I’ve argued that Darwin’s mechanism probably isn’t powerful enough to produce proteins with fundamentally new structures.  If that’s correct it’s a serious problem for the old theory, because we know that new protein structures—new folds, as they are known—appeared well over a thousand times in the history of life. If Darwinism doesn’t account for these then whatever else it may be, it isn’t a complete theory of biological origins.
New protein functions don’t always call for completely new structures, though. There are numerous examples of proteins that use very similar structures to perform tasks that are genuinely distinct, meaning that one cannot replace the other. Recognizing this, Ann Gauger and I set out to test how well Darwin’s mechanism works on this more modest scale where things that already work are adjusted to work differently.
We began by analyzing the members of a large ‘family’ of enzymes (proteins that carry out chemical reactions) in order to find a pair with very high structural similarity but distinct functions. Then we performed a series of experiments hoping to demonstrate in the lab the kind of functional transition that ought to be a snap (if you believe the Darwinian story).
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.  Here we’ll keep it simple.
Based on our experimental observations and on calculations we made using a published population model , 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 :
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.