Here is how our author defines the different versions of naturalism:
The self-imposed convention of science that limits inquiry to objective observations of the world and generally seeks natural accounts for all phenomena is called methodological naturalism.
We have also noted that methodological naturalism is often conflated with metaphysical naturalism, which assumes that reality itself is purely natural, that is, composed solely of material objects.
Methodological naturalism can still be applied without implying any dogmatic attachment to metaphysical naturalism. (God: The Failed Hypothesis, 29)
Stenger writes that he will “use the words natural and supernatural as synonymous with material and nonmaterial.” (14) This is rather confusing. If metaphysical naturalism is equivalent to materialism, then it suffers from all the problems identified with materialism. But if, say, substance dualism is true, are not animal souls entirely “natural”? Are human actions guided by intelligence supernatural? What of the ideal numbers and sets and propositions and possible worlds and so on? Must we delete them from our ontology simply because we are committed to materialism? Is every “special science” merely applied physics? Are praxeology and economics not legitimate sciences?
Clearly, materialism, apart from other unlovely things about it, strongly suggests scientism, that is, the view that the correct methodology of every science must imitate the methodology of physics. I don’t know why Stenger would want to import materialism, with all its liabilities, into his unsuccessful search for God.
Suppose now that metaphysical naturalism / materialism is false. Should we nonetheless still abide by methodological naturalism? But why? If there are immaterial entities both immanent and beyond this universe, why must we deny them all causal efficacy? Why listen to the bureaucrat Stenger instead of going where the evidence leads? If our investigation inclines us to postulate a designing intelligence, then shouldn’t we do just that?
Stenger agrees; his point is that the “hypothesis” of the existence of God is falsifiable and, in fact, is falsified. This is a welcome change from the views of those atheists who refuse to countenance the idea that nature can, at least in principle, yield insights about God.