It would be interesting to draw your friend out a bit more on what he means by the scientific method. Is he including non-behaviorist psychology, in which it is permissible to describe and explain people's subjective experiences, employing introspection? Does he include history? Or is his domain only the natural sciences? Even addressing these questions will, I believe, bring to light that your friend is operating on something that goes beyond the "scientific method"; he is employing a philosophy of science. Science alone (physics....) will not tell you that it is the only reliable basis of knowledge, and if a physicist says this, then she is being more than a physicists; she is a philosopher of physics or science. In any case, questions about ethics, religion, and meaning go beyond science (I suggest) and in fact science as a practice must presuppose some ethics (minimally one must be trustworthy / not falsify data, etc) in order to be practiced at all. Questions about whether or not there is a God or objective values, etc, seem to me to be the sorts of things that require a philosophical investigation, an assessment, for example, of why it is that there is a cosmos in which science is so successful. To make one further observation that I hope is helpful: these days, philosophers rarely speak in terms of "proofs." It is very difficult even to prove that radical skepticism is wrong (do I know that I am not in the Matrix? ). In most contexts, we refer instead to good or bad arguments. So, I am sympathetic with your friend it is good to discuss the reasons for and against theism but I suggest you do so, drawing on, but not limited to science alone. Good wishes to you both!
Read another response by Charles Taliaferro
I have a friend who is an Atheist because he claims that the burden of proof (for the existence of God/other practices and belief's) is on religion and he has not been satisfied with any proof set forth. He says, "if you propose the existence of something, you must follow the scientific method in your defense of its existence. Otherwise, I have no reason to listen to you." Should one believe in God or practice religion only if it can be proven by the scientific method? What do you think of his reasoning? Is it rational to believe in a God/Religion without the SM? Thanks and I'm a huge fan of the site!