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

Comments

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!Nakashima_{May 23, 2010
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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.DonaldM_{May 22, 2010
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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! ;)Nakashima_{May 20, 2010
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Actually Nak, I think self imposed prison is a better analogy: Creed - My Own Prison http://www.youtube.com/watch?v=_YoUuwDZuW0bornagain77_{May 20, 2010
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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=ybjSSExktzIbornagain77_{May 20, 2010
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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.jerry_{May 20, 2010
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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.Nakashima_{May 20, 2010
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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?Nakashima_{May 20, 2010
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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?mullerpr_{May 20, 2010
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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?mullerpr_{May 20, 2010
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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.Nakashima_{May 20, 2010
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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.mullerpr_{May 20, 2010
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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.Nakashima_{May 20, 2010
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"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."Ilion_{May 20, 2010
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"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.Ilion_{May 20, 2010
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"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.Ilion_{May 20, 2010
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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 TKIkairosfocus_{May 20, 2010
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"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.jerry_{May 20, 2010
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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!DonaldM_{May 20, 2010
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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.Nakashima_{May 20, 2010
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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.Nakashima_{May 20, 2010
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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.mullerpr_{May 20, 2010
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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.Nakashima_{May 20, 2010
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... 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."]Ilion_{May 20, 2010
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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.Ilion_{May 20, 2010
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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)F2XL_{May 19, 2010
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@kairosfocus Thanks so much for clearing it up. :)above_{May 19, 2010
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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.Nakashima_{May 19, 2010
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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.Nakashima_{May 19, 2010
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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.Nakashima_{May 19, 2010
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