Science itself assumes a metaphysical reality. Science can only make observations on the material world. Science cannot confirm or deny metaphysical underpinnings.

I think classical vs quantum physics is a good example. It gave us information on determinism, but it didn't explain who / what is setting the odds.

Science can give us estimates for all the universal constants. It cannot tell us how they came to being.

We know there was a big bang, we don't know in which medium the big bang occurred.