At one time it was said that God guided the Earth around the sun, but Newton figured out orbits, and more.
Newton did indeed push God out of the equation to some significant extent, but still invoked His hand at the limit of his own understanding. He felt that the actions of planets on each other, and other bodies such as comets, would conspire to create orbital irregularities that needed to be corrected by some sort of divine intervention (lest the solar system eventually be thrown into disarray).
A perfect example of the progress of science, it's gradual diminishing of the role of God in natural affairs, and the subsequent revision of that role into something that is itself also destined for further revision in the future (we understand orbits much better than Newton did).
Somehow, though, we are supposed to believe that this process has stopped. That the unsolved mysteries of the present age will remain unsolved until the end of time. Really? Please.