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Over and over I have stated that the genetic coding mechanism promised to be extremely complex. Coupled with the this the observation that discoveries of increased complexity would proportionally reduce the odds for the chance production of life from inorganic matter.-How true is seen in the following article. The RNA pieces in so-called'junk' DNA are now seen to be a large and complicated secondary RNA code of direct gene expression and varying gene expression. Methods are now developed to begin that decoding. This is a computer system within a computer system. I think other levels of code will appear.-http://www.nature.com/news/2010/100505/full/465016a.html

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A Time magazine article on the amazing advances in epigenetics. And I repeat my same argument; the odds for a chance production of this code system are nil. Only an intelligence can create an adaptive system this complex. Not enough computer power to study it thoroughly, as the article states:-http://www.time.com/time/health/article/0,8599,1951968-1,00.html

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For balance, I would just like to make the point that I also regard the development of epigenetics ideas as valuable advances in our knowledge of biology and evolution, but I don't see how it supports the "intelligent design" scenario. In fact the occurrence of years of low and high crop yields and the resulting nutrition effects all seem pretty random. So it supports evolution by natural selection from chance variation. I didn't notice in the paper any account taken of the people keeping stocks of grain in good years to offset famine years. Surely there was some such activity, unless they were all totally stupid.

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GPJ

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For balance, I would just like to make the point that I also regard the development of epigenetics ideas as valuable advances in our knowledge of biology and evolution, but I don't see how it supports the "intelligent design" scenario. In fact the occurrence of years of low and high crop yields and the resulting nutrition effects all seem pretty random. So it supports evolution by natural selection from chance variation. I didn't notice in the paper any account taken of the people keeping stocks of grain in good years to offset famine years. Surely there was some such activity, unless they were all totally stupid.-I really don't see how George's analogy follows at all. Since Reznick's guppy study in South America in the early 90's, in which guppies change their size under predation pressure in a two year period, man ystudies have shown rapid adaptations that didn't wait for a lucky mutation. the Time article is quite clear. This is an extensive mechanism with a number of layers of controls to allow for Lamarkian events. George should study it.

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For balance, I would just like to make the point that I also regard the development of epigenetics ideas as valuable advances in our knowledge of biology and evolution, but I don't see how it supports the "intelligent design" scenario. In fact the occurrence of years of low and high crop yields and the resulting nutrition effects all seem pretty random. So it supports evolution by natural selection from chance variation. I didn't notice in the paper any account taken of the people keeping stocks of grain in good years to offset famine years. Surely there was some such activity, unless they were all totally stupid.
> 
> I really don't see how George's analogy follows at all. Since Reznick's guppy study in South America in the early 90's, in which guppies change their size under predation pressure in a two year period, man ystudies have shown rapid adaptations that didn't wait for a lucky mutation. the Time article is quite clear. This is an extensive mechanism with a number of layers of controls to allow for Lamarkian events. George should study it.-And I don't see how guppies changing size is anything other than genetic variation. My hair is blond. My wife's is brown. I'm tall, she's short. To me this is exactly the kind of variation that has been predicted in textbook evolution...-Again, it's something that I don't see as an issue, though you keep making it one... I still don't get it. Sexual recombination, pressure selection for smaller guppies... none of this refutes evolution by natural selection!

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\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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> And I don't see how guppies changing size is anything other than genetic variation. > 
> Again, it's something that I don't see as an issue, though you keep making it one... I still don't get it. Sexual recombination, pressure selection for smaller guppies... none of this refutes evolution by natural selection!-It is the issue. The guppies change themselves in a different river in a two year period to allow natural selection to protect them.No time to wait for chance mutations. Small guppies were out into a river where the predators like small guppies and big guppies were put in a river where predators liked big guppies. Look up Reznick's work, which I believe is ongoing.This is epigenetics preparing for trouble. The organism does the initial work and then natural sdlection takes over. Who is the prime mover??

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> > And I don't see how guppies changing size is anything other than genetic variation. > 
> > Again, it's something that I don't see as an issue, though you keep making it one... I still don't get it. Sexual recombination, pressure selection for smaller guppies... none of this refutes evolution by natural selection!
> 
> It is the issue. The guppies change themselves in a different river in a two year period to allow natural selection to protect them.No time to wait for chance mutations. Small guppies were out into a river where the predators like small guppies and big guppies were put in a river where predators liked big guppies. Look up Reznick's work, which I believe is ongoing.This is epigenetics preparing for trouble. The organism does the initial work and then natural sdlection takes over. Who is the prime mover??-Yeah, to me this sounds like stress hormones acting on the genome; it wasn't my area of specialty, but I remember this being fairly well documented over the last ten years. -To answer your question, the prime mover would be the stimulus that stresses the organism and forces selection. It's like evolution within a generation, but... maybe its just the way I think, but I don't see this as threatening any paradigms...

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\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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> To answer your question, the prime mover would be the stimulus that stresses the organism and forces selection. It's like evolution within a generation, but... maybe its just the way I think, but I don't see this as threatening any paradigms...-The Darwin paradigm as presented by Charles himself was that of slow and gradual changes, step by step. Darwin could not have guessed at what we are finding now, but some of his followers still think that way. Gould's PE has come to the fore, and the Cambrian Explosion certainly shows that species appear full-blown. The Dawkins whale series shows a series of differing forms, but large gaps between each one. There is no evidence of Darwin's step by step
guess. "IF" the first Archaia had adaptive mechanisms in the genome to stresses presented by environment, that is suggestive of design. The first organisms
at 3.6 bya had to face enormous environmenal changes. The Earth was still cooling down, CO2 and O2 were still altering their levels enormously,'snowball' Earth was still to be experienced, etc. Without those initial adaptive abilities
it is unlikely life would have survived. I believe as research advances, it will be fully confirmed that the earliest organisms had adaptation built in. Your answer will be that we can only study living organisms now, and more simplistic organisms preceded what we see presently. That is no more proveable than my theory which views life as surviveable only if complete with good adaptive defenses.

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David believes that the mechanisms leading from the simplest forms of life to the most complex were all in place from the very beginning. I'll select some salient quotes from the Complexity thread and the Ain't nature wonderful thread:-"[..] recent work is showing that the earliest organisms appear to have a very complex adaptation mechanism in the genome."-"The first organisms at 3.6 bya had to face enormous environmental changes. [...] Without those initial adaptive abilities it is unlikely life would have survived."-"If Archaia have these adaptive processes from the beginning, then these rapid adaptation mechanisms drive evolution forward to the more and more complex forms. [...] presuming Archaia haven't changed much, epigenetics was there from the beginning."-I find all of this convincing, but the sting is in the tail, which leads me to a whole string of questions. Archaia adapted in order to remain Archaia. Adaptation does not explain innovation. There is therefore an additional problem of origin, quite apart from that of life itself: how do we explain the origin of new organs and indeed of new species? (Natural selection doesn't innovate.) There has to be a mechanism for random, occasionally beneficial, inheritable mutations (which of course might also be triggered by the environment), and if that was in place from the start, would there not also have been such mutations from the start? -The same applies to complexity. The earliest known complex forms are now believed to date back 2.1 billion years (Gabon fossils). So what do you reckon went on during the first 1.5 billion years, if mechanisms for innovation and increasing complexity were already in place? Of course we may never know, but if you're right, might we not expect to find even older complex forms? And if the Cambrian explosion was caused by dramatic changes in the environment but the mechanisms for adaptation and innovation were already present right from the start, wouldn't the "enormous environmental changes" 3.6 bya and onwards have caused similar explosions? -It seems to me that innovation adds to the complexity of the mechanisms (which reinforces the argument against chance), but the apparent stasis for 1.5 billion years and the presumption that Archaia haven't changed much do nothing to reinforce the argument that all the mechanisms for evolution were in place from the beginning. However, I still can't see why it makes any difference to the design (or chance) theory whether they were or weren't in place then.

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> [...] presuming Archaia haven't changed much, epigenetics was there from the beginning[/i]."
> 
> I find all of this convincing, but the sting is in the tail, which leads me to a whole string of questions. Archaia adapted in order to remain Archaia. Adaptation does not explain innovation. There is therefore an additional problem of origin, quite apart from that of life itself: how do we explain the origin of new organs and indeed of new species? (Natural selection doesn't innovate.) There has to be a mechanism for random, occasionally beneficial, inheritable mutations (which of course might also be triggered by the environment), and if that was in place from the start, would there not also have been such mutations from the start?-Thank you for reviewing and summarizing my theory, but the intent of my comment re' Archaia staying the same, is different than your interpretation. We don't know what Archaia were like 3.6 bya. It is only by presuming they are unchanged that I can reach certain tentative conclusions about their condition then.--> The same applies to complexity. The earliest known complex forms are now believed to date back 2.1 billion years (Gabon fossils). So what do you reckon went on during the first 1.5 billion years, if mechanisms for innovation and increasing complexity were already in place? -We really don't know mujch about the Gabon fossils. They could be interesting mats of bacteria, or very simple multicelluar sheets in wavy form. They may relate to a jump in oxygen at that time, the same theory for the Cambrian Explosion. They don't seem directly related to any existing phyla. They may have been an attempt at multicellularity that went awry, and disappeared. They do suggest that life has a built-in propensity to become complicated when given the right stimulus.-> 
>Of course we may never know, but if you're right, might we not expect to find even older complex forms? And if the Cambrian explosion was caused by dramatic changes in the environment but the mechanisms for adaptation and innovation were already present right from the start, wouldn't the "enormous environmental changes" 3.6 bya and onwards have caused similar explosions?-Those explosions may be there waiting for discovery, but the Cambrian did not reach a blind end, and earlier ones may have. -
> 
> It seems to me that innovation adds to the complexity of the mechanisms (which reinforces the argument against chance), but the apparent stasis for 1.5 billion years and the presumption that Archaia haven't changed much do nothing to reinforce the argument that all the mechanisms for evolution were in place from the beginning. However, I still can't see why it makes any difference to the design (or chance) theory whether they were or weren't in place then.-From my previous comments, I think you can see why I do not agree with your above conclusion. Epigenetic innovation creates inheritable genes. The apparent stasis may be only that and we will turn up 'starts and stops' in that ancient time period. If I presume that archaia are unchanged, I can then state that the arrow of increasing complexity in evolution is not due to the Gould effect, i.e., that it could only grow more complex, because it started so relatively simply. Epigenetics is the method of complexity, and chance only relates to changes in the Earth's challenging environment, and development of alternate enemies in differing organisms. Chance mutations are not worth much, as stated any times. -And as a final point, I believe there are still layers of genome control within the organisms that are not yet discovered. Our knowledge of genome complexity will still grow a bit. I can't explain the Cambrian Explosion just on oxygen increase. The oxygen allowed the genome to perform and create new organs and organisms. Again, all my theory of the past 10 years, and the new discoveries seem to keep on confirming more and more of it.

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David has given me a pretty comprehensive answer to the questions I asked in my post of 23 August at 19.02. Thank you. The gist seems to be that the Proterozoic era remains as much of a mystery as ever: Archaia may or may not have changed, we can't be sure of the significance of the Gabon fossils, the apparent stasis may not have been one, and there may even have been Cambrian-like explosions. It seems to me that our knowledge of life over this vast stretch of time is so scant that no matter what new discoveries are made concerning genome complexity, it is impossible to say with any degree of certainty whether all the mechanisms needed for evolution were already present in the earliest forms of life. (I also wonder how one can talk of an explosion when we know so little about the forms of life that existed beforehand!) Like Darwin himself, you can only rely on the thesis that the geological record is "imperfect". It seems entirely logical to me, though, that the early forms must have been adaptable, as you say, since life could not have survived otherwise in a rapidly changing environment, but adaptability is still a far cry from innovation, which is the problem I find most puzzling.-Interestingly, however, you say in relation to the Cambrian Explosion that the increased oxygen "allowed the genome to perform and create new organs and organisms", and it would be immensely helpful if you could elaborate on this, even if you think there must have been other factors too. No change of any kind happens in the abstract ... the genome can only "perform" within existing individual organisms. Darwin's gradual step-by-step process would scarcely have helped an individual organism to survive in an environment it could not cope with, and so either the changes had to be rapid, or they were not essential for survival. We're talking here about a wide variety of apparently new species, but new species can only evolve from old species, while new organs can only come into existence in organisms that didn't have them before. I'm not questioning that evolution happened, and of course natural selection played its part in preserving advantageous changes, but I'm trying to fill the gap between adaptation and innovation, following the same line of argument as before: that if organisms have not changed, their adaptability sheds no light on evolutionary diversification or advancement. That requires innovation. Why and how, then, do you think the rise in oxygen would have allowed (forced?) the genome of existing organisms to create NEW organs and NEW organisms?

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> It seems to me that our knowledge of life over this vast stretch of time is so scant that no matter what new discoveries are made concerning genome complexity, it is impossible to say with any degree of certainty whether all the mechanisms needed for evolution were already present in the earliest forms of life. (I also wonder how one can talk of an explosion when we know so little about the forms of life that existed beforehand!)-No we cannot be certain that Archaia are unchanged. So far the scarcity of pre-existing forms may be real, but the jump from Edicaran sheets of cells is all we have, so 'explosion'.
>
> but adaptability is still a far cry from innovation, which is the problem I find most puzzling.-You are mising my point. I'll repeat: Epigenetic changes in the genome can be heritable, and thus adaptations can become innovations.
> 
> Interestingly, however, you say in relation to the Cambrian Explosion that the increased oxygen "allowed the genome to perform and create new organs and organisms", and it would be immensely helpful if you could elaborate on this, even if you think there must have been other factors too.-This is the current Darwinian explanation. I know of no other factors. These forms appear 'out of thin air'.
>
> I'm not questioning that evolution happened, and of course natural selection played its part in preserving advantageous changes, but I'm trying to fill the gap between adaptation and innovation. -I feel they are one and the same. Inheritable adaptations can gradually or quickly become innovations. Darwin guessed at 'slow' change. He was watching the work of breeders. We now recognize that evolution can move rather quickly. It appears we are finding both stasis followed by puctuated equilibrium advances, and just punctuated advances with no stasis preceding.

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Here is a fascinating article combining global warming and adaptation of a carnivore species. 50 Mya there was a global warming period of 15 degrees F. and a species shrunk to half its size. Possible factors are discussed:-http://news.ufl.edu/2010/08/24/global-warming-3/

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David,-Emphasis Added
> >
> > [...] presuming Archaia haven't changed much, epigenetics was there from the beginning[/i]."
> > 
> Thank you for reviewing and summarizing my theory, but the intent of my comment re' Archaia staying the same, is different than your interpretation. We don't know what Archaia were like 3.6 bya. It is only by presuming they are unchanged that I can reach certain tentative conclusions about their condition then.
> -Your conclusion that life was made by design is anything but tentative! You've already admitted that you take this on faith. So please, lets not mince words here. -
> ...They do suggest that life has a built-in propensity to become complicated when given the right stimulus.
> -Again, if epigenetics are the cause of evolution, we will be able to demonstrate that evolution happens with no stimulus at all. ->
... Chance mutations are not worth much, as stated any times. 
> -Something tells me that cri du chat kids might serve as a counterexample to the sentence "Chance mutations are not worth much..." But I think you mean to aim not at chance mutations but at chance stimuli? -> And as a final point, I believe there are still layers of genome control within the organisms that are not yet discovered. Our knowledge of genome complexity will still grow a bit. I can't explain the Cambrian Explosion just on oxygen increase. The oxygen allowed the genome to perform and create new organs and organisms. Again, all my theory of the past 10 years, and the new discoveries seem to keep on confirming more and more of it.-My comp.bio brothers are working hard on this, :-P

--
\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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David,
> 
> Emphasis Added
> > >
> > > [...] presuming Archaia haven't changed much, epigenetics was there from the beginning[/i]."
> > > 
> > Thank you for reviewing and summarizing my theory, but the intent of my comment re' Archaia staying the same, is different than your interpretation. We don't know what Archaia were like 3.6 bya. It is only by presuming they are unchanged that I can reach certain tentative conclusions about their condition then.
> > 
> 
> Your conclusion that life was made by design is anything but tentative! You've already admitted that you take this on faith. So please, lets not mince words here.-My observations came first, and faith second. I can see, at this stage of our knowledge, no other mechanism that will work in the way we observe evolution to proceed. I'm not mincing words. I've made a theoretical choice, because I choose to, rather than sit on a fence. I may well be wrong, but if I can live long enough, I think my approach will be justified.
> 
> 
> > ...They do suggest that life has a built-in propensity to become complicated when given the right stimulus.
> > 
> 
> Again, if epigenetics are the cause of evolution, we will be able to demonstrate that evolution happens with no stimulus at all. -Not so. The epigenetic mechanisms generally provide rapid adaptation to onerous stimuli. The genetic changes are inheritable, so that a series of environmental challenges could produce a new species thru epigenetics. 
> 
> >
> ... Chance mutations are not worth much, as stated many times. 
> > 
> 
> Something tells me that cri du chat kids might serve as a counterexample to the sentence "Chance mutations are not worth much..." But I think you mean to aim not at chance mutations but at chance stimuli? -No, chance mutations. (Cru du Chat?; I don't know French, but I detect the word for cat??) 
> 
> > And as a final point, I believe there are still layers of genome control within the organisms that are not yet discovered. Our knowledge of genome complexity will still grow a bit. I can't explain the Cambrian Explosion just on oxygen increase. The oxygen allowed the genome to perform and create new organs and organisms. Again, all my theory of the past 10 years, and the new discoveries seem to keep on confirming more and more of it.
> 
> My comp.bio brothers are working hard on this, :-With great appreciation from me.

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How DNA is protected from mistakes in replication. There are two paths. Acetylation is a key component.-http://www.physorg.com/news/2011-03-scientists-key-dna.html

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> > To answer your question, the prime mover would be the stimulus that stresses the organism and forces selection. It's like evolution within a generation, but... maybe its just the way I think, but I don't see this as threatening any paradigms...
> 
> The Darwin paradigm as presented by Charles himself was that of slow and gradual changes, step by step. Darwin could not have guessed at what we are finding now, but some of his followers still think that way. Gould's PE has come to the fore, and the Cambrian Explosion certainly shows that species appear full-blown. -You make the same assertion as young-earth creationists here however, that the fossils in the Cambrian literally were the only appearing organisms in the record, that no previous forms of those creature existed. This is an argument that simply takes advantage of the fact that we have no complete link from every intervening generation from Archaea to now. -The Dawkins whale series shows a series of differing forms, but large gaps between each one. There is no evidence of Darwin's step by step
> guess. "IF" the first Archaia had adaptive mechanisms in the genome to stresses presented by environment, that is suggestive of design. The first organisms-Fine. Then look at the evolution of horses which when I visited the Smithsonian this July, was pretty conclusive. Several (sometimes hundreds of ) thousands of years between each form. Your argument is identical to the creationists here. "Because we have gaps in the fossil record, and some of the gaps are far too short for it to have evolved by natural selection."-This argument fails for the following reasons:
1. We must be able to demonstrate what the normal rate of mutation actually was; for this we can only go by modern measurements which just like weather--are far too recent to be able to accurately push backwards into the model. Only by comparing actual to expected can the argument be made that "it's just too fast." -2. We must be able to demonstrate that the conditions during these periods were happening under some kind of balance--we need to be able to remove environmental and predatory conditions. This must be done because in order to establish "epigenetics" as the "prime mover" we need to be able to demonstrate change without selection pressure. Epigenetics can only be the cause of speciation if and only if it can create species without selective pressure. This point of mine is incisive: if this cannot be demonstrated than it means that the cause of speciation itself cannot be reduced to a single moving part. My position is that speciation begins only from a stimulus. (Which can be a collection of non-deleterious frameshifts, etc.) -> at 3.6 bya had to face enormous environmenal changes. The Earth was still cooling down, CO2 and O2 were still altering their levels enormously,'snowball' Earth was still to be experienced, etc. Without those initial adaptive abilities
> it is unlikely life would have survived. I believe as research advances, it will be fully confirmed that the earliest organisms had adaptation built in. Your answer will be that we can only study living organisms now, and more simplistic organisms preceded what we see presently. That is no more proveable than my theory which views life as surviveable only if complete with good adaptive defenses.-The present evidence shows clear movement from uncomplex to complex. No research can be done of the kind you're talking about if we don't have access to the information needed for my points 1 & 2. Especially the environmental issues. Before you can demonstrate that the world was truly hostile to life, we need a really good example of what it actually was. Shapiro claims that we don't have a good enough picture of this.

--
\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

5246 views


> You make the same assertion as young-earth creationists here however, that the fossils in the Cambrian literally were the only appearing organisms in the record, that no previous forms of those creature existed. This is an argument that simply takes advantage of the fact that we have no complete link from every intervening generation from Archaea to now.-I agree. If you will carefully follow the discussion I've had with dhw, you will see I have made the point that other 'explosions' may still be hidden and awaiting discovery. It is interesting that the Burgess shale at Emerald Lake, Canada, was discovered by Walcott in 1909. Gould assumed in 'Wonderful Life' that this finding was one of a kind, and made very erroneous assumptions as a result. We arrive through very miraculous contingencies, to paraphrase him .......Conway-Morris went to shales in China, and you know the result. We have several different branches of ancentors before us (Notochordate forms), much less contingency, and more of a picture that evolution is driven. The point is, we have expanded our knowledge of the Cambrian Expl. and found no other explosions so far. 
> 
> The Dawkins whale series shows a series of differing forms, but large gaps between each one. There is no evidence of Darwin's step by step
 
> Fine. Then look at the evolution of horses which when I visited the Smithsonian this July, was pretty conclusive. Several (sometimes hundreds of ) thousands of years between each form. Your argument is identical to the creationists here. "Because we have gaps in the fossil record, and some of the gaps are far too short for it to have evolved by natural selection."-I am a form of creationist. I am not dismissing natural selection. Competition has to act on epigentic progress. I've said so to dhw. My point is that we have NEVER found any evidence of step by step. I think the reason is the rapid responses of epigentics creating new species which then face survival in the face of selection. Both processes are at work and work together.
> 
> This argument fails for the following reasons:
> 1. We must be able to demonstrate what the normal rate of mutation actually was; for this we can only go by modern measurements which just like weather--are far too recent to be able to accurately push backwards into the model. Only by comparing actual to expected can the argument be made that "it's just too fast."-Answered by the above comment. You misunderstand my thinking. 
> 
> 2. We must be able to demonstrate that the conditions during these periods were happening under some kind of balance--we need to be able to remove environmental and predatory conditions. This must be done because in order to establish "epigenetics" as the "prime mover" we need to be able to demonstrate change without selection pressure. Epigenetics can only be the cause of speciation if and only if it can create species without selective pressure. -This is exactly opposite my point of view. Epigenetics can drive speciation under pressures for adaptation.
> 
> > at 3.6 bya had to face enormous environmenal changes. The Earth was still cooling down, CO2 and O2 were still altering their levels enormously,'snowball' Earth was still to be experienced, etc. Without those initial adaptive abilities
> > it is unlikely life would have survived. I believe as research advances, it will be fully confirmed that the earliest organisms had adaptation built in. Your answer will be that we can only study living organisms now, and more simplistic organisms preceded what we see presently. That is no more proveable than my theory which views life as surviveable only if complete with good adaptive defenses.
> 
> The present evidence shows clear movement from uncomplex to complex. No research can be done of the kind you're talking about if we don't have access to the information needed for my points 1 & 2. Especially the environmental issues. Before you can demonstrate that the world was truly hostile to life, we need a really good example of what it actually was. Shapiro claims that we don't have a good enough picture of this.-Shapiro' book is about 25years old in publication, older than that in preparation. Presently, we do know a tremendous lot more about ancient climate, throuht ice core studies, etc. For example, Shapiro did not know about extremophiles at the writing of his book. I admire Shapiro, but you are misusing him.

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See the genome in action, the nucleosome separating DNA:-http://www.physorg.com/news201956505.html

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David,
> 
> > Fine. Then look at the evolution of horses which when I visited the Smithsonian this July, was pretty conclusive. Several (sometimes hundreds of ) thousands of years between each form. Your argument is identical to the creationists here. "Because we have gaps in the fossil record, and some of the gaps are far too short for it to have evolved by natural selection."
> 
> I am a form of creationist. I am not dismissing natural selection. Competition has to act on epigentic progress. I've said so to dhw. My point is that we have NEVER found any evidence of step by step. I think the reason is the rapid responses of epigentics creating new species which then face survival in the face of selection. Both processes are at work and work together.
> > 
> > This argument fails for the following reasons:
> > 1. We must be able to demonstrate what the normal rate of mutation actually was; for this we can only go by modern measurements which just like weather--are far too recent to be able to accurately push backwards into the model. Only by comparing actual to expected can the argument be made that "it's just too fast."
> 
> Answered by the above comment. You misunderstand my thinking. -I've admitted as much... I'm still unclear. Probably just because of our differences in normative argumentation...-> > 
> > 2. We must be able to demonstrate that the conditions during these periods were happening under some kind of balance--we need to be able to remove environmental and predatory conditions. This must be done because in order to establish "epigenetics" as the "prime mover" we need to be able to demonstrate change without selection pressure. Epigenetics can only be the cause of speciation if and only if it can create species without selective pressure. 
> 
> This is exactly opposite my point of view. Epigenetics can drive speciation under pressures for adaptation.-Here's the rub; if you're right and epigenetics are the "cause" of speciation, then we should be able to force evolution artificially without need of reproduction or intervening generations. If we can't do this, then the argument must go "Stimulus-->Response-->Filter" where as the response (epigenetics) is only the middle step from stimulus to new species. The cause is clearly the stimulus, and the end result is clearly via natural selection (Filter). Again, via computer science, the filter is the only thing that matters in the end, because we only care about what gets left behind...-> > 
> > > at 3.6 bya had to face enormous environmenal changes. The Earth was still cooling down, CO2 and O2 were still altering their levels enormously,'snowball' Earth was still to be experienced, etc. Without those initial adaptive abilities
> > > it is unlikely life would have survived. I believe as research advances, it will be fully confirmed that the earliest organisms had adaptation built in. Your answer will be that we can only study living organisms now, and more simplistic organisms preceded what we see presently. That is no more proveable than my theory which views life as surviveable only if complete with good adaptive defenses.
> > 
> > The present evidence shows clear movement from uncomplex to complex. No research can be done of the kind you're talking about if we don't have access to the information needed for my points 1 & 2. Especially the environmental issues. Before you can demonstrate that the world was truly hostile to life, we need a really good example of what it actually was. Shapiro claims that we don't have a good enough picture of this.
> 
> Shapiro' book is about 25years old in publication, older than that in preparation. Presently, we do know a tremendous lot more about ancient climate, throuht ice core studies, etc. For example, Shapiro did not know about extremophiles at the writing of his book. I admire Shapiro, but you are misusing him.-Ice cores can be discarded--we know that the early earth was too hot. As for the rest of this here, we have no firm basis to argue from at this point (and this goes for abiogenesis as well.) The oldest rocks are 4.5Bn years old; everything prior to that was recycled into the earth's crust and we can only glean small glimpses into what happened prior--which might well be necessary if life began in extremophile conditions.

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\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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> > This is exactly opposite my point of view. Epigenetics can drive speciation under pressures for adaptation.
> 
> Here's the rub; if you're right and epigenetics are the "cause" of speciation, then we should be able to force evolution artificially without need of reproduction or intervening generations. If we can't do this, then the argument must go "Stimulus-->Response-->Filter" where as the response (epigenetics) is only the middle step from stimulus to new species. The cause is clearly the stimulus, and the end result is clearly via natural selection (Filter). Again, via computer science, the filter is the only thing that matters in the end, because we only care about what gets left behind...-Agreed. But I think it will require direct stimulation of the epigenetic mechanisms. If the organism is threatened, there are probably somewhat slow chemical mediators to turn on the epigenetics, and that may confuse the results of your proposed experiment.-By the way: Cru du Chat? please translate!

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> > > This is exactly opposite my point of view. Epigenetics can drive speciation under pressures for adaptation.
> > 
> > Here's the rub; if you're right and epigenetics are the "cause" of speciation, then we should be able to force evolution artificially without need of reproduction or intervening generations. If we can't do this, then the argument must go "Stimulus-->Response-->Filter" where as the response (epigenetics) is only the middle step from stimulus to new species. The cause is clearly the stimulus, and the end result is clearly via natural selection (Filter). Again, via computer science, the filter is the only thing that matters in the end, because we only care about what gets left behind...
> 
> Agreed. But I think it will require direct stimulation of the epigenetic mechanisms. If the organism is threatened, there are probably somewhat slow chemical mediators to turn on the epigenetics, and that may confuse the results of your proposed experiment.
> -This is precisely what I mean by "...should be able to force evolution artificially without need of reproduction or intervening generations."-Where my confusion still lies in interpreting your thinking, is, if we have agreement that Stimulus-->epigenetic response-->Natural Selection is the "correct" model... then I don't see how your thinking is actually different than the current textbook model. This generalized process is exactly what I learned in college only 4 years ago. It is the de facto position I've seen evolutionary biologists (Massimo Pigliucci) use consistently. --> By the way: Cru du Chat? please translate!-It should have been "Cri du chat" which translates to "Crying cat." It's a birth defect cause by... I think it's a deletion of part of an entire chromosome. The resulting baby is severely retarded and when cries, sounds like a howling cat.

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\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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> This is precisely what I mean by "...should be able to force evolution artificially without need of reproduction or intervening generations."
> 
> Where my confusion still lies in interpreting your thinking, is, if we have agreement that Stimulus-->epigenetic response-->Natural Selection is the "correct" model... then I don't see how your thinking is actually different than the current textbook model. -The usual interpretation of evolution is that, a' la Darwin, it is in slow tiny steps. Our difference in interpretation is speed. I believe large jumps can occur and it is usually the way evolution proceeds. Small changes are reversible adaptations, like Darwin's six species of finches, with beaks adjusting cyclically with climate changes in cycles.

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> > This is precisely what I mean by "...should be able to force evolution artificially without need of reproduction or intervening generations."
> > 
> > Where my confusion still lies in interpreting your thinking, is, if we have agreement that Stimulus-->epigenetic response-->Natural Selection is the "correct" model... then I don't see how your thinking is actually different than the current textbook model. 
> 
> The usual interpretation of evolution is that, a' la Darwin, it is in slow tiny steps. Our difference in interpretation is speed. I believe large jumps can occur and it is usually the way evolution proceeds. Small changes are reversible adaptations, like Darwin's six species of finches, with beaks adjusting cyclically with climate changes in cycles.-Okay... I think, coupled with your post in "Ain't Nature Wonderful" I think I FINALLY understand you;-1. Adaptability is a necessary component to life, as much as reproduction and respiration. -2. Adaptability itself isn't something you view as "creatable by chance."-These two underpinnings seem to be the hinge. -Assuming I have this right, I need to get some clarifications. -First; how does your epigenetics differ from stimulus/response? An example would make this more clear. It has been demonstrated that the human body of baseball pitchers modifies itself to what the pitcher does best; bones thicken and provide more surface area for muscle attachment, thus allowing for faster pitches, for longer games. To me, this would read as an "epigenetic" trait, because this is an inherent ability that will get passed to his offspring. (The ability to change, not the bone structure itself.) The same thing when I exercise; I tear muscle, get weak, and then my body repairs more strongly. To me, it seems your epigenetics aren't differentiable from these physiological processes. Could you explain the differences you see, if any?

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\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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> like Darwin's six species of finches, with beaks adjusting cyclically with climate changes in cycles.-The finches are not changed!! They are like Roger's arm below, adapting to 90 mile an hour pitches. Roger's son can make the same adaptation BUT they are both really the same species.
> 
> Okay... I think, coupled with your post in "Ain't Nature Wonderful" I think I FINALLY understand you;
> 
> 1. Adaptability is a necessary component to life, as much as reproduction and respiration. 
> 
> 2. Adaptability itself isn't something you view as "creatable by chance."
> 
> These two underpinnings seem to be the hinge. 
> 
> Assuming I have this right, I need to get some clarifications. 
> 
> First; how does your epigenetics differ from stimulus/response? -I guess in the meaning of word descriptions. "Stimulus/response" is descriptive, and doesn't clarify genetic levels of change, Like Aristotle I'm getting to underlying cause and mechanism. Epigenetics changes the core genetics of the organism as a whole. It is back to Reznick's guppies. The entire organisms get bigger in size and this size remains the same from generation to generation unless put back into a different river with preditors who like large guppies on their menu. Roger's grandson will not have a large arm unless he starts to pitch. And his kids won't have enlarged arms unless they pitch. Each generation of Clemens is not irreversibly changed, like the finches.

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A Time magazine article on the amazing advances in epigenetics. And I repeat my same argument; the odds for a chance production of this code system are nil. Only an intelligence can create an adaptive system this complex. Not enough computer power to study it thoroughly, as the article states:
> 
> http://www.time.com/time/health/article/0,8599,1951968-1,00.html-I'm rather late to this thread (go figure) but the argument that "there isn't enough computing power" irks me a little. -Simulations of this nature typically are trying to "search" across a very broad number of permutations. A lack in power in this doesn't put a single point of argument in favor of design; computing complexity is purely a measurement of how much time it takes to search--not how complex life is.

--
\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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Over and over I have stated that the genetic coding mechanism promised to be extremely complex. Coupled with the this the observation that discoveries of increased complexity would proportionally reduce the odds for the chance production of life from inorganic matter.-
Today, Uncommon Descent has an excellent article on the origin of information in DNA from a therodynamic perspective, arguing against chance.-http://www.uncommondescent.com/

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Over and over I have stated that the genetic coding mechanism promised to be extremely complex. Coupled with the this the observation that discoveries of increased complexity would proportionally reduce the odds for the chance production of life from inorganic matter.-
I noted that I misspelled 'thermodynamic' on the last entry. I'll try to be a better self-taught typist. Today let's look at jumping genes, transposons. These allow for rapid gene change and therefore rapid adaptation. It is another complicated controlled mechanism that is not a chance point mutation.-
http://www.sciencedaily.com/releases/2010/06/100601171838.htm

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More on genetic compexity: exons are the coding portion of genes. Introns are interruption areas in genes, so that genes are not one continuous strip of code. This degree of interruption developed in early evolution and is most prominent in humans. Its development is now being studied in cyanobacteria, one of the earliest forms of bacteria. The interruptions allow for iRNAs to piece together different parts of a gene to create different functions of the gene, allowing the whole gene to do several jobs. This is probably why we have so few genes for so many functions. And this is why we have so many layers of control of this mechanism, as well as review and repair mechanisms to insure accuracy of all processes of copying. See this article:-http://www.physorg.com/news195236809.html

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The fact that this paper by Macintosh has passed peer review is unsurprising -http://www.uncommondescent.com/intelligent-design/andy-mcintoshs-peer-reviewed-id-paper-note-the-editors-note/-when one finds that he is on the editorial advisory group and that the first name on the list of editors is his old creationist mate Stuart Burgess of University of Bristol. -http://journals.witpress.com/pages/08jdne/default.asp-They were both speakers at the Creationist Conference in Leicester that I attended a few years ago. The "Wessex Institute of Technology" which publishes the journal is known for dubious editorial practices in the past:-http://www.cg.tuwien.ac.at/~wp/videa-paper.html-Macintosh is an out-and-out Young-Earth Creationist. His lecture was more like an evangelical sermon, very passionate and emotional. He twists his expertise in thermodynamics to fit this preconceived scenario.

--
GPJ

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> Macintosh is an out-and-out Young-Earth Creationist. His lecture was more like an evangelical sermon, very passionate and emotional. He twists his expertise in thermodynamics to fit this preconceived scenario.-George is certainly correct in his objections to Macintoch. M is an IDer. But the question still remains. Where did the informaion in the various layers of codes in the genetic mechanism come from? Arise by chance? Not any code we have seen developed on this Earth. Each point change by chance mutation introduces new information hidden in the code. Each transposition does the same thing. Each methylation does it. Each deletion introduces hidden code infomation. There is coded information at each level of control in the genetic mechanism. the point still remains. How did that information appear? I think chance is the least likely.

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But the question still remains. Where did the informaion in the various layers of codes in the genetic mechanism come from? Arise by chance? Not any code we have seen developed on this Earth. There is coded information at each level of control in the genetic mechanism. the point still remains. How did that information appear? I think chance is the least likely.-Another level of micro RNA control found. As usual more complexity and less and less 'junk' DNA. Eventually my theory will triumph!-http://www.nature.com/nature/journal/v466/n7306/edsumm/e100729-14.html

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Over and over I have stated that the genetic coding mechanism promised to be extremely complex. Coupled with the this the observation that discoveries of increased complexity would proportionally reduce the odds for the chance production of life from inorganic matter.
> 
> How true is seen in the following article. The RNA pieces in so-called'junk' DNA are now seen to be a large and complicated secondary RNA code of direct gene expression and varying gene expression. Methods are now developed to begin that decoding. This is a computer system within a computer system. I think other levels of code will appear.
> 
> http://www.nature.com/news/2010/100505/full/465016a.html-Here is another study of RNA influence, again reducing the regions of 'junk' to 'functional'. Human cells need less than 25,000 genes becuase of this layer of activity:-http://www.physorg.com/news200656763.html-And another article on very simple ancient sponges http://www.nature.com/news/2010/100804/full/466673a.html, their genes and cell death (apoptosis):

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Over and over I have stated that the genetic coding mechanism promised to be extremely complex. Coupled with the this the observation that discoveries of increased complexity would proportionally reduce the odds for the chance production of life from inorganic matter.-
An article in Science on 'positive selection' is a great insight how the genome manages to have rapid selection, while chance mutation and natural selection is cumbersome, chancy and slow.-http://www.sciencemag.org/cgi/content/full/329/5993/740

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Unfortunately, David, this article is only available to subscribers - or you have to buy it. Maybe that's what they mean by 'positive selection'!

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Sorry the article didn't open. The summary doesn't explain much. A major example given of 'positive selection' is that Tibetans adapted to high altitudes in just 4,000 years. The gene is identified. This is a much faster rate than the known rates of random mutation and natural selection can provide. Therefore, it is concluded there are subtle mechanisms that can push adaptive evolution.- http://www.sciencemag.org/cgi/content/summary/329/5993/740

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> http://www.sciencemag.org/cgi/content/summary/329/5993/740-Here are selected paragraphs from the above article:-Human Evolution: 
Tracing Evolution's Recent Fingerprints
Ann Gibbons 
 -
"For Rasmus Nielsen, it was a revelatory moment. He was analyzing the frequency of different mutations in the genomes of Tibetans living at high altitude, searching for adaptations that allow them to thrive in thin air. His team's analysis had generated a graph in which most of the mutations were clustered together. But two stood apart, indicating they existed in almost all Tibetan highlanders but not in their close relatives, the Han Chinese. The high frequency of the mutations showed that this was a radical example of rapid evolution, with strong natural selection acting on a single gene. It was the most radical of a flurry of recent discoveries of human genes that evolution has strongly favored, a process called positive selection. They now realize, however, that plenty of positive selection exists, but it is subtler and harder to trace than originally anticipated. Using new statistical methods, they have found many less dramatic mutations that, for example, also help highland Tibetans survive at high altitude. A growing number of researchers now think it is rare for a particular mutation to spread rapidly to most people within a population, as was the case with the Tibetan gene. "There have been a bunch of papers that show very consistently selection across a lot of our genome, but of a type that doesn't leave these massive footprints," says Gilean McVean, a population geneticist at the University of Oxford. -Seeking selection 
Many researchers have argued that most of the obvious differences between humans today are the result of recent positive selection rather than mutations that accumulated randomly over time. All living humans are remarkably similar genetically because we all descended from a small founder population that arose in Africa about 200,000 years ago. As these modern humans moved around and, eventually, out of Africa in the past 80,000 years or so, they evolved genetic differences that helped them adapt to new climates, digest novel foods, and fight off new illnesses and parasites. -
With the sequencing of the complete human genome for the first time a decade ago, researchers were able to get a better handle on how selection has shaped the genome. Several large-scale projects used different methods to identify millions of single-nucleotide polymorphisms (SNPs) from across the genomes of people in different populations in Europe, Asia, and Africa. By comparing SNPs at the same sites in individuals from different populations, researchers could detect those where positive selection had driven a mutation to high frequencies in a population. 
 The identification of so many regions of the genome under positive selection prompted some researchers to conclude that evolution had accelerated as humans spread around the globe and adapted to new challenges.
 
Soft sweeps 
Yet McVean and others were convinced that positive selection had shaped much of the genome but lay beneath the radar of methods used to detect it. Consequently, earlier this year Pritchard and his colleagues proposed an alternative to strong selection on single new mutations. In Current Biology, they argued that selection on more than one gene at once could allow a new traitâincreased heightâto sweep more rapidly through a group. -
 While several teams are developing new methods to identify polygenic soft sweeps, others are working to pinpoint more precisely the DNA under positive selection. Sabeti's team was able to home in on 64 regions containing just a single gene, which narrows the search for a SNP that may boost an adaptive trait. 
Many groups are also ramping up efforts to do functional studies of the gene variants they have identified. Finally, many researchers are looking forward to the complete genomes of 1000 individuals in the 1000 Genomes Project.
As researchers look forward to scanning these new data sets, they say that the key question is no longer how much positive selection is in the genome."-
Think about it. Geneticists are now showing us that the genome is responding actively to environmental pressures, not passively as Darwin expected. This is done at the RNA level, methylation of DNA, SNP's, etc. Watson/Crick DNA is a copy code for the raw material of life, not a very effective code for rapid evolutionary advances. This is an obvious conclusion. Many other layers of the genome are operative to allow these rapid advances. Chance mutation and natural selction are a totally passive mechanism. Scientists are discovering much more beyond Neo-Darwinism.

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David has referred us to two websites, both of which as a non-scientist I find puzzling. I'll explain why, and then perhaps someone can shed some light on the issues.-http://www.physorg.com/news200842170.html-This deals with the discovery of a bacterium which researchers at Yale say is a remnant from the time before DNA. The cells use "ancient RNA technology to control modern gene expression", an ability "once believed to be possessed solely by proteins." Prof. Ron Breaker believes that early forms of life depended on such "RNA machines". So far so good. However, Breaker concludes with the statement that "a lot of sophisticated RNA gadgetry has gone extinct, but this study shows that RNA has the power needed to carry out complex biochemistry. [...] It makes the spontaneous emergence of life on earth much more palatable." -Without climbing aboard the ID bandwagon, I would just like to know how the newly discovered complexities of RNA make the case for "spontaneous emergence" more palatable. -The second article, available only in summary to non-subscribers, is on: -http://www.sciencemag.org/cgi/content/summary/329/5993/740-but David has kindly provided us with salient extracts. It illustrates "positive selection", e.g. Tibetans adapting to high altitudes in "just 4000 years". David says that this "is a much faster rate than the known rates of random mutation and natural selection can provide. Therefore, it is concluded there are subtle mechanisms that can push adaptive evolution."-Firstly, I don't understand the relevance of random mutations anyway. Why on earth would Tibetans have randomly acquired an ability to cope with high altitudes prior to being exposed to such an environment? Doesn't common sense tell us this is "adaptative evolution", not random mutation? If you can't cope with high altitude, you'll either die or you'll get back down to where you can breathe again. Presumably, Tibetans were gradually able to venture higher and higher, as each generation got more acclimatized, but even a single generation of animals can adapt to a changing environment. Otherwise the lions of Longleat (a safari park here in Britain) would hardly have survived our winters when the park first opened in 1966. Also I wonder how the researchers hit on the figure of 4000 years. If you take that as the equivalent of say 200 generations, it seems a mighty long time for the Tibetans to be huffing up and down. (I'm not disputing the arguments of the experts. I'm just explaining why I don't understand them, and I'm asking for help.)-Secondly, as we have said repeatedly on this forum, the mechanism allowing for potential adaptation must have been built into early forms of life ... otherwise there would have been no evolution ... and so I can't see what is so revelatory about "positive selection". Right from the start of evolution, natural selection has meant the survival of those features that are best adapted to the environment, and this has to be "positive". Negative selection ultimately means goodbye.-DAVID: Geneticists are now showing us that the genome is responding actively to environmental pressures, not passively as Darwin expected. [...] Chance mutation and natural selection are a totally passive mechanism.-Of course Darwin didn't know what we now know about genetics, but he certainly viewed adaptability as an integral feature of living things: "I am inclined to look at adaptation to any special climate as a quality readily grafted on an innate wide flexibility of constitution, which is common to most animals." (Origin, 'Laws of Variation', section on 'Acclimatisation'). I think David is right about the passiveness, since Darwin attributed acclimatisation to "mere habit" and/or natural selection working on "different innate constitutions", but again I don't see what this has to do with chance mutation, which seems to me to be a totally different subject from adaptation. I'd always thought of the former as a random, entirely internal change (which may or may not be useful), and the latter as an internal change arising from interaction with external conditions. Am I missing something here?

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David has referred us to two websites, both of which as a non-scientist I find puzzling. I'll explain why, and then perhaps someone can shed some light on the issues.
> 
> http://www.physorg.com/news200842170.html
> 
> This deals with the discovery of a bacterium which researchers at Yale say is a remnant from the time before DNA. The cells use "ancient RNA technology to control modern gene expression", an ability "once believed to be possessed solely by proteins." Prof. Ron Breaker believes that early forms of life depended on such "RNA machines". So far so good. However, Breaker concludes with the statement that "a lot of sophisticated RNA gadgetry has gone extinct, but this study shows that RNA has the power needed to carry out complex biochemistry. [...] It makes the spontaneous emergence of life on earth much more palatable." 
> 
> Without climbing aboard the ID bandwagon, I would just like to know how the newly discovered complexities of RNA make the case for "spontaneous emergence" more palatable. -Thank you, dhw. Of course I noted that stupid final comment by the researcher. And usually I comment on those obligatory bows to the dying theory of an "RNA world" has to come first. I'm delighted others of us notice. The key issue in the article is the exact point I just made yesterday to George: these modifying mechanisms are probably ancient, and if so suggest design.

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David has referred us to two websites, both of which as a non-scientist I find puzzling. > 
> The second article, available only in summary to non-subscribers, is on: 
> 
> http://www.sciencemag.org/cgi/content/summary/329/5993/740
> 
> but David has kindly provided us with salient extracts. It illustrates "positive selection", e.g. Tibetans adapting to high altitudes in "just 4000 years". David says that this "is a much faster rate than the known rates of random mutation and natural selection can provide. Therefore, it is concluded there are subtle mechanisms that can push adaptive evolution."
> 
> Firstly, I don't understand the relevance of random mutations anyway. Why on earth would Tibetans have randomly acquired an ability to cope with high altitudes prior to being exposed to such an environment? Doesn't common sense tell us this is "adaptative evolution", not random mutation? 
 
Of course it is adaptive evolution. Just as Reznick's guppies take two years to adapt to danger. The Tibetans migrated uphill and forced the adaptation. They didn't have to wait for random help from cosmic rays, or some other chance mechanism, creating a mutation. As stated yesterday in discussion with George, Darwin made some amazing guesses, but could not know what we are finding today. This type of research started in the early 1990's, and has developed quite a story of adapability, directed changes, not chance.->
> Also I wonder how the researchers hit on the figure of 4000 years. If you take that as the equivalent of say 200 generations, it seems a mighty long time for the Tibetans to be huffing up and down. (I'm not disputing the arguments of the experts. I'm just explaining why I don't understand them, and I'm asking for help.)-I don't either fully. It is done by identifying genes, and studies of changes from the past. I know I can go to 11,000 feet and walk around. I've done this at the top of Pike's Peak after taking the cog railroad up. I know if I stay there I'll get more red blood in my system and acclimate in a few days. I've done this at Cusco, Peru at 10,500 feet and then went to Machu Picchu at 8,500 feet very comfortably, toured Quito, Equador at 11,000 feet, over a two week period. And we started at Lima, at sea level. This is done by rapid temporary adaptation of the body, but eventually genes should take over and make the adaptation permanent.-
> 
> Secondly, as we have said repeatedly on this forum, the mechanism allowing for potential adaptation must have been built into early forms of life ... otherwise there would have been no evolution ... and so I can't see what is so revelatory about "positive selection". Right from the start of evolution, natural selection has meant the survival of those features that are best adapted to the environment, and this has to be "positive". Negative selection ultimately means goodbye.-I think it is a matter of bowing to Darwin verbiage: natural selection has both positive and negative sides to it, depending upon genetic response rate to adaptation. Too slow and you are gone as I previously stated: 
> 
> Geneticists are now showing us that the genome is responding actively to environmental pressures, not passively as Darwin expected. [...] Chance mutation and natural selection are a totally passive mechanism. 
> 
> Of course Darwin didn't know what we now know about genetics, but he certainly viewed adaptability as an integral feature of living things. but again I don't see what this has to do with chance mutation, which seems to me to be a totally different subject from adaptation. I'd always thought of the former as a random, entirely internal change (which may or may not be useful), and the latter as an internal change arising from interaction with external conditions. Am I missing something here?-Only that the "positive selection" proposal implies that there are internal processes that can change the genome to respond quickly to external pressures of the environment, immediately as those pressures are recognized. They do not allow the negative possibility implied in relying upon 'natural selection' alone to act in a random fashion.

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More articles on the micro-RNA function in controlling cell activity:-http://www.physorg.com/news201173119.html-http://www.physorg.com/news201174605.html

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More complexity. This summary of an article describes newly-found functions for non-coding RNAs:-http://f1000.com/5601958?key=pvf5hhgm9nltp41

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This article demonstrates that DNA is very bendable, and controllable by certain enzymes. the enzymes are modeled:-http://blog.the-scientist.com/2010/12/13/lets-twist-again/

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Another article on the complex functions of RNA. How RNA in dangerousbacteria can manipulate the genome:-http://www.physorg.com/news200842170.html

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An article discusses using bacteria for codes messages. The key sentences is in the second paragraph, in which the researchers suggest that they can use bacterial DNA for the coding. Life is a living computer!-http://www.physorg.com/news/2011-09-chemists-bacteria-encode-secret-messages.html

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A new repair enzyme has been found for DNA repair. Each discovery makes the genome more complex, and makes the question of 'chance development' more problematic:-http://www.physorg.com/news/2011-09-biochemists-genetic-code-tool.html

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I thought this comment on a discussion on the Dawkins forum might be of interest. It estimates the enormous number of generations in the process of evolution from the simplest cell to humans. More than enough for chance and natural processes to evolve all manner of complexity.-http://richarddawkins.net/discussions/499667-how-many-generation-estimated-from-first-cell-to-modern-human-How-many-generation-estimated-from-first-cell-to-modern-human?-In The Ancestors Tale Richard Dawkins gives an estimate of 
how many generations have gone between each branch point concerning 
the human line (which turns into the 'ape line' then the 'mammal line' 
then... etc.) to us modern day humans (there are about forty such 
branch points on our line - surprising no?). So the fisrt branch point 
is between us and chimps, 250 thousand generations ago (which spans 
6 million years). Reptiles and birds branched off at 310 million years 
ago, 170 million generations ago. Of course, the average generation 
time for a human is something like 20 years, whilst mouse might be 
only about 2 years - so that has to be factored in (and since we are 
dealing with long extinct animals, some guesswork is required).-Anyway, the last branch point, which Dawkins ventures a guess at the 
amount of generations past, is at the branch point between humans 
and protostomes (worms, molluscs, insects and crustaceans etc.) 
This is a little after 'phylems to be' such as plants, animals and 
fungi have appeared. Dawkins estimates about 310 million genertions 
have passed in that 600 million year(!) gap.-So Dawkins deosn't even try to guess at how many generations have 
gone between us and our single celled ancestors. Were are probably 
talking anywhere between 1 and 4 billion years of single celled life. 
Some single celled animals today have a geration time of a few hours. 
How many generations can you pack into a few billion years, given a 
generation time as short as that?-Hell if I know, but the margin of error would be collosal.-Addition: Assuming two and half billion years of single celled life, 
with an average generation time of 6 hours. There would have been 
3'650'000'000'000 (3.65 trillion) generations before you even start 
with multicellular life.

--
GPJ

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I thought this comment on a discussion on the Dawkins forum might be of interest. It estimates the enormous number of generations in the process of evolution from the simplest cell to humans. More than enough for chance and natural processes to evolve all manner of complexity.-Your observation and Dawkins' is exactly correct. Quadrillions of generations, but the ever-present Archaia and the other bacteria have been the same for 3.5 billion years. Then we see changes, punctuated equilibrium, the Cambrian Explosion, and actually intermediate forms, (i.e. the whale series), but the fossil record has never provided Darwin's little-step-at-a-time proposal. Darwin was extremely prescient, but at a huge disadvantage to what we can study today. -To me it is necessary to take the next step. Your multitudinous generations provide time for the development of the processes I have been presenting. Evolution can speed up, driven by necessity, and by processes in the genome to allow rapid adaptation. Where you and I will disagree, is I expect it to be found that many of these adaptive processes are present in Archaia from the beginning, and to me that means design. If on the other hand, the processes developed over the 3.6 billion years of life, and are a recent phenomenon, then you are correct and there in no design, only chance. At present, neither of us knows the 'true' answer, only our individual biases.

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George has drawn our attention to a discussion on the Dawkins forum concerning the enormous number of generations in the process of evolution from the simplest cell to humans ... "more than enough for chance and natural processes to evolve all manner of complexity."-David expects it to be found that "many of these adaptive processes are present in Archaia from the beginning, and to me that means design. If on the other hand, the processes developed over the 3.6 billion years of life, and are a recent phenomenon, then you are correct and there is no design, only chance."-I have no difficulty at all following George's logic. Once you take the plunge of accepting chance as the originator of life plus its mechanisms of reproduction with potential variation, the rest is plain sailing. But if you haven't taken that plunge, I can't see why recentness should lessen the complexity argument. If you follow the design scenario, it's perfectly conceivable that a designer might leave the original simple forms of life alone for a billion or so years, and then decide enough's enough and endow them with new innovative or adaptive mechanisms. Either you believe these mechanisms to be too complex for chance to assemble, or you don't ... regardless of the time factor. Scientists can juggle with time, generations and mathematical odds as much as they like, but firstly such calculations can only be speculative (different conditions, missing species, "Dawkins ventures a guess", "Dawkins estimates"...) , and secondly each of us has his own boundaries of credulity. I have myself repeatedly argued that the mechanisms for change must have been present in early forms of life for evolution to have taken place, but if you tell me those mechanisms didn't appear for say a billion years (i.e. a billion years elapsed before evolution began to produce more complex forms of life), I'm still confronted with the conundrum of how they managed to put themselves together. David says quite rightly that neither he nor George knows the 'true' answer and therefore each is left with his individual bias. I'm just puzzled as to why the bias has a temporal cut-off point.-Thank you, David, for your clear and comprehensive answers to my post of Monday 16 August at 12.51. No further questions!

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> David expects it to be found that "many of these adaptive processes are present in Archaia from the beginning, and to me that means design. If on the other hand, the processes developed over the 3.6 billion years of life, and are a recent phenomenon, then you are correct and there is no design, only chance-Exactly as I feel.
> 
> I have no difficulty at all following George's logic. Once you take the plunge of accepting chance as the originator of life plus its mechanisms of reproduction with potential variation, the rest is plain sailing. -Let me explain. As you state below there is the 'if' of complexity. George's thinking is not plain sailing. There is a time factor of creating the genome's newly discovered complexity. Therefore, if there is only some complexity in the genome in Archaia and massive complexity in humans, George is correct. But if it turns out that the same massive complexity is in Archaia and humans then there has been design. 
> 
> If you follow the design scenario, it's perfectly conceivable that a designer might leave the original simple forms of life alone for a billion or so years, and then decide enough's enough and endow them with new innovative or adaptive mechanisms. Either you believe these mechanisms to be too complex for chance to assemble, or you don't.- I cannot conceive of a God who keeps fiddling with his creation. It is either designed from the beginning or we will agree George is correct and it all evolved with those interesting paroxysms of puctuated equilibium thrown in to confuse us. IT IS TOO COMPLEX for evolution to do it by chance.-I don't have the whole article, but more evidence of complexer and complexer than we ever imagined, since Watson/Crick announced their (as it is turning out) simplistic code.-http://www.nature.com/nrg/journal/v11/n9/execsumm/nrg2843.html

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Here is another short essay which defines my position and view of what we are finding in the complex coding within the genome.-http://www.plosbiology.org/annotation/listThread.action?inReplyTo=info%3Adoi%2F10.1371%2Fannotation%2F15134b58-7375-48e7-9553-42979b51bb5d&root=info%3Adoi%2F10.1371%2Fannotation%2F15134b58-7375-48e7-9553-42979b51bb5d

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DAVID: [...] if there is only some complexity in the genome in Archaia and massive complexity in humans, George is correct.-George believes we are the product of chance and not design. Sitting as always on my fence, and therefore looking in all directions at the same time, I see no reason why a designer shouldn't leave things simple for a billion years or so, and then decide to try something a bit more ambitious.-DAVID: I cannot conceive of a God who keeps fiddling with his creation. It is either designed from the beginning or we will agree George is correct with those interesting paroxysms of punctuated equilibrium thrown in to confuse us. IT IS TOO COMPLEX for evolution to do it by chance.-Please forgive me my obtuseness, but the point you are making is so fundamental both to your faith and to my own indecision that I need to have it clarified on two counts. Firstly, I have no trouble following the argument that the genome is too complex to have evolved by chance. What I don't understand is why it had to be present in all its complexity right from the start, and if it wasn't, then ALL its complexities have come about by chance. Surely it is or it isn't too complex for chance, regardless of the time factor. -Secondly, if in fact the choice is between chance and a God who occasionally fiddles around, I'm surprised that you would go for chance, especially as you have always insisted that we should not make any assumptions about the UI. Given your belief in his deliberate creation of life, is there any reason why he should not deliberately have intervened if he felt like it? Isn't it just as much an imposition of attributes to argue that he doesn't intervene as to argue that he does?

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> Secondly, if in fact the choice is between chance and a God who occasionally fiddles around, I'm surprised that you would go for chance, especially as you have always insisted that we should not make any assumptions about the UI. Given your belief in his deliberate creation of life, is there any reason why he should not deliberately have intervened if he felt like it? Isn't it just as much an imposition of attributes to argue that he doesn't intervene as to argue that he does?-To answer please review my most recent discussion with Matt. I admit my preference (obviously I don't 'know') for everything being in place from the beginning. However, recent work is showing that the earliest organisms appear to have a very complex adaptation mechanism in the genome. Of course, work is done on current represenatives of ancient bacteria, and presumes they are relatively unchanged. As you have admitted previously, such mechanisms would drive evolution toward more complexity. Secondly, life is run by codes, driven by codes. It can't exist without codes. Why should they not be complete from the beginning? The fact that the genome can manipulate it own genes should not come as a surprise. The manipulation completes an ideal structure to manage life. Living matter is diffrent than the 'brick' or a rock. Living matter has to have the ability to adapt to environmental change, or that great stalker, natural selection takes over.-And finally, I agree that we should not make any assumptions about the UI, but the evidence is pointing more and more to a beginning that was complete, with no subsequent fiddling. Remember, the amoeba has a DNA slightly longer than human DNA, but only six genes. A blank slate waiting to be filled.

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> I cannot conceive of a God who keeps fiddling with his creation. It is either designed from the beginning or we will agree George is correct and it all evolved with those interesting paroxysms of puctuated equilibium thrown in to confuse us. IT IS TOO COMPLEX for evolution to do it by chance.-
More complexity: ncRNA is important in activating and de-activating genes:-http://www.cell.com/retrieve/pii/S0092867410010111-
And a more complete discussion of transcriptones, ncRNAs, that monitor and guide development:-http://f1000.com/5601958?key=pvf5hhgm9nltp41

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> > I cannot conceive of a God who keeps fiddling with his creation. It is either designed from the beginning or we will agree George is correct and it all evolved with those interesting paroxysms of puctuated equilibium thrown in to confuse us. IT IS TOO COMPLEX for evolution to do it by chance.-
This article shows the layers upon layers of genome complexity that are becoming very clear. This dscribes worm and fruit fly studies, just published:-http://www.the-scientist.com/news/display/57899/ -As these articles come out they form a pattern of discovery that leads us far beyond the simplifed beginnings when DNA was starting to be decoded.

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This article shows how the ribosome uses a careful method of cleavage to construct very accurate protein molecules. The mistakes are roughly one in 10 thousand.:-http://www.sciencedaily.com/releases/2010/12/101222131133.htm

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> I cannot conceive of a God who keeps fiddling with his creation. It is either designed from the beginning or we will agree George is correct and it all evolved with those interesting paroxysms of puctuated equilibium thrown in to confuse us. IT IS TOO COMPLEX for evolution to do it by chance.
> 
> I don't have the whole article, but more evidence of complexer and complexer than we ever imagined, since Watson/Crick announced their (as it is turning out) simplistic code.
> 
> http://www.nature.com/nrg/journal/v11/n9/execsumm/nrg2843.html-This article is a great story of RNA research and how RNA is the protein maker, taking instructions from DNA, and then acting very much on its own. Way too complex a system to have designed itself, and as I predicted in my book, getting complexer and complexer as research digs into the system of the genome.-http://www.the-scientist.com/2010/9/1/34/1/-
"The fact is that the scientific evidence that we have is full of holes, or mysteries. At one time people believed in the God of the Gaps and then retreated from that position because the gaps seemed to be getting smaller and smaller and threatened to close up altogether. But that is not the case today: the gaps are getting bigger and bigger; the chances of the world that we live in happening by accident are vanishingly small. The chances of a strand of DNA assembling itself by accident are infinitesimal, too small to be worth considering. The world is an essentially mysterious place. Science has not got it all sorted out, whatever Stephen Hawking says: science has only deepened the mysteries. In the face of the mysteries of life there are only two responses, a shrug of the shoulders, or faith in God."-From:-Martin Down is the author of Deluded by Darwinism, pubished by David C. Cook 2007

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Sometimes it seems like this world is a giant fractal design. Just when your current perspective seems to have closed all the gaps, you find yourself able to zoom in, dig deeper, look closer, and find that all those closed gaps have formed once again. I have a hunch that this will be true no matter how deep we are able to look, how far we are able to see, or how many questions we are able to answer.

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Sometimes it seems like this world is a giant fractal design. Just when your current perspective seems to have closed all the gaps, you find yourself able to zoom in, dig deeper, look closer, and find that all those closed gaps have formed once again. I have a hunch that this will be true no matter how deep we are able to look, how far we are able to see, or how many questions we are able to answer.-It's called job security for scientists-And regarding complexity in general
http://www.dhbailey.com/papers/dhb-probability.pdf-and thermodynamic point of view.
http://2ndlaw.oxy.edu/evolution.html

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> And regarding complexity in general
> http://www.dhbailey.com/papers/dhb-probability.pdf
> 
> and thermodynamic point of view.
> http://2ndlaw.oxy.edu/evolution.html-Hemoglobin in chimps and humans is the same, but we are close relatives, and when going back to preceding organisms below primates, one cannot find an evolutionary pattern (Michael Denton's, "Evolution"). For the second website, in meteorites, only eight of the 20 amino acids essential for life have been found, and organic compounds react very slowly unless organic enzymes are present. And the latter tend to be huge molecules.-My view of your references is that they are very old from the standpoint of progress in science discoveries.

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Many thanks to David and Romansh for a number of articles that pull us first one way and then another. If scientists can't agree, what are the rest of us supposed to believe?
 
The only section I feel qualified to comment on is the paragraph quoted from Martin Down in David's post on 9 January at 17.23. Down says firstly: - "The fact is that the scientific evidence that we have is full of holes, or mysteries."-We don't know what evidence he's referring to, but since science is at present incapable of fathoming the origin and nature of the universe, the origin of life plus the mechanisms that gave rise to evolution, and the nature of consciousness, I don't see how anyone can disagree when he goes on to say that "science has not got it all sorted out."-However, his conclusion is a different matter: "In the face of the mysteries of life there are only two responses, a shrug of the shoulders, or faith in God." -Perhaps it's unfair to criticize such a sentiment without knowing the full context, but the stark alternative makes my own general scepticism seem about as sharp as a marshmallow. Are science and philosophy supposed to grind to a halt in January 2011? Should people like ourselves either turn away from life's mysteries or bow to Martin Down's deity? -The time has come to shake your head,
To shut your eyes and close your mind.
As Jesus really should have said:
"Give up and ye shall find."-The third response is to have faith in chance, while the fourth ... and in my view the best ... is to keep searching for solutions to life's mysteries, always bearing in mind that science may not be the only way to find them.

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An article has appeared that basically describes the genome as an orchestra, with layers upon layer of symphonic controls. The most cogent observation is that every cell serving a specific purpose has the same DNA as every other cell. A heart muscle cell as the same DNA as a liver cell, but they are enormously different. It all starts with a sperm and egg making one cell with that same DNA sequence. The article gives a good description of the epigenetic mechanisms that change gene expression and are inheritable. Only a tiny understanding of the orchestra and its fine tuning is known at this time. Finding DNA was only an early beginning. Noting the cooperative interconnections of all the manufacturing and controlling parts of the genome makes one realize that the 'selfish gene', a ghost concept of polemic writers, is just that, a marketing tool and conceptualization that is nonsense.-http://www.thenewatlantis.com/publications/getting-over-the-code-delusion-As the author notes from the stacked turtles story, the genome is layer upon layer of life all the way down. The DNA code is alpha. No one yet can see the omega. Watson and Crick had no idea of what they had really uncovered. And all developed by chance, as recently departed George would defend from his faith.

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An article has appeared that basically describes the genome as an orchestra, with layers upon layer of symphonic controls. 
 
> http://www.thenewatlantis.com/publications/getting-over-the-code-delusion-&... told this site will not open for those in England. Try using Uncommon Descent website. Go to the Denyse O' Leary article of 1/24/11 and click on 'Steve Talbot' muses. It comes up for me. It is a very detailed review, about 20 pages long, and my previous comments cover the salient points.

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David has drawn our attention to a long article about the genome, which consists of "layer upon layer of life all the way down". David says that "the DNA code is alpha. No one can yet see the omega."-I don't see how anyone can with confidence maintain that such an intricate mechanism could fashion itself by accident, but I was particularly struck by statements near the very end of the article, which raise all manner of questions:-"Having plunged headlong toward the micro and molecular in their drive to reduce the living to the inanimate, biologists now find unapologetic life staring back at them from every chromatogram, every electron micrograph, every gene expression profile. Things do not become simpler, less organic, less animate."
"The hopeful thing is that molecular biologists today â slowly but surely, and perhaps despite themselves â are increasingly being driven to enlarge their understanding through a reckoning with genetic contexts. As a result, they are writing "finis" to the misbegotten hope for a non-lifelike foundation of life, even if the fact hasn't yet been widely announced. It is, I think, time for the announcement."-I may have totally misunderstood this, and do please correct me if I have, but I presume he means that this research heralds the death knell of the theory that life can come into being from non-living materials (abiogenesis). At first glance, this may seem like a poke in the eye for our materialist, atheist friends, but is it? If Planet Earth had a finite beginning, and indeed if our whole material universe had a finite beginning, where did life spring from, if not from a non-lifelike foundation? Even if our material universe didn't have a finite beginning, but has been here for ever, the same question has to be asked. And the answer can't be a supernatural power that deliberately created the mechanism, because if it had been deliberately created, that power must also have used non-living materials.-No matter how many layers of life it may have, the genome is still material, and so we're left with the argument that material life has always been there ... shades of BBella's views, linked to aspects of process theology? ... which runs counter to every theory of finite beginnings, and makes God the Creator superfluous. I'd have thought that for theists as much as for atheists, the hope for a non-lifelike foundation of life still burns bright.-What have I missed?

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David has drawn our attention to a long article about the genome, which consists of "layer upon layer of life all the way down". David says that "the DNA code is alpha. No one can yet see the omega."
> 
> I don't see how anyone can with confidence maintain that such an intricate mechanism could fashion itself by accident.-I agree absolutely. - "The hopeful thing is that molecular biologists today â slowly but surely, and perhaps despite themselves â are increasingly being driven to enlarge their understanding through a reckoning with genetic contexts. As a result, they are writing "finis" to the misbegotten hope for a non-lifelike foundation of life, even if the fact hasn't yet been widely announced. It is, I think, time for the announcement."
> 
> I may have totally misunderstood this, and do please correct me if I have, but I presume he means that this research heralds the death knell of the theory that life can come into being from non-living materials (abiogenesis).-No, I think he has a different point of view. He points out that Watson and Crick, and everyone else at that time thought the research was about over. They had the code. But what happened as research went foward, layer upon layer of manufacturing units, checking units, and Lamark units turned up, all coordinated like a symphony orchestra, although we have no yet found or proven a composer or a conductor. I don't think he ever said that life did not come from inorganic materials, but he did not say how life began. I see none of that discussion in the paper.-> 
> No matter how many layers of life it may have, the genome is still material, and so we're left with the argument that material life has always been there ... shades of BBella's views, linked to aspects of process theology? ... which runs counter to every theory of finite beginnings, and makes God the Creator superfluous. I'd have thought that for theists as much as for atheists, the hope for a non-lifelike foundation of life still burns bright.
> 
> What have I missed?-What I have described. No discussion of how life started but a deeply detailed description of what an amazingly complex factory the genome is. Nowhere near as simple as Darwinian-leaning and atheistic scientists presumed and are finding hard to admit at this time. The author (Talbot) of this paper is a design leaner.-Note this quote from the paper: -The one decisive lesson I think we can draw from the work in molecular genetics over the past couple of decades is that life does not progressively contract into a code or any kind of reduced "building block" as we probe its more minute dimensions. Trying to define the chromatin complex, according to geneticists Shiv Grewal and Sarah Elgin, "is like trying to define life itself." Having plunged headlong toward the micro and molecular in their drive to reduce the living to the inanimate, biologists now find unapologetic life staring back at them from every chromatogram, every electron micrograph, every gene expression profile. Things do not become simpler, less organic, less animate. The explanatory task at the bottom is essentially the same as the one higher up. It's rather our understanding that all too easily becomes constricted as we move downward, because the contextual scope and qualitative richness of our survey is so extremely narrowed.-The search for precise explanatory mechanisms and codes leads us along a path of least resistance toward the reduction of understanding. A capacity for imagination (not something many scientists are trained for today) is always required for grasping a context in meaningful terms, because at the contextual level the basic data are not things, but rather relations, movement, and transformation.

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More complex findings: gene transfer is the primary way evolution advances in bacteria and other prokaryotes. -http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001284-Also more commentary:-http://www.the-scientist.com/news/display/57962/

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David drew our attention to an article about the genome, one aspect of which I have queried, as its ramifications are enormous. -DAVID: I don't think he ever said that life did not come from inorganic materials.-The symphonic image and the complexity of the genome are clear, but there are two passages that aren't. You've repeated one of my quotes: "things do not become simpler, less organic, less animate." The other quote ends: "[Molecular biologists] are writing "finis" to the misbegotten hope for a non-lifelike foundation of life, even if the fact hasn't yet been widely announced. It is, I think, time for the announcement."-What do you think he means, then, by "a non-lifelike foundation of life", in the context of things NOT becoming less organic, less animate? Who do you think is hoping for a non-lifelike foundation? What do you think is the announcement? -Sorry for the third degree!-Thank you for the latest posts about horizontal gene transfer. This appears to shed light on how prokaryotes adapt to changing conditions, but does it have any bearing on the emergence of totally new organs and species? (I'm asking because I'm not sure whether I've understood all the implications.)

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David drew our attention to an article about the genome, one aspect of which I have queried, as its ramifications are enormous. 
> 
> DAVID: I don't think he ever said that life did not come from inorganic materials.
> 
> The symphonic image and the complexity of the genome are clear, but there are two passages that aren't. You've repeated one of my quotes: "things do not become simpler, less organic, less animate." The other quote ends: "[Molecular biologists] are writing "finis" to the misbegotten hope for a non-lifelike foundation of life, even if the fact hasn't yet been widely announced. It is, I think, time for the announcement."-Your first quote is right on 'his' mark. With the discovery of the triplet code in DNA, many atheistic scientists assumed they had found the Rosetta Stone of genetics. Far from it, the new research is revealing an enormous number of layers, and when the molecles are 'watched' in their dance of coding and control, each type of molecule acts as if it has a life of its own. Not exactly true but it looks like it. Those molecules are under tight controls. But the choreography is at a level of a great ballet company doing Nutcracker. Nothing 'looks' inorganic. Nothing is simple. And he expects that further research will only make the schemata more and more complex. Quote 2 is a metaphor for giving up on Darwin from his the original suppositions: 'misbegotten hope for a non-lifelike foundation of life', parses as the foundation of life 'is life'. (Parallels his comment on turtles all the way down) 
>
 What do you think is the announcement? -Very simple: Life is alive in all the layers. It may have started from inorganic matter, but that matter has changed into an animate-like construction of extreme complexity in which the organization of the parts has resulted in an emergence of living matter, most highly developed in the human brain with so-far unexplained consciousness. Like Stuart Kauffman's theories of emergence from complex systems. There is no simple explanation for this observation. The parts are so carefully intertwined chance construction is extremely unlikely. It looks 'irreducably complex'. -We need to follow this fellow (Talbot). I'll bet he discusses design in future articles.-
> Thank you for the latest posts about horizontal gene transfer. This appears to shed light on how prokaryotes adapt to changing conditions, but does it have any bearing on the emergence of totally new organs and species? (I'm asking because I'm not sure whether I've understood all the implications.)

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David drew our attention to an article about the genome, one aspect of which I have queried, as its ramifications are enormous. 
> > 
> > DAVID: I don't think he ever said that life did not come from inorganic materials.
> > 
> > The symphonic image and the complexity of the genome are clear, but there are two passages that aren't. You've repeated one of my quotes: "things do not become simpler, less organic, less animate." The other quote ends: "[Molecular biologists] are writing "finis" to the misbegotten hope for a non-lifelike foundation of life, even if the fact hasn't yet been widely announced. It is, I think, time for the announcement."
> 
> Your first quote is right on 'his' mark. With the discovery of the triplet code in DNA, many atheistic scientists assumed they had found the Rosetta Stone of genetics. Far from it, the new research is revealing an enormous number of layers, and when the molecles are 'watched' in their dance of coding and control, each type of molecule acts as if it has a life of its own. Not exactly true but it looks like it. Those molecules are under tight controls. But the choreography is at a level of a great ballet company doing Nutcracker. Nothing 'looks' inorganic. Nothing is simple. And he expects that further research will only make the schemata more and more complex. Quote 2 is a metaphor for giving up on Darwin from his the original suppositions: 'misbegotten hope for a non-lifelike foundation of life', parses as the foundation of life 'is life'. (Parallels his comment on turtles all the way down) 
> >
> What do you think is the announcement? 
> 
> Very simple: Life is alive in all the layers. It may have started from inorganic matter, but that matter has changed into an animate-like construction of extreme complexity in which the organization of the parts has resulted in an emergence of living matter, most highly developed in the human brain with so-far unexplained consciousness. Like Stuart Kauffman's theories of emergence from complex systems. There is no simple explanation for this observation. The parts are so carefully intertwined chance construction is extremely unlikely. It looks 'irreducably complex'. 
> 
> We need to follow this fellow (Talbot). I'll bet he discusses design in future articles.
> 
> 
> > Thank you for the latest posts about horizontal gene transfer. This appears to shed light on how prokaryotes adapt to changing conditions, but does it have any bearing on the emergence of totally new organs and species? (I'm asking because I'm not sure whether I've understood all the implications.)-Prokaryotes can have horizontal gene transfer. These are single-celled organisms. Eukaryotes are multicelled. They have organs, and there is some small evidence for gene transfer at this level of development. Prokaryotes can form new species with gene transfer, but the evidence of gene transfer forming new organs in eukaryotes does not exist. And I doubt we will find evidence for this.

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My thanks to David for his comprehensive answers to my questions concerning horizontal gene transfer, and especially about Steve Talbott's article on the genome ... with its intriguing reference to "the misbegotten hope for a non-lifelike foundation of life". -You remark at the end: "We need to follow this fellow [Talbott ... he has two Ts]. I'll bet he discusses design in future articles."-I think you're right ... in which case, the "non-lifelike foundation" may yet turn out to be a metaphorical shot in the theological foot!

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My thanks to David for his comprehensive answers to my questions concerning horizontal gene transfer, and especially about Steve Talbott's article on the genome ... with its intriguing reference to "the misbegotten hope for a non-lifelike foundation of life". 
> 
> You remark at the end: "We need to follow this fellow [Talbott ... he has two Ts]. I'll bet he discusses design in future articles."
> 
> I think you're right ... in which case, the "non-lifelike foundation" may yet turn out to be a metaphorical shot in the theological foot!-I insist that his metaphore refers to the 'hope' of atheist scientists. His article refutes them all the way down. Life is the foundation of life in life's chemistry. The scientists have wounded feet!

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The latest article in Nature on gene codes finds that certain base pairs can be reversed by DNA in an 'excited state'creating an even broader code mechanism. Look at this abstract:- http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09775.html-Hoogsteen base pairs expand the information available. In life it is information all the way down! And here, in a sense, the DNA can call up its own mutations when necessary. Fit this into Neo-Darwinism, if you can.

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A new article in Nature describes plant genes ramping up defenses against pathogens according to their circadian rhythms for light and dark:-http://www.the-scientist.com/news/display/57972/

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Daphnia pulex, the water flea, is a crustacian used to study water contamination. In 200 million bases it has 31,000 genes, apparently developed for protection against toxic chemicals in water. My guess is that this is the penultimate example of epigenetics in action. 50% more genes than we have! And many not like ours.-
http://www.sciencedaily.com/releases/2011/02/110203141822.htm-http://www.physorg.com/news/2011-02-crustacean-genome-sequenced.html

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Complexer and complexer. Now the discovery of an RNA mechanism that appears to act on its own to change DNA instructions. It is stop and change:-http://www.sciencenews.org/view/generic/id/331345/title/Loophole_found_in_genetic_traffic_laws

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We have no idea why a Japonese plant has 50 times the base pairs of human DNA:-http://www.the-scientist.com/article/display/57932/

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There is confusion among scientists about the importance of a gene regulation mechanism, which is the extent of the influence of 'Alu' segments:- http://sandwalk.blogspot.com/ look for Feb. 12th.-Review by Science Daily: -http://www.sciencedaily.com/releases/2011/02/110209131828.htm

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How one riboswitch can can respond to more than one energy protein, turning genes on and off. Note the three-dimensional changes of the Riboswitch. It is as though the molecule has a brain, or at least carries control information: -http://www.physorg.com/news/2011-02-rna-onoff.html

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Note the complexity of RNA in yeast, 3,000 of them identified:-http://www.nature.com/nature/journal/v467/n7311/abs/nature09322.html?lang=en

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Nice animated video here-http://www.youtube.com/watch?v=4PKjF7OumYo-showing how DNA works in the cell.

--
GPJ

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Introducing inteins, epigenetic molecules that both splice out and splice together proteins as they are made. Known about 20 years, and can hop from genome to genome. Please read to the end: the final paragraphs have loads of interesting material as to function and theory:-http://www.the-scientist.com/blog/display/57690/

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An interesting article. I just wish there were more detail on the actual study.

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An interesting article. I just wish there were more detail on the actual study.-As I've told Matt, I watch the free stuff and will buy an article if it is really significant. The work in epigenetics is at full speed with stuff popping up daily. The last review article I purchased was OK but not great in the Quart. Rev. Biology. I'll wait for the next review to purchase. Someone will write a good epigenetics book shortly, and I'll watch for it.

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Over and over I have stated that the genetic coding mechanism promised to be extremely complex. Coupled with the this the observation that discoveries of increased complexity would proportionally reduce the odds for the chance production of life from inorganic matter.-
A very clear description of how chromosomes are handled in cell division, and how epigenetic factors work into the process. -http://www.sciencedaily.com/releases/2010/09/100917101814.htm

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Another example of mRNA managing protein production at two different rates:-http://www.the-scientist.com/blog/display/57692/

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Even at the most fundamentally basic parts of our biology, we are still wonderfully complex. Thanks for sharing.

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It is more than the genome that is amazingly complex. This synopsis of energy delivery by the ATP-ADP system shows it is enormously complex:-Biochemistry: 
Flexible Exchange Rates
Gilbert Chin - 
CREDIT: WATT ET AL., PROC. NATL. ACAD. SCI. U.S.A. 107, 16823 (2010)
 
 -The membrane-bound enzyme F-ATPase serves an important function in almost all walks of life. It makes ATP (from ADP and inorganic phosphate) by converting the passage of protons down an electrochemical gradient first into mechanical energy and thence into chemical energy. The parts of the enzyme (red and yellow) that bind ADP lie mostly outside the membrane, and three such binding sites are converted sequentially from open to loose to tight conformations. The energy contained in the movement of protons is extracted by forcing them through a membrane-embedded ring (brown) of identical subunits, each of which captures a single proton on a glutamate residue. Turning this ring rotates a central stalk (blue, purple, and green) at 6000 rpm, which drives the cycle of conformational changes. Watt et al. describe the crystal structure of the mitochondrial ring and show that it contains eight subunits, leading to a ratio of eight protons for three ATPs synthesized. What is puzzling is the range of stoichiometries documented thus far, with 10 to 15 subunits found in the F-ATPases of fungi, bacteria, and chloroplasts. All of these enzymes possess the canonical trio of ADP-binding sites, which means that the cost of each ATP varies from as little as 2.7 protons in animals to as many as 5in microbes. -Proc. Natl. Acad. Sci. U.S.A. 107, 16823 (2010).

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Thre is a webinar available on recent work in epigenetics:-For more information and complimentary registration visit:
www.sciencemag.org/webinar-Webinar Description -Epigenetics is being recognized as an increasingly important area of research that involves an understanding of the molecular mechanisms that influence the phenotypic outcome of the genome without alteration of the DNA sequence. These effects are mediated by the covalent attachment of chemical groups to DNA and its associated histone proteins. Such modifications, including methylation, acetylation, ubiquitination, and phosphorylation, often result in the alteration of gene expression levels that determine cell fate. Epigenetic marks are somatically inherited and therefore can be passed on as diseased cells replicate. In this webinar, viewers will gain insight into the current status of epigenetics research, with an emphasis on understanding the mechanism and effects of DNA methylation. Current methods associated with epigenetics research will be discussed, as well as how these technologies are advancing the development of new diagnostics and biomarkers.

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A partial description of how the chromosomes are split by various protein molecles in the process of mitosis, making two daughter cells.-Location, Location, Location- 
CREDIT: KELLY ET AL.
 
 
Cell division is orchestrated by a complex signaling pathway that ensures the correct segregation of newly replicated chromosomes to the two daughter cells. The pathway is controlled in part by restricting the activity of critical regulators to specific subcellular locations. For example, the chromosomal passenger complex (CPC) is recruited to chromosomes during mitosis where it oversees kinetochore activity and cytokinesis (see Perspective by Musacchio). Wang et al. (p. 231, published online 12 August), Kelly et al. (p. 235, published online 12 August), and Yamagishi et al. (p. 239) now show that the phosphorylation of the chromatin protein, histone H3, acts to bring the CPC to chromosomes, thereby activating its aurora B kinase subunit. The Survivin subunit of CPC binds specifically to phosphorylated H3, with the phosphorylation at centromeres being carried out by the mitosis-specific kinase, haspin. Furthermore, Bub1 phosphorylation of histone H2A recruits shugoshin, a centromeric CPC adapter. Thus, these two histone marks in combination define the inner centromere. -From this week science mag.

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This is a marvelous, but complex description, of how B-cells manufacture antibodies, and how germ cells (sperm or egg) are created. The author has made every attempt to make it sound simple. It isn't. It is a beautiful example of natural nanotechnology.-http://www.uncommondescent.com/intelligent-design/comments-on-kathryn-applegate%e2%80%99s-may-posts-on-biologos/#more-15176-Don't be frightened that it comes from uncommon descent. The author, Caroline Crocker, has no polemics in her essay. In fact she disagrees with another author, who is trying to use this information to interpret God.

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Using the complexity of gene codes to sort out evolutionary family relationships. The role of microRNA:-http://www.the-scientist.com/news/display/57752/

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The mediator of bacterial gene transfer has been found. Where did it come from in the evolutionary process, out of thin air?-
http://www.nature.com/news/2010/100930/full/news.2010.507.html

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The mediator of bacterial gene transfer has been found. Where did it come from in the evolutionary process, out of thin air?
> 
> 
> http://www.nature.com/news/2010/100930/full/news.2010.507.html-So... God used virii to speed evolution? How could you differentiate this from chance?

--
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The mediator of bacterial gene transfer has been found. Where did it come from in the evolutionary process, out of thin air?
> > 
> > 
> > http://www.nature.com/news/2010/100930/full/news.2010.507.html
> 
> So... God used virii to speed evolution? How could you differentiate this from chance?-The article says 'virus-like'. This particle has a specific function. The developmednt requires the particle to appear. If virus-like it is not fully alive, but requires contact with the bacteria to be 'alive'. Then there is the issue of bacteria with a transferable gene and another bacteria with a need for that transfer. I cannot image how all of this fell together by chance. Just-so story anyone?

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How do cell types stay the same if they all have the same DNA? There are 200 different cell types in humans. It's RNA to the rescue:-http://www.physorg.com/news/2011-03-molecular-cell-identity.html

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Once again, many thanks to David for alerting us to new findings concerning the makeup of cells:-http://www.physorg.com/news/2011-03-molecular-cell-identity.html-"If a big bunch of your brain cells suddenly went rogue and decided to become fat cells, it could cloud your decision-making capacity a bit. Fortunately, early in an organism's development, cells make firm and more-or-less permanent decisions about whether they will live their lives as, say, skin cells, brain cells or, well, fat cells. -Those decisions essentially boil down to which proteins, among all the possible candidates encoded in a cell's genes, the cell will tend to make under ordinary circumstances. But exactly how a cell chooses its default protein selections from an overwhelmingly diverse genetic menu is somewhat mysterious.-A new study from the Stanford University School of Medicine may help solve the mystery. The researchers discovered how a particular variety of the biomolecule RNA that had been thought to be largely irrelevant to cellular processes plays a dynamic regulatory role in protein selection."-May I make two brief comments on this? Firstly, it seems to be happening more and more frequently that what had previously been thought to be x is now thought to be y. At the risk of being a bore, let me say yet again that even though it's heartening to see science constantly correcting itself, every correction should sound a warning signal that we can take nothing for granted when the "experts" make their pronouncements.
 
Secondly, it's striking that the article talks of cells making decisions and choosing. Once again, I feel there's a parallel here between bodies and societies. Ants and bees and other social organisms also make decisions and choose. Our cells are not under our control, and if it's the biomolecule RNA taking the decisions, the question still remains as to what kind of "thoughts" govern the process, and where they come from. David thinks it's all been pre-programmed by a universal intelligence. I suggested earlier that all living things including cells may be endowed with some sort of intelligence and even inventiveness - hence new combinations leading to innovations leading to new organs and new species. Just as great-grandpa termite and colleagues invented and built the first hill, maybe great-great-grandpa Geniucell and colleagues (cooperation is essential in all contexts) invented and built the first leg, wing, eye etc. The net outcome would be the same, but my scenario leaves open the origin of the mechanism. Fantasy? Is it any more fantastic than a universal and eternal intelligence, or unthinking blobs of matter just happening by chance to create all these amazing machines?

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Here we go again. Another thoughtful article about epigenetic research and how complicated it is, because epigenetic controls are extremely complex:-http://www.the-scientist.com/article/display/58005/

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Look at how this monster mechanism works. Made by chance, huh?-http://www.physorg.com/news/2011-03-rna-exporting-machine-deciphered.html

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An award to the discoverers of miRNA, a very active sublayer of gene function:-http://www.pauljanssenaward.com/sites/default/files/pdf/DPJA_Winner_Announcement_Press_Release-Final_Approved_6_19_12.pdf

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