Brown 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.
Last April a paper by Summers et al. (see my summary here) appeared in the Proceedings of the National Academy of Sciences confirming that at least two mutations to the protein PfCRT are required before chloroquine resistance appears in the malaria parasite, as I had surmised in The Edge of Evolution. I wrote a series of posts (here, here, and here) analyzing the result, and another one that challenged Kenneth Miller and PZ Myers (who had downplayed the unsettling implications of the result for Darwinism) to provide their own quantitative — not verbal — account for the extreme rarity of chloroquine resistance. Last month Miller posted an 11-page reply.
The first two and a half pages of the PDF version of Miller’s essay consist of stage-setting and throat-clearing. The last six pages are a reprise of his review of The Edge of Evolution and a defense of the evolutionary musings of University of Chicago biologist Joseph Thornton from my skepticism. I’ll deal with those later. Miller’s only response to my take on the importance of Summers et al. is in the section "Parasites and Drugs." Although the section is less than three pages (including several large figures), as we shall see it includes a number of serious mistakes.
Unfortunately, Miller dodges my challenge to provide a quantitative account of the rarity of the origin of chloroquine resistance. I had asked him to "Please keep the rhetoric to a minimum." Alas, to no avail. He cites no relevant numbers, makes no calculations — just words.
Miller begins the section by questioning whether the mutation K76T (which replaces a lysine, "K," at position 76 with a threonine, "T") in the protein PfCRT is important to its ability to transport chloroquine:
There is indeed one required mutation in the PfCRT protein, which is a change of an amino acid at position number 76 from lysine to threonine…. But Behe was dead wrong about it being "strongly deleterious." In fact, it seems to have no effect on transport activity at all.
It’s nothing short of incomprehensible to claim that the K76T mutation has "no effect on transport activity." Figure 2 of Summers et al. — the very paper to which Miller is referring — shows that one variant of PfCRT (dubbed "D39") with a particular mutation (N75E) has no chloroquine transport activity. When the K76T mutation is added to it to make a double mutant (variant D32), it gains such activity. So it had no effect? Variant E1 has three mutations (none are K76T) but no activity. When K76T is added to those mutations to make the Ecu variant, activity appears. The only difference between the non-transporting and transporting variants is the addition of K76T, but Miller maintains it has no effect on transport activity?
Summers et al. did show in their Figure 4 that, on the background of the mature malaria resistant variant Dd2, which has a total of eight mutations, other amino acid residues could replace T at position 76 and retain activity. But that has nothing to do with the claim that a K76T mutation would have "no effect on transport activity" in a strain that is newly developing chloroquine resistance.
Miller writes, "Quite frankly, [Be]he must be secretly hoping that nobody actually looks at the details in the PNAS paper." Actually, I’m very publicly encouraging everyone to read it with a lot more attention to detail than he did. Anyone who relies on Miller’s characterization of the paper will be badly misled.
Miller’s claim that the paper shows K76T isn’t deleterious is equally unsupported. Summers et al. did not even try to test whether the K76T mutation is deleterious. The word doesn’t even appear in their paper. Rather, the workers were interested mostly in testing what mutations were required just for chloroquine transport activity.
To test if a certain mutation were itself "strongly deleterious" takes particular conditions. That mutation would at least have to be examined: 1) alone on the background of the wild-type sequence (that is, with no other mutations present; more about this later); and 2) in the relevant organism. Yet most of the work described in the Summers et al. paper used frog eggs (X. laevis) as a test system, not malaria (P. falciparum). Whether a mutation has "no effect on transport activity" in frog eggs says nothing at all about whether it would be deleterious to malaria.
Summers et al. did test a PfCRT variant ("D38") that had only the K76T mutation. It did not transport chloroquine, showing that multiple mutations are needed — which is by far the most ominous result for Darwinism. But since the test system was frog eggs, that of course couldn’t determine whether K76T might have any deleterious effect in malaria. The authors did also test five PfCRT variants (encoded on plasmids) in malaria cells in the lab to see how they would affect the cells’ survival in the presence of chloroquine. But all had multiple mutations — not K76T alone — so that couldn’t determine possible deleterious effects of the single mutation. What’s worse, the malaria cells also retained their own, genomic, functional, wild-type PfCRT, which would likely mask any deleterious effects of a nonfunctional plasmid-encoded mutant protein.
One of the variants ("E2") had three mutations, including K76T. The protein could transport chloroquine modestly well in frog eggs, but in malaria cells in the lab it didn’t help increase survival rate much above background. That result may possibly indicate that more than those three mutations are needed for net beneficial activity in the wild. But it says nothing about whether a single K76T mutation would be deleterious to malaria cells.
Miller’s reading of Summers et al. is seriously mistaken. Sadly, a person who can’t accurately report the results of a paper makes for an unreliable guide. I urge everyone who has sufficient background to read at least the disputed parts of Summers et al. Determine for yourself which account is correct.