Philosopher and photographer Laszlo Bencze on a reasonable understanding of methodological naturalism.
Galileo was a methodological naturalist because he was not a methodological supernaturalist, the only other option. Galileo was interested in the natural world, specifically the movements of the planets and their moons. He studied these movements via natural methods, i.e., he observed them through a telescope. He did not use supernatural methods in his studies. What might “supernatural methods” be? He might have written his questions about the solar system on slips of paper and burned them with incense in expectations of receiving visions explaining everything. Of course that “supernatural methodology” sounds very silly. I’m not aware of any serious Christian thinker who ever used that method of inquiry. All of them understood that if a person wished to understand the workings of a non contingent God in the world created by God there was no choice but to study that world directly. Its functioning could not be predicted from first principles as Aristotle thought. Nor could any human presume to question God directly to receive answers. That approach was unsuccessful for Job and would be equally unsuccessful for anyone else. God is not a cosmic librarian who is compelled to satisfy idle curiosity on demand.
The admission that the only way to understand the natural world is by observing it most certainly does not preclude the existence of a supernatural world. But direct study of the supernatural world by observation is not possible. Understanding of the supernatural world comes via revelation and via the normal actions of the rational mind. In fact rational thought necessarily leads to the conclusion that a supernatural world must exist. The rational mind is itself a mystery because it partakes of qualities which are supernatural though it exists in our natural realm. Thus the mind is a kind of hybrid between the two realms. So we have the perplexing difficulty of assigning logic and mathematics to either the natural world or the supernatural world. The modern prejudice is to assign both to the natural world, the world of material things, and say that they “emerge” from that world. That view makes little sense. I say that God equips us with the ability to understand both logic and mathematics as a result of being made in his image. He gives us the tools to understand things that are immaterial and beyond physics (hence “metaphysical”).
Thus by combining our minds with our observations of the natural world through normal means we come to that understanding which we call science. The methodology of science is natural insofar as it allows no supernatural shortcuts to knowledge. Yet it is supernatural insofar as the mental tools it relies upon cannot be explained as artifacts of the natural world. Hence when used fairly and correctly, the term “methodological naturalism” is nothing more than an admission of man’s limited place in the world. We cannot conjure answers directly from supernatural realms. We can only persist doggedly in observations of what is open to observation. Yet, our reliance on methodological naturalism in no way limits our world to that which can be observed because the very act of observing relies upon that great, mysterious, non-natural thing: the human mind.
See also: Why the human mind remains a mystery to naturalists.
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