However, there are quite a few unexplained areas of particle physics that defy explanation, but that only means we haven't found the cause yet. One by one, the holes get patched.
Some people start with the belief that an active, Creationist God is the fact, and that science then must conform. I absolutely believe in intelligent design and that God had intentions for the Universe and for each person in it, but that for God to interfere and direct things, He would have to interfere with laws of physics, laws that He wrote. Ah, but some say that quantum mechanics allows for such tinkering. Well, no. QM is governed by strict laws of probability, and tinkering would put those out of balance. A god that needs to interfere with his own laws doesn't say very much about his power.
Yet it should be obvious that the Universe is well designed and life is not a violation of the Third Law of Thermodynamics (entropy). Clearly there is purpose and a design that we see all about us.