Before the mid-nineteenth century, scientists were called “natural philosophers”—seeking to know the natural world. Natural philosophers of the High Middle Ages developed a practical guide for studying the causes of what they saw in the nature. As Christian intellectuals (almost always in holy orders), they did not doubt that God is the primary cause of everything; the debate was about how God operates in the natural world. Does God directly make happen each and every event in nature—every wind that blows, every wave that crashes? Or does God create “secondary causes” that are part of the natural world we can perceive, like air and water, as well as the rules that govern the capabilities and behavior of these secondary or natural causes?
Reflecting their Greek as well as Hebrew roots, Christian philosophers relied heavily on reason to guide their thinking on this question and concluded very early on that God operates through secondary causes (with the exception of true miracles, when God is presumed to momentarily suspend the rules). Only secondary causes, which are natural (material), should be invoked to explain natural events. Rational explanation hits a dead end when we cite supernatural causes, because we can’t know what such causes really are. That’s what makes them supernatural, literally above and beyond our world of experience.
Given this truly practical and liberating intellectual convention, natural philosophers could focus on productively exploring the natural world and the rules that govern its operation without having to get into highly rational but ultimately irresolvable theological arguments about what created nature and its rules or why or how. This is methodological naturalism. It is an intellectual tool.
A useful tool is always subject to misuse. Natural philosophers, now scientists, must resist a tendency to be so focused on nature that it becomes for them all there is—really believing that nothing exists outside the natural world. Failing to resist this temptation allows methodological naturalism to morph into philosophical naturalism—also known as materialism, in which the supernatural is categorically excluded from existence.
In the nineteenth century, this philosophical position became, for many, “scientific materialism” or “scientism” or “atheism.” These are not intellectual tools but worldviews, comprehensive understandings of existence. Note that they all would be ruled out of order in the long tradition of natural philosophy, because they make assertions about the supernatural. To say the supernatural does or does not exist is a theological speculation, regarding which certainty can come only through faith, not reason. By this logic, both theism and atheism are faith-based and ruled out of order as “science.”
For intellectuals solidly committed to the Christian worldview, methodological materialism remained a conceptual ‘rule of the road,’ enabling safe conduct of scientific inquiry. In contrast, for those like Charles Darwin who had lost faith in the truth of Christianity or even a notion of spiritual enchantment of nature, materialism slipped easily from method into mantra—nothing exists but the material/natural world, what is available to our senses, even if only when aided by instruments and mathematics. This is philosophical materialism.
As would many others of his time, Charles took his materialism further, into reductionism. He sought to simplify understanding of complex phenomena by breaking them into smaller and smaller pieces and treating complexity as merely the aggregate of millions of pieces cobbled together to form something like a jigsaw puzzle. To a reductionist like Charles, humanity could be reduced to biology, which could be explained as elaborate chemistry, which could be further reduced to the physics of interacting atoms.
By applying his materialist, reductionist approach to understanding human beings, even the human mind, Charles categorically excluded any spiritual (supernatural) dimension of humanity—not just from scientific explanations but from the realm of possibility. Charles was viscerally offended by any attempts to reconcile his materialistic explanations with alternatives that invoked supernatural influences. In consequence, Charles consciously parted company with most of his intellectual peers, including his close scientific friends Charles Lyell, Asa Gray, and Alfred Russel Wallace.
The purist reductionist dismisses higher-order (even if natural) causes of complexity as unnecessary to understand the universe and all within. While this approach provides a very useful start for understanding complex phenomena, we know now how further research has always revealed far greater and higher order complexity than can be explained through reductionism.
For example, in the nineteenth century, scientists contended that Newton’s physics offered a complete understanding of mass and motion in the universe, then in the twentieth century they discovered the relativistic nature of physics at the cosmological level and the probabilistic nature of physics at the sub-atomic level of reality.
Nineteenth-century scientists learned that living creatures are aggregates of cells, but they had only an inkling of how remarkably complex are the biochemistry and microstructure inside each cell, much less the interactions of cells.
Sociologists like Karl Marx attempted to explain human society and history solely in terms of class structure and economic motivations. Early twentieth-century psychologists were tempted to explain animal and even human behavior as simply composed of innate and learned responses to external and internal stimuli. The nineteenth century was a hotbed of over-simplification by over-confident scientists and philosophers unaware of just how complex reality is in fact. They offer a cautionary tale for twenty-first-century scientists and philosophers.