In this paper, I call into question a commonly assumed principle in science known as methodological naturalism, which is the idea that science should only accept natural, as opposed to supernatural, explanations. In support of MN, two arguments are commonly thrown against the idea of theistic explanation in science: the science stopper argument and the God-of-the-gaps argument. The science stopper argument states that appealing to theistic explanations hinders science from making steady progress; it simply stops science from its tracks. In (...) other words, abandoning MN spells the death of science. The God-of-the-gaps argument states that appealing to God when explaining phenomenon is a form of an argument from ignorance, what critics call God-of-the-gaps thinking, which is considered to be fallacious reasoning. Any gap in nature that is explained by God, so the argument goes, is simply an appeal to our ignorance that we have no yet found the correct explanation to such natural mystery. In this scenario, an appeal to God is assumed to simply show our lack of knowledge with regard to the workings of nature. After introducing these arguments, I assess their strength by looking at the history of methodological naturalism. I then show how the history of science does not only fail to support these arguments but actually refutes them. (shrink)