The steps toward evolutionary progress

Over at the Discovery Institute's Media Complaints Division, Michael Behe seems to be a wee bit concerned by the attention that a recent Nature paper is getting, moaning that, "It seems some scientists have discovered that one way to hype otherwise-lackluster work is to claim that it discredits ID."

OK. To start with, watching Michael Behe whine about someone else using ID to hype "otherwise-lackluster work" creates a concentration of irony so dense that four mining firms have put in bids for that post. Sorry, but I had to get that one out of my system. Now that I've more or less managed to get that minor issue out of the way, let's look at what, for lack of a better term, we will have to call the "substance" of Behe's complaints.

The January 25th issue of Nature carries a "Progress" paper by Poelwijk et al that's touted on the cover as "Plugging Darwin's Gaps," and cited by its authors as addressing concerns raised by proponents of intelligent design. The gist of the paper is that some amino acid residues of several proteins can be altered in the lab to produce proteins with properties slightly different from those they started with.

. . .

Quite unsurprisingly, the current paper shows that microevolution can happen. Small changes in a protein may not destroy its activity. If you start out with a protein that does something, such as bind DNA or a hormone, it's not surprising that you can sometimes find a sequence of changes that can allow the protein to do something closely similar, such as bind a second sequence of DNA or a second, structurally-similar hormone.

That's Behe's description of what the paper is doing. Now, let's go for the reality-based summary:

Despite the plethora of modern genetic tools, something that is little changed since Darwin's time is our reliance on evolutionary outcomes to unravel the process of evolution. The lack of evolutionary intermediates leaves the door ajar for the proponents of intelligent design. But a new technique could help fill the gaps. It involves the construction of evolutionary intermediates in the lab, and the search for viable paths between them. The resulting 'fitness landscapes' map viable routes between accessible evolutionary paths.

That's the editor's summary for that article. I realize that it isn't quite as reader-friendly as Behe's summary, so let me try to sum up the summary: scientists are using new lab techniques to take a step-by-step, mutation-by-mutation look at the various paths that evolution might have taken.

Looking at what I just wrote, I think an example might be called for. A good one can be found in a recent paper in Science that was referenced in this Nature article.

There are some bacteria that have a version of a particular enzyme that makes them 100,000 times more resistant to certain antibiotics (like penicillin). We know that there are five differences that separate this version of the enzyme from the basic version, and we know what those mutations are. In theory, if the mutations happened one at a time, there are 120 possible ways that the enzyme could go from the original form to the resistant form. (For example, mutation 1 could have happened first, mutation 2 second, mutation 3 third, mutation 4 fourth, and mutation 5 fifth, or mutation 2 could have happened first, mutation 1 second, mutation 3 third . . . or mutation three could have happened first . . . and so on until all the possibilities are exhausted. )

Scientists then were able to construct possible intermediate forms of the enzyme - varieties that contained some, but not all 5, of the mutations, and test their resistance to the antibiotic. What they found was that 12 of the 120 possible paths from the original form to the new form increased resistance with every additional mutation. That's pretty cool - it shows that not only could natural selection drive the changes in this enzyme, but also that there are 12 different ways it could have happened.

The Nature article that Behe is bitching about looks at the ways in which that type of approach is being used to study evolution at the cellular level, mutation by mutation. That's a bit different from Behe's description of the article: "the gist of the paper is that some amino acid residues of several proteins can be altered in the lab to produce proteins with properties slightly different from those they started with." Actually, we already know that proteins can be altered to slightly change their properties. What this paper is discussing is how we can study, in the lab, the mutation-by-mutation paths that natural selection can take in moving a protein from one form to another. That's something that any scientist with even marginal reading comprehension skills could figure out from skimming the paper. So why is Behe trying to obfuscate what the paper is really about?

It might have something to do with statements like this:

Not only would I need a step-by-step, mutation by mutation analysis, I would also want to see relevant information such as what is the population size of the organism in which these mutations are occurring, what is the selective value for the mutation, are there any detrimental effects of the mutation, and many other such questions.

That quote was taken from Behe's testimony during the Kitzmiller trial. Behe was talking about the immune system there. The current studies are a long way from systems like that, but they do show mutation-by-mutation paths, with selective values for each step, in the development of some new traits. (Like it or not, a 100,000-fold improvement in antibiotic resistance is a new trait.) Some of the other studies cited in the paper look at even more things, like the possible effects of taking paths that are longer than the shortest possible paths investigated in the bacterial resisitance study, by looking at things like the effect of a muation that is gained then lost along the way.

Under the circumstances, it's really no surprise that Behe is trying to obfuscate these studies and minimize their significance. Our understanding of evolution keeps improving, and his complaints about the things we don't yet understand sound weaker and weaker every day.

Reference

Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins
Daniel M. Weinreich, Nigel F. Delaney, Mark A. DePristo, and Daniel L. Hartl
Science 7 April 2006 312: 111-114 [DOI: 10.1126/science.1123539]