Home » Intelligent Design » A Code That Isn’t Universal

A Code That Isn’t Universal

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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52 Responses to A Code That Isn’t Universal

  1. 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)

  2. 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?

  3. 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/infor.....issue-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.

  4. 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.

  5. 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.

  6. 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.

  7. 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/.....rticle/171

    etc.. etc..

  8. 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.....netic-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-rays

  9. 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”.

  10. 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.

  11. 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.

  12. *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.

  13. 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.

  14. 14
    Granville Sewell

    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.

  15. 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?

  16. 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.

  17. 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.

  18. 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/showt.....038;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/showt.....ost6067200 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?

  19. “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.

  20. 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.

  21. 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 TKI

  22. 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.”

  23. Mr Mullerpr,

    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.

    Well, that is certainly true of what humans do with codes we create. If you found a second or third instantiation of the genetic code in nature in which the same code was instantiated as magnetism vs polarisation of light beams, that would be a very strong evidence that it did not occur via the channels we now are investigating. Even if a second instantiation was found to exist, you’d have to show that one did not derive from the other, that they are historically independent.

    However, the single instance of the code we now know of in nature can’t be said to exhibit multiple instaniations. There are amino acids, which we know can arise abiotically. There are short nucleotide sequences, which we’re pretty sure can arise abiotically. There are circumstances of temperature, pressure, concentration, etc that would allow both kinds of molecules to live long enough to knock against each other. Under these circumstances, some nucleotide sequences preferentially associate with the amino acids that we know they are associated with in the genetic code. The genetic code is a table of associations between amino acids and RNA triples, that’s all.

  24. Mr Jerry,

    That a designer would make use or create conditions that facilitate this is not surprising.

    No, it isn’t. But, as a variation of the “that isn’t common descent, that is common design” argument, it’s not evidence for ID either. The Designer Who only uses found objects is indistinguishable from Nature.

  25. Hi above @17,

    Thank you for the request to elaborate.

    You are right, the stereochemical hypothesis is only a part of the puzzle of how the code came into existence as we see it today. As the research I linked to shows, it does not explain all of the associations we see in the code, only some of them.

    Right now, the code is a fairly strict 1 to 1 association of RNA triplets to amino acids. What we see as a table on a web site is really a collection of tRNA molecules in each cell.

    If we want to apply generic evolutionary thinking to the code, we have to ask two things:

    1 – can it vary, and are those variations natual occurences?
    2 – do the variations create any advantage for the organism that has them?

    Let’s look at 1) first.
    Yes, the code can vary. We know that there are different codes in some species. We know that we can take all the tRNA out of a cell that associates the triple AGG with its normal amino acid, and replace it with artificially created tRNA that associates it with another amino acid, perhaps not even one of the standard 20 amino acids. (There are many more amino acids than those used in biology.) This kind of substitution has been done in synthetic biology research to build protein chains that could never be built by normal cells.

    We also know that the current code (in tRNA form) isn’t perfect. Sometimes leucine and isoleucine substitute for each other because they have a similar shape. If you wanted your table to capture that ambiguity, you’d have to introduce probabilities into the table, and say the RNA triplet actually associates 95% with isoleucine and 5% with leucine.

    Can these variations occur naturally? Today they don’t, because the planet is full of life that will eat poor performers. They might have in the past – that is what question 2 is about. But just looking at it physically, yes. tRNA is built from 4 RNA hairpins – very common short RNA structures. We don’t have any evidence today that would lead us to believe that the tRNAs in existence today are the only ones possible.

    On to point 2) – is there selectable advantage in table variations?

    The answer from studies of the code is definitely yes. Some codes are much better at preserving protein function than others, because a change in a nucleotide maps to another triplet that maps to the same protein, or to another protein with the same properties (size, hydrophbicity, etc.). So a bag of molecules containing one set of tRNAs will replicate faster, with fewer errors, that another bag with a different set of tRNAs.

    So the theory of evolution, applied at this molecular level would lead you to expect a pretty functional bag of tRNAs to dominate after a while. Actuarial science would lead you to expect that after a long while, the descendants of only one kind will still be around.

    That is what we see today.

    Can the code occur naturally? Can 4 RNA hairpins get mashed together with random associations of triplets at one end, and AA carriers at the other end, and then have that set get winnowed down to what we see today. Yes. As opposed to many ‘bignum’ calculations in the OOL debate, there are only 64*20 or 64*22 possibilities, because there are only 64 positions in the table, and only 20 amino acids. A little bag of molecules could have many many copies of each of those.

  26. @kairosfocus

    Thanks so much for clearing it up. :)

  27. Regarding the existence of multiple genetic codes, does this mean that the 3 base pair (condon) sequence code for amino acids varies from species/kingdoms, or something to that effect?

    (Condon table as I learned it)

  28. F2XL,
    In that table (once called “universal,” now called “canonical”) are listed twenty DNA-triplet codon -> amino acid translations, plus the ‘stop‘ codon. As you can see, some amino acids are coded for by multiple codons, but all sixty-four possible codons are accounted for by exactly one translation to one specific amino acid. There are no codons unaccounted for.

    With the discovery of the 21st and 22nd amino acids, we have the situation in which a particular codon translates to one specific amino acid in most species (or, at any rate, is assumed/believed to do so), but in some other species that some codon translates to a different amino acid.

    That is, before the discovery of the 21st amino acid, the DNA code was believed to be a one-to-many encoding; now it is known to be a many-to-many encoding.

  29. … and so, Nakashima’s “explanation” @ 16 doesn’t really hold up to scrutiny:
    ["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."]

  30. Mr Ilion,

    … and so, Nakashima’s “explanation” @ 16 doesn’t really hold up to scrutiny:

    Srsly? Which part of the peer reviewed scientific studies I referenced have been refuted? I look forward to reading the papers you reference.

  31. Mr. Nakashima;

    “If you found a second or third instantiation of the genetic code in nature in which the same code was instantiated as magnetism vs polarisation of light beams, that would be a very strong evidence that it did not occur via the channels we now are investigating.”

    I really hope you see the circular argument in this. You start by claiming that the genetic code is a “naturally occurring code” and then you use it to distinguish it from other code systems – which form the basis of your argument.

    You first need to establish beyond reasonable doubt that it actually is “the only naturally occurring code”. You have not done so with your effort to simplify the interactions that the code baring medium has with nature. In fact your simplification should be applicable to all potential code baring media in nature, and yet we don’t see code baring patterns all over. Statistically there are media that can more easily be endowed with “randomly generated messages”. Yet we don’t see them around.

    Your proposed mechanism is flawed and certainly not supported by observation.

  32. KF-san,

    3 –> And if the atmosphere is more reducing, you get UV disintegration of complex molecules. So, off to convenient caves and deep sea vents.

    IOW, I’d prefer to be distractive than to admit there are solutions to this problem. Indeed, rather than a problem, high energy photons are an important source of the energy gradient necessary for life, even today.

    4 –> next problem: chirality.

    Next solution, late afternoon sunlight. Remember you were just saying how strong it was back then? Or some other process:

    Imitating Prebiotic Homochirality on Earth

    From the abstract:

    The process can start with a miniscule excess and in one step generate water solutions with L/D ratios in the over 90% region. Kinetic processes can exceed the results from equilibria. We have also examined such amplifications with ribonucleosides, and have shown that initial modest excesses of the D-nucleosides can be amplified to afford water solutions with D to L ratios in the high 90’s.

  33. Mr Mullerpr,

    I’m sorry, you misunderstand the purpose of my example. Your initial objection was that a code can be instantiated in multiple ways. That is certainly true of codes in general, and we see that humans do instantiate codes in different ways. However, the genetic code is only found in nature instantiated in one way, as the association of RNA triplets and amino acids. Failing evidence of multiple independent instantiations, we have no warrant that the code exists as an abstraction prior to, or independent of, that particular instance in nature.

    I did not argue that the genetic code was the only naturally occuring code. I agree that there are other naturally occuring media that can host coded information. For example, patterns of magnetic reversals – we use these on our hard drives, and they do occur in nature. There could be patterns of L vs D enantiomers, or open vs closed chromatin. The problem is that nature does not create a lasting association between any of these.

    While the word ‘code’ is common and appropriate, it is also freighted with numerous associations that might not be appropriate when considering the origin of the code. If we just called it an association or bijection there might be less of that.

    The stereochemical hypothesis is not a complete explanation, but it is supported by observation. I refer you to the paper already linked or the results of a Google search.

  34. Granville:

    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.”

    In other words, despite decades of claims that evolution is a “fact, fact, fact…”, and that biological systems are replete with examples of evolution “in action” (ie, the peppered moths), New Scientist admits that its not until 2008 that we “finally” caught evolution in the act! And then…only after intervention on the part of an intelligent agent! Got it! Thanks for clearing that up!

  35. “The Designer Who only uses found objects is indistinguishable from Nature.”

    If I build a house out of stones and wood, then I am indistinguishable from nature. This is one of Nakashima’s stupider comments and he is not a stupid person but he was forced to do something. He may want to rethink this particular claim. This is a desperate attempt to get out of a hole he dug for himself.

    Nakashima tries hard and it is rare when he admits a little support or understanding for the ID position but then he saw what he did and had to try and cover immediately. Anti ID people must be 100% anti and lack any sympathy or even understanding for an ID position. Thus, we have sympathy for the stupid comment. It was necessary to show he has not been corrupted.

    Way to go, Nakashima. You make the ID case every time you come here because you are smart and try the hardest but then come up with nothing. What better support for our position could we ask for.

  36. Follow up notes:

    1: Above, I suggest a read through of the online book on he controversy over Signature in the cell, here. (It will also give you a pretty good idea of the level of critiques out there.)

    2: I already corrected my error, on spotting it in JT;s cite [I really must be getting tired], and it is 7 bits per letter [I am using an assumption of basic ASCII, not extensions up to 8 or 16 bits.]

    3: Nakashima-san, UV disintegrates complex, energetically unfavourable molecules, overwhelmingly. Indeed, I have seen it argued that this is what keeps the beaches on certain Caribbean islands bathe-able, by killing off bacteria in the clear water. And if R/DNA molecules in pre biotic environments were strong UV absorbers, then that would translate into they were rapidly broken up, not just that hey rotated, stretched and vibrated their bonds more intensely. The Ozone shield is vital to keeping life going on earth today. My point was, there is a double challenge: reducing atmosphere [which is not credible on other grounds] no Ozone shield. Oxygen, and required paths are poisoned by oxygen, an extremely reactive species. That is what sent OOL speculators to deep sea vents and to comets etc.

    4: Similarly, I observe the chirality generation abstract to say in its first sentence: “We show how the amino acids needed on prebiotic earth in their homochiral L form can be produced by a reaction of L-alpha-methyl amino acids—that have been identified in the Murchison meteorite—with alpha-keto acids under credible prebiotic conditions.” First, the meteorite as I recall was recovered in a sheep farm, so its credibility for natural origin of L-form molecules is suspect. Since we are dealing with essentially geometry, abiotic chemical processes strongly tend to produce racemic forms, which are generally energetically equivalent. To get homo-chirality, you have to start with same, which can indeed in certain cases pick it out in a racemic context. So, the article’s premise of pre-exisitng presumably meteoric L-form amino acids to start the cascade, is suspect.

    5: Further, I see that “With copper ion a square planar complex with two of the reaction intermediates is formed, and now there is the desired L to L transformation, producing small enantioexcesses of the normal L-amino acids. We also show how these can be amplified, not by making more of the L form but by increasing its concentration in water solution.” Le Chetalier and relief of constraints is the obvious explanation, but the question arises: how does one increase concentration sans Chemists and apparati, in a real world watery matrix which will have many other cross-interfering reagents and reaction paths that on concentration will most likely eat up the relevant reagents?

    6: In short, we are back to the Shapiro-Orgel exchange on OOL scenarios, and implausible chemistry.

    7: And, we have not yet got to the issue of the spontaneous origin of a von Neumann Replicator on such chemistry, complete with codes, algorithms, data structures and storage, code readers and algorithm effectors, plus either metabolic machines to build components or reservoirs of components; all in a compass of a few microns.

    GEM of TKI

  37. Srsly? Which part of the peer reviewed scientific studies I referenced have been refuted? I look forward to reading the papers you reference.

    Exactly the sort of response one expects of persons unconcerned with reasoning properly.

  38. This is one of Nakashima’s stupider comments and he is not a stupid person but he was forced to do something.

    Exactly. DarwinDefenders aren’t stupid people … they just constantly make incredibly stupid assertions because that “logic” of attempting to protect Darwinism from critical and rational scrutiny requires it of them.

  39. That is, before the discovery of the 21st amino acid, the DNA code was believed to be a one-to-many encoding; now it is known to be a many-to-many encoding.

    Though, I did mean to write “many-to-one,” not “one-to-many.”

  40. Mr Jerry,

    If I build a house out of stones and wood, then I am indistinguishable from nature.

    If your house looks like a pile of rocks or a tree, then yes. If you’ve pushed the rocks into a circle, you’re doing at least as well as a seagull. If you’ve piled sticks and branches up around and empty space, you’re doing at least as well as a beaver. The design of these houses is distinguishable from nature. If you point me at some boulders left over from an avalanche and say “I designed it.” then I have a hard time distinguishing your work from Nature.

  41. Nakashima,

    I think I did not misunderstand your argument, however you might have misunderstood my argument. To highlight the conclusion of my argument regarding the independence of a code from the medium that contains it was stated as follows:

    @20 “The media does not “select” to be a code system on its own account. There is an intentional coder, message & decoder necessary.”

    I considered the following article on your proposed mechanism:
    Coding coenzyme handles: A hypothesis for the origin of the
    genetic code
    (ribozymes/RNA world/origin of life)
    EORS SZATHMARY*
    http://www.pnas.org/content/90/21/9916.full.pdf

    Maybe someone can inform me why this is not a just so story. Dependent on the same question begging arguments presented here.

    I still hold that there is no reason to accept the argument that the only natural occurring code is the DNA code, therefore the DNA code is a naturally occurring code. This is exactly the argument you use to distinguish between human generated code and the DNA code.

    The ID argument sounds much better and is not begging the question. Intelligence at work is the only known code generating phenomenon.

  42. KF-san,

    Thank you for a direct questioning of the science involved. I appreciate that you are willing to question and challenge the facts and results as reported.

    your 3 – What does UV do to RNA? From the above linked paper:

    RNA/DNA strongly absorb ultraviolet radiation at around 260 nm at 1 atmosphere pressure
    (Haggis, 1974; Chang, 2000) due to the 1 pi-pi * electronic excitation of the bases (Voet et al.,
    1963; Callis, 1983). Most noteworthy, these molecules are ultra-fast at converting the
    electronic excitation energy into heat through internal conversion; that is, into vibrational
    motion of the atoms of the surrounding water molecules (Pecourt et al., 2000, 2001). This non-radiative process occurs on the sub-picosecond time scale, making RNA/DNA a very efficient absorber since the molecule promptly returns to the ground state, ready to absorb another photon.

    So I agree that our intuition might be that absorbing UV would break the molecule. It seems that our intuition is wrong by not taking into account how rapidly this particular kind of chemical bond can convert a high energy photon into vibrational energy and dissipate it as heat into the surrounding water.

    (The Zinc World hypothesis also assumes that RNA tethered to the surface of ZnS can share the energy with that bulk material faster than the RNA can break apart.)

    your 4&5 – in part you say:
    how does one increase concentration sans Chemists and apparati, in a real world watery matrix which will have many other cross-interfering reagents and reaction paths that on concentration will most likely eat up the relevant reagents?

    As with the paper above, and many other OOL hypotheses, you work in the topmost microlayer, or in tidal pools (closer Moon, faster rotaton = more tidal action). There are plenty of places where evaporation can raise concentration.

    7: And, we have not yet got to the issue of the spontaneous origin of a von Neumann Replicator …

    Yes, there is so much exciting chemistry still to be discovered! It is wonderful to live in a time of such great advances.

  43. Nakashima,

    You might feel unfairly treated since your argument is actually: The DNA code is only instantiated in the living cell and therefore it is naturally occurring. Even so, it boils down to the same self-referential argument.

    Explain to me how uniqueness of the code bearing can possibly convince anyone of its purely natural origin?

  44. Sorry I missed a word, #42 should end with:

    Explain to me how can the uniqueness of the code bearing MEDIUM possibly convince anyone of its purely natural origin?

  45. Mr Mullerpr,

    Thank you for being patient with me, if I have misunderstood you.

    The article you reference is a discussion of a speculative hypothesis, as the first sentence of the abstract says. It presents no experimental results in favor of the hypothesis, only suggests that the hypothesis can be tested.

    It is important to distinguish this kind of sharing of hypotheses from the publication of experimental results which do or do not support a particular hypothesis. The paper I have referenced is a report of experimental results, and it does support the stereochemical hypothesis for some amino acids while not supporting it for other amino acids. Both positive and negative results are published.

    I’ve tried to make a distinction between a code and an instantiation of a code. I don’t think the genetic code is the only natural code possible, and I don’t think the media of amino acids and RNA triplets are the only natural media that can participate in a code.

    I do think that the only instantiation in nature of the genetic code is the association of AA and RNA.

    If I understand your position, you hold that there are at least two competing hypotheses:

    H1 – An intelligent designer composed the genetic code in the abstract, and then implemented it in organic matter as a number of interacting chemicals.

    H2 – A number of chemicals slowly assumed more and more definite associations over time, with more elaborate mechanisms to enforce that definiteness.

    Is that correct?

  46. Mr Mullerpr,

    Explain to me how can the uniqueness of the code bearing MEDIUM possibly convince anyone of its purely natural origin?

    It doesn’t. Whereas multiple independent instantiations might be a warrant that a code is an intelligent design, lack of evidence for one hypothesis is not positive evidence for another hypothesis.

  47. Nakashima,

    There is an old saying,

    “It is a good thing to follow the first law of holes; if you are in one, stop digging.”

    Quit digging and get out of the hole and move on. You are looking foolish and as I said, you are a smart person.

  48. Well Jerry, I don’t think its possible for Nak to stop digging holes. I believe he lives in a self imposed box,

    http://www.crystalinks.com/outsidebox.jpg

    A self imposed box where it is impossible for him to even consider the possibility of not digging holes (to think outside the box):

    Dig it – From the Disney Movie “Holes” – song
    http://www.youtube.com/watch?v=ybjSSExktzI

  49. Actually Nak, I think self imposed prison is a better analogy:

    Creed – My Own Prison
    http://www.youtube.com/watch?v=_YoUuwDZuW0

  50. Mr Jerry,

    You are very kind, thank you.

    Actually this is a demonstration of quantum tunneling. By Heisenberg’s Uncertainty Principle, the more certain you are that I am in the hole, the faster I’ll be out of it! ;)

  51. Nakashima in #40

    If your house looks like a pile of rocks or a tree, then yes. If you’ve pushed the rocks into a circle, you’re doing at least as well as a seagull. If you’ve piled sticks and branches up around and empty space, you’re doing at least as well as a beaver. The design of these houses is distinguishable from nature. If you point me at some boulders left over from an avalanche and say “I designed it.” then I have a hard time distinguishing your work from Nature.,

    With respect to this response, one wonders exactly what features, then, would indicate intelligent design as opposed to the blind, purposeless forces of nature. Would, say, an irreducibly complex biological system also be “indistinguishable” from nature? You’ve practically tripped over one of the major foci of ID: distinguishing between undirected, natural causes and intelligent causes. From the example list you provided above, perhaps you might indicate precisely what characteristics would tell you that something is not the result of undirected, natural cause.

  52. Mr DonaldM,

    You’re quite right, this is the foci of ID. In the spirit of the Rev Paley, if I go walking through the forest and happen upon a log cabin, I will conclude design, while if I happen upon a deadfall, I will conclude nature acting by chance. Suddenly, a woodsmen appears out of the forest and claims to have designed the deadfall. What is the evidence he can bring that would convince me?

    Would, say, an irreducibly complex biological system also be “indistinguishable” from nature? You’ve practically tripped over one of the major foci of ID: distinguishing between undirected, natural causes and intelligent causes.

    As we can see from the fact that you dropped it from your second sentence, the phrase “irreducibly complex” adds nothing to the issue. As an attempt at problemizing complexity, it has failed.

    From the example list you provided above, perhaps you might indicate precisely what characteristics would tell you that something is not the result of undirected, natural cause.

    Even if I didn’t see a beaver make it, the marks of the beaver’s teeth on the sticks would be one strong clue. Craig Venter’s synthetic DNA strand also contains makers marks.

    BTW, since we have been discussing the genetic code earlier, I see that according to Wikipedia there are 23 versions of the genetic code already documented!

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