Science Explains Everything

As science advances, doesn't it leave less and less for God to do?

The objection, at its strongest:

1. Things once attributed to God — storms, disease, the origin of species — now have natural explanations.
2. The gaps where God was invoked keep shrinking.
3. So God is an outdated placeholder for what we do not yet understand.

This is essentially Aquinas's second objection, that natural and human causes are a complete explanatory set, leaving God redundant:

It is superfluous to suppose that what can be accounted for by a few principles has been produced by many. But it seems that everything we see in the world can be accounted for by other principles, supposing God did not exist. For all natural things can be reduced to one principle which is nature; and all voluntary things... to human reason or will. Therefore there is no need to suppose God's existence.

— Summa Theologiae I, Q. 2, A. 3, obj. 2

In response:

• This attacks a "God of the gaps" no serious theist defends. Classical theism does not put God inside the causal chain as one force among others, filling holes in our knowledge. It asks why there is a lawful, intelligible chain to investigate at all. Better science does not shrink that question; it sharpens it.
• Science and God answer different questions. Physics describes how the world behaves; it presupposes but cannot supply the why is there anything, and why is it ordered that grounds the whole enterprise. Explaining the mechanism of a kettle does not remove the person who wanted tea.
• This is not a gap that waits to be closed. It is tempting to reply: "Science couldn't explain lightning once either; give it time, and 'why is there anything at all' will fall too." But this mistakes the kind of question it is. Science advances by finding deeper mechanisms: a prior cause, a finer law. "Why is there any lawful, existing world for mechanisms to operate in?" is not a missing mechanism further down the same road; it is a question about the road itself. No amount of progress along the chain explains why there is a chain, so this is not a shrinking gap; it is a question science presupposes every time it succeeds.
• Science rests on assumptions it cannot prove. That the universe is rational, that its order is stable and discoverable, that our minds track truth: these are not results of science but conditions for it. A created, intelligible cosmos makes better sense of why science works than brute, unexplained regularity does.
• The history cuts both ways. Many founders of modern science pursued it because they expected a law-giver's ordered world. The success of science is comfortable company for theism, not its refutation.

Aquinas answers that nature and human reason are not the bottom of the explanation at all. Both of them change and can fail, so both are themselves caused, which means they point beyond themselves rather than settling the matter:

Since nature works for a determinate end under the direction of a higher agent, whatever is done by nature must needs be traced back to God, as to its first cause. So also whatever is done voluntarily must also be traced back to some higher cause other than human reason or will, since these can change or fail.

— Summa Theologiae I, Q. 2, A. 3, ad 2

That nature is directed to an end rather than self-explaining is developed in the Fifth Way — Governance.