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Scientists acknowledge that methodological naturalism underlies their research, but point out that they have little choice in the matter. Scientists must assume, when they perform an experiment or make some measurements, that no supernatural entity is disturbing the experimental setup while they perform the experiment, for otherwise no repeatable empirical study could rationally be performed. After all, making controlled experiments, where the "variables" are fixed one by one, is a key foundation stone of the scientific method. Yet by definition, a scientist cannot vary, rule out or "control" in any way the actions of an omnipotent Being who exists beyond the realm of the natural universe and acts beyond its natural laws. Thus supernatural effects lie, one way or the other, lie outside the realm of scientific investigation [Scott2009, pg. 19, 56].
Scientific philosopher Robert Pennock explains this issue in these terms [Pennock2001, pg. 89-90]:
Once such supernatural explanations are permitted they could be used in chemistry and physics as easily as Creationists have used them in biology and geology. Indeed, all empirical investigation beyond the purely descriptive could cease. ... Methodological Naturalism is not a dogmatic ideology that simply is tacked on to the principles of the scientific method; it is essential for the basic standards of empirical evidence.
Perhaps a better question is the extent to which some scientists assume a full-fledged "scientific naturalism", or even a more extreme form known as "philosophical naturalism" (or "scientism") -- the notion that the only truths that deserve the name "truth," and the only truths worth believing or investigating, are those that are derived from the process of scientific research. Several of the "new atheists," for example, presume this stronger worldview in their writings -- see Atheists.
But the "scientific naturalism" (or "philosophical naturalism" or "scientism") worldview is not one that can itself be established within the methodology of science. No "experiment" can be devised to conclusively affirm that scientific truth encompasses all truth, any more than an "experiment" can establish the existence of God. As Catholic philosopher John Haught writes [Haught2008, pg. 11]:
[Scientism] is a belief for which there can be no "sufficient" scientific or empirical "evidence" either. There is no way, without circular thinking, to set up a scientific experiment to demonstrate that every true proposition must be based in empirical evidence rather than faith. The censuring of every instance of faith, in the narrow new atheist sense of the term, would have to include the suppression of scientism also. ... Moreover, the claim that truth can be attained only by reason and science functioning independently of any faith is itself a faith claim. Complete consistency would require that the new atheists' world of thought be cleansed of scientism and scientific naturalism as well.
See also the articles
Natural law and