Methodological naturalism assumes that there is a natural cause for all things, and is the basis of the scientific method. Supernaturalism assumes that there are entities, energies, forces and phenomena that will forever elude the scrutiny of scientists. The first problem with supernaturalism is this; if something is beyond the realm of scientific proof then it is completely indistinguishable from being non-existent, and if it is within the realm of proof then it is no longer a supernatural phenomena.
We cannot assume supernaturalism when it comes to science, because if we do then anything goes. We cannot prove that gravity is not actually undetectably minute entities pulling one object towards another, but why make this assumption? Just because we cannot prove it wrong doesn’t mean it has any credibility. Supernaturalism forever hides in the realm of ‘you can’t prove me wrong’ – but that’s no refuge for the rational. I can think of any number of ridiculous propositions that you cannot prove wrong; I have an invisible pet dragon that doesn’t interfere with matter in any way, I can play the piano excellently, but I can’t if anyone is watching or listening, and so on. You can’t prove these things wrong, does that give them any credibility whatsoever? Absolutely not.
In order for a proposition to have any worth it has to be falsifiable. ‘Tomorrow it will rain’ is a falsifiable claim because if it doesn’t rain then I stand proven wrong. Any claim made about the world is only of use if you can prove it wrong. Science is not what is proven to be right, it is what hasn’t yet been proven wrong. A strong scientific theory is one that can be proven wrong, but hasn’t been to date.
This is the main advantage of naturalism over supernaturalism – naturalistic ideas can be proven wrong, whereas supernatural ideas are ridiculous and have nothing that inherently distinguishes them from the non-existent. Naturalism has also been of demonstrable benefit to humanity. Methodological naturalism brings us scientific advances whether it’s technology or medicine and so on, these things would not have been possible had we clung to the supernatural explanations of our ancestors. How far would we have got if we never got past the belief that diseases were the result of God’s wrath, or some other kind of curse? Or that sacrificing a goat to a particular god was the key to a successful crop?
Naturalism works because it is within the realm of disproof. Supernaturalism is meaningless because it cannot be distinguished from other unfalsifiable claims and it cannot be distinguished from the non-existent. Naturalism is by far the more advantageous viewpoint to assume.