Ontology is the branch of philosophy that deals with conceptions of reality and the nature of being, while metaphysics investigates principles of reality transcending those of any particular science, traditionally including cosmology and ontology. Ontological naturalism, or metaphysical naturalism, describes the belief that nothing exists except the natural world that can be studied, at least in principle, through the scientific method (methodological naturalism). This excludes the supernatural from study not merely because only the natural is available for study but also because the supernatural is held not to have existence outside its conceptualization. The scientific method follows upon the assumption that observable effects in nature are best explainable only by natural causes, without reference to, or an assumption of, the existence or non-existence of supernatural notions.
The supernatural is conceived of as pertaining to entities, events or powers that are regarded as being beyond nature, in that they cannot be explained from the laws of the natural world. How convenient for those who wish to believe in miracles!
I—and scientific others—maintain that because we could not even suspect the existence of such entities or powers if they did not interact with the physical world, then that such entities or powers are necessarily part of the physical world—are natural—by virtue of such interactions. As soon as something manifests within the physical world then it is part of the physical world. In fact, the supernatural is a special invented category that made intuitive sense to pre-scientific thinkers and that has remained convenient to religionists, creationists, and intelligent design creationists.
Frederick Crews argues that metaphysical naturalism is a valid and rational extension of methodological naturalism. This is contrary to Ruse and to the people at NCSE (e.g., Eugenie Scott). Stenger states that according to our best knowledge, the world of matter is all that exists. Massimo Pigliucci wrote in 1998 that the methological-metaphysical distinction is "technically correct" but lacking in "philosophical courage." Trotskyist, Joe Kay, thinks that the methodological-metaphysical distinction is untenable.
Why are these methodological and ontological distinctions important?
Proponents of creationism or intelligent design creationism refer to methodological naturalism as 'scientific materialism' or as 'methodological materialism' and conflate it with metaphysical naturalism. In an attempt to discredit the findings of science that exclude religious explanations, they resort to this assertion in order to support their claim that modern science has an atheistic bias. To do so ignores the fact that even if science did have an atheistic bias, this would not indicate that creationism is a viable explanatory alternative. Creationists favor a revived natural philosophy that welcomes supernatural explanations for natural phenomena in supports of claims for "theistic science" or pseudoscience.
Blog: comments on Letter to an non-atheist New Atheist.
Here's an interesting critique of a critique of scientific approaches.
Websites: Butterflies and wheels article : Naturalism is an Essential Part of Science and Critical Inquiry : The Oxford Handbook of Philosophy of Religion, 11: GOD, SCIENCE, AND NATURALISM : Philosophy Now: The Alleged Fallacies of Evolutionary Theory : Statement on Intelligent Design : Science and fundamentalism : Justifying Methodological Naturalism : Methodological Naturalism and Philosophical Naturalism : Naturalism is an Essential Part of Science : Robert T. Pennock, Supernaturalist Explanations and the Prospects for a Theistic Science or "How do you know it was the lettuce?" : Kitzmiller v. Dover: Whether ID is Science :
On the Origins of Methodological Naturalism : Kitzmiller trial: testimony of Robert T. Pennock :
creationism, intelligent design, metaphysical naturalism, metaphysics, methodological naturalism, ontology, ontological naturalism, science, scientific method, supernatural