Saturday, December 1, 2012

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

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.

91 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?

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    1. Who is George?! I guess "George" is better than something like dufus, but still the least you can do is show some respect and call the guy by his preferred name!

      Delete
  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.

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  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.

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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.

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    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?

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    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]

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    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?

      Delete
    5. Oh dear. Those numbers. How tiresome.

      Why are they tiresome?

      Delete
    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.

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    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

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    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.

      Delete
    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.

      Delete
  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?

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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

      Delete
  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.

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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

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  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."

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    1. Well then, that settles it doesn't it?

      This is the kind of posts evolutionists post when they have no answers for the problem at hand.

      Materialists are willing to believe any miraculous thing as long as it doesn't involve the supernatural.

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  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)

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    1. DaleFlannery

      (Cornelius should remove both our comments since neither is addressing the topic of the post)


      Actually mine is directly addressing it. As has already been pointed out, the headline of the OP is false and deliberately misleading.

      Lying is what Creationists do.

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  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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  9. Jeff

    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.


    If you're so sure you have the goods to expose this "scam", why don't you or CH or any on the other IDiots write up your evidence and submit it to the leading scientific journals? Send a copy to Faux News too, they'll scream it all over the airwaves.

    Why limit this monumental discovery that would shake modern science to its foundations to just high-fiving yourselves on some backwater ID-incestuous blogs?

    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.


    Er...I'm not the one who has had dozens of posts removed for obscenities, accusations of pedophilia, and threats of physical harm to others. That would be your YEC friend Pal Joey.

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  10. The scam is that there is no naturalistic theory which, when applied to the relevant initial conditions, implies any of the relevant, subsequent events/effects. And if you, or anyone else for that matter, knew of such a prediction, you would post it right here and now. Not holding my breath.

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  11. Jeff

    The scam is that there is no naturalistic theory which, when applied to the relevant initial conditions, implies any of the relevant, subsequent events/effects. And if you, or anyone else for that matter, knew of such a prediction, you would post it right here and now. Not holding my breath.


    I just showed you one - insular dwarfism.

    Why do Creationists always think if they go "LALALA I DON'T SEE ANY EVIDENCE" it somehow magically makes the evidence go away?

    Here's another evolutionary prediction - the loss or degradation of unused functions. When the environment changes and a particular feature of an animal costs more energy to maintain than the survival benefits it provides, the feature will disappear, degrade, or occasionally take on another function. That's exactly why we see flightless birds that have small non-flight capable winglets, vestigial eyes in blind cave fish, vestigial leg bones in cetaceans.

    I'd love to hear your ID explanation for the above features, but we both know you don't have one.

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    1. Umm ID is OK with Darwinian mechanisms breaking and degrading things. However there isn't any evidence that those mechanisms can produce the original structures in the first place.

      And vestigial leg bones in cetaceans exist only in the minds of evos.

      Delete
  12. Thorton:

    Designed things break down. If the break isn't critical then the designed thing can still function.

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  13. And I understand that the vestigal leg bones in whales still support the reproductive organs so they serve a purpose. Please correct me if I'm wrong.

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    1. natschuster

      Designed things break down. If the break isn't critical then the designed thing can still function.


      Individual units that have already been produced break down. What kind of an incompetent Designer makes products that all are already broken down?

      And I understand that the vestigal leg bones in whales still support the reproductive organs so they serve a purpose. Please correct me if I'm wrong.

      Poor nat the troll, still can't read.

      Thorton; "the feature will disappear, degrade, or occasionally take on another function.

      Why did your incompetent designer have to use degenerated leg bones for that function?

      Delete
    2. Maybe the designer designed all birds as flying. In some species, the ability was lost. In some populations of cave fish, eyesight was lost.

      And it is considered good design practice to use pre-existing components so why wouldn't a designer use degenerate legs for another purpose. And they might not be degenerate anyway.

      Delete
  14. Thorton: I'd love to hear your ID explanation for the above features, but we both know you don't have one.

    Jeff: None of those things you mention are implied by any naturalistic theory applied to the relevant initial conditions (Precambrian conditions). You're just utterly confused.

    Your absurd contention, taken to its logical conclusion, implies that cars were never designed if they ever lose any function. And this, in turn, means that no cars are or were designed. So, as I said, Thorton, I'm not holding my breath waiting on the likes of you and your ilk to respond with anything relevant.

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  15. Jeff

    None of those things you mention are implied by any naturalistic theory applied to the relevant initial conditions (Precambrian conditions). You're just utterly confused.


    As expected, no Intelligent Design Creation explanation for the empirical data.

    What were the relevant initial Precambrian conditions? Please be specific and supply the details as determined by your IDC research. Why are they the only ones science should consider relevant?

    Your absurd contention, taken to its logical conclusion, implies that cars were never designed if they ever lose any function.

    Cars aren't living populations that reproduce with heritable traits. How many times does that need to pointed out to the ignorant Creationists?

    So, as I said, Thorton, I'm not holding my breath waiting on the likes of you and your ilk to respond with anything relevant.

    When will you be submitting your amazing falsification of Evolutionary Theory to any mainstream science journals for publication? I'm not holding my breath.

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    1. When will mainstream science put up positive evidence that unguided evolution can actually construct structures as opposed to breaking and degrading existing structures?

      BTW thorton, the reproduction part is what your position can't explain. So stop already with the "cars can't reproduce" cowardly spewage.

      Got that? Living populations are the very things that need to be explained so you just can't use them to do the explaining. But then again you don't seem to know much of anything.

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  16. Thorton: What were the relevant initial Precambrian conditions?

    Jeff: Pick any kind of reproducing organism for the common ancestor you wish. It makes no difference. The subsequent phenotypes are not known to be the natural result of any set of event regularities whatsoever, much less at the time you suppose they originated.

    Thorton: When will you be submitting your amazing falsification of Evolutionary Theory to any mainstream science journals for publication? I'm not holding my breath.

    Jeff: That's the point, Thorton: UCA is unfalsifiable by any criteria of falsifiability your willing to apply to it. That's why it's just a metaphysical belief for you guys rather than a logical inference.

    But, on the other hand, SA is currently the best inference by logical induction criteria (i.e., parsimony, etc).

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    1. Jeff

      Pick any kind of reproducing organism for the common ancestor you wish. It makes no difference. The subsequent phenotypes are not known to be the natural result of any set of event regularities whatsoever, much less at the time you suppose they originated.


      Science doesn't have to model and identify every last step taken 500 million years ago to have evidence of what happened. Your IDiot claim is like saying we find a pile of rocks at the bottom of a mountain, but unless we can identify the original position and pathway each rock took in falling that gravity wasn't the cause of them being there.

      That's the point, Thorton: UCA is unfalsifiable by any criteria of falsifiability your willing to apply to it.

      Your ignorance is showing again Jeff. UCA is very falsifiable. Demonstrating that the phylogenetic tree created from DNA data is vastly discordant with the one created from the fossil data would do it easily. You seem to be another clueless wonder who confuses unfalsifiable with unfalsified.

      You just don't get this science stuff at all, do you?

      Delete
    2. thorton-

      The problem is every experiment ever conducted puts a damper on evolutionism. And imagination is not evidence. Evolutionism is OK with any phylogenetic tree.

      Your position can't even be tested so forget about falsification.

      Why is it that every time I ask you to provide a testable hypothesis along with supporting evidence for your position you always throw a hissy fit but never, under any circumstances, do as requested?

      It's as if you are proud to be a bluffing, equivocating coward.

      Delete
    3. Thorton: "Science doesn't have to model and identify every last step taken 500 million years ago to have evidence of what happened. Your IDiot claim is like saying we find a pile of rocks at the bottom of a mountain, but unless we can identify the original position and pathway each rock took in falling that gravity wasn't the cause of them being there."

      No it is not when the pile of rocks falls in such a way as to spell a word. In the cell, we have much more than one word, we have volumes and volumes of information, codes, machines, software, design, life itself, etc. That is a far cry from "a pile of rocks." If the rocks spelled out a word or two, you might want to reevaluate your assumption that they fell in that pattern, eh?

      You overlooked the possibility that someone placed the rocks in a pile. That is the problem with materialism. you only allow certain explanations for the problem, even when the rocks spell out a long sentence, you only allow for naturalistic explanations.

      Delete
  17. Thorton: Cars aren't living populations that reproduce with heritable traits. How many times does that need to pointed out to the ignorant Creationists?

    Jeff: So articulate the relevance of this additionally-provided point to my statement and your original claim. Either designoids can lose function or not. Clearly they can. So connect the dots.

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    1. Jeff,

      thorton doesn't get it- his position cannot account for living organisms so he doesn't get to use them to explain anything.

      As you have noticed he is just very upset because he cannot provide anything to support his position, but he sure can bluff and equivocate.

      Delete
    2. Jeff

      Either designoids can lose function or not. Clearly they can.


      So you're saying that flightless birds were originally "designed" with flying wings, blind cave fish were originally "designed" with seeing eyes and cetaceans were originally "designed" with walking legs.

      When were the original "designs" done, and where? What is the process called whereby the original "design" made these large morphological changes?

      Delete
    3. thorton- there isn't any evidence that cetaceans had walking legs. And fish LOSING their eyes does not explain the eyes in the first place.

      As for birds, flightless birds could be designed. And the form we see today would be degenrated via random mutations.

      Delete
  18. Right, Joe. When it comes to evolutionary theory, the desire of those who want to believe it supports the hypothesis of UCA, etc. somehow shuts down their rational processes. To be fair, plenty of religious folks do the same thing with theology. But that doesn't justify the pot calling the kettle black.

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  19. Thorton: So you're saying that flightless birds were originally "designed" with flying wings, blind cave fish were originally "designed" with seeing eyes and cetaceans were originally "designed" with walking legs.

    When were the original "designs" done, and where? What is the process called whereby the original "design" made these large morphological changes?

    Jeff: You are misunderstanding something about both natural and final causality (note, final/libertarianly-free CAUSALITY, not the final effect). In the non-psychological sciences, we infer which putative, empirically-observed conditions are causal (i.e., necessary and sufficient) of effects. What we don't observe empirically is their necessity and sufficiency to produce the effect. Those properties of the conditions are abstract, not observable. You can't even prove, given your rejection of benevolent/competent design, that you ever observe anything empirically. Eastern philosophy acknowledges this and accepts it stoically.

    Likewise, libertarianly-free causality is involved when we strategically allocate conscious attention (http://www.newyorker.com/reporting/2009/05/18/090518fa_fact_lehrer?printable=true) unto mental states that are believed to be means to forethought ends. What we don't observe is the fact that such allocation of attention is strategic (i.e., teleological) in nature. That property, too, is abstract and non-empirical.

    Thus, the causal relation is never observed empirically. It is believed to exist intuitively and specific causes of specific effects are inferred. For all we know empirically, there is no such relation as causality. Once again you demonstrate your oblivion to basic logic and, therefore, science of every kind.

    As for when the original designoids were configured, that is not provable from the fossil record. There is no reason to believe we know actual stratigraphic ranges of critters since 1) known stratigraphic ranges increase relatively frequently and 2) we have searched precious little of the fossil record with any thoroughness. Furthermore, there is no reason to believe actual stratigraphic ranges correspond to existential ranges of critters. Because tons of erosion has occurred, and fossilization is not a particularly probable event in the first place, etc (also, see http://sp.lyellcollection.org/content/358/1/63.short for the difficulty involved in ascertaining when such inferences are sound/plausible).

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    1. Shorter Jeff:

      "I'm as ignorant of evolutionary theory and evidence as a sack of doorknobs, so therefore all of science must be ignorant too!"

      Good luck swaying the scientific community with that one.

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    2. The scientific community can't even sway the public with their nonsense.

      Delete
  20. Thorton: Science doesn't have to model and identify every last step taken 500 million years ago to have evidence of what happened.

    Jeff: What is the evidence, then, for UCA? It's not cladistics, because cladistics has no known correspondence to mutational and environmental effects. It's not observation, because we haven't observed any of the grand hypothetical lineages you posit actually occur. It's not theoretical corroboration, for there is no set of event regularities that we can apply yet to any conceivable initial conditions and deduce the relevant effects at the relevant times. So WHAT pray tell is the evidence?

    Thorton: Your IDiot claim is like saying we find a pile of rocks at the bottom of a mountain, but unless we can identify the original position and pathway each rock took in falling that gravity wasn't the cause of them being there.

    Jeff: In case you don't realize it, I can bring a rocks to the bottom of a mountain and set them down there. The mere existence of rocks at the bottom of a mountain doesn't prove they got there by gravity moving them there from higher up the mountain. That might be a plausible inference because of their arrangement. But it is not the only explanation conceivable. Furthermore, we know rocks fall down from mountains from observation. We've never seen the kinds of grand genealogical lineages you posit can occur naturally. You're just really confused. Your analogy is worthless.

    Thorton: Your ignorance is showing again Jeff. UCA is very falsifiable. Demonstrating that the phylogenetic tree created from DNA data is vastly discordant with the one created from the fossil data would do it easily.

    Jeff: Stratigraphic ranges are not known to be existential ranges in the first place. So the fossil record has nothing to do with it. As for the DNA data, it implies nothing about whether the hypothetical transitional phenotypes ever did or could have existed by natural means. You're just really confused.

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    Replies
    1. Jeff

      What is the evidence, then, for UCA?


      Just every last piece of consilient, corroborating data from the genetic and fossil records ever collected.

      What is the evidence for SA? Answers In Genesis' "baraminology" page?

      But it is not the only explanation conceivable.

      Guess what Jeff - science doesn't much care if you can *conceive* of a magic designer poofing everything into existence. Evolution and a UCA is the only explanation that fits all the available empirical evidence.

      We've never seen the kinds of grand genealogical lineages you posit can occur naturally.

      Dumb Creationist argument #3B: "Were you there??? Did you see it???" We don't have to see an event happen in real time to know it occurred. It's enough to determine the event's occurrence from the evidence it leaves behind.

      Seriously Jeff, have you ever been within 1000 yards if a college level science class in your life? Because your ignorance of the most basic scientific concepts is just pitiful.

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    2. thorton is lying because there isn't any genetic data that supports any UCA. And thorton is equivicating with the word "evolution", as usual.

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  21. Thorton: Just every last piece of consilient, corroborating data from the genetic and fossil records ever collected.

    Jeff: Thorton, data that is not predicted by applying a naturalistic theory to some plausible initial conditions corroborates nothing. You are confused beyond belief.

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    1. This comment has been removed by a blog administrator.

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    2. Jeff

      data that is not predicted by applying a naturalistic theory to some plausible initial conditions corroborates nothing. You are confused beyond belief


      Tell you what Jeff - go ahead and write that up, submit it to the scientific community. Tell them that analysis of empirical data mean nothing. See how far that gets you.

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    3. And what would make you think that "scientists" as dense as you understand corroboration any better than you? You're really confused.

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    4. Jeff, when will you be posting that scientific evidence for your "Separate Ancestry" claims?

      I keep asking, you keep evading. Seems like you're caught in a fib and don't have any.

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    5. Thorton, the evidence for ID-style SA is the fact that is highly analogical and requires WAY less ad-hoc hypotheses than does naturalistic UCA. Indeed, the naturalistic UCA hypothesis is only conceivable by positing kazillions of ad-hoc hypotheses for which there is no theory to support their plausibility.

      Oh, and that's IF UCA is at least teleological in nature. But you deny even that, rendering your view hopelessly absurd. You can't even account for the correspondence view of warranted belief when you start off assuming your mind isn't intentionally-designed to correspond to an "external" world. You're so confused it's mind-boggling.

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    6. Excuse after excuse from thorton, but still no scientific evidence for the claimed UCAs, nor how they could have possibly diversified into what we now observe.

      Imagination is not evidence.

      And no one has determined the created kinds yet. That is what science is for- to help make that determination.

      Linneas started the scientific quest for the created kind when he came up with his classification scheme- Linnean taxonomy is based on a common design.

      He put the Kind at the level of "Genus", however today creationists say it all depends on the organism.

      And their methodology doesn't seem to be very different from determining "species". You can actually read all about it. Or you can keep attacking for the sake of attacking.

      Delete
    7. Still no scientific evidence from Jeff to support his SA claims.

      At least tell us what the originally created "separate ancestry" lineages are Jeff, and how you determined them. You Creationists usually call them "kinds".

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    8. Still no scientific evidence from the dancing queen to support her UCA claims.

      Quite a bit of obfuscation, though. I wonder why?

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    9. Thorton, it matters not what the separate ancestors might have been in one sense. Because there is no natural theory that explains the subsequent relevant evolution from the relevant initial conditions for SA or UCA.

      However, with SA, we can use a lot more analogical reasoning by which to extrapolate. And the SA'ist need not posit anywhere NEAR as many ad-hoc hypotheses as the UCA'ist does. And the SA'ists ad-hoc hypotheses are at least related to analogical reasoning, unlike kazillions of those posited for UCA.

      Delete
    10. OK, so you don't have even one piece of positive scientific evidence for SA.

      Hopefully we'll be hearing no more about SA nonsense from you then.

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    12. The only normative inductive criteria for two or more hypotheses, that are not actually explanatory of the data/effects/etc their adherents believe is naturally caused as per those respective hypotheses, are such criteria as greater analogical relationality, smaller quantity of ad-hoc hypotheses required to render the original hypotheses coherent, etc.

      I'm sorry that you think induction can provide you such absurd criteria as, "there is no libertarianly-free causality," etc. This just means you're clueless. Court systems regularly apply inductive criteria to questions around the involvement or lack of involvement of self-control (i.e., libertarian causality). You'll never see such non-sense as what you UCA'ists believe in a logic book. It has nothing to do with logic.

      What you UCA'ists do is adopt a metaphysics which is not known to be possible or plausible and then try to force inductive criteria within that metaphysics. But logic doesn't function that arbitrarily. It deals with logical possibilities in terms of inductive criteria like parsimony, etc without imposing any such arbitrary constraints as UCA'ists impose on themselves.

      Sane people will never join you in your arbitrariness (i.e., irrationality). And, again, none of this implies that UCA is false. It just means it fares MUCH worse in terms of inductive criteria than does certain versions of SA.

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    13. thorton:
      OK, so you don't have even one piece of positive scientific evidence for SA.

      Just every observation and experiment ever conducted. Prokaryotes give rise to prokaryotes. Humans give rise to humans. Chimps give rise to chimps. Bats give rise to bats. Fish give rise to fish- and so on.

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    14. Jeff

      blah blah blah inductive criteria blah blah blah libertarian causality blah blah blah metaphysics blah blah blah


      There's nothing quite so pathetic or boring as a clueless Creationist philosophy student trying to BS his way through a scientific discussion.

      You have no scientific positive evidence for "Separate Ancestry", period.

      Game over. You Creationist idiots lose.

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    15. Chubby Joe G

      Just every observation and experiment ever conducted. Prokaryotes give rise to prokaryotes. Humans give rise to humans. Chimps give rise to chimps. Bats give rise to bats. Fish give rise to fish- and so on.


      ...and primates give rise to primates, mammals give rise to mammals, vertebrates give rise to vertebrates, chordates give rise to chordates.

      Does your Creationist "after its kind" blithering have a point?

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    16. dancing queen:
      ...and primates give rise to primates, mammals give rise to mammals, vertebrates give rise to vertebrates, chordates give rise to chordates.

      And unguided evolution cannot account for primates, mammals, vertebrates nor chordates.

      Did you have a point other than to show your position is ignorant abd useless?

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    17. dancing queen:
      You have no scientific positive evidence for "Separate Ancestry", period.


      How would you know? It is quite obvious that you don't know what "scientific positive evidence" is as you cannot provide any for unguided evolution.

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    18. Chubby Joe G

      It is quite obvious that you don't know what "scientific positive evidence" is as you cannot provide any for unguided evolution.


      Evolution isn't unguided Chubs. It's a feedback system that responds to changes in the environment.

      Unless you wish to claim your Magic Designer is somehow consciously manipulating the environment to direct the evolution of specific species down consciously selected paths.

      Is that your latest assertion Chubs?

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    19. Fatboy Joe G

      and 38 Nobel laureates say:

      Logically derived from confirmable evidence, evolution is understood to be the result of an unguided, unplanned process of random variation and natural selection.


      Sorry idiot, they are saying evolution is not CONSCIOUSLY guided, which it isn't. Its direction is still determined by unconscious, unplanned environmental changes.

      Just how stupid are you Chubs?

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    20. thorton:
      Its direction is still determined by unconscious, unplanned environmental changes.

      BWAAAAHAHAHAHAHAAAAAAAHAHAHAHAAAAAHAHHAHA

      That "direction" = whatever. Evolution does NOT have a "direction" other than "survival", which isn't a direction.

      Whatever survives and whatever is good enough survives (Mayr).

      Just how stupid are YOU, queenie? Mevermind, we already know that you are very stupid...

      Delete
    21. Can evolution make things less complicated?





      Instead, the data suggest that eukaryote cells with all their bells and whistles are probably as ancient as bacteria and archaea, and may have even appeared first, with bacteria and archaea appearing later as stripped-down versions of eukaryotes, according to David Penny, a molecular biologist at Massey University in New Zealand.



      Penny, who worked on the research with Chuck Kurland of Sweden's Lund University and Massey University's L.J. Collins, acknowledged that the results might come as a surprise.



      “We do think there is a tendency to look at evolution as progressive,” he said. “We prefer to think of evolution as backwards, sideways, and occasionally forward.”


      So the "direction" is every which way, including loose...

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    22. Chubby Joe G

      So the "direction" is every which way, including loose...


      That's right fatboy. Evolutionary processes can and do produce new features when those features are beneficial to survival, and evolutionary processes can and do remove features, even complexity, when they no longer are "cost effective" for reproductive success.

      Again that's Evolution 101, but since you're never studied the subject its no surprise you're so ignorant of it.

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    23. queenie:
      Evolutionary processes can and do produce new features when those features are beneficial to survival, and evolutionary processes can and do remove features, even complexity, when they no longer are "cost effective" for reproductive success.

      So more equivocation. You need to demonstrate that all evolutionary processes are blind and undirected chemical processes. You can't do that. So as far as you know evolutionary processes are DESIGN processes.

      It's amazing that you think that your ignorance means something.

      Delete
    24. Thorton, your last reply to me was so challenging that I had to really give some thought about my next reply. But I finally came up with something that someone with your level of intelligence might get:

      Thorton,

      blah blah blah inductive criteria blah blah blah libertarian causality blah blah blah metaphysics blah blah blah

      There's nothing quite so pathetic or boring as a clueless UCA'ist trying to BS his way through a scientific discussion.

      You have no scientific positive evidence for "UCA", period.

      Game over. You UCA'ist idiots lose.

      -- so tell me, could you understand that response, at least? Since it's on your intellectual level?

      Delete
    25. Poor Jeff. Still too ignorant to understand phylogenetic analysis. Still no evidence for his claimed SA. Still an IDiot.

      Delete
    26. Poor thong-boy- too ignorant to understand that phylogenetic analysis is not evidence for any UCA. Still an equivocating coward.

      Delete
    27. Guess that last one was still over your head, Thorton. Let me try another one:

      Poor Thorton. Still too ignorant to understand phylogenetic analysis. Still no evidence for his claimed UCA. Still an idiot.

      Does that help?

      Delete
    28. Poor Jeff. Still too ignorant to understand phylogenetic analysis. Still no evidence for his claimed SA. Still an IDiot

      Now watch the IDiot attempt his "I'm rubber you're glue" childish retort a dozen more times.

      Delete
    29. Indeed, because you're so stupid, you've already proven you'll follow right in line. It's awesome showing people just HOW stupid UCA'ists are! LOL! So you ready? Here we go again. I'm gonna try to get a level of discussion you can understand:

      Poor Thorton. Still too ignorant to understand phylogenetic analysis. Still no evidence for his claimed UCA. Still an absolute idiot.

      Now watch the moronic Thorton attempt his "I'm rubber you're glue" childish retort a dozen more times.

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    30. Thorton: "Now watch the IDiot attempt his "I'm rubber you're glue" childish retort a dozen more times."

      Jeff the IDior philosophy student: Neener neener I know you are but what am I!!"


      Q.E.D.

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    31. Let me try harder to get it on your level, Thorton. How's this? --

      Thorton the true believer who needs no evidence: Neener neener I know you are but what am I!!

      Q.E.D.

      -- Does that help, Thorton?

      Delete
    32. That's right Jeff, I forgot you're the guy with the 3rd grade maturity level who has to have the last word.

      Go ahead, copy this post word for word since it's all you know how to do. You'll still be an idiot and a scientifically illiterate philosophy student tomorrow, and the scientific community will still be laughing at you, not with you.

      Delete
    33. I guess I have to work harder to get it on your level that YOU are the one that insists on the last word. You just can't resist. And that's what's so funny about it. So here goes:

      "That's right Thorton, I forgot you're the guy with the 3rd grade maturity level who has to have the last word.

      Go ahead, respond to this post without defining evidence since it's all you know how to do. You'll still be an idiot and a scientifically illiterate philosophy student tomorrow, and the the scientific community will still be laughing at you, not with you."

      Does that help? BTW, by scientific community, I mean those who do science. You know, that which can actually be demarcated from the pseudo-science you fideists do.

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  23. Evolutionists believe their myth IN SPITE of the evidence, not because of it. The more we learn about biology, the more we realize how absurd it is to believe materialistic evolution is the cause.

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  24. I) Anyone care to defend the title of this post. Deceptive at best, isn't it?

    II) I realize you'll reject it without reading it if I present it, so here is a nice, empirical refutation of the big numbers game from a ID/creation perspective:

    http://toddcwood.blogspot.co.uk/2012/10/biochemistry-tour-de-force-in-nature.html

    ".... McLaughlin et al., authors of a new study published in Nature that managed to accomplish that very project. For the protein, they picked a small one called PSD95pdz3, which binds to other proteins and is involved in cell signaling. McLaughlin et al. mutated every position one at a time to every other possible amino acid, resulting in 1577 variants of the native protein. They then checked these variants for their ability to bind to a short peptide that represents the normal binding partner of PSD95pdz3.

    Their results confirm some of what protein biochemists have long believed about protein sequence and function. Substitutions at most sites (about 75%) had little effect on the protein function, and some sites tolerated substitutions of very dissimilar amino acids with little to no functional consequence"

    "Within the creation/evolution debate, these results have quite important consequences. You've probably heard creationists and ID advocates claim that mutations are bad and ruin protein function. As a person with a background in protein biochemistry, I've always thought that claim was exaggerated at best."

    "Their second experiment of examining binding to a nonnative binding partner speaks to the ongoing research project of some ID scholars who want to show that a protein really can't evolve even a new function. ... The results of these studies have shown that multiple substitutions are necessary to convert one protein function to another, which is consistent with McLaughlin et al.'s discovery that two substitutions are necessary to fully change the specificity of PSD95pdz3 to a different binding partner. Whereas ID scholars have concluded based on their research that such conversions are improbable (impossible?) because they involve coordinated mutations, McLaughlin et al. found a plausible intermediate, Gly330Thr, which binds to both binding partners. Since there's a functional intermediate, it's at least plausible that this protein could evolve a new function."

    Referenced paper:
    http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11500.html

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    1. Robert C-

      The problem is that your position cannot account for any proteins.

      Delete
    2. And why is that Joe?

      Because you happen to think functional ones are exceedingly rare in sequence space? Are you sure?

      Did you bother to read Wood's post?

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    3. That's because your position cannot account for any proteins forming in a scenario in which there aren't any existing proteins.

      And yes I read Todd's post and it has nothing to do with what I am saying.

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    4. II) I realize you'll reject it without reading it if I present it, so …

      So first, come here and make unrealistic claims about protein evolution, and then return with false indignation that it’s my fault.

      here is a nice, empirical refutation of the big numbers game from a ID/creation perspective:

      No, the McLaughlin paper does not accomplish what you believe it does. You think it refutes the “big numbers game,” which is the scientific finding that chance events are not likely to construct complicated machines, such as proteins. Proteins are convenient because we actually can obtain some numerical estimates. As I pointed out above, even optimistic estimates for short proteins show a deficit ranging from 20 to 56 orders of magnitude (i.e., the number of searches evolution could possibly perform is ~10^20 to 10^56 times fewer than the number of searches that would be required to get lucky and find a native protein).

      This is what you refer to as the “big numbers game.” Actually it is just an obvious result. It is intuitively obvious that chance events aren’t likely going to create amazingly complex machines.

      This hasn’t stopped evolutionists from trying. As I mentioned, the 10^20 to 10^56 range results from optimistic estimates. For example, evolutionists estimated the number of searches that evolution could perform to be between 10^21 and 10^43. This is ridiculously optimistic. This is just silly and yet you blame me for playing a “big numbers game.” Even so, estimates for the number of searches required far exceed these numbers.

      The reason why the number of searches required is so large is because the protein landscape is rugged and native proteins tend to lose their function with a relatively small percentage of mutations. So the landscape seems to be something like narrow spikes in an otherwise fairly flat but rugged landscape. The spikes are narrow because for many proteins, while a few percent mutations don’t degrade the function too much, not too many more can be tolerated. The function seems to fall off rapidly with the number of mutations.

      Now what the McLaughlin paper shows is that given a native protein as your starting point, a *single* mutation often can be tolerated.

      So what? Interesting numbers, great study, but it doesn’t suddenly make protein evolution any easier. But then again, I guess I’m just not “reading” the right stuff.

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