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Overlapping genetic code is … stories embedded in stories, using the exact same words?

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And not even just a different story read backwards, like I thought?

Liberty University biology prof David A. DeWitt, author of Unraveling the Origins Controversy, commented on my characterization of the overlapping codes of the genome. Seeing that Christianity Today is actually taking BioLogos and yesterday’s science seriously, I had written,

A friend, a faithful Christian in science, was dismayed by the story. He is an information theorist. … The genome, to take one small point, is full over overlapping codes. (It’s as if a short story read backwards is a flawless different short story, and sections of it, read letter by letter down the right hand side are a flawless paragraph.)

and DeWitt replies,

In the mitochondrial genome the overlapping codes are for different subunits of the same protein complex (ATP Synthase). So it is not even that “backwards is a flawless different short story” it is another volume in a series of short stories involving the same characters!

which all happened, of course, merely by the magic of Darwin’s natural selection acting on random mutations. But presumably Christian Darwinists are free to dress it their unbelievable scenario in God talk as long as they feel like it.  Only, 

BioLogos: Yesterday’s science as if reality didn’t matter.

Christianity Today: News coverage for Christians as if trashing our heritage and grovelling to yesterday’s science will make people stop hating serious Christians.

Yoo hoo!! Is anyone else out there sick of that whole narrative? Looking for solutions?

Read Uncommon Descent. We make it our business to tell you what is really happening because we cannot afford not to know, in the way that institutional Christian media can. We don’t even think of ourselves as Christian media. It’s true that the whole slate of list guvs here are trad Christians, but that’s just how we found each other.

What should mater to you is, we are united in thinking that you deserve news as if you and reality mattered.

Comments
A simple example of a poly-functional word would be LIVE, which backwards is EVIL. To change LIVE to HIVE might be desirable, but it turns EVIL which has meaning, to EVIH, which is meaningless. So this dual-meaning word, like the other examples above, is poly-constrained, precisely because it is poly-functional. ~ John Sanfordbevets
June 5, 2011
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p.s. that last comment was not meant to reflect on any of your prior comments in this thread, though I see now that it could be interpreted that way. Please don't interpret it as an insult to anything you've written. Thanks.Mung
June 4, 2011
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Elizabeth:
Do we agree that some polymorphisms are “silent” (result in an identical protein) and others result in a slightly different protein with different phenotypic effects?
Let's dispense with the technical terms if we can, unless they become relevant somehow, ok? In general, yes, I agree. For a given protein, we can substitute different amino acids at certain sites, and the different amino acid that is introduced may or may not change how the protein functions. If it does change how the protein functions, that may or may not affect the organism's reproductive rate compared to other organisms of the same "type." Are we together so far? So the first evolutionary hurdle that we must overcome is the one in which changes take place but they are not visible to selection. Or in search terms, the organism must "find" a new configuration in the amino acid sequence that actually makes a difference in terms of it's rate of reproduction. Are we still together? Anything objectionable so far? Must be getting late there. I've begun to employ a strategy where I post later so that you ladies over there across the pond are tired and not on your best game ;)Mung
June 4, 2011
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As I’ve said, I think letters and words are a very bad analogy. Codon triplets specify amino acids, a sequence of which then forms a protein.
Letters and words are perfectly fine as an analogy. To me it seems you just don't care for them because of where that leads us, which is that there must be a code to get from the letters of DNA to the letters of proteins. Codon triplets, by themselves, specify nothing. The genetic system is not just analogous to a communication system, it is a communication system. Messages are being read, encoded, transmitted, decoded, and interpreted. The reason, again imo, that you are so uncomfortable with this is that it significantly increases the problems that had to be solved by a supposedly mindless, non-future-oriented, non-teleological process which at it's very core is based upon pure happenstance. luck. fortune. magick. the fates. the gods. We have empirical evidence of one single source for such systems. Intelligent agents. Now you would have us believe that you're fine with the idea that God created the first cell and that it could have been highly complex for all you care, but I think we all know the truth about that. If miracles are allowed to account for the existence of these communications systems in the first place, then there is no warrant for excluding miracles from their further development, and indeed, other miracles which introduce completely new systems, and there is then no reason for Darwinism. You don't strike me as the sort to cut off your nose to spite your face, so I conclude that you're not serious and just attempting to evade via rhetorical means. F/N: Messages, as we all know, are constructed of words, which are constructed of letters. There's nothing wrong with the analogy and in fact it can even be developed more fully.Mung
June 4, 2011
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Mung:
So time for a bit of a review. DNA contains sequences of “letters” that must be read in order for them to have any effect (keeping in mind that a simple reading of those letters may in fact have no effect whatsoever). So it is entirely possible, and in fact I fail to see how it is not a requirement for the theory of evolution, that DNA be changed.
Absolutely. Without heritable variation, and unless that variation results in differential reproduction, evolution won't occur. [quote]But how many of these changes are not even read in the first place? IOW, how many are completely invisible to selection? A lot. Some changes do nothing, because they are not read. Others do nothing because they result in exactly the same protein. Some have neutral effects (at least in the current environment). Some have a net neutral effect in most genotypes.
And if DNA changes and is not read, then the search isn’t at all like Elizabeth makes it out to be.
I don't follow. Clearly changes that have no phenotypic effects won't be subject to selection (by definition). Changes that do have phenotypic effects will. Many changes have phenotypic effects. I'm not seeing your point, I'm afraid.
It really is that simple. And that is just the first step in the evolutionary story. Elizabeth would have us believe that all DNA gets read (the technical term, iirc, is transcription) and not only that, but then that it is also translated, and then that it also gets incorporated into a protein, and than that the amino acid just happens to have a selective effect. We know that is not the case.
Well, I clearly need to hone my presentation skills! No, I would certainly not "have you believe that all DNA gets read"! Not only does all DNA not get read, but most of what is read only gets read under certain circumstances, and is ignored under all others. And of what is read, only some gets translated into protein. And I certainly would never say that "an amino acid has a selective effect". It is true that a polymorphism that results in an alternate amino acid in a protein can have phenotypic effects, as I said, and phenotypic effects are, of course, "selectable" i.e. may result in phenotypic variants with different probabilities of reproducing successfully. But by no means all phenotypic effects are the result of alternate amino acids. Other variants can give rise to proteins with the same functions but with slightly different properties, and still more variants can alter regulatory genes and gene networks, including regulatory genes implicated in embryogenesis and development (with phenotypic effects on, for example, leg length, or cortical development), or on, to take another example, neurostransmitter expression. All these variants are expressed in the phenotype, and therefore potentially selectable.
Therefore we know her description of evolutionary search is simplistic and misleading and could even reasonably be called false.
Well, if I was saying what you thought I was saying, then I would agree! But I most certainly am not. Hope that has clarified my position a little. Cheers LizzieElizabeth Liddle
June 4, 2011
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Mung, I thought I was pretty clear. But I'll try again:
The reason that you don’t think it is the same thing is because you either are not thinking clearly or your argument lacks the necessary precision. Codon triplets are not the “letters” of protein “words.” Can we agree on that?
We certainly can. As I've said, I think letters and words are a very bad analogy. Codon triplets specify amino acids, a sequence of which then forms a protein. But several triplets can specify the same amino acid, so the same protein can result from different DNA sequences, if the only difference is that one or more of the amino acids is specified by an alternate codon.
The “letters” of proteins are amino acids, and it is true that different amino acid sequences can specify the same protein. That should also be unobjectionable.
No, and it's what I said. There are two kinds of differences that can result in the same functional protein; one will result in an identical protein (a "silent" polymorphism), because exactly the same sequence of amino acids is specified. The other will result in a slightly different protein, with different amino acids (e.g. methionine instead of valine), but which is expressed under the same conditions, and performs the same function. However it is not exactly the "same protein" - it will have some different properties, and may result in some phenotypic differences.
But that hardly helps your case.
Do we agree that some polymorphisms are "silent" (result in an identical protein) and others result in a slightly different protein with different phenotypic effects?Elizabeth Liddle
June 4, 2011
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So time for a bit of a review. DNA contains sequences of "letters" that must be read in order for them to have any effect (keeping in mind that a simple reading of those letters may in fact have no effect whatsoever). So it is entirely possible, and in fact I fail to see how it is not a requirement for the theory of evolution, that DNA be changed. But how many of these changes are not even read in the first place? IOW, how many are completely invisible to selection? And if DNA changes and is not read, then the search isn't at all like Elizabeth makes it out to be. It really is that simple. And that is just the first step in the evolutionary story. Elizabeth would have us believe that all DNA gets read (the technical term, iirc, is transcription) and not only that, but then that it is also translated, and then that it also gets incorporated into a protein, and than that the amino acid just happens to have a selective effect. We know that is not the case. Therefore we know her description of evolutionary search is simplistic and misleading and could even reasonably be called false.Mung
June 4, 2011
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Second, no it isn’t the same thing. There can be multiple ways of “spelling the exact same protein” because some amino acids are specified by more than one triplet.
The reason that you don't think it is the same thing is because you either are not thinking clearly or your argument lacks the necessary precision. Codon triplets are not the "letters" of protein "words." Can we agree on that? The "letters" of proteins are amino acids, and it is true that different amino acid sequences can specify the same protein. That should also be unobjectionable. But that hardly helps your case.Mung
June 4, 2011
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Elizabeth states: 'I would say that searching for a “meaningful” DNA sequence is not a “problem” for at least five reasons:' And I would say it is a severe problem: Especially since the generation of a novel gene by purely material processes has never been demonstrated!!! ,,,Many times evolutionists are very deceptive in saying that evolutionary processes can generate functional information, as with the duplicate gene scenario, when in fact no one has ever demonstrated a gain in functional information, above a parent species, that would violate the principle of genetic entropy. These following articles reveal some of the many elaborate ploys evolutionists have used in the past to try to deceive the public into thinking evolutionary processes can easily generate functional information: Assessing the NCSE’s Citation Bluffs on the Evolution of New Genetic Information - Feb. 2010 http://www.evolutionnews.org/2010/02/assessing_the_ncses_citation_b.html How to Play the Gene Evolution Game - Casey Luskin - Feb. 2010 http://www.evolutionnews.org/2010/02/how_to_play_the_gene_evolution.html further notes: Is Antibiotic Resistance evidence for evolution? - 'The Fitness Test' - video http://www.metacafe.com/watch/3995248 Testing Evolution in the Lab With Biologic Institute's Ann Gauger - podcast with link to peer-reviewed paper Excerpt: Dr. Gauger experimentally tested two-step adaptive paths that should have been within easy reach for bacterial populations. Listen in and learn what Dr. Gauger was surprised to find as she discusses the implications of these experiments for Darwinian evolution. Dr. Gauger's paper, "Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness,". http://intelligentdesign.podomatic.com/entry/2010-05-10T15_24_13-07_00 “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.(that is a net 'fitness gain' within a 'stressed' environment i.e. remove the stress from the environment and the parent strain is always more 'fit') http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/ Michael Behe talks about the preceding paper on this podcast: Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time - December 2010 http://intelligentdesign.podomatic.com/player/web/2010-12-23T11_53_46-08_00bornagain77
June 4, 2011
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Can we agree, for the sake of argument, that for it to be “meaningful” it would need to have a discernible effect on differential survival?
We could. Or we could, which I would prefer, regard it as "meaningful" if it had phenotypic effects, whether or not they had net effect on the probability of survival in the current environment.
Now doesn’t the question answer itself? Please think about it. I am trying to follow your own line of reasoning in this matter, because I really do hope that you will come to see that the line you have chosen does not lead where you think it does.
I appreciate that.
Try to anticipate what my next question or argument will be before you post a response. Thanks.
Well, won't it depend on my response? I would say that searching for a "meaningful" DNA sequence is not a "problem" for at least five reasons: First: every possible base triplet potentially "codes" for an amino acid - at that level there is no redundancy (i.e no combos that have no meaning). In that sense, written English text is a very bad analogy. Second: combinations with no phenotypic effect will not be propagated except by drift. Third: combinations with beneficial phenotypic effects will be preferentially replicated, and so "found" by natural selection. Fourth: Because combinations with neutral, and even slightly deleterous effects on the phenotype will also stand a chance of propagating through the population due to drift, a rich pool of potentially beneficial combinations is maintained. Fifth: gene-gene interactions mean that no one gene is likely to be critical; this means that the whole pool of alleles can move smoothly with changing environmental pressures in order to maintain a population optimally adapted to its environment, the less commonly useful alleles reducing in frequency, the more commonly useful alleles increasing in frequency as required.Elizabeth Liddle
June 4, 2011
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Elizabeth you state: 'There are also multiple versions of a protein which fulfull the same function.' So??? ,,,and in language we have Synonyms, and yet the existence of synonymous proteins does absolutely nothing to tell us how such 'extremely rare' proteins came to be in the first place; It seems, once again, you are being very disingenuous to the evidence Elizabeth!!! you then state; ,As for your more recent post, I didn’t say that there weren’t similarities. In some ways there are. There are also profound differences.' You are right there are 'profound differences', where the analogy breaks down is that genetic sequences are far beyond, in terms of integrated functional complexity, any coded sequence man has ever devised in his most advanced computer programs. So yes Elizabeth there are very 'profound' differences, but they certainly are not the types of 'profound differences' I would figure someone of neo-Darwinian persuasion, such as yourself, would care to dwell on very much??!!??. Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information - David L. Abel and Jack T. Trevors - Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8 "No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms' genomes programmed?" http://www.biomedcentral.com/content/pdf/1742-4682-2-29.pdf There’s No Such Thing as a ‘Simple’ Organism - November 2009 Excerpt: In short, there was a lot going on in lowly, supposedly simple M. pneumoniae, and much of it is beyond the grasp of what’s now known about cell function. http://www.wired.com/wiredscience/2009/11/basics-of-life/ Human DNA is like a computer program but far, far more advanced than any software we've ever created. Bill Gates, The Road Ahead, 1996, p. 188 Bill Gates, in recognizing the superiority found in Genetic Coding compared to the best computer coding we now have, has now funded research into this area: Welcome to CoSBi - (Computational and Systems Biology) Excerpt: Biological systems are the most parallel systems ever studied and we hope to use our better understanding of how living systems handle information to design new computational paradigms, programming languages and software development environments. The net result would be the design and implementation of better applications firmly grounded on new computational, massively parallel paradigms in many different areas. http://www.cosbi.eu/index.php/component/content/article/171 3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell - Oct. 2009 Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip -- while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication. http://www.sciencedaily.com/releases/2009/10/091008142957.htm Quantum Dots Spotlight DNA-Repair Proteins in Motion - March 2010 Excerpt: "How this system works is an important unanswered question in this field," he said. "It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It's akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour." Dr. Bennett Van Houten - of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot. http://www.sciencedaily.com/releases/2010/03/100311123522.htm Systems biology: Untangling the protein web - July 2009 Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. "Combine all this and you can start to think that maybe some of the information flow can be captured," he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. "The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent," he says. "The simple pathway models are a gross oversimplification of what is actually happening." http://www.nature.com/nature/journal/v460/n7253/full/460415a.html Though material processes have NEVER shown the ability to produce ANY functional information whatsoever (Abel - Null Hypothesis), Darwinists are adamant that material processes produced more information, of a higher complexity than man can produce, than is contained in all the libraries of the world: “a one-celled bacterium, e. coli, is estimated to contain the equivalent of 100 million pages of Encyclopedia Britannica. Expressed in information in science jargon, this would be the same as 10^12 bits of information. In comparison, the total writings from classical Greek Civilization is only 10^9 bits, and the largest libraries in the world – The British Museum, Oxford Bodleian Library, New York Public Library, Harvard Widenier Library, and the Moscow Lenin Library – have about 10 million volumes or 10^12 bits.” – R. C. Wysong etc.. etc..bornagain77
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Mung: First, yes, I know that "protein language" is not the same as "DNA language". Actually I think neither are languages, but I agree that they are not the same. I also agree that they have some parallels with language. Second, no it isn't the same thing. There can be multiple ways of "spelling the exact same protein" because some amino acids are specified by more than one triplet. There can also be multiple versions of a protein that fulfill the same function, but which incorporate different amino acids (valine vs methionine, for instance). In the first case, the result is sometimes called a "silent" SNP, as it results in the exact same protein, e.g. GUG and GUA both result in valine. In the latter case an SNP (e.g. GUG and AUG) results not in a different "spelling" of the amino acid,but a different "spelling" of the protein (methionine instead of valine). The "val" version of the protein might have different survival value (depending on context) than the "met" version. Interestingly, even "silent" mutations can have phenotypic effects, possibly due to differential efficiency in the production of the protein.Elizabeth Liddle
June 4, 2011
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Why is finding “meaningful words” in DNA a problem?
Can we agree, for the sake of argument, that for it to be "meaningful" it would need to have a discernible effect on differential survival? Now doesn't the question answer itself? Please think about it. I am trying to follow your own line of reasoning in this matter, because I really do hope that you will come to see that the line you have chosen does not lead where you think it does. Try to anticipate what my next question or argument will be before you post a response. Thanks.Mung
June 4, 2011
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Lizzie:
What I said is that there are multiple ways of spelling a protein, which is true.
But let's not forget that "protein language" is not the same as "DNA language."
There are also multiple versions of a protein which fulfull the same function.
Which is just another way of saying that there are multiple ways of spelling a protein. You've added no new information!Mung
June 4, 2011
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Why is finding "meaningful words" in DNA a problem? Oh, and I'm not complaining. I'm delighted to be here :)Elizabeth Liddle
June 4, 2011
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Elizabeth @10:
I think it’s a huge mistake to draw analogies between DNA and English text. They differ in countless ways.
1. That's because you don't understand the analogy. 2. Analogies differ. That's why we call them analogous.
I know I’ve said this before, but it’s worth repeating
But the last time you said it was as a red herring. You did better this timne :)
There are far more functional ways of “spelling” a protein, than there are ways of “spelling” a word, and far more sequences that “spell” a viable protein than “spell” an English word.
So what? You're just acknowledging you don't grasp the real intent of the analogy. As has been pointed out to you on numerous occasions since you've begun posting here, the problem is one of finding "meaningful words" in DNA. Until you do, "nature" nothing to see, and nothing to choose. Or as a nod to your preferred way of putting it (see, I do read what you write), the problem is one of coming up with "words" in DNA that have a real impact on differential survival. The analogy to english language is not that far fetched, but I do think a better one could be developed. But it also would rely on codes, symbols and alphabets and meaning. In the cell, we have not just one alphabet, but two. And not just one language, but two. And we need to translate the words of one language into the words of another language. It's more like translating English into Russian perhaps. but that doesn't help the evolutionist, because now we're not just trying to find a functional English word, we're also trying to find a functional Russian word, and on top of that, we have to find the right mapping. So we're really trying to simplify things for you guys (and gals), so please stop complaining. ;)Mung
June 4, 2011
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Joseph: however, stochastic processes can clearly result in a different protein being made.Elizabeth Liddle
June 4, 2011
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Joseph, I didn't say there was. ba77: What I said is that there are multiple ways of spelling a protein, which is true. There are also multiple versions of a protein which fulfull the same function. I'm not sure why you think what you posted is a rebuttal to what I said. As for your more recent post, I didn't say that there weren't similarities. In some ways there are. There are also profound differences. I think those differences matter, particularly when arguing by analogy.Elizabeth Liddle
June 4, 2011
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Thus, If we change (mutate) any letter we may get a new meaning for a single reading read any one way, as in Dawkins weasel program, but we will consistently destroy the other 3 readings of the message with the new mutation.
What we have there is a redundant message, which makes it much less amenable to the message being corrupted by any single letter change. There's a huge difference between four different messages being encoded within the same text and the same message being encoded four times.Mung
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Elizabeth also made this comment; 'I think it’s a huge mistake to draw analogies between DNA and English text. They differ in countless ways.' And yet the actual fact is: A New Design Argument - Charles Thaxton Excerpt: "There is an identity of structure between DNA (and protein) and written linguistic messages. Since we know by experience that intelligence produces written messages, and no other cause is known, the implication, according to the abductive method, is that intelligent cause produced DNA and protein. The significance of this result lies in the security of it, for it is much stronger than if the structures were merely similar. We are not dealing with anything like a superficial resemblance between DNA and a written text. We are not saying DNA is like a message. Rather, DNA is a message. True design thus returns to biology." http://www.arn.org/docs/thaxton/ct_newdesign3198.htm Information Theory, Evolution, and the Origin of Life - Hubert P. Yockey, 2005 Excerpt: “Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.” http://www.cambridge.org/catalogue/catalogue.asp?isbn=9780521802932&ss=exc further note: John Sanford, a leading expert in Genetics, comments on some of the stunning poly-functional complexity found in the genome: "There is abundant evidence that most DNA sequences are poly-functional, and therefore are poly-constrained. This fact has been extensively demonstrated by Trifonov (1989). For example, most human coding sequences encode for two different RNAs, read in opposite directions i.e. Both DNA strands are transcribed ( Yelin et al., 2003). Some sequences encode for different proteins depending on where translation is initiated and where the reading frame begins (i.e. read-through proteins). Some sequences encode for different proteins based upon alternate mRNA splicing. Some sequences serve simultaneously for protein-encoding and also serve as internal transcriptional promoters. Some sequences encode for both a protein coding, and a protein-binding region. Alu elements and origins-of-replication can be found within functional promoters and within exons. Basically all DNA sequences are constrained by isochore requirements (regional GC content), “word” content (species-specific profiles of di-, tri-, and tetra-nucleotide frequencies), and nucleosome binding sites (i.e. All DNA must condense). Selective condensation is clearly implicated in gene regulation, and selective nucleosome binding is controlled by specific DNA sequence patterns - which must permeate the entire genome. Lastly, probably all sequences do what they do, even as they also affect general spacing and DNA-folding/architecture - which is clearly sequence dependent. To explain the incredible amount of information which must somehow be packed into the genome (given that extreme complexity of life), we really have to assume that there are even higher levels of organization and information encrypted within the genome. For example, there is another whole level of organization at the epigenetic level (Gibbs 2003). There also appears to be extensive sequence dependent three-dimensional organization within chromosomes and the whole nucleus (Manuelides, 1990; Gardiner, 1995; Flam, 1994). Trifonov (1989), has shown that probably all DNA sequences in the genome encrypt multiple “codes” (up to 12 codes). Dr. John Sanford; Genetic Entropy 2005 Cells Are Like Robust Computational Systems, - June 2009 Excerpt: Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. ,,,,"We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail."bornagain77
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Elizabeth states: 'I know I’ve said this before, but it’s worth repeating :) There are far more functional ways of “spelling” a protein, than there are ways of “spelling” a word, and far more sequences that “spell” a viable protein than “spell” an English word.'; And yet, contrary to Elizabeth once again, the actual evidence states: Stephen Meyer - Proteins by Design - Doing The Math - video http://www.metacafe.com/watch/6332250/ Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681 Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe: Excerpt: Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function. The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences. http://www.ncbi.nlm.nih.gov/pubmed/15321723 Correcting Four Misconceptions about my 2004 Article in JMB — May 4th, 2011 by Douglas Axe http://biologicinstitute.org/2011/05/04/correcting-four-misconceptions-about-my-2004-article-in-jmb/ The Case Against a Darwinian Origin of Protein Folds - Douglas Axe - 2010 Excerpt Pg. 11: "Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin." http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.1 Shortcuts to new protein folds - October 2010 Excerpt: Axe concludes that all of these putative shortcuts are dead ends. The Darwinian search mechanism is not capable of finding new protein folds by random sampling and all the shortcuts to new folds are dead ends. http://idintheuk.blogspot.com/2010/10/shortcuts-to-new-protein-folds.html The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway - Ann K. Gauger and Douglas D. Axe - April 2011 Excerpt: We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions. But evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.1/BIO-C.2011.1 When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied. http://biologicinstitute.org/2011/04/16/when-theory-and-experiment-collide/ Even if evolution somehow managed to overcome these impossible hurdles for generating novel proteins by totally natural means, evolution would still face the monumental hurdles of generating complimentary protein/protein binding sites, in which the novel proteins would actually interact with each other in order to accomplish the specific tasks needed in a cell (it is estimated that there are least 10,000 different types of protein-protein binding sites in a 'simple' cell; Behe: Edge Of Evolution). What does the recent hard evidence say about novel protein-protein binding site generation? "The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable." Michael J. Behe PhD. (from page 146 of his book "Edge of Evolution") Nature Paper,, Finds Darwinian Processes Lacking - Michael Behe - Oct. 2009 Excerpt: Now, thanks to the work of Bridgham et al (2009), even such apparently minor switches in structure and function (of a protein to its supposed ancestral form) are shown to be quite problematic. It seems Darwinian processes can’t manage to do even as much as I had thought. (which was 1 in 10^40 for just 2 binding sites) http://www.evolutionnews.org/2009/10/nature_paper_finally_reaches_t.htmlbornagain77
June 4, 2011
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EL:
There are far more functional ways of “spelling” a protein, than there are ways of “spelling” a word, and far more sequences that “spell” a viable protein than “spell” an English word.
I know I have said this before but it is worth repeating: There isn't any evidence that stochastic process can produce a protein (in the absence of a living organism).Joseph
June 4, 2011
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I still don't see why overlapping genes are like making a complex sentence that can be read in two reading frames. Genes are not like complex sentences, nor are their products. For example, the number 103.579 can be made to read as a very different number simply by moving the reading frame and writing it as 10.3579. Both numbers are perfectly sensible numbers. Similarly with genes - if a sequence read one way gives a useful protein, and read a different way also gives a useful protein, and if it turns out that a tweak to a regulatory gene results in one protein given one input, and the other given another, then, if the result is beneficial, the tweak will tend to be selected. I think it's a huge mistake to draw analogies between DNA and English text. They differ in countless ways. I know I've said this before, but it's worth repeating :) There are far more functional ways of "spelling" a protein, than there are ways of "spelling" a word, and far more sequences that "spell" a viable protein than "spell" an English word.Elizabeth Liddle
June 4, 2011
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I have blogged about overlapping genes: Since the Human Genome Project was completed some 10 years ago we have discovered that only about 20,000-25,000 genes encode 100,000-200,000 proteins. We have discovered two mechanisms that make this so- alternative gene splicing- in which introns are removed and exons spliced back together in different packages producing different proteins from the same gene- editting and splicing, evidence for design. We have alo discovered overlapping genes- that is one gene actually being two or more genes. That means there has to be a start codon and stop codon for each gene along the same sequence. Have you even tried to make more than one complex sentence out of a given complex sentence just by shifting your starting point to the right or left? Can you think of what planning and foresight is required to accomplish such a feat? Think about it, genes have only one start codon.Joseph
June 4, 2011
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hmm. I am not seeing "overlapping code" in the genome as being analogous to
...a short story read backwards is a flawless different short story, and sections of it, read letter by letter down the right hand side are a flawless paragraph
Can someone explain how the analogy works?Elizabeth Liddle
June 4, 2011
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bevets; here is the example John Sanford used in his book 'Genetic Entropy".;,,, S A T O R A R E P O T E N E T O P E R A R O T A S Which is translated ; THE SOWER NAMED AREPO HOLDS THE WORKING OF THE WHEELS. This ancient puzzle, which dates back to 79 AD, reads the same four different ways, Thus, If we change (mutate) any letter we may get a new meaning for a single reading read any one way, as in Dawkins weasel program, but we will consistently destroy the other 3 readings of the message with the new mutation.bornagain77
June 4, 2011
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It is a challenge to find even single short words (I found a few others). The exercise gives an appreciation for the difficulty in finding (let alone creating) overlapping code -- especially code that will yeild a meaningful/coherent/complex/aesthetic result. It also illustrates the constraints on mutations -- if a mutation falls on a bolded letter, it will probably be fatal. This should be a UD contest.bevets
June 4, 2011
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What makes overlapping code difficult in my experience is the need to preserve the integrity of the original, while interleaving a second, secondary code. Bevets' examples are very good, but the oddness of the full form would surely attract attention.O'Leary
June 4, 2011
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Michael Denton, whose first book, Evolution: A Theory in Crisis, first awakened me from my Darwinian stupor, has described it all as "wheels of complexity within wheels of complexity." As far as I can discern, having read both of his books, Denton is an agnostic and clearly has no theological axe to grind. He seems to have some vague notion of teleology concerning the universe and living systems, but that is as far as he goes.GilDodgen
June 3, 2011
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Overlapping code: No, I save on final perusal – a sure plan if no evasion. [a spine] Name no side in Eden, I’m mad! A maid I am, Adam mine; denied is one man. [seen mad] Madam in Eden, I’m Adam [amen]bevets
June 3, 2011
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