Note the form of scientific action: "If A is true, then B should result. I perform an experiment to test A, and the result is B. Therefore A is true." As any logician will confirm, this is a logical fallacy known as "affirming the consequent." After all, there might be many other reasons why B followed the test of A, and A had nothing to do with it. However, because there is a knowable order in the universe, this process actually works. We do get cause and effect sorted out.
You may enjoy this definition from a 1959 Catholic reference book, “Origin of Man” The original was written in French by a Priest/Theologian but I think the translation holds up well:
The Coming of Science
Just as philosophy replaced poetry and mythology in explaining the origins of the world and of man, so has science for the last few centuries taken over the quest from philosophy.
Science differs from philosophy in that it is concerned not with the “final causes of things”, but with their proximate and immediate causes. It refuses to go beyond the facts. A scientific fact is a fact of physical observation, a fact registered by the senses and by the innumerable instruments which man has called in to supplement his senses. The facts once observed and registered are subjected when possible to precise verification in the form of experiments. But science ventures beyond the facts in attempting to explain them. This she achieves by first framing hypotheses and then, after verification, giving them the force of laws if their validity as explanation is confirmed. From this it follows that a hypothesis leads on to fresh observations, and is thus a kind of working tool. But a hypothesis aspires to become a scientific law, and becomes one as soon as it has successfully passed the test of experiment which it has itself set in train.
He also has some other thoughts on atheism vs. Theism but I am heading out the door right now, will post later.
Cheers!