Naturalism is divided into two philosophical stances:
- Naturalized epistemology (or Methodological naturalism or scientific naturalism) which focuses on epistemology: This stance is concerned with knowledge: what are methods for gaining trustworthy knowledge of the natural world? It is an epistemological view that is specifically concerned with practical methods for acquiring knowledge, irrespective of one's metaphysical or religious views. It requires that hypotheses be explained and tested only by reference to natural causes and events. Explanations of observable effects are considered to be practical and useful only when they hypothesize natural causes (i.e., specific mechanisms, not indeterminate miracles). Methodological naturalism is the principle underlying all of modern science. Some philosophers extend this idea, to varying extents, to all of philosophy too. Science and philosophy, according to this view, are said to form a continuum. W.V. Quine, George Santayana, and other philosophers have advocated this view.
- Metaphysical naturalism, (or ontological naturalism or philosophical naturalism) which focuses on ontology: This stance is concerned with existence: what does exist and what does not exist? Naturalism is the metaphysical position that "nature is all there is, and all basic truths are truths of nature."
The ideas and assumptions of philosophical naturalism were first seen in the works of the Ionian pre-Socratic philosophers. One such was Thales, considered to be the father of science, as he was the first to give explanations of natural events without the use of supernatural causes. These early philosophers subscribed to principles of empirical investigation that strikingly anticipate naturalism .
The modern emphasis in methodological naturalism primarily originated in the ideas of medieval scholastic thinkers during the Renaissance of the 12th century:
- By the late Middle Ages the search for natural causes had come to typify the work of Christian natural philosophers. Although characteristically leaving the door open for the possibility of direct divine intervention, they frequently expressed contempt for soft-minded contemporaries who invoked miracles rather than searching for natural explanations. The University of Paris cleric Jean Buridan (a. 1295-ca. 1358), described as "perhaps the most brilliant arts master of the Middle Ages," contrasted the philosopher’s search for "appropriate natural causes" with the common folk’s habit of attributing unusual astronomical phenomena to the supernatural. In the fourteenth century the natural philosopher Nicole Oresme (ca. 1320-82), who went on to become a Roman Catholic bishop, admonished that, in discussing various marvels of nature, "there is no reason to take recourse to the heavens, the last refuge of the weak, or demons, or to our glorious God as if He would produce these effects directly, more so than those effects whose causes we believe are well known to us."
- Enthusiasm for the naturalistic study of nature picked up in the sixteenth and seventeenth centuries as more and more Christians turned their attention to discovering the so-called secondary causes that God employed in operating the world. The Italian Catholic Galileo Galilei (1564-1642), one of the foremost promoters of the new philosophy, insisted that nature "never violates the terms of the laws imposed upon her." 
Pierre Simon de Laplace, when asked about the lack of mention of God in his work on celestial mechanics, is said to have replied, "I have no need of that hypothesis."
During the Enlightenment, a number of philosophers including Francis Bacon and Voltaire outlined the philosophical justifications for removing appeal to supernatural forces from investigation of the natural world. Subsequent scientific revolutions would offer modes of explanation not inherently theistic for biology, geology, physics, and other natural sciences.
The term "methodological naturalism" for this approach is much more recent. According to Ronald Numbers, it was coined in 1983 by Paul de Vries, a Wheaton College philosopher. De Vries distinguished between what he called "methodological naturalism," a disciplinary method that says nothing about God's existence, and "metaphysical naturalism," which "denies the existence of a transcendent God." The term "methodological naturalism" had been used in 1937 by Edgar Sheffield Brightman in an article in The Philosophical Review as a contrast to "naturalism" in general, but there the idea was not really developed to its more recent distinctions.
In a series of articles and books from 1996 onwards, Robert T. Pennock wrote using the term methodological naturalism to clarify that the scientific method confines itself to natural explanations without assuming the existence or non-existence of the supernatural, and is not based on dogmatic metaphysical naturalism as claimed by creationists and proponents of intelligent design, in particular Phillip E. Johnson. Pennock's testimony as an expert witness at the Kitzmiller v. Dover Area School District trial was cited by the Judge in his Memorandum Opinion concluding that "Methodological naturalism is a "ground rule" of science today"
Naturalism as epistemology
W. V. Quine describes naturalism as the position that there is no higher tribunal for truth than natural science itself. There is no better method than the scientific method for judging the claims of science, and there is neither any need nor any place for a "first philosophy", such as (abstract) metaphysics or epistemology, that could stand behind and justify science or the scientific method.
Therefore, philosophy should feel free to make use of the findings of scientists in its own pursuit, while also feeling free to offer criticism when those claims are ungrounded, confused, or inconsistent. In this way philosophy becomes "continuous with" science. Naturalism is not a dogmatic belief that the modern view of science is entirely correct. Instead, it simply holds that science is the best way to explore the processes of the universe and that those processes are what modern science is striving to understand. However, this Quinean Replacement Naturalism finds relatively few supporters among philosophers.
Karl Popper equated naturalism with inductive theory of science. He rejected it based on his general critique of induction (see problem of induction), yet acknowledged its utility as means for inventing conjectures.
A naturalistic methodology (sometimes called an "inductive theory of science") has its value, no doubt. […] I reject the naturalistic view: It is uncritical. Its upholders fail to notice that whenever they believe to have discovered a fact, they have only proposed a convention. Hence the convention is liable to turn into a dogma. This criticism of the naturalistic view applies not only to its criterion of meaning, but also to its idea of science, and consequently to its idea of empirical method.
– Karl R. Popper, The Logic of Scientific Discovery (Routledge, 2002), pp. 52-53, ISBN 0-415-27844-9.
Popper instead proposed the criterion of falsifiability for demarcation.
Contemporary philosopher Alvin Plantinga has argued that evolutionary naturalism is incoherent. In Science and Theology News he attacks the conclusions of the Kitzmiller trial and suggests that the term "science" denotes any activity that is:
- a systematic and disciplined enterprise aimed at finding out truth about our world, and
- has significant empirical involvement. Any activity that meets these conditions counts as science.
He concludes "if you exclude the supernatural from science, then if the world or some phenomena within it are supernaturally caused – as most of the world's people believe – you won't be able to reach that truth scientifically."
Steven Schafersman contends methodological naturalism is "the adoption or assumption of philosophical naturalism within scientific method with or without fully accepting or believing it … science is not metaphysical and does not depend on the ultimate truth of any metaphysics for its success (although science does have metaphysical implications), but methodological naturalism must be adopted as a strategy or working hypothesis for science to succeed. We may therefore be agnostic about the ultimate truth of naturalism, but must nevertheless adopt it and investigate nature as if nature is all that there is." 
This definition rules out recourse to the supernatural. Pennock contends that as supernatural agents and powers "are above and beyond the natural world and its agents and powers" and "are not constrained by natural laws", only logical impossibilities constrain what a supernatural agent could not do, and "If we could apply natural knowledge to understand supernatural powers, then, by definition, they would not be supernatural". As the supernatural is necessarily a mystery to us, it can provide no grounds on which to judge scientific models. "Experimentation requires observation and control of the variables … But by definition we have no control over supernatural entities or forces." Allowing science to appeal to untestable supernatural powers would make the scientist's task meaningless, undermining the discipline that allows science to make progress, and "would be as profoundly unsatisfying as the ancient Greek playwright's reliance upon the deus ex machina to extract his hero from a difficult predicament."
Naturalism of this sort says nothing about the existence or nonexistence of the supernatural which by this definition is beyond natural testing. Other philosophers of science hold that some supernatural explanations might be testable in principle, but are so unlikely, given past results, that resources should not be wasted exploring them. Either way, their rejection is only a practical matter, so it is possible to be a methodological naturalist and an ontological supernaturalist at the same time. For example, while natural scientists follow methodological naturalism in their scientific work, they may also believe in God (ontological supernaturalism), or they may be metaphysical naturalists and therefore atheists. This position does not preclude knowledge that derives from the study of what is hitherto considered supernatural, but considers that if such a phenomenon can be scientifically examined and explained naturally, it, then, by definition, ceases to be supernatural.
Notes and references
- Methodological Naturalism and Philosophical Naturalism: Clarifying the Connection (2000), Barbara Forrest, Retrieved 2007-05-20.
- "Naturalism", in The Encyclopedia of Philosophy, Macmillan, 1996 Supplement, 372-373.
- Jonathan Barnes's introduction to Early Greek Philosophy (Penguin)
- Ronald L. Numbers (2003). "Science without God: Natural Laws and Christian Beliefs." In: When Science and Christianity Meet, edited by David C. Lindberg, Ronald L. Numbers. Chicago: University Of Chicago Press, p. 267.
- Nick Matzke: On the Origins of Methodological Naturalism. The Pandas Thumb (March 20, 2006)
- ASA March 2006 - Re: Methodological Naturalism
- Kitzmiller trial: testimony of Robert T. Pennock
- Kitzmiller v. Dover: Whether ID is Science
- Stanford Encyclopedia of Philosophy: Naturalized Epistemology
- Naturalism is an Essential Part of Science - Steven Schafersman
- Robert T. Pennock, Supernaturalist Explanations and the Prospects for a Theistic Science or "How do you know it was the lettuce?"
- Mario De Caro and David Macarthur (eds) Naturalism in Question. Cambridge, Mass: Harvard University Press, 2004.
- Friedrich Albert Lange, The History of Materialism, London: Kegan Paul, Trench, Trubner & Co Ltd, 1925, ISBN 0-415-22525-6
- Naturalist Newsletter
- Center for Naturalism
- Naturalism: The Naturalistic Worldview
- Naturalism David Papineau, The Stanford Encyclopedia of Philosophy
- The Craig-Taylor Debate: Is The Basis Of Morality Natural Or Supernatural? William Lane Craig and Richard Taylor October 1993, Union College (Schenectady, New York)
- Naturalism Jon Jacobs, The Internet Encyclopedia of Philosophy
- Naturalism article in the Catholic Encyclopedia
- Dennis Polis, God, Science and Mind: The Irrationality of Naturalism
- Alvin Plantinga (1994). Naturalism Defeated. http://www.calvin.edu/academic/philosophy/virtual_library/articles/plantinga_alvin/naturalism_defeated.pdf. (pdf)
- Victor Reppert, C. S. LEWIS'S DANGEROUS IDEA: In Defense of the Argument from Reason
- Shaun Connell, The Natural Verses Supernatural False Dichotomy
- A shorter version of C. S. Lewis' Dangerous Idea
- Philip Johnson's Evolution as Dogma: The Establishment of Naturalism from First Things
- Robert A. Delfino's (2007) Replacing Methodological Naturalism
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