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Monday, 3 December 2012

Now Evolution Must Have Evolved Different Functions Simultaneously in the Same Protein by Cornelius Hunter

Every so often a Creation versus Evolution Blogpost will catch my eye, and I think it vaguely understandable enough for the rest of us non-scientists. Sometimes, like listening to modern classical music compositions, the thing isn't to expect to get it all in one hit....but merely to expose yourself to it and hope something sticks!!!
This post is from here  via   Uncommon Descent


Proteins consist of a long sequence of amino acids and those amino acids are supplied by the so-called transfer RNA, or tRNA, molecules.
The tRNA molecules, in turn, are loaded with the right amino acid by the so-called aminoacyl-transfer RNA synthetases, or aaRS, proteins. There are several different versions of aaRS proteins, which load the different tRNA molecules with the different kinds of amino acids. These aaRS proteins hang around the ribosome where proteins are constructed. But as I discussed in the previous post, the lysine aaRS, also known as LysRS, has an interesting dual role. Normally it hangs around the ribosome where it binds to another LysRS to form what is known as a dimer. In this dimer configuration, there is a weak binding between (i) the 207th amino acid (a serine) of one of the LysRS proteins and (ii) the 540th and 541st amino acids (a glycine and a leucine, respectively) of the other LysRS protein. The serine side chain consists of a hydroxyl group attached to a methyl group and when the 207th amino acid’s hydroxyl group is phosphorylated (the hydrogen is replaced by a phosphate group), its binding to the opposing 540th and 541st amino acids is broken. Not surprisingly this allows the serine dimer to loosen. But this is only the beginning of a series of events caused by the phosphorylation of that serine. The serine molecules move away from the ribosome, enter the cell’s nucleus, interact with a DNA transcription factor causing (i) the production of a signaling molecule, diadenosine tetraphosphate, (ii) release of one of the transcription factor’s proteins and (iii) expression of the transcription factor’s target genes. Simply put, depending on the phosphorylation state of its 207th amino acid, LysRS has two different structural and functional states. When not phosphorylated LysRS is a crucial part of the translation process, supplying lysine amino acids to tRNA molecules. When phosphorylated it regulates gene expression. This is a major problem for evolutionary theory.

The dual role of LysRS is not viewed as a challenge to evolutionary theory by evolutionists. This is not because evolutionary theory predicts or easily accommodates this finding, but rather because evolutionists assume evolution to be true to begin with, so there can be no real challenges, only unsolved research problems.

In fact, evolutionists have accepted so many contradictions and false predictions that new contradictions have little impact. Evolutionists simply make vague speculations and move on.

But the dual role of LysRS is not easily accommodated by evolutionary theory. In fact, it is a major challenge. This is because evolution calls for a gradual buildup of functionality. New designs do not simply appear out of nowhere. Instead, rudimentary capability is supposed to have slowly been refined by chance events such as DNA mutations.

This makes the evolution of molecular machinery and processes—such as proteins and protein synthesis—not likely without a multiverse to provide a near infinite number of tries.

But ignoring such problems and assuming that proteins and processes could somehow evolve, evolutionists must now believe that random mutations and natural selection simultaneously evolved LysRS for two completely different functions.

LysRS must have had rudimentary capabilities in both translation and transcription, and both capabilities must have been refined by evolution. The phosphorylation of that key serine must have just happened to arise. The transport of LysRS from nearby the ribosome to inside the cell nucleus must have just happened to arise. And the transcription functions of LysRS must have been refined.

All of this while LysRS was refining its translation function. We don’t have scientific evidence for the evolution of these designs, but the point here is that now we must imagine two such refinements, for two different functions, evolving simultaneously.

Or evolutionists could say LysRS evolved only for its translation function, and it just so happened that its design also fulfilled a crucial transcription function as well. It was a lucky strike. And so was the phosphorylation capability of the key amino acid just at times when it was needed.

Now none of this can be proved to be impossible. And perhaps all of this did occur somehow. But the science that we currently have does not indicate this. What we know at this time tells us that the evolution of biological machines, such as LysRS and its surrounding cellular context is, far from a fact. If we are looking for scientific facts to proclaim, the fact is evolution is unlikely.

Simply put, evolution either must have evolved two independent designs simultaneously in the same protein, or it must have been a two-fer, evolving the one design and getting the second for free. Either way the evidence does not bode well for evolution.

We can argue that the metaphysics requires evolution to be true. Or we can argue that all will be well in the future when evolution is vindicated by findings yet to come. But these are not scientific arguments.

From a scientific perspective, evolution is a deeply flawed idea. People believe it is true, and their beliefs should be respected. And who knows, perhaps future discoveries will point to evolution. But for now, gene sharing findings such as with LysRS continue to add yet more scientific problems for the theory.

20 comments:

  1. "The transport of LysRS from nearby the ribosome to inside the cell nucleus must have just happened to arise. And the transcription functions of LysRS must have been refined."

    How many years of evolution before the nucleus emerges George?

    Please.

    For goodness sakes, that a molecule has one function, and a secondary (10^? years later, and in which organisms?) function becomes a problem, as "Evolve(ing) Different Functions Simultaneously" is too improbable?
    Reply
  2. For goodness sakes, that a molecule has one function, and a secondary (10^? years later, and in which organisms?) function becomes a problem, as "Evolve(ing) Different Functions Simultaneously" is too improbable?

    As I said, “The dual role of LysRS is not viewed as a challenge to evolutionary theory by evolutionists. This is not because evolutionary theory predicts or easily accommodates this finding, but rather because evolutionists assume evolution to be true to begin with, so there can be no real challenges, only unsolved research problems.”

    You believe that protein evolution is not a problem, in spite of the facts. So it is not surprising that dual function is not a problem for you. But whether LysRS evolved its two functions simultaneously or in series, the evolutionary search becomes that much more unlikely. If in series, for example, you have a mature protein with an important function. It is likely that more than a few mutations are not well tolerated as function falls off rapidly. So the purefying selection greatly complicates the search for the second function. And if it was the case that only a few mutations would have been required, then evolution got lucky. Another case of evolutionary serendipity.
    Reply
  3. "But whether LysRS evolved its two functions simultaneously or in series, the evolutionary search..."

    "Now Evolution Must Have Evolved Different Functions Simultaneously in the Same Protein"

    So you are unsure whether LysRS evolved its two functions simultaneously or in series, but you title the post "Evolution Must Have Evolved Different Functions Simultaneously in the Same Protein?"

    Nice.
    Reply

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    1. So you are unsure whether LysRS evolved its two functions simultaneously or in series, …

      I was never good at keeping up with all the possible just-so stories.

      but you title the post "Evolution Must Have Evolved Different Functions Simultaneously in the Same Protein?" Nice.

      The problem that LysRS poses for evolution is independent of the just-so story. Whether its dual functions are supposed to have evolved in parallel, in series, or just by luck, either way you have now escalated the search or the serendipity problem. The search problem was already 27 orders of magnitude in the red, and that was based on the evolutionist’s optimistic estimates.
    2. Can you reference the evidence that "Evolution Must Have Evolved Different Functions Simultaneously" re: LysRS?

      Or did you conjure this out of thin air? You're not exactly defending the title of your post, George. I think "simultaneous" and a couple o' billion years might not be the same thing to an average reader.

      "The search problem was already 27 orders of magnitude in the red"

      Big number. Calculation please?
    3. Big number. Calculation please?

      In one study evolutionists estimated the number of attempts that evolution could possibly have to construct a new protein. Their upper limit was 10^43. The lower limit was 10^21.

      http://rsif.royalsocietypublishing.org/content/5/25/953.long

      These estimates are optimistic for several reasons, but in any case they fall short of the various estimates of how many attempts would be required to find a small protein. One study concluded that 10^63 attempts would be required for a relatively short protein.

      http://www.ncbi.nlm.nih.gov/pubmed/2199970

      And a similar result (10^65 attempts required) was obtained by comparing protein sequences.

      http://www.sciencedirect.com/science/article/pii/0022519377900443

      Another study found that 10^64 to 10^77 attempts are required.

      http://www.ncbi.nlm.nih.gov/pubmed/15321723

      And another study concluded that 10^70 attempts would be required. In that case the protein was only a part of a larger protein which otherwise was intact, thus making the search easier.

      http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000096

      These estimates are roughly in the same ballpark, and compared to the first study giving the number of attempts possible, you have a deficit ranging from 20 to 56 orders of magnitude. Of course it gets much worse for longer proteins.

      [edited for clarity]
    4. Oh dear. Those numbers. How tiresome.

      I'd love it if Doug Axe, for example, would ever cite his first publications that show folding is plastic, and that enzymes (barnase) tolerate a huge range of substitutions and remain active. Rugged terrain or not?

      But we digress.

      No response to my first question: can you reference the evidence that "Evolution Must Have Evolved Different Functions Simultaneously" re: LysRS?

      Do you have ANY defense of the title of the post?
    5. Oh dear. Those numbers. How tiresome.

      Why are they tiresome?
    6. I'd love it if Doug Axe, for example, would ever cite his first publications that show folding is plastic, and that enzymes (barnase) tolerate a huge range of substitutions and remain active. Rugged terrain or not? But we digress.

      Digressing or not, that is not a typical result. Protein function doesn’t don’t generally tolerate very many mutations.
    7. No response to my first question: can you reference the evidence that "Evolution Must Have Evolved Different Functions Simultaneously" re: LysRS?

      http://darwins-god.blogspot.com/2012/12/now-evolution-must-have-evolved.html?showComment=1354421549847#c8191811156858130424
    8. Mostly because they implicitly or explicitly reject your hypothesis.

      From your first reference:

      "Finally, we conclude that the number 20^100 and similar large numbers (e.g. Salisbury 1969; Maynard Smith 1970; Mandecki 1998; Luisi 2003; Carrier 2004; de Duve 2005) are simply ‘straw men’ advanced to initiate discussion in the same spirit as the ‘Levinthal paradox’ of protein folding rates (Levinthal 1969; Zwanzig et al. 1992). 20100 is now no more useful than the approximate 2×101 834 097 books present in Borges' (1999) fantastical ‘Library of Babel’ and has no connection with the real world of amino acids and proteins. Hence, we hope that our calculation will also rule out any possible use of this big numbers ‘game’ to provide justification for postulating divine intervention (Bradley 2004; Dembski 2004)."

      I mean, damn. That reference burns you. It calls you and Dembski a "big numbers game" that postulates divine intervention without merit. But you cite it. As your first reference against me. Did you miss the burn? Do you read these papers?

      So yeah, tiresome.

      Did Axe forget his data? Ask him sometime for me.
    9. I mean, damn. That reference burns you. It calls you and Dembski a "big numbers game" that postulates divine intervention without merit. But you cite it. As your first reference against me. Did you miss the burn? Do you read these papers?

      Yes, I do read these papers. And no, I did not miss that passage. You obviously did not catch the context. The authors believe there is no problem because they believe their estimates of the fraction of protein sequence space that evolution can feasibly search easily exceeds what is required to find native proteins. Therefore they conclude anyone claiming there is a protein evolution problem is playing a “big numbers game,” and their results should put an end to such games.

      But to understand this conclusion of theirs, you need to understand the context. The paper estimates the fraction of protein sequence space that evolution can feasibly search. It is an optimistic estimate, but at least it is an estimate.

      As for the fraction of protein sequence space that evolution is required to search to find native proteins, the Introduction of the paper merely refers to conjecture that only two types of amino acids are required (from 20), and on top of that only a subset of a protein’s amino acids even matter. They also refer to other conjectures that the required search space can be narrowed yet further. They conclude that the search space reduces dramatically.

      This conjecture has no correspondence with reality, as indicated by the various experimental results that are available which are nowhere close to their optimistic conjectures. Likewise their estimate of the fraction of protein sequence space that evolution can feasibly search is equally off base.

      So what you are doing is placing their lattice-based, back of the envelope, conjecture of the search space required over and above several detailed and experimental studies that all converge on the same neighborhood.
  4. Active barnase variants with completely random hydrophobic cores.

    Axe DD, Foster NW, Fersht AR.
    Proc Natl Acad Sci U S A. 1996 May 28;93(11):5590-4.

    Atypical? Or well supported empirical result?
    Reply

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    1. Atypical? Or well supported empirical result?

      Why the dichotomy? It is a complicated problem, we don’t have exact numbers, and there are bound to be exceptions. But the empirical evidence suggests that, generally, function drops off pretty rapidly with only a few percent amino acid substitutions. Here is how one paper describes it:

      “The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability—the ability of proteins to acquire changes in sequence and function.”

      http://www.ncbi.nlm.nih.gov/pubmed/19765975
  5. No response to my first question: can you reference the evidence that "Evolution Must Have Evolved Different Functions Simultaneously" re: LysRS?

    http://darwins-god.blogspot.com/2012/12/now-evolution-must-have-evolved.html?showComment=1354421549847#c8191811156858130424

    Yeah, I've been here for the whole comment thread. Still missing your proof that the functions evolved simultaneously.
    Reply

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    1. RobertC, 'big number game' aside (Godel), please cite the exact empirical evidence of a completely new functional protein sequence evolving from a existing functional protein sequence:

      When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
      Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
      http://www.biologicinstitute.org/post/18022460402/when-theory-and-experiment-collide

      "Biologist Douglas Axe on Evolution's (non) Ability to Produce New (Protein) Functions " - video
      Quote: It turns out once you get above the number six [changes in amino acids] -- and even at lower numbers actually -- but once you get above the number six you can pretty decisively rule out an evolutionary transition because it would take far more time than there is on planet Earth and larger populations than there are on planet Earth.
      http://intelligentdesign.podomatic.com/entry/2012-10-15T16_05_14-07_00

      Collected notes on the severe limits found for the ability of proteins to ‘randomly’ evolve to new functions, for new binding sites, for new domain-domain interactions, and for new ORFan genes/proteins:
      https://docs.google.com/document/d/11VRNz03ox-vXauBTVonqmRM7amD5CbUWwu6wxr2ABr4/edit

      Where's the substantiating evidence for neo-Darwinism?
      https://docs.google.com/document/d/1q-PBeQELzT4pkgxB2ZOxGxwv6ynOixfzqzsFlCJ9jrw/edit
  6. When reading this blog, UD, or anything from the DI it's good to keep in mind the prophetic words of professional educator William J. Bennetta:

    "In all of these efforts [to push Creationism], the creationists make abundant use of a simple tactic: They lie. They lie continually, they lie prodigiously, and they lie because they must."
    Reply

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    1. Nice projection by Willaim J. Bennetta as evolutionism is all lies all of the time. And thorton is a pathological liar
  7. I think that Bennetta's words apply to evolution's religious adherents such as yourself, Thorton. Though of course, if I repeat his words that would constitute an ad hom, which implies I have no valid argument to present :-P

    (Cornelius should remove both our comments since neither is addressing the topic of the post)
    Reply
  8. Dale, Thorton has a strategy. He knows there is no evidence for UCA, much less for naturalistic UCA. But he doesn't like to see the scam exposed for what it is. So he purposely blogs in a way that will tempt CH to shut off the blogging again.

    Good call, Thorton. I would want the blogging shut down too if I were you. ;)

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