When you look at the history of the world, you see thousands -- tens of thousands, arguably hundreds of thousands or more -- of phenomena for which a supernatural explanation has been replaced by a natural one. Why the sun rises and sets; what thunder and lightning are; how and why illness happens and spreads; why people look like their parents; how people got to be here in the first place… all these things, and thousands more, were once explained by gods or spirits or mystical energies. And now all of them have natural, physical explanations.
Natural explanations, I should point out, with mountains of solid, carefully collected, replicable evidence to support them.
Now, how many times in the history of the world has a natural explanation of a phenomenon been supplanted by a supernatural one?
As far as I am aware, exactly zero.