Methodological naturalism is a strategy for studying the world, by which scientists choose not to consider supernatural causes - even as a remote possibility. There are two main reasons for pursuing this strategy. First, some scientists believe that there is no supernatural: they begin with the assumption that God does not exist (see atheism) and that there is no life after death (see also spiritual world). Second, some scientists believe it is possible that supernatural causes (such as God and angels) may exist, but they assume that any supernatural action would be arbitrary or haphazard and therefore impossible to study systematically.
The first methodological naturalist is sometimes considered to have been Thales, who explained earthquakes (which were traditionally attributed to the anger of the god Poseidon) with an early theory of plate tectonics .
According to Christian philosopher Alvin Plantinga, "The philosophical doctrine of methodological naturalism holds that, for any study of the world to qualify as "scientific," it cannot refer to God's creative activity (or any sort of divine activity)."  The possibility of divine intervention in nature is not only neglected, but positively dismissed. 
This kind of approach is the result of application of the epistemology of either of the empirical philosophies of pragmatism or logical positivism, and (because it is a methodology developed without first establishing the ontological principles of the world) is unfounded.
This is the reason that presuppositionalists do not subscribe to methodological naturalism, relying on the intelligent design Programme instead. Presuppositionalists also contend that methodological naturalism is inherently atheistic, since it would be a meaningless exercise to define the rules of empirical inquiry in an entirely arbitrary manner. Since we define the rules of empirical inquiry in such a way that the ontological systematicness of the world is reflected in the method, the methodological naturalist's claim that methodological naturalism is independent of ontological naturalism is disingenuous.
Defenders of methodological naturalism point out that it in no way requires or implies philosophical naturalism.
- Methodological Naturalism? by Alvin Plantinga
- Methodological Naturalism? Part 2 by Alvin Plantinga
- Methodological Naturalism? by Alvin Plantinga - From Perspectives on Science and Christian Faith 49 (September 1997): 143-154.
- The Rules of the Game by Carl Wieland
- Padamsee, Hasan. Unifying the Universe: the Physics of Heaven and Earth. CRC Press, 2003. Page 15.
- "The methods of science, it is claimed, "give us no purchase" on theological propositions--even if the latter are true--and theology therefore cannot influence scientific explanation or theory justification. Alvin Plantinga, Department of Philosophy, Decio Hall, University of Notre Dame