Let’s begin by being clear about our terminology. As we are using it here, “naturalism” is a philosophical term and “naturalists” are not those who study nature, but rather those who hold certain tenets about nature. In particular, metaphysical naturalists maintain that there is no such being as God and there is no realm of being that transcends the physical; all that exists are material substances and processes and things that emerge from them. A methodological naturalist may or may not believe that metaphysical naturalism is true, but maintains that for the purposes of science one cannot appeal to transcendent causes, and therefore scientific research must be pursued as if metaphysical naturalism were true. In other words, a methodological naturalist believes that, for the purposes of doing science, the Universe (all of nature) must be treated as a closed system of physical causes and effects.
Needless to say, Christians reject metaphysical naturalism as false; but why, then, would they be seduced into embracing its methodological handmaiden? The only plausible explanation for their acceptance of the unacceptable is that methodological naturalism has been sold as a foundational principle for the practice of science and that, quite appropriately, they believe that science is an important and productive activity in which Christians should be involved. Indeed it is, but – with all due respect to the district judge in Kitzmiller v. Dover whose philosophical naiveté was exploited by the ACLU – this does not mean that methodological naturalism is a foundational principle for the practice of science.
What is foundational to the practice of science is the assumption of uniformity in the causal structure of nature, that is, uniformitarianism. Some think that uniformitarianism is equivalent to methodological naturalism – after all, they assert, if God “intervened” to change the course of nature this deviation would disrupt natural regularity and destroy the possibility of science – but this assertion is mistaken on multiple levels and it’s easy to see that uniformitarianism and methodological naturalism are distinct ideas.
First of all, suppose God occasionally acts in such a manner that nature deviates from the path it would have taken had God not acted in this way, would such divine action destroy the overall regularity of nature in a way that rendered science impossible? Stated thus, the silliness of the suggestion is evident. All that is required for scientific investigation is confidence that nature will behave regularly in the neighborhood being investigated, and this is not disrupted by the recognition that God can, and for good reasons sometimes does, act contrary to nature’s normal course in special circumstances and for particular purposes. Secondly, an arbitrary declaration on the part of human beings that God cannot act because causal closure is an assumption (mistakenly) thought necessary to the practice of science does not mean that God will not act. It is fair to say that this decision is not up to us. And if God so acts, it is entirely possible in special cases that this action has an effect that bears the marks of having an intelligent cause, for if theism is true, God does act, and there are well-defined mathematical principles that allow the discernment of particular intelligent causation in relevant special cases. Thirdly, uniformity in the causal structure of nature is not the same thing as assuming the inviolability of natural causes. The latter assumption presumes something about the nature of nature that the former does not. This point is fundamental. If, as most Christians believe, the causal structure of nature has its ontological basis either in God’s active maintenance of secondary causes or in his direct divine action, then nature’s causal structure is properly grounded in supernatural causation, not natural causation. In fact, if direct divine action is the fundamental source of natural regularity – as occasionalists maintain – there is no such thing as “natural” causation where inanimate nature is concerned. The historically orthodox Christian understanding of God’s essential role in the existence of natural regularities is therefore the precise opposite of causal closure. Nature is regular not because it is closed to divine activity, but rather because (and only because) divine causality is operative. In orthodox Christian understanding therefore, it is precisely the failure of causal closure, and thus the falsity of methodologically naturalistic assumptions, that provides the metaphysical basis for the regularity of nature and the possibility of doing science. God’s existence and action are not prohibitive of science; rather, they are the ontological basis for it in much the same way that the creation of humanity in God’s image is the epistemic basis for the intelligibility of nature, another assumption necessary to the practice of science. Since what is necessary for the practice of science is just the regularity and intelligibility of nature, not the absence of the very supernatural causation that provides the basis for them, from a Christian perspective the doctrine of methodological naturalism succeeds in being both gratuitous and heterodox in equal measure. As Christians, we not only can do without it, we should do without it. Uniformitarianism, properly understood, will suffice.
Finally, by precluding intelligent causation and begging the question as to the true nature of nature, methodological naturalism blocks the path of inquiry by preventing the discernment of intelligent causation if and when it is present. By contrast, uniformitarian reasoning infers past causes from present effects under the assumption that the causal structure of the world has remained constant and permits reliable inferences. In this regard, we have a very clear conception of what will happen in the regular course of nature that forms a stable background to human activity, which can then be contrasted with what lies outside the regular course of nature and requires the particular and directed action of an intelligent cause. In the course of providential action, God is responsible both for nature’s regularity and for certain exceptional events, but the mode of divine action (regular versus exceptional) is sometimes distinguishable by its characteristics. As Stephen Meyer has observed, the fact that uniform repeated experience confirms to us that the only presently acting cause sufficient to the production of complex specified information is intelligence means – in accordance with uniformitarian principle – that intelligent design is the best explanation available for such information when it is discovered in the universe or in living systems. It is thus uniformitarian analysis based on our knowledge of the causal structure of the world that provides the warrant for a design inference when specified complexity is found in nature. Only by rejecting methodological naturalism as a stricture on science, therefore, can we avoid begging the question against transcendent causation and the nature of nature itself, and thereby free the path of scientific inquiry to explore all possibilities and follow the evidence where it leads.