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Philosophy of science
Methodological naturalism is the label for the required assumption of philosophical naturalism when working with the scientific method. Methodological naturalists limit their scientific research to the study of natural causes, because any attempts to define causal relationships with the supernatural are never fruitful, and result in the creation of scientific "dead ends" and God of the gaps-type hypotheses. To avoid these traps scientists assume that all causes are empirical and naturalistic, which means they can be measured, quantified and studied methodically.
However, this assumption of naturalism need not extend beyond an assumption of methodology. This is what separates methodological naturalism from philosophical naturalism — the former is merely a tool and makes no truth claim, while the latter makes the philosophical — essentially atheistic — claim that only natural causes exist.
“”If a philosopher or social scientist were to try to encapsulate a single principle that yoked together the intellectual process of [civilization], it would be a gradual dismantling of presumptions of magic. Brick by brick, century by century, with occasional burps and hiccups, the wall of superstition has been coming down. Science and medicine and political philosophy have been on a relentless march in one direction only — sometimes slow, sometimes at a gallop, but never reversing course. Never has an empirical scientific discovery been deemed wrong and replaced by a more convincing mystical explanation. ("Holy cow, Dr. Pasteur! I've examined the pancreas of a diabetic dog, and darned if it's NOT an insulin deficiency, but a little evil goblin dwelling inside. And he seems really pissed!") Some magical presumptions have stubbornly persisted way longer than others, but have eventually, inexorably fallen to logic, reason and enlightenment, such as the assumption of the divine right of kings and the entitlement of aristocracy. That one took five millennia, but fall it did.
Methodological naturalism and theism
The majority of scientists do not believe it is possible to combine methodological naturalism with theistic or supernatural philosophical belief systems. Even in the United States, a majority of scientists embrace full philosophical naturalism — although a significant minority (40%-45%) describe themselves as "theistic evolutionists" or hold other religious beliefs.
Stephen Jay Gould's Non-Overlapping Magisteria is a form of methodological naturalism that allows for the acknowledgement of supernatural beliefs. It is an attempt to compartmentalize the role of science and religion, and maintain them completely separate from each other: assigning each an equal but different role in human understanding. There are still many prominent modern-day proponents of this "dual path" within the sciences; most notable are probably Ken Miller and his book Finding Darwin's God  and Francis Collins' The Language of God. Miller was one of the primary witnesses against the school board in Kitzmiller v. Dover Area School District, and a prominent opponent of "intelligent design" and creationism, while Collins was the former head of the Human Genome Project and a convert to Christianity.
Methodological naturalism and the anti-science movement
Methodological naturalism has become an important buzzword in the culture wars with the anti-science movement. The battle hinges around intelligent design and creationism advocates who claim the theory of evolution is a religion. The modern form of this started with Phillip Johnson and his publication of Darwin on Trial where he not only created a list of repeatedly refuted creationist claims but also tried to put forward the idea that teaching evolution was a violation of the establishment clause of the United States Constitution. Johnson's main argument centered around confounding philosophical naturalism and methodological naturalism and claiming that teaching evolution was an endorsement of philosophical naturalism and thus impinged on the religious beliefs of students. Eugenie Scott described Johnson's error in her review:
“”The scientific definition of evolution makes no mention of theological issues such as whether God created. Science as practised today is methodologically naturalistic: it explains the natural world using only natural causes. Science cannot explain (or test explanations about) the supernatural. There is also an independent sort of naturalism, philosophical naturalism, a belief (not science, but belief) that the universe consists only of matter and energy and that there are no supernatural beings, forces, or causes. Johnson's crucial error is not distinguishing between these two kinds of naturalism. That some individual scientists are philosophical naturalists does not make science atheistic any more than the existence of non-believing bookkeepers makes accounting atheistic.
While Johnson and the creationists may have started the ball rolling it is the intelligent design advocates that have really embraced the rhetoric surrounding the evils of methodological naturalism. The Discovery Institute ("DI") as the primary public relations firm for "ID" has been beating this drum in every possible direction. The DI claims many things at once, and the fact that they may contradict each other never seems to bother them. They just like to throw a bunch of bullshit out there and see what sticks.
They claim that:
- Methodological naturalism is not really the accepted approach in Science.
- Intelligent design actually follows methodological naturalism because it doesn't say who or what the designer is.
- Answering the kinds of questions that intelligent design and evolution ask can not be handled by methodological naturalism.
- Evolution is as much a religion as Intelligent design because of its reliance on naturalism.
All of these arguments together are pretty self-defeating, but they are also wrong individually. Methodological naturalism is a cornerstone of science, embraced by both practitioners and philosophers of science. There is always disagreement in philosophy, and that includes philosophy of science. The fact that intelligent design doesn't talk about the designer is a major hit against it as a hypothesis, and it certainly doesn't save it from violations of methodological naturalism.
The value of methodological naturalism comes from the ability to quantify, measure, and study the causes of phenomena. Intelligent design removes our ability to predict, measure and quantify, whether the intelligent designer is a deity or an alien. The questions that evolution answers are rooted as firmly in empirical evidence and methodological naturalism as any other science. Arguments that claim it is not are really holdover ideas from creationists, who like to claim that unless it's directly observed in a laboratory, "it's not science". Sometimes the DI likes to mix in issues of morality and ethics, and claims evolution addresses those questions, but this is simply the naturalistic fallacy. Finally, the last argument that evolution is a religion is the same old Johnson argument — all over again — that Scott and others have had to address ad nauseum.
Arguments against methodological naturalism
While the reality of methodological naturalism, and its importance to practicing scientists, cannot be denied by any rational person, that has not shielded it from criticism. Criticism of methodological naturalism comes primarily from two camps, and for opposite reasons.
The first is the religious and spiritual position that accepts its existence as a reality but feels that supernatural causes are directly observable and measurable and should be embraced by the scientific community (so long as it doesn't reach results that contradict their beliefs).
The second is from philosophical naturalists, who also believe that the supernatural is testable but that it has failed all the tests and should be tossed. Essentially, they argue that the success of methodological naturalism, and the complete failure of other systems, means it is a logical leap to say that we don't just use naturalism as an assumption in methodology, but that naturalism is actually the reality of the Universe.
Religious and spiritual arguments
By far the most vocal arguments stem, once more, from those who deny the reality of evolution. Answers in Genesis (AIG) embraces the most common argument trying to separate out what it calls "operational science" versus "origin science." AIG claims that "operational science" can embrace methodological science all it wants and that's fine, but that "origin science" cannot. "Operational science", to AIG, is the thing that makes your computer work and lets medical science develop new drugs, while "origin science" is basically evolution, abiogenesis and the Big Bang. The presumed reasoning in this break is that origin science relies in part on historical evidence, therefore somehow this violates methodological naturalism and means that they are perfectly within their rights to bring "God" and miracles — and everything else — into the picture.
This is as illogical as any argument from the DI-ists as could ever be. Historical science is grounded in prediction and observation just like any other form of science, and the value of methodological naturalism in keeping things quantifiable, measurable and falsifiable applies as much to historical evidence as to laboratory evidence.
Another attack that's often made is that naturalistic explanations are "missing" something in the analysis. For example: one of the more common points of contention surrounds evolutionary explanations for altruism. Arguments that link altruist deeds to nepotism and inclusive fitness, or demonstrating that there is no "true altruism", only reciprocal altruism, are often met by religious individuals by claiming it's completely wrong and that religion and God can explain "true altruism" and should be embraced in any such study.
Finally, another popular approach is to claim that the supernatural can be studied using the scientific method. This group is a hodgepodge of people, from faith healers, ghost hunters, psychics, dowsers, and astrologers to the more mainstream religious researchers claiming to study the power of prayer. Essentially, these arguments say that the supernatural claims they make have repeatable specific predictions that can be studied and therefore should be embraced by science. The fact that all of these things have been studied and shown to have no effect whatsoever doesn't seem to faze anyone in this group.
They are right about one thing; those bodies of wonderlore have made specific and testable predictions. And to the extent that any of these hypotheses make specific and testable predictions, it begins to lose its supernatural character. It becomes a reliable part of our world and human minds will bejigger it to see how it works. As Arthur C. Clarke might have said, "any sufficiently advanced magic is indistinguishable from science."
Arguments from philosophical naturalism
Taking off from where the last arguments of the spiritualists leave off are the proponents of philosophical naturalism. Most of these individuals agree with the basic premise that most supernatural claims can be studied using the scientific method, and that they have been studied and shown to not exist. These individuals argue that the logical leap is then to realize that these things really do not exist and that naturalism is reality.
Perhaps the best known proponent of this viewpoint in recent times is Richard Dawkins with his recent best-selling book The God Delusion. Others include Christopher Hitchens with his book God is not Great  and Sam Harris with Letter to a Christian Nation . These authors point out that empirical evidence can be derived that falsifies the existence of an interventionist god such as the "Christian" god. They argue that science should embrace its ability to demonstrate the falsehood of any claim and comes out against the reality of religion.
Others have focused less on religion in general and more on the specific claims of spirituality — particularly as it emerges from the pseudoscience movements. James Randi has offered a million dollar prize to anyone who can offer proof of supernatural claims such as the ability to talk to the dead or make psychic readings. He has personally overseen and arranged for many hundreds of controlled experiments on these claimed abilities. Every single one of those tested has failed. Randi makes several excellent points that it is possible for science to study these kinds of claims using standard methodology, and that the mounting evidence of failure is evidence that these claims are bogus.
Perhaps one of the strongest arguments for philosophical naturalism stems from the success of methodological naturalism. Nothing else in human knowledge has come anywhere close to the ability of science to predict, understand, and control the world around us. From landing a man on the Moon, to the creation of the personal computer and the Internet, humanity has been gifted beyond measure by the assumption of methodological naturalism. At some point, doesn't the amazing success of assuming naturalism when asking questions about reality mean that naturalism is not only a good assumption — but the underlying reality of the Universe? It's not conclusive, of course, but it does seem a reasonable argument at this point.
- Many Scientists See God's Hand in Evolution by Larry Witham, National Center for Science Education (Archive.org copy from February 19, 2006).
- New Survey: Scientists "More Likely Than Ever" To Reject God Belief Web Posted: July 25, 1998 (Archive.org copy from December 6, 2008).
- Miller, K. R. (2007). Finding Darwin's God: A Scientist's Search for Common Ground Between God and Evolution. Harper Perennial.
- Collins, F. S. (2007). The Language of God: A Scientist Presents Evidence for Belief. Free Press.
- Johnson, P. E. (1993). Darwin on Trial. InterVarsity Press.
- DARWIN ON TRIAL: A Review — Eugenie Scott from the National Center for Science Education
- Pennock to the Court: "Methodological Naturalism is all there is, or was, or ever will be" Casey Luskin the DI's toy attorney
- A Review of The Right Darwin: Evolution, Religion and the Future of Democracy — Seth Cooper Intellectual Conservative October 11, 2006
- On Evolution Sunday, It's Give Me That Old Time Darwinist Religion — Discovery Institute press release
- Who's really pushing bad science? Dr. Jonathan Sarfati, AiG–Australia
- For examples of solid predictions in evolutionary theory from historical science see The incontrovertible evidence of common descent.
- Plantinga, A. (1997). Methodological Naturalism? Perspectives on Science and Christian Faith, Philosophical Analysis Origins & Design 49(3), 143-154. Retrieved from 
- Dawkins, R. (2006). The God Delusion. Houghton Mifflin.
- Hitchens, C. (2007). God is not Great: How Religion Poisons Everything. Twelve Books, Hachette Book Group.
- Harris, S. (2006). Letter to a Christian Nation. Knopf.
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- Log of applicants for challenge