This distinction between methodological assumption and metaphysical assertion is critical, yet frequently the two are conflated. One can scarcely fail to have enormous respect for the natural sciences per se and for their astonishing, ever-expanding capacities for exploring and explaining reality at every scale, from the subatomic to the cosmological, according to their respective methods and assumptions.2 Naturalism is a methodological assumption shared by all of the natural sciences, and quite properly so: it means, for the purposes of scientific explanation, regarding the universe as a whole and everything in it as if it were a closed system of nothing but and nothing more than matter-energy explicable through the mechanistic, efficient causality of natural forces. By definition and as a stipulation for doing science, no reference to anything supernatural or transcendent is permissible, nor is reference allowed to any intention, meaning, value, or purpose. The results have been remarkable since methodological naturalism was pioneered in seventeenth-century mechanics, was extended to nineteenth-century biology through Darwinism, and in the last century has been further applied in so many disciplines, including post-Newtonian physics, cosmology, genetics, and neuroscience. Provided the sciences remain within their stipulated self-limitations, including naturalism as a methodological assumption, they are constantly adding to our knowledge of reality. No problem; quite the contrary.
The problem is rather that the exponential increase in scientific knowledge has been taken by some as a warrant to inflate its methodological postulate of naturalism into a metaphysical assertion. Naturalism has been made into a comprehensive claim about reality as such, a worldview that now constitutes part of the de facto framework of our prevailing intellectual culture and of all academic disciplines in universities. When a methodologically provisional «as if» becomes a metaphysically assertive «is» naturalism almost always functions essentially as a synonym for materialism and atheism. Its self-consciously abstractive, reductionist explanatory method shifts from the proper recognition that questions about transcendence, meaning, purpose, and values are simply not part of its intellectual enterprise, to the unwarranted insistence that, its methods having failed to find anything transcendent or any inherent meaning in reality, none exists. (This is bizarre, to say the least – of course none of the natural sciences have discovered what they are prohibited from even considering, as a corollary of their own self-constitutive methodological mandate.) Relatedly, the expanding explanatory power of the natural sciences is wedded to a constantly repeated historical narrative about a seismic, modernizing shift from pre-scientific ignorance, superstition, and religious credulity to enlightened knowledge, observation, and secular rationality. The narrative seems to gain further traction from wider processes of secularization, themselves influenced by consumerist practices that erode the familial relationships and other social solidarities traditionally anchored in communities of faith, practices that depend on the application of technologies in industrial manufacturing that are in turn based on burgeoning scientific knowledge. As Pope Francis tersely put it in Laudato si’, «everything is connected.»3 More apparent confirmation for metaphysical naturalism, at least culturally and institutionally, comes from the dominance of the STEM disciplines in universities all around the world: they attract the big government and corporate money bestowed as investments in the hope that new knowledge can be turned into patentable, lucrative technologies.
Note that none of this has any intellectual bearing on whether naturalism as a methodological postulate might legitimately support or develop into naturalism as a metaphysics and worldview. But this is lost on many people in society at large, not to mention on the ideologues and polemicists who proselytize for naturalism as a worldview, such as the so-called New Atheists. And it would be naïve to remain blind to the ways in which metaphysical naturalism seems to become ever more plausible to the unwary because of the power of the natural sciences, including medicine and all the branches of engineering, through the transformative impact of its technological applications in all domains of human life. Since the late nineteenth century, these disciplines have called the shots in research universities because of their spectacular success in producing «useful knowledge.»4
As a corollary, when naturalism’s methodological postulate becomes metaphysical assertion, science is nearly always conjoined with scientism: the ideological position that only the empirical, observational, experimental, mathematizing methods of the natural sciences are justifiable means of pursuing and discovering any truth about reality. In effect: «look how much the sciences have explained – perhaps they will eventually explain everything! But whether they can or not, nothing else can tell us anything true about reality.» This epistemological imperialism is not only false, but mistaken in its aspiration in principle, just as metaphysical naturalism is mistaken because it is based on a fundamental irrationalism; more on this below. Yet warranted and necessary criticisms of scientism do not and should not challenge any genuine findings of the natural sciences; and even though naturalism is an irrational worldview, it remains a legitimate, demonstrably productive methodological postulate for the natural sciences’ self-limited, restricted mode of inquiry.
Another distinction about which it is important to be clear, lest the argument at hand be misunderstood: notwithstanding my criticism of scientism as an epistemological ideology, it is important to retain a commitment to the unicity and integral character of all knowledge in principle, ultimately as a matter of logic (and thus of the exercise of reason). In the traditional scholastic formulation, truth cannot contradict truth; everything that is true must ultimately hang together, even though there obviously is a great deal we don’t know, and even if we can’t see how what we do know coheres. But we certainly have some capacity to relate to each other the distinctive types of knowledge gained from the inquiries characteristic of different disciplines. We can grasp, for example, that in eighteenth-century Brandenburg, Johann Sebastian Bach could not have written any of his sublime keyboard music apart from neurons firing in his central nervous system; or without the capacity for symbolic thought that seems to have arisen in our species around 50,000 years ago; or if hominid evolution had not been part of the evolution of life on earth, extending back more than four billion years; or unless the physical elements in the chemical compounds in the molecules of Bach’s body had been forged in processes of stellar and supernova nucleosynthesis, and in the case of helium and hydrogen at the time of the Big Bang, billions of years ago. Every human creative act, every aesthetic experience, every heartfelt embrace, and every compassionate smile presupposes what is studied by neuroscientists and neurologists, archaeologists and evolutionary anthropologists, evolutionary and cell biologists, biochemists and organic chemists, particle physicists and cosmologists. But this neither means nor implies that, for example, knowledge of Bach’s genetic makeup or ancestry tells us anything about the structure and harmonies of his Toccata and Fugue in D-Minor. It doesn’t, nor can it.
Why should a Reformation historian concern himself with these issues? Because of the conditions of our shared academic environment. Regardless of one’s discipline or field, whether we like it or not, the predominant framing assumptions of universities today increasingly include scientism and materialist naturalism. This means we inhabit an intellectual milieu characterized by contracted, restricted reason. There is enormous professional and social pressure to conduct our academic lives as if all reality consists of nothing but and can be nothing more than the natural order of matter-energy in motion, as if the universe is a closed