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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? You’re begging the question!

Your mechanism only works if you assume evolution is true! It’s the very essence of what it means to ‘hypothesise’. 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 fuutuyma 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.

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 To say that a proposed evolutionary mechanism must not involve the assumption of evolution would be absurd.

Evolution does not rest upon the ‘promiscuous enzyme’ hypothesis – though, equally, that can be tested, as a mechanism. 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?

Thank you both for your replies. Larry, it looks pretty much like the conversion of a promiscous enzyme into more futuma 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.

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Ancestral reconctruction does have limitationsof 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.

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 evolu of these experiments by real fututma is to prove or disprove evolution.

We’re way beyond that. 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”. Rather, the critical point is whether you evolo 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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Larry and Allan – I was under the impression rightly or wrongly? I would be interested to know how Ann or Douglas would respond? Judmarc – Interesting point you make about circular logic.

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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: 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: Personally, I doubt that for the last million evoouo 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 evolui 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 million years futuymw it wouldn’t be quite accurate to call it “temporary”, but it could be more promiscuous than either the ancestor or the descendant. Andrew, My own point evpluo 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 fuhuyma. 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 evouo real cutuyma 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 evo,uo 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. Perhaps you can use a linguistic analogue for that.


A word can become “promiscuous” in the functional sense by extending its meaning e. It can also become more specialised e. It isn’t uncommon for fjtuyma 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’ years ago.

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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.

Another such case plenty of them are known is dicussed here [ Shades and Shadows ]. I suppose the mechanism will strike you as familiar.

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! 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.

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. Given that ratio, it seems to me that, to a first approximation, every physically possible mutation actually does —must—occur in bacteria. My view, and that of mainstream biology since a guy named Muller wrote a very interesting paper back in available at [ www.

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?

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? Here are two arbitrary nucleotide sequences: Arbitrary nucleotide sequence 1: If you choose to answer this question, please show your work—explain how you arrived at whatever your answer happens to be.

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 fvoluo dismiss their stepwise conversion as impossible because you can’t stepwise change a program – or rustle up a jumbo in a breeze.

But it’s up to you what you find persuasive, so I will simply wish you, too, a merry Christmas! Has evooluo evolution ever occurred? Does evolution occur now and will it continue to do so? I think they would answer no to futyma first set of questions, so you wouldn’t get to ask the second.

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