Imagine the following conversation between a theist (T) and a metaphysical naturalist (MN) who justifies metaphysical naturalism on the basis of the evidential form of the problem of evil and who then attempts to justify methodological naturalism on the basis of metaphysical naturalism.
MN: If one is a metaphysical naturalist then one should be a methodological naturalist, i.e., refuse ever to postulate nonphysical entities as the cause of physical events. One should not believe in nonnatural entities without good evidence. There is no good evidence for nonnatural entities. Indeed, in the case of God, the chief candidate for a nonnatural entity, the existence of evil constitutes positive evidence against His existence. Therefore one should accept metaphysical naturalism and, by logical extension, methodological naturalism.
T: I disagree that there is no good evidence for nonnatural entities. I propose to show you that there is evidence that God causes some physical events and that this positive evidence for God outweighs any presumed negative evidence based on the existence of evil.
MN: Such positive evidence cannot exist.
T: Why not?
MN: Because any investigation of the causes of physical events must employ methodological naturalism, i.e., must assume that it is never, even in principle, legitimate to posit a nonnatural cause for a physical event.
T: Why should one accept methodological naturalism?
MN: Because there is good reason to think metaphysical naturalism is true, and methodological naturalism follows logically from the truth of metaphysical naturalism.
T: Remind me once more of your good reason for thinking metaphysical naturalism is true.
MN: The good reason for thinking that metaphysical naturalism is true is that there is no good evidence that nonnatural entities exist. Further, given that evil constitutes evidence against the existence of God, the primary candidate for a nonnatural entity, it seems clear that metaphysical naturalism is justified.
T: Would methodological naturalism ever permit one to posit a nonnatural entity as the cause of a physical event.
MN: No. I have already made that clear.
T: Let me get this right. Your acceptance of metaphysical naturalism is based on the fact that there exists no evidence that nonnatural entities ever cause physical events?
MN: Yes. That along with the evidence provided by the existence of evil.
T: And your endorsement of methodological naturalism follows from your acceptance of metaphysical naturalism?
T: This seems question-begging. You endorse metaphysical naturalism on the basis that there exists no evidence that nonnatural entities ever cause physical events, yet adopt a methodology which rules out the possibility of ever recognizing evidence of nonnatural causes. You are using your metaphysic to justify your acceptance of methodological naturalism, but your acceptance of methodological naturalism serves to guarantee that even if evidence for the existence of nonphysical causes exists it can never be recognized as such.
MN: Are you not forgetting that evil constitutes positive evidence against God’s existence?
T: Assuming that evil does in fact constitute evidence against God’s existence, it only makes God’s existence improbable if there is not a body of positive evidence that outweighs the body of negative evidence. By adopting methodological naturalism you guarantee that such a body of positive evidence will not be recognized, even if it exists. You use your metaphysical naturalism to justify methodological naturalism and you use methodological naturalism to justify your metaphysical naturalism. Your metaphysical naturalism supposedly justifies your methodological naturalism, but your methodological naturalism serves to insulate your metaphysical naturalism from any possible challenge. This is viciously circular. It begs the important question of whether there exists sufficient evidence to justify belief in nonnatural entities and thus disbelief in metaphysical naturalism.