Following my discussion of Boltzmann Brains, I wanted to mention its relation to yet another argument for God.
The argument goes that a low-entropy initial condition is extremely unlikely unless God exists. Therefore, God probably exists.
(This argument is not to be confused with the argument that evolution contradicts the Second Law, a mistake once made by PZ Myers.)
My response is that we don't know that the initial condition is extremely unlikely. It's only extremely unlikely if we assume all microstates are equally likely initial conditions. Also, saying that we do not have an explanation is not the same as saying we do have an explanation and we call that explanation God.
Let's say that I have a differential equation that I can't solve (a common scenario in physics). A common practice is to posit the existence of a solution and call that solution something like the Bessel Function or the Legendre Function. But I can't posit a solution and call that solution God. Got the distinction? The analogy isn't perfect though; in differential equations we have existence theorems, in metaphysics we do not.
Rationalist atheism does not claim that science has all the answers, but rather, that religion has none of the answers.