This is a question for those of you who have greater facility with Bayes' Theorem than I do. (In other words, this is a question for just about everyone.) Let's suppose that either theism is true or evolutionary naturalism is true and to keep things simple let's say that neither hypothesis is more likely than the other. (This is a gross simplification, but let it slide to keep the calculations simple. The second assumption is an assumption Plantinga makes in his initial presentations of the EAAN.) Let 'T' stand for theism, let '~T' stand for evolutionary naturalism, and let 'R' stand for the proposition that our faculties are reliable. Suppose for the sake of this discussion that Plantinga is right that:
(1) P(R/T) > P(R/~T).
(2) P(R/T) is high.
(3) P(T) = P(~T).
Given these three assumptions, doesn't evidence against R count as evidence against T? Playing with the numbers just a bit, suppose that we say that P(R/T) is .9 and P(R/~T) is .2. If we further suppose that P(T) = P(~T), P(~T/~R) is .8889. It seems that there is some evidence that we are unreliable in certain kinds of cognitive tasks that I'd think that we wouldn't expect ourselves to be particularly good at given the background assumption of evolutionary naturalism but would expect ourselves to be good at given the background assumption of theism. Having a bit too much fun with trolleys and chalk the other day, I discovered that the vast majority of my students start judging that they ought to engage in actions that they themselves deemed to be murderous only weeks earlier when we have 4 option trolley cases rather than the 2 option cases I initially presented to them. I started having my dose of Darwin's Doubt!
Now, I know there's the worry that if you accept ~T and P(R/~T) is low, you are supposed to acquire a defeater for everything you believe. But, it seems that this problem is easily avoided. I think Sober pointed this out in an article some years ago. We should focus on the reliability of certain kinds of methods and processes for discovering the truth instead of focusing on reliability across the board. There's ample evidence against reliability across the board but little evidence for the proposition that every faculty we have is unreliable. It would be self-defeating (perhaps) to believe that every faculty is unreliable, but not to believe that we are not reliable across the board. That we are unreliable moral judges does not mean that we oughtn't trust our scientific judgments. But, here's the kicker. This sort of move seems helpful to the naturalist but I don't think that the theist wants to say that the conditional probability that we are good moral judges on the assumption of theism is low or inscrutable.
Anyway, I think this is interesting. It seems that if the assumptions Plantinga often introduces in the course of setting up the EAAN he might have given the naturalist some assumptions to use to construct an empirical argument for God's non-existence. Roughly, we should expect to be competent moral judges if God exists but not if evolutionary naturalism is true. Given evidence of incompetence and the initial use of the principle of indifference to justify the starting assumption that P(T) = P(~T), we ought to decrease our confidence in theism accordingly.
I have no confidence in the above, by the way. I'm sure there are details that need to be ironed out, assumptions that need to be added in, and responses that are so damn obvious that any fool could see them. That's what the comments box is for.