There has been a bit of talk about methodological naturalism (MN) around lately, with David Heddle and Joe Carter posting about it and I just wanted to bring a few things together...
David's definitions will suffice
Philosophical Naturalism: the belief that the natural world is all that there is.
Methodological Naturalism: the belief that the natural world is all that is accessible for scientific inquiry.
Joe makes the following claim
Conclusion: If God can be discerned from the evidence of creation, than the evidence of God is detectable by empirical observation and study of the natural world. The Christian must therefore completely reject philosophical naturalism. We might also conclude that methodological naturalism is flawed and a hindrance to science. Though the method may be adequate for some purposes, it is unnecessarily self-limiting and should be rejected.
This all makes sense, but many scientists claim that supernatural explanations (and class Intelligent Design as one) are also outside the scope of science, mostly arguing that supernatural causes can never be observed.
Let me make this very clear...this is a gigantic double standard....Craig Rusbult explains why
Can scientists logically infer the existence of things they cannot observe? Yes, if an unobservable cause produces observable effects. This cause-and-effect principle is used in operations science. For example, even though electrons and ideas cannot be observed, modern theories propose electrons (in chemistry) and ideas (in psychology). Why? Because our observations are explained in the most satisfactory way by theories proposing the existence of unobservable causes (electrons and ideas) that produce the effects we observe.
Similarly, in historical science we can logically infer the existence of causes we did not observe, if these unobserved causes produced effects we can observe. Therefore, when skeptics ask "Were you there? Did you see it?", they are ignoring the principle that scientific logic depends mainly on observable effects, not observable causes. Because of this principle, even if an event or process was not directly observed, a plausible scientific theory can propose that the event or process did occur.
So when someone excludes supernatural causes from science on the basis of that they cannot be observed, yet include the vast multitude of natural causes that cannot be observed as science, what they are really doing is practicing philosophical naturalism (PN).
This assumption of PN essentially means that science is no longer looking for the best explanation or 'the truth', but instead merely looking for the best naturalistic explanation. The once noble aim of science is reduced to an atheistic propaganda machine.