Philosophical Naturalism (PN) holds that there is nothing outside of nature. Everything in our experience can be accounted for by pure natural forces.
Obviously then, a person who holds to PN cannot believe in miracles (defined as events that cannot be explained by pure natural forces). The non-existence of miracles is assumed by definition. Just as it would be impossible to believe in a married bachelor it is impossible – logically – to believe in miracles.
Now note this: PN cannot be itself established by science since, by definition, science only studies natural (not supernatural) events. PN defines the parameters of science; viz., everything in nature. This definition of “science” does not nor cannot prove PN. As philosopher Richard Purtill states, “a position that describes natural laws as simply a summary of what happens cannot even make the contrast between miracles and nonmiraculous events” (“Defining Miracles,” in A Defense of Miracles: A Comprehensive Case for God’s Action in History, eds. Douglas Geivett and Gary Habermas, 70).
Philosopher Winfried Corduan adds, "By virtue of their assumptions about the nature of science the naturalists [adherents of PN] will never be convinced that a miracle has actually occurred... We can now see that the naturalists have laid out the rules of the game in such a way that they cannot possibly lose" ('Recognizing a Miracle," in Ib., 101).
Any attempt to argue from this notion of science that miracles do not happen is to beg the question.