Hmm ... that's a very lucid and expressive summary of selection, which is something I've never really received before. Thank you for it. And sorry if I'm being dense here, but some questions remain for me: if "a reproductive bias results toward the genotype that is more advantageous for that environment," doesn't this in the long term result in the characteristics of the species being trained to the environment? And even though the gene didn't try to fit the environment, it seems that the "reproductive bias" did. To what exactly are we attributing agency here? And is it not still a characteristic of the species in question? We would simply have to say, it seems, that a different aspect of the equation is performing the selection, that something is still selecting. Or have I missed it entirely?

All that aside, I doubt the finer mechanisms of evolution could foil a synchronization with theism for Plantinga. Or if they could for him, I daresay that would evidence a problem in his approach. Reconciling apparent randomness of systems with theological determinism is an old game among theistic philosophers, and it only falls flat when the starting point is an overly anthropomorphic view of divine will. When these run amok, their logic is seldom more persuasive than that of Manifest Destiny (i.e., we brutally took the land, we now therefore have the land, therefore God must have always wanted us to have the land). Or, to state in non-theistic terms, "it happened in this way. Therefore, it could not have happened in any other way."

Wow, the God Helmet! Thanks for the link. I've heard of connected studies, but not this actual item -- which, by the way, sounds like something out of the Dungeon Master's Guide. This connects directly to the book I wanted to recommend to you the other evening, which I've just finished reading. It's a novella called "Flying to Nowhere," in which, among other threads, an Abbots slips towards madness (or epiphany?) whilst secretly dissecting cadavers in search of the seat of the human soul. Interestingly enough, the object of his inquiry is the pineal gland, a thing I keep running across of late. Being a medical physicist (est-ce vrai?), you're probably more familiar with it than I, but just in case, the wiki page ain't too shabby:

http://en.wikipedia.org/wiki/Pineal_gland

Not only did the likes of Rene Descartes consider it to be "the principal seat of the soul," but many have noted its handy correspondence to the third eye, the ajna chakra. While chakras and meridians, considered axiomatic in eastern medicine and religion, await anything resembling confirmation by western scientific method, such coincidence across widely disparate traditions seems at the very least interesting, if not significant.

But here's the kicker: even if we were to grant the effects of the God Helmet and the metaphysical significance of the third eye, our conclusions would still result, not from such evidence, but from our presuppositions. Once again, we're left with the same simple chicken and egg question. Does the brain have a God-senser so that it can sense God? Or does it merely sense God because it has a God senser? And this is why I find most debates between atheists and theists ultimately doomed, though fascinating. Almost invariably, predisposition determines conclusion, especially where ideology is concerned. The conversion of such basic inclinations is rare.