Excursus on the Origin of Life and Evolution of Biological Complexity (Part 24): Methodological Naturalism

August 08, 2025

Methodological Naturalism

Last time I argued that, contrary to what you often hear on both sides of the creation-evolution debate, the contemporary theory of biological evolution does not assert that mutations are undirected or unguided and that therefore the evolutionary process is purposeless. Rather we saw that what evolutionary biologists mean when they say that mutations occur randomly is that they occur irrespective of the benefit that they might bring to the host organism. That definition is not at all incompatible with the evolutionary process’ being directed or guided by God or even with God's miraculously intervening in the evolutionary process to cause key mutations that would bring about evolutionary advance.

This raises a related issue – methodological naturalism. Many philosophers and scientists would argue that science by its very nature is committed to a sort of methodological naturalism. It's important to understand that this is not synonymous with metaphysical naturalism. Metaphysical naturalism is a thesis about the nature of reality – that reality consists simply of space-time and its contents (the physical world). That's metaphysical naturalism. But methodological naturalism holds that science seeks only natural explanations for phenomena in the world. It's simply part of the methodology of science to seek natural explanations for various effects. Therefore supernatural explanations of some phenomenon would not even be permitted into the pool of live explanatory options. When you look at the pool of live explanatory options for some body of empirical data, science would not even look at supernatural explanations because it is methodologically committed to the quest to find natural explanations of the data. So these supernaturalistic explanations wouldn't even come into consideration. Therefore even many Christian scientists would agree that they are restricted methodologically to seeking for natural explanations. This would of course then preclude appealing to God as an explanation of the origin of life and the evolution of biological complexity.

What might we say about methodological naturalism? I think what's striking about methodological naturalism is that it is not a scientific viewpoint but rather a philosophical viewpoint. It is not an issue to which scientific evidence is relevant. Rather, it is about the philosophy of science – the nature of science. As such we should ask ourselves: Why should we be committed to this philosophical thesis? As the intelligent design theorist William Dembski has pointed out, methodological naturalism would prevent us from inferring design even if we were to discover that every atom in the universe carried a label on it “Made by God.” You still would be prohibited methodologically from inferring that God has made these things.

More seriously, suppose that life and biological complexity really were the result of creative, miraculous interventions at various points in the past on the part of God. Suppose that we actually do live in a world like that – where God has intervened in the evolutionary process to bring about forms that would not have otherwise evolved. It would be a tragedy – wouldn't it? – both scientifically and personally if we were debarred from discovering the truth about reality simply because of a methodological constraint. Methodology is supposed to aid us in the discovery of the truth about reality not hinder us in it. So there are, I think, serious questions that can be raised about a strict methodological naturalism.

But leave that point aside. The more important point that I want to make is that we are not now concerned with what a scientist might infer as the best explanation of biological complexity. Rather, our question, as we've seen, is: How, from a theological standpoint, should we integrate what the Bible teaches with what we discover through empirical evidence? We are not trying to justify a design inference. Rather, we are trying to integrate our theology with the empirical evidence. We are trying to understand how these two bodies of truth fit together best. Even if the scientist works within the constraints of methodological naturalism, there is no such constraint on the systematic theologian, who is free to craft an integrative or synoptic view of the world that takes account of both the data of modern science and the data of divine revelation.

So the systematic theologian could admit that the current theory of biological evolution may very well be the best naturalistic theory that we've got. If, as a result of methodological naturalism, the pool of live explanatory options is limited to naturalistic hypotheses then (at least until relatively recently) the neo-Darwinian theory of biological evolution driven by the mechanisms of random mutation and natural selection was basically the only game in town. Rival naturalistic hypotheses just could not equal its explanatory power, explanatory scope, and plausibility. It was the best naturalistic account. No matter how improbable it might seem, no matter how enormously far its explanatory mechanisms had to be extrapolated beyond the testable evidence, no matter the lack of evidence for many of its tenets, it was still the best naturalistic explanation because there wasn't any other naturalistic explanation that even came close to it.

As theologians we are going to approach our question from a theological standpoint and ask how, given the biblical data and the empirical evidence, we should best understand the origin of life and the development of biological complexity. As we do so, I want to emphasize that I approach these questions, not as a professional scientist but rather as a theologian with a layman's interest in these scientific questions.