Monday, December 08, 2014

Ann Gauger keeps digging

Ann Gauger and her creationist collaborator, Doug Axe, have been swapping amino acid residues in one kind of protein hoping to show that they cannot change it into another. They have deliberately ignored any clues that might be derived from assuming that evolution happened.

They have succeeded in their goal. None of their constructs have a different activity. They conclude that evolution is disproved.

This may seem a bit illogical, and indeed it is. Nevertheless, Ann Gauger set out to show that her logic is sound in a post entitled "Is Evolution True? Laying Out the Logic." In that post she made up a strawman version of an evolutionary argument. It goes like this ...
  1. Evolution is true. That is, enzymes have evolved new functions by a process of random mutation and natural selection.
  2. Modern enzymes can't evolve genuinely new functions by random mutation and natural selection but can only tinker with existing functions.
  3. Therefore, ancient enzymes must have been different, capable of carrying out a broad range of enzyme activities.
  4. Those enzymes underwent duplication and diverged from one another, becoming specialized.
  5. How do we know this happened? Because we now see a broad array of specialized enzymes. Evolution is the explanation.
Ann Gauger thinks this is a flawed argument because it assumes the very thing that one is attempting to prove; namely, evolution.
This begs the question of whether evolution is true. It is a circular argument unsubstantiated by the evidence and unfalsifiable. No one can know what ancient enzymes actually looked like, and whether they really had such broad catalytic specificities.
I wanted to discuss the logic of her argument that evolution can't happen so I posted a comment on the same day that her post appeared [A creationist argument against the evolution of new enzymes]. I outlined a more reasonable argument in support of the evolution of two enzymes with different functions from a common promiscuous ancestor. Here's my reasoning ...

Before looking at her version of logic, let me outline the standard evolutionary explanation for the evolution of enzymes with new functions from pre-existing enzymes with different functions.
  1. Evolution is a proven fact. It can be easily observed in the lab.
  2. The evidence that evolution has occurred in the past is overwhelming. This is especially true of molecular evolution. It would be perverse to ignore all this evidence and claim that genes have not evolved over billions of years.
  3. Primitive enzymes were probably promiscuous—they were able to catalyze reactions with a large range of related substrates [The Evolution of Enzymes from Promiscuous Precursors]. Many modern enzymes have broad specificity.
  4. Homologous enzymes with different, but related, specificities probably evolved from promiscuous ancestral enzymes following a gene duplication event and subsequent specialization of the two copies. Evolution in the two lineages occurs by a combination of natural selection and random genetic drift.
  5. It's possible to deduce the amino acid sequence of an ancient enzyme from a phylogenetic tree. Some ancient enzymes have been constructed and some of them react with multiple related substrates (promiscuous) as predicted.
  6. Therefore, it's reasonable to conclude that homologous enzymes with different specificities can evolve from promisuous enzymes in this manner.
I think you can see the difference between what Ann Gauger wrote and what I wrote. I don't ASSUME that evolution occurs, I state that it is a proven fact. It has been shown repeatedly that the frequencies of alleles in a population change over time and that natural selection and random genetic drift are responsible for those changes.

I then go on to say that there is overwhelming evidence to support the idea that genes have evolved in the past over a period of billions of years. This is not an assumption. It is supported by scientific evidence.

Given that evolution occurs, I then go on to outline a scenario for the evolution of two related enzymes with different specificities. In several case those predictions have been proven by reconstructing the ancestral enzyme and showing that it can catalyze a broad range of reactions. I've posted one example of duplicated genes caught in the act of diverging [Evolution of a New Enzyme]. In another case, you have the related enzymes lactate dehydrogenase and malate dehydrogenase that catalyze different reactions but you can convert lactate dehydrogenase to malate dehydrogenase by changing only one amino acid [The Evolution of Enzymes from Promiscuous Precursors].



Seems like a pretty sound argument to me.

Ann Gauger doesn't think so: Is Evolution True? Laying Out the Logic, Part 2. Here's why she thinks I am mistaken ...
Moran's statements #1 and #2 amply indicate that he believes evolution is true. The evidence for evolution that Moran says is so overwhelming is no doubt based on how similar things are, on the observation that they can (sometimes, considering some traits) be arranged in hierarchical groupings, and that they have changed over time. I acknowledge those facts. But that does not prove things got that way by a process of random mutation, selection, and drift. That has to be demonstrated.
That's a very interesting kind of logic. I assume she accepts the fact that antibiotic resistance can evolve by mutation and natural selection but balks at the idea that this process took place in the past. Even Michael Behe agrees that chloroquine resistance can evolve by mutation and natural selection.

I assume she knows that the genetic differences between humans and chimps are consistent with mutations and fixation of neutral alleles and that this data is roughly consistent with known mutation rates and rates of fixation according to population genetics [Why are the human and chimpanzee/bonobo genomes so similar? ]. I can only imagine how she manages to accept these facts but reject evolution.

Is she really saying that she accepts all the scientific facts but that she has a better explanation that accounts for all the data?
You see? Moran begins by assuming evolution is true, then hypothesizes a mechanism for how enzymes must have evolved, then concludes that his explanation is reasonable. But how much would he accept the story about ancestral proteins being promiscuous if he didn't believe wholeheartedly that enzymes had evolved by the standard evolutionary mechanism? His conclusion is based on his stated assumption.

That circularity, you may have noticed, is precisely what I said about evolutionary logic.
Do the IDiots actually believe this nonsense? Is she really saying that all evolutionary biologists are wrong because their entire field is based on a false assumption and false logic that is patently obvious to Intelligent Design Creationists but not to scientists?


107 comments :

  1. I have to say that I understand Ann´s logic but fail to see yours!

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    1. Only if you take the explicit contrary position - evolution is NOT true - could you dismiss out of hand the hypothesis that one possible mechanism of producing specific modern enzymes could be by differential tuning of alternative functions from a common ancestor.

      What are evolutionists supposed to do? "Evolution cannot be true because ..." "Well, here's a possible mechanism ..." "Hah! You're begging the question! Your mechanism only works if you assume evolution is true!". Well, duh. It's the very essence of what it means to 'hypothesise'.

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    2. Thank you for clarifying. I will give it some thought.

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    3. If evolutionists are skeptical about the findings of Ann´s results then they should either re-validate the test (if needs be re-run in an independent lab); perform their own tests to ´prove´ their point else accept Ann´s findings and move on.

      "..here´s a possible mechanism..." - By all means hypothesize but if the mechanism proposed cannot be tested then don´t claim it as science and certainly don´t claim it as ´a proven fact´ it is an assumption.

      To me Ann´s logic remains sound, Larry´s is circular and therefore flawed.

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    4. Ann is saying the protein equivalent of "you cannot turn a gorilla into a chimp, therefore evolution cannot be work that way". And she is restricting the mutational landscape to point mutation. Evolution is not proposed to work in either of those ways (or not exclusively, in the second case). I don't see how you conclude that her logic is thereby sound. There's not really anything to re-validate, experimentally.

      As to whether Larry's is circular, could you express his argument in a semi-formal manner, and demonstrate the circularity? It does not appear to be of the form

      X is true because of Y.
      Y is true because of X.

      eg
      "evolution is true because a promiscuous enzyme may have led to two descendant enzymes with different function.
      A promiscous enzyme may have led to two descendant enzymes with different function because evolution is true.".

      The truth of the matter may involve some other mechanism entirely, or there may indeed be no evolution. Nonetheless, if a promiscous enzyme leads to two descendant enzymes with different function ... that IS evolution, by definition (descent with modification). To say that a proposed evolutionary mechanism must not involve the assumption of evolution would be absurd.

      "..here´s a possible mechanism..." - By all means hypothesize but if the mechanism proposed cannot be tested then don´t claim it as science and certainly don´t claim it as ´a proven fact´ it is an assumption.

      Evolution does not rest upon the 'promiscuous enzyme' hypothesis - though, equally, that can be tested, as a mechanism.

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    5. Andrew Campbell says,

      If evolutionists are skeptical about the findings of Ann´s results then they should either re-validate the test (if needs be re-run in an independent lab); perform their own tests to ´prove´ their point else accept Ann´s findings and move on.

      I have provided you with links to several blog posts where I discuss published results from real scientists. They have deduced the structure of ancient enzymes and shown that they have broad specificity.

      They have shown that a series of mutations of this putative ancient enzyme can lead to two (or more) modern enzymes with different substrate specificities.

      To me that looks very much like direct test of a hypothesis.

      Allan, what does it look like to you and how do you interpret those results? Why do you think Ann Gauger fails to mention them?

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    6. Thank you both for your replies. That´s given me an awful lot more to think about!

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    7. Allan, what does it look like to you and how do you interpret those results? Why do you think Ann Gauger fails to mention them?

      Larry, it looks pretty much like the conversion of a promiscous enzyme into more specific ones! I certainly wasn't casting doubt on the plausibility or testability of the mechanism, but more on the argument that such an evolutionary explanation (or any other) would be 'circular'. As noted, evolution doesn't rest upon it, but nor is it untestable.

      Ancestral reconctruction does have limitations, of course, and hence conclusions must be tentative. But the findings are still more likely to be robust than Ann's method, as a guide to the capability of evolutionary mechanisms. By making the evolutionary assumption, you explore the likelier evolutionary paths. Throw away the evolutionary assumption, and your method can waddle up all the blind alleys you like, in proving that the mechanism you dismiss couldn't have gone there.

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    8. Allan Miller

      I'm not making an arbitrary "evolutionary assumption" in the way that Ann Gauger claims. The idea that two very similar proteins might share a common ancestor is supported by a huge amount of evidence. It would be perverse to ignore that data and postulate that they were independently created by some gods.

      Ann Gauger seems to imagine that the goal of these experiments (by real scientists) is to prove or disprove evolution. We're way beyond that.

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    9. To me Ann´s logic remains sound, Larry´s is circular and therefore flawed.

      It's been pointed out by mathematician Mark Chu-Carroll that any true statement eventually must reduce to a tautology (the more formal name for "circular argument"). For example, 2+2=4, once you perform the addition, becomes 4=4. So the critical point is not whether you can make a "circular argument" (in fact if you can't, it should worry you, because that means it's not true - 2+2 != 5).

      Rather, the critical point is whether you can either factually verify the point, or, without violating the rules of logic, get to the point from what can be factually verified. And what Larry has said is that indeed this critical requirement has been satisfied: The occurrence of these proteins as a result of evolution from a common ancestor is the result of well-verified facts and the logical implications of those facts.

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    10. @Larry and Allan - I was under the impression (rightly or wrongly?) that you assumed "..ancient enzymes must have been different.." If this is not the case (and sadly I do not have the expertise to know) then I am unable to answer your questions. I would be interested to know how Ann or Douglas would respond?

      @Judmarc - Interesting point you make about circular logic. I can see what you mean in the use of equations - Ohm´s law:- if V=10V and R=1k then I=10mA; and if R=1k and I=10mA then V=10V etc. While this is a useful check it doesn´t help if we ´assume´ any parameter to start with e.g. if V=10V but we assume R=2k then we can only ever assume I=5mA and then if we complete the circle it works because we end up with R=2k and erroneously deduce R MUST be 2k. Any error in any assumption ripples through to all derived parameters.

      So unless I am mistaken the crux of the issue is down to the statement highlighted by bFast and made by Larry: "I don't ASSUME that evolution occurs, I state that it is a proven fact." and whether it has been assumed or not. As much as I would like to I am unable to answer this with any certainty. Therefore I have to retract my accusation and leave it for others to address :-)

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    11. @Andrew: Personally, I doubt that for the last 500 million years at least, that enzymes have generally grown more specific or less promiscuous. Not as a general rule. However, where evolutionary theory applied to phylogenies would lead us to infer that an ancestral enzyme changed from an old function to a new one, most of the time it would go through an intermediate state that was promiscuous. That intermediate state could last 100 million years so it wouldn't be quite accurate to call it "temporary", but it could be more promiscuous than either the ancestor or the descendant.

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    12. Andrew,

      My own point was that 'making an assumption' is simply part of the scientific method. You take the position that something is a fact, and look for the consequences you would expect if that fact were true. Ideally, you also try to look for other explanations of the same data, and try to be your own severest critic. I think ID science sometimes omits that last check.

      Of course, evolution went beyond the 'hypothesis' stage years ago - even before the nature of the genetic material and code were established. I think this is why Larry bristles at my suggestion that the promiscuous enzyme mechanism involves an 'assumption'. It does only in the sense that all hypothesis testing does, but there are many independent verifications of evolution - it is not the hypothesis being tested.

      One sees the same 'circular' argument given against the statistical methods used to generate 'best fit' trees to molecular datasets based on their degree of sequence or structure similarity. The methods 'assume' that there is a real tree of common descent, and try to find the closest arrangement of the data that fits that assumption, and often incorporate other evolutionary 'assumptions' such as transition-transversion bias, property conservation etc. The fact that well-supported trees can be recovered from such datasets is actually a confirmation of the 'assumption' that they exist. One can test this by generating artificial data, one set involving copying and error, and another a bit more random, and setting your method loose on them. It will have a go at generating trees for both sets, but its 'assumption' in the second set is invalid, and the data sets can be clearly distinguished.

      If you have two different proteins with a high degree of sequence similarity, it is a very reasonable assumption that they are commonly descended. If (as Thornton does) you attempt to use the differences to 'reverse out' the changes, back to a common ancestor, and you find that the result is promiscuous, you have supported your simple assumption (common ancestry) and provided supporting evidence for the 'promiscuous enzyme' path. There are other potential mechanisms, though - not instead of, but as well as. But ultimately, all proposed evolutionary mechanisms must naturally 'assume' evolution, just as hydrology 'assumes' water.

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    13. Diogenes: However, where evolutionary theory applied to phylogenies would lead us to infer that an ancestral enzyme changed from an old function to a new one, most of the time it would go through an intermediate state that was promiscuous.

      Perhaps you can use a linguistic analogue for that. A word can become "promiscuous" in the functional sense by extending its meaning (e.g. a mouse is now, among other things, a computer appliance -- something it wasn't forty years ago. It can also become more specialised (e.g. the Old English precursor of the word meat meant '(any kind of) food'). It isn't uncommon for a word to become promiscuous and then specialised, so that its meaning crawls like an amoeba in semantic space. For example, the word knight (spelt cniht in old English) meant 'boy' 1200 years ago. Then it acquired numerous secondary meanings ('page', 'male attendant', 'servant of the shire', 'armed retainer', 'mounted warrior', etc.). About a century after the Norman Conquest, one of those extra meanings, a rather narrow one, but very important in the new social context of England as a feudal kingdom ('a member of the land-holding ruling class, owing military service to his lord and fighting on horseback') became dominant, and the original meaning ('boy') became rare by the thirteenth century. The word underwent quick specialisation, losing most of the intermediate meanings as well'.

      There are also many cases when a word with a rather general meaning becomes duplicated and each "copy" gets specialised. For example, moon and month were once declensional variants of one and the same "promiscuous" Proto-Germanic word meaning both 'moon' and 'month' (= lunar cycle). Another such case (plenty of them are known) is dicussed here [Shades and Shadows]. I suppose the mechanism will strike you as familiar.


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    14. @Diogenes, Allan & Piotr - thank you for your comments, they HAVE helped me as a layman to understand the biology somewhat. However I remain skeptical as to whether the diversity of life can be accounted for just by multiple unguided mutations and filtering, that is an extrapolation too far! And then there is Irreducible Complexity (I am sure you have views on that too!). Lastly my expertise is in Linear-Feedback-Shift-Registers, Pseudo-Random sequences, Correlation etc. and hence Information. I find it fascinating that although we have never met, the information you have generated in your consciences has entered my conscience and vice versa (a connection of information has been made.) You have correctly discerned that you have been conversing with a fellow human by recognizing patterns of ascii characters in these posts, yet why do some people discern design in nature while others only see the ´appearance of´ design? For me Information trumps Matter, and whether I am ridiculed or not I think Intelligent Design is the best fit so far. May you each have a happy Christmas.

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    15. Any error in any assumption ripples through to all derived parameters.

      That's why you test assumptions - to see whether the answers you get as they "ripple through" to the end of the calculation/scenario turn out to correctly reflect reality. And again, that's what Larry was talking about - the fact that these assumptions (a/k/a hypotheses) have been tested against reality and thereby proved.

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    16. sez andrew campbell: "…I remain skeptical as to whether the diversity of life can be accounted for just by multiple unguided mutations and filtering, that is an extrapolation too far!"
      Why?
      Last time I checked, the Earth's total population of bacteria is something like 10^30, and has been for quite some time, and the typical bacteria's genome is made of something like 2*10^6 base pairs. So there’s about 10^24 times as many individual bacteria as there are individual base pairs in any bacteria’s genome. Given that ratio, it seems to me that, to a first approximation, every physically possible mutation actually does —must—occur in bacteria. So, again to a first approximation, the simple occurrance of any given mutation X isn’t a problem; rather, the problem is whether or not any given mutation X occurs in an environment within which mutation X will be beneficial.

      "And then there is Irreducible Complexity (I am sure you have views on that too!)."
      Sure: My view, and that of mainstream biology since a guy named Muller wrote a very interesting paper back in 1918 (available at [ www.genetics.org/cgi/reprint/3/5/422 ]), is that Irreducible Complexity isn’t a problem for unguided evolution. Since you disagree, perhaps you might want to read the paper I provided a link to, and get back to us on where (you believe) Muller went wrong?

      “Lastly my expertise is in Linear-Feedback-Shift-Registers, Pseudo-Random sequences, Correlation etc. and hence Information.”
      That’s nice. As best I can tell, all “information”-based arguments ID-pushers have made against evolution are crap, and the reason they’re crap is that they can’t friggin’ measure the information content of arbitrary nucleotide sequences. Well, that’s one reason. Another reason is that they can’t explain how the hell the Designer installs “information” into nucleotide sequences. Nor can they explain how the exact same change-in-sequence can have vastly different consequences, based solely and entirely on whether that change-in-sequence is installed by a Designer (in which case, sure it can produce novelty and yada yada yada) or by an unguided mutation (in which case, no it can’t produce novelty and yada yada yada). Nor… well… let’s just say that ID-pushers have one king hell monster lot of work to do if they want to actually, like, support their anti-evolutionary assertions.
      You say don’t be silly, ID-pushers don’t need to measure the information content of arbitrary nucleotide sequences ? Well, perhaps not—but if that’s the case, how the hell do ID-pushers know whether or not unguided mutations can or cannot insert this ‘information’ stuff into arbitrary nucleotide sequences? Answer: ID-pushers do not and cannot know that—not unless they actually have some way to, you know, measure the information content of arbitrary nucleotide sequences.
      You say no, wait, ID-pushers can, too, measure the information content of nucleotide sequences, honest they can ? Great! Here are two arbitrary nucleotide sequences:

      Arbitrary nucleotide sequence 1: “gag tac aac gcc cta taa gtc atc gac ctt cat aag acc cga tag ttg agt ttc gtt tta”
      Arbitrary nucleotide sequence 2: “aaa tag gaa ctt gcg ctg atg tat atc taa tat gct aac caa acg aga att tgg cac atc”

      My question to you is, which of these two nucleotide sequences contains more information? If you choose to answer this question, please show your work—explain how you arrived at whatever your answer happens to be.

      “…why do some people discern design in nature while others only see the ´appearance of´ design?”
      This one’s easy: The ones who “discern design in nature” started out with the pre-installed presupposition that yes, Nature definitely was Designed. The ones who “only see the ´appearance of´ design”, contrariwise, didn’t start out with that presupposition.

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    17. Andrew,

      My background is biochemistry, but my job is computing, and I don't think that a viewpoint informed by engineering, either of the 'soft' or 'hard' varieties, really works. Information is clearly involved, with copying and translation, but what is produced is a 3-dimensional chemical structure - a functional RNA or protein. You have to take account of the degrees of freedom available to such structures, and the patterning of 'functional space', before you can dismiss their stepwise conversion as impossible because you can't stepwise change a program - or rustle up a jumbo in a breeze. They're just ... different! But it's up to you what you find persuasive, so I will simply wish you, too, a merry Christmas!

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  2. "I don't ASSUME that evolution occurs, I state that it is a proven fact."
    'nuf said.

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  3. If Gauger and Axe weren't hiding in the ENV sanctuary and would come here I would ask them:

    Has any evolution ever occurred? Does evolution occur now and will it continue to do so?

    If evolution has occurred and/or does/will occur, but not due to "the standard evolutionary mechanism" (random mutation, natural selection, and drift), can and will you name and demonstrate the mechanism(s) by which evolution has, does, and/or will occur?

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    1. I think they would answer no to your first set of questions, so you wouldn't get to ask the second.

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    2. "can and will you name and demonstrate the mechanism(s) by which evolution has, does, and/or will occur?"

      In my opinion, this is a fool's argument. One should not need to prove an alternative theory to be correct to falsify the existing theory. This particular study is an attempt to do just that -- an attempt to produce evidence that proves that, at least in this case, random mutation + natural selection cannot explain the proposed evolutionary mechanism.

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    3. TWT: "If Gauger and Axe weren't hiding in the ENV sanctuary and would come here I would ask them:

      Has any evolution ever occurred? Does evolution occur now and will it continue to do so? "


      Don't ever expect a satisfying answer.

      Gauger usually says something along the lines that, sure, some evolution happens but we don't know how much of what we observe is the result of evolution (roughly because models=assumptions). Her strategy is to turn this into her and Axe being more open-minded than evolutionary biologists who accept that evolution is the cause, because they don't assume evolution but claim they are open to it.

      For example, I would love Gauger to explain exactly what she thinks ancestral AA sequence reconstructions show if not approximations of ancestral AA sequences--why functional proteins can be produced this way, and why the patterns of increased substrate specificity that have been discussed here by Larry emerge. But specific answers will never be forthcoming from Gauger or from Axe because they are carefully working only to produce some negative results against a caricature of evolution, and not to create new ways of looking at the world. They want only to create doubt within which ID can exist. It is the genetical programme of the Wedge Strategy, and the last thing they want to do is replace their carefully cultured wedge with anything more concrete than doubt, and certainly not with anything testable.

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    4. This particular study is an attempt to do just that -- an attempt to produce evidence that proves that, at least in this case, random mutation + natural selection cannot explain the proposed evolutionary mechanism.

      And just how does it do that? If someone claims he is your cousin and you didn't believe him, how would you disprove his claim? Would you look at his children and see if any of them were your identical clone? You would if you were an IDiot like Anne Gauger.

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    5. bFast said: "One should not need to prove an alternative theory to be correct to falsify the existing theory. This particular study is an attempt to do just that -- an attempt to produce evidence that proves that, at least in this case, random mutation + natural selection cannot explain the proposed evolutionary mechanism."

      Thanks for admitting that IDiots have no positive evidence for ID. And no one is saying that IDiots have to "prove" their alternative, but IDiots do claim that their alternative (ID) is a scientific "theory" with positive, supported, scientific evidence and testable (and tested) scientific hypotheses/tools/methods, so it's not unreasonable to expect them to provide much more than bald assertions, evasiveness, religious sermons, misrepresentations, endless repetition of already refuted claims, blatant lies, false accusations, irrelevant and/or misleading experiments, and attacks on evolutionary theory and the non-IDiots who study evolution and other aspects of nature.

      Whenever IDiots are asked what the ID 'mechanism' is (or pretty much anything else about ID) they either don't respond, move the goal posts, spew religious crap, demand overwhelming evidence of every nano-detail of all evolution throughout all time, claim that there's no such thing as evolutionary theory (Joe G, etc.), misrepresent and attack evolutionary theory and non-IDiots, and/or or say that 'design' is the mechanism. When they're asked or challenged to provide details, evidence, new avenues of research, etc., in regard to the ID mechanism, they either don't respond, move the goal posts, go into attack mode, and/or baldly reassert that design is the mechanism and that they don't need to provide 'no stinking details, evidence, new avenues of research, etc.' They need to do a lot better than that if they expect to be taken seriously by honest, sane, scientifically minded people.

      And before you say it, yeah, science, including evolutionary theory, doesn't have all the answers, but IDiot-creationists have no positive, productive answers that were/are provided by using so-called ID "theory".

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    6. "This particular study is an attempt to do just that -- an attempt to produce evidence that proves that, at least in this case, random mutation + natural selection cannot explain the proposed evolutionary mechanism."

      Then why didn't they correctly perform their study with a set of enzymes from which we can elucidate their evolutionary history? Why did Axe and Gauger choose mutations from one extant enzyme, thought to be related to another for structure-functional reasons but with almost zero sequence based phylogenetic signal, to insert directly into another extant enzyme, when this is not what evolution postulates happened?

      Please explain in what way evolution is being tested with this strangely illogical methodology. Are you even capable of doing that? Do you understand that they are actually not testing evolution here because the method they are using is not what evolution says happened. How can their test then constitute a falsification of evolution?

      Please use your brain, stop being so credulous just because they are trying to prove something you already agree with.

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    7. Konrad said: "I think they would answer no to your first set of questions, so you wouldn't get to ask the second."

      I would agree that if they were 'honest' they would answer no. Even if they accept changes in the life on Earth I don't believe that they accept changes as 'evolution'. They obviously hate the word evolution and what it means (or what they think it means).

      Since IDiots are notoriously dishonest and evasive, Paul McBride's advice is good: "Don't ever expect a satisfying answer."

      Paul, I agree with your comments about Gauger's and Axe's strategy. Even though their strategy doesn't work on many people it does work on the rubes who prefer oogity boogity over reality. There's a sucker born every minute. :)

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    8. bFast: "One should not need to prove an alternative theory to be correct to falsify the existing theory. This particular study is an attempt to do just that -- "

      Stop right have. Are you saying that alleged "problems" of evolution are NOT evidence for intelligent design? This directly contradicts the long-standing policy of the Discovery Institute. We ask them "Where are the peer-reviewed publications presenting evidence supporting intelligent design?" and they, besides pointing to crackpot, fake-peer-reviewed articles in their vanity journal BIO-Complexity, list articles that only describe alleged "problems" of evolution, like Behe and Smoke 2004. This strategy presupposes that evidence against evolution is evidence for ID.

      So you admit they were wrong all along?

      "an attempt to produce evidence that proves that, at least in this case, random mutation + natural selection cannot explain the proposed evolutionary mechanism."

      Uh, as we have pointed out over and over, Axe and Gauger never tested this, or any, proposed evolutionary mechanism. Evolution says that A and B evolved by two separate pathways from a common ancestor C, which lacks the distinctive characters of A or B. So Axe and Gauger deliberately ignore that, start with A and try to intelligently design in one pathway straight to B, skipping C altogether. They fail; so that is a failure of the design hypothesis, not of evolution, because they were trying to design B.

      Typical creationist logic: "We have never seen B being designed by an intelligent being, therefore B was designed by an intelligent being."

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  4. There's enough independent evidence for evolution. It is still there even if you falsify the hypothesis that enzyme A is related to enzyme B via a common ancestor. To assume that evolution occurs is not illegal or circular here, because the hypothesis being tested is not, "Evolution is true." What's so difficult to understand here?

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    1. Gęsiarowski,

      Have you lost your mind...?

      What is the "independent evidence for evolution"? Is it some kind of crea-evoluo hybrids hiding in the Amazon rainforest who all of the sudden support evolution...? Why don't you just say: "I want to believe that evolution is true..." Or more correctly... "I need people to think that evolution is true..." without it you are just ... just less than an average linguist...

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    2. "Have you lost your mind...?"

      Says the troll who obviously never had one.

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    3. "There's enough independent evidence for evolution. It is still there even if you falsify the hypothesis that enzyme A is related to enzyme B via a common ancestor. "

      Good point. Of course, to falsify the hypothesis of the relation of enzyme A to enzyme B, you actually have to test the evolutionary hypothesis, not some strange design mechanism of your own fevered halluscination the way Axe and Gauger did. And not a single IDiot has spotted the error. I'm not at all surprised, they are the most credulous lot in existence. The higher ups in the IDiot movement has merely to open their mouthes and they are taken to be right by definition. Never a critical thought exchanged between them.

      I would like to see what kind of "peer review" Axe and Gauger's "paper" wen't through in their Bio-Complexity "journal".

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    4. I suppose Axe reviewed Gauger's contribution and vice versa. Axe is the managing editor and Gauger a member of the editorial board, so why drag in any outsiders?

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    5. without it you are just ... just less than an average linguist...

      Quest, let's pretend for a moment that I can take you seriously. We linguists often do the same thing when we establish relationships between languages resulting from shared ancestry. We reconstruct the common ancestor and all the steps leading to the modern forms. If you want to check whether French fils, pronounced [fis], and Spanish hijo [ixo] are related, you use the methods of historical linguistics and your independently gained knowledge of the history of the Romance languages to trace them back to a common ancestor, which happens to be Latin fīlius with minor complications (the Spanish word goes back to the accusative sg. fīlium). You don't attempt to reconstruct their history in a vacuum, ignoring what you already know.

      What Axe and Gauger do is the following: they show that [ixo] can't plausibly be derived from [fis] or vice versa, ergo they can't be related. If you point out that the actual ancestor was a Latin word, they will protest, IDiotically, that you assume a historical relationship between French and Spanish (via Latin as their common ancestor) instead of proving it. The objective of the exercise, however, is not to prove or disprove such a relationship (it has already been established beyond reasonable doubt), but to see whether a particular pair of words can be regarded as related, and how they have developed.

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    6. I love the analogy to language. It so completely blows away the common objections like random errors not being able to create new information (for example, the many random errors through history that led to me not writing to you in Middle English just now); microevolution (e.g., Middle English developing into Modern English) sharing nothing in common with macroevolution (e.g., Latin developing into French and Spanish); the need for two members of a species to evolve at once so they can reproduce (obviously one would require two people to begin speaking and writing French at the same time, otherwise they'd have no one to talk to, right?)....

      Of course now we will have the Language Institute present the alternative of Tower of Babelism, showing it is correct by finding problems with modern linguistics.

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    7. Let me just add that cognacy in linguistics is defined strictly in terms of common descent, no matter if the words in question are similar formally or functionally (i.e. express the same meaning). For example, Latin deus and Greek theós look vaguely similar and mean roughly the same thing ('a god' or 'God' in the cultural context of Christianity), but a common ancestor (with separate Greek and Latin derivations) cannot be reconstructed for them, so we conclude (for this and a variety of other reasons) that they are historically unrelated and the similarity is accidental. Now I suppose Axe and Gauger could take this negative result as "proof" that languages can't evolve, while in fact it only shows that etymological hypotheses are falsifiable.

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    8. Piotr, I have been trying to come up with a simple example of an analogy from the etymology of words to the biological idea of a "transitional fossil" or intermediate form. Specifically, I find many creationists define "transitional fossil" in ridiculous, Kafkaesque ways, e.g. as an animal that has a half-leg and half-wing and neither is functional, so it must die. Or they create phony and ridiculous phylogenies, like "cat evolving into dog", "bird evolving to horse", "snake to human", "cow to whale", "earthworm to vertebrate", "jellyfish to gorilla", etc. (These are all real creationist arguments BTW.)

      I wanted to succinctly shoot down all "cat to dog" claims of creationists by very simply defining a common ancestor of A and B as, e.g. having the common features of A and B but lacking the distinguishing features of A and B. And then maybe giving an example of an intermediate form between the common ancestor and one of the modern form "A"-- an intermediate that has some, but not all, of the derived features of "A", at least more derived features than the common ancestor.

      With biology I can think of many examples, but I was trying to think up a simple etymological case of two words deriving from a common ancestor, where

      1. some features of the ancestor can be reasonably guessed at from the modern words, and

      2. an intermediate form exists between the common ancestor and a modern word, which has more derived characters than the ancestor, but less than the modern word.

      Your example of fils / hijo / filium is interesting, but I don't think I could ever guess at any characters of "filium" just by knowing the modern words fils / hijo alone, nor could I explain to a lay audience how we could predict any characters of "filium".

      I don't know enough to build a concrete example, but I was thinking of things like how "frail" and "fragile" in English come from the same French word, or how "flood, flux, fluid and flow" all (I would presume) come from a common source. Help me out?

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    9. Diogenes,

      (Part 1)

      Reconstruction is a complex process. In biology, at least the genetic code is by and large fixed for all organisms; in linguistics, the "letters" of the code (language-specific sound systems) evolve, as do their sequences (morphemes and words). However, speech-sound changes tend to be regular, which means that the same sound in the same context usually changes in the same way. This makes it possible to group words into "lexical sets" based on phonetic criteria -- for example, French words beginning with [f] followed by a vowel. If you compare them with Spanish words with approximately the same meaning, you will discover that many of the Spanish counterparts begin with a orthographic h, no longer pronounced in modern Spanish. They may or may not be superficially similar to their French counterparts (e.g. faire : hacer, feuille : hoja, fumée : humo), but what counts is that the correspondence is systematic and high above the expected level of chance agreement. It must therefore mean something, and in fact it does: Latin [f] regularly changed into Medieval Castilian [h] in word-initial position, and that [h] regularly dropped out in the transition to Modern Spanish. French, however, has retained the original pronunciation (though it has accumulated many other changes). The Latin prototypes in the words above were, respectively, facere, folia, fūmus.



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    10. (Part 2)

      If you compare just two languages and don't know much about their "family background", high-resolution reconstruction may be impossible. But if you include a larger number of related linguistic taxa, things become much clearer. For example, beside hijo and fils we have Italian figlio, Portuguese filho, Galician fillo, Catalan fill, Romanian fiu, etc. Some of them can be regarded as "transitional" between Franch and Italian (with the same reservations as in biology). You see at a glance that Spanish is the odd man out with its mute h instead of [f], and since there is no reason to believe that Spanish is the "basalmost" Romance language (actually, in most respects it's very close to Portuguese and Galician), it follows that the original character state must be [f], and its word-initial loss is a Castilian innovation. This is of course confirmed by our direct knowledge of Latin (and by attested "transitional fossils" like Old Spanish fijo), but even if Latin were unattested, we would still be able to reconstruct "Proto-Romance" *f for this word. In fact, we reconstruct lots of languages not documented in written form, e.g. Proto-Germanic, Proto-Celtic, Proto-Indo-European, Proto-Bantu, Proto-Austronesian, etc. They are all "hypothetical constructs", but their reconstruction is based on the rigorous application of the comparative method (the most important part of which is the study of regular sound correspondences).

      "Horizontal transfer" is one major complication. Languages not only inherit and modify lexical stuff within the same historically continuous speech community, but often borrow words from other languages. Spanish has words inherited from the colloquial Latin of the former Roman province of Iberia, but it also has words borrowed from literary Latin in more recent times, words borrowed from other Romance languages, and words influenced by their Latin form. They stand out in the lexicon, since they don't conform to mainstream developments. For example, falso 'false' is a loan from Latin, not an inherited word, and hierro 'iron' has the variant fierro, influenced by Latin ferrum.

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    11. (Part 3)

      frail and fragile are a similar pair. They have the same source but different trajectories. Frail was borrowed by English from Old French fraile, which is a regular development of inherited Latin fragilis. The same word was borrowed into 14th-century French from book Latin as a literary word, and then from French into English as fragile. But apart from spawning families of paralogues in French and English, Latin fragilis and the related verb frangō 'break', also have an orthologue in English (and more generally in Germanic). Its identification is easier if you know that some instances of Latin [f] regularly correspond to Germanic [b] (cf. frāter : brother), and that Latin [g] regularly corresponds to Germanic [k] (genu : knee). To cut a long story short, English break and Latin frango are related; they shared a common ancestor a few thousand years ago.

      English flood and flow are both inherited and not borrowed from French. They both go all the way back to reconstructed Proto-Indo-European but -- quite surprisingly -- derive from two different (though similar) verb roots, bot meaning 'flow, float'. These roots may be ultimately related, but if so, it's a case of "deep coalescence", pre-dating the MRCA of Latin and English. Flux and fluid are Latin borrowings, and -- even more surprisigly -- are not historically related to flow despite the alliteration (though they are related to each other within Latin). The real Latin cousin of flow is pluit 'it rains', showing the same regular correspondence of the initials as father : pater, fish : piscis, or feather : penna (no kidding -- they are cognate). The fact that unrelated words with the same meaning may have a similar form is usually due to pure coincidence, but occasionally the similarity may be due to onomatopoeic convergence (a sequence like /pl-/ may be favoured in words associated with water and the noises it can make: plip-plop, plunge, splosh).

      I am not going to test Larry's patience by lecturing on historical linguistics here. I hope some analogies between linguistic and biological phylogenetic reconstruction are clear.

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    12. I made some spelling errors... let's create a course based on that.. Let students sped their valuable time to thing about it because that's what evolution of languages is all about... and we all need to know it or we are going to be deprived of true knowledge...

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    13. Piotr, thanks for all that explication, I will steal some of it.

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    14. Piotr has delivered an excellent rendition of Grimm's Law, the same German brothers who made a famous collection of fairey tales.

      Exactly this kind of analysis can be employed to deconstruct the Bible, determine the intent of the original texts before bowdlerizations not to mention the historical Jesus who bears little resemblance to the fantasy of the Current Gospels.

      But again we digress my apologies

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    15. But since Piotr brought up the subject of philology...

      Here is my favorite spoof on the subject

      Again my apologies

      Subject: Plucking the Yew! Before the Battle of Agincourt in 1415, the French, anticipating victory over the English, proposed to cut off the middle finger of all captured soldiers. Without the middle finger it would be impossible for the English soldiers to draw the renowned English longbow and therefore incapable of fighting in the future. The famous bow was made of the English Yew tree and the act of drawing the longbow was known as "plucking the yew" or "pluck you". Much to the bewilderment of the French, the English won the battle and began mocking the French by waving their middle fingers at the defeated French and saying "We can still pluck yew. Pluck you". Since "pluck yew" is rather difficult to say, the difficult consonant cluster at the beginning has gradually changed to a labiodental fricative 'F' and thus the words often used in conjunction with the one-finger salute. It is also because of the pheasant feathers on the arrows used with the longbow that the symbolic gesture is known as "giving the bird". And yew thought that yew knew everything.

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    16. A former colleague of mine once explained to me how she had (partially) reconstructed from scratch, a dead language from a small area in South Amercia. A language which hadn't been spoken nor written in over 150 years.
      Really fascinating stuff, lots of statistics involved, because she also had to reinvent the grammar and discover the usage of f.e. vowels combinations which weren't common compared to the modern 'western languages'. She did have a slightly better documented but also dead reference language from a nearby area with which she could reconstruct common ancestors of words. And work from there in reconstructing the dead language.

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  5. Gaugers mistake is the same mistake made by many IDers and Creationists. They think the interpretation of scientific data is akin to the description of a glass as half empty or half full: one can interpret it any way ones like depending on ones previous assumptions. While previous assumptions often do determine what is tested and what observations are made that doesn't mean the results will necessarily fit the assumptions.

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  6. It's really funny that "His conclusion is based on his stated assumption" is intended as a criticism. On what are we to base our conclusions if not on our premises?

    But actually her thinking begins to make sense once one realises that she misunderstands the whole point of the argument. She thinks that the point is to prove that evolution happened, which would indeed be non-sensical and circular to try to do in this way. She cannot see the difference between concluding that "homologous enzymes with different specificities can evolve from promisuous enzymes" (which is not a premise of the argument) vs concluding that "evolution happens" (which is a premise of the argument and would therefore be circular).

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    1. Konrad, "she misunderstands the whole point of the argument. She thinks that the point is to prove that evolution happened"

      Or you misunderstand what she is contending. She is not arguing that evolution (change over time) happened. She is questioning whether the mechanisms of random mutation + natural selection is capable of producing the evolution that did happen. Big difference.

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    2. Yes, that is also possible. In which case the only explanation for her accusation of circularity is that she is either stupid or disingenuous. I was trying to give her the benefit of the doubt, but sadly you may be right.

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    3. She is not arguing that evolution (change over time) happened. She is questioning whether the mechanisms of random mutation + natural selection is capable of producing the evolution that did happen. Big difference.

      Yes. And ancestral protein reconstruction shows that they are able to produce the very entities which she denies evolution can produce (without help from Jesus, that is). So just what is she missing? More to the point: What are you missing?

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    4. Gauger is very confused, and I think much of the confusion rests on ambiguity of the word "evolution". She equates it with natural selection and random mutation (and, just possibly, drift).

      Yet ancestral sequence reconstruction relies on none of this. It relies on another meaning of evolution, i.e. common descent with branching. The mechanisms by which changes (fixations) are introduced into the tree is irrelevant to reconstruction, just the branching sequence and lengths of the branches. It's hard to tell whether she denies that. She may be carefully avoiding taking a position, or she may not understand the difference. Either way, a problem for her.

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    5. John Harshman: "She may be carefully avoiding taking a position, or she may not understand the difference."

      The former, I'm sure. She spends lots of time discussing the limitations of phylogenetic models and their assumptions, and her conclusions are usually along the lines of the jury now being out on something those damned evolutionists thought was sewn up. Her focus is strongly on creating doubt, and then being able to step back and say "Who knows?" as if hers is the open-minded position. I think it's quite a deliberate strategy.

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    6. "Or you misunderstand what she is contending. She is not arguing that evolution (change over time) happened. She is questioning whether the mechanisms of random mutation + natural selection is capable of producing the evolution that did happen. Big difference."

      Which is a totally fine question worth asking. But to answer it requires you actually do the experiment correctly, by mimicking the proposed evolutionary history of the enzymes in question. She didn't, so her test can't be used to conclude what she wants to. I have already given several hefty criticisms here and in the previous thread and I contend she and Axe went out of their way to make their test unsuccessful.

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    7. Harshman: "Yet ancestral sequence reconstruction relies on none of this. It relies on another meaning of evolution, i.e. common descent with branching. The mechanisms by which changes (fixations) are introduced into the tree is irrelevant to reconstruction, just the branching sequence and lengths of the branches."

      Well no, that's not the whole story. The mechanism by which changes are introduced is not irrelevant, bevause Thornton and others doing ASR did not just theoretically deduce the ancestral sequence, they resurrected it and intermediates leading to it, and tested them to see if viability went up or down at each step. That's relevant to showing NS made the changes.

      Ancestral Sequence Reconstruction does not test the mechanism of change, but Ancestral Sequence Resurrection does test the mechanism.

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    8. In my limited understanding, ASR incorporates models of substitution and/or insertion in trying to retrodict the past versions of molecules at the branch points(incorporating knowledge of the genetic code also, such that we are able to make probability estimates concerning whether a substitution is likely to result in a codon-change to another amino-acid). If we did not have such models, I don't see how it would even be possible to elucidate what the ancestral state most probably would have looked like. For example, that transition mutations are more frequent than transversions, and which transitions are more likely than others etc.

      When such models are used to calculate the probable ancestral states, and the ancestral state is biochemically resurrected and tested for it's function, that the mechanism by which the modern versions arose was through the modeled mechanism used to retrodict the ancestor molecule. In other words, ASR does test the mechanism by which the modern versions arose, it is the very mechanism, the mechanism of substitutions for known chemical reasons, that gave rise to the extant molecules from the ancestor in the first place.

      No IDiot has grasped this point. I have never even seen them discuss or even attempt to criticize ASR in any of their work. It is either being dismissed out of hand with no explanation (it's assumptions, as we see Gauger do above) or plainly ignored as if it doesn't exist. It is obvious why, it utterly annihilates their work.

      I can only repeat myself from the previous thread with a KEY QUESTION FOR IDiots: If evolution did not take place, and mutations invariably always degrade and destroy god's supernaturally designed proteins, why did ancestral sequence reconstruction, a method based on assumptions about how molecular evolution takes place (mutations producing branching patterns of descent), manage to reconstruct a functional and promiscous enzyme ancestor? How's this possible when the process is only based on trees and substitution models, not on structure or function? Shouldn't functional molecules supposedly be totally isolated and unreachable in sequence space?

      I have yet to hear from a IDiot creationist who even understands the question.

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    9. BFast: "She is not arguing that evolution (change over time) happened. She is questioning whether the mechanisms of random mutation + natural selection is capable of producing the evolution that did happen."

      I like how whenever IDcreationists are proven factually wrong, they claim they're just "questioning" evolution. Creationists never ask questions; they make statements, and we show their statements are factually wrong, and instead of conceding that they were wrong, they say, "I was just askin' a question." No you weren't. Creationists never ask questions; they make confident statements that are flat wrong.

      Axe and Gauger once claimed to have proven that functional protein sequences occur in only 1 out of every 10^77 possible amino acid sequences. This number was wrong-- they started with a half-crippled mutant enzyme, and made mutants off that, but tested the mutants for just one function, not for all possible functions-- but if hypothetically that were true, it would demolish intelligent design.

      Thornton and coworkers use ASR to reconstruct the common ancestral sequences of modern proteins, assuming evolution back to a common ancestor is true. They resurrect the ancestral protein and test it. It's functional. If evolution were true, we expect that to happen. If ID were true, the odds against the sequence being functional are 1 in 10^77. Which hypothesis would you believe?

      Thornton et al. go beyond that and construct intermediates between the ancestral and the modern proteins. Some of those are functional too, enough to pick out an evolutionary pathway. Suppose Thornton et al. resurrect and test 3 ancestral or intermediate sequences and they're all functional. If ID were true and evolution were not true, the odds against that happening are 1 in (10^77)^3 which is 1 in 10^231. Which hypothesis would you believe?

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    10. lutesuite: "And ancestral protein reconstruction shows that they are able to produce the very entities which she denies evolution can produce (without help from Jesus, that is)." I seem to recall that Steve Benner and his group did exactly that with alcohol dehydrogenase around 20 years ago (I heard him talk about it in 1996, so presumably he did the experiments before that). I've had difficulty tracking down the reference, so I'll quote from memory, which may of course be faulty. They deduced from sequence analysis what the ancestral enzyme should have been like (both in sequence and properties) before the appearance of the flowering plants. They then synthesized it, and found that it had the properties that they predicted. Something like that, anyway.

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    11. Ancestral sequence reconstruction models, as far as I know, do not incorporate selection; they may incorporate it indirectly, as observed rates of substitution may be used to estimate parameters. But most models implicitly assume neutrality.

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    12. @John Harsman

      You are correct, ASR does not assume selection took place, only that the mechanism responsible for substitutions is chemical(the well-known reasons for transition vs transversion bias). This is what implies the different enzymes weren't produced by deliberation, as in a designer choosing which amino acids to insert, but that the extant sequences arrived through series of mutations over generations. Whether these were retained through selection or drifted is immaterial with respect to that point.

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    13. Thanks for the transition vs. transversion point. I didn't know what that was, looked it up, and learned something.

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    14. Mikkel,

      Sorry, but that doesn't say the designer didn't do it, as long as he's a designer who works by fixing specific mutations at various points in history. Which is apparently exactly the designer Michael Behe believes in.

      Gauger, not so sure. I think she's actually denying common descent. Hard to tell, because most IDiots who are "poof" creationists won't come out and say it. They only "have doubts" or say "the evidence is weak". Gauger, Meyer, and Dembski are like that.

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    15. Well no, it doesn't deductively prove that the designer was not a chemical reaction, I have to concede that. There is no observation that cannot be ad-hoc rationalized with "that's what the designer wanted" :P

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    16. Sorry, but that doesn't say the designer didn't do it, as long as he's a designer who works by fixing specific mutations at various points in history. Which is apparently exactly the designer Michael Behe believes in.

      Is that really what Behe believes? I thought he believed that God causes certain mutations to occur together at the right time. Not that he has, to my knowledge, ever clearly spelled out exactly how he thinks the "designer" operates.

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    17. He's never specified any pathway, to my knowledge, other than that if multiple mutations are required, he commonly assumes that they are individually deleterious and so must have happened simultaneously. He never says that multiple mutations must be simultaneous in other situations.

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    18. No, Behe has actually specified the mechanism of biological change quite precisely.

      Larry Arnhart writes: "A few years ago, I lectured at Hillsdale College as part of a week-long lecture series on the intelligent design debate. After Michael Behe's lecture, some of us pressed him to explain exactly how the intelligent designer created the various "irreducibly complex" mechanisms that cannot--according to Behe--be explained as products of evolution by natural selection. He repeatedly refused to answer. But after a long night of drinking, he finally answered: "A puff of smoke!" A physicist in the group asked, Do you mean a suspension of the laws of physics? Yes, Behe answered. Well, that's not going to be very persuasive as a scientific answer. And clearly Behe and other ID proponents prefer not to answer the question."

      [Larry Arnhart, Sept. 7, 2006]

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  7. In the case presented whether evolution otherwise is proven is beside the point.
    She is making a scientific investigation and so its based on the test.

    Yes all evolutionary biologists could be demonstrated to be wrong by the flaws in simple logic of their claims.
    Wrong ideas can be the fault of wrong reasoning without being the fault of thoughtful speculation.
    Its not shocking that the small circles of paid evolutionists got it wrong.
    Evolution was never based on biological scientific evidence. ot was based on other evidences. However it included flaw reasoning.

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    1. "She is making a scientific investigation and so its based on the test."

      The test she is performing is a test of a design-postulate: Similar structures were derived from each other by purposeful design. She picks an enzyme that is structurally and functionally similar to another, then she starts inserting mutations from one enzyme into the other to see if she can convert it's function into the other enzyme. She fails, in that she produces a dead protein that does not catalyze any of the desire reactions. Therefore, her design methodology has failed. What we can conclude is that her design-methodology is not working, that's not how the designer operated.

      Oddly enough, every time we can reconstruct the histories of related enzymes and proteins, it looks like the designer was using evolution to do it's work.

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  8. In contrast to Robert Byers I look at the facts.
    Gauger said This begs the question of whether evolution is true. It is a circular argument unsubstantiated by the evidence and unfalsifiable. No one can know what ancient enzymes actually looked like, and whether they really had such broad catalytic specificities.

    Since there is in fact very much evidence that evolution is true, It makes no senes doing ghat Gauger does, starting from a preconveid claim that evolution is not true and make circular arguments from there on.

    AFAIK, much is known about enzymes and autocatalytic reactions and there are very good reasons we should not jump to conclusions about what is impossible like Gauger does.

    It takes quite a bit more effort than what Gauger is capable of to falsify the theory of evolution. Would Byers care to compare his "small number of paid evolutionists" to the number of paid creationists - and their credentials?

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    1. Odd statement! Gauger is making a test. This test might not end evolutionary ideas once and for all but its adding to it.
      I think she has a good hunch of how to seriously test evolutions presumptions.
      Its strange on this thread how much the evolutionists cling to EVOLUTION IS TRUE as opposed to proving hjer test fails.
      HMMM.
      I bet there is a lot of tests like this.
      How many paid evolutionists are there ic Canada or toronto??
      Who actually think, write about, write papers, do research on evolution.!
      Not mere students repeating things.
      I don't know. i suspect its in the dozens, or hundreds, only.
      creationism is not fighting very many people.
      Thats why evolution sticks around too long and why a few creationists really are agents of change.
      its very small circles about great conclusions.
      The error of evo bio will fall in our time. too many thinkers, like Gauger, smell blood and a chance to be revolutionaries in intellectual pursuits.

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  9. Strange how chipping away at a protein gorilla cannot turn it into a protein chimp, and yet essentially random synthetic peptides are found with promiscuous activity that can rescue function in multiple different E Coli nutritional knockout mutants, from a tiny (1.5 million) random subset of the 10^52 possible variants.

    http://pubs.acs.org/doi/abs/10.1021/jp212438h

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    1. Interesting study. I dug through the references and alighted upon this recent one that has some intersting implications for early evolution and origin of life research:
      Short peptides self-assemble to produce catalytic amyloids

      Simple, 7-amino acid long peptides with a whole host of useful biological functions. If Axe and Gauger's idiotic "only 1 in 10^77 polymers is functional"-assertion was correct, this study should simply not be possible. It is also interesting how such short peptides still turn out to be functional biocatalysts in conjunction with metal cofactors, despite their lack of ability to fold into larger structures alone.

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    2. Oh, come on! Defending science with science is circular reasoning! ;)

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    3. Mikkel,

      Yes, another interesting link. It's interesting how many catalytic peptides actually grab a metal ion and use it as a kind of 'spot-welder'.

      An important aspect of both papers is the essential modularity of protein construction. It's a naive view to suppose that 100-acid protein space is probed by point mutation from a random 100-acid start point. In fact, units such as a single turn of an alpha helix can be produced from very few residues, and with high probability since it simply requires a patterned alternation of hydrophilic and hydrophobic sites. End-join two such units together, or further join larger modular chunks, and you can soon produce a lengthy spiral. If you want to eliminate evolutionary pathways, you have to make sure such modular insertions and deletions are blocked off too, not just the point-mutational route. The space has many more dimensions.

      All that said, I do give Axe and Gauger credit for at least attempting to tackle the issue experimentally, for all the apparent misunderstandings.

      I'm just waiting for someone to notice that, in both the linked papers, there was an element of 'design'!

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  10. "So Axe and Gauger deliberately ignore that, start with A and try to intelligently design in one pathway straight to B"

    If evolution is true, why don't squirrels evolve into birds? That's the question being asked by Axe and Gauger.

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  11. "Therefore, her design methodology has failed."

    What Gauger and Axe have demonstrated is that design is impossible, at least design by their methods. Their experiment does not speak to the possibility of extant sequences having evolved from a common ancestor that is neither.

    But it is good of them to call attention to this site. That's a worthwhile thing.

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  12. Larry,

    I don't think that promiscuous is a good way to talk about ancestral enzymes. After all, biochemists measure enzyme specificity in comparative terms, as in lactate dehydrogenase catalyzes conversion between lactate and pyruvate 1000 times better than conversion between malate and oxaloacetate. Attempts at converting LDH to MDH work on this specificity measure (and have been quite successful). This would mean that, in principle, enzymes might be promiscuous today, not just in the past, only their specificities can move at times much, at times little.

    The second issue is that enzymes work at a wide range of actual binding and catalytic constants, so evolution works with two thingies, maybe at the same time, whatever. One of them as above, specificity (one substrate over another), the other is the actual kcat. That thing varies a lot between enzymes and their preferred substrates. So, there we have some degrees of freedom for evolution too.

    Anyway, my point is that the proposal of "promiscuous" enzymes in the past is unnecessary and misleading, since promiscuity is a rather vague term, and since there's no reason to propose such a thing in order to understand the evolution of new and improved enzymes from gene duplication. What we need is proper understanding of chemistry and biochemistry.

    I hope that was clear enough. Not much we can do in a blog comment.

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    1. I don't think that promiscuous is a good way to talk about ancestral enzymes.

      I agree. It makes them sound slutty. The religious already have enough reason to reject science without adding that to the list.

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  13. I'll briefly summarize the entire research career of Axe and Gauger, and all their research results, and all their arguments. Let's imagine they're presenting their experimental results to a real scientist, let's say, Joe Thornton.

    Axe and Gauger: Proteins A and B both exist in distantly related organisms alive today. Therefore, Darwinists believe A turns into B.

    Scientist: No, evolutionary theory says that A and B descended from a common ancestor.

    Axe and Gauger: So, to test Darwinism, I hit A repeatedly with a hammer and it did not turn into B. Therefore, Darwinism is falsified.

    Scientist: No, evolutionary theory does not say that B was created by repeatedly hitting A with a hammer... It says A and B descended from a common ancestor.

    Axe and Gauger: But I hit A with a hammer many times.

    Scientist: &%#$... There aren't any &%#% hammers. Evolutionary theory says that A and B descended from a common ancestor, which was neither A nor was it B.

    Axe and Gauger: My results make sense, because if a giant tornado were to randomly scramble all the parts in A, they wouldn't assemble into B by blind chance.

    Scientist: Look, evolutionary theory does not say that B was created by a giant tornado randomly scrambling all the parts of A, it says A and B descended from a common ancestor through processes of random mutation, genetic drift, and non-random natural selection. There aren't any %#$! tornadoes.

    Axe and Gauger: Next we broke up A into its substituent atoms, and the atoms did not spontaneously assemble into a Toyota Prius. Therefore, Darwinism is falsified.

    Scientist: Evolutionary theory is about biological complexity, living organisms. With like sex organs and stuff, that make babies, and have DNA, and get mutations! It's not about a $%#! Toyota Prius that doesn't have any of those things!

    Axe and Gauger: We cut open a frog and its guts spilled out. Its guts did not spontaneously re-insert into the frog. Therefore, Darwinism is falsified.

    Scientist: Evolutionary theory does not say that frog guts evolved by spontaneous insertion into a frog! It says amphibians descended from a fish-like animal that already had a gut!

    Axe and Gauger: You're begging the question. You're assuming that fish exist. Sure, Darwinists say these things called "fish" exist, but has anyone ever seen one?

    Scientist: It's not begging the question if we have independent $%#! evidence that FISH exist!

    Axe and Gauger: We're just askin' a question. Why do you get mad at people for questioning evolution?

    Scientist: That's not how you "question" a theory! To question a theory, you can't just make stuff up. You have to first assume the theory is true, and then compare your real-world observations against those testable predictions which logically follow from the theory!

    Axe and Gauger: So you're admitting that you just assume evolution is true. That's circular logic.

    Scientist: %$#!... That's how you test theories! You have to assume a theory is true, in order to determine what are its testable predictions that you should compare against observations!

    Axe and Gauger: Hitler was a Darwinist.

    Scientist: Hitler wasn't a $%#! Darwinist! Hitler never even said the name "Charles Darwin"!

    Axe and Gauger: Well now there's a controversy. Why aren't schools allowed to teach the controversy? Why do you get mad at people just for questioning evolution?

    ReplyDelete
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    1. A couple additions:

      1) The hammer is a ball-peen. Take proteins that range from 2/3 to 4/5 different, make 10^5 or so variants, select. Pretty pathetic. How can they extrapolate to their big-big numbers from tiny samples?

      2) Ignore that many modern enzymes have been readily modified to greater specificity. The literature is out there. Conclude instead that: "Modern enzymes can't evolve"

      3) Ignore that there are enzymes, in nature, that catalyze the BioF and Kbl reactions from the same active site: http://www.ncbi.nlm.nih.gov/pubmed/22484932

      Do NOT use those as a starting point in making more specific enzymes.

      Conclude instead: "Kbl2 is comprehensively suited to one function, while
      BioF2 is comprehensively suited to another."

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    2. Dino-gene,

      Didn't you claim that Larry and his students have been doing experiments in his lab with proteins and their results supposedly contradicted Axe and Gauger experiments and not speculations...? When are we going to see the papers that apparently were published...? Please tell me that they are not still peer-reviewed...? Or even worst they got " Dr. No " stamp on the abstract.... LMAO!!!

      Delete
    3. Pest: Didn't you claim that Larry and his students have been doing experiments in his lab with proteins and their results supposedly contradicted Axe and Gauger experiments and not speculations...?

      No. I made no statements about Larry's work nor his students. Be more specific and I might know what you're talking about.

      Delete
    4. The only thing I remember was that it was either you or Larry or both claiming that Axe and Gauger's experiments reg. Protein evolution and their claims were not valid; that there is not enough time in Earth's history for proteins to evolve beyond 6 or 7 mutations... you both possibly said "...Larry's undergrads are doing experiments and publishing papers that disproved Axe and Gauger's claims..." that is all I can recall but I may be wrong about the exact details...

      Delete
    5. Diogenes I bow my head in awe of your brilliance!

      Quest- pluck yew

      Delete
  14. "I've posted one example of duplicated genes caught in the act of diverging [Evolution of a New Enzyme]. In another case, you have the related enzymes lactate dehydrogenase and malate dehydrogenase that catalyze different reactions but you can convert lactate dehydrogenase to malate dehydrogenase by changing only one amino acid [The Evolution of Enzymes from Promiscuous Precursors]."

    So you can step an a stone near the shore and you conclude that you can safely cross the ocean by random walk.

    Professor Moran I ask a hundred times What is your best you can demonstrate by random errors?

    Professor Behe has demonstrated that all you've got is nothing. Every time you show us that all you've got is nothing.

    further questions: what is the last common ancestor of Kbl2 and BioF2. What are the ancestors up to their last common ancestor?

    ReplyDelete
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    1. Hey unknown, you must have traced every single one your ancestors back to 'Adam and Eve', because otherwise you don't exist.

      In 6K years, that would mean somewhere between 100 to 150 generations. Do tell, who's your 75th grandmother of your mother? And the 45th grandfather of your father?

      Delete
    2. Hey Ed, stick to the subject instead of asking stupid irrelevant questions.

      Delete
  15. M Behe on an ancestral protein reconstruction:

    "1) This continues the venerable Darwinian tradition of making grandiose claims based on piddling results. There is nothing in the paper that an ID proponent would think was beyond random mutation and natural selection. In other words, it is a straw man.

    2) The authors (including Christoph Adami in his commentary) are conveniently defining “irreducible complexity” way, way down. I certainly would not classify their system as anywhere near IC. The IC systems I discussed in Darwin’s Black Box contain multiple, active protein factors. Their “system”, on the other hand, consists of just a single protein and its ligand. Although in nature the receptor and ligand are part of a larger system that does have a biological function, the piece of that larger system they pick out does not do anything by itself. In other words, the isolated components they work on are not irreducibly complex.

    3) In the experiment just two amino acid residues were changed! No new components were added, no old components were taken away.

    4) Nothing new was produced in the experiment; rather, the pre-existing ability of the protein to bind several molecules was simply weakened. The workers begin their experiments with a protein that can strongly bind several, structurally-very-similar steroids, and they end with a protein that at best binds some of the steroids ten-fold more weakly. (Figure 4C)

    5) Such results are not different from the development of antibiotic resistance, where single amino acid changes can cause the binding of a toxin to a particular protein to decrease (for example, warfarin resistance in rats, and resistance to various AIDS drugs). Intelligent design proponents happily agree that such tiny changes can be accomplished by random mutation and natural selection.

    6) In the “least promising” intermediate (L111Q) the protein has essentially lost its ability to bind any steroid. In the “most promising” intermediate protein (the one that has just the S106P alteration) the protein has lost about 99% of its ability to bind DOC and cortisol, and lost about 99.9% of its ability to bind aldosterone. (Figure 4C)

    7) Although the authors imply (and Adami claims directly) that the mutated protein is specific for cortisol, in fact it also binds aldosterone with about half of the affinity. (Compare the red and green curves in the lower right hand graph of Figure 4C.) What’s more, there actually is a much larger difference (about thirty-fold) in binding affinity for aldosterone and cortisol with the beginning, ancestral protein than for the final, mutated protein (about two-fold). So the protein’s ability to discriminate between the two ligands has decreased by ten-fold.

    8) One would think that the hundred-fold decrease in the ability to bind a steroid would at least initially be a very detrimental change that would be weeded out by natural selection. The authors do not test for that; they simply assume it wouldn’t be a problem, or that the problem could somehow be easily overcome. Nor do they test their speculation that DOC could somehow act as an intermediate ligand. In other words, in typical Darwinian fashion the authors pass over with their imaginations what in reality would very likely be serious biological difficulties.

    9) The fact that such very modest results are ballyhooed owes more, I strongly suspect, to the antipathy that many scientists feel toward ID than to the intrinsic value of the experiment itself.

    10) In conclusion, the results (and even the imagined-but-problematic
    scenario) are well within what an ID proponent already would think Darwinian processes could do, so they won’t affect our evaluation of the science. But it’s nice to know that Science magazine is thinking about us!"

    ReplyDelete
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    1. Could "Unknown" be Michael Behe? He seems utterly enfatuated with everything he says, almost as if Behe is a reincarnation of Jesus. Behe has merely to type something on his computer and "Unknown" is sold. Behe has spoken, the matter is settled!

      Delete
    2. Behe's a professor of biochemistry, don'tcha know?

      If the aldosterone binding result is a big yawn, perhaps Unknown could suggest a peptide pair that does display IC? Preferably two with some sequence homology.

      Delete
    3. Mikrael the ventologist,

      I think Witon got out... He used to love quoting Behe, Ventor and what's his name...? the guys with the bird...

      Delete
    4. Unknown,

      You are going to get slaughtered here by Larry, Dino-genes, Johnny Harsh and our beloved Joe Franks... These people eat Behe and his work for breakfast... Don't be fooled by their resistance to answer the big questions... Larry promised me and his bloggers that he was going to answer ALL MY QUESTIONS when he was absent from the blog for over a month... when Larry says he will do it, he surly will... the only tiny problem might be the timeframe...I have no idea when or where those answers are coming but hopefully before Larry retires...

      Delete
    5. Hey "Unknown", what happened to your demand we write an "open letter" to the clown of Dover? You were all into that. Then I said I'd go you one better than your "open letter", I'd debate Behe face-to-face in his home state of Pennsylvania. He can bring along Dembski, Axe, Gauger, Ray Comfort, Megan Fox, Kent Hovind after he gets out, any creationist he can find who's not in jail. On this condition: ENV must have an open comment policy forevermore.

      I said I'd debate the clown of Dover and you clammed up pretty quick and ran off for a few weeks. Whyzat?

      Bock bock bock.

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    6. Dino-gene,

      What debate...? Did I miss something interesting...? Who and what issues did you want to debate...?

      Delete
  16. Enzyme expert exposes evolution’s error

    Former Darwinist Dr Matti Leisola obtained his D.Sc. (Tech) in biotechnology from the Helsinki (Finland’s capital) University of Technology in 1979. His extensive career includes winning the Latsis Prize for a significant young researcher in 1987 in Switzerland, being Director of Research (1988–1997) in an international Biotech company, and most recently Dean of the Faculty of Chemical and Materials Sciences at the new Finnish Aalto University. He has published over 120 papers, mainly on enzyme research, authored 20 articles in books or conference proceedings, and obtained six patents. Dr Leisola’s scientific articles are cited about 1300 times in the scientific literature.

    etter known to the scientific community as an expert in his area of enzymes. Dr Leisola explains:

    “I like to call enzymes ‘the tools of life’. They are a type of protein—a macromolecule (large molecule) made out of specifically arranged amino acids. They are life’s catalysts—that is, they greatly speed up specific chemical reactions of living cells. Enzymes recognize, convert, transfer, transport, oxidize, reduce, join molecules together and break them apart.”

    The instructions to build them are encoded on our DNA. Dr Leisola explains that just as the Finnish language has 29 letters,1 so the enzyme language has 20 biochemical ‘letters’ (amino acids), each of which is coded by three-letter ‘words’ in the DNA language (which has four different letters). For example, ‘Matti Leisola’ is a specific combination of 12 letters and one space. “This combination is so specific that it helps anybody to find me out of all the people in the world since no one else I know of has this same combination. An average enzyme contains about 300 biochemical letters. This makes each enzyme very specialized for a given task.”

    stockphoto.com
    A model of the enzyme xylanase—a complex machine made up of precise sequence of amino acids
    A model of the enzyme xylanase—a complex machine made up of precise sequence of amino acids
    For example, Matti’s group studied an enzyme called xylanase (see diagram right). It breaks down one of the most abundant carbohydrate polymers on earth called xylan, found in plant cell walls. This fibre makes up about 30% of the birch tree. The xylanase enzyme contains about 200 amino acids. Its protein code is a sentence that means: ‘degrade xylan’. Mammals lack this enzyme, so they can’t digest xylan.

    Using a different letter for each different amino acid, the protein ‘sentence’ can be written as:

    ASINYDQNYQTGGQVSYSPSNTGFSVNWNTQDDFVVGVGWTGSS
    APINFGGSFSVNSGTGLLSVYGWSTNPLVEYYIMEDNHNYPAQGTVK
    GTVTSDGATYTIWENTRVNEPSIQGTATFNQYISVRNSPRTSGTVTVQ
    NHFNAWASLGLHLGQMNYQVVAVEGWGGSGSASQSVSN

    As with all enzymes, it is this sequence which enables this molecular machine to carry out its task. There is nothing about the chemistry or the physics of the amino acids that make up xylanase that will cause them to be ordered in the correct way. The order—the information—is imposed upon the matter via the sequence in which the amino acids are assembled, under programmed instructions within the cell.

    Rejecting evolution

    We interviewed Dr Leisola because he is known as a skeptic of molecules-to-man evolution, which he calls “story-telling”. But he was not always skeptical, as he explains:

    “I believed the standard story till I was about 22 years old. I used it (as I then thought) as a powerful weapon to argue against the Christian God. Without realizing it, I was a typical product of the western naturalistic educational system and I certainly wanted to remain autonomous, and actually hated the idea of God interfering with my life.”

    ouch..

    Ful article:

    http://creation.com/matti-leisola-interview

    ReplyDelete
    Replies
    1. I beg your pardon -- what error does Dr Leisola expose?

      Delete
    2. Bacteria-to-biologist evolution has no bearing on real scientific work, but many claim that mimicking evolution, i.e. random changes and artificial selection, has enabled new enzymes to be produced. However, Dr Leisola is actually an expert in this area, and points out:

      “These methods—even when under careful control—do not create anything but minor adaptations or variations on a theme. My research group has, for instance, engineered enzymes to function better in extreme conditions, and microorganisms to produce novel molecules. But these achievements have a well-designed enzyme to start with, are intelligently controlled, and there is always a limit to the extent of the change. It’s no wonder that living cells resist random changes because these are almost always downhill.”

      Is that true? A well-designed enzyme? .... hmmmmm

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    3. "Living cells resist random changes"? What's this supposed to mean? The most charitable reading of this paragraph is that there are limits to what intelligent engineering "under careful control" in his lab has achieved. OK, this may suggest that intelligent design is rubbish, but we've known it all along.

      I wouldn't believe everything what a notorious young-earth creationist has to say. I don't doubt he's a skilled technician, but if he's managed to convince himself that the world is a few millennia old and Noah's Flood really happened, he must be very, very good at ignoring any amount of scientific evidence.

      Delete
    4. "But these achievements have a well-designed enzyme to start with,"

      Note circular logic: we know they're designed because they're designed.

      "are intelligently controlled, and there is always a limit to the extent of the change."

      Another failure of intelligent design.

      So, in our uniform past experience, we've never observed new protein functions being created by an intelligent being. Therefore, all protein functions were created by an Inttelligent Being.

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    5. This is one sentence in this that stands out for its extraordinary dishonesty:

      The xylanase enzyme contains about 200 amino acids. Its protein code is a sentence that means: ‘degrade xylan’.


      What garbage. There is nothing like human language in any gene or protein sequence. No verbs, no grammar, nothing. "Degrade xylan" is a sentence in human language created by HUMANS to describe its molecular interactions-- interactions that only occur in a specific context. It's as stupid ss saying baking soda is a "sentence" that reads, "mix with vinegar, then explode." Those are our HUMAN descriptions of functions, but nothing in the sequence translates to that, or to anything.

      Teleology + lying.

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    6. ....and with that, we have the most extraordinary dishonest reply from the fastidiously pendantic diogenes.

      His response is like saying human vocal chords dont utter words, they only makes sounds, which come from impulses from nerves originating in the brain, which said brains just happen to generate electrical impulses for some mysterious reason.

      So vocal chords dont utter language, nerves dont transmit language, the brain doesnt generate language.

      Its all just physics and chemistry doing weird stuff.

      People, dont think you are intelligent!! Its an illusion. We are just molecules doing weird stuff.

      Get over yourselves people. YOU ARE NOTHING, not no thing.

      Get it????!!!!!!

      Brave, this new world??!! Naw, just pretty lame.

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    7. But you know, Steve, that the tongue, the epiglottis, the larynx and the vocal folds occur in all mammals, and in many of them "they only makes sounds", as you would put it. You know it, don't you, Steve? You are aware of the fact that other mammals also have brains and nerves, right? Our so-called "organs of speech" are in fact slightly modified organs of -- well -- lots of other things. They had existed in our pre-human ancestors tens of millions of years before we evolved articulated speech. serving other functions. As a matter of fact, they still serve many of those phylogenetically older functions in humans. The larynx, together with the vocal folds, still protects your trachea as you swallow food. The tongue still houses your taste buds, manipulates the food in your mouth, and cleans the teeth. Phonetic articulation is their secondary application, not a purpose they were originally "designed" for. Similarly, the brain did not originally evolve for abstract thinking, and even language has always had other uses beside being a tool for meaningful communication. Something that superficially looks like a message may turn out to be just a lot of noise emitted to disturb other people's communication. See above for a typical example of a tale told by an IDiot, full of sound and fury, signifying nothing.

      Delete
    8. Piotr unwittingly just made a case for the intelligent multi-functionality of our organs.

      But nothing in what Piotr says supports the notion that nature didn't design anything.

      Piotr cant wrap his brain around the fact that intelligence must precede any use of a system, whether its a digestive, sensory, defensive, or motility.

      How does an organism discover a nub can turn into a transportation mechanism? How does an organism discover that a nutrient can be turned into fuel? How does an organism discover that another organism has discoved it is food and better run?

      Piotr would have us believe that the transformation of any system lacks any intelligent work.

      Nature was intelligent way before Man walked this earth.

      enough of the facile commentary already Piotr.

      Delete
    9. How does an organism discover that a nutrient can be turned into fuel?

      Same way oxygen molecules "discover" they can bind with hydrogen.

      Delete
    10. Steve demonstrated that while anti-evolutionists can emit sentences in human languages, they cannot understand sentences in human language.

      I say: There is nothing like human language is any gene or protein sequence. No verbs, no grammar, nothing.

      Not only can anti-evolutionists not refute that argument, they can't even understand it!

      So Steve comically says I said:
      His [Diogenes'] response is like saying human vocal chords dont utter words, they only makes sounds, which come from impulses from nerves originating in the brain, which said brains just happen to generate electrical impulses for some mysterious reason.

      So vocal chords dont utter language, nerves dont transmit language, the brain doesnt generate language.


      I say: X is not a subset of Z.

      Steve says I said: Z is not a subset of Z.

      Forget about refuting scientific arguments; creationists can't even understand arguments. Steve can emit sentences in English but is not able to understand sentences in English. Like a mynah bird.

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