Methodological naturalism is the idea that it’s imprudent to invoke supernatural intervention as an explanation when such miraculous intervention may not be necessary. This is a pillar of mainstream science.

And how do you determine whether supernatural intervention was necessary for some observation?

By assuming, for the sake of argument, that something supernatural did not intervene, and then genuinely attempting to find a sufficient natural (that is, mechanistic) explanation.

The Relentless Robot Thought Experiment

You live on planet Chalybos, and you’ve been taught from birth that the core of the planet is made of an indestructible substance. You begin a mission to search for that indestructible substance.

You’re not the first Chalyban to have this idea. Many people have before begun similar digging adventures.

The first such explorer hit a really tough substance 50 meters down. He was convinced that this was the indestructible core. He wailed on the substance for weeks, but it wouldn’t break. Finally, after failing to dig any deeper, he proclaimed that he had, indeed, found the core.

Later, a different explorer brought a team along with him. After months of working at the stubborn material, they broke through. The material wasn’t indestructible at all; the core had not been reached.

This happened again and again in the history of Chalybos. A team would reach a layer seemingly invulnerable, and proclaim their victory in terms of having discovered the planet’s core. But then a subsequent team would work a little harder and longer and break through what before was claimed to be the core.

And then, the cycle would repeat.

To deal with this, you decide to build a robot that is programmed to dig downward. Even if the robot hits a surface that he has trouble with, he never gives up. He always treats anything he encounters as if he can break through.

• In some ways, this robot has a weakness: He is stuck in full-throttle dig-mode. He has no perceptions and no decisionmaking faculties. Furthermore, if indeed he does hit the true core one day, he’ll continue digging into it, fruitlessly, forever.
• In other ways, this robot has a strength: He will never give up too soon and falsely proclaim victory, as so many explorers before you had done.

Here are a few opinions of fellow Chalybans:

• Seeing this repetitive pattern of false victories and deeper digs, some conclude that there is no indestructible core at all. There is only an “indestructible core of the gaps,” shrinking every time a team breaks through and digs deeper.
• Eventually, the robot hits a surface that he spends years working against with no success. Some, at this point, say, “We believe the robot has finally arrived at the core — but we must keep him powered, forever, because there is a chance that we’re wrong.”
• Others say, “He has certainly arrived at the core. We should save our energy and shut the robot off. His job is finished.”
• Etc.

No Obvious Answer

Can you see the reasoning behind the skeptics who reject the idea of an indestructible core? Can you see the reasoning behind those who believe the core has been found, but refuse to disconnect the robot? And can you see the reasoning behind those who believe the core has been found, and thus the robot should be disconnected?

I can see the reasoning behind all of these perspectives. None of them are completely meritless nor certainly meritorious.

Methodological naturalism is like the relentless robot. It chews through superstition and baseless supernatural conjecture. Layer after layer, it refuses to quit. To some, this is evidence that there’s no indestructible core at all, that is, there is nothing in existence that does lacks an mechanistic and explanatory underpinning. But I don’t think that necessarily follows. Methodological naturalism is a preference heuristic, not dogma.

I say, “keep the robot going,” while simultaneously putting faith in a God who I believe has interacted with my life in a meaningful, powerful, and efficacious way. This is what Stephen Jay Gould meant by “non-overlapping magisteria.” My beliefs about the core are orthogonal to the activity and revelations of the robot, though they are updated if and when the robot forces it.