rationalskepticism.org

Part of the problem believers have is they confuse informational 'tools" with motivational "tools". Suppose one is a religious scientist. One may regard nature as god's works, and thus believe science as a form of worship of god's works, as presented in nature. This sentiment is a great motivational tool, but a poor informational one. One could believe that god is nature, but it is scientifically untestable. Thus Newton could believe in a god who was the creator of a clockwork universe. However, we can only test the model of the universe as a clockwork mechanism, and not the watchmaker. Thus even if the universe was clockwork, Newton did not prove god as its watchmaker. In any case, we now know via Einstein that the Universe is not quite as clockwork as Newton imagined it to be.
An atheist scientist, who would not make the presumption of a celestial clock-maker in any case, is freer to propose models of less prejudice. He would simply ask if the universe is clock-like or not.