Does science prove there is no such thing as miracles? Does it make God a mere superintendent of the world He created? Part of this depends on what we mean by science. Are we talking about the science people wanted or the science they actually found?
One of the assumptions of the early advocates of science was that science would find a deducible universe. That is, one could start with a few basic intellectually obvious premises and from that deduce the rest of the system. The obvious analogy to this is mathematics. You start with certain basic mathematical premises and from that deduce the rest of mathematics as far as algebra and calculus. The idea is nature's laws work the same way. Now nothing can stop God, if there is a God, from miraculously interfering, but this does produce difficulties regarding God's providential control of the world. I am not saying this could not be reconciled with the Christian idea of God, but there are problems. But is it true?
We have not yet found the basic premises from which all scientific laws are deducible, but they look to be extremely complex rather than intellectually obvious. We have to take into account things like Einstein's theory of relativity, which, while it does not say all things are relative, does say that the world is more complicated than we expect from our normal experiences. But trying to deduce all events from those premises involves difficulties. There is quantum mechanics, which says that light is both a wave and a stream of particles (something which is beyond human understanding), and that at a certain level of smallness we can only know the behavior of particles in terms of probabilities rather than certainties. Then there is chaos theory, which says, when things are sufficiently complex, a minor difference in initial behavior can cause a huge effect later on. (The flapping of a butterfly's wings in Kansas can cause a tornado in Brazil.) While there are, in my opinion, huge holes in Neo-Darwinian Evolution, if it is true it says that living creatures are what they are because of chance mutations which happened to be advantageous in the particular environment the creature lived in.
The bottom line is the deducible universe does not fit modern scientific knowledge. It looks unlikely we will ever make it back to that concept. Therefore the universe is either the result of a intelligent creator or a sophisticated game of chance. Perhaps a better analogy than mathematics is language. As in mathematics, you start with certain basic premises and work from them in an orderly manner. But there is not the precise, necessary, logical connection you find in mathematics. You cannot start with the alphabet and deduce Milton's "Paradise Lost" or Mark Twain's "Adventure's of Tom Sawyer." Which at least suggests the idea of an intelligent creator behind it all. Maybe God is not primarily a mathematician; perhaps He is an artist.
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