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This is the reason that [[Presuppositionalist Metaphysics|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 [[deceit|disingenuous]].

This is the reason that [[Presuppositionalist Metaphysics|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 [[deceit|disingenuous]].

Defenders of methodological naturalism point out that it in no way requires or implies [Philosophical naturalism]. Many scientists of faith nevertheless adopt naturalism in their studies. This is because there is simply no way for an experiment to investigate forces which by their nature cannot be investigated scientifically.{{fact-science}} And the assumption that a supernatural force is not going to affect the outcome of an experiment is no more unreasonable than the assumption that supernatural forces are not going to miraculously poison all the apples in the supermarket.<ref>http://www.talkorigins.org/indexcc/CA/CA301.html</ref>

Defenders of methodological naturalism point out that it in no way requires or implies [Philosophical naturalism]. Many scientists of faith nevertheless adopt naturalism in their studies. This is because there is simply no way for an experiment to investigate forces which by their nature cannot be investigated scientifically.{{fact-science}} And the assumption that a supernatural force is not going to affect the outcome of an experiment is no more unreasonable than the assumption that supernatural forces are not going to miraculously poison all the apples in the supermarket.<ref>http://www.talkorigins.org/indexcc/CA/CA301.html</ref>