Natural explanations to former supernatural ideas

[Won2blv]

A common reasoning I have heard from atheists or secular type people for why they don't believe in god or the bible is, natural explanations to former supernatural explanations. I was talking to one guy that said, god use to explain thunder, lighting, rain, etc. But now we have natural explanations to such things. So I am looking for biblical examples of such ideas. Miraculous events excluded. I understand that Joshua asking god to make the sun stand still is more than likely not scientifically possible but it is not equal to lighting being the product of thor. The creation account is probably another one that will be brought up a lot so I'd prefer other examples if you know of any. Not discounting the creation account, I just have never believed that it was to be read as a literal 6 24 hour creative days. Thanks!