Maarten Boudry, Ghent UniversityHere's the problem. You can't just arbitrarily restrict science to methodological naturalism. That's like ruling out supernatural explanations by fiat and not by logic. If God exists, then there's no reason why supernatural explanations can't be a legitimate part of science. This is one of the arguments made by Philip Johnson and it hasn't been adequately addressed by most philosophers.
Methodological Naturalism as an Intrinsic Property of Science: A Grist to the Mill of Intelligent Design Theory
In recent rounds of debate between evolutionists and supporters of Intelligent Design, the principle of methodological naturalism (MN) has been an important battleground. Creationists and intelligent design proponents have previously claimed that the commitment of evolutionists to naturalism and materialism constitutes a philosophical prejudice on their side, because it rules out any kind of supernatural causes by fiat. In response to these charges, some philosophers and scientists have argued that science is only committed to something they call methodological naturalism: Science does not deal with supernatural causes and explanations, but that does not mean that the latter do not exist. However, there has been some philosophical discussion about the correct understanding of MN. The principle of MN is often conceived of as an intrinsic and self-imposed limitation of science, as something that is part and parcel of the scientific enterprise by definition. According to this view (Intrinsic MN or IMN) - which is defended by people like Eugenie Scott, Michael Ruse and Robert Pennock and has been adopted in the ruling of Judge John E. Jones III in the Kitzmiller vs. Dover case - science is simply not equipped to deal with the supernatural and therefore has no authority on the issue. It is clear that this depiction of science and MN offers some perspectives for reconciling science and religion. Not surprisingly, IMN is often embraced by those sympathetic to religion, or by those who wish to alleviate the sometimes heated opposition between the two.
However, we will argue that this view of MN does not offer a sound rationale for the rejection of supernatural explanations. Alternatively, we will defend MN as a provisory and empirically grounded commitment of scientists to naturalistic causes and explanations, which is in principle revocable by future scientific findings (Qualified MN or QMN). In this view, MN is justified as a methodological guideline by virtue of the dividends of naturalistic explanation and the consistent failure of supernatural explanations in the history of science.
We will discuss and reject four arguments in favour of IMN: the argument from the definition of science, the argument from lawful regularity, the science stopper argument, and the argument from procedural necessity. Moreover, we will argue that defining the supernatural out of science is a counterproductive strategy against ID creationism, and, for that matter, against any theory involving supernatural explanations. More specifically, IMN has been eagerly exploited by proponents of ID to bolster their false claims about the philosophical and metaphysical prejudices of evolutionists. As ID proponent Philip Johnson rhetorically noted, if science is about following the evidence wherever it leads, why should scientists exclude a priori the possibility of discovering evidence for the supernatural? Therefore, IMN is actually grist to the ID mill.
We conclude that IMN is philosophically artificial and that its attempt to reconcile science and religion is ill-conceived. QMN, alas, does not provide any such ready reconciliation either, but it does offer a sound rationale for the rejection of supernatural designers in modern science.
But there's another problem with using methodological naturalism as a defense of accommodationism. How do draw the line between methodological naturalism and philosophical naturalism? Obviously, there's no difference for an atheist; in fact, the distinction seems rather silly. If supernatural explanations are never found to be necessary in explaining the natural world then doesn't it make sense to conclude that fairies and Santa Claus don't exist?
But for theists it's important to make a distinction so that they can adhere to methodological naturalism as scientists without having to abandon their belief in supernatural beings outside of the laboratory.
Where is the boundary and how do you tell when the line has been crossed? Accommodationists are absolutely convinced that they can tell the difference between methodological naturalism and philosophical naturalism but they are never very clear about explaining this difference to others.
Here's your chance. Let's see if anyone can come up with a good way of telling when the practice of methodological naturalism becomes philosophical naturalism.
) but since he'll be here in a few months I'm sure his sister will take him to Waterloo. 
