I've cited Francis Collins here before in his excellent defense of the compatibility of science and Christianity. And he accurately critiques the hold philosophic naturalism has on the field of science, dictating only certain kinds of answers. But I have to disagree with his comments in this interview.
God can't have used Darwinian evolution to design the world because they are definitionally at odds. Darwinianism is specifically a random, directionless process of natural selection. That is in contradiction to God's design or plan or direction. Theistic evolution is a oxymoron. Randomness and design don't mix. It's not a matter of being beyond our comprehension; it's a matter of contradiction in the terms.