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The Very Neutral Kenneth Miller

51aLrvnMXUL._SY344_BO1,204,203,200_.jpgBrown University biologist Kenneth R. Miller has posted a reply to my challenge to him to give a quantitative account for the extreme rarity of the origin of chloroquine resistance in malaria. I’m grateful to him for doing so. Although I strongly disagree with nearly everything he wrote, his essay gives the public a chance to see directly how one informed Darwinist reacts to a basic empirical challenge to the theory. This is the second in a series of four responses to it. See yesterday’s post here.

In the last post I showed Miller’s claim that the K76T mutation in the chloroquine-resistance protein factor PfCRT had "no effect on transport activity" was simply wrong. Also wrong was his claim that Summers et al. had shown the single mutation not to be deleterious. Here I rebut several other statements of Miller’s concerning whether the mutation is selectively neutral. He writes:

In fact, a 2003 study recommended against using the K76T mutation to test for chloroquine resistance since that same mutation was also found in 96% of patients who responded well to chloroquine. Clearly, K76T wouldn’t have become so widespread if it were indeed "strongly deleterious," as Behe states it must be. This is a critical point, since Behe’s probability arguments depend on this incorrect claim.

Wrong again. A mutation could easily be both deleterious by itself yet widespread in a population if an organism has acquired other, compensating mutations that block its injurious effects. In the case of malaria this could happen in the following highly plausible scenario. First, as chloroquine is deployed in an afflicted country, the initial ultra-rare two required mutations eventually appear together in one cell (the deleterious-by-itself K76T plus a second mutation that confers transporting activity) and are selected to survive in the presence of chloroquine.

After those first two required mutations get their proverbial foot in the door and allow the altered gene to increase in the population, subsequent additional helpful mutations could do two things: 1) improve chloroquine-transporting, and 2) compensate for the destabilizing effect of K76T and/or other mutations on the normal, required function of PfCRT. (Malaria cells cannot survive without that protein, even in the absence of chloroquine.) The next milestone is that, once that multi-mutated protein becomes widespread, chloroquine is rendered medically useless and is prescribed much less frequently in the geographic region. With diminished pressure from chloroquine, the protein can then back-mutate to improve its necessary native function and spread in the population, without regard to maintaining the now-unnecessary transporting ability.

Consistent with this scenario are all of the following: The study Miller cites (Vinayak et al. 2003) did not check for other, possibly compensating mutations in PfCRT, only for K76T. Chloroquine had been the drug of choice in India, the locale of the study, but was discontinued as the first-line drug way back in 1973 — thirty years before the study Miller cites — when chloroquine-resistant malaria became endemic (Farooq & Mahajan 2004). Work in Malawi (Kublin et al. 2003) and China (Wang et al. 2005) has shown that chloroquine resistant malaria are replaced rapidly by sensitive malaria once the drug is discontinued in a region, likely reflecting selective pressure to alter the PfCRT protein in the absence of chloroquine. Although the Malawi work showed simple replacement of the resistant strain by the original unmutated one, other reversion pathways may well be possible. In doing so the PfCRT from the study Miller cites could easily have retained K76T if it also retained compensating mutations.

The result — widespread, chloroquine-sensitive K76T PfCRT in a population — is medically and epidemiologically interesting, but would have nothing to do with how resistance originally arose. It shouldn’t need pointing out to professional biologists that the major unsolved problem for Darwinian evolution is to explain how a new beneficial property first appears under a new selective pressure — in this case, how chloroquine resistance arises from the wild-type protein — not how a feature decays once selective pressure is removed.

Here’s a homey analogy to help explain. Suppose you wanted to replace the support columns of an old porch. If you simply pulled one away, the porch roof might collapse. But if you first braced the roof with strong poles, the columns could safely be replaced. Ken Miller is in the position of someone who points to a braced porch under repair, and claims that shows removing a column from a normal, unbraced structure would not be harmful.

He writes:

A neutral mutation like this can easily propagate through a population, and field studies of the parasite confirm that is exactly what has happened.

In my last post I showed Miller’s claim that Summers et al. found K76T to be selectively neutral was incorrect. Above I showed that the study he cites, showing the mutation is found in chloroquine-sensitive malaria, is easily compatible with its being deleterious on its own. But is there any direct, positive, experimental evidence indicating whether a single, uncompensated K76T mutation is deleterious or neutral?

Yes, there is. As I wrote earlier, to see if a mutation is harmful by itself, at the very least you have to test it without any other mutations present in the relevant organism. Lakshmanan et al. did this carefully in the lab in 2005:

To test whether K76T might itself be sufficient to confer VP-reversible [chloroquine resistance] in vitro … we employed allelic exchange to introduce solely this mutation into wild-type pfcrt (in GC03). From multiple episomally transfected lines, one showed evidence of K76T substitution in the recombinant, full-length pfcrt locus (data not shown). However, these mutant parasites failed to expand in the bulk culture and could not be cloned, despite numerous attempts. These results suggest reduced parasite viability resulting from K76T in the absence of other pfcrt mutations. This situation is not reciprocal however, in that parasites harboring all the other mutations except for K76T (illustrated by our back-mutants) show no signs of reduced viability in culture. [Emphasis added.]

Frankly, it was never a good bet that the K76T mutation — a nonconservative change in a required protein that’s likely to be near a binding site — would be selectively neutral. The best relevant experimental evidence indicates that K76T is indeed strongly deleterious by itself in the wild-type protein, but not if compensatory mutations are present. Miller’s claim that the individual mutation is neutral is wrong.

Michael J. Behe

Senior Fellow, Center for Science and Culture
Michael J. Behe is Professor of Biological Sciences at Lehigh University in Pennsylvania and a Senior Fellow at Discovery Institute’s Center for Science and Culture. He received his Ph.D. in Biochemistry from the University of Pennsylvania in 1978. Behe's current research involves delineation of design and natural selection in protein structures. In his career he has authored over 40 technical papers and three books, Darwin Devolves: The New Science About DNA that Challenges Evolution, Darwin’s Black Box: The Biochemical Challenge to Evolution, and The Edge of Evolution: The Search for the Limits of Darwinism, which argue that living system at the molecular level are best explained as being the result of deliberate intelligent design.