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‘That is why no findings of empirical science can undermine the claims of metaphysics and the philosophy of nature. It is also why no findings of empirical science can undermine the Aristotelian-Thomistic arguments for the existence of God, for these are grounded in premises drawn, not from natural science, but from metaphysics and the philosophy of nature. Now that does not mean that these arguments of natural theology are not susceptible of rational evaluation and criticism. What it means is that such evaluation and criticism will have to be philosophical and metaphysical, rather than empirical, in nature. Nor is natural theology in this regard at all different from atheism. Atheists who think they are arguing from “purely scientific” premises never really are. They are, without exception, arguing from metaphysical assumptions — and usually unexamined ones at that — that are first read into empirical science and then read back out, like the rabbit the magician can pull out of the hat only because he’s first hidden it there.’

Edward Feser on science and metaphysics – from his The Last Superstition.