Methodological naturalism, unlike philosophical naturalism, is the sensible, neutral working principle which confines the science of the day to natural causes. The scientific naturalism (or philosophical naturalism or scientism) worldview is not a worldview which is self-evident in scientific methodology. In contrast, methodological naturalism is a more restricted worldview in which supernatural phenomena cannot or should not be used in scientific methods. Take philosophical naturalism as a view that no supernatural entities exist–no person such as God, for instance, but no other supernatural entities either, or anything at all similar to God.
There is also a separate kind of naturalism, philosophical naturalism, which is the belief (not science, but belief) that the universe is composed of only matter and energy, and there are no supernatural beings, forces, or causes. The vast majority of modern philosophers will gladly embrace naturalism as simply described–that is, they will simultaneously reject supernatural entities, while allowing science to be one possible route, though not necessarily the only route, to crucial truths about the human spirit. Essentially, philosophical naturalists claim that the success of methodological naturalism, as well as the total failure of other systems, means it is a leap in logic to claim not merely that we are using naturalism as a hypothesis of methodology, but that naturalism is in fact the reality of the universe.
Methodological naturalists confine their scientific inquiry to examining natural causes, since any attempts to determine causation from the supernatural are never productive, leading to the creation of dead ends and scientific “God-of-the-Gaps”-type hypotheses. Methodological naturalists are willing to acknowledge the possibility of supernatural causes, but are committed to acting as though there are none. Philosophical naturalists are committed to a position in which natural properties and causes alone do exist. In view of the difficulties moral non-naturalism faces, most modern moral philosophers have instead chosen some species of naturalist views.
Those philosophers who have comparatively weak commitments to naturalism are tempted to conceive of naturalism unrestrictedly, lest they be thereby disqualified from being naturalists, whereas those who endorse stronger naturalistic doctrines are content to raise the standard of naturalism. That some take a priori views about philosophical naturalism into the sciences, whereas others take a posteriori views that derive from methodological naturalism (as in the case of the philosopher Barbara Forrest) is regrettable, but irrelevant for the aim of methodological naturalism, which is neutral about the metaphysics (as for Forrest).
Properly understood, the principles of methodological [naturalism] demand that one should remain neutral toward God; one cannot, wearing ones scientific hat, say whether or not God does or does not act. The converse, however, is that if science is limited by methodological [naturalism] due to our failure to check an intervention of a power with all the potential for harm, then either God does or God does not do this fails as scientific proposition. Science cannot prove nor disprove the actions of God (or of his plan) in our world.
If we have no idea if history has always been all-natural, then the best scientific strategy to seek the truth is an open science, where scientists humbly ask the question rather than haughtily presume the answer. I believe that the answer is yes, since Christians–who do believe non-natural miracles occur, and therefore must see a naturalistic science as just one facet of a larger search for truth, which takes into account all possibilities, including non-natural ones–can embrace methodological naturalism, rejecting extending it beyond the sciences. You can pursue natural science just like a nonbeliever, this line of thinking goes, but still be a believer on matters of religion. For instance, although natural scientists practice methodological naturalism in their scientific work, they might also believe in God (ontological supernaturalism), or they might be metaphysical naturalists, and thus atheists.
Science is said to be neutral with respect to religion, if only because science and religion are epistemically different in their essence. Science is simply a human endeavor to investigate nature, subject to rigorous, peculiar rules, and it does not (at this point) take into account God. Many philosophers of science have held that the fundamental requirement for scientific inquiry is that it be empirically testable, effectively restricting it to studying and explaining the natural world. However, the mathematician William Dembski has suggested that methodological naturalism actually hinders scientific progress because it restricts science to only investigating natural causes.
This stance is taken by creationists, such as the Institute for Creation Research and Creation Science, whose Web site states that methodological naturalism limits science to the non-invoking of supernatural causes, and that methodological naturalism cannot be justified as the governing principle of all types of science–without doing damage to science as an endeavor for the pursuit of truth . Most advocates of philosophical naturalism accept the fundamental premise that most supernatural claims can be investigated using the scientific method, and have been investigated and shown to not exist. The first is a religious and spiritual stance, which accepts methodological naturalisms being true, but believes supernatural causes are directly observed and measured, and that they should be accepted by the scientific community (so long as it does not produce results contradicting their beliefs). The first is underlying application of scientific method to science, that makes a methodological assumption that observed events in nature are explained by only natural causes, while making no assumptions about supernatural existence or non-existence, and therefore does not accept supernatural explanations of those events.
Naturalism is a commitment to explaining the world by means of natural properties and causes, in contrast to supernatural or spiritual explanations. Furthermore, Arthur K. Danto has said that naturalism, as it is currently used, is a variety of philosophical monism according to which everything that exists or happens is natural, meaning it is explainable by methods which, though exemplified paradigmatically in the natural sciences, are continued across the domains of objects and events. Theistic science is not a monolithic mode of thought, as theistic science may result in varying theological claims concerning God, nature, and science.
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