It’s a big year for all things Darwin. This month, two centuries after his birth, we commemorate the man and his accomplishments. And in November, a century and a half after On the Origin of Species was published, we commemorate the beginnings of the theory by which we all know him.
But how exactly should we think of his theory? Is it to be remembered the way we remember the man—as an important part of the past? Or is it to be remembered as something more than that—as an intellectual seed that grew into something that thrives to this day?
Many, of course, would like to think of Darwin’s theory in these flourishing terms. But the growth of something else makes this view increasingly hard to hold. We refer here to the seldom discussed but steadily expanding body of peer-reviewed scientific work that refuses to square with Darwinism.
Take a look at the recent Genetics paper by Rick Durrett and Deena Schmidt.  They’ve done the math to calculate how long it would take for Darwin’s mechanism to accomplish a particular kind of functional conversion. And their eagerness to “expose flaws in some of Michael Behe’s arguments”  shows that they think they’ve resuscitated Darwinism after Behe pronounced it dead. 
Maybe the answer depends on how vigorous a theory you were hoping for. Part of what ails Darwinism, in other words, may be that people have such high expectations of it.
If you think Darwinism explains how life acquired the great variety of forms we see around us (the grand vision that Darwin himself had) you’ll probably be disappointed with Durrett and Schmidt’s findings. Darwin’s vision is chock-full of conversions of the most profound kind—all complex life forms originating from one or a few simple forms. Whereas the conversions that Durrett and Schmidt examine are nothing like that.
Theirs are conversions not from one body plan to another, or from one organ or tissue or cell type to another, or even from one protein molecule or gene to another, but rather from one binding site to another. These binding sites are DNA sequences about one hundredth the size of a gene that affect how a nearby gene is switched on and off. Conversion is accomplished by two point mutations occurring in succession:
We think of the A mutation [i.e., the first] as damaging an existing transcription factor binding site and the B mutation as creating a second new binding site at a different location within the regulatory region. … We used the word ‘damage’ above to indicate that the mutation may only reduce the binding efficiency, not destroy the binding site. However, even if it does, the [A] mutation need not be lethal. 
Now, there are two important questions to be asked here. The first, which Durrett and Schmidt address, is the question of whether this kind of two-step conversion can evolve in a Darwinian fashion—and if so under what circumstances. The second, which they largely avoid, is the question of relevance to Darwin’s grand vision. That is, even if we knew these binding-site conversions to be feasible, would that give us any reason to think that the more profound conversions are feasible?
As things stand, scientific caution dictates a ‘no’ answer to this second question. The right kind of evidence could conceivably change that answer, but there are good reasons to think no such evidence will appear. The main reason is simply that converting one binding site to another accomplishes no significant structural reorganization, whereas transitions to new life forms would require radical structural reorganization. It’s not that a binding site change can have no effect (indeed, it could be lethal), but rather that it cannot have the required effect—the complete top-down reorganization needed for a transition to a substantially different form of life.
By way of analogy, you might easily cause your favorite software to crash by changing a bit or two in the compiled executable file, but you can’t possibly convert it into something altogether different (and equally useful) by such a simple change, or even by a series of such changes with each version improving on the prior one. To get a substantially new piece of software, you would need to substantially re-engineer the original code knowing that your work wouldn’t pay off until it’s finished. Darwinism just doesn’t have the patience for this.
Furthermore, returning to the first question, it seems that even humble binding-site conversions are typically beyond the reach of Darwinian evolution. Durrett and Schmidt conclude that “this type of change would take >100 million years” in a human line , which is problematic in view of the fact that the entire history of primates is thought to be shorter than that .
Might the prospects be less bleak for more prolific species with shorter generation times? As it turns out, even there Darwinism appears to be teetering on the brink of collapse. Choosing fruit flies as a favorable organism, Durrett and Schmidt calculate that what is impossible in humans would take only “a few million years” in these insects. To get that figure, however, they had to assume that the damage caused by the first mutation has a negligible effect on fitness. In other words, they had to leap from “the mutation need not be lethal” to (in effect) ‘the mutation causes no significant harm’. That’s a big leap.
What happens if we instead assume a small but significant cost—say, a 5% reduction in fitness? By their math it would then take around 400 million years for the binding-site switch to prove its benefit (if it had one) by becoming fully established in the fruit fly population.  By way of comparison, the whole insect class—the most diverse animal group on the planet—is thought to have come into existence well within that time frame. 
Do you see the problem? On the one hand we’re supposed to believe that the Darwinian mechanism converted a proto-insect into a stunning array of radically different life forms (termites, beetles, ants, wasps, bees, dragonflies, stick insects, aphids, fleas, flies, mantises, cockroaches, moths, butterflies, etc., each group with its own diversity) well within the space of 400 million years. But on the other hand, when we actually do the math we find that a single insignificant conversion of binding sites would reasonably be expected to consume all of that time.
The contrast could hardly be more stark: The Darwinian story hopes to explain all the remarkable transformations within 400 million years, but the math shows that it actually explains no remarkable transformation in that time.
If that doesn’t call for a serious rethink, it’s hard to imagine what would.
The truth of the matter, much to the chagrin of contemporary biology, is that Darwin’s theory should have been laid to rest some time ago. It certainly deserved all the interest it generated in its day, but at some later point that interest was transformed from the critical kind to the credulous kind. Regrettably, that change took hold before the most conclusive data came to light.
But all is not lost—even wrong ideas can make big contributions to the advancement of science. Few biologists want to see Darwin’s theory filed in that category, but if that is its rightful place, then you can be sure that’s exactly where one bold generation of biologists will file it—someday.
The timing of such things is hard to predict, but we suspect that many members of the bold generation will be in polite attendance at the Darwin celebrations this year.
 Behe M (2007) The Edge of Evolution. Free Press.
 Calculated by multiplying their figure of 4325 years (pg. 1507, col. 1, line 4) first by 100 (pg. 1507, col. 1, line 14) and then by rho, which is calculated to be about 900 according to their formula (pg. 1507, col. 1, line 17).