Thanks for the constructive criticisms. You're right about Darwin, of course. That was badly worded on my part, and I made the change in the article.
Regarding clever apologetics, I was speaking somewhat facetiously in the way Jerry Coyne does about "sophisticated theology." Certainly, there's a difference between crude, literalistic fundamentalism, and the mystical, more obfuscatory theology of the priestly class, including the metaphysical arguments you find in the Greek Orthodox Church. Whether the sophisticated theology amounts to more than a pseudoscience is another matter.
You seem to be on top of the argument from design. This is still one of the theist's stronger arguments, though, because the physical constants puzzle physicists themselves. It's a classic god of the gaps argument: mystagogues leap on ongoing mysteries in science and declare that God did it. It's the same with consciousness.
For me, the question is what a finished scientific theory of everything would even look like. Is the notion of such a theory oxymoronic for the sociological reasons I lay out in "Atheism and the Endlessness of Explanation"?
