Uncommon Descent Serving The Intelligent Design Community

Yet another layer of complexity

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Plant study reveals a “deeply hidden” layer of transcriptome regulation.

“Cells keep a close watch over the transcriptome – all parts of the genome that are expressed in any given cell at any given time.

Before RNA transcripts can guide protein synthesis or take on regulatory functions, they have to undergo a strict mRNA surveillance system that degrades defective, obsolete, and surplus transcripts.

By stopping the function of the exosome, a multi-unit complex molecular machine in charge of controlled RNA degradation, researchers found evidence for widespread exosome-mediated RNA quality control in plants and a ‘deeply hidden’ layer of the transcriptome that is tightly regulated by exosome activity.

The common notion was that the exosome plays a central role in bulk RNA turnover so they expected to find the levels of all transcripts increasing when they inactivated the exosome complex. Instead the exosome mechanism seems to be very tightly regulating an already very specific group of transcripts.”

It is wonderous in the extreme to find the exosome “a multi-unit complex molecular machine” but there is also some separate information and control mechanism using the exosome to be “in charge of controlled RNA degradation”. These multiple layers of design and control engineering are clearly outside the ability of RM and NS to create.

Comments
xcdesignproponentsists: I have just read your answer (#12). Here are some notes about what you say: "If you want to assert that every scientific discovery only raises a hundred new questions, I will readily agree with you. That is the nature of scientific inquiry. However, to simply claim that something so complex cannot be explained by mutation and selection is not positive evidence for ID". No, you evidently misunderstand ID and me in particular. In brief, the ID argument is as follows: 1) A specific type of complexity is abundantly observed in living beings (CSI, IC). 2) That complexity has not always been there. It was built, more or less gradually, on our planet. 3) A theory exists (or a group of similar theories, if you prefer) which states that it can explain the emergence of biological information according to certain mechanisms. Be careful, darwinian evolution is not a "vague" faith that perhaps biological information will some day be explained. It is a very definite attempt to explain it with a specific theory. It is the only "naturalistic" theory available, but that does not make it different from any other theory. 4) Like any other scientific theory, it cannot be ultimately verified. But it can , indeed, be falsified. As I have said many times, the first step in ID is to falsify darwinian evoution. That has been vastly made at two different levels: a) Logical level, showing that the theory is internally inconsistent, because its logical and mathematical premises are completely false. That has been done in many ways, but essentially by Dembski with the concept of CSI, and by Behe with the concept of IC. b) Empirical level, showing that no existing empirical observation really supports the theory, while a lot of empirical observations are against it. That has been done in many ways, for example by Behe in his last book. Now, I understand that you don't agree with all these considerations, and you have all the rights to believe what you believe. I am just saying that these are the questions about ID, and that nothing in them is an argument from incredulity. Debating each single aspect of ID is not possible here, but we do that every day on various threads in this blog. And believe me, we don't do that from arguments of incredulity, but with very specific arguments and debates. You are welcome to take part in them. You say: "However, to simply claim that something so complex cannot be explained by mutation and selection is not positive evidence for ID". No, saying that (and demonstrating it) is poositive evidence "against" darwinian selection. That means falsifying it, which is a perfectly natural scientific endeavor. Positive evidence against something is not "negative evidence". Positive evidence for ID is, instead, the observation that intelligent designers "can" produce that kind of complex information, and that indeed they do that constantly. Besides, all examples of that kind of information in nature (except biological information, which is exactly the object of inquiry) are always the product of an intelligent designer. That is positive evidence for ID. It is called "The design inference". You say: "On what basis do any of these findings “falsify” random mutation and natural selection? It’s completely absurd to say that." No, it's not absurd. Obviously, I have not given in my post a detailed discussion about CSI or IC (it was not my goal to do that there). But, if you know the arguments I am citing, then you can understand that the continuous discovery of new, and ever more conspicuous, levels of CSI and IC certainly strengthens the ID arguments. Obviously, if you don't agree with the basic arguments, you will not agree with the above point. But that's really trivial. You say: "It’s essentially the same negative argument that has existed for many years. There is no new evidence" No. First of all, I have shown that ID arguments are never negative. One is a positive argument against darwinism. The other is a positive argument for ID. In no case it is a negative argument. Secondly, I think you are a litlle bit confused about the meaning of the words "argument" and "evidence". Even if we could agree that, in the last year for instance, there have been no new "arguments" for ID (that's not true, there have been, but let's accept that as a starting hypothesis here), still there is certainly a lot of new "evidence". For instance, if the "argument" of IC made by Behe some years ago is still the same (and why should it be changed, it is so strong and beautiful!), still each new example of IC discovered in nature is new "evidence" in favor of that argument (and the article cited in this post is certainly an example of that). But, for instance, the argument from malaria in Behe's TEOF is, indeed, a new argument, and an empirical one. You say: "Attempting to shift the burden of proof will not help the validity of your position. It’s like saying “till you prove that Russell’s teapot does not exist, then it means that it exists" I am not shifting anything. The burden of proof of darwinian theory is, and has always been, of darwinists. In the same way, the burden of proof of ID theory is, obviously, of IDists (and we are proud of that!). Everyone has the burden to prove what he is saying. You say: "Furthermore, it would be sufficient merely to show that certain structures “can” evolve from naturalistic processes in order to falsify your position that they “cannot”." That's perfectly right. Then, why don't you do that? I really believe that ID is falsifiable, both in its first part (falsification of darwinian evolution) and in its second part (affirmation of the design inference). I do believe that ID "is" falsifiable, but that it will not be falsified. So, why don't darwinists falsify it, instead of stating today that it is not falsifiable, while trying tomorrow (without suceeding) to falsify it?gpuccio
January 7, 2008
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gpuccio:
The “credulity argument” is not that. It is believing that, as you can vaguely imagine that some result could possibly happen due to naturalistic causes, you do believe that, although you have no real evidence for that, and although there are important evidences, both logical and empirical, against that. That is credulity, being ready to believe something just for “sentimental reasons”, like the faith in “naturalistic explanations”.
The "no real evidence" claim is misleading, as is the claim that there is empirical and logical evidence against evolution without an Unidentified Intelligent Agent (UIA). The evidence is there is to suggest that naturalistic processes can create biological novelty and give rise to complexity.
No, there isn’t sufficient evidence. That is the problem. There is some evidence, well known, that mutation can modify an existing function, usually reducing it, and that, when special environmental pressures are present, like antibiotic use, that “modification” in function may have some indirect advantage. That is well known.
Considering that evolution can be summarized as descent with modification, it's hardly that surprising is it? A large percentage of the genes in your body probably arose from gene duplication events. Furthermore, small modifications to regulatory genes can result in fairly signficant variation as evolutionary developmental biologists are discovering. Even then, there is scope for novelty in evolution e.g. the evolution of the anti-freeze protein in Antarctic fish. No one is suggesting that biological complexes evolved from scratch into their modern-day forms in a single mutational event - well, perhaps thats how some ID proponents think it is supposed to work.
But to believe that such observations are “enough evidence” to believe that that’s the way biological information is built really requires tons of “credulity”.
You mean just like it's "credulity" to believe that chemical cues may be involved in the differentiation of certain embyrological cell types, even if they have not been identified as yet? Or that a plant could naturally produce an alkaloid extracted from it, even though one does not know the exact biochemical pathway involved?
I will not repeat here the many arguments ID has made against that credulity. You know where to find them, so please read them, or if you have already done that, please address them specifically. But if you come here just stating that observations like antibiotic resistance in bacteria or the selection of S hemoglobin due to malaria are a good empirical foundation for the darwinian theory, then your credulity is much greater than I thought.
The examples of mutations go far beyond those two textbook examples.
A last note about negative evidence and positive evidence. It is the darwinian theory which has been built and arrogantly passed as “fact” in a complete lack of any evidence. ID, in its first (negative) aspect, is only remarking that. That means falsifying darwinian evolution on both logical and empirical grounds, which is a perfectly legit scientific endeavor.
I hope you realize that arguments from incredulity do not suffice to falsify a theory.
On the other hand, the positive aspect of ID (the design inference) suggests an alternative explanation based on strict logical and empirical observations. The design inference is perfectly “naturalistic”, if you stick to the real meaning of “naturalistic”: nature, indeed, is full of designers, we can observe at least a few billions of them constantly operating on our planet, and so we are perfectly correct in observing the phenomena of intelligent design and in studying the laws which allow to infer its presence. And that is, absolutely, positive evidence.
I'm baffled by the sheer inconsistency of your position. You demand that evolutionists show you in detail how certain structures have naturalistically evolved in a stepwise fashion, or else you condemn their theory as a falsehood. On the other hand, you gladly cling to ID by making a flimsy "design inference" in the absence of demonstrating positively how a UIA goes about designing things. If these desigers are indeed naturalistic as you claim, then its well within the bounds of science. Where is the experimental evidence that identifies these agents and shows them at work?xcdesignproponentsists
January 7, 2008
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Really? That is what Michael Behe’s book recently tried to do. Pin down in observations exactly what mutations could do.
I haven't read The Edge of Evolution, but the impression I've had from proponents of Behe's ideas is that he arbitrarily imposes "limits" on what mutation can do with more arguments from ignorance. It's become the trademark of Behe's argumentative style, which is probably why he feels the need to come up with empty rhetoric like "argument from credulity".
I generally find the arguments to rely on Darwin-of-the-Gaps. There has to be a naturalistic answer, therefore there is a naturalistic answer.
Is this part of the beef with "methodological naturalism" that some ID proponents seem to have? Let me just say that I'm glad Laplace felt that way.
And what’s wrong with a negative argument? So what? I think we are talking about a philosophical premise than an actual demonstration of natural mutation producing something.
Mutations have produced lots of "things". Do you disagree?xcdesignproponentsists
January 7, 2008
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xcdesignproponentsists: You say: "The evidence for mutation and selection are not based solely on what you term a “credulity argument”, which I’m assuming is of the form “I believe A, therefore A is true”. It is based on positive evidence - observations of the role of mutation in creating variation within a population, and the role of selection and genetic drift" The "credulity argument" is not that. It is believing that, as you can vaguely imagine that some result could possibly happen due to naturalistic causes, you do believe that, although you have no real evidence for that, and although there are important evidences, both logical and empirical, against that. That is credulity, being ready to believe something just for "sentimental reasons", like the faith in "naturalistic explanations". You say: "There is sufficient evidence to show that mutation can “build” things of utility to living organisms; it’s not merely a “credulity argument”." No, there isn't sufficient evidence. That is the problem. There is some evidence, well known, that mutation can modify an existing function, usually reducing it, and that, when special environmental pressures are present, like antibiotic use, that "modification" in function may have some indirect advantage. That is well known. But to believe that such observations are "enough evidence" to believe that that's the way biological information is built really requires tons of "credulity". I will not repeat here the many arguments ID has made against that credulity. You know where to find them, so please read them, or if you have already done that, please address them specifically. But if you come here just stating that observations like antibiotic resistance in bacteria or the selection of S hemoglobin due to malaria are a good empirical foundation for the darwinian theory, then your credulity is much greater than I thought. A last note about negative evidence and positive evidence. It is the darwinian theory which has been built and arrogantly passed as "fact" in a complete lack of any evidence. ID, in its first (negative) aspect, is only remarking that. That means falsifying darwinian evolution on both logical and empirical grounds, which is a perfectly legit scientific endeavor. On the other hand, the positive aspect of ID (the design inference) suggests an alternative explanation based on strict logical and empirical observations. The design inference is perfectly "naturalistic", if you stick to the real meaning of "naturalistic": nature, indeed, is full of designers, we can observe at least a few billions of them constantly operating on our planet, and so we are perfectly correct in observing the phenomena of intelligent design and in studying the laws which allow to infer its presence. And that is, absolutely, positive evidence.gpuccio
January 7, 2008
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"The evidence for mutation and selection are not based solely on what you term a “credulity argument”, which I’m assuming is of the form “I believe A, therefore A is true”. It is based on positive evidence - observations of the role of mutation in creating variation within a population, and the role of selection and genetic drift." Really? That is what Michael Behe's book recently tried to do. Pin down in observations exactly what mutations could do. I generally find the arguments to rely on Darwin-of-the-Gaps. There has to be a naturalistic answer, therefore there is a naturalistic answer. And what's wrong with a negative argument? So what? I think we are talking about a philosophical premise than an actual demonstration of natural mutation producing something.geoffrobinson
January 7, 2008
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Lutepisc:
Fascinating comment, Undesigned. Sounds as it it’s finely tuned, doesn’t it?
"Finely tuned" by processes like selection or an unidentified Intelligent Agent?
Materialists need to explain how a process which relies on errors (mutations, etc.) would create an error-control mechanism.
Materialists? Does that mean ID is exempt, or can it reasonably fall under the boundaries of "materialism"? Nonetheless, it's a loaded question. You could conversely ask how a process that relies on minimizing errors could create an error-control mechanism.xcdesignproponentsists
January 7, 2008
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gpuccio:
You seem to ignore all the multiple and detailed arguments made by ID (CSI, IC, OOL, fossil, etc.), none of which has ever been really addressed by darwininsts. I don't ignore them, I'm simply not convinced they have any validity.
I think that what idnet.com.au is saying is simply that, as ever new complex and deep layers of organization are discovered, explanations based on RM and NS are more and more a virtual impossibility,
Again, the question arises as to how you make that conclusion. If you want to assert that every scientific discovery only raises a hundred new questions, I will readily agree with you. That is the nature of scientific inquiry. However, to simply claim that something so complex cannot be explained by mutation and selection is not positive evidence for ID.
and ID arguments are more and more strengthened. ID arguments would have been valid even at the times of Darwin, but certainly there was much less evidence in their favor then. At the middle of the past century, when molecular biology was born, ID arguments would have been much more believable, if only the scientific community had not been hypnotized by its arrogance for a few important successes in understanding some mechanisms in biology.
The arguments for ID are not strenghtening. It's essentially the same negative argument that has existed for many years. There is no new evidence; merely more appendices to the same unprovable argument. If ID wants to strengthen its position, it needs to come up with positive evidence for its claims rather than relying on the gaps in our knowledge.
But today, with the developments of, say, the last ten years in molecular biology, ID arguments are strong like steel. Each new discovery, each single day, is falsifying the RM + NS model, and is making the ID point of view stronger. The scientific paper cited in the post is only the last of many similar advancements in our understanding of the intelligent and organized nature of biological realities, and believe me, we are only at the beginning.
On what basis do any of these findings "falsify" random mutation and natural selection? It's completely absurd to say that.
First of all, we “do” know that molecular complexes cannot evolve through naturalistic processes, and have shown that many times.
Uh-huh...so where is the experimental evidence that indicates this? There have only been misguided attempts to show that they cannot, which remain arguments from ignorance e.g. Behe's hijacking of "irreducible complexity".
At this point, it’s you, the darwinist field, who should clearly show how “exactly” you know that molecular complexes “can” evolve through naturalistic processes. Indeed, you should clearly show not only that they “can”, but also that they “have”. That would be science. All the rest (practically, all darwinian theory of evolution) is just an “argument from credulity”, and nothing else.
Attempting to shift the burden of proof will not help the validity of your position. It's like saying "till you prove that Russell's teapot does not exist, then it means that it exists". Furthermore, it would be sufficient merely to show that certain structures "can" evolve from naturalistic processes in order to falsify your position that they "cannot". Your "argument from credulity" claim is rhetorical hogwash, because it would extend to virtually every other branch of science.xcdesignproponentsists
January 7, 2008
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geoffrobinson: "Materialists need to explain how a process which relies on errors (mutations, etc.) would create an error-control mechanism" Very well said. What is rarely emphasized is that, if a single function (specific protein) is already a perfect example of CSI, and therefore beyond the scope of RM + NS, the "regulation" of a function, both quantitavely and qualitatively (including error-control), so that it can be just fine-tuned to constantly changing conditions, is really a new layer of complexity, even more difficult to explain in blind terms. And think for a moment about complex networks of functions, and about the regulation of those networks! And, if you want, networks of networks, and so on. Biological beings, especially multicellular ones, are literally filled with such multiple levels of organization and interdependency, regarding, in humans, no less than 10^13 - 10^14 different living cells, witn myriads of different microscopic and macroscopic patterns of physical organization (tissues, organs, and so on) and myriads of myriads of functional connections (biochemical, with thousands of different cytochines, and neuro-electro-chemical, like in the about 10^14 synapses connecting 10^10 - 10^11 neurons). And that is only a superficial list of the many interrelations developing in our body from a single genome, which is always the same in each cell! And all of that is not only perfectly engineered, but also constantly regulated and modified, and error checked, according to constantly changing environmental challenges, both outside and inside the body. And we, poor ID folks, have just timidly tried to affirm the irreducible complexity of the bacterial flagellum... Sometimes I really think we are too shy. Materialists, indeed, have a lot to explain. But we have the duty to remain constantly aware of the greatness and the beauty of what we experience everyday in the living world, because it is very easy to forget, and to take it for granted.gpuccio
January 7, 2008
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kairos:
But DNA is, from the chemical point ov view, a pretty perfect “neutral” framework for nucleotides sequences.
What do you mean by "neutral"?
So, we are almost left only with RM+NS wher it’s mere science to ask: what are the chances to perform a non-teleological search of the solution space? Please let me ask for a provocatio. Isn’t instead to claim that RM+NS could have done it a pretty “credulity argument”?
The evidence for mutation and selection are not based solely on what you term a "credulity argument", which I'm assuming is of the form "I believe A, therefore A is true". It is based on positive evidence - observations of the role of mutation in creating variation within a population, and the role of selection and genetic drift. Evolution is only a "credulity argument" if you think black holes, plate tectonics, etc are also credulity arguments. On the other hand, the fallacious argument presented vis-a-vis the ability of naturalistic processes to give rise to complex cellular processes is based primarily on a lack of evidence rather than any positive evidence.
No, what it’s unplausible is to claim that Stonehange could have been built by earthquakes and tornados.
And evolutionary biologists claim no such thing. To equate mutation and selection to forces like earthquakes and tornadoes shows a profound misunderstanding of the former processes. There is sufficient evidence to show that mutation can "build" things of utility to living organisms; it's not merely a "credulity argument".xcdesignproponentsists
January 7, 2008
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Materialists need to explain how a process which relies on errors (mutations, etc.) would create an error-control mechanism.geoffrobinson
January 7, 2008
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I’d say if QC were any less perfect, evolution would not occur in the first place. Clever that its just imperfect enough to let life adapt to its surroundings. Love it.
Fascinating comment, Undesigned. Sounds as it it's finely tuned, doesn't it?Lutepisc
January 7, 2008
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At this point, it’s you, the darwinist field, who should clearly show how “exactly” you gpuccio Indeed, you should clearly show not only that they “can”, but also that they “have”. That would be science. That's correct. And let's remember what skeptics routinely say about the possible existence of teleological phenomena "extraordinary claims need extraordinary proofs". OK gentlemen, but this should first and mainly applied to NDE claims, and this is every day more true. All the rest (practically, all darwinian theory of evolution) is just an “argument from credulity”, and nothing else. It seems that we have at the same time had the same idea about :-)kairos
January 7, 2008
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xcdesignproponentsists: You seem to ignore all the multiple and detailed arguments made by ID (CSI, IC, OOL, fossil, etc.), none of which has ever been really addressed by darwininsts. I think that what idnet.com.au is saying is simply that, as ever new complex and deep layers of organization are discovered, explanations based on RM and NS are more and more a virtual impossibility, and ID arguments are more and more strengthened. ID arguments would have been valid even at the times of Darwin, but certainly there was much less evidence in their favor then. At the middle of the past century, when molecular biology was born, ID arguments would have been much more believable, if only the scientific community had not been hypnotized by its arrogance for a few important successes in understanding some mechanisms in biology. But today, with the developments of, say, the last ten years in molecular biology, ID arguments are strong like steel. Each new discovery, each single day, is falsifying the RM + NS model, and is making the ID point of view stronger. The scientific paper cited in the post is only the last of many similar advancements in our understanding of the intelligent and organized nature of biological realities, and believe me, we are only at the beginning. So, instead of speaking of "argument from incredulity" for ID (which is a totally false perspective), let's speak of "argument from credulity" for the RM + NS model. Saying: "How exactly do you know that molecular complexes cannot evolve through naturalistic processes?" is indeed an argument from credulity. From completely acritical credulity. First of all, we "do" know that molecular complexes cannot evolve through naturalistic processes, and have shown that many times. That's exactly what the ID arguments are about. You may not agree about the conclusions, but certainly you cannot affirm that ID has not addressed and extensively discussed that point. At this point, it's you, the darwinist field, who should clearly show how "exactly" you know that molecular complexes "can" evolve through naturalistic processes. Indeed, you should clearly show not only that they "can", but also that they "have". That would be science. All the rest (practically, all darwinian theory of evolution) is just an "argument from credulity", and nothing else.gpuccio
January 7, 2008
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Oops I forgot to quote and comment the last statement. It seems a bit like saying that Stonehenge could never have been built without cranes or modern-day machinery. No, what it's unplausible is to claim that Stonehange could have been built by earthquakes and tornados.kairos
January 7, 2008
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Can anyone say “argument from incredulity”? How exactly do you know that molecular complexes cannot evolve through naturalistic processes? Naturalistic processes do involve only chemical laws and RM+NS. But DNA is, from the chemical point ov view, a pretty perfect "neutral" framework for nucleotides sequences. So, we are almost left only with RM+NS wher it's mere science to ask: what are the chances to perform a non-teleological search of the solution space? Please let me ask for a provocatio. Isn't instead to claim that RM+NS could have done it a pretty "credulity argument"? It seems a bit like saying that Stonehenge could never have been built without cranes or modern-day machinery.kairos
January 7, 2008
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Quality control on the genetic level is far from perfect. You see fused chromosomes, duplicated sections, missing information, frame errors, deactivated centromeres and offspring with different features from their parents. I'd say if QC were any less perfect, evolution would not occur in the first place. Clever that its just imperfect enough to let life adapt to its surroundings. Love it.Undesigned
January 7, 2008
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These multiple layers of design and control engineering are clearly outside the ability of RM and NS to create.
Can anyone say "argument from incredulity"? How exactly do you know that molecular complexes cannot evolve through naturalistic processes? It seems a bit like saying that Stonehenge could never have been built without cranes or modern-day machinery.xcdesignproponentsists
January 7, 2008
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Transcription regulation is, indeed, a total mystery, and the real future of biological research. It is the "dark energy" problem of biology: no known theory or mechanism even begins to explain how it could work. Even in the iD field, many usually think of the cell as some well structured machine where, once the right information is packed in the genome about proteins, and in a certain order, everything goes on mechanically according to principles which, although not known in detail, are at least generally understood. That is not true, especially for multicellular organisms. Transcription regulation from the genome is as difficult to explain as the emergence of biological information in the genome. They are, indeed, two questions for which no satisfying answer still exists, except that they both scream intelligency and design. ID usually focuses on the secon problem, but I am convinced that the two problems are strongly interrelated, as even the darwinists in the bfield of evo-devo seem to have understood. But no mechanical and reductionist theory is going to explain those two problems. A completely new approach is needed, and it will have to take into basic account the concepts of consciousness, intelligence, design and purpose. And, probably, a wholly new conception of physics and biophysics.gpuccio
January 7, 2008
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