Can Darwinian Evolution Explain Life? The C.O.D.E. Argument for Intelligent Design

In his book The Blind Watchmaker, one of the most well-known atheists wrote, “Biology is the study of complicated things that give the appearance of having been designed for a purpose.” He then argues that such “apparent design” is actually the byproduct of blind physical forces and genetic replication driven by random mutations. Is this true?

Can the complexities we see at the heart of life be adequately explained by blind and unguided processes (such as natural selection)? It will be argued here that Darwinian evolution cannot account for the complexities we see within life itself, which, in our everyday experience, always come from an intelligent mind. There are too many critical problems that Darwinian evolution runs into. To illustrate this, I came up with an acronym—C.O.D.E. It's best explained with an illustration.

Imagine that all the parts of a laptop, such as the motherboard, screen, keyboard, processor, cooling system, and battery, were all scattered across a beach. Now imagine that through nothing but the natural forces of wind, waves, and the sand, those parts somehow came together. Would you trust that laptop to turn on and function properly?

Of course not. But why not? Because functioning systems don’t arise from disorder alone—they require intelligence to bring about organization and design. This illustration provides four reasons to question Darwinian evolution, forming the acronym C.O.D.E., which stands for Compartments, Organization, Design, and Epistemology. Let’s review this further below.

C- Compartments

You may have noticed in our laptop illustration that the various parts of the laptop were assumed to already exist and were scattered on the beach. This is no minor point and should not be overlooked. How did the parts get there?

In the same way, before evolution could even get started, life itself would already have to be present. But how did life first come about, minus any form of intelligence?  How does life come from non-life? How do mindless chemicals produce the first living cell? This is the problem of the origin of life.

Life depends on highly sophisticated systems already being in place. Even the simplest cell is astonishingly complex. DNA stores information.  RNA participates in protein synthesis. Ribosomes function like molecular machines. So, how did life come to be? Mindless chemicals banging around? That seems incredibly implausible.

However, many Darwinists will beg to differ, specifically those who conduct origin-of-life research. They aim to show that life can arise naturally without a supernatural source. However, there is a glaring problem with such research, as Dr. William Dembski described on the Truthful Hope Podcast:

“All of origin of life research does not take the form of simply randomly sloshing around chemicals. It’s all based on going to a chemical supply company, getting some RNAs, getting some chemicals, mixing them together in various purities and concentrations with various elaborate instruments. How much of that was available on the early Earth? How much of that is a realistic prebiotic simulation? None of it is!”[1] 

In other words, the issue is that origin-of-life experiments are often presented as if they simulate the early Earth, but in reality, they require highly controlled laboratory conditions, purified chemicals, and intelligent scientists directing the process. That’s precisely the point. The intelligence is already built into the experiment.

It’s not just the information we see in DNA and the various sophisticated systems that need explanation; one must also explain how life could have come about at the chemical level! Dr. James Tour, a Nanotechnologist and synthetic chemist at Rice University, pulled no punches when speaking about this problem for Darwinists:

“But even if one were given all the molecules needed in complete stereochemical purity, and the information code, could a cell be constructed using the chemical and biochemical tools that we have today? I have written about such a hypothetical experiment, and how it would be impossible, using today’s expertise, to even construct the lipid bilayer, namely the exterior packaging that holds the cell’s nanomachinery in place. Just the lipid bilayer (which itself surrounds thousands of nanosystems) is beyond our ability to synthesize. The conclusion of that thought experiment is that ‘life based upon amino acids, nucleotides, saccharides and lipids is an anomaly. Life should not exist anywhere in our universe. Life should not even exist on the surface of the earth.’ ‘Yet we are led to believe that 3.8 billion years ago the requisite compounds could be found in some cave, or undersea vent, and somehow or other they assembled themselves into the first cell.’”[2]

That said, while natural selection may explain survival, it cannot explain arrival. Given this, many naturalists will draw a distinction between evolution and abiogenesis (the origin of life from non-life). I agree they are distinct, but the point is that a full naturalistic worldview still needs to account for how life began.

So, the first question in the CODE argument is:  Where did the components come from? This is a major challenge for a fully naturalistic account of life’s origins. The question can be phrased as follows: How does life arise from non-life?

O – Organization

How do the various parts of the laptop work together? Even if all the parts are present (which again, is a problem in and of itself), that still doesn’t mean you have a working computer. The parts must be arranged in a very specific way. This is where we encounter the problem (for Darwinists) of irreducible complexity.

Irreducible complexity (IR) is a system that is composed of many well-matched parts, where if you remove any one part from that system, it no longer works. So, if you reduce the complexity, it stops functioning. Therefore, the complexity is irreducible. In other words, some systems only function when all the essential parts are present at the same time. Remove one part, and the entire system fails—said systems are all-or-nothing.

Dr. Michael Behe, the one who discovered and popularized IR in his monumental book, Darwin’s Black Box, gives a practical illustration of a mousetrap. Take away the spring, the base, or the bar, and it no longer works. You need all the parts of the mousetrap together at the same time for the device to function properly. How does this relate to evolution? Charles Darwin once said,

“If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case.”[3] 

To no fault of Darwin, we have since found biological systems that could not have formed in such a manner, rendering his theory untenable. Like the mousetrap, we see systems that are all-or-nothing. If a mousetrap were to come about through Darwinian means (through numerous successive steps by slight modifications), we would never arrive at a mousetrap! For a mousetrap without a board or the spring would not be functional and thus would not be “selected” for any advantage. We see this at the biological level as well.

Rather than referring to a complex organism like humans, Behe draws on one of the simplest life forms—bacteria. Specifically, he highlights the bacterial flagellum, which is a microscopic rotary motor with multiple coordinated parts. Take away any of its parts, and it no longer functions. The bacterial flagellum is irreducibly complex and could not have evolved through numerous successive slight modifications. This is just one of many irreducible complex systems and parts within life.

While many objections have been raised to Behe’s argument, one of the most popular is called co-option. Namely, a structure originally serving one function may later be repurposed for another. Many will point to the secretion system as resembling the flagellum, therefore, arguing that the latter came from the former. So, as it would be argued, irreducible complexity (like the flagellum) can evolve through co-option (repurposed parts).  However, the question is not whether parts can be repurposed, but whether the coordinated functional integration itself is sufficiently explained.

Moreover, just because two systems share similar parts does not necessarily mean one evolved from the other, especially when they perform very different functions. Secondly, research has shown that the flagellum actually came first, and the secretion system evolved after.[4] Lastly, even if some parts were repurposed, that still does not explain how all the necessary pieces are coordinated into a fully functioning system, such as the rotary motor. The deeper issue is whether blind and unguided natural processes can realistically account for that level of organized complexity.  

Going back to our laptop, the same problem arises. Remove the fan, and the processor overheats. Remove the heat pipe, and the heat has nowhere to go. These systems depend on the organization. The question becomes:  How do blind processes produce systems that require all parts working together at once? That is the O in CODE — Organization.

D – Design

Let’s say at this point, we (somehow) have laptop parts scattered on the beach that have miraculously come together to form a laptop. And it turns on! But then you see, “Enter your password.” Well, this is another major problem. Why is there meaningful information? This deals with what is called specified complexity.

Specified complexity is the kind of information that, in our experience, always comes from an intelligent mind. Something is considered complex if it’s unlikely and it’s specified if it matches an independent pattern.

For example, imagine you and your friend are walking on the beach, and you see written in the sand, “10434.” That would be unusual (complex), but perhaps you could imagine a natural explanation, whether from the wind or the waves. But now imagine you both walk a bit further along the shore, and you see written in the sand, “Mary loves James.” Immediately, you infer intelligence, for it would be foolish to say that this message came about by natural forces. Why?

Because it is not merely complex — it is specified. It communicates meaning. It matches an independent pattern. This is no different than how we infer intelligent life on other planets when receiving “messages,” in that we look for specified complexity and intuitively infer intelligence. This is exactly what we see in DNA.

DNA is not just chemistry. It functions analogously to information-bearing code, in that sequences carry functional instructions that produce proteins with highly specific functions. In other words, life is built upon coded information. And in every other realm of our experience, coded information points back to a mind. Therefore, our DNA, the building blocks of life, is literally a library of information far more complex than anything humanity can think of.

Arguing that such specified complexity that we see at the very heart of life is the byproduct of random mutations through an unguided process is just as absurd as saying the phrase “Mary Loves James” in the sand came about by the winds and crashing of waves or that the sketching of the faces on Mount Rushmore came about by erosion. This is D in CODE—Design.

E – Epistemology

At this point, the parts of the laptop were scattered, the parts came together, and messages were generated…all without any intelligence or guidance! It gets worse! Without any intelligent mind behind creation, we are no different from a laptop. Given this, how can we understand and rationalize the messages that come forth from our miraculous laptop? How do we make sense of the messages?

Before proceeding further, it’s important to clarify what epistemology means. This is a branch of philosophy that studies knowledge and how we know things. Apologies are warranted for those who were thrown off by this word in the acronym (I couldn’t think of a better word for E).

Nevertheless, this concerns the problem of the existence and reliability of reason itself, most famously known as the argument from reason (AR). The AR was famously developed and popularized by C.S. Lewis from his book, Miracles, where he wrote:

“Thus, strict materialism refutes itself for the reason given long ago by Professor Haldane: ‘If my mental processes are determined wholly by the motions of atoms in my brain, I have no reason to suppose that my beliefs are true…and hence I have no reason for supposing my brain to be composed of atoms.’…[Naturalism] discredits our processes of reasoning or at least reduces their credit to such a humble level that it can no longer support Naturalism itself.”[5]

Lewis argued that if naturalism is true, then our thoughts are ultimately the result of blind physical processes aimed at survival rather than truth. But if our beliefs are only the product of atom movements selected for survival, then why should we trust them as true? Including the belief in naturalism itself? This makes naturalism appear self-defeating. Darwin himself wrestled with this issue:

“With me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would anyone trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?”[6]

Can natural selection bring about rationality? Natural selection is blind and unconscious; therefore, it could not possibly select the few beliefs that are true to reality while weeding out the others.

 Instead, natural selection is merely the description of traits passed on to offspring that have adapted for survival, not for beliefs that accurately reflect reality. Natural selection is descriptive, not prescriptive. Moreover, natural selection will aid the development of reasoning faculties only so long as it aids survival, which truth statements, such as that physical reality has an atomic and molecular structure, do not.

Therefore, a naturalist may respond that evolution “selects” for reliable cognition. However, survival advantage does not necessarily require truth, since false beliefs can still produce adaptive behavior. It makes far more sense that human rationality can be grounded in the rational, true nature of an intelligent Designer. More specifically, given Christianity, human beings are made in the image of a rational Creator (Gen. 1:27; James 3:9).

So, the final question is:  Why trust reason if reason is only the byproduct of blind matter? That is the E in CODE — Epistemology and concludes the C.O.D.E. argument.

Conclusion

It's likely that, throughout the article, the naturalist may have thought (numerous times) that the CODE argument is nothing more than God of the gaps (filling in a gap in our knowledge with God). However, the CODE argument is not based on what we don’t know, but it’s based on what we do know.  

Given this, it seems evident that Darwinian evolution cannot adequately explain the complexities of life, at least no more than we can trust the existence and reliability of our made-up laptop. A far better explanation is that there is an intelligent Designer behind creation.

This is not to specify who/what this Designer is, for that requires further argumentation. But I would much rather debate WHO the Designer is rather than WHETHER there is a Designer, for then we are one step closer to the Gospel of Jesus Christ.

Footnotes

[1] The Truthful Hope Podcast, “The Design Inference: Dr. William Dembski on the Mathematics Behind Intelligent Design,” November, 2025. https://youtu.be/uwFcOqL0yMY?si=Qvi2-0mTzHf_UrKQ.

[2] James Tour, “Evolution/Creation,” James Tour Group, August 2019. https://jmtour.com/evolution-creation/. (emphasis added)

[3] Charles Darwin, Origin of Species. Online Variorum of Darwin's Origin of Species (1872). https://darwin-online.org.uk/Variorum/1872/1872-146-dns.html.

[4] Sophie S. Abby and Eduardo P.C. Rocha, “The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems,” PLoS Genet 8, no. 9 (2012), doi: 10.1371/journal.pgen.1002983.

[5] C.S. Lewis, Miracles (New York: HarperCollins, 1947), 22.

[6] Charles Darwin, “Letter to William Graham Down,” in The Life and Letters of Charles Darwin, vol. 1, ed. Francis Darwin (London: John Murray, 1887), 285.