Apologetics · Intelligent Design — what finding one working protein actually asks of chance
Most conversations about design never get past the slogans. Somebody says the universe looks engineered. Somebody else says that is just an argument from ignorance. Both men go home convinced.
So let us put the slogans down and look at one narrow, concrete, measurable question that working biochemists actually argue about. Not the whole cell. Not the origin of life. One protein.
What a Protein Is, and Why Shape Is Everything
A protein is a chain. The links are amino acids, and in living things there are twenty kinds in common use. The cell strings them in a specified order, and then the chain folds into a precise three-dimensional shape.
The shape is the whole point. A protein does its job the way a key does — by geometry. Hemoglobin carries oxygen because of a pocket of a particular size. An enzyme speeds a reaction a million-fold because its surface holds two molecules at the exact angle where they react. Change the order of the links and the fold changes. Change the fold and you do not get a slower machine. You generally get a tangled strand the cell has to haul off and destroy.
That is the feature that makes this question answerable. Function here is not a matter of taste. It either folds and works, or it does not.
First, the Size of the Haystack
Take a modest protein of 150 links. At each position, twenty choices. The number of possible chains of that length is twenty multiplied by itself one hundred fifty times — roughly ten to the one hundred ninety-fifth power. A one followed by 195 zeros.
Put that against the physical universe for scale. There are something on the order of ten to the eightieth atoms in the observable universe. The physicist Seth Lloyd calculated an upper bound on the total number of elementary logical operations the universe could have performed since its beginning at around ten to the one hundred twentieth. The space of possible 150-link chains is vastly larger than either figure — not by a factor, by dozens of orders of magnitude.
Now, that number alone proves nothing, and anyone who stops there is arguing badly. A lottery has an enormous number of possible tickets and somebody still wins. The size of a search space is only half the problem.
The Real Question Is How Many Needles
The honest question is density. Of all those possible chains, what fraction fold into something stable and useful? If functional sequences are common — if one in a thousand chains does something — then a big search space is no obstacle at all. If they are vanishingly rare, the search space becomes decisive.
This is where the actual scientific dispute lives, and it is worth knowing both numbers that get quoted.
Douglas Axe, working in a Cambridge molecular biology lab, published an estimate in 2004 in the Journal of Molecular Biology based on mutational experiments on a beta-lactamase domain. His figure for the prevalence of sequences capable of producing that functional fold was about one in ten to the seventy-seventh. If that is anywhere near right, undirected search is not in the running. There is not enough matter, time, or opportunity in the universe to stumble onto a single fold at that density.
Against that, Anthony Keefe and Jack Szostak reported in Nature in 2001 that when they screened random 80-link sequences, roughly one in ten to the eleventh could bind ATP. One in a hundred billion is a long shot; it is not an impossible one. Critics of Axe have also argued that his experimental setup, which worked from an already-functional enzyme under stringent conditions, measures something narrower than the real frequency of useful folds, and therefore understates it.
Both of those studies are real. They are also measuring different things. Binding a molecule is a low bar; a stable fold that catalyzes a specific reaction and integrates with the rest of a cell is a high one. The gap between those two numbers — sixty-six orders of magnitude — is the live argument, and anyone who tells you it is settled is selling you something.
The Four Objections That Deserve Real Answers
If you are going to make this argument, make it against the strongest replies, not the weakest.
- “You do not need one specific sequence.” Correct, and the better design arguments never claimed otherwise. The target is not a single chain but a set of chains that produce the fold. That is precisely why the density question is the right question instead of a hand-wave about one-in-a-trillion odds.
- “Evolution does not search at random — natural selection guides it.” This is the strongest objection and it is partly right. Selection is a powerful ratchet. But selection can only preserve what already does something. It has nothing to grip until a sequence is already functional. So selection explains the refinement of a working protein beautifully; the question on the table is how the first working version of a novel fold was reached.
- “New proteins come from old ones — duplication, then divergence.” Granted, and well documented. Much protein novelty is clearly tinkering with existing parts. But that relocates the question rather than answering it: the folds themselves are a limited and ancient set, and the origin of a genuinely new fold is the thing in dispute.
- “Deep time solves it.” Only if you do the arithmetic. Four billion years is about ten to the seventeenth seconds. Even generous estimates of total microbial reproductive events across earth history land far below ten to the fortieth. Against a density of one in ten to the seventy-seventh, more time barely moves the decimal.
Why This Is an Inference, Not a Gap
The standard dismissal is that this is an argument from ignorance — we cannot explain it yet, therefore God. If that were the structure of the argument, the dismissal would be fair.
But that is not the structure. The design inference is a positive one, and it runs on something we actually know. We know, from a thousand ordinary cases, what kind of cause produces a long sequence of symbols that is both highly improbable and specified in advance by a function. Sentences. Software. Sheet music. Blueprints. In every single case where we can observe the cause directly, the cause is a mind. We are not reasoning from an absence. We are reasoning from the one cause with a demonstrated track record of doing this exact thing.
And it should be said plainly: this is an inference to the best explanation, which means it is answerable to evidence. If someone demonstrates that functional folds are dense in sequence space, the argument weakens, and honest people will say so. A Christian has no stake in a bad argument. We have a stake in what is true.
Where Believing Christians Differ
It is worth being clear about the room. Not everyone who affirms God as Creator lines up here, and the differences are not between the faithful and the compromised.
Young-earth creationists read Genesis 1 through 11 as straightforward history and hold to a recent creation and a global flood. Old-earth and progressive creationists accept the conventional age of the earth while holding firmly to a real Adam, a real Fall, and direct creative acts. Some sincere believers accept common descent and understand God to have worked through the process. These are genuine disagreements with genuine stakes, and the men on each side include careful exegetes and serious scientists.
What the protein question speaks to is narrower than any of those positions. It asks whether undirected mechanisms are a sufficient explanation for functional biological information. A young-earth creationist and an old-earth creationist can stand together on that answer while continuing to disagree about Genesis 1 and the rock record — and they should argue that out with open Bibles rather than caricatures.
Scripture Said It First, and Said It Differently
What strikes me about all of this is not that science has caught up with the Bible. It is the category Scripture chose to put at the foundation of everything.
In the beginning was the Word, and the Word was with God, and the Word was God. The same was in the beginning with God. All things were made by him; and without him was not any thing made that was made.
John 1:1–3 (KJV)
Not force at the bottom of reality. Not matter. A Word. Meaning, intent, speech — and a person. Two thousand years before anyone knew a cell runs on a four-letter code read three letters at a time, Scripture put language at the origin of everything that exists.
And he is before all things, and by him all things consist.
Colossians 1:17 (KJV)
Consist here means hold together. Not wound up once and abandoned — sustained, continuously. And David, with no microscope, described himself as curiously wrought in the lowest parts of the earth, written in a book before his members were formed (Psalm 139:15–16). Curiously wrought is an old phrase for skillfully embroidered. He had the right instinct about his own body with none of the data.
What an Argument Can and Cannot Do
Now the confrontation, and it cuts toward the believer as much as the skeptic.
An argument like this clears brush. It can take an honest man’s confident materialism and turn it into an open question, and that is worth doing. Paul says creation leaves men without excuse — the invisible things of God are clearly seen, being understood by the things that are made (Romans 1:20). The evidence is doing real work.
But no man was ever argued into the kingdom. You can be fully persuaded that life was designed and remain exactly as far from God as you were before, because the problem was never a shortage of evidence. Design tells you there is a Designer. It does not tell you He is good, or that He knows your name, or what He has done about what you did last year.
For that you need the rest of John 1 — the Word who made the folds came down and wore one. And the Word was made flesh, and dwelt among us (John 1:14). The One whose speech specified every sequence in your body stepped into a body, and went to a cross, and settled the actual debt. That is not an inference. That is history, and it is an invitation.
Learn the argument. Use it honestly. Then get past it to the Person, because the Person is the point.
Teaching the Word. Watching the Times.
— SmithForChrist