I heard on a podcast a theist say that he had a problem with Victor Stenger. The critique was phrased something like, that Dr Stenger put his atheism first in his explanations, that he has a presupposition against against using God as an explanation, a presupposition against the supernatural. Something struck me as odd about this perspective, and then I realized that one never hears this sort of perspective in scientific circles.
Why not? I think it's because, in science, it is recognized that the natural world will correct any wrong presupposition...the truth will out. So, if someone has a presupposition, just let it ride out and see if it works. Einstein had a presupposition for a static universe - he even "corrected " his theory to get rid of the dynamics when it was pointed out to him that that was a consequence. Once the data came in that was best explained with a dynamics universe, he modified the theory and said it was a big mistake.
Another example comes from my own experience teaching astronomy. For years I taught the prevailing wisdom that there were two possibilities for the end of the universe. Either the expanding universe, initiated at the Big Bang, would have enough mass to collapse again in a Big Crunch or it would expand forever, slowing but never stopping. It was never on the radar that it could be accelerating, and had anyone suggested it, I would have said it was unreasonable. Of course the universe doesn't care about my bias, lack of imagination, or presupposition and it does appear to be accelerating nonetheless.
So, if someone has a presupposition against God as an explanation, indulge them! If they are wrong, then at some point it will make a bad prediction and fail. If not, then we've learned that, for the thing explained, the concept of God is not necessary. Don't complain about the presupposition. Know that the truth will out, eventually. On the other hand, I would love to know what predictions the God theory makes (not post-dictions), so that it can be tested.