Thanks Joshua. I didn’t have a chance to read all the posts but I was picking up on questions in a post from @jrfarris that seemed to intersect with my own work. My apologies if it was not clear who I was responding to.
I would agree that we have all methodologies that we use. I was really speaking of the ideal, popular since the 19th century, that there was a single methodology (e.g, Popper, Lakatos) underlying all successful science. That assumption has not been helpful for the conversation between science and religion, in my opinion.
I think my use of “bottom-up” gave a misleading impression of what I am arguing (I was using it the way John Polkinghorne uses it). I am not asking to change ground rules of science, for example. Rather I am making the point that classic philosophy of science (and its search for :"the scientific method), which has had a large influence on the Christianity and Science conversation, has often been too isolated from actual practice to be of much use. But I wonder if my arguments are addressing a different set of worries and problems than you have been addressing here.