Intelligent Design

Evolution Professor: DNA Code Indicates Common Descent Because … Why?

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In my previous post we saw that evolutionist Jerry Coyne claimed that “Darwin showed that ‘design-like’ features could arise from a purely naturalistic process.” That whopper was not even thinly disguised. What is particularly striking about Coyne’s lie is that the science ever since Darwin has not demonstrated this either. It is not as though Coyne was merely confusing something Darwin showed with something that was discovered after Darwin. We are nowhere remotely close to showing that “design-like” features can arise from a purely naturalistic process. Is it possible? Sure, anything is possible. But Coyne wasn’t referring to theoretical possibilities. Unfortunately it turns out this was not simply a rare fib from the University of Chicago evolutionist. In another post from the same day Coyneinformed his readers that the universal genetic code indicates common descent from a single ancestor:  Read more

44 Replies to “Evolution Professor: DNA Code Indicates Common Descent Because … Why?

  1. 1
    Mung says:

    It is the near-universality of this code … that gives us confidence that modern life traces back to a single ancestor. If there was more than one origin of life, and its descendants independently developed the DNA—>protein system, it would be very unlikely that all modern species would have the same code.

    Coyne forgot to use the obligatory scare quotes around “code.”

    Sheesh. It’s not like it’s really a code.

  2. 2
    Mung says:

    How is it that educated evolutionists can believe in a “warm little pond” from which life emerged but then can also hold that only one living entity emerged from that pond and everything else descended from that one?

  3. 3
    ppolish says:

    I have a tough time with Coyne’s writing style. Don’t think I have ever made it more than a quarter of the way through any of his blog posts. I stopped trying,

    But does Jerry say One Pond in One Place at One Time? That would seem awfully silly.

  4. 4
    Mung says:

    Evolutionist (aka Pedant):

    Nobody is claiming that life could not have evolved more than once.

    Great!

    Then why does Coyne (amongst others) claim that the genetic code is evidence for universal common ancestry?

    Perhaps different self-replicating but non-living molecules were present in Darwin’s warm little pond but they all for some reason shared the same code and extant life all came from this pond but did not all share the same common ancestor.

    Perhaps there is reason to believe that the code is a matter of natural law and not just a historical accident (aka miracle). If pressed, I bet even an evolutionist could think of one.

    But evolutionists don’t know. And Darwin forbid that they actually produce some probability calculations according to which their claims appear not just plausible but likely.

  5. 5
    Mung says:

    “But does Jerry say One Pond in One Place at One Time? That would seem awfully silly.”

    Of course not. That would be to conflate the evolution of life with the origin of life!

  6. 6
    Eric Anderson says:

    The real key here — as hinted at by a couple of other posters — is that evolutionists are essentially running a probability analysis when they proclaim that all life is related.

    The thought process is that it is just too improbable for the genetic code to have arisen more than once by chance. Indeed, you would have to be a gullible fool to believe so. As a result, evolutionist are essentially engaging in an explanatory-filter-based preliminary design analysis, but instead of admitting that chance is also unable to produce such a system, they are forced — beyond all rationality — to rely on chance. At least once.

    Unfortunately, they are unwilling to apply the same strict and careful thinking to the question of whether the code arose even once by chance. The possibility that it didn’t is ruled out of bounds from the outset by a priori philosophical assumptions that the code must have arisen by chance at least once — because the alternative is unthinkable.

    Furthermore, the evolutionist’s careful analysis about the probabilities is regularly jettisoned when they consider all of the examples of alleged convergent evolution and when they consider the fact that the genetic code is not the only code operating in living systems.

    The whole evolutionary mythology is a crapshoot: whatever we see in the living world must have been able to arise by purely natural mechanisms; what we don’t see either couldn’t or just by happenstance didn’t.

    This is Grand Evolutionary Explanation for all things:

    Stuff Happens.

  7. 7
    vividbleau says:

    Using this logic one must conclude that all of English literature has one common author after all they all contain the same letters found in the English alphabet what more proof do you need????
    Berlinski wrote something a few years back that was so funny I was in tears. Something to do with how the author of Don Quixote is responsible for all of English literature. I hope someone knows what piece I am referring to and post it here. Absolutely hilarious.
    Vivid

  8. 8
    Mung says:

    Eric:

    The real key here — as hinted at by a couple of other posters — is that evolutionists are essentially running a probability analysis when they proclaim that all life is related.

    BINGO!

    But then they fail to share that analysis.

    So it cannot be tested.

    And it is not scientific.

  9. 9
    vividbleau says:

    Found it. From Deniable Darwin.

    On the Derivation of Ulysses from Don Quixote

    I imagine this story being told to me by Jorge Luis Borges one evening in a Buenos Aires cafe.

    His voice dry and infinitely ironic, the aging, nearly blind literary master observes that “the Ulysses,” mistakenly attributed to the Irishman James Joyce, is in fact derived from “the Quixote.”

    I raise my eyebrows.

    Borges pauses to sip discreetly at the bitter coffee our waiter has placed in front of him, guiding his hands to the saucer.

    “The details of the remarkable series of events in question may be found at the University of Leiden,” he says. “They were conveyed to me by the Freemason Alejandro Ferri in Montevideo.”

    Borges wipes his thin lips with a linen handkerchief that he has withdrawn from his breast pocket.

    “As you know,” he continues, “the original handwritten text of the Quixote was given to an order of French Cistercians in the autumn of 1576.”

    I hold up my hand to signify to our waiter that no further service is needed.

    “Curiously enough, for none of the brothers could read Spanish, the Order was charged by the Papal Nuncio, Hoyo dos Monterrey (a man of great refinement and implacable will), with the responsibility for copying the Quixote, the printing press having then gained no currency in the wilderness of what is now known as the department of Auvergne. Unable to speak or read Spanish, a language they not unreasonably detested, the brothers copied the Quixote over and over again, re-creating the text but, of course, compromising it as well, and so inadvertently discovering the true nature of authorship. Thus they created Fernando Lor’s Los Hombres d’Estado in 1585 by means of a singular series of copying errors, and then in 1654 Juan Luis Samorza’s remarkable epistolary novel Por Favor by the same means, and then in 1685, the errors having accumulated sufficiently to change Spanish into French, Moliere’s Le Bourgeois Gentilhomme, their copying continuous and indefatigable, the work handed down from generation to generation as a sacred but secret trust, so that in time the brothers of the monastery, known only to members of the Bourbon house and, rumor has it, the Englishman and psychic Conan Doyle, copied into creation Stendhal’s The Red and the Black and Flaubert’s Madame Bovary, and then as a result of a particularly significant series of errors, in which French changed into Russian, Tolstoy’s The Death of Ivan Ilyich and Anna Karenina. Late in the last decade of the 19th century there suddenly emerged, in English, Oscar Wilde’s The Importance of Being Earnest, and then the brothers, their numbers reduced by an infectious disease of mysterious origin, finally copied the Ulysses into creation in 1902, the manuscript lying neglected for almost thirteen years and then mysteriously making its way to Paris in 1915, just months before the British attack on the Somme, a circumstance whose significance remains to be determined.”

    I sit there, amazed at what Borges has recounted. “Is it your understanding, then,” I ask, “that every novel in the West was created in this way?”

    “Of course,” replies Borges imperturbably. Then he adds: “Although every novel is derived directly from another novel, there is really only one novel, the Quixote.”

  10. 10
    Eric Anderson says:

    Let me put it this way:

    Skeptic: How do you know that all life is related?

    Coyne: Well, all life shares a similar genetic code.

    Skeptic: Couldn’t such a code have arisen more than once by chance?

    Coyne: Preposterous! Just look at what we’re dealing with — the physical structure of DNA, the semiotic system that translates one piece of information into another, and on and on. It is obvious that such a system would never arise more than once by chance.

    Skeptic: But if it is so unlikely to have arisen twice by chance, how can we be so sure that it ever arose even once by chance?

    Coyne: Well, we know it arose once by chance because life exists. So obviously it happened at least once, thank goodness, or we wouldn’t be here to talk about it.

    Skeptic: My understanding is that there are other options than just pure chance. For instance, isn’t it possible that the genetic code could have been purposely designed? Wouldn’t that be more consistent than saying that the code couldn’t possibly have arisen twice, but that it could arise once?

    Coyne: What are you a creationist!? If you want to believe in Bible stories, that’s your business. I’m dealing with real science.

    Skeptic: I didn’t say anything about the Bible or creationism. I’m just asking whether design might be a possibility and whether it makes sense to say that chance can’t create life twice, but it could create it once. What is the basis for the distinction?

    Coyne: Well, we’re here aren’t we? Obviously chance was able to create life once.

    Skeptic: No, it isn’t obvious. You’re just assuming it. The same probabilities that you applied to determine whether it could happen twice should also be applied to whether it could happen once.

    Coyne: I’m not debating this anymore. You obviously have a religious agenda. Science only deals with natural causes. You should just accept that life came about by purely natural causes, and if you can’t deal with that because you aren’t as Bright as I am, that is your problem. I’m not going to waste my time debating the issue with creationists.

    . . .

    Objective Outside Observer: What is with that Coyne guy? He is allowing his metaphysics to override his physics.

  11. 11
    Eric Anderson says:

    vividbleau:

    Thanks for the reminder. Everyone who has any interest at all in the evolution debate owes it to himself to read, and occasionally re-read, The Deniable Darwin.

    Regarding the section you cited, my favorite part is: “. . . and then as a result of a particularly significant series of errors, in which French changed into Russian, Tolstoy’s The Death of Ivan Ilyich and Anna Karenina.”

    That is right down the lines of what we are being asked to believe happened with DNA over the aeons by our materialistic friends. It is so preposterous that I am often left without words to describe the pure, unadulterated, bald-faced outrageousness of the materialist creation myth.

  12. 12
    Querius says:

    Eric Anderson,

    Love it! 🙂

    -Q

  13. 13
    vividbleau says:

    Eric,

    Yeh first Spanish evolves into French, then French into Russian and then

    “Late in the last decade of the 19th century there SUDDENDLY emerged, in English, Oscar Wilde’s The Importance of Being Earnest, ”

    Man does Berlinski nail it in away that demonstrtatrs the absurdity of it all. So funny

    Vivid

  14. 14
    Moose Dr says:

    Common descent or common design, there is something unquestionably common about all DNA. All life use the same translation logic to convert from DNA to protein. Some of the most complex genes are universal to all life, and very usually ultra-conserved.

    There is unquestionably a unity in the DNA. All DNA based data comes from the same, one, root. This is the best case we have to prove that the designer is singular, not plural. (Or as I always note, it could be a group acting together as a single unit.)

  15. 15
    HeKS says:

    @Eric Anderson #6

    You’ve hit at least one of the nails right on the head. I’m working on an article at the moment about falsifiability as it relates to ID vs Evolution and the methods that have been proposed to falsify evolution. The issue of the single genetic code is one of the things I’m addressing, including whether multiple genetic codes would actually falsify evolution, or even common descent in a non-trivial sense. SPOILER ALERT: I conclude that it wouldn’t.

  16. 16
    Sebestyen says:

    Didn’t they find out that it is exactly not the case that there’s only one genetic code but instead several ones that differ in how some of the condons translate?

    Here’s a list of 25 recognized codes: NCBI Taxonomy

    Examples:

    1. In vertebrates, AGA and AGG are termination codons, but in invertebrates they both code for Serine.

    2. In yeast, CTx codons code for Leucine, but in vertebrates and invertebrates all four code for Threonine. Also, AGA and AGG are neither termination codons nor code for Serine but code for Arginine instead.

    3. In bacteria, ATA codes for Isoleucine, TGA is a termination codon and AGA/AGG code for Arginine while in vertebrates ATA codes for Methionine, TGG for Tryptophane and AGA/AGG are termination codons.

    Apparently there are also some more differences within one code depending on the species.

    Sebestyen

  17. 17
    Sebestyen says:

    3. In bacteria, ATA codes for Isoleucine, TGA is a termination codon and AGA/AGG code for Arginine while in vertebrates ATA codes for Methionine, TGG for Tryptophane and AGA/AGG are termination codons.

    Correction:

    3. In bacteria, ATA codes for Isoleucine, TGA is a termination codon and AGA/AGG code for Arginine while in vertebrates ATA codes for Methionine, TGA for Tryptophane and AGA/AGG are termination codons.

    Sebestyen

  18. 18
    kairosfocus says:

    Seb, and don’t forget the Mitochondria code! KF

  19. 19
    Axel says:

    Eric Anderson @ #10

    Jerry Coyne is a simple-minded chap, Eric. I believe he’s convinced his hairy arms are a vindication of Darwinism.

    I started this off as a joke, but on reflection, it seems to be how they think.

  20. 20
    Axel says:

    Save you looking it up in #10, the operative line is:

    ‘Objective Outside Observer: What is with that Coyne guy? He is allowing his metaphysics to override his physics.’

    Sorry. I forgot to copy it.

  21. 21
    bornagain77 says:

    a brief comment as to different codes in life

    A glimpse into nature’s looking glass — to find the genetic code is reassigned: Stop codon varies widely – May 22, 2014
    Excerpt: While a few examples of organisms deviating from this canonical code had been serendipitously discovered before, these were widely thought of as very rare evolutionary oddities, absent from most places on Earth and representing a tiny fraction of species. Now, this paradigm has been challenged by the discovery of large numbers of exceptions from the canonical genetic code,,,
    Approximately 99% of all microbial species on Earth fall in this category, defying culture in the laboratory but profoundly influencing the most significant environmental processes from plant growth and health, to the carbon and other nutrient cycles on land and sea, and even climate processes.,,,
    “We were surprised to find that an unprecedented number of bacteria in the wild possess these codon reassignments, from “stop” to amino-acid encoding “sense,” up to 10 percent of the time in some environments,” said Rubin.
    Another observation the researchers made was that beyond bacteria, these reassignments were also happening in phage, viruses that attack bacterial cells.,,,
    The punch line, Rubin said, is that the dogma is wrong.
    “Phage apparently don’t really ‘care’ about the codon usage of the host.
    http://www.sciencedaily.com/re.....141422.htm

    The reason why deviating from the canonical code is so ‘unexpected’ to the Darwinian worldview is best xplained by Dawkins himself:

    Venter vs. Dawkins on the Tree of Life – and Another Dawkins Whopper – March 2011
    Excerpt:,,, But first, let’s look at the reason Dawkins gives for why the code must be universal:
    “The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation…this would spell disaster.” (2009, p. 409-10)
    http://www.evolutionnews.org/2.....44681.html

    Of humorous note is this video from a few years before in which Venter almost made Dawkins have a cow when Venter denied that common descent was as well supported as Dawkins thought it was:

    Dr. Craig Venter Denies Common Descent in front of Richard Dawkins! – video
    Quote: “I think the tree of life is an artifact of some early scientific studies that aren’t really holding up.,, So there is not a tree of life. In fact from our deep sequencing of organisms in the ocean, out of, now we have about 60 million different unique gene sets, we found 12 that look like a very, very deep branching—perhaps fourth domain of life. ”
    – Dr. Craig Venter, American Biologist involved in sequencing the human genome
    http://www.youtube.com/watch?v=MXrYhINutuI

    Moreover, to make matters much worse for Darwinists, ‘alternative splicing codes’ are found to be species specific

    Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012
    Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,,
    A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species.
    On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,,
    http://www.the-scientist.com/?.....plicing%2F

    Here is how the ‘species specific’ alternative splicing codes are deciphered

    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

    This finding is far more devastating for Darwinism than most people realize. The reason why finding drastically different alternative splicing codes/schemes between species would be, to use Richard Dawkins term, ‘instantly catastrophic’ for neo-Darwinism is because of what is properly termed ‘Shannon Channel Capacity’:

    “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

    Shannon Information – Channel Capacity – Perry Marshall – video
    https://vimeo.com/106430965

    The bottom line is that if any code, such as the alternative splicing code, is ‘randomly changed’ in part, it throws the entire code out of whack and will be ‘instantly catastrophic’, to use Richard Dawkins most appropriate term, thus rendering gradual change to the code impossible. In other words, the entire code must be implemented ‘top down’, all at once, when the species is created and the code cannot be arrived at gradually.!

    Moreover, alternative splicing codes are part of the developmental gene regulatory network (dGRN). Yet mutations in the dGRN are shown to be ‘always catastrophically bad’

    A Listener’s Guide to the Meyer-Marshall Debate: Focus on the Origin of Information Question -Casey Luskin – December 4, 2013
    Excerpt: “There is always an observable consequence if a dGRN (developmental gene regulatory network) subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way.” –
    Eric Davidson
    http://www.evolutionnews.org/2.....79811.html

    Stephen Meyer – Responding to Critics: Marshall, Part 2 (developmental Gene Regulatory Networks) – video
    https://www.youtube.com/watch?v=Cg8Mhn2EKvQ

    Darwin or Design? – Paul Nelson at Saddleback Church – Nov. 2012 – ontogenetic depth (excellent update) – video
    Text from one of the Saddleback slides:
    1. Animal body plans are built in each generation by a stepwise process, from the fertilized egg to the many cells of the adult. The earliest stages in this process determine what follows.
    2. Thus, to change — that is, to evolve — any body plan, mutations expressed early in development must occur, be viable, and be stably transmitted to offspring.
    3. But such early-acting mutations of global effect are those least likely to be tolerated by the embryo.
    Losses of structures are the only exception to this otherwise universal generalization about animal development and evolution. Many species will tolerate phenotypic losses if their local (environmental) circumstances are favorable. Hence island or cave fauna often lose (for instance) wings or eyes.
    http://www.saddleback.com/mc/m/7ece8/

    ,,, If neo-Darwinism were a normal science, instead of being primarily a cornerstone of the atheistic religion which is impervious to empirical falsification, these findings, along with many other lines of evidence (J. Shapiro etc,,), would be more than enough to overturn neo-Darwinism as a hypothesis of serious consideration in science.

  22. 22
    DavidD says:

    Pedant:

    “Nobody is claiming that life could not have evolved more than once.”

    Mung: “Great!

    Then why does Coyne (amongst others) claim that the genetic code is evidence for universal common ancestry?”

    Uncle Walley Walt = Pedant is a sort of bitter old fart on the verge of a heart attack if you really look at his posts which angry bluster, but no substance. Walley and Coyne are committed or shackled to a religiously driven ideology and cannot give a complete explainable hypothesis for how the codes developed in the first place. So rather than any intelligent explanation, which get soap box Faith Affirmations of “It’s proof of common descent” as opposed to, “Written by the same Author & Programmer” which are both vitriol spewing Evo bad Boys consider the later blasphemous and heretical options. Walley’s retired, but Coyne is still acting Pastor at his church and has to tickle the ears of his parishioners or be booted out for not defending the faith. Hence, we’re all treated stupid one liner comments as mere appetizers with no satisfying main course do follow. And you can forget about dessert.

  23. 23
    the bystander says:

    From Coyne’s Guest post:

    The strict universality of the code was not a law, nor even a requirement. The only requirement is that any divergence from this assumption can be explained within the framework of evolution, and through testable hypotheses about the history of organisms. This has been amply met.

    Amply met? Will someone explain how is that claim valid ?

  24. 24
    Lesia says:

    It’s always been a mystery to me how evolutionists calculate their probabilities and certainly there’s bias present in their thinking. When two spieces are genetically close we say they are related (like us and chimps). Why? Of course due to low probabilities of things being the other way round (the same sequences couldn’t’ve arisen twice independently). Evolutionists used this argumentation in, for instance, Kitzmiller vs. Dover (pseudogenes) – same mistakes won’t happen twice! But then again sometimes species can share homologous sequences in their genomes and not be closely related (like dolphins and bats) and we explain this by introducing the so-called convergent evolution. Why not come out and say, hey, we share the same genes with monkeys, but that’s due to convergence, not common ancestry! If an improbable and even impossible (convergent evolution) happened somewhere according to their storytelling once (and even one example is enough to invalidate the law), how on earth do they distinguish between these two cases (convergent evolution and common ancestry)?

  25. 25
    Lesia says:

    Eric Anderson @10 Yes, that’s how it is!

  26. 26
    bornagain77 says:

    A few more notes on codes. The genetic code, despite its inability accidentally originate through material processes,,,

    “A code system is always the result of a mental process (it requires an intelligent origin or inventor). It should be emphasized that matter as such is unable to generate any code. All experiences indicate that a thinking being voluntarily exercising his own free will, cognition, and creativity, is required. ,,,there is no known law of nature and no known sequence of events which can cause information to originate by itself in matter.
    Werner Gitt 1997 In The Beginning Was Information pp. 64-67, 79, 107.”
    (The retired Dr Gitt was a director and professor at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt, Braunschweig), the Head of the Department of Information Technology.)

    ,,,and despite the genetic code’s inability to evolve into a more complex code once it is in place,,

    “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

    Shannon Information – Channel Capacity – Perry Marshall – video
    https://vimeo.com/106430965

    Collective evolution and the genetic code – 2006:
    Excerpt: “The genetic code could well be optimized to a greater extent than anything else in biology and yet is generally regarded as the biological element least capable of evolving.”
    http://www.pnas.org/content/103/28/10696.full

    Ode to the Code – Brian Hayes – 2004
    Excerpt: “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

    The Finely Tuned Genetic Code – Jonathan M. – November 2011
    Excerpt: Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?,” that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology. –
    Eugene Koonin and Artem Novozhilov
    http://www.evolutionnews.org/2.....52611.html

    ,,, despite the genetic code’s inability to evolve, into a more complex code once the code is in place, the genetic code is still found to be opitimal,,,

    Get Out of Jail Free: Playing Games in an RNA World – September 23, 2013
    Excerpt: “The genetic code, the mapping of nucleic acid codons to amino acids via a set of tRNA and aminoacylation machinery, is near-universal and near-immutable. In addition, the code is also near-optimal in terms of error minimization,”
    http://www.evolutionnews.org/2.....77021.html

    “The genetic code’s error-minimization properties are far more dramatic than these (one in a million) results indicate. When the researchers calculated the error-minimization capacity of the one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution. Researchers estimate the existence of 10^18 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 means of 10^18 codes few, if any have an error-minimization capacity that approaches the code found universally throughout nature.”
    Fazale Rana – From page 175; ‘The Cell’s Design’

    Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement – 2009
    Excerpt: A molecular dynamics calculation of the amino acid polar requirement is used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code, an order of magnitude more than any previously known measure, effectively ruling out a vertical evolution dynamics.
    http://pre.aps.org/abstract/PRE/v79/i6/e060901

    A New Study Adds Further Depth to the Information Story – JonathanM – March 2012
    Excerpt: The conventional genetic code involves 20 different amino acids, which map to 64 different triplets of nucleotides called codons. Since there are many more codons than amino acids, this means that there is an element of redundancy because amino acids can be specified by multiple codons. As I noted before, this redundancy allows the genetic code to be exquisitely fine-tuned to minimize error. The paper explains that “redundancy in the genetic code allows the same protein to be translated at different rates.” In other words, even so-called silent substitutions (that is, those mutations that exchange a nucleotide for another without changing the amino acid specified by the codon) can have an impact on the rate of translation of the protein product.
    http://www.evolutionnews.org/2.....58051.html

    ‘Snooze Button’ On Biological Clocks Improves Cell Adaptability – Feb. 17, 2013
    Excerpt: Like many written languages, the genetic code is filled with synonyms: differently spelled “words” that have the same or very similar meanings. For a long time, biologists thought that these synonyms, called synonymous codons, were in fact interchangeable. Recently, they have realized that this is not the case and that differences in synonymous codon usage have a significant impact on cellular processes,,
    http://www.sciencedaily.com/re.....134246.htm

    ,,, and as was made clear with the ‘species specific’ alternative splicing code which was mentioned in post 21, there is more than just one code, i.e. the genetic code, in life. In fact, Dr. Johnson states,,

    “In the last ten years, at least 20 different natural information codes were discovered in life, each operating to arbitrary conventions (not determined by law or physicality). Examples include protein address codes [Ber08B], acetylation codes [Kni06], RNA codes [Fai07], metabolic codes [Bru07], cytoskeleton codes [Gim08], histone codes [Jen01], and alternative splicing codes [Bar10].
    Donald E. Johnson – Programming of Life – pg.51 – 2010

    Moreover, there are ‘codes within codes’

    Codes Within Codes: How Dual-Use Codons Challenge Statistical Methods for Inferring Natural Selection – Casey Luskin – December 20, 2013
    Excerpt: In fact, one commentator observed that on the same analysis, codons may have more than two uses: “By this logic one could coin the term “trion” by pointing out that histone binding is also independently affected by A-C-T-G letter frequencies within protein-coding stretches of DNA.”
    But this isn’t the first time that scientists have discovered multiple codes in biology. Earlier this year I discussed research that found an analog code in the DNA that helps regulate gene expression, in addition to the digital code that encodes primary protein sequence. In other cases, multiple proteins are encoded by the same gene! And then of course there’s the splicing code, which helps control how RNAs transcribed from genes are spliced together in different ways to construct different proteins (see here and here).
    It boggles the mind to think about how such “codes within codes” could evolve by random mutation and natural selection. But now it turns out that evidence of different functions for synonymous codons could threaten many standard methods used to infer selection in the first place,,,
    http://www.evolutionnews.org/2.....80381.html

  27. 27
    bornagain77 says:

    In fact the genetic code is nearly optimal for allowing additional information within protein-coding sequences ,,,

    The genetic code is nearly optimal for allowing additional information within protein-coding sequences – Shalev Itzkovitz and Uri Alon – 2006
    Excerpt: Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes…. the present findings support the view that protein-coding regions can carry abundant parallel codes.
    http://genome.cshlp.org/content/17/4/405.full

    And overlapping parallel codes in the same sequences are now being found

    Second, third, fourth… genetic codes – One spectacular case of code crowding – Edward N. Trifonov – video
    https://vimeo.com/81930637

    In the preceding video, Trifonov elucidates codes that are, simultaneously, in the same sequence, coding for DNA curvature, Chromatin Code, Amphipathic helices, and NF kappaB. In fact, at the 58:00 minute mark he states, “Reading only one message, one gets three more, practically GRATIS!”. And please note that this was just an introductory lecture in which Trifinov just covered the very basics and left many of the other codes out of the lecture. Codes which code for completely different, yet still biologically important, functions. In fact, at the 7:55 mark of the video, there are 13 codes that are listed on a powerpoint, although the writing was too small for me to read.

    Concluding powerpoint of the lecture (at the 1 hour mark):
    “Not only are there many different codes in the sequences, but they overlap, so that the same letters in a sequence may take part simultaneously in several different messages.”
    Edward N. Trifonov – 2010

    Since Darwinian evolution can’t even account for the origination of the one ‘optimal’ genetic code, it is certainly extremely difficult to imagine how unguided Darwinian processes can account for multiple overlapping codes within the same sequence,,

    DNA as Poetry: Multiple Messages in a Single Sequence – James Shapiro – 2012
    Excerpt: Another question is harder to answer: How do multiple messages come to be inscribed in a single sequence in the course of evolution? This is an evolutionary mystery, especially when the second message has a complex structure. ,,,,
    Moreover, known mechanisms for duplicating and inserting copies of a complex DNA signal at multiple locations generally disrupt coding capacity. Further, as in mammalian dual-coding regions, we do not understand how both strands evolve simultaneously to encode functional protein segments.
    At a time when we pride ourselves for being able to read DNA sequences with increasing speed, it is salutary to keep in mind that we are still far from knowing how to interpret the complex overlapping meanings contained in the genomic texts we store in our databases. DNA, like poetry, often has to be read in several ways.
    http://www.huffingtonpost.com/.....29190.html

    ‘It’s becoming extremely problematic to explain how the genome could arise and how these multiple levels of overlapping information could arise, since our best computer programmers can’t even conceive of overlapping codes. The genome dwarfs all of the computer information technology that man has developed. So I think that it is very problematic to imagine how you can achieve that through random changes in the code.,,, and there is no Junk DNA in these codes. More and more the genome looks likes a super-super set of programs.,, More and more it looks like top down design and not just bottom up chance discovery of making complex systems.’ –
    Dr. John Sanford

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – published online May 2013
    Excerpt: In the last decade, we have discovered still another aspect of the multi-dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43].,,,
    Conclusions: Our analysis confirms mathematically what would seem intuitively obvious – multiple overlapping codes within the genome must radically change our expectations regarding the rate of beneficial mutations. As the number of overlapping codes increases, the rate of potential beneficial mutation decreases exponentially, quickly approaching zero. Therefore the new evidence for ubiquitous overlapping codes in higher genomes strongly indicates that beneficial mutations should be extremely rare. This evidence combined with increasing evidence that biological systems are highly optimized, and evidence that only relatively high-impact beneficial mutations can be effectively amplified by natural selection, lead us to conclude that mutations which are both selectable and unambiguously beneficial must be vanishingly rare. This conclusion raises serious questions. How might such vanishingly rare beneficial mutations ever be sufficient for genome building? How might genetic degeneration ever be averted, given the continuous accumulation of low impact deleterious mutations?
    38. Sanford J (2008) Genetic Entropy and the Mystery of the Genome. FMS Publications, NY. Pages 131–142.
    39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432.
    40. Trifanov EN (1997) Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654.
    41. Kapranov P, et al (2005) Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997.
    42. Birney E, et al (2007) Encode Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816.
    43. Itzkovitz S, Hodis E, Sega E (2010) Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589.
    http://www.worldscientific.com.....08728_0006

    Moreover, on top of all those overlapping codes within the same DNA sequences there is also a ‘species specific’ bioelectric code, which is not reducible to DNA sequences, that is ‘jaw dropping’

    An Electric Face: A Rendering Worth a Thousand Falsifications – Cornelius Hunter – September 2011 – video
    Excerpt: The video suggests that bioelectric signals presage the morphological development of the face. It also, in an instant, gives a peak at the phenomenal processes at work in biology. As the lead researcher said, “It’s a jaw dropper.”
    https://www.youtube.com/watch?v=0VULjzX__OM

    podcast – Jonathan Wells: Is There Biological Information Outside of the DNA?, pt. 3 – Bioelectric code
    http://intelligentdesign.podom.....5_52-07_00

  28. 28
    tjguy says:

    OK, so there are various genetic codes in existence in nature, although one dominant one. Is this why some have said that maybe life evolved a couple of times on earth? I don’t have any quotes or anything, just a memory that the idea has been floated.

    Also, if the existence of multiple codes and the absence of any real ‘tree of life’ spells the doom of evolution, doesn’t it also spell the doom of common descent?

    (Unless of course, you take a ‘God of the gaps’ type of argument and add God to the mix to save the theory.)

    But my question is, if the evidence for common descent just isn’t there – as seen by the existence of multiple codes – why do we feel like we need to save it by adding God to the mix?

    Doesn’t this fit better with the creationist idea that God created various kinds and then there was a measure of evolution within each kind?

    So, yes, a certain amount of evolution can take place, but the amount of change possible is limited by the genetic information present in the original pair of created organisms.

    So instead of a ‘tree of life’, we have an orchard of life made up of small bushes.

    Here is an article that discusses this entitled: “Is the evolutionary tree turning into a creationist orchard?” and is written by Pierre Jerlström.

    http://creation.com/is-the-evolutionary-tree-changing-into-a-creationist-orchard

    And here are a few key quotes from the article:

    As a result, the once simple tree with a single trunk, rooted to a hypothetical 3.5 billion year old, ancient prokaryote, has become a tangled brier (see trees A and B in diagram), causing much frustration and discouragement.

    ‘There’s so much lateral transfer that even the concept of the tree is debatable.’ 4

    ‘It is as if we have failed at the task that Darwin set for us: delineating the unique structure of the tree of life.’5

    As the evolutionary’ picture of origins is still unclear, scientists are hoping that analysis of additional genomic sequences and molecular phylogeny will bring some new light. However, they admit that, ‘Now new hypotheses, having final forms we cannot yet guess, are called for.’11

    Comparisons of the DNA sequence data from the recently sequenced genomes[not sure when this was written, but the latest quote listed was from the year 2000 so it is probably a bit old by now], which have been determined by testable and repeatable scientific means, conflict with Darwin’s single evolutionary tree of life. As a result, polyphyly, in one sense the opposite of evolution or common ancestry, has been embraced in the form of HT(horizontal gene transfer) and a community of ancestral cells. This is not surprising, as ReMine predicted that evolutionary ideology is bound to naturalism and simply ‘accommodates’ all evidence to fit reworked evolutionary models, thus showing that it is not falsifiable and therefore not scientific according to science philosopher Carl Popper’s primary criterion.12 He even predicted that evolutionists would increasingly resort to such lateral transfer.

    If we tease apart the evolutionary brier and remove the hypothesised evolutionary HT ‘links’ between the branches, we obtain separate trees with individual trunks and roots. This is highly reminiscent of the creationist ‘orchard’, a biblical model for the origin and diversity of all life (see tree C in diagram) which was predicted by the scientific creation movement at its inception.13

    In the creationist orchard, the trunk of each tree represents an original created kind or baramin, and the branches correspond to the diversity within a kind due to (limited) speciation, as for example, seen in the dog/wolf/jackal/coyote kind.

    Like I said, it might have been written over 10 years ago, but I highly doubt the data discovered since then has done anything to change the conclusion. In fact, with all these codes listed, it seems to further confirm the conclusion!

  29. 29
    bornagain77 says:

    Talking Back to Goliath: Some Advice for Students in the Evolutionary Biology Classroom – Paul Nelson – September 30, 2014
    Excerpt: (if neo-Darwinism) is true, we should be able to find in the scientific literature the detailed explanations for the origin of complex structures and behaviors, rendered strictly in terms of random variation plus natural selection.
    Guess what? Those explanations aren’t there; they don’t exist. If anyone doubts this, he should try looking for himself. Choose any complex structure or behavior, and look in the biological literature for the step-by-step causal account where the origin of that structure (that is, its coming-to-be where it did not exist before) is explained via random variation and natural selection.
    You’ll be looking a long time. The explanations just aren’t there, and this fact is well known to evolutionary biologists who have become disenchanted with received neo-Darwinian theory. When proponents of the received theory, such as Richard Dawkins, face the task of making random variation and natural selection work, they resort to fictional entities like Dawkins’s “biomorphs” — see Chapter 3 of The Blind Watchmaker (1986) — or flawed analogies such as the “methinks it is like a weasel” search algorithm scenario. No one would have to employ these toy stories, of course, if evidence were available showing the efficacy of random variation and selection to construct novel complexity.
    “Research on selection and adaptation,” notes Mary Jane West-Eberhard, a disenchanted evolutionary theorist, “may tell us why a trait persisted and spread, but it will not tell us where a trait came from….This transformational aspect of evolutionary change has been oddly neglected in modern evolutionary biology” (2003, p. 197).,,,
    http://www.evolutionnews.org/2.....90141.html

  30. 30
    bornagain77 says:

    OT: podcast – Dr. William Dembski: Inspired by Richard Dawkins
    http://www.discovery.org/multi.....d-dawkins/

  31. 31
    Guillermoe says:

    You got this quite wrong. The fact is that the genetic code of all living organisms on Earth is written basically in the same code (RNA and DNA).

    The question is: HOW did this happen?

    One possible answer is that all living organisms share common ancestors. That would explain the fact that we all have our genetic codes coded with the same material.

    The other possibility is… what?

    The purpose of scientific theories is to answer question, not to accuse other thoeries of not answering them. So, instead of trying to prove that the answer above is not valid, ID should provide another answer. A scientific answer: clear, specific, demonstrable.

  32. 32
    Querius says:

    Guillermo,

    I didn’t think it was all “basically”the same, depending on your criteria. Nevertheless . . .

    The other possibility is… what?

    That the sentient beings we’re hunting for with SETI used earth as a graduate study lab for bioengineering. This might explain some of the genetic mysteries that result in the baseless speculations about the evolution of the same feature multiple times, the unexplained stasis of several genomes over millions of years (aka living fossils), and the discovery of several types anachronistic fossils (routinely ignored). Plus there was some obvious plagiarism as is readily apparent in the platypus genome.

    There. This speculation is logically equivalent to the majority of Darwinism.

    IMHO, ID is not a theory, it’s a paradigm. We assume something is designed, so we dig longer and deeper. The result is that, from a pragmatic evaluation, the ID paradigm is profoundly more successful than the random junk paradigm.

    ID doesn’t make any speculation of who, how, and where the design took place. If we did, we’d be as bad at science as many Darwinists.

    -Q

  33. 33
    Guillermoe says:

    “That the sentient beings we’re hunting for with SETI used earth as a graduate study lab for bioengineering.”

    Ok, what evidence you have of their existence?

    “There. This speculation is logically equivalent to the majority of Darwinism.”

    No, because we know biological evolution is real. Populations of living organisms change. We have observed it. So, assuming that biodiversity is the result of a real process of gradual change is not the saem as assuming it’s the result of imaginary aliens.

    “ID is not a theory”

    There are several sources that say ID is a scientific theory.

    “We assume something is designed”

    I know. You don’t prove it’s designed. You assume it.

    “the ID paradigm is profoundly more successful than the random junk paradigm”

    In what? What knowledge does ID produce? That living organisms are designed, which was assumed from the beginning?

    “ID doesn’t make any speculation of who, how, and where the design took place”

    It would if it was science. That speculation would lead to hypotheses, and the would lead to the confirmation of the who, who, where.

  34. 34
    Upright BiPed says:

    So, assuming that biodiversity is the result of a real process of gradual change is not the same as assuming it’s the result of imaginary aliens

    Yet, without any doubt whatsoever, you do merely assume the unguided rise of the physical conditions required for Darwinian evolution to exist.

  35. 35
    Querius says:

    Q: “That the sentient beings we’re hunting for with SETI used earth as a graduate study lab for bioengineering.”

    G: Ok, what evidence you have of their existence?

    Q: The same level of reliability as Darwinian evolution. An assumption.

    Q: “There. This speculation is logically equivalent to the majority of Darwinism.”

    G: No, because we know biological evolution is real.

    Q: Haha. No we don’t.

    G: Populations of living organisms change. We have observed it.

    Q: All we observe is changes in allele frequency. Show me a chihuahua that evolved wings, or a bear that turned into a whale.

    G: So, assuming that biodiversity is the result of a real process of gradual change is not the saem as assuming it’s the result of imaginary aliens.

    Q: The imaginary process of magically evolving chemical cycles that are a billion billion billion billion billion billion billion billion times more complex than anything humans have ever designed is far less likely than the hypothesized aliens that “musta” experimented with genetics on our planet.

    Q: “ID is not a theory”

    G: There are several sources that say ID is a scientific theory.

    Q: So what? I contend that ID is a paradigm.

    Q: “We assume something is designed”

    G: I know. You don’t prove it’s designed. You assume it.

    Q: Right. That’s how paradigms work. Just the same way you assume that organisms “musta” evolved leaving lots of junk and vestigial organs behind. You assume it.

    Q: “the ID paradigm is profoundly more successful than the random junk paradigm”

    G: In what? What knowledge does ID produce? That living organisms are designed, which was assumed from the beginning?

    Q: For example, by not dismissing “junk” DNA as junk. By not dismissing the thyroid as a useless vestige of evolution. And so on.

    Q: “ID doesn’t make any speculation of who, how, and where the design took place”

    G: It would if it was science. That speculation would lead to hypotheses, and the would lead to the confirmation of the who, who, where.

    Q: Not true. I said it’s a paradigm. Another paradigm is cause-effect moving forward in time. Do you ask who, when, where was responsible for cause and effect? You might say that this is obvious and a law. Fine, but Quantum Mechanics consistently violates the “law.”

    -Q

  36. 36
    Joe says:

    The fact is that the genetic code of all living organisms on Earth is written basically in the same code (RNA and DNA).

    The question is: HOW did this happen?

    Most likely via intelligent design.

  37. 37
    Guillermoe says:

    PB:

    “Yet, without any doubt whatsoever, you do merely assume the unguided rise of the physical conditions required for Darwinian evolution to exist”

    No, we know species evolve because we have observed it.

  38. 38
    Upright BiPed says:

    #37.

    That is a non-sequitur.

    Your comment doesn’t have anything to do with the comment you were responding to.

  39. 39
    Guillermoe says:

    Q

    ” The same level of reliability as Darwinian evolution. An assumption”

    We have observed species evolve. It’s not an assumption based on a process WE KNOW IS REAL.

    ” No we don’t”

    Yes, we do. Biological evolution is the gradual change in allele frequency in a population of living organisms caused by some selective pressure. We have observed that happening.

    “All we observe is changes in allele frequency”

    Yes, that’s called biological evolution.

    “Show me a chihuahua that evolved wings, or a bear that turned into a whale.”

    I can’t show you because you won’t live a million years. But if that’s a problem, check this: show me a description of the intelligent designer. Show me how the intelligent designer designs. It goes both ways, you see?

    “The imaginary process of magically evolving chemical cycles that are a billion billion billion billion billion billion billion billion times more complex than anything humans have ever designed is far less likely than the hypothesized aliens that “musta” experimented with genetics on our planet.”

    No, if we have evidence of chemical recombination and no evidence of aliens.

    Now, this is important: “is far less likely” is a subjective argument. It is less likely TO YOU, because you feel that way.

    ” Just the same way you assume that organisms “musta” evolved leaving lots of junk and vestigial organs behind. You assume it.”

    Yes, we assumed that because biological evolution (change in allele frequency) is a real process.

    What’s the real process involved in ID? What’s any process involved in ID of life on Earth?

    “For example, by not dismissing “junk” DNA as junk.”

    Bullshit, we know junk DNA is not junk because of genetics, not because of ID.

    “By not dismissing the thyroid as a useless vestige of evolution”

    We know thyroid is not a useless vestige because of physiology, not because of ID.

    What knowledge has been produce from ID?

  40. 40
    Guillermoe says:

    Joe:

    “Most likely via intelligent design”

    What happens when intelligent design happens? Nobody has explained that yet, so saying “it happened via intelligent design” is as explicative as “it happened via fañlfalksdjfaldfa”..

  41. 41
    Guillermoe says:

    UB:

    “Your comment doesn’t have anything to do with the comment you were responding to”

    It does. If I observe something, I am not assuming it.

  42. 42
    jerry says:

    Yes, we do. Biological evolution is the gradual change in allele frequency in a population of living organisms caused by some selective pressure. We have observed that happening.

    This is modern day genetics and is meaningless in the evolution debate. People confuse the two. There is no evidence that this process has ever led to anything but trivial changes in gene pools.

    Anybody that suggests that is had is ill informed.

  43. 43
    Upright BiPed says:

    But you have never observed the “rise of the physical conditions required for Darwinian evolution to exist.”

  44. 44
    Querius says:

    Guillermoe,

    Biological evolution is the gradual change in allele frequency in a population of living organisms caused by some selective pressure.

    Sorry, but neither natural or artificial methods will breed coacervates into chihuahuas. Changes in allele frequency have never ever been observed to result in new alleles.

    Bullshit, we know junk DNA is not junk because of genetics, not because of ID.

    And out comes the abuse indicating you’ve lost. The necessity of “junk” DNA first hypothesized by Susumo Ohno as the genetic “fossil” evidence of evolution among other things has been grimly defended by Darwinists despite mounting evidence to the contrary.

    IDers assumed non-coding DNA would have a designed purpose (and kept looking for one), while Darwinists gleefully assumed (and still assume) it’s junk and used it as Yet Another Example (TM) of random processes, vestiges, and poor design as a proof of the evolutionary process.

    This is a good example of how Darwinists have been slowing scientific progress!

    -Q

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