Here is my take, very briefly:
— No Darwinian evolution of the supposedly new gene was shown. It was only discovered in that strain of maize
Maize is not subject to Darwinian evolution? This remark makes no sense at all.
— The ability of a random sequence of DNA to form a 4-helix bundle when transcribed beggars belief. It would not be expected to happen in many, many tries. That alone makes it seem very likely that the sequence was not random.
As you said, Bill, Behe grants that T-urf13 is pretty remarkable.
— The authors of the review write: “Although novel when discovered, it is now apparent that many other CMS genes have arisen by recombinational events involving other mitochondrial-encoded genes. In fact, mitochondrial DNA rearrangements are a significant force in changing the genome organization and in causing mutations in the mitochondrial genomes of higher plants (Mackenzie et al., 1994).” A distinct possibility implied by this, it seems to me, is that plant mitochondrial DNA is in fact built to provide easily accessible functional variability. In other words, intelligently provided, pre-existing information was tapped for this protein.
Doesn’t this sound sort of circular? Anyways, how would one determine this, without assuming the conclusion Behe wishes to draw?
Hopefully, Behe can take a bit more time and offer some more commentary about my essay.
One more comment - that “the 4-helix bundle is a challenge to explain through random mutation” is only a valid argument if one grants that protein functionality is rare in sequence space. It is pretty clear that this is not the case.