Sean Carroll Fails to Scale The Edge of Evolution (Part IV): Mistaking Protein Sequence Similarity for Natural Selection
[Editor's Note: This is Part 4 of a 4-part response. The full response can be read here.]
In Part I of this series, I discussed Sean Carroll's misrepresentations of Michael Behe's arguments in The Edge of Evolution. Part II exposed a citation referenced by Carroll which, rather than refuting Behe, actually confirms him. Part III explained the fact that many of Carroll's citations discuss meager examples of evolution that Behe finds fall well within the humble creative capabilities of Darwinian evolution. Carroll has thus far failed to engage Behe's actual arguments. Carroll does make an attempt to tackle the origin of a couple complex biological features. Yet these attempts fail because they confuse the evidence for common descent from sequence similarity with evidence for natural selection. Again, Behe anticipates this mistake and provides ample rebuttals to Carroll's citations. As discussed below, Carroll badly miscites one paper as showing that "new protein interactions ... can evolve fairly rapidly."
Carroll Spins the Flagellum
When discussing the flagellum, Carroll cites Pallen and Matzke's review paper on the evolution of the flagellum. Yet this paper itself admits that "the flagellar research community has scarcely begun to consider how these systems have evolved." Those that read the Pallen/Matzke paper will find vague generalities and nothing remotely approaching a specific step-by-step model for the evolution of the flagellum. In fact, readers will find attempts to give evidence of protein homology, evidence which Behe readily anticipates by citing to Pallen's work and noting that "modern Darwinists point to evidence of common descent and erroneously assume it to be evidence of the power of random mutation." (Behe, Edge of Evolution, pg. 95) None of the work cited by Carroll remotely attempts to explain the evolution of the complexity of flagellar assembly discussed in Appendix 3 of The Edge of Evolution.
Carroll's Questionable Citation
Behe's recognition that evidence for common descent is not evidence for natural selection also provides a poignant rebuttal to one of Carroll's prized citations. Carroll relies on his claim that "new protein interactions ... can evolve fairly rapidly." Carroll's cites Budovskaya et al., "An evolutionary proteomics approach identifies substrates of the cAMP-dependent protein kinase," Proceedings of the National Academy of Sciences, Vol. 102:13933--13938 (Sept. 27, 2005). But this paper epitomizes Behe's recognition that "modern Darwinists point to evidence of common descent and erroneously assume it to be evidence of the power of random mutation." (Behe, Edge of Evolution, pg. 95)
The study's methods were essentially as follows: (1) take a protein that is acted upon by a particular enzyme (called a cAMP-dependent kinase), (2) search protein databases to find proteins with similar sequences, and then (3) study those proteins with similar sequences to determine if they are acted upon by the same enzyme, the cAMP-dependent kinase. In fact, the paper didn't even look for a function as such of these proteins; it merely demonstrated that the proteins identified by sequence analysis are likely targets of the same kinase. Budovskaya et al. (2005) even admits that it merely "uses sequence information to identify the biologically relevant occurrences of a protein motif of interest." In other words, the raw data is mere comparison of proteins through sequence similarity, and there's no direct testing of random mutation and natural selection here.
Indeed, the paper recognizes that its results support a strong correlation of "structure-function," due to the fact that one can completely remove common descent and Darwinian evolution from this picture and get the same results: All the study truly found was the mundane result that proteins with similar sequences tend to be acted upon by similar enzymes. Big deal. The paper then adds a lot of evolutionary gloss, but that's all it is: inference based upon assumptions, not hard evidence. It in no way demonstrates the power of random mutation and natural selection, and at best provides an example of how "Darwinists point to evidence of common descent and erroneously assume it to be evidence of the power of random mutation" (Behe, Edge of Evolution, pg. 95) (and even then, this assumes that sequence similarity is necessarily evidence for common ancestry).
Even if this paper had demonstrated natural selection, it still would fall well below Behe's edge of evolution. By citing this paper, Carroll is referring to the interaction between enzymes that modify or cleave other proteins, and the protein binding sites recognized by those enzymes may be quite short. Carroll equivocates over the term "interaction motifs": Behe is talking about the kinds of protein interactions that build enzyme complexes or structures like the ribosome or the cilium or the replication machinery of the cell. These kinds of interactions are stabilized by many amino acids, not the short motifs studied in this paper. These kinds of short motifs may be necessary for building molecular machines, but they are far from sufficient to build molecular machines where two or more proteins must dock together and stably interact.
Finally, even if Budovskaya et al. had demonstrated random mutation and natural selection (which it doesn't), Carroll cites this paper to claim that protein-protein interactions "can evolve fairly rapidly," yet the paper studied proteins in "a group of budding yeast species that are separated by up to 800 million years of evolutionary distance." 800 million years is not "fairly rapidly"--in fact, it represents nearly 1/4 of the entire history of life on earth. There appears to be no legitimate grounds whatsoever for Carroll citing Budovskaya et al. (2005) to claim that "new protein interactions ... can evolve fairly rapidly."
In the end, what is starkly missing from Carroll's review is anything that actually demonstrates the evolution of something that Behe argues is beyond the edge of evolution. It seems that Carroll is afraid of heights -- by citing a number of irrelevant or unsupportive papers, Carroll never comes remotely close to meeting Behe's challenge to explain the step-by-step Darwinian origin of anything beyond Behe's proposed edge of evolution.