The very definition of science has undergone a subtle yet significant shift. Historically, science was understood as the pursuit of knowledge, a quest to understand the world around us through observation and reason. This pursuit inherently necessitates certain presuppositions: that the universe operates with causal connections, that truth is knowable, and that we can have confidence in our ability to discern it. However, modern science has often become synonymous with methodological naturalism, a philosophy that restricts scientific inquiry to natural causes, excluding any possibility of non-natural or supernatural agency. The RationalWiki page on Methodological Naturalism introduces the concept like so:

Methodological naturalism is the label for the required assumption of philosophical naturalism when working with the scientific method. Methodological naturalists limit their scientific research to the study of natural causes, because any attempts to define causal relationships with the supernatural are never fruitful, and result in the creation of scientific “dead ends” and God of the gaps-type hypotheses. To avoid these traps, scientists assume that all causes are empirical and naturalistic, which means they can be measured, quantified, and studied methodically.

However, this assumption of naturalism need not extend beyond an assumption of methodology. This is what separates methodological naturalism from philosophical naturalism — the former is merely a tool and makes no truth claim, while the latter makes the philosophical — essentially atheistic — claim that only natural causes exist.

The distinction between methodological and ontological naturalism, while often presented as this clear boundary, is, in practice, a strategic rhetorical move. Methodological naturalism purports to be a neutral, non-ontological framework for scientific inquiry. It claims to be a mere rule of engagement—that science should only investigate natural phenomena using natural explanations. Yet, in its application, it inexorably leads to ontological conclusions. By systematically excluding the possibility of non-natural causes a priori, science creates a worldview in which naturalism appears to be the only viable explanation for everything. This isn’t a discovery; it’s a foregone conclusion derived from the very rules of the game.

The assumptions underpinning science are the most glaring example of this flawed logic. Science demands that phenomena be testable, repeatable, and observable, yet it rests on a foundation of unproven, non-empirical assumptions. We must assume logic, order, and consistency in nature—presuppositions that are not themselves testable by the scientific method. This creates a paradox: science, in its pursuit of knowledge, relies on foundational truths that are, by its own criteria, unscientific.

This arbitrary limitation is particularly problematic when we consider the concept of agent causation. In fields like forensics, we readily distinguish between natural and volitional causes. We can conclude, based on empirical evidence, that an event was caused by an agent’s intent or will, even though that intent is not a physical object we can measure. There is already a precedent for including non-material causes in our models of reality. Science, as a system for making models that account for data, should be open to all potential causal explanations, not just those that fit within a pre-approved, naturalist box. By artificially fixing its scope to exclude supernatural causes, science pre-determines its own conclusions and, in doing so, sacrifices the pursuit of a more complete truth about reality. It becomes a system for confirming its own biases, rather than an open-ended quest for knowledge.

Further, this limitation creates a profound epistemological problem. Consider the analogy of a painting: while analyzing the physical components of the paint and canvas can provide valuable information, it does not explain the origin or intent of the artwork. Even if we limit the inquiry to all natural processes and we found how the components could have been put together in this fashion through totally naturalistic processes, that doesn’t mean that this is the only explanation nor the most parsimonious explanation.
Again forensics, but not just forensics, but archaeology, information theory, search for extraterrestrial intelligence (SETI), and geography. We routinely investigate both natural and non-natural causes. Embedded within these fields is the idea of agent causation, intentionality, and will. Archaeology examines artifacts to understand the cultural and intellectual agency of past civilizations. Information theory can examine material, in respect to its environment, which is high in free energy. This is usually simply described as complex and specified information. The Search for Extraterrestrial Intelligence (SETI) demonstrates that science can test for non-natural causes, such as intelligent signals from distant galaxies. Geography can also seek an understanding of how humans have impacted the natural processes and landforms of their environments through various farming and infrastructure.

Why, then, is natural science uniquely restricted?

The claim that science will eventually explain all phenomena through natural processes creates a logical contradiction. Methodological naturalism, by its very nature, cannot detect non-natural causes. Therefore, any conclusions drawn from this limited methodology are inherently incomplete. Scientific methodology is rooted in epistemological assumptions, and flawed assumptions lead to incomplete or inaccurate conclusions. Pragmatism, while useful, is insufficient for pursuing truth if it ignores potential causal factors.

Counterexamples abound, highlighting that science is not always confined to strict naturalism. Studies on prayer and near-death experiences, for instance, explore non-natural influences. These examples underscore the fact that the a priori rejection of non-natural causes is a philosophical position that requires justification, especially given the prevalence of dual-causal investigations in other fields.

From a creationist perspective, excluding supernatural processes as potential causal explanations is not only unscientific but also detrimental to the pursuit of true knowledge. The goal of science should be to determine the causes and mechanisms underlying observed phenomena, regardless of whether they are natural or involve intelligent agency. The term “supernatural” refers to causes that are not due to physical laws and chemistry, such as programming or other information input. Excluding these potential causes compromises the integrity of scientific inquiry.

A true scientist must follow all leads and consider all possibilities to ensure that the most accurate and comprehensive model is upheld. Science is grounded in the principles of evidence-based reasoning, and the evidence may lead to non-natural or supernatural causes. If naturalism is to be a consistent and reliable methodology, it must be applied across all scientific disciplines, including forensics and historical sciences.

In conclusion, the pursuit of knowledge should not be constrained by arbitrary philosophical limitations. By embracing a broader definition of science that includes the possibility of non-natural causes, we can move closer to a more complete and accurate understanding of the universe. This approach aligns with the creationist worldview, which recognizes the intelligent design and purpose inherent in the natural world.