Wednesday, March 13, 2013

What's Wrong with This Statement?

Read the following statement from the Wikipedia article on the Genetic Code.
... the genetic code used by all known forms of life is nearly universal with few minor variations. This suggests that a single evolutionary history underlies the origin of the genetic code.
What wrong with this statement? Cornelius Hunter says that the statement "... is false—at least from a scientific perspective" [Here is Why the DNA Code is a Problem]. Can you guess why this IDiot would make such a claim?

In contrast, an anonymous source at Uncommon Descent asks, "Does the Genetic Code Bear A Signature of Intelligence?." He/she posts the following abstract ...
It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but stronger in noise immunity is the genetic code. The code is a flexible mapping between codons and amino acids, and this flexibility allows modifying the code artificially. But once fixed, the code might stay unchanged over cosmological timescales; in fact, it is the most durable construct known. Therefore it represents an exceptionally reliable storage for an intelligent signature, if that conforms to biological and thermodynamic requirements. As the actual scenario for the origin of terrestrial life is far from being settled, the proposal that it might have been seeded intentionally cannot be ruled out. A statistically strong intelligent-like “signal” in the genetic code is then a testable consequence of such scenario. Here we show that the terrestrial code displays a thorough precision-type orderliness matching the criteria to be considered an informational signal. Simple arrangements of the code reveal an ensemble of arithmetical and ideographical patterns of the same symbolic language. Accurate and systematic, these underlying patterns appear as a product of precision logic and nontrivial computing rather than of stochastic processes (the null hypothesis that they are due to chance coupled with presumable evolutionary pathways is rejected with P-value < 10–13). The patterns display readily recognizable hallmarks of artificiality, among which are the symbol of zero, the privileged decimal syntax and semantical symmetries. Besides, extraction of the signal involves logically straightforward but abstract operations, making the patterns essentially irreducible to natural origin. Plausible ways of embedding the signal into the code and possible interpretation of its content are discussed. Overall, while the code is nearly optimized biologically, its limited capacity is used extremely efficiently to pass non-biological information.

According to Uncommon Descent, the article is written by two scientists. They turn out to be two mathematicians from the Republic of Kazakhstan [The “Wow! signal” of the terrestrial genetic code].

Can you guess why the IDiots would believe such a ridiculous claim?

I wonder if Cornelius Hunter thinks this is science?


30 comments :

  1. Kazakhstan? The darkies will be trying to do science next!

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    1. yeah, I know...not a trace of snobbism in writing that they 'turn out' to be two mathematicians from the Republic of Kazakhstan, is there?
      If Larry wanted only to make the point that mathematicians are not scientists (which I think many mathematicians would argue against) the country where they do their work wouldn't really make much difference, would it?
      Besides, their names, Vladimir shCherbak and Maxim Makukov seem like traditional Russian names to me. So the assertion that they are 'from' Kazakhstan just seems like yet another in Larry's history of jumps to conclusions.

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    2. Here's a fairly balanced essay addressing the question as to whether or not mathematicians are scientists;
      http://andrewlias.blogspot.jp/2004/08/is-mathematics-science.html

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    3. They're not scientists. End of story.

      "A mathematician may say anything he pleases, but a physicist must be at least partially sane." -- Josiah Willard Gibbs

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    4. @Andy

      Don't worry Andy, they'll be scientists again soon enough. As soon as someone goes on one of their rambling 'science is the only thing of value in the whole wide world' diatribes.

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  2. "Besides, extraction of the signal involves logically straightforward but abstract operations, making the patterns essentially irreducible to natural origin."

    What? What is a "logically straightforward but abstract operation", and why isn't it reducible to a natural origin?

    Or how about this gold-nugget: "Accurate and systematic, these underlying patterns appear as a product of precision logic and nontrivial computing"

    Accurate and systematic? Praise jesus. And precision logic too? Holy lord. NONtrivial computing? As opposed to trivial.. guessing? I'm sure this all sounds really impressive to the usual IDiot fans.

    Looks to me like apologetics camouflaged as science with a coat of technobabble. No doubt one of their acolytes will be here soon to tell me I don't understand what it means, the quintessential refuge of charlatans trying to hide their bullshit in mindless gobbledygook.

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  3. It sounds very similar in style to the self-citing chain of "publications" by notorious YEC and "origin of life foundation" David Abel. It would be wholly unsurprising if he's an anonymous guest-poster on UD.

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    1. Here's one of his more recent technobabbling papers:
      http://www.tbiomed.com/content/9/1/8

      Try and go back through his self-refences and see the mountains of wharblegarble the man produces.

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  4. Don't they mean the Wawawewow signal?

    If they can't accurately explain what a p-value means, why should we believe the rest? P-values are the percentage of times that you will draw 'this sample' from a larger population if that population is 'random', not the 'likelyhood that this pattern is random'.

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  5. Cornelius is an imbecile of incalculable magnitude.

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  6. The point in all this is that its the first and best conclusion the creator of physics would use the same principals and laws in creating biology and so DNA should be along the same lines.
    The DNA being , at root, the same for all speaks loudly for a creator.
    If it evolved it would not be so universal!
    It is a common foundation expression and and merely represents biology as a parts department.
    So like parts equals like DNA.
    Its not a trail of biological heritage.
    Any ideas that it is ARE anyways just speculation and not genetic scientific investigation.
    Just lines of reasoning.

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  7. Byers, it's not the DNA that is 'the same', it's the coding, the way it's read, that is being considered.
    Are you saying that the fact that the code is conserved means it was designed? What about the fact that it is a little variable? How would the code look if it was not naturally produced, why wouldn't it be conserved?

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    1. I'm only saying that a creator WOULD make the foundations and laws of genetics just as he did in physics.
      It would predicted the DNA code would be the same at its basic core.
      How its read etc is not my knowledge circle.
      Evolutionism tries to say DNA is the evidence for common descent and I'm just bringing up it is just a line of reasoning to see like DNA as meaning like origin.
      It would be that way also from a common blueprint and unrelated to speculations about common descent.
      Its just a parts score and not a trail.
      otherwise I can't get too deep into this.

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  8. Larry: Cornelius Hunter says that the statement "... is false—at least from a scientific perspective" [Here is Why the DNA Code is a Problem]. Can you guess why this IDiot would make such a claim?

    I can guess, without clicking the link. Dr. Cornelius will say it is based on "metaphysical presuppositions", which is ID cultic bafflegab for "I'm invoking an ad hominem attack against damned atheists."

    The use of "metaphysical presuppositions" as a trope for rehabilitating the ad hominem attack, an approach popularized by pig-ignorant lawyer Phillip Johnson, was the ultimate tu quoque, in which religious fanatics with no knowledge of science basically say to the world's scientists, "Oh yeah? I'm religious? Well, you're even MORE religious, Nyah Nyah!"

    See also: our friend Rapey, who makes this very accusation on this very blog 50-100 times a day, every day. He'll be along in a moment.

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  9. Ah, 37, prime numbers, it's biochemical Kabbalah.

    I wonder if the completely deranged (although he is getting tough competition recently) former, now banished, commenter Atheistoclast/Joseph Esfandiar Hannon Bozorgmehr has upped and moved to the Republic of Kazakhstan to collaborate with the two mathematicians, fresh from the heady success of getting his "The Genetic code and the Latin language" paper published.

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    1. shCherbak seems to be obsessed with the beauty and magical properties of the decimal system (which he believes is the system of the human mind and a hallmark of intelligence in general). His publications are mostly about things decimal (and divisibility by 37, and numerological mysticism in general). How he manages to smuggle such stuff past reviewers is a mystery to me (unless the journals in question are nor really peer-reviewed). I suppose the number of digits in first tetrapods was fixed as 5 so that their distant descendants could use their fingers as a portable calculator.

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  10. Xposted to Darwin's God:

    Cornelius Hunter: ... the genetic code used by all known forms of life is nearly universal with few minor variations. This suggests that a single evolutionary history underlies the origin of the genetic code.

    Larry Moran: What wrong with this statement?

    The actual history of the genetic code was very complex, and included a myriad of competing lineages. The extant code is only what survived of that epic struggle. Of course, that can be considered a single history, as long as you understand it's not a single lineage.

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    1. By the way, this represents one of many inverted pyramids of diversity in evolutionary history, such as the Cambrian Explosion. This occurs when life diversifies, experimenting with various adaptations, when filling a new niche.

      (Probably not where you were going, but anyway.)

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  11. "...the genetic code used by all known forms of life is nearly universal with few minor variations. This suggests that a single evolutionary history underlies the origin of the genetic code..."

    Last time I’ve checked, there were 24 variants of the genetic code listed at: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

    I'm not sure if that’s what you had in mind Larry, but I'm sure that you, or a couple of other clever guys on this blog will have no problem coming up with a testable theory how the genetic code has evolved, since the alternative is probably not acceptable. Not to you anyhow.

    Cheers,

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    1. You do realize that there is nothing inconsistent between "nearly universal with few minor variations" and "24 variants of the genetic code" ?

      Perhaps you may also know that it is extremely unlikely that any direct evidence for the evolution of the genetic code will ever be discovered.

      The best that could be accomplished would be to demonstrate that self replicating molecules could develop from non self replicating molecules, but this would only serve to demonstrate that this is possible but would provide no real insight into how it actually happened on planet Earth.

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    2. A theory for code evolution?

      There's been an easy to understand video on YOUTUBE of all places for over 5 years now. http://www.youtube.com/watch?v=rtmbcfb_rdc


      And that's really just one of the several different models suggested for the origin of the genetic code.

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    3. Att: Rumraket and steve oberski

      The variants are mainly the result of codon reassignment, especially stop codons (mycoplasmas). Therefore the reassignments must taken place by the disappearance of a codon from coding sequences, and then by its reappearance in a new role. This means that at the same time, a changed anticodon must have reappeared etc.

      While I am a big admirer of science, I am not a big fan of fairy tales told by evolutionists who come up with stories like that i.e. "...it had to happen like that..." I just don’t buy that. That’s all. Sorry.

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    4. I am not a big fan of fairy tales told by evolutionists who come up with stories like that i.e. "...it had to happen like that..." I just don’t buy that. That’s all. Sorry.

      I already addressed the evolution of genetic code variants in my comment, below.

      Creationists have, on countless occasions, falsely asserted that TESTABLE theories, confirmed by observation, are "fairy tales told by evolutionists who come up with stories like that i.e. "...it had to happen like that...""

      Most creationists are fucking allergic to doing a PubMed search, and make grand announcements of "just so stories" without doing a PubMed search, with zero familiarity with the literature, and what's in the literature, they lie about.

      For example, Michael Behe saying there were no detailed models of genetic evolution on the witness stand at Dover, even when confronted by 58 papers just on the evolution of the immune system.

      He simply misrepresented the literature as non-testable "just so stories", and since the judge could see he was lying, the creationists lost at Dover, with Behe's outright lies a big part of the reason cited by the judge.

      Since then there's been more research into molecular evolution, for example, Joe Thornton's work on resurrecting and testing ancestral gene sequences. Behe simply dismissed Thornton's work on step-by-step evolution as "piddling", as expected.

      So here we have another IDiot calling testable theories "just so stories." Your side lost at Dover with that argument-- even non-scientists can see you're either lying or ignorant.

      No IDiot in any lab has ever observed 40,000 generations of E. coli waiting for a genetic change to be caused by an invisible, intangible spook. IDiots all act like their Intelligent Designer is dead or retired.

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    5. When you stop foaming, just send me the link to the study that observed the supernatural event of codone caputre in action because, I can write novels too. I just have a hard time believing in this shit. You can believe all you want but you seem to miss the reality of the shit you believe. I'm not surprised. There are a lot of people who want to belive in what they want to believe. I'm not surprised.

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    6. http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0040127

      Abascal F, Posada D, Knight RD, Zardoya R (2006) Parallel Evolution of the Genetic Code in Arthropod Mitochondrial Genomes. PLoS Biol 4(5): e127. doi:10.1371/journal.pbio.0040127

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    7. There you go Dominic,

      together we've delivered at least four references on testable theories of how the genetic code evolved.

      Perhaps you can cite a paper describing a testable theory on how the genetic code appeared magically.

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    8. Dominic,

      The variants are mainly the result of codon reassignment, especially stop codons (mycoplasmas). Therefore the reassignments must taken place by the disappearance of a codon from coding sequences, and then by its reappearance in a new role. This means that at the same time, a changed anticodon must have reappeared etc.

      Add mitochondria to those reassigned stop codons. Now, take a look and these have smallish genomes. If a stop codon gets a tRNA, which can happen by a single mutation, then, for most organism with large genomes, could be catastrophic. Tons of proteins would be longer. For an organelle or for an organism with a smallish genome it is a few proteins that become longer. Might not be such a big deal, and that's it. Presto. New genetic code variant. From that point on, mutations that put that codon inside a coding sequence would be tolerated because now it is no longer a stop, but a codon. If the introduced amino-acid is compatible with the structure, then the new codon starts being used more and more.

      Besides the smallish genomes, also take into account that codons and amino-acids are not equally abundant, and you will start to understand that the evolution of these code variants from a standard genetic code is not far-fetched at all.

      Be as skeptical as you want. Just learn that not everything has to be perfect for an organism to survive, which allows for a lot in evolutionary terms.

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    9. (Of course, to a scientist it is not enough that we can easily understand why these changes could have happened. Look at the example Diogenes wrote about below. Scientists have made many further analyses to try and see if there's evidence about how these things have happened. And they have found such evidence.)

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  12. Nikel: I'm sure that you, or a couple of other clever guys on this blog will have no problem coming up with a testable theory how the genetic code has evolved, since the alternative is probably not acceptable

    WHAT alternative theory? "It happened by magic" is not an alternative theory. Theories must make testable predictions. Nikel's belief, "It happened by magic" is an allegation of cause, not a theory. "It happened by magic" accommodates all data, predicting nothing.

    the alternative is probably not acceptable. Not to you anyhow.

    You are right as far as the alternative hypothesis (not theory) is not acceptable to us because we're scientists and the scientific method requires that theories make testable predictions.

    Anyway, Nikel wants some testable work on the evolution of variants of the genetic code.

    He could have searched PubMed, but IDiots are fucking allergic to literature searches.

    This is from Prof. David Levin, regarding specifically evolution of variants of the genetic code in yeast. "A Portugese molecular biologist named Manuel Santos has done the best work on the evolution of the genetic code in yeast. The links below are to literature reviews he has written. The first gives a good overview (not too detailed).

    http://www.ncbi.nlm.nih.gov/pubmed/16498697

    http://www.ncbi.nlm.nih.gov/pubmed/19941859

    In general, the way codon reassignment works is that it starts with a mutant tRNA that puts in the wrong amino acid at a particular codon. In the case of Candida species, this was a serine tRNA that mutated to recognize the CUG (leucine) codon. This was not a lethal event because the normal leucine tRNA was still present. It just created an ambiguity whereby sometimes a Ser was put into a protein where a Leu should have been. It's important to note that some of the protein would have the normal Leu in that position. This is important, because this is not like mutating every CUG Leu codon so that it reads as a Ser. The ambiguity results in some normal and some abnormal versions of every protein.

    This strain would likely have been at a slight selective disadvantage. The next step was to start mutating CUG codons to others that still unambiguously encode Leu (UUG, UUA, CUU, CUA, or CUC). Note that a CUG can be mutated to any of these Leu codons (except UUA) by a single change. Remarkably, there is strong evidence for such codon reassignment. Based on genomic comparisons, it appears that only 2% of the expected 30,000 CUG codons were retained in Candida. This is clear evidence for a historical selection against CUG codons in the evolution of Candida species.

    The final step was mutational loss of the original CUG Leu tRNA to eliminate the ambiguity. The evidence for this is that in certain Candida species, the ambiguity remains because the original CUG Leu tRNA is still present. This ambiguity appears to have arisen about 272 MYA and has been driving codon reassignment for much of that time."

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  13. I hate when even scientists refer to genes as "information" and DNA as a "code". These are analogies useful for helping laymen grasp what these things do and represent in human terms, but they're just analogies. The problem is that creationists seize on them as literal in all the same ways they typically don't want their Bible taken as literal, and run with them through the fog to their supposed goal line of "therefore, Jesus is Lord".

    Information "informs". That's a process that occurs between minds. There are no minds involved in what DNA does (not evidentially, anyway; if God is using DNA to tell little protein fairies which atoms to squish together, that needs to be established). I'm led to understand that all DNA actually is is four chemicals with a particular affinity for one another that, when arranged in accord with their chemical properties, form a catalytic acid whose shape subsequently determines the shape of various proteins. Calling that "information" is like calling a hole "information" for forming a puddle. It "informs" no one, nor is anyone "informing" anyone else by dint of the shape of the hole... though you could CALL it "information" for shaping a puddle by metaphor if it's that important enough to you. But it's still only a metaphor.

    We, as human beings, can take facts about the world around us and USE them as information... but they are not intrinsically information, they do not "inform", until we choose to do so and promote them as such. That oxygen has eight protons is a natural fact; it becomes knowledge when that a mind becomes aware of that fact, and subsequently becomes information when I relate it to you, or you to me, as conscious agents capable of informing and being informed. But not before.

    I wish real scientists would stop feeding the trolls this way. I really do.

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