For example, consider an auto mechanic trying to figure out why a car is making a funny noise. He may hypothesize that a part is worn out, or that a coupling is loose, that some parts have come out of alignment, etc. But he probably won't seriously consider supernatural causes such as ghosts, gremlins, or demons. This mechanic is using methodological naturalism. If this mechanic is also a theist, then he uses methodological naturalism in his job, but does not subscribe to philosophical naturalism.
"Once miracles are admitted, every scientific explanation is out of the question."
- — Johannes Kepler
Methodological naturalism and science
Some critics, notably Intelligent design proponents, charge that this is an arbitrary restriction that blocks exploration of potentially fruitful areas of research.
However, science is eminently practical. The reason scientists don't consider supernatural explanations is that there is no way to test them to see whether they're correct. In the example above, an auto mechanic may hypothesize that a problem was caused by evil spirits, but there is no reliable way to either confirm or disconfirm this hypothesis. To put it bluntly, the reason that scientists don't consider supernatural explanations is that they don't work.
Note that it is conceivable that someone might some day come up with a testable explanation for some phenomenon that involves a supernatural entity. If a genuine miracle ever occurred, this rule would have to be revisited. In the meantime, given supernaturalism's track record, it seems safe for scientists to avoid it.
Naturalism ignores intelligent design
- "...their preconceived ideology-naturalism-prevents them from even considering an intelligent cause."
If God was observable, even indirectly, he would be considered "natural" in this context. The problem is divine intelligence is not observable (so far). In fact, the lack of evidence is the real reason that divine explanations are generally ignored by scientists. Obviously, the argument from ignorance does not count as evidence.
- "As we've mentioned before, science is a search for causes. Logically, there are only two types of causes: intelligent and nonintelligent (i.e., natural)"
This is incorrect: intelligence, at least when it is observable, is natural (in the context of naturalism). That is why psychology proceeds using scientific means but still adheres to naturalism.
Naturalism cannot explain the profound questions
- "If it can’t answer the fundamental questions of the origin of the world or the origin of life, it’s not a viable box top [world view]."
That is not a reasonable claim. The apologists have not demonstrated that these questions are answerable, particularly the origin of the universe. Also, their "god-did-it" hypothesis does not explain anything because an explanation must be founded on known entities, rather than using one mystery to "solve" another. Naturalism may also be able to answer these questions and assuming they will not is god of the gaps and argument from ignorance.