A friend of mine, handed me a book a few days ago and asked for my thoughts on it. The book was Only a Theory: Evolution and the Battle for America’s Soul by Kenneth R. Miller — a 2008 volume from Viking that has been pressed on Christians for almost two decades as the answer to their unease about evolution. Miller is a professor of biology at Brown University, a practicing Roman Catholic, and one of the most articulate defenders of the position called theistic evolution — the claim that God, somehow, used the long, blind processes of Darwinian descent to make the living world we know.
The book is well-written. Miller is gracious where he could be acidic, careful where he could be loose, and he writes about science with the clarity that comes from years of teaching it. I do not want to begin by undervaluing any of that. What I want to do in this post is exactly what Josh asked me for: tell him — and tell you — what I found inside the covers, and why, after working through it page by page, I cannot follow Miller where his book wants to take us.
Because that is the real question this book puts to a believing reader. Miller is not simply asking you to learn some new science. He is asking you to accept a particular settlement between Genesis and Darwin — a settlement in which Genesis quietly moves to the back of the room and Darwin keeps the chair at the front. He calls this a “bigger tent.” I think, after a careful reading, it is a smaller one than he admits, and the cost of entry is higher than he is willing to say out loud.
Let me show you what I mean.
What Miller Is Really Asking
The book is organized across seven chapters, but the heart of it is a sustained attempt to dismantle the two most famous arguments for Intelligent Design (ID), originally made by the biochemist Michael Behe: the irreducible complexity of the bacterial flagellum, and the blood-clotting cascade in mammals. Miller spends real ink on each. He then broadens the lens, accuses ID of misusing information theory, draws an unflattering parallel between the ID movement and postmodern academic relativism, and closes with his “bigger tent” vision in which scientifically literate Christians make their peace with neo-Darwinian evolution and stop being a nuisance to American science.
That is the case. The flagship arguments come from the laboratory; the framing comes from a court case (Kitzmiller v. Dover, 2005, which ruled that ID is religion and may not be taught in public-school science classes); and the closing appeal comes from civic concern about America’s place in world science. It is meant to feel inevitable — the kind of book that closes the question.
It does not close the question. It opens several. Let me walk through the most important ones.
The Flagellum and the “Co-option” Story
Behe’s famous claim about the bacterial flagellum was that it is irreducibly complex — a tiny rotary motor made of dozens of interacting protein parts, with no plausible step-by-step evolutionary pathway because no subset of those parts produces a functional motor. Take any one out, and the thing simply does not run.
Miller’s reply is what he calls co-option. He points to the Type III Secretory System (T3SS), a needle-like apparatus that certain bacteria use to inject proteins into host cells, and notes that the T3SS shares roughly ten proteins with the base of the flagellum. So, Miller argues, evolution must have borrowed the secretory system and slowly repurposed it into a motor. The pieces were already lying around; selection assembled them.
It is a clean story. The trouble is that the science, in the years since Miller wrote, has steadily moved against it.
A 2012 phylogenetic study in PLOS Genetics by Abby and Rocha indicates that the injectisome (the T3SS structure) is more likely derived from the flagellum than the other way around. The flagellum appears to be older and more widely distributed across bacterial lineages. Miller’s arrow, in other words, may be pointed in the wrong direction; the device he claims is the ancestor looks more and more like the descendant. Microbiologist Scott Minnich, at the University of Idaho, has carried out systematic knockout experiments showing that approximately 35 proteins are necessary and non-redundant for the flagellum to function. Even granting the T3SS as a source for ten of them, the origin of the remaining two dozen — their precise amino-acid sequences, the assembly instructions that put them together in the correct order, and the regulatory networks that switch their expression on and off at exactly the right time — is untouched by Miller’s account.
The deeper problem with co-option is that it confuses parts with plans. Borrowing the spring from a stapler does not explain how a mousetrap was designed and built. Pointing to a shared component does not explain the blueprint that decides where the component goes, when, and in what arrangement. Miller’s story tells us where some of the bricks may have come from. It does not tell us who, or what, drew the building.
The Blood, the Puffer Fish, and a Quietly Circular Argument
The second of Behe’s two challenges concerned the mammalian blood-clotting cascade — a tightly choreographed chain of more than a dozen proteins in which each step activates the next, and the absence of almost any link is fatal. Miller answers by pointing to simpler clotting systems in dolphins and puffer fish and arguing that those simpler systems demonstrate an incremental, evolutionary build-up of the mammalian cascade.
If you are quick, you may notice that this argument quietly assumes exactly what is in question. It is only evidence of evolutionary build-up if you have already granted that dolphins, puffer fish, and humans share a common ancestor through descent with modification. A reader who has not granted that assumption — and a thoughtful Christian has both scientific and theological reasons not to grant it — sees something else. We see the variation in clotting systems we would expect a wise Creator to author across created kinds. The same data, read through a different framework, says something entirely different.
This is the move you will find again and again in books like Miller’s. The framework of evolution is used to interpret the data, and then the interpretation is offered back as a proof of the framework. It is not a fallacy in the formal sense, but it is a circle, and the reader needs to see it as such.
Two Naturalisms, Not One
Now we come to the philosophical hinge of the whole book, and it is the place where I think Miller’s argument quietly comes apart.
There is a phrase that gets used a great deal in conversations like this: methodological naturalism. It means, simply, the working rule that science, as a method, looks only for natural causes. As a working rule, that is unobjectionable. Plumbers do not look for angels in the pipes. Investigators do not invoke demons to explain a fingerprint at a crime scene. For most of what science does, looking for natural causes is not only sensible but unavoidable.
But there is a second word, only one letter different, that means something entirely different: metaphysical naturalism. This is no longer a working rule. It is a claim about reality — the claim that nothing exists, and nothing has ever acted, except natural causes. It is, in other words, a philosophical worldview. It cannot be proved by science, because science (as Miller defines it) is committed to it from the start.
Miller’s book repeatedly slides from the first to the second without telling you. He declares that Intelligent Design is “not science” because it invokes a non-natural cause. But that judgment depends on a prior definition of science that already rules out non-natural causes — and that definition is itself a philosophical commitment, not a discovery of the laboratory. You cannot use a definition you assumed at the start to prove a conclusion at the end. That is the very shape of a circle.
The right question is not, “Does ID fit our current definition of science?” The right question is, “Does the evidence in front of us — the precise, specified, code-like information at the heart of every living cell — point to a mind, or does it not?” The answer to that question may surprise you. It is one Miller never really lets the reader ask.
The Information Problem He Never Solves
Which brings us to the deepest unanswered question in the book — the one that, in my judgment, no naturalistic account has ever met, and certainly not this one.
DNA is not merely a complex molecule. It carries information. Long, specified, functional sequences of chemical letters that code for the proteins on which every living thing depends. The information is not in the chemistry of the letters themselves — any letter can sit in any position, just as any sequence of English letters can be assembled in any order. What makes a stretch of DNA meaningful is the specification: the particular arrangement that produces a functioning protein. Get the arrangement wrong, and the cell gets nothing useful — often, it gets something fatal.
In every other realm of human experience, when we encounter long, specified, functional information — a book, a piece of music, a computer program — we infer, without hesitation, that a mind put it there. We do not credit the wind, or erosion, or random chance with composing Hamlet. We know better.
Miller’s response, when he reaches information theory, is to argue that ID theorists have misused Claude Shannon’s concept of information. There is a narrow technical point to be made there, and Miller makes it. But it does not touch the real argument. The challenge is not about Shannon information, which is merely a measure of unpredictability. The challenge is about specified information — sequences that not only could go many ways but go this way, the one way that yields a working biological function. No undirected process has ever been observed to produce that kind of information. Not in the laboratory. Not in the field. Not in any simulation that does not smuggle a designer in through the back door.
You will read the entire book and you will not find an answer to this. You will find rhetorical maneuvers. You will find appeals to court rulings. You will find unflattering comparisons to the ID movement’s strategy memos. But you will not find an account of where the specified information in even a single bacterial cell actually came from. Because no one yet has one — and the silence in this book is, in the end, eloquent.
The Theological Cost Miller Does Not Count
So much for the science. The harder question, for any Christian reader, is what Miller’s settlement actually requires the church to give up.
It requires more than he admits. If evolution is true — if death, predation, disease, and extinction are the mechanism by which God has been creating for billions of years — then death cannot be the result of Adam’s sin. It must have been part of the world long before Adam was anywhere on the scene. But Genesis 1 says God looked at what He had made and pronounced it very good (Genesis 1:31). And Paul, the apostle, builds the very logic of the gospel on the opposite assumption:
Just as sin entered the world through one man, and death through sin, and in this way death came to all people, because all sinned. — Romans 5:12
Paul says it again, even more sharply, in 1 Corinthians 15:21–22: “For since death came through a man, the resurrection of the dead comes also through a man. For as in Adam all die, so in Christ all will be made alive.” Adam is not, for Paul, a flexible symbol. He is the first man, the federal head of the human race, whose historical disobedience explains why every funeral ever held has been necessary. And Christ is the second Adam, whose historical obedience is the only reason any of those funerals is not the end of the story.
Pull Adam out of history, and Paul’s argument does not merely become awkward. It becomes incoherent. You cannot rest the work of the Second Adam on the failure of a First Adam who was never there. Miller is a sincere believer, and I do not doubt his intentions. But the theological account his book quietly assumes does not preserve the gospel. It dissolves the load-bearing wall on which Paul’s gospel was built — and once that wall is gone, the rest of the house leans.
The Scriptures are not coy about this. “By the word of the Lord were the heavens made,” sings the psalmist, “and all their host by the breath of his mouth” (Psalm 33:6). “Without him nothing was made that has been made,” writes John (John 1:3). “By him all things were created… and in him all things hold together,” writes Paul (Colossians 1:16–17). The God of the Bible is not a clockmaker who left the room. He is a Speaker whose words still ring through the things He spoke into being, and whose fingerprints, as Paul says, are “clearly seen” in what He has made (Romans 1:20).
What Miller Gets Right
Honesty requires me to say what Miller gets right, because he gets some important things right.
He is right that Christians must engage the world of science with intellectual seriousness, not retreat into a defensive crouch that can only embarrass the gospel. He is right that faith and reason are not meant to be permanent enemies — they have the same Author. He is right that the church’s public credibility depends, in part, on whether her members can think clearly about empirical claims. These are the very points that thoughtful creationist and ID scholars — from William Dembski to Jonathan Wells to the patient teachers at Answers in Genesis — have been making for years. The desire to build a thoughtful, engaged Christian intellectual culture is one Miller and his critics share. We just disagree, profoundly, about the conclusions that culture should reach.
Standing on Genesis with Open Eyes
So that is my answer for Josh, and for any reader who has wondered whether Only a Theory is the book that finally settles the question. It is not. It is an intelligent, well-written defense of a settlement that does not, in the end, hold — neither scientifically, where its flagship arguments have weakened with time and the information problem has only grown sharper, nor theologically, where it asks the church to part with the historical Adam and, with him, the structure of Paul’s gospel.
What I want to leave you with is this. The believer who reads Miller and feels a flicker of doubt is not a fool, and the doubt is not a sin. Miller is a smart man writing on his home field, and any honest reader will feel the pressure of his argument. But pressure is not proof. And the moment you look closely at what the argument actually delivers — a partial homology dressed up as an origin story, a circle disguised as a chain of inference, a philosophical commitment passed off as a scientific finding, and a quiet rewriting of Romans 5 — you will see what is really being offered. It is a smaller settlement than it appears. The cost is the foundation.
The foundation can stay. The Word of God is not a primitive thing we tolerate for sentimental reasons until the science catches up. It is the bedrock. “The grass withers and the flowers fall, but the word of our God endures forever” (Isaiah 40:8). It will outlast every confident theory of our generation, as it has outlasted every confident theory of every generation before. The believer who stands on it is not standing on yesterday’s science. He is standing on the speech of the One who was there.
Read Only a Theory if you want to understand the best case for the other side. Read it carefully. Read it with an open Bible. And when you finish, you may find what I found — that the book makes the strongest possible case for a position that, even at its strongest, cannot do what it claims to do, and cannot pay what it asks the church to give.
The theory is only a theory. The Word still stands.
Father, thank You that You are the Speaker behind every speaking thing — that the heavens were made by Your word, that nothing was made apart from Your Son, and that in Him all things hold together. Where I have been intimidated by confident voices, give me courage. Where I have been confused by clever arguments, give me clarity. Teach me to read carefully, to think honestly, and to stand without apology on what You have said. Let my mind serve my faith and my faith ground my mind. And in a generation that prizes theory, hold me steady on Your unshakable Word. In Jesus’ name, amen.
Scripture at the heart of this devotional: Genesis 1:31; Psalm 33:6; Isaiah 40:8; John 1:3; Romans 1:20; Romans 5:12–21; 1 Corinthians 15:21–22; Colossians 1:16–17.