There’s a brief article here about Darwin, his loss of faith, and a general argument meant to establish that evolution defeats itself: if (according to Evolutionary Theory) all that matters about us is successful replication of our genes, then we have no reason to think that our brains are any good at coming up with true theories; and thus we have no reason to think Evolutionary Theory is true. (This argument has been raised to me by students a couple of times, so I thought this link may be of interest.)
The article doesn’t quite come around to answering the objection. The author observes, “our minds evolved to deal with commonplace reality,” and so from this one might harbor the hope that our brains track truth after all. But the next part of the sentence is “and we must doubt whether they are adequate instruments for speculating so far beyond that.” So the question is whether Evolutionary Theory is well-enough supported by observations of commonplace reality. I think it is: the brilliant thing about Darwin’s idea is how incredibly simple it is, and how extensive its explanatory reach is. This isn’t enough to prove it true, I suppose, but it is enough to defend it from Plantinga’s argument.