The philosopher Thomas Nagel recently published a dense, searching review of Alvin Plantinga's new book, Where the Conflict Really Lies, which argues for the compatibility of religious faith and science. Nagel ends his essay by admitting Plantinga has pointed to something essential:
I say this as someone who cannot imagine believing what he believes. But even those who cannot accept the theist alternative should admit that Plantinga’s criticisms of naturalism are directed at the deepest problem with that view—how it can account for the appearance, through the operation of the laws of physics and chemistry, of conscious beings like ourselves, capable of discovering those laws and understanding the universe that they govern. Defenders of naturalism have not ignored this problem, but I believe that so far, even with the aid of evolutionary theory, they have not proposed a credible solution. Perhaps theism and materialist naturalism are not the only alternatives.
Jerry Coyne seizes on that paragraph to scold Nagel:
Nagel has fallen for the God-of-the-gap trap. The credible solution is to do more work to find out how the structure of the mind produces consciousness, and how natural selection might have acted to promote that feature. Does Nagel think that science has used all its resources on this problem, and failed? Does he not know how relatively primitive neurobiology is right now? Nagel has just thrown up his hands and said, “You people haven’t explained it, therefore perhaps Plantinga is right.” Or there might be “another alternative.” Curious that Nagel doesn’t propose what that alternative might be.
Sean Carrol broadens the debate, attacking Plantinga's understanding of faith:
Even if your faith is extremely strong in some particular proposition, e.g. that God loves you, it’s important to recognize that there’s a chance you are mistaken. That should be an important part of any respectable road to knowledge. So you are faced with (at least) two alternative ideas: first, that God exists and really does love you and has put that belief into your mind via the road of faith, and second, that God doesn’t exist and that you have just made a mistake.
The problem is that you haven’t given yourself any way to legitimately decide between these two alternatives. Once you say that you have faith, and that it comes directly from God, there is no self-correction mechanism. You can justify essentially any belief at all by claiming that God gave it to you directly, despite any logical or evidence-based arguments to the contrary. This isn’t just nit-picking; it’s precisely what you see in many religious believers. An evidence-based person might reason, “I am becoming skeptical that there exists an all-powerful and all-loving deity, given how much random suffering exists in the world.” But a faith-based person can always think, “I have faith that God exists, so when I see suffering, I need to think of a reason why God would let it happen.”