A Code That Isn’t Universal

_{Cornelius Hunter

May 18, 2010

Intelligent Design}

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The DNA code, which translates DNA sequences into protein sequences, has always been claimed as extremely compelling evidence for evolution. The code was first described in the mid twentieth century and, among other things, was found to be universal, or nearly so. The same DNA code is used in the cells in your brain and your big toe. The same DNA code is used in different species. The same DNA code is even used across the major kingdoms. All tissues, all species use the same code? Surely they were not independently created—they must have evolved. And if the code varied, on the other hand, evolution would surely be falsified. In one fell swoop, the DNA code not only is another compelling evidence for evolution, it also demonstrates that evolution is falsifiable, a badge that is crucial for evolutionists who seek to distinguish themselves from those religious rascals. But now a new code has been discovered and, believe it or not, it is not universal. Read more

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PS: H/W; Figure out the questions being begged in Bob Allen's 1278 here: "Thus, Perry, in answer to your question about the so-called “Code of DNA” – the Cosmic Evolution of matter from inorganic matter to organic matter – creates a natural, non-directed, random-event occurring Code, known as DNA! This answers your question of having someone point out just one, naturally occurring code. I provide the answer that you seek. By the by, I am an Atheist."kairosfocus_{May 19, 2010
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Above: You are right to be suspicious:
this guy claims (after reading the entire post) that simply based on the fact that carbon is created in stars, that is evidence that DNA can be materialistically created. Am I missing something or do others find this conclusion rather dubious?
1 --> The conditions for a cosmos that creates the key elements of life and sets up second genersaiton long term stable stars in Galactic Habitable Zones with suitable terrestrial planets are extraordinarily fine-tuned. [Watch here and here for starters.] 2 --> All that has got you is elements in a rocky, watery planet that may have an atmosphere that has enough Oxygen to shield from high energy rays -- then that Oxygen will poison reaction paths to create biologically relevant monomers. 3 --> And if the atmosphere is more reducing, you get UV disintegration of complex molecules. So, off to convenient caves and deep sea vents. 4 --> next problem: chirality. Life chemistry is dependent on precise geometrical key-lock fitting of molecules, most of which have mirror-image handedness, like left and right hands [Proteins are basically L handed, and D/RNA is right handed]. When such molecules form out side of life settings, they strongly tend to form in 50-50 handedness mixes called racemic forms. And the odds of getting the right handedness combination for enough molecules to form a life functional system are astronomical. 5 --> Well maybe there was a frozen accident in a mythical self-replicating RNA molecule that could hen template off molecules of he right handedness. But, such will form in media that have cross interfering relatively chemically active compounds and bye bye replicator, you just got eaten up by something else. 6 --> And so on. 7 --> Bottomline: there is no credible lucky noise information generating free lunch to get to the cluster of information-rich organised molecules that implement a von Neumann type self-replicating molecule. 8 --> Your man is indeed begging he question bigtime. 9 --> Which should tell us the significance of the imposed rule that blocks the obvious conclusion on seeing the code based information -processing systems in cells. 10 --> until one of these rebuttals can show us a credible physically demonstrated, observed case where under plausible conditions, a self-replicating entity SPONTANEOUSLY forms that also carries out metabolic-related processes such as protein synthesis [cf here], we can safely conclude that we are looking at materialistic question-begging. G'day GEM of TKIkairosfocus_{May 19, 2010
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Nakashima, My objection to nature creating a code system should be clear from the fact that a code system is independent of the medium that represent it physically. Think of the fact that a binary code is sometimes represented by 1 and 0 and can be captured in various media. The DNA's 4 letter code can be represented on various media in various ways. The media does not "select" to be a code system on its own account. There is an intentional coder, message & decoder nessesary. This should be clear from the "monkeys typing the works of Shakespeare" example. The act of the monkeys is meaningless even if there is enough statistical resources and the event actually happens, because if there is no significance to the works of Shakespeare in the first place (initial objective/aim/goal), the works would in itself be just as random as the proposed process that created it. It is humans that selected the code system (Typewriters) and the message (Shakespeare's works) in the first place. Saying that nature created the DNA code system and computational machines contained in the cell and then present it as the proof that nature is capable of creating code is the fallacy of begging the question.mullerpr_{May 19, 2010
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"So nature, the laws of physics and chemistry, creates the code" No, the laws of nature are such that certain affinities are more likely than others to be used (not created) in developing a code for protein building. There are about 1500+ proteins necessary to get from the code to the actual amino acid assembly that are required to implement the actual code. And the code for these 1500 proteins must also be in the code. That a designer would make use or create conditions that facilitate this is not surprising. "If you are in favor of cosmic fine tuning arguments, the results that support the stereochemical hypothesis could be considered supportive of that outlook." Way to go Nakashima. You have come a long way and have admitted some of the of the ID side's perspective. Now we just have to explain how those 1500 proteins that are necessary for the transcription and translation process can arise by naturalistic means and we are on our way to showing how the fine tuning process led to a very essential but small part of life. We could then all consider the Theistic Evolution thesis as more tenable. But those pesky fine tuning findings are still a great big thorn in the atheist's side. Just too many coincidences. But there is always the multiverse and infinity to save them.jerry_{May 19, 2010
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I have been reading about Perry Marshall's information argument here: http://www.cosmicfingerprints.com/ and it sounds a lot like the arguments put forth by several people here (tgpeeler and kairosfocus come to mind). I also wanted to read the responses from the opposing camp so I visited: http://www.freeratio.org/showthread.php?t=135497&page=1 where there was a very long discussion on the matter. I run into the following post which seemed informed but rather misleading as an attempt to undermine Marshall's argument. The conclusion of the poster was: "Again, all nucleic acids and proteins are long chain-like arrangements of carbon-rich molecules. Moreover, carbon finds creation through the Cosmic evolution of exploding Super Nova – forging the necessary heat for the fusion of carbon from hydrogen and helium. Thus, it is impossible ever to talk about organic carbon-based organic Life without including a discussion of inorganic Cosmic evolution. In short – Darwin falls short of placing the Evolution of Life within the larger context of Cosmic Evolution. Thus, Perry, in answer to your question about the so-called “Code of DNA” – the Cosmic Evolution of matter from inorganic matter to organic matter – creates a natural, non-directed, random-event occurring Code, known as DNA! This answers your question of having someone point out just one, naturally occurring code. I provide the answer that you seek." The post is too long to include here so you can read the whole thing at: http://www.freeratio.org/showthread.php?p=6067200#post6067200 post #1278 My understanding is that there is significant question begging and unproven assumptions (taken as certainties) in this guy’s response. It seems to me that this guy claims (after reading the entire post) that simply based on the fact that carbon is created in stars, that is evidence that DNA can be materialistically created. Am I missing something or do others find this conclusion rather dubious?above_{May 19, 2010
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Nakashima, I'm not sure if it's the way you phrased it or what you actually mean, but my understanding from what you said is that this sterochemical hypothesis facilitates the creation of the code as opposed to actually programming it. Feel free to elaborate.above_{May 19, 2010
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Mr Mullerpr, Can anyone tell me how nature can create a code system? There is evidence that at least some of the associations of codon to amino acid in the genetic code exist because of chemical affinities between these specific molecules. So nature, the laws of physics and chemistry, creates the code. This is called the stereochemical hypothesis. If you are in favor of cosmic fine tuning arguments, the results that support the stereochemical hypothesis could be considered supportive of that outlook.Nakashima_{May 19, 2010
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Thanks Granville. I actually read about that and also saw one of Behe's interview that was talking about that. Is that really all there is?above_{May 19, 2010
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above:
I took the time to read through much of the evolutionary literature but I could not find any experiments that provided evidence for materialistic macro evolution. I know about experiments with fruitflies and bacteria and all… But those changes are rather minor. Any experiments out there that provide more substantive evidence?
Richard Lenski's 20-year E.coli experiments, which Michael Behe says [in The Edge of Evolution] were all due to "breaking some genes and turning others off," and which according to Behe produced "nothing fundamentally new," were hailed by a June 9, 2008 New Scientist article as "the first time evolution has been caught in the act." So that should answer your question.Granville Sewell_{May 19, 2010
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The "code within a code" thing was my next point to be enlightened on. Something I need to know in this particular case. Is it simply the DNA code that is used to create another code or is it a specific "gene message" that is used to generate a new code system? Both are possible (when a mind is involved) but my knowledge of biological terms are not sufficient to discern which type of new code has been generated in this instance. If the "Code within a code" is actually a "Code within a message", than things looks even worse for natural processes to be the cause. A message implies meaning & the new code would be dependent on the meaning to remain the same to ensure the code to remain valid. Having a code is one thing. Using a code is a totally different matter. Embedding codes within messages is great for compression. This should actually be considered an ID prediction.mullerpr_{May 18, 2010
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*A point of clarification. I am not asking for fossil records, DNA similarities or evidence for common descent. But rather, an experiment that provides hard evidence of one one organism radically changing to something different, to put it simply.above_{May 18, 2010
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A little side question. I took the time to read through much of the evolutionary literature but I could not find any experiments that provided evidence for materialistic macro evolution. I know about experiments with fruitflies and bacteria and all... But those changes are rather minor. Any experiments out there that provide more substantive evidence? This question I would much like to hear from the atheist/materialist readers of the blog.above_{May 18, 2010
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mullerpr, I am with you when you state: "I need some honest guidance, not being a biologist. A universal code system for DNA being proof of evolution is not parsimonious in any sense." I can show you this though mullerpr: 1st, all codes we know the origination of come from a mind: The DNA Code - Solid Scientific Proof Of Intelligent Design - Perry Marshall - video http://www.metacafe.com/watch/4060532 and 2nd, all information we know the origination of within a code comes from a mind as well: Stephen C. Meyer - The Scientific Basis For Intelligent Design - video http://www.metacafe.com/watch/4104651 ------------ What makes this paper Dr. Hunter cites so interesting to me is that, in my very limited ability, it appears to me that the "second code", which is over-layed on top of the DNA codon code, is a unique code which is tailored to each different kind of species. Thus whereas before the evolutionists could kind of forget the nagging problem that he has no explanation for the original DNA code, that "forgotten" problem has just magnified exponentially. So I am with you 100% on this mullerpr in that "I need some honest guidance" to see how far this goes.bornagain77_{May 18, 2010
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I need some honest guidance, not being a biologist. A universal code system for DNA being proof of evolution is not parsimonious in any sense. The simplest answer would be a single or integrated code generator created/caused this particular code. Claiming that code generator to be an evolutionary mechanism would also not be the simplest explanation, because apart from intelligent agents there is no known phenomenon that can create code systems. Evolution as a code generator is still unproven. Can anyone tell me how nature can create a code system? Surely you need a form of consciousness that has a message to transfer that turns some part of nature into a code baring medium. Furthermore that code, in most instances does not decode itself... and so the naturalistic troubles keeps growing. Surely someone like Hubert Yockey knows this and has spoken on the matter. What does the evolutionary biologists think of his work? Another point of ignorance is regarding the difference between a code system and a message captured by using that system. How is it possible that some of the messages are the same across different branches of the "Tree of Common Descent"? Does that have no implication for the proposed method / mechanism by which these messages "evolved". Is there a known mechanism that help messages to jump between genes? Again the simplest answer with our current knowledge of physical phenomenon is the act of some form of intelligence. Why should I reject this view? It is falsifiable by any other proven "message sharing" mechanism acting on the genes of species in the proposed "Tree of common descent".mullerpr_{May 18, 2010
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this may interest you as well llion: Deciphering Design in the Genetic Code Excerpt: When researchers calculated the error-minimization capacity of one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution where the naturally occurring genetic code's capacity occurred outside the distribution. Researchers estimate the existence of 10 possible genetic codes possessing the same type and degree of redundancy as the universal genetic code. All of these codes fall within the error-minimization distribution. This finding means that of the 10 possible genetic codes, few, if any, have an error-minimization capacity that approaches the code found universally in nature. http://www.reasons.org/biology/biochemical-design/fyi-id-dna-deciphering-design-genetic-code DNA Optimized for Photostability Excerpt: These nucleobases maximally absorb UV-radiation at the same wavelengths that are most effectively shielded by ozone. Moreover, the chemical structures of the nucleobases of DNA allow the UV-radiation to be efficiently radiated away after it has been absorbed, restricting the opportunity for damage. http://www.reasons.org/dna-soaks-suns-raysbornagain77_{May 18, 2010
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llion, I said universal for convenience: Ode to the Code - Brian Hayes The few variant codes known in protozoa and organelles are thought to be offshoots of the standard code, but there is no evidence that the changes to the codon table offer any adaptive advantage. In fact, Freeland, Knight, Landweber and Hurst found that the variants are inferior or at best equal to the standard code. It seems hard to account for these facts without retreating at least part of the way back to the frozen-accident theory, conceding that the code was subject to change only in a former age of miracles, which we'll never see again in the modern world. https://www.americanscientist.org/issues/pub/ode-to-the-code/4 This may be of interest to you llion; DNA - The Genetic Code - Optimal Error Minimization & Parallel Codes - Dr. Fazale Rana - video http://www.metacafe.com/watch/4491422 Biophysicist Hubert Yockey determined that natural selection would have to explore 1.40 x 10^70 different genetic codes to discover the optimal universal genetic code that is found in nature. The maximum amount of time available for it to originate is 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that is optimal. Put simply, natural selection lacks the time necessary to find the optimal universal genetic code we find in nature. (Fazale Rana, -The Cell's Design - 2008 - page 177) 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 The Coding Found In DNA Surpasses Man's Ability To Code - Stephen Meyer - video http://www.metacafe.com/watch/4050638 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 etc.. etc..bornagain77_{May 18, 2010
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"Thus as you can see, though the DNA code is universal ..." But it's not universal. That idea had to be set aside when the 21st amino acid was discovered (to say nothing of the 22nd). Further, these "non-canonical" codon -> amino acid translations show that the genetic code is, in fact, a code. By that, I mean that these two discoveries make it clear that there is no chemical necessity that any particular codon sequence code for any particular amino acid product.Ilion_{May 18, 2010
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Dr. Hunter, this could be very interesting. It seems that a unique coded "alphabet" is generated from their method by "an input a collection of exons and surrounding intron sequences and data profiling how those exons are spliced in different tissues". Yet this method of coding they have deciphered will present insurmountable difficulties for the Darwinists since,,, “Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible” Donald E. Johnson – Bioinformatics: The Information in Life Thus as you can see, though the DNA code is universal and the evolutionists have appealed to a onetime "frozen accident" to explain its optimality, The evolutionists will now basically have to argue for a discontinuous series of frozen accidents to explain the origination of each next "higher level" unique code. i.e. each "next" unique code found for a higher number of exons and introns. As well,, Seeing as the codes generated by this method code could very well produce radically different "alphabets" which each must be accounted for with their own point of origination, I think the argument for universal common ancestry from the evolutionists is effectively crushed. This could be a very interesting turn of events.bornagain77_{May 18, 2010
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Here is the article: Canadian Team Develops Alternative Splicing Code from Mouse Tissue Data By Andrea Anderson NEW YORK (GenomeWeb News) – A University of Toronto-led research team reported online today in Nature that they have come up with a computational method for predicting tissue-specific alternative splicing patterns in mice. The approach, which relies on incorporating information on hundreds of RNA features to tease apart an alternative splicing code, predicted a slew of tissue-specific splicing patterns as well as splicing differences between adult and embryonic mouse tissues that may point to previously unappreciated regulatory mechanisms. Those involved with the effort say the work also sets the stage for similar studies in human tissues. "What we've achieved here is really the first step," senior author Brendan Frey, an engineering and molecular genetics researcher affiliated with the University of Toronto and the Canadian Institute for Advanced Research, told GenomeWeb Daily News. "We and other researchers can use the same framework and the same methodology for [studying alternative splicing in] humans." Nearly all genes with more than one exon can be spliced in a variety of ways. This alternative splicing is thought to help explain how humans accomplish such biological complexity with relatively few genes, Frey noted. "Before we can understand how genes work, we have to understand how splicing works," he said. But rather than looking gene-by-gene or protein-by-protein, he explained, the team decided to tackle splicing complexity across the genome using a coding approach similar to that used by the biological system itself. "Our method takes as an input a collection of exons and surrounding intron sequences and data profiling how those exons are spliced in different tissues," Frey and his co-authors wrote. "The method assembles a code that can predict how a transcript will be spliced in different tissues." The team used an algorithm developed by co-lead author Yoseph Barash, a postdoctoral researcher in Frey's lab, to create a code based on data for 3,665 alternative exons in 27 mouse embryonic and adult tissues. After bringing together information on 171 known exon and intron sequence motifs, as well as 326 new motifs, 460 short motifs, and 57 features associated with specific transcript structures, the researchers narrowed in about 200 of the most informative features. These included a wide range of features, from specific motifs to transcript features such as exon length, Frey said, hinting at complex regulation of alternative splicing. "It is apparent from examining the splicing code deciphered in the present study that large numbers of sequence features are generally required to achieve tissue-regulated splicing," he and his co-workers wrote. When the researchers grouped the dozens of tissues into four categories — central nervous system tissues, muscle tissues, digestive system tissues, and embryo/embryonic stem cell tissues — they were able to begin characterizing the extent of tissue specific splicing. "In most cases that we looked at, there were changes between tissues," Frey said. In addition, their method predicts patterns in the mouse tissues that could only be explained by previously unappreciated regulatory mechanisms. For example, the researchers found a class of genes that is expressed in both embryonic and adult tissues but doesn't seem to be functional in the adult. Based on their predictions and follow up experiments, the team concluded that such differences stem from the inclusion of exons with premature termination codons in adult tissues that stimulate nonsense mediated mRNA decay. Indeed, Frey noted, they found roughly 100 examples of genes in which NMD-causing exons seem to get skipped in embryonic tissue. While instances of this had been detected for individual genes in past studies, Frey explained, "there was no understanding of whether this was general or not." Overall, about 3,000 of the splicing events predicted by the newly developed splicing code were subsequently validated using microarrays, Frey noted, while 14 exons were verified in 14 tissues using reverse transcription PCR. The team also followed up on some of the predictions using mutagenesis and other experiments. The team has now started doing similar alternative splicing analyses in 20 or more human tissues using RNA sequencing and microarray data, Frey noted. They eventually hope to broaden their analyses to include information on non-coding RNAs, polyadenylation patterns, and more, he added. Nevertheless, Frey cautioned, the alternative splicing picture is far from complete, even in mice. He predicts that researchers' understanding of the splicing code identified in the current study will continue expanding as more transcript data — including information on additional tissue types — becomes available. An online tool for investigators interested in determining whether a particular exon is likely to undergo alternative splicing is available at the Website for Alternative Splicing Prediction. "The tool can scan previously uncharacterized exons, predict tissue-dependent splicing patterns, and produce downloadable exploratory feature maps linked to the UCSC genome browser," the researchers noted.bornagain77_{May 18, 2010
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Here is a article on the code within the code for those who don't have access to Nature, Canadian Team Develops Alternative Splicing Code from Mouse Tissue Data Excerpt: "Our method takes as an input a collection of exons and surrounding intron sequences and data profiling how those exons are spliced in different tissues," Frey and his co-authors wrote. "The method assembles a code that can predict how a transcript will be spliced in different tissues." http://www.genomeweb.com/informatics/canadian-team-develops-alternative-splicing-code-mouse-tissue-data Thus it seems that a unique splicing code will be "assembled" for each genome studied: This hints very strongly at a signature of individuality.bornagain77_{May 18, 2010
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Dr Hunter, Can you believe such an amazing thing? That the three dimensional structure somehow affects the meaning of the code which in turn affects function. The analogy if one exists would be for a programmer to push his handy assembler code through some computer and then depending on the exact properties of the material the electrons move through (as opposed to just their ordering) would result in modified end code that performs a slightly different function than the original code intended! This defies a natural explanation. When are evolutionists going to accept at least the possibility of the elephant being in the room?aqeels_{May 18, 2010
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Dr. Hunter, I found this quote of yours very interesting: "The new massive study systematically analyzed how genes are alternatively spliced in four different types of mouse tissue: central nervous system tissue, muscle tissue, digestive system tissue, and whole embryos. The study found significant signals that the splicing machinery seem to use to decide how to do its splicing. This splicing code is extremely complicated, using not only sequence patterns in the DNA transcript, but also the shape of transcript, as well as other factors. What is also complex about the new code is that it varies substantially across the four tissue types. There is still much to learn, but there certainly is no question that this is no universal code. Is evolution still falsifiable? Thus my question, Dr. Hunter, is, Do you think this "signature of individuality" for the splicing code that varied substantially for the four tissue types in the mouse, will be found to produce the same signature of individuality once they expand their study to other species? (if they have not expanded already)bornagain77_{May 18, 2010
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