Atheist: A supernatural explanation of the universe is wrong because it cannot be explained by natural causes.
Response: Your assertion reveals an a priori commitment to naturalism. You conclude that all things must be explained by natural causes by assuming that all things must be explained by natural causes. This is a viciously circular argument - an arbitrary assertion, and as such, it is irrational. Why dismiss the possibility of creation? Any philosophy which arbitrarily (without justification) does away with ideas which are potentially true is poor philosophy.
Everyone has ultimate presuppositions which undergird their thinking but only the biblical explanation makes sense of the data of the real world we live in. The naturalistic explanation cannot account for things which underly the world, including logic, morality, free agency, meaning and the uniformity of the cosmos. The atheist uses all these things on a daily basis, of course, but cannot account for them. In fact, when held consistently, his view contradicts them. He is forced to behave AS IF these things have a basis, which is another way of saying he must pretend. On the other hand, the biblical view can account for all of them.