Last year, in an episode of the Mind Matters News podcast, Dr. Angus Menuge and Dr. Robert J. Marks hosted a compelling conversation with philosopher Dr. Robert Larmer. They delved into the philosophical assumptions behind methodological naturalism , the idea that science must limit itself to natural causes.  

While often portrayed as a neutral rule for scientific inquiry, the guests argued that methodological naturalism may not be as neutral — or necessary — as many suppose. Instead, they suggested that rigid adherence to it may stifle both scientific and theological insights.

A subset or a constraint?

The conversation began with the observation that, from a Christian or broader theistic perspective, the relevant question is not whether God is involved in the workings of the world, but how He is involved. This perspective does not reject naturalistic mechanisms; rather, it considers the possibility that God could work through such means or, at times, through direct action. Historical examples — from the abandonment of spontaneous generation to the discovery of cellular complexity — illustrate a consistent trend: Increased scientific understanding has not eliminated wonder or purpose, but has

instead revealed deeper layers of design and intentionality.

Methodological naturalism was initially introduced as a kind of pragmatic truce. As Larmer noted, the term was coined by Paul de Vries, a Christian philosopher at Wheaton College, and was earlier referenced by Edgar Brightman (1884‒1953). The idea was simple: believers and non-believers alike could work side by side in the lab by focusing only on secondary natural causes. But over time, this methodological stance has hardened into a metaphysical commitment, leaving little room for any explanation for anything other than material causes.

The problem with “neutral” methodology

Larmer raised a significant objection: if science declares in advance that all explanations must be naturalistic, it effectively limits the scope of inquiry. In doing so, it precludes the possibility that God could act directly in the world in ways that natural processes cannot explain. “You are, as it were in advance, committing God to working in a certain way,” Larmer said. That commitment may reflect philosophical naturalism more than it reflects sound science.

The conversation highlighted the need to follow the evidence wherever it leads — even if it leads to the possibility of divine intervention. If the observable data points to outcomes that natural causes cannot adequately explain, then ruling out supernatural causes from the outset is not scientific humility — it’s dogma.

Rule of thumb or rule of faith?

Dr. Angus Menuge offered a potential middle ground. He suggested that methodological naturalism could be viewed as a “rule of thumb” rather than an inflexible rule. In areas where it has produced  fruitful results, such as chemistry and physics, it makes sense to start with naturalistic explanations. However, this practical approach differs greatly from a dogmatic insistence that no other explanations can ever be considered. “What’s wrong is assuming in advance there can’t be anything other than a natural cause,” Menuge explained.

Larmer responded that such a middle ground might be overly generous. He argued that many of history’s most important scientists — such as Robert Boyle and Johannes Kepler — did not operate with anything like methodological naturalism. Instead, they sought the best explanation available, whether it was natural, supernatural, or a blend of both. These early scientists saw no conflict between faith in divine design and the pursuit of empirical understanding. Kepler, for instance, viewed the laws of nature as direct reflections of God’s providence.

Implications beyond science

The discussion then turned to the broader consequences of methodological naturalism, particularly for natural theology and the debate over intelligent design. According to Larmer, strict adherence to methodological naturalism leads some theistic scientists — such as those affiliated with BioLogos — to argue that while they may personally believe in design, such design is undetectable through empirical means. In essence, design becomes a matter of private faith rather than public knowledge.

Robert J. Marks noted that intelligent design is often supported by abductive reasoning—inferring the best explanation from available evidence. Yet, as Larmer pointed out, such reasoning is frequently dismissed as “unscientific” simply because it appeals to design. This creates a circular problem: design cannot be considered because it is ruled out by methodological naturalism, even when it might be the most reasonable inference.

A call for open inquiry

Larmer’s chapter in Minding the Brain (Discovery Institute Press 2023) addresses these issues in greater detail, inviting readers to reconsider whether methodological naturalism serves science or constrains it. For theists and non-theists alike, the challenge is to approach scientific inquiry with intellectual openness — not with blind allegiance to a particular methodology. In the end, the real question isn’t whether methodological naturalism should be used or ignored but whether it should be allowed to function as a philosophical gatekeeper. Science, if it is to remain true to its core values, must be willing to follow the evidence — wherever it leads. And sometimes, that path might just lead beyond the natural.