A statement recently crossed my social media feed from an Intelligent Design advocate: “Science is the study of Intelligent design in Nature.” It’s the kind of declaration that sounds profound in a tweet-sized format and seemingly affirms both God and science simultaneously. What’s not to like?

Quite a lot, actually. The more I turned this statement over in my mind, the more I realized it manages to get almost everything wrong. Wrong about what science is, about what the Intelligent Design movement claims, and even about what Christians should believe about God’s relationship to the natural world. It is a statement that flatters the hearer into thinking they’ve reconciled science and faith when they’ve actually confused both.

When I saw this statement, I recognized this an opportunity to say some things I’ve wanted to say about Intelligent Design theory (I cringe a bit calling it a theory) for a long time. I’ve had a lot of half-written unpublished blog posts on this but now I’m putting them together. So this is going to be a long one. Probably not the thing to say when you just started reading but it’s a bit of my manifesto on the ID movement and those who share these sort of IDish statements.

I want to take this statement seriously, not because it represents careful philosophical thinking—it doesn’t—but because it reflects a widespread confusion among Christians about the nature of science, the meaning of “design,” and how God relates to the creation He sustains. As a Reformed Christian who affirms that this world is indeed the product of divine intention, I find myself in the curious position of objecting to this statement not despite my theology but because of it.

The Equivocation at the Heart of the Claim

The first and most fundamental problem with “Science is the study of Intelligent design in Nature” is that it trades on an equivocation—a classic logical fallacy in which the same word is used in two different senses within the same argument, creating the illusion of coherence where none exists. The word doing all the heavy lifting here is “design.”

In everyday theological language, Christians use the word “design” to refer to God’s purposeful creation and sustaining of the universe. When the psalmist declares that “the heavens declare the glory of God” (Psalm 19:1), or when Paul writes that God’s “invisible attributes, namely, his eternal power and divine nature, have been clearly perceived, ever since the creation of the world, in the things that have been made” (Romans 1:20), they are expressing a conviction about the ultimate origin and purpose of reality. This is what we might call theological design—a claim about God’s relationship to all of creation.

But the Intelligent Design movement, as represented by the Discovery Institute and figures like Michael Behe, William Dembski, and Stephen Meyer, uses “design” in a very different and much narrower sense. For the ID movement, “design” is a technical claim about specific features of the natural world—the bacterial flagellum, the blood-clotting cascade, the Cambrian explosion—that allegedly cannot be explained by natural processes and therefore require the direct intervention of an intelligent agent. This is what we might call empirical design. It’s a claim about detectable gaps in natural causation.

These two meanings of “design” are not the same thing, and conflating them is not just sloppy thinking—I believe it is corrosive to both good science and good theology. When the ID advocate says “Science is the study of Intelligent design in Nature,” they want you to hear it in the broad theological sense (of course God designed everything!) while smuggling in the narrow empirical sense (and science proves it by finding things natural processes can’t explain!). The equivocation allows the statement to feel self-evidently true while actually making a highly specific and contested philosophical claim.

What Does Science Actually Study?

Let’s set aside the ID framing for a moment and ask a more basic question: What is science, and what does it study? Philosophers of science have spent centuries wrestling with this question, and while there is no perfect consensus, there are some things I think we can say with confidence.

Science is a systematic enterprise that builds and organizes knowledge in the form of testable explanations and predictions about the natural world. The key word there is “testable.” Scientific claims must, in principle, be capable of being shown wrong. This criterion of falsifiability, most famously articulated by Karl Popper in the mid-20th century, is not the only feature of science, but it captures something essential about how science differs from other ways of knowing. A scientific hypothesis makes predictions that can be checked against observation. If the predictions fail, the hypothesis should be revised or discarded.

Notice what’s missing from this description: purpose. Science, as a method, is agnostic about whether the patterns it discovers were “intended” by anyone. A physicist studying gravitational waves is not studying whether gravity was designed; she or he is studying how gravity behaves. A molecular biologist mapping a gene regulatory network is not investigating whether those regulatory connections were planned; he is investigating how they function. The extraordinary success of science over the past four centuries has come precisely from this methodological restraint—from asking “how does this work?” rather than “who made this work?”

This approach is sometimes called methodological naturalism, and it is widely misunderstood. Methodological naturalism is not atheism. It is not a philosophical commitment to the claim that nothing exists beyond the natural world. It is a procedural principle: when doing science, we look for natural explanations. The reason is practical, not philosophical. Natural explanations are testable. They make predictions. They can be confirmed or refuted by observation. Claims about the direct intervention of an intelligent agent, by contrast, are generally not testable in the same way, because an intelligent agent could, in principle, do anything.

Consider the difference between these two explanations for the same observation. If I were examining a sandstone formation in Utah I might explain its cross-bedding patterns as evidence of ancient sand dunes shaped by wind. These are natural processes that we can model, predict, and test. An alternative “explanation” that says “An intelligent agent arranged the sand grains in this pattern” is not really an explanation at all, because it makes no predictions.  It doesn’t tell us what pattern to expect in the next formation, or what we should find when we analyze the grain sizes, or how this formation should relate to the ones above and below it. The natural explanation is scientifically productive; the design “explanation” is a dead end.

Even Young-Earth Creationists (YECs) yield this point in practice as witnessed by the work of Dr. Whitmore who claims the patterns of sandstone of the Coconino sandstone are the result of underwater deposition rather than wind. Whitmore never appeals to design via supernatural action but rather believes he can explain the deposition by natural processes.  His theories are judged by the strength of the evidence he bring to bear on the subject. Nearly all geologists and I find his evidence and interpretation unconvincing but the rejection of his hypothesis is not a question of evidence of deign or not. 

So when the ID advocate says “Science is the study of Intelligent design in Nature,” they have the relationship exactly backwards. Science does not start with the premise that nature is designed and then study that design. Science starts with observations and develops natural explanations for those observations. If someone holds the theological conviction that God is behind all natural processes—as I do—that is a perfectly respectable metaphysical commitment, but it is not itself a scientific claim, and conflating the two helps neither science nor theology.

The Demarcation Problem and Why It Matters

Philosophers of science refer to the challenge of distinguishing science from non-science as “the demarcation problem.” It’s one of the oldest and thorniest questions in philosophy of science, and it is directly relevant to evaluating the ID claim. The Intelligent Design movement has, from its inception, struggled with this problem. The core claim of ID is that certain biological features are “irreducibly complex” and therefore cannot have arisen through natural processes. As a result they are structured in a peculiar way. It is essentially a negative argument: “We can’t explain X through natural processes, therefore X was designed.” But this argument form, known as an argument from ignorance or a “god of the gaps” argument, has a fatal flaw: it mistakes the current limits of our knowledge for the actual limits of nature.

History provides abundant examples of why this reasoning fails. In the 18th century, many natural philosophers argued that the complexity of the eye proved direct divine design—no natural process could produce such an intricate organ. Darwin spent considerable effort in On the Origin of Species addressing this very objection, showing how intermediate stages of light-sensitive organs exist across the animal kingdom and how natural selection could, in principle, produce the eye through a series of small, functional improvements. Today, we have detailed evolutionary models of eye development, supported by comparative anatomy, developmental genetics, and the fossil record.

Michael Behe’s famous example of “irreducible complexity,”, the bacterial flagellum, has followed a similar trajectory. When Behe first proposed in Darwin’s Black Box (1996) that the flagellum could not have evolved because removing any single part renders it nonfunctional, it seemed like a powerful argument. But subsequent research identified the type III secretion system. This is a subset of flagellar components that functions as a toxin injection apparatus that demonstrates that components of the flagellum did indeed have independent functions. The “irreducibly complex” system turned out to be reducible after all.

The pattern here is instructive. ID identifies a gap in current scientific knowledge, declares the gap to be evidence of design, and then watches as ongoing scientific research fills the gap. This is not a recipe for productive science. It is a recipe for a perpetually retreating argument.

A Reformed Christian Perspective: Providence, Not Intervention

Now I want to address this from my own theological tradition, because I think the Reformed understanding of God’s relationship to nature actually provides a much richer and more coherent framework than what the ID movement offers.

The Westminster Confession of Faith (1647), which I affirm, states that “God from all eternity, did, by the most wise and holy counsel of His own will, freely, and unchangeably ordain whatsoever comes to pass” (WCF III.1). It further teaches that God “upholds, directs, disposes, and governs all creatures, actions, and things, from the greatest even to the least, by His most wise and holy providence” (WCF V.1). This is the doctrine of divine providence—the teaching that God is not an absentee landlord who occasionally tinkers with creation, but the sovereign Lord who sustains and directs all things at all times through the means He has established.

This has profound implications for how we think about science. If God governs all natural processes—if gravity, natural selection, plate tectonics, and gene regulation are all means through which God accomplishes His will—then discovering natural explanations for phenomena does not diminish God’s role one bit. It describes God’s providential activity. The secondary causes that science investigates are the very means of God’s governance.

The ID movement, by contrast, operates with what I would call a semi-deistic framework, even though its advocates would never use that label. By arguing that certain features of nature can only be explained by direct intervention—by a designer stepping in to assemble the bacterial flagellum or front-load the Cambrian explosion—ID implicitly suggests that the rest of nature runs on autopilot. The designed bits are where God shows up; the naturally-explained bits are just mechanism. This is profoundly un-Reformed. If natural selection can produce the eye, the ID advocate sees that as a point against divine involvement. But the Reformed Christian should see natural selection as no less God-directed than if an angel had sculpted each eye by hand. Providence means that there is no “merely natural” process, because God is the one who established and sustains every natural process.

In this framework, the ID movement’s entire project is based on a theological category error. It assumes that demonstrating natural causation is equivalent to demonstrating the absence of God—and then tries to find places where natural causation fails, in order to insert God back into the picture. But God never left the picture. He doesn’t need gaps in natural causation to be present in His creation, because He is present in the natural causation itself.

John Calvin, writing in the 16th century, already saw this clearly. In his commentary on Genesis, Calvin warns against the temptation to invoke miraculous divine action where ordinary providence suffices. God, Calvin argued, normally works through the natural order He established, and our task is to study and marvel at that order—not to search for exceptions to it. The Dutch Reformed tradition captured this beautifully in the concept of “common grace”: God’s providential care extends to the entire created order, sustaining it through regular, predictable processes that science can investigate.

The Irony of Natural Theology

There is a deep historical irony in the ID movement’s central claim, and understanding it helps illuminate what’s gone wrong. The argument that features of nature prove the existence of a designer is not new. It is, in fact, one of the oldest arguments in Christian theology, stretching back at least to the Stoics and developed extensively in the Middle Ages by Thomas Aquinas (the “Fifth Way”). Its most famous modern formulation came from William Paley, whose Natural Theology (1802) opened with the famous watchmaker analogy: if you found a watch on a heath, you would infer a watchmaker, and similarly, the complexity of nature implies a cosmic designer.

The irony is that Paley’s Natural Theology was published just 57 years before Darwin’s On the Origin of Species (1859), and Darwin himself described the Origin as one long argument against Paley’s reasoning. Darwin did not deny that organisms look designed; he provided a natural mechanism—natural selection acting on heritable variation—that could produce the appearance of design without an external designer’s intervention at each step. The crucial insight was that the appearance of design and the reality of design are not the same thing, and that natural processes can produce complex, functional structures through iterative, undirected steps.

The ID movement is essentially an attempt to rehabilitate Paley’s argument with updated scientific examples—substituting the bacterial flagellum for Paley’s watch, and the Cambrian explosion for Paley’s eye. But the fundamental logical structure is identical, and it remains vulnerable to the same objection: just because we cannot currently explain something by natural processes does not mean it cannot be so explained. Our ignorance is not evidence of design; it is evidence of ignorance.

This is not just a philosophical point. It has practical consequences for how science is done. If you believe that certain features of nature are the direct product of an intelligent designer’s intervention, what do you do next? You can describe the feature, admire it, and declare it designed—but you cannot investigate its origin, because its origin is an untestable miraculous event. The history of science is a history of natural explanations replacing supernatural ones, not because scientists are atheists, but because natural explanations are productive—they lead to new questions, new predictions, and new discoveries—while appeals to design are conversation-stoppers.

William Dembski’s Design Inference

The most sophisticated attempt to put “design detection” on rigorous footing came from William Dembski, whose “explanatory filter” was supposed to provide a reliable method for distinguishing designed events from natural ones. Dembski proposed that if an event is both highly improbable and matches an independently given pattern (what he called “specified complexity”), we can infer design. This was supposed to be the mathematical backbone of ID. This was a rigorous criterion that could move design detection beyond mere intuition.

The problems with this framework are numerous and have been extensively documented by philosophers and mathematicians. The most fundamental is that Dembski’s filter requires us to calculate the probability of an event occurring by natural processes. However, in the biological cases that ID cares about, this probability is precisely what we don’t know. How probable is it that a bacterial flagellum could evolve by natural selection? We don’t know, because the evolutionary pathway is complex and only partially understood. Dembski’s method requires as input the very information that is in dispute, rendering it circular.

Moreover, Dembski’s concept of “specified complexity” turns out to be remarkably difficult to apply in practice. In over two decades since Dembski first proposed it, no one—including Dembski himself—has ever successfully applied the explanatory filter to a real biological system and produced a rigorous, peer-reviewed demonstration of design. The filter exists as an abstract philosophical framework, not as a working scientific tool. When the flagship method of your movement has never been successfully applied in a real case, that tells you something important about whether your movement is producing genuine science.

What the Statement Reveals About the ID Movement’s Strategy

Let’s return to the original statement: “Science is the study of Intelligent design in Nature.” Beyond its philosophical problems, this statement reveals something important about the rhetorical strategy of the ID movement. By defining science itself as the study of design, the statement attempts to redefine the boundaries of science to include ID by default. If science just is the study of design, then ID isn’t an outsider trying to get into the scientific conversation—it’s what science has been doing all along.

This is a clever rhetorical move, but it only works if you accept the equivocation on “design” that I identified earlier. Scientists who study the structure of proteins, the dynamics of ecosystems, or the formation of galaxies are not studying “design” in the ID sense. They are studying patterns, processes, and mechanisms. The word “design” is being imposed on their work from outside, reinterpreting their findings within a framework they never adopted.

It’s worth noting that this redefinition strategy has been a hallmark of the ID movement since the famous Wedge Document, an internal Discovery Institute memo leaked in 1999, which described a long-term plan to “reverse the stifling dominance of the materialist worldview, and to replace it with a science consonant with Christian and theistic convictions.” The document was remarkably candid about the movement’s cultural and political goals, and the statement we’re examining fits neatly into that larger project of redefining what counts as science.

As a scientist and a Christian, I find this strategy deeply troubling—not because I object to faith, but because I object to intellectual dishonesty. You don’t honor God by distorting what science is. You don’t strengthen the case for divine creation by weakening the standards of evidence. And you certainly don’t help Christians navigate the relationship between science and faith by conflating categories that need to be kept distinct.

Does Science Point to God?

At this point, a sympathetic reader might object: “Okay, but doesn’t the order and beauty of nature at least suggest a creator? Isn’t there something to the intuition that the universe looks designed?” And my answer is: yes, I think there is. But the way you get from that intuition to a meaningful conclusion matters enormously, and the ID movement takes a path that ultimately undermines the very conclusion it’s trying to reach.

There is a vast difference between saying “The order, beauty, and intelligibility of nature are consistent with—and may even suggest—the existence of a wise Creator” and saying “Specific features of nature cannot be explained by natural processes and therefore prove the intervention of a designer.” The first is a reasonable philosophical and theological reflection. The second is a scientific claim that is currently unsupported and historically unsuccessful.

The great Christian tradition of reflecting on nature as a pointer to God (what theologians call “general revelation”) does not require finding gaps in natural causation. It requires precisely the opposite: marveling at the comprehensive order and coherence of the natural world. When a physicist discovers that the same mathematical laws governing the fall of an apple also govern the orbit of Jupiter, the appropriate response is not “Where’s the gap?” but “How extraordinary that such unity and elegance pervades the whole of creation.”

The intelligibility of nature, the fact that the universe operates according to regular, discoverable laws that the human mind can grasp, is itself a profound feature of reality that science assumes but cannot explain. Why should mathematics, a product of human thought, describe the physical world with such uncanny precision? This is what Eugene Wigner famously called “the unreasonable effectiveness of mathematics,” and it is a genuine philosophical puzzle. But notice: it is not a gap in natural causation. It is a feature of the entire framework within which natural causation operates. It is the kind of observation that makes theism a reasonable metaphysical position, without requiring science to become something it isn’t.

The Danger of Making Faith Dependent on Scientific Gaps

Perhaps the most important reason to reject the ID framing—and by extension, the statement that “Science is the study of Intelligent design in Nature”—is pastoral. Every time we identify God’s activity with gaps in scientific knowledge, we create a faith that is hostage to the progress of science. When the gap closes, as gaps in scientific knowledge tend to do, the “evidence” for God’s action disappears, and the believer is left wondering whether God was there at all.

I have seen this dynamic play out countless times in my interactions with students and fellow Christians. A young person is taught that the complexity of DNA “proves” that God designed life. Later, they take a molecular biology course and learn about the extensive evidence for the natural evolution of genetic systems. Because they were taught that the evidence for God was in the gap, closing the gap feels like losing God. Their faith was built on sand—not because faith in God is unreasonable, but because it was made dependent on a scientific argument that turned out to be wrong.

A Reformed understanding of providence avoids this trap entirely. If God’s activity is in and through the natural processes—not in the gaps between them—then every scientific discovery is a revelation of how God works, not a threat to the belief that He works. The more we learn about the stunning complexity of gene regulation, the intricate dance of protein folding, the vast timescales of stellar evolution, the more we see of the means through which God accomplishes His purposes. Science becomes a window into providence, not a competitor to it.

This is not just better theology; it’s also better for the church. We need young Christians who can fully engage with the scientific enterprise—who can become excellent biologists, geologists, physicists, and chemists—without feeling that their faith is under siege every time they learn something new. The ID framework, with its insistence on finding design in scientific gaps, makes enemies of science and faith where none need exist.

Getting Both Science and Theology Right

“Science is the study of Intelligent design in Nature.” It’s a pithy statement, and I understand why it appeals to Christians who feel beleaguered by a culture that often treats science and faith as incompatible. But good intentions don’t make good arguments, and this statement fails on every level.

It fails philosophically, because it rests on an equivocation between the broad theological meaning of “design” and the narrow empirical meaning used by the ID movement. It fails scientifically, because science does not study design—it studies natural processes, patterns, and mechanisms, and it does so without presuming anything about ultimate purpose. It fails theologically, because the Reformed doctrine of providence teaches us that God’s activity extends to all natural processes, not just the ones we can’t currently explain. And it fails pastorally, because building faith on scientific gaps is a recipe for crisis when those gaps inevitably close.

As Christians, we can do better. We can affirm that the heavens declare the glory of God without insisting that they do so by displaying gaps in natural causation. We can marvel at the intelligibility and beauty of the created order without claiming that science is secretly studying design. We can fully embrace both the scientific enterprise and our theological convictions, recognizing that they address different questions—the “how” and the “why”—and that both are gifts from the God who made us curious enough to ask.

The universe is not less extraordinary because we can describe its workings in natural terms. If anything, it is more extraordinary. A God who creates a universe capable of generating stars, planets, continents, ecosystems, and conscious minds through the outworking of natural laws is not a lesser God than one who must constantly intervene to patch things together. He is a God whose wisdom and power exceed our ability to comprehend—which is exactly what Scripture teaches and exactly what the evidence, rightly interpreted, suggests.

I believe the world is designed because I believe it is created by the Triune God. But that does not mean science is the study of Intelligent Design in nature. Science studies the natural world. Christians, in turn, understand that world as the creation of God.

That distinction is not a retreat. It is a more coherent account of both science and faith.

And in the long run, coherence is more valuable than slogans.

Blessings,

Joel