We have the physical world, governed by scientific law, and a spiritual or supernatural realm, qualitatively distinct and working in ways that science cannot explain. Most people don't have a clue, however, as to how these two worlds could possibly coexist. Of course, science exists. I am, I admit, taking some rhetorical license here. I believe that the method used by science is, in fact, the universal method of all productive thinking, whether in science, in poetry, in philosophy or in any other form of human expression.
Science studies quarks and the human genome.
It does not study the nature of science itself and the nature of the inferences that constitute its method. This is not because those who seek to understand this method have reservations about its utility and power. On the contrary, those who have tried to pin this method down are some of science's staunchest friends. They've come to appreciate that the scientific method may be as complex as some of the phenomena science itself studies. This should not cause excessive rejoicing on the part of religious believers and theologians, however.