The naturalism that science adopts is methodological naturalism. It
does not assume that nature is all there is; it merely notes that
nature is the only objective standard we have. The supernatural is not
ruled out a priori; when it claims observable results that can be
studied scientifically, the supernatural is studied scientifically
(e.g., Astin et al. 2000; Enright 1999). It gets little attention
because it has never been reliably observed. Still, there are many
scientists who use naturalism but who believe in more than nature.
The very same form of naturalism is used by everyone, including
creationists, in their day-to-day lives. People literally could not
survive without making naturalistic assumptions. Creationism itself is
based on the naturalistic assumption that the Bible has not changed
since the last time it was read.
Naturalism works. By assuming methodological naturalism, we have made
tremendous advances in industry, medicine, agriculture, and many other
fields. Supernaturalism has never led anywhere. Newton, for example,
wrote far more on theology than he did on physics, but his theological
work is largely forgotten because there has been no reason to remember
it other than for historical curiosity.
Supernaturalism is contentious. Scientific findings are based on hard
evidence, and scientists can point at the evidence to resolve disputes.
People tend to have different and incompatible ideas of what form
supernatural influences take, and all too often the only effective way
they have found for reaching a consensus is by killing each other.
Astin, J. A., E. Harkness and E. Ernst. 2000.
The efficacy of "distant healing": a systematic review of randomized
trials. Annals of Internal Medicine 132(11): 903-910.
Enright, J. T. 1999. Testing dowsing: The failure of the Munich
experiments. Skeptical Inquirer 23(1): 39-46.