Uh OH! Essential reading for evo supporters. 
When Theory and Experiment Collide
......As other scientists have found with other enzymes, it turned out not to be a snap. The technical details are reported in a paper just published in BIO-Complexity. [2] Here we’ll keep it simple.
Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
Now, if I were a Darwinist a result like this would bother me. I’m sure some of my fellow Darwinists would try to dismiss it as irrelevant… but that would bother me all the more.
The excuse for shrugging it off would, I expect, be that the transition we examined isn’t actually one that anyone thinks occurred in the history of life. That’s true, but it badly misses the point. As Ann and I made clear in the paper, our aim wasn’t to replicate a historical transition, but rather to identify what ought to be a relatively easy transition and find out how hard or easy it really is. We put it this way in the paper [2]:
But that’s not an easy thing to say with a straight face, is it?
Having always believed the bottom picture to be correct, my alter ego would be very reluctant to reject it. And yet he wouldn’t be able to deny the obvious. There is in fact a jaw-dropping, ludicrous, even grotesque inconsistency between the top picture and the bottom picture. They can’t possibly both be true. But that realization, of course, forces an uncomfortable decision.
And here I must confess to feeling more than a little sympathy for my alter ego. I think it’s because of what we have in common.
He loves science.
So do I.
He loves stories.
So do I.
He sees a role for stories in framing scientific ideas.
So do I.
And he has said to himself, “The progress of science has invalidated my alter ego’s favorite story.”
So have I.
----------------
The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway
.....This leads Koonin and Wolf
to reject convergent evolution (extensive similarity appearing
by evolution from dissimilar starting points) as implausible.
But from this they conclude that homology, while not
formally proven by similarity, is nonetheless overwhelmingly
supported in cases where chance convergence is implausible.
The problem with this is that all non-chance alternatives
must be considered once chance is ruled out. Yet Koonin and
Wolf consider only one of these alternatives—the standard
Darwinian one.
We agree with their rejection of chance, but we argue here
that the Darwinian explanation also appears to be inadequate.
Its deficiencies become evident when the focus moves from
similarities to dissimilarities, and in particular to functionally
important dissimilarities—to innovations. The extent to which
Darwinian evolution can explain enzymatic innovation seems,
on careful inspection, to be very limited. Large-scale innovations
that result in new protein folds appear to be well outside
its range [5]. This paper argues that at least some small-scale
innovations may also be beyond its reach. If studies of this
kind continue to imply that this is typical rather than exceptional,
then answers to the most interesting origins questions
will probably remain elusive until the full range of explanatory
alternatives is considered.
When Theory and Experiment Collide
......As other scientists have found with other enzymes, it turned out not to be a snap. The technical details are reported in a paper just published in BIO-Complexity. [2] Here we’ll keep it simple.
Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
Now, if I were a Darwinist a result like this would bother me. I’m sure some of my fellow Darwinists would try to dismiss it as irrelevant… but that would bother me all the more.
The excuse for shrugging it off would, I expect, be that the transition we examined isn’t actually one that anyone thinks occurred in the history of life. That’s true, but it badly misses the point. As Ann and I made clear in the paper, our aim wasn’t to replicate a historical transition, but rather to identify what ought to be a relatively easy transition and find out how hard or easy it really is. We put it this way in the paper [2]:
Whether or not a particular conversion ever occurred as a paralogous innovation (or the direction in which it occurred if it did) is not the point of interest here. Rather, the point is to identify the kind of functional innovation that ought to be among the most feasible […] and then to assess how feasible this innovation is.So, if I had a Darwinist alter ego, here’s the problem he’d be facing right now. To dismiss our study as irrelevant, he’d have to say (in effect) that he sees no inconsistency between these two assessments of the power of Darwin’s mechanism:
But that’s not an easy thing to say with a straight face, is it?
Having always believed the bottom picture to be correct, my alter ego would be very reluctant to reject it. And yet he wouldn’t be able to deny the obvious. There is in fact a jaw-dropping, ludicrous, even grotesque inconsistency between the top picture and the bottom picture. They can’t possibly both be true. But that realization, of course, forces an uncomfortable decision.
And here I must confess to feeling more than a little sympathy for my alter ego. I think it’s because of what we have in common.
He loves science.
So do I.
He loves stories.
So do I.
He sees a role for stories in framing scientific ideas.
So do I.
And he has said to himself, “The progress of science has invalidated my alter ego’s favorite story.”
So have I.
----------------
The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway
.....This leads Koonin and Wolf
to reject convergent evolution (extensive similarity appearing
by evolution from dissimilar starting points) as implausible.
But from this they conclude that homology, while not
formally proven by similarity, is nonetheless overwhelmingly
supported in cases where chance convergence is implausible.
The problem with this is that all non-chance alternatives
must be considered once chance is ruled out. Yet Koonin and
Wolf consider only one of these alternatives—the standard
Darwinian one.
We agree with their rejection of chance, but we argue here
that the Darwinian explanation also appears to be inadequate.
Its deficiencies become evident when the focus moves from
similarities to dissimilarities, and in particular to functionally
important dissimilarities—to innovations. The extent to which
Darwinian evolution can explain enzymatic innovation seems,
on careful inspection, to be very limited. Large-scale innovations
that result in new protein folds appear to be well outside
its range [5]. This paper argues that at least some small-scale
innovations may also be beyond its reach. If studies of this
kind continue to imply that this is typical rather than exceptional,
then answers to the most interesting origins questions
will probably remain elusive until the full range of explanatory
alternatives is considered.
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