Ok, so science is a methodology, a way of examining phenomena, their causes and effects, measuring them, replicating them and either protecting against them or making them useful or both. Science is by nature analytic -taking things apart , separating them into their components.
Philosophy studies the basic or fundamental nature of knowledge, thought, existence and reality with a view to placing the intelligent being cporectly within the context of the Universe. It is synthetic, bringing together many different ideas and facts.
Metaphysics is a branch of philosophy concentrating on the fundamental nature of reality, including first causes.
Naturalism is a branch of applied philosophy that takes the methodology of science and tries to turn it into an explanation of reality/existence. Some scientists share it, others don't.
Theism is a philosophical position which assumes an intelligent first cause, then sets out to prove it, using all kinds of arguments in lieu of any empirical evidence.
Religion is a political structure, loosely based upon Theism. It is used to enforce specific behaviours within communities in order toi maintain the current political and power structures as well as ensuring the privileged social position of its priests (most of whom are not believers in anything but gravy trains).
All of these are, of course, circumscribed by the limitations of our senses and comprehension. I tend to the opnion that there is an awful lot of reality we are unaware of and couldn't understand if we were able to perceive it. I suspect some scientists share that view as they consistently attempt to increase our powers of perception and understanding. But as matters currently stand, we lack the data to succesfully theorise on the true nature of reality, so are unlikely to come up with any valid answers any time soon!
I aslo strongly suspect that if God, the First Cause, Nature, Azathoth or whatever you want to call Them were even aware of us, Their view would be along the lines of "Not my circus, not my monkeys."
