria, but currently nowhere else. Since no new species are popping up, do you infer previously speciating brilliant cells have stopped?


dhw: Meanwhile, what evidence has been found to prove the theoretical existence of a divine, 3.8-billion-year old programme for every innovation, lifestyle, strategy, natural wonder in the history of evolution. What evidence is there for an unknown, sourceless mind named God theoretically intervening to specially design every innovation etc. in the history of evolution (99% of which are/were irrelevant to what you say was his one and only purpose)?

Same old complaint. The designs of life require a desiging mind.[/i]

DAVID: I faithfully presented Shapiro as an historical figure in the debate.

dhw: You faithfully quoted his exact summary of his theory, e.g. “evolutionary novelty arises from the production of new cell and multicellular structures as a result of cellular self-modification and cell fusions.” Stop pretending that I have “blown it up”.

DAVID: What you have blown up is that cells have the intelligence to create irreducible complexity in living forms.

dhw: I have never mentioned the “irreducible complexity” of anything. I have repeated word for word Shapiro’s theory, and added that it is perfectly possible that your God designed the original cells and their intelligence. Please stop dodging the issues and inventing arguments I have never used.

The issue is that Shapiro proposed the bacterial ability to edit their DNA might explain evolution! You morphed that into brilliant cell committees running evolution. And further you see the tiny factories that are our cells as intelligent, when they are designed to run intelligently and constantly repeat their processes.

LUCA latest: Shapiro redux

by dhw, Monday, July 24, 2023, 09:23 (248 days ago) @ David Turell

DAVID: All we see are epigenetic editing, nothing close to speciation. Nothing 'major' in current research.

dhw: It’s a theory! Nobody knows how speciation happens! But if we know that “minor” autonomous editing does occur, why should we discount the possibility that “major” autonomous editing could also have occurred when conditions required it?

DAVID: It is still happening in bacteria, but currently nowhere else. Since no new species are popping up, do you infer previously speciating brilliant cells have stopped?

Of course, just as in your theory your God has stopped speciating. We are going through a period of stasis, just as earlier species did. Who knows what will happen in the next thousand million years? I went on to ask what evidence there was for your illogical theories.

DAVID: Same old complaint. The designs of life require a designing mind.

Same old dodge. Shapiro’s theory offers you designing “minds” (intelligent cells) and I suggest that these may have been designed by your God.

DAVID: I faithfully presented Shapiro as an historical figure in the debate.

dhw: You faithfully quoted his exact summary of his theory, e.g. “evolutionary novelty arises from the production of new cell and multicellular structures as a result of cellular self-modification and cell fusions.” Stop pretending that I have “blown it up”.

DAVID: The issue is that Shapiro proposed the bacterial ability to edit their DNA might explain evolution! You morphed that into brilliant cell committees running evolution.

Please stop ignoring what Shapiro wrote. Read the above! It doesn’t say bacterial editing ability might explain evolution. It says cellular self-modification produces evolutionary novelty, and the rest of the summary you quote in your book lists all those qualities of cells which denote their intelligence.

DAVID: And further you see the tiny factories that are our cells as intelligent, when they are designed to run intelligently and constantly repeat their processes.

You always focus on those cellular processes which have become established and hence automatic, and you don’t seem to have grasped the elementary fact that all those processes, except for those present in the original first cells (possibly designed by your God) were once new, and new species can only be formed when instead of or in addition to repeating their processes, cells introduce new ones. (Shapiro calls them “evolutionary novelty”.) Hence evolution from single cells to trilobites, dinosaurs, the duck-billed platypus and humans.

LUCA latest: Shapiro redux

by David Turell @, Monday, July 24, 2023, 17:04 (248 days ago) @ dhw

DAVID: I faithfully presented Shapiro as an historical figure in the debate.

dhw: You faithfully quoted his exact summary of his theory, e.g. “evolutionary novelty arises from the production of new cell and multicellular structures as a result of cellular self-modification and cell fusions.” Stop pretending that I have “blown it up”.

DAVID: The issue is that Shapiro proposed the bacterial ability to edit their DNA might explain evolution! You morphed that into brilliant cell committees running evolution.

dhw: Please stop ignoring what Shapiro wrote. Read the above! It doesn’t say bacterial editing ability might explain evolution. It says cellular self-modification produces evolutionary novelty, and the rest of the summary you quote in your book lists all those qualities of cells which denote their intelligence.

Yes, I quoted Shapiro's theory, pure theory! All we know currently for fact is bacteria edit DNA.


DAVID: And further you see the tiny factories that are our cells as intelligent, when they are designed to run intelligently and constantly repeat their processes.

dhw: You always focus on those cellular processes which have become established and hence automatic, and you don’t seem to have grasped the elementary fact that all those processes, except for those present in the original first cells (possibly designed by your God) were once new, and new species can only be formed when instead of or in addition to repeating their processes, cells introduce new ones. (Shapiro calls them “evolutionary novelty”.) Hence evolution from single cells to trilobites, dinosaurs, the duck-billed platypus and humans.

Your bold skips over the fact that we do not know how speciation happens, and I believe God did it by designing new forms.

LUCA latest: Shapiro redux

by dhw, Tuesday, July 25, 2023, 09:05 (247 days ago) @ David Turell

DAVID: I faithfully presented Shapiro as an historical figure in the debate.

dhw: You faithfully quoted his exact summary of his theory, e.g. “evolutionary novelty arises from the production of new cell and multicellular structures as a result of cellular self-modification and cell fusions.” Stop pretending that I have “blown it up”.

DAVID: The issue is that Shapiro proposed the bacterial ability to edit their DNA might explain evolution! You morphed that into brilliant cell committees running evolution.

dhw: Please stop ignoring what Shapiro wrote. Read the above! It doesn’t say bacterial editing ability might explain evolution. It says cellular self-modification produces evolutionary novelty, and the rest of the summary you quote in your book lists all those qualities of cells which denote their intelligence.

DAVID: Yes, I quoted Shapiro's theory, pure theory! All we know currently for fact is bacteria edit DNA.

So will you please stop pretending that I have blown his theory up, and have morphed it into something he did not say. And stop ignoring the fact that over and over again I have agreed that it is a theory – just as your God’s existence and your interpretation of his purpose, method and nature are all theories.

DAVID: And further you see the tiny factories that are our cells as intelligent, when they are designed to run intelligently and constantly repeat their processes.

dhw: You always focus on those cellular processes which have become established and hence automatic, and you don’t seem to have grasped the elementary fact that all those processes, except for those present in the original first cells (possibly designed by your God) were once new, and new species can only be formed when instead of or in addition to repeating their processes, cells introduce new ones. (Shapiro calls them “evolutionary novelty”.)

You have completely ignored this all-important distinction between repetition of processes and the fact that new species can only arise through changes in the processes!

dhw: Hence evolution from single cells to trilobites, dinosaurs, the duck-billed platypus and humans.

DAVID: Your bold skips over the fact that we do not know how speciation happens, and I believe God did it by designing new forms.

I have stated over and over again that we don’t know how it happens, and that is why we can only theorize, and then test our theories to see how feasible they are. I know what you believe: that your God either popped in over and over and over again to do a dabble or he preprogrammed every species 3.8 billion years ago. And you reject my theistic version of Shapiro’s theory, that he might have endowed the original cells with the intelligence to do their own designing, because although cells act as if they are intelligent, you know they are not.

LUCA latest: Shapiro redux

by David Turell @, Tuesday, July 25, 2023, 17:12 (247 days ago) @ dhw

DAVID: Yes, I quoted Shapiro's theory, pure theory! All we know currently for fact is bacteria edit DNA.

dhw: So will you please stop pretending that I have blown his theory up, and have morphed it into something he did not say. And stop ignoring the fact that over and over again I have agreed that it is a theory – just as your God’s existence and your interpretation of his purpose, method and nature are all theories.

Don't deny you use Shapiro to tout brilliant designing cells!!!


dhw: You have completely ignored this all-important distinction between repetition of processes and the fact that new species can only arise through changes in the processes!

Wrong!! New species cells use the same processes old species cells used! What changes is morphology that can perform new tasks.


dhw: Hence evolution from single cells to trilobites, dinosaurs, the duck-billed platypus and humans.

DAVID: Your bold skips over the fact that we do not know how speciation happens, and I believe God did it by designing new forms.

dhw: I have stated over and over again that we don’t know how it happens, and that is why we can only theorize, and then test our theories to see how feasible they are. I know what you believe: that your God either popped in over and over and over again to do a dabble or he preprogrammed every species 3.8 billion years ago. And you reject my theistic version of Shapiro’s theory, that he might have endowed the original cells with the intelligence to do their own designing, because although cells act as if they are intelligent, you know they are not.

What I know is cells act intelligently from intelligently designed instructions from God.

LUCA latest: Shapiro redux

by dhw, Wednesday, July 26, 2023, 12:59 (246 days ago) @ David Turell

Now transferred to More Miscellany PART TWO.

LUCA latest: Shapiro redux

by David Turell @, Wednesday, July 26, 2023, 17:05 (246 days ago) @ dhw

dhw: Now transferred to More Miscellany PART TWO.

Answered there.

Shapiro redux: experiments with minimal genes forms

by David Turell @, Wednesday, August 09, 2023, 17:44 (232 days ago) @ David Turell

They evolve:

https://www.quantamagazine.org/even-synthetic-life-forms-with-a-tiny-genome-can-evolve-...

"Seven years ago, researchers showed that they could strip cells down to their barest fundamentals, creating a life form with the smallest genome that still allowed it to grow and divide in the lab. But in shedding half its genetic load, that “minimal” cell also lost some of the hardiness and adaptability that natural life evolved over billions of years. That left biologists wondering whether the reduction might have been a one-way trip: In pruning the cells down to their bare essentials, had they left the cells incapable of evolving because they could not survive a change in even one more gene?

"Now we have proof that even one of the weakest, simplest self-replicating organisms on the planet can adapt. During just 300 days of evolution in the lab, the generational equivalent of 40,000 human years, measly minimal cells regained all the fitness they had sacrificed, a team at Indiana University recently reported in the journal Nature. The researchers found that the cells responded to selection pressures about as well as the tiny bacteria from which they were derived. A second research group at the University of California, San Diego came to a similar conclusion independently in work that has been accepted for publication.

“'It turns out life, even such simple wimpy life as a minimal cell, is much more robust than we thought,” said Kate Adamala, a biochemist and assistant professor at the University of Minnesota who was not involved in either study. “You can throw rocks at it, and it’s still going to survive.” Even in a genome where every single gene serves a purpose, and a change would seemingly be detrimental, evolution molds organisms adaptively.

“'It’s a stunning achievement,” said Roseanna Zia, a physicist at the University of Missouri whose research aims to build a physics-based model of a minimal cell and who was not involved in the study. The new work showed that even without any genome resources to spare, she said, the minimal cells could increase their fitness with random changes in essential genes.

***

"They calculated that the original minimal cell had lost 53% of its relative fitness along with its nonessential genes. The minimization had “made the cell sick,” Lennon said. Yet by the end of the experiments, the minimal cells had evolved all that fitness back. They could go toe-to-toe against the ancestral bacteria.

“'That blew my mind,” said Anthony Vecchiarelli, a microbiologist at the University of Michigan who was not involved in the study. “You would think that if you have only essential genes, now you’ve really limited the amount of evolution that … can go in the positive direction.”

***

"When Lennon and Moger-Reischer adjusted for the relative fitness of the organisms, they found that the minimal cells evolved 39% faster than the synthetic M. mycoides bacteria from which they were derived.

***

"The researchers found that most of the beneficial mutations favored by natural selection in their experiments were in essential genes. But one critical mutation was in a nonessential gene called ftsZ, which codes for a protein that regulates cell division. When it mutated in M. mycoides, the bacterium grew 80% larger. Curiously, the same mutation in the minimal cell didn’t increase its size. That shows how mutations can have different functions depending on the cellular context, Lennon said. (my bold)

***

"'They observed a “fear-greed trade-off,” a tendency also seen in natural bacteria to evolve mutations in genes that will help it grow rather than mutations that would produce more DNA repair proteins to correct the errors." (my bold)

Comment: pure experimentation in a Shapiro mold. My first bold notes the use of natural selection to explain the issue, when we know bacteria can edit DNA, not natural selection. The second bold shows they recognized Shapiro's work.

Shapiro redux: experiments with bacteria & Yeast

by David Turell @, Tuesday, August 15, 2023, 16:31 (226 days ago) @ David Turell

Suport for Shapiro:

https://www.quantamagazine.org/andreas-wagner-pursues-the-secrets-to-evolutionary-succe...

"Quanta spoke to Wagner over the phone recently about his new book, evolution as exploration, and the grand patterns that underlie biology.

***

"...when the bacterium Escherichia coli enters the human intestinal tract, the environment contains oxygen. But as it gets deeper into the bowel, the environment starts to lack oxygen. E. coli needs to express different genes depending on whether oxygen is there or not.

"It turns out E. coli has evolved this anticipatory response where as soon as it enters the gastrointestinal tract, it starts to turn on the needed genes before it hits the anoxic zone. Its foresight might have evolved out of the thousands of millions of times it has gone through intestinal tracts: When it gets warm or the pH drops, or whatever it is, then it needs to turn on these genes, because soon it’s going to run out of oxygen.

"We wanted to find out whether you could evolve something like that in the laboratory. So we cycled yeast between different stressful environments. Once yeast went through the cycle multiple times, would they start to turn on the genes for handling oxidative stress [from too much reactive oxygen] before the oxidative stress hit? We found some evidence that they did.

***

"I study evolution...There have been many life forms that were not very successful by any standard when they originated. They didn’t radiate into hundreds of species, and they didn’t cover large areas of the planet’s surface. But wait long enough, and they became very successful.

"The best example is grasses. Today, grasses are one of the most successful families of organisms on the planet. They cover huge amounts of territory on most continents and have evolved enormous diversity, with about 10,000 very different species. They range in size from the tiny tufts of Antarctic grasses to huge bamboo forests in Asia. Grasses are old. We find grass pollen in fossilized dinosaur dung from 65 million years ago. But what’s quite remarkable is that when grasses originated and for many millions of years thereafter, they were just eking out a living at the margins of the biosphere. For that to change, they had to wait literally 40 million years for their spot in the sun.

"We see similar patterns in a lot of organisms. Mammals originated more than 100 million years before they first became successful. Evolution experimented with different mammalian life forms and ways of life, such as flying like bats or water living like otters, or tree living, and so forth. A lot of these originated and went extinct again. They were so unsuccessful that they actually had to be reinvented by evolution. That happened in some mammalian lineages multiple times before mammals became really successful.

"We see analogous phenomena in bees and other insects. So many, many different life forms were not very successful in the beginning and then became successful.

***

"It was when we found this kind of phenomenon in the lab that I became interested in it. We took E. coli and exposed them to an environment that contains a lot of an antibiotic called ampicillin. Most of them will die in the presence of that antibiotic. But bacteria are extremely rapid at evolving antibiotic resistance, so within a few weeks, they have absolutely no problem surviving high dosages of it.

"We were interested in other traits that these bacteria acquired as a byproduct of that evolutionary process. To find out what they might be, we exposed the bacteria to hundreds of other toxic environments containing other antibiotics or toxins such as heavy metals or solvents. We knew from previous work that in many of these environments, bacteria could not survive or survive very poorly.

"The important thing to realize is that these bacteria had encountered none of those environments before our experiments. But we found that in 20 or so of these environments, the bacteria could survive pretty well. It was remarkable that as a byproduct of evolution for one thing you get something else altogether. And not just one thing, but multiple viability traits.

"When we see a property that’s evolved in an organism, we have this reflex of thinking that it’s a product of natural selection, right? That at some point, the property was useful to the organism’s survival, and that’s why we see it today. But as these kinds of experiments show, that’s not necessarily the case at all.

[Quanta] "It could have been selection for something completely different."

"Exactly. It could just be a byproduct. And so it’s probably not prudent to always take an adaptationist or selectionist viewpoint. There may be a lot of traits that exist for no good reason at all. (my bold)

***

"It could seem almost like these bacteria are clairvoyant, you know? Like they anticipated that at some point they would need to be resistant against antibiotics when humanity came along, right? But there’s a very mundane explanation that has to do with these latent kinds of traits that we identified in experiments in the lab. So these traits really exist out in nature. They’re not just artifacts of experiments."

Comment: Simple live on-their-own bacteria and yeast must have these abilities to survive and then evolve into our complexity where only minor adaptations can occur. A designer God would naturally do this with simple organisms.

Shapiro redux: experiments with bacteria & Yeast

by dhw, Wednesday, August 16, 2023, 11:51 (225 days ago) @ David Turell

DAVID: Support for Shapiro

https://www.quantamagazine.org/andreas-wagner-pursues-the-secrets-to-evolutionary-succe...

QUOTES: Mammals originated more than 100 million years before they first became successful. Evolution experimented with different mammalian life forms and ways of life, such as flying like bats or water living like otters, or tree living, and so forth. A lot of these originated and went extinct again. They were so unsuccessful that they actually had to be reinvented by evolution. That happened in some mammalian lineages multiple times before mammals became really successful.

"We see analogous phenomena in bees and other insects. So many, many different life forms were not very successful in the beginning and then became successful.”

DAVID: Simple live on-their-own bacteria and yeast must have these abilities to survive and then evolve into our complexity where only minor adaptations can occur. A designer God would naturally do this with simple organisms.

The quotes makes it abundantly clear that the authors are not confining their conclusions to simple organisms or to minor adaptations. You are right, this all provides support for Shapiro, and it could also provide support for other theories. Evolution does not “experiment” with anything. It’s not a being but a process. Nobody would say evolution has a conscious mind! And so we might justifiably regard this whole article as support for the theory that your God did the experimenting, or Shapiro’s intelligent cells (possibly invented by your God) did it. One theory which the diversity and constant comings and goings does not support is that of an all-powerful, all-knowing God setting out with the sole purpose of designing H. sapiens and his food.

Shapiro redux: experiments with bacteria & Yeast

by David Turell @, Wednesday, August 16, 2023, 18:24 (225 days ago) @ dhw

DAVID: Support for Shapiro

https://www.quantamagazine.org/andreas-wagner-pursues-the-secrets-to-evolutionary-succe...

QUOTES: Mammals originated more than 100 million years before they first became successful. Evolution experimented with different mammalian life forms and ways of life, such as flying like bats or water living like otters, or tree living, and so forth. A lot of these originated and went extinct again. They were so unsuccessful that they actually had to be reinvented by evolution. That happened in some mammalian lineages multiple times before mammals became really successful.

"We see analogous phenomena in bees and other insects. So many, many different life forms were not very successful in the beginning and then became successful.”

DAVID: Simple live on-their-own bacteria and yeast must have these abilities to survive and then evolve into our complexity where only minor adaptations can occur. A designer God would naturally do this with simple organisms.

dhw: The quotes makes it abundantly clear that the authors are not confining their conclusions to simple organisms or to minor adaptations. You are right, this all provides support for Shapiro, and it could also provide support for other theories. Evolution does not “experiment” with anything. It’s not a being but a process. Nobody would say evolution has a conscious mind! And so we might justifiably regard this whole article as support for the theory that your God did the experimenting, or Shapiro’s intelligent cells (possibly invented by your God) did it. One theory which the diversity and constant comings and goings does not support is that of an all-powerful, all-knowing God setting out with the sole purpose of designing H. sapiens and his food.

Aagreed.

Shapiro redux: experiments with bacteria and bacteriophages

by David Turell @, Thursday, November 09, 2023, 21:36 (140 days ago) @ David Turell

A rapidly moving evolutionary fight:

https://phys.org/news/2023-11-bacteria-virus-arms-rare-window-rapid.html

"Borin and Meyer set bacteria and viruses together in a closed laboratory flask—just two teaspoons large—to study coevolution in action. As viruses infect their bacterial neighbors, the bacteria evolve new defensive measures to repel the attacks. The viruses then counter these adaptations with their own evolutionary changes that work around the new defensive measures.

"In only three weeks, this accelerated arms race between bacteria (Escherichia coli) and viruses (bacteriophage, or "phage") results in several generations of evolutionary adaptations. The new findings, published in the journal Science, reveal the emergence of distinct evolutionary patterns.

"'In this study we show the power of evolution," said Meyer, an associate professor in the Department of Ecology, Behavior and Evolution. "We see how coevolution between bacteria and phage drive the emergence of a highly complicated ecological network. Evolution doesn't have to be slow and gradual as Darwin thought."

***

"As bacteria and viruses adapted to each other's presence over time, two prominent repeating patterns emerged. These included nestedness, a development in which narrow interactions between bacteria and virus specialists are "nested" within a broader range of generalist interactions; and modularity, in which interactions between species form modules within specialized groups, but not between groups.

"'We were amazed to discover that our evolution experiment in tiny flasks had recapitulated the complex patterns that had been previously observed between bacteria and viruses collected at regional and transoceanic scales," said Borin."

Comment: I looked at the article itself to see if Shapiro was mentioned in the text or in the references. Strange since this fits exactly with his finding that bacteria can actively edit their DNA.

Shapiro redux: humans edit yeast DNA

by David Turell @, Friday, November 10, 2023, 15:33 (139 days ago) @ David Turell

And grow functional yeast:

https://www.sciencemagazinedigital.org/sciencemagazine/library/item/10_november_2023/41...

"A 17-year project to craft a synthetic genome for yeast cells has reached a watershed. Researchers revealed this week in 10 new papers that they have created designer versions of all yeast chromosomes and incorporated almost half of them into cells that can survive and reproduce. “It’s a milestone we have been working on for a long time,” says geneticist Jef Boeke of NYU Langone Health, director of the project.

"Researchers have tinkered with the genomes of yeast and many other organisms using editing technologies such as CRISPR. But building a new version from the ground up opens the way to making bigger changes to an organism’s genome and delving deeper into its organization, function, and evolution.

***

"The researchers didn’t attempt to redesign the genome one nucleotide at a time. Instead, they revised the native yeast genome, adding thousands of modifications that simplify its structure, boost its stability, and make it easier to study. For instance, they carved out the transposons, itinerant stretches of DNA that can leap from location to location in the genome, disrupting DNA sequences.

"They also pruned the genome by excising many of the introns, segments of DNA that don’t code for portions of proteins. And to make the new yeast genome easier to manipulate in future experiments, the team included several hundred short DNA sequences that can prompt sections of chromosomes to rearrange.

"In most cases, the researchers left genes on their original chromosomes. But a team led by synthetic biologist Yizhi “Patrick” Cai of the University of Manchester, international director of the project, created a new, 17th chromosome to house yeast’s 275 tRNA genes. They code for RNA molecules that transport amino acids, the building blocks of proteins.

"Although tRNAs are essential for protein synthesis, their genes “are a lot of trouble for the genome,” Cai says, because “they are DNA damage hotspots” that can cause breaks. By isolating these disruptive genes on one chromosome, the researchers hoped to tame them. They found that yeast cells could survive and grow—albeit more slowly than unmodified cells—with this newfangled chromosome, they report in Cell. Synthetic biologist Paul Freemont of Imperial College London calls this work “a tour de force.”

***

"Boeke and colleagues repeatedly mated cells harboring different synthetic chromosomes, eventually producing yeast that contained six full-size synthetic chromosomes and a fragment of another, but not the extra tRNA chromosome.

"This yeast grew slower than normal because of some harmful genomic glitches, but after the researchers identified and corrected them, the strain grew about as fast as unaltered cells, the team reported in a second Cell paper. They then used a similar mating approach to add another synthetic chromosome, bringing the total to 7.5. In these cells, more than 50% of the DNA is synthetic. “We are more than halfway there,” Boeke says.

***

"The team is now working to integrate the remaining chromosomes into a yeast cell and correct any genomic problems that arise. Boeke expects a yeast with a fully synthetic genome to debut in about a year."

Comment: now we ae doing God's work, not speciating in a real sense. Remember we are using living material to do the editing, so our editing is secondhand. We do not know how genes really produce their results. We simply know what genes produce.

Shapiro redux: humans edit a new monkey

by David Turell @, Friday, November 10, 2023, 19:56 (139 days ago) @ David Turell

A hybrid from an embryo and stem cells from another monkey:

https://www.nature.com/articles/d41586-023-03473-w?utm_source=Live+Audience&utm_cam...

"Scientists have produced an infant ‘chimeric’ monkey by injecting a monkey embryo with stem cells from a genetically distinct donor embryo1. The resulting animal is the first live-born chimeric primate to have a high proportion of cells originating from donor stem cells.

***

"But the monkey chimaera had to be euthanized when it was only ten days old because of hypothermia and breathing difficulties, highlighting the need for further optimization of the approach and raising ethical concerns, say researchers.

"Scientists have long sought to make animal chimaeras using embryonic stem cells, which are derived from an embryo’s inner region and can develop into a wide variety of tissues. Such stem cells can be genetically edited before being added to a recipient embryo.

***

"Esteban and his colleagues created recipient embryos by collecting eggs from female cynomolgus monkeys (Macaca fascicularis) and fertilizing the eggs.

"Meanwhile, the researchers extracted embryonic stem cells from one-week-old cynomolgus embryos and genetically edited the cells to display a green fluorescent signal. To grow the stem cells in the laboratory, the team finetuned the nutrients and growth-promoting proteins in the liquid in which the stem cells were grown. They then injected up to 20 green embryonic stem cells into each of the recipient embryos, yielding 74 chimeric embryos with a strong fluorescent signal.

***

"The team found that, on average, 67% of the cells across the 26 tested tissues, including the brain, lungs and heart, were descendants of the donor stem cells. The highest level of chimerism was seen in the adrenal gland: the progeny of donor stem cells made up 92% of total cells.

"The low birth rate of chimeric monkeys and the poor health of the one survivor suggest that the donor embryonic stem cells did not perfectly match the developmental state of the recipient embryo, says reproductive biologist Zhen Liu at the Chinese Academy of Sciences in Shanghai. The team plans to optimize this in future, he adds.

“This work is both impressive and commendable,” says stem-cell biologist Irene Aksoy at the Stem-cell and Brain Research Institute in Lyon, France, who was not involved in the study.

"The method might be used to grow human organs in pig or non-human primate tissues, says developmental cell biologist Shoukhrat Mitalipov, director of the Oregon Health and Science University in Portland.

“'If we can delete the genes encoding for, say, the kidney, in a large animal such as a pig or primate, we could introduce human cells to produce that organ instead,” he says. But he adds that using human–animal chimaeras for organ collection, especially if human embryonic stem cells contribute to the nervous system, brain or reproductive cells, comes with many ethical concerns." (my bold)

Comment: it turns out, we are not yet God-like. Growing organs in surrogate animals is really God-like and ethically frightening. Can we guarantee perfection when God doesn't?

Shapiro redux: bacterial resistance

by David Turell @, Tuesday, November 28, 2023, 19:14 (121 days ago) @ David Turell

New math approach:

https://www.quantamagazine.org/evolving-bacteria-can-evade-barriers-to-peak-fitness-202...

"Over the course of the last hundred years, evolutionary biologists have used mathematical models and, increasingly, lab experiments with living organisms to explore how populations of all sizes can move through fitness landscapes (sometimes called adaptive landscapes). Now, in a study just published in Science, researchers have engineered more than a quarter-million versions of a common bacterium and plotted each strain’s performance to create one of the largest lab-built adaptive landscapes ever. It enabled them to ask: How hard is it to get from any given point to the peaks?

***

"As huge as the fitness landscape in Wagner’s new paper is, it shows only what the bacteria are capable of in a single specific environment. If the researchers changed any of the particulars — if they changed the dose of the antibiotic or raised the temperature, say — they would get a different landscape. So although the findings seem to suggest that most E. coli strains can evolve antibiotic resistance, that outcome might be either far less likely or far more likely in the real world. All that seems certain is that most strains probably aren’t irrevocably sabotaged by their own minor successes.

***

"Wagner and Papkou are hoping to explore other versions of the landscape in future work. Papkou notes that it is not possible to map every permutation of even a single gene comprehensively — the landscape would explode to astronomical size almost immediately. But with lab-built landscapes and theoretical models, it should still be possible today to begin exploring whether universal principles undergird how an evolving entity can change in response to its environment.

“'The bottom line is: It is pretty easy for Darwinian evolution to start in a suboptimal position and move by force of natural selection to a high fitness peak,” Papkou said. “It was pretty astonishing.'”

Comment: Shapiro all over again. Bacteria have a definite way to protect themselves by editing DNA. Why? They started life and have stayed around to contribute positively to so many aspects of life like our gut microbiome.

Shapiro redux: bacteria make giant proteins

by David Turell @, Monday, December 11, 2023, 21:16 (108 days ago) @ David Turell

To fight all:

https://www.nature.com/articles/d41586-023-03937-z?utm_source=Live+Audience&utm_cam...

"Jacob West-Roberts, a computational biologist at the University of California (UC) Berkeley, was scouring microbial DNA sequences for giant genes and discovered what he thought was a whopper: a gene encoding a protein made up of 1,800 amino acids. The average protein has a few hundred.

“'Wait till you see this,” responded his PhD adviser, UC Berkeley environmental microbiologist Jillian Banfield, and pointed out proteins longer than 30,000 amino acids, already known from sequencing data.

"Their team has now found dozens of even bigger proteins, including what might be the longest ever: an 85,000-amino-acid behemoth. The mega-molecules could help an enigmatic group of environmental microorganisms to feed on other microbial cells, the researchers propose. They describe their findings in a preprint posted on bioRxiv1 last month.

“It’s a good study,” says Brian Hedlund, a microbiologist at the University of Nevada, Las Vegas. “They essentially doubled the size of the largest known predicted proteins from 40,000 to 85,000 amino acids, which are all insane.”

***

"Giant proteins were especially common in Omnitrophota, a bacterial phylum first discovered in Yellowstone National Park in the northern United States in the 1990s and now commonly found in environmental samples. In total, the researchers found 46 Omnitrophota genes encoding proteins longer than 30,000 amino acids, including the 85,804-amino-acid-colossus, which turned up in waste water. “They were just absolutely everywhere,” says West-Roberts.

***

"Genome sequencing identified a gene predicted to encode a protein nearly 40,000 amino acids long, and matching protein fragments turned up in a biochemical assay. Harder’s team might even have caught a glimpse of the giant in electron micrographs of the Omnitrophota cells, which seemed to show them attacking and devouring other bacteria and microbes called archaea.

***

"The AI predictions of the proteins’ structures revealed more cell-wall-binding regions, but also a big surprise: a very long tube-like apparatus unlike anything researchers have ever seen. This structure could be involved in delivering molecules to prey, or could attach to other cells before the host microbe devours them.

***

"The fact that giant proteins are so common in Omnitrophota is especially surprising because of the microbes’ tiny physical size, says Oleg Reva, a bioinformatician at the University of Pretoria in South Africa. The study shows that giant proteins are “sophisticated weapons wielded by the diminutive microbial hunters in their pursuit of bacterial and archaeal prey”, he adds.

"The discovery of genes encoding proteins as longer than 85,000 amino acids does not mean that the molecules exist in this state in cells, researchers say. One possibility is that the protein is chopped into smaller pieces after it’s made, and these portions take on a range of functions in cells. That could explain why Harder’s team was able to find only pieces of its giant protein. “Currently I don’t see experimental evidence that these large proteins exist,” Harder says.

"Many of the giant proteins contain protein-breaking enzymes called peptidases, which could chop the Goliaths down into Davids, West-Roberts and his team say. Firm answers might require researchers to grow Omnitrophota cells, something that only Harder’s team has managed to do so far. “All the others, they’re just imaginary,” says Harder. “There’s a lot of mystery to solve.'”

Comment: I carefully looked for a reference to Shapiro in all the references. None. A shame. I assume God helped with the DNA editing as the molecules are so large.

Shapiro redux: bacterial resistance

by David Turell @, Tuesday, December 26, 2023, 16:55 (93 days ago) @ David Turell

Another study on Salmonella:

https://www.the-scientist.com/news-opinion/bacteria-go-dormant-to-survive-antibiotics-a...

"Infections that can’t be treated are a significant problem. To search for ways to fight this growing health threat, Peter Hill and his colleagues at Harvard Medical School teased apart how antibiotic tolerance and persistence arise. They recently reported in Cell Host & Microbe that tolerance comes from mutations in genes related to nutrient production while persistent bacteria activate a specific DNA repair pathway to survive. (my bold)

***

"To find out which mutations were responsible for tolerance, Hill’s team infected macrophages with a strain of Salmonella that causes recurrent diarrheal disease,3 induced tolerance by exposing them to antibiotics, and sequenced the genomes of the surviving bacteria. They found mutations that stopped the bacteria from making certain molecules essential for life. Bacteria that cannot make these compounds grow slowly, which causes them to survive in the face of antibiotics that target dividing cells. Because tolerant bacteria only grow in nutrient-rich environments, Hill saw that the tolerant Salmonella were sensitive to antibiotics once they moved to favorable conditions.

"Next, the team studied antibiotic persistence, which results from a phenotypic switch that temporarily slows or stops growth in a small portion of antibiotic-susceptible bacteria. Like the tolerant bugs, the persistent bacteria grew slowly, if at all, within macrophages treated with antibiotics. But the researchers found that persistent Salmonella came alive in the macrophages once they removed the antibiotic stress.

"Because persistence arises from a phenotypic shift rather than a mutation, Hill and his colleagues performed RNA-sequencing on the persisters to see how antibiotic treatment affected gene expression in this dormant population. They observed an increase in a stress response pathway that bacteria induce in response to DNA double-strand breaks (DSBs)—a common side effect of genome replication within hostile macrophages.

***

"Testing macrophages in a lab offers a lot of information, but Hill and his team wanted to know what happens during infections in the human body. They obtained patient samples of a similar Salmonella strain and sequenced the bacterial genomes. To their surprise, they did not identify any of the tolerance mutations that showed up in their cell culture experiments. Instead, the isolates’ growth in antibiotic-treated macrophages mimicked that of persistent bacteria; there was a subpopulation that was not as susceptible to antibiotics and had robust activation of the DNA repair response. (my bold)

“'The observation that clinical isolates seem to behave closer to the persisters in terms of the [DNA repair] response is very interesting,” Nathalie Balaban, a professor at the Hebrew University of Jerusalem who was not involved in this study, wrote in an email. “It would be also good to see whether [the clinical isolates] reinfect macrophages better.”

"Understanding the role of DNA repair in driving persistence and tolerance will help researchers develop other treatment strategies for bacterial infections. Blocking the DNA repair necessary for Salmonella survival in combination with antibiotic treatment may stop infection relapse and slow the development of antibiotic resistance."

Comment: a marvelous example of how bacteria manipulate their DNA to survive.

Shapiro redux: bacterial resistance

by David Turell @, Wednesday, January 10, 2024, 20:37 (78 days ago) @ David Turell

Persister study:

https://phys.org/news/2024-01-notorious-cell-subpopulation-key-antibiotic.html

"Antibiotic overuse can lead to antibiotic resistance, but classic antibiotic resistance might not completely explain why antibiotics sometimes fail. Sub-populations of bacteria called persister cells can survive in the presence of lethal doses of antibiotics for prolonged periods. Although persister cells have been intensively researched, evidence linking them to poor patient outcomes has been limited.

"Scientists led by UNC School of Medicine microbiologist Brian Conlon, Ph.D., and Duke School of Medicine infectious diseases fellow Josh Parsons, MD, Ph.D., have now shown that E. coli can evolve in patients to produce increased persister cells and this leads to increased survival to antibiotics.

***

"Using clinical E. coli bacteremia isolates—bacteria from the blood of patients—Conlon, first author Joshua Parsons, MD, Ph.D., an infectious diseases fellow at Duke University, and colleagues found that high-persister mutants evolved in patients. The researchers then documented a 100-fold increase in persisters in one such mutant when challenged with the exact antibiotic doctors had used to treat patients from which the E. coli had been isolated.

"The mutant bacteria showed no loss of fitness in a mouse infection model and displayed a 10-fold increase in survival following the antibiotic challenge.

"Importantly, Conlon said his team documented the infections and treatment protocols of patients who had been prescribed antibiotics to clear E. coli infections. Conlon said that classical antibiotic resistance was not responsible for the poor outcomes in patients who did not clear infection with antibiotics.

"'Because of this research, we think persister formation is likely a significant contributor to antibiotic treatment failure in patients," Conlon said. "Our research strongly suggests that persister formation is an important metric to consider when treating patients with antibiotics."

"He also said that researchers should develop techniques to identify mutants that are likely to respond poorly to antibiotics because such information would influence treatment choices or duration of treatment. Additionally, developing new therapeutic approaches to target and kill persisters may improve patient treatment outcomes."

Comment: Shapiro showed how bacteria can edit DNA for survival. This is a prime example.

From the article: https://www.pnas.org/doi/10.1073/pnas.2314514121

*In the relapsed E. coli strain with the greatest increase in persisters (100-fold relative to initial isolate), we determined that the increase was due to a loss-of-function mutation in the ptsI gene encoding Enzyme I of the phosphoenolpyruvate phosphotransferase system. The ptsI mutant was equally virulent in a murine bacteremia infection model but exhibited 10-fold increased survival to antibiotic treatment. This work addresses the controversy regarding the clinical relevance of persister formation by providing compelling data that not only do high-persister mutations arise during bloodstream infection in humans but also that these mutants display increased survival to antibiotic challenge in vivo." (my bold)

Comment: this fits Behe's thesis that most evolution of this type involves loss of function. To me this means evolution of major new species is over.

Shapiro redux: bacterial DNA controls

by David Turell @, Thursday, January 11, 2024, 15:42 (77 days ago) @ David Turell

Using ncRNA changes:

https://www.sciencedirect.com/science/article/abs/pii/S2451945623004415

"Commensal and pathogenic bacteria continuously evolve to survive in diverse ecological niches by efficiently coordinating gene expression levels in their ever-changing environments. Regulation through the RNA transcript itself offers a faster and more cost-effective way to adapt than protein-based mechanisms and can be leveraged for diagnostic or antimicrobial purposes. However, RNA can fold into numerous intricate, not always functional structures that both expand and obscure the plethora of roles that regulatory RNAs serve within the cell. Here, we review the current knowledge of bacterial non-coding RNAs in relation to their folding pathways and interactions. We posit that co-transcriptional folding of these transcripts ultimately dictates their downstream functions. Elucidating the spatiotemporal folding of non-coding RNAs during transcription therefore provides invaluable insights into bacterial pathogeneses and predictive disease diagnostics. Finally, we discuss the implications of co-transcriptional folding and applications of RNAs for therapeutics and drug targets.

"In order to survive and thrive, bacteria must constantly tune their metabolism and overall gene expression to adjust to their ever-changing environment and ecological niches. Because of the competition between species, it is crucial for their survival that bacteria adapt quickly to transient nutritional resources as well as external threats such as antibiotics and toxins. (my bold)

***

"In bacteria, a single multi-subunit RNA polymerase (RNAP) enzyme is responsible for the synthesis of all RNA transcripts within the cell. The core enzyme forms a conserved architecture4 comprising all of the regulatory functions necessary for the efficient and accurate synthesis and folding of the transcripts during all phases of transcription, namely initiation, elongation, and termination. RNAP is subject to multiple types of regulatory processes that, in combination, determine the overall levels of expression of all genes.

***

"Maintaining a temporal balance between transcription progress, folding, and RNA functional action is key to the survival of bacteria. Slight changes in the timing of transcription (too fast or too slow) therefore can have deleterious effects, leading to competitive disadvantages or even loss of viability. Examining the importance of the relative timescales of transcription and RNA folding therefore will allow for a deeper and more nuanced understanding of critical biomolecular processes.

***

"ncRNAs have emerged as significant players in gene regulation in all domains of life, including bacteria. Unlike coding RNAs, which are translated into proteins, ncRNAs are not recruiting the ribosome for translation, but instead typically perform regulatory functions at the transcriptional or post-transcriptional level (Figure 1). There are diverse classes of ncRNAs, varying in length and structure, with roles encompassing regulation of basal gene expression, stress responses,

***

"ncRNAs fold co-transcriptionally into intricate structures on a rugged energy landscape
Whereas a plethora of ncRNAs such as sRNAs are thought to modulate gene expression at the post-transcriptional level, increasing evidence points toward a more complex regulation that operates during the transcription process itself. RNA molecules in general, and ncRNAs such as riboswitches in particular, are complex structures folded into unique three-dimensional shapes."

Comment: this is a clear expression of why bacteria can edit their DNA so precisely. Shapiro's work is not mentioned.

Shapiro redux: bacterial phage defences

by David Turell @, Thursday, January 11, 2024, 18:17 (77 days ago) @ David Turell

They use a specific molecular module against the phage:

https://phys.org/news/2024-01-reveals-unexpected-strategy-competition-bacteria.html

"Understanding how Gabija and other elements of bacterial defense systems look and work—along with the mechanisms that viruses known as phages use to overcome these defenses and infect bacteria—promises to illuminate broader aspects of immunity, including human immunity and immune responses to cancer.

"Already, the team has revealed an unexpected strategy that phages might use to neutralize Gabija in the evolutionary arms race between bacteria and phages.

"'This is the importance of basic science," said Kranzusch, senior author of the paper. "We're learning how cells defend against infection."

"Gabija is one of hundreds of defense systems found in bacteria. It is present in about 15% of all bacteria whose genes have been sequenced.

"'It's one of the most prevalent bacterial defense systems," said Antine, who is first author of the study. "Yet very little was known about how it works or how viruses that infect bacteria can evade the system."

***

"Gabija, she learned, is a very large complex. It is about one-quarter the size of the ribosome, which is a huge molecular machine that performs the incredible task of using information from RNA to make proteins.

"Antine also learned that Gabija is formed using the instructions from just two genes, GajA and GajB. GajA forms proteins that connect in groups of four to form the center of the structure. GajB forms proteins that connect to form the outer winglike portions of the structure.

***

"It isn't yet clear how this large complex recognizes and defeats the phage. But Antine and Kranzusch suspect that the complex recognizes a specific structure formed by phage DNA and then degrades it.

"'Gabija has exquisitely evolved to hunt and destroy a very particular target," said Kranzusch.

***

"...she found that the phage evolved DNA that encodes a very large protein that surrounds Gabija and inactivates it.

""The protein forms this huge web around the entire outside of the complex," said Kranzusch. "This evasion technique creates a massive complex. It was a surprising result that changes the way we think about how phages interact with these defense systems."

"Phages are often thought of as small and simple, but Kranzusch has found that that's not always true. The phages he and Antine are studying are large, with DNA that holds hundreds of genes.

"Phages are also considered entities rather than living organisms because they require a host cell to replicate. Yet they actively evolve and change under pressure from defense systems like Gabija.

"'They are complex and can evolve and adapt with their host. They shape evolution," said Kranzusch.

"For next steps, Antine will dive into the precise mechanisms Gabija uses to defeat phages. These mechanisms are the result each side finding new ways to defeat the other. The same kind of one-upmanship goes on in cancer, as tumor cells find increasingly clever ways to evade the immune system and cancer treatments.

"'There are parallels between immunity in human cells and in bacteria," says Antine. "We're interested in the diversity, the many ways that immune systems combat something that is actively evolving against it."

Comment: it seems cancer cells, phages and bacteria all can edit DNA. And humans are now editing DNA. The appearance of multicellularity has removed that ability in those organisms' cells.

Shapiro redux: from prey to predator

by David Turell @, Wednesday, January 24, 2024, 19:17 (64 days ago) @ David Turell

Raied in hot or cold makes the switch:

https://www.newscientist.com/article/2413791-a-bacterium-switches-from-prey-to-predator...

Growing up at a different temperature seems to transform common prey bacteria into predators, suggesting that bacterial ecology is more fluid than we thought.

Two species of bacteria appear to reverse which is predator and which is prey depending on the temperature. Just a small temperature change is enough to cause the switch.

"The soil bacteria Myxococcus xanthus is a social species that hunts in packs – it forms temporary, multicellular “swarms” of individuals that chemically tear apart and soak up nutrients from other microbes. And its prey includes Pseudomonas fluorescens, a bacterium common in both soil and water.

***

"...when P. fluorescens was reared at 32°C, M. xanthus destroyed most of the population within four days. But surprisingly, the P. fluorescens reared at 22°C “slaughtered M. xanthus to extinction”, Vasse and her colleagues wrote in the paper. They realised that cooler-reared P. fluorescens secreted a chemical compound that could degrade and destroy other bacteria.

"In addition, the team observed that P. fluorescens grew rapidly after wiping out M. xanthus. This means that it was probably consuming nutrients from, and thus preying on, its one-time predator.

“'[This research] challenges the idea of having ‘fixed’ roles within communities,” says Vasse. “They can change so fast, so easily and so radically. It’s very brutal.”

Comment: this study is no surprise to Dr. Shapiro. However, we should note, the species is still the same adapted species. Bacteria as free-living-alone organisms must have altered defenses they can bring into play.

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