Here’s another thought to consider. Science is not the only academic discipline to insist more or less firmly on methodological naturalism.
Sociology does, for example, so that investigation of the supernatural experiences of people (“supernatural” not the category I like, but the most comprehensible to make the point here) - such experiences must be interpreted naturalistically in the literature.
Likewise historians have a strong tradition of excluding the supernatural by methodological necessity as ahistorical. For history only studies the kind of events events that are known to occur in the common experience. This has significance because it applies not only to reports of miracles in Augustine or Bede, but par excellence in the field of biblical studies, which consider themselves to be guilds of specialised historians. Jesus’s miracles, or his resurrection, are not the stuff of academic history, and therefore not a subject for empirical study - hence all those distinctions between the “Jesus of history” and the “Jesus of faith.”
Accordingly, since the miracles are claimed as actual events, not simply as “beliefs”, then methodological naturalism also extends to theology: we cannot do theology on the basis that God actually acts in the world (because the historians, sociologists and scientists deal with the empirical world, and don’t do the supernatural. And theology depends on biblical studies, which are historical disciplines).
It seems, then, that not only physical sciences, but all empirical fields, have the same insistence on methodological naturalism in the Academy. So my question is, are these academic disciplines any less justified than the physical sciences in sharing their methodological naturalism. And if so, why, other than the assumed right of practitioners to decide their proper boundaries?
One can, of course, argue that it enables these disciplines to be pursued on an equal footing by those of all faiths and none. Theology shouldn’t, after all, be the domain only of the religious…