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I stress in Chapter 3 that in the case of malarial resistance to chloroquine, multiple necessary mutations did happen in the membrane protein PfCRT. I also of course emphasize that it took a huge population size, one that would not be available to larger organisms. But Carroll seems uninterested in making distinctions.

Carroll cites several instances where multiple changes do accumulate gradually in proteins. (So do I. I discuss gradual evolution of antifreeze resistance, resistance to some insecticides by “tiny, incremental steps — amino acid by amino acid — leading from one biological level to another”, hemoglobin C-Harlem, and other examples, in order to make the critically important distinction between beneficial intermediate mutations and detrimental intermediate ones.)

In fact, if one takes the trouble to look up the references Carroll cites, one sees that a short amino acid motif is not enough for function in a cell. For example, Budovskaya et el (Proc. Nat. Acad. Sci USA 102, 13933-8, 2005) show that the majority of proteins in the yeast Saccharomyces cerevisiae containing a motif recognized by a particular protein kinase were not phosphorylated by the enzyme. What does that mean? It just means that the simple motifs, while necessary for binding, are not sufficient. Other features of the proteins are necessary, too, features which Sean Carroll ignores.

In his enthusiasm Carroll seems not to have noticed that, as I discuss at great length in my book, no protein binding sites — neither short linear peptide motifs nor any other — developed in a hundred billion billion (1020) malarial cells. Or in HIV. Or E. coli. Or in human defenses against malaria, save that of sickle hemoglobin. Like Coyne, Carroll simply overlooks observational evidence that goes against Darwinian views. In fact, Carroll seems unable to separate Darwinian theory from data. He writes that “what [Behe] alleges to be beyond the limits of Darwinian evolution falls well within its demonstrated [my emphasis] powers”, and “Indeed, it has been demonstrated [my emphasis] that new protein interactions (10) and protein networks (11) can evolve fairly rapidly and are thus well within the limits of evolution.”

Yet if one looks up the papers he cites, one finds no “demonstration” at all. Those papers show, respectively, that: A) different species have different protein binding sites (but, although the authors assume Darwinian processes, they demonstrate nothing about how the sites arose); or B) different species have different protein networks (but, again, the authors demonstrate nothing about how the networks arose). Like Jerry Coyne, Sean Carroll simply begs the question. Like Coyne, Carroll assumes whatever exists in biology arose by Darwinian processes.