Many scientists who are atheist or agnostic (as most are) nonetheless feel that science should stay out of religion, based on an idea that Stephen Jay Gould called "Non-Overlapping Magisteria" or NOMA. In this series, I refute NOMA and similar ideas that would tell us not to say what we actually think is true.In this second installment, I offer some analogies to show how "methodological naturalism" (which a lot of NOMA proponents hide behind) only makes sense if naturalism is true, in which case NOMA would fail.