Cornelius Hunter is still harping on Ken Miller's "scientific misrepresentations" in the Kitzmiller v. Dover case. After rehearsing his arguments that shared pseudogenes are not evidence for evolution (since some pseudogenes do have functions, and therefore cannot possibly be vestiges (structures that lack the primary but not necessarily all the functions of their homologs in allied and related species), he moves on to Miller's testimony about human chromosome two. This chromosome (with its vestigial centromere and telomere, and its homologies to two separate chromosomes in chimps, gorillas, and orangutans) is so obviously a fusion of two ancestral chromosomes that Hunter does not bother to dispute the point. Rather, his argument is that we have no reason not to suppose that this fusion happened to two chromosomes in a human species that does not share ancestry with any other primates: it doesn't prove common ancestry. That, to be sure, is correct as far as it goes, though Miller's point was that given that humans have 23 pairs of chromosomes, whereas other great apes have 24 pairs, common descent implies that one of our chromosomes must be the result of a fusion of two separate chromosomes, and the evidence of fusion in human chromosome two is a confirmation of this prediction.
Miller, Hunter complains, was "deceiving" Judge Jones because Miller did not explicitly discuss what one would expect of a Creator in his court testimony, although Miller did discuss it in his book Finding Darwin's God. This is, as Hunter sees it, a deliberate attempt to obscure the point that the only evidence for evolution is the "metaphysical" and "religious" assumption that God would not have made things the way we see them. But then, it is hard to see how it can be purely scientific to invoke God as a Explanation for a scientific phenomenon, but somehow become "religious" as soon as one tries to consider the properties God would have for a creation miracle to account for the data we actually see. Of course, the problem is that Hunter's only evidence is the assertion that "Darwinism" cannot account for the evidence (principally, the "evidence" in this case is every case where an evolutionist guessed or hypothesized wrongly about anything, whether his hypothesis was logically implied by common descent or not), and the non sequitur that therefore the true explanation must be Design. He cannot acknowledge that evolution is indeed confirmed by some evidence, and would be disconfirmed by others, in ways that "design" would not be, or that the vestiges of fusion in chromosome 2 are a small part of that evidence.