Metaphysical naturalism is the claim that nothing exists but the natural world. There are substantial variations in naturalist views, but all agree there is no such thing as intervention from a supernatural source, no possibility of miracles, and no intelligence or purpose beyond that of the universe itself. For most who hold this view, metaphysical naturalism is identical to materialism, the belief that matter and energy are ultimately all that exist.
Metaphysical naturalism is fundamentally different from methodological naturalism, a general-purpose approach to explaining observations. Methodological naturalism, as the name implies, is a technique—a method—used in research and assessment, especially science. For example, seeking to explain why water expands when it freezes, researchers look for a physical mechanism. There’s an assumption that mundane things are usually explained by natural mechanisms, and exploration generally supports that idea.
Contrary to what some naturalists claim, methodological naturalism’s usefulness in most practical situations does not prove metaphysical naturalism. In philosophy, metaphysics is the category of describing the actual nature of the universe. A metaphysical claim is a suggestion about how things “really are.” Metaphysical naturalism would consider the assertion “nothing exists but matter and energy” to be a statement of absolute reality. Attempting to make this conclusion based on the common use of methodological naturalism is irrational.
As a parallel, consider a man in a one-person submarine at the bottom of the ocean. He falls asleep, then awakes to find words in his journal that he does not remember writing. The most “natural” explanation is that either forgot about writing them or is having a breakdown. The suggestion that someone sneaked into his submarine, thousands of feet underwater, seems impossible to square with what he knows. Therefore, it makes sense to assume a more “natural” explanation, at least until more evidence surfaces. That is the essence of methodological naturalism. Pursuing that line of thought, the man in the submarine would try to piece together information to see when or how he might have written something and not remembered.
However, if the words in the journal were written in red pen, and all the man has on board the submarine are pencils, that’s a different story. If searching the tiny sub produces no red pens, then the “unnatural” idea that someone stole in from the outside is not entirely off the table. The absence of red pens doesn’t absolutely prove an interloper, but, sooner or later, mounting evidence might leave that as the only logical option. Continuing to look for a more “natural” explanation, while also realizing that further investigation might imply an intruder, still accords with methodological naturalism.
On the other hand, if the man absolutely rejects the possibility of a visitor and forces all evidence to be explained in conformity to that axiom, he’s taking the path of metaphysical naturalism. In that case, the man in the submarine is starting from a conclusion—there is no possible way anyone else could get in here—and interpreting his observations accordingly. That would be particularly irrational if he found evidence incompatible with his “natural” assumption, such as someone else’s wedding ring lying on the floor. The more evidence he sees that some other person has been in his submarine, the less reasonable it would be to simply keep stating, “Well, that can’t happen, so this evidence has to mean something else” (see Proverbs 18:17).
The key to unlocking methodological naturalism from metaphysical naturalism is summed up in a quote from the fictional detective Sherlock Holmes:
“When you have eliminated all which is impossible, then whatever remains, however improbable, must be the truth” (Sir Arthur Conan Doyle, “The Adventure of the Blanched Soldier,” 1926).
When exploring topics such as the origin of life or of the universe itself, natural explanations eventually fall short. In those instances, it’s perfectly rational to propose something beyond the natural as an explanation.
The Bible obviously contradicts the idea of metaphysical naturalism (Psalm 14:1), but it supports methodological naturalism. Contrary to what popular culture might think, Scripture does not propose that miracles are frequent occurrences. Rather, it indicates God has overtly intervened in history only on rare occasions and only to demonstrate or prove some divine message. The idea that God mostly allows creation to operate according to consistent rules (methodological) does not mean He cannot or will not intervene (metaphysical). In point of fact, the belief that the universe runs according to consistent, reliable rules—allowing for methodological naturalism—was a uniquely Judeo-Christian concept that drove the development of the scientific method.