Methodological naturalism
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Methodological naturalism (MN) is the philosophical tenet that, within scientific enquiry, one can only use natural explanations - i.e. one's explanations must not make reference to the existence of supernatural forces and entities. Note that methodological naturalism does not hold that such entities or forces do not exist, but merely that one cannot use them within a scientific explanation. Methodological naturalism is often considered to be an implied working rule of all scientific research and logically entails neither philosophical naturalism nor atheism, though some would argue that it implies such a connection.
History
The term "methodological naturalism" itself probably does not originate much earlier than the 1980s; Phillip E. Johnson acknowledges taking it (or "methodological atheism") from Nancey Murphy, a theologian with training in the philosophy of science. Arguably, MN itself dates to the Ionian pre-Socratic philosophers of the 4th century BCE; see, e.g., Jonathan Barnes's introduction to Early Greek Philosophy (Penguin), which describes them as subscribing to principles of empirical investigation that strikingly anticipate MN. Benjamin Wiker traces the historical development of the modern materialist perspective starting with the choice of the Epicureans to focus exclusively on the natural realm as a necessary step toward their goals; see his book "Moral Darwinism; How We Became Hedonists".
Methodological Naturalism vs. Traditional Religion
Because Methodological Naturalism explicitly excludes supernatural entities, it has met resistance from some religious groups. These groups conclude that if supernatural forces do exist, limiting science to natural explanations forces it to come to false conclusions. Generally opponents of MN prefer an open science or even a theistic science that would allow scientists to incorporate supernatural propositions in their theories.
Supporters of Methodological Naturalism believe that it is a necessary part of working science. They claim that open science and theistic science often fail to provide any means of making the supernatural falsifiable, removing the key criteria of testability from science and reducing the whole enterprise to subjectivity.