For thirty years the genome was Exhibit A against design. Then somebody actually read the parts they had thrown away.
It was one of the better arguments the other side ever made, and it deserves to be stated at full strength before anyone answers it.
Roughly ninety-eight percent of human DNA does not code for proteins. For decades that stretch was labeled junk — broken genes, viral wreckage, repeated sequences copied over and over for no reason anyone could see. And the argument wrote itself: no competent engineer builds like this. A designer would ship clean code. What we actually find looks like a hard drive nobody has emptied in four billion years. That is not the signature of a mind. That is the signature of a process that keeps whatever does not kill you.
That is a real argument. It is not a straw man, it was made by serious people, and for a long stretch it was the strongest empirical card in the deck.
So here is the interesting question, and it is not the one people usually ask. Forget for a moment who is right. Ask instead: which assumption sent researchers into that ninety-eight percent to look?
What happened when they looked
Beginning in the 2000s, large-scale projects went into the non-coding genome with better instruments, and the picture that came back was not an attic full of trash.
They found regulatory switches — sequences that decide which genes turn on, in which cell, at which stage of development. They found promoters and enhancers, some working on genes a long distance away. They found genes that never make protein at all but produce RNA that does real work. They found structural regions that organize how a chromosome physically folds, which turns out to matter enormously for what a cell can read.
Even the repeated elements — the most obvious “junk” of all — turned out in many cases to be doing something: providing regulatory sites, contributing to genome architecture, participating in development.
The 2012 ENCODE consortium put a headline number on it and said something like eighty percent of the genome shows biochemical function. And a serious scientific fight broke out immediately.
The objection, stated fairly
Critics — many of them excellent scientists — pushed back hard, and they had points worth taking.
“Biochemical activity” is not the same as “biological function.” A stretch of DNA that gets transcribed occasionally may just be noise; cells are wet, crowded places and the machinery is not perfectly precise. Define function loosely enough and you can call almost anything functional.
And there is the onion problem, which is genuinely awkward. A common onion has about five times more DNA than a human being. Some salamanders have far more still. If every base pair were precisely engineered, that is difficult to explain.
So let me say plainly what I think the evidence supports: some genomic material almost certainly is non-functional. The honest position is not that every letter is load-bearing. The honest position is that the fraction doing real work is vastly larger than the confident consensus of 1980 said it was, and it has been revised in one direction — upward — for forty straight years.
The part that is actually about worldviews
Here is the point, and it is narrower and more durable than “junk DNA is dead.”
Two frameworks produced two research bets. One said: this is accumulated debris, do not expect much. The other said: if this system was designed, unexplained does not mean useless — keep digging.
One of those bets aged well.
This is not the first time. In the late nineteenth century, anatomists compiled a list of well over a hundred “vestigial” human organs — leftovers with no purpose, offered as proof of an unguided history. The tonsils were on it. The thymus was on it. The appendix was on it, and we now understand it plays a role in immune function and in maintaining gut flora. The list did not shrink because theologians complained. It shrank because people kept investigating and found out what the parts were for.
There is a pattern in that. “We do not know what this does” gets promoted to “this does nothing,” and “this does nothing” gets promoted to “therefore no one designed it.” That is an argument from ignorance wearing a lab coat — and it has a poor track record specifically because ignorance is temporary.
What design actually claims
Let me be careful here, because the design argument is regularly caricatured as a lazy shrug — we cannot explain it, so God did it.
That is precisely backward. The design inference is not built on what we do not know about biology. It is built on what we do know about information. In every case where we can observe the cause of a functional, specified, coded sequence — a sentence, a legal contract, a line of software — the cause is a mind. Never once, in the entire body of human experience, has anything of that description arisen from an undirected process.
The genome is a coded sequence that runs a machine. Treating that as evidence of intelligence is not a retreat from science. It is the same inference an archaeologist makes about scratches on a rock and a cryptographer makes about a string of characters — applied consistently, to the one system where consistency is unwelcome.
And design, unlike a shrug, predicts something and can be embarrassed by the result. It predicted that apparent waste in a coded system would keep resolving into unrecognized function. That prediction has been paying out for four decades.
Where the Bible already put us
None of this should surprise a man who has read the Psalms.
I will give thanks to You, for I am fearfully and wonderfully made; Wonderful are Your works, And my soul knows it very well. My frame was not hidden from You, When I was made in secret, And skillfully wrought in the depths of the earth; Your eyes have seen my unformed substance; And in Your book were all written The days that were ordained for me, When as yet there was not one of them.
Psalm 139:14–16, NASB1995
David had no microscope. He nevertheless described being skillfully wrought, an unformed substance seen by God, and a book containing what he would become before any of it existed. That is not a scientific paper and I will not pretend it is. But a man who believes that verse will never approach an unexplained portion of the human body assuming it is garbage.
Scripture also gives an explicit posture toward the unexplained:
It is the glory of God to conceal a matter, But the glory of kings is to search out a matter.
Proverbs 25:2, NASB1995
Concealment is not absence. God hides things the way a father hides a gift — to be found. That verse is a mandate for research, not a stop sign, and the modern scientific enterprise was largely built by men who believed it.
What this does and does not prove
Three guardrails, because overclaiming here would be its own kind of dishonesty.
- Functional DNA does not by itself prove God. It removes an argument that was aimed at design. That is a smaller claim, and it is the true one.
- Do not build your faith on a research result. Data moves. If your confidence in the Creator rises and falls with the next paper, you have made a scientific consensus into a god, and it is a poor one.
- Do not sneer at the people who were wrong. They were reasoning from what they had. The lesson is about humility in the face of a system we have barely begun to read — and that lesson has our name on it too.
The book that was already written
Step back from the genome and the argument gets simpler and much more personal.
Somebody looked at the most sophisticated information system in the known universe, could not read most of it, and concluded it was worthless.
Men do that to each other constantly. And men do it to themselves — most of all to themselves. You look at a stretch of your own life you cannot make sense of and file it under junk. Wasted years. Broken sequence. Nothing there worth keeping.
But you are not the one who wrote it, and you are not qualified to call it waste. The One who ordained your days when there was not one of them yet has never lost a chapter, and He specializes in using the parts you were ready to throw out.
For since the creation of the world His invisible attributes, His eternal power and divine nature, have been clearly seen, being understood through what has been made, so that they are without excuse.
Romans 1:20, NASB1995
The evidence has been there the whole time. The trouble was never that the code was empty. The trouble is that we had not learned to read, and we called it junk to avoid saying so.
Teaching the Word. Watching the Times.
— SmithForChrist