Pondero,
I can appreciate where a scientist cannot attribute something to God and still be doing science. But a scientist can attribute something to God and still be a scientist; I know because I am one and I do that.
You are right, the clockwork universe was a good place to start. (To be in accordance with Catholic teachings, you had to make an allowance for the possibility of the clockmaker putting his finger on the works to move them around occasionally, but that is a different subject.) But it isn’t tenable any more. Certainly large numbers of molecules do tend to follow certain statistical “laws” virtually all the time, but those statistical laws are not ironclad. The fact that a molecule bounced one way rather than another will eventually have a macroscopic effect, sort of an extreme version of the “butterfly effect” of chaos theory.
I calculated once (some decades ago, so I’m a little fuzzy on the details) that if you did the following:
(1) opened a box full of air (instantaneously) in a vacuum,
(2) some time later reversed the velocity of each air molecule (again instantaneously, and as perfectly as the uncertainty principle would allow you to), and
(3) had the air molecules track their trajectories backwards back into the box,
the air molecules would not go back into the box perfectly. The uncertainty in the position or velocity would make a difference in the trajectories as they went backwards. I forget whether it was seconds or milliseconds that it would take for the velocities of the air molecules to be completely randomized and unpredictable, but it was something in that area.
Certainly God is free to do as He pleases, but Catholicism states that He has done things in a certain way. If you say that He did them differently, then you are being incompatible with Catholicism. If you say that God kick-started a clockwork universe and exclude any possibility of the miraculous, that is incompatible with Catholicism.