One more quickie
Bud over at Dead Logic linked to a great blog of PZ Myer's from back in '09 when he took down Alvin Plantiga – one of those "sophisticated" Christian philosophers. I liked Myers' post, but I really liked this comment from the user "Sastra":
This argument (often called The Argument from Reason) comes up regularly in comments, and you've done a great job pointing out some of its major flaws. In addition to the false dichotomy (either we have 'warrant' to trust our brains completely, or anything goes), it suffers from the same problem most theistic reasoning suffers from: they can't get away from the childish idea that Like comes only from Like.
Reason, free will, life, consciousness, morals, love, you name it. If things didn't start out there, they can't get there. Nothing new comes gradually out of increasingly complex patterns and interactions. Nothing grows. Nope. We get Reason from a Reason Force which is made out of Reason and has always been and never was anything else. We get life from a Life Force. How does the brain create mind? It doesn't. There's a Mind Force which uses the brain. Morals come from a Moral Force. And so on and so forth.
You hit the nail on the head. Evolution would give us brains which would be 'good enough' for most things, but which are inclined to error. What it won't give us is a sensus divinitus -- a certain way of 'knowing' God through our intuition. That couldn't "grow." It would have to be "gifted."
I find it remarkable that theists and New Agers love to trot out evidence that our biases mislead us as part of their case against science. See, the fact that we're biased entails that science is also a bias, and therefore we can't trust it any more than we trust our intuitions. But of course, the more flawed we are, the stronger the case for our need for objective methods, which evolved over time to help us cope with the problem.