What the Neutral Theory Taught
In 1968 the Japanese geneticist Motoo Kimura proposed what became known as the Neutral Theory of Molecular Evolution. The following year Jack King and Thomas Jukes published a similar paper in Science under the bold title “Non-Darwinian Evolution.” Their claim was simple. Most mutations that harm an organism are quickly removed by natural selection. Mutations that help are so rare that they hardly matter. So the great majority of the genetic changes that become fixed in a species, the differences we see when we compare the DNA of one creature with another, are neutral: they do nothing, and they spread through populations by sheer chance, a process called genetic drift.
This was a remarkable admission. For a century, Darwin’s followers had taught that natural selection was the creative force behind life’s variety. Kimura argued that at the level of the genes, selection was not the main driver at all; chance was.
Why Kimura Needed It
Kimura did not propose the Neutral Theory out of nowhere. He was answering a problem that troubled evolutionists then and troubles them still. In 1957 the British geneticist J. B. S. Haldane calculated the “cost” of natural selection: for a beneficial gene to replace the old one throughout a population, many individuals carrying the old gene must die or fail to reproduce. Haldane estimated that in a typical case a species could afford about one such replacement every 300 generations. At that pace, he noted, it would take some 300,000 generations to produce a difference of 1,000 genes between two species. The problem became known as “Haldane’s dilemma.”
When protein sequencing in the 1960s revealed far more differences between species than selection could have paid for at Haldane’s rate, Kimura used Haldane’s own reasoning to conclude that most of those changes could not have been driven by selection. They must be neutral, costing nothing. In other words, the Neutral Theory was, from the beginning, partly a rescue: a way of explaining how so much genetic change could have happened within evolution’s timescale without selection having to accomplish it.
The Theory That Built the Molecular Clock
The Neutral Theory soon became one of the pillars of modern evolutionary biology. If most changes are neutral, then they should pile up at a steady rate, like the ticking of a clock. This “molecular clock,” first suggested by Emile Zuckerkandl and Linus Pauling in the early 1960s, became the standard method for estimating when two species supposedly shared a common ancestor. The dates we read in textbooks and museums, that humans and chimpanzees split some six or seven million years ago, or that various animal groups diverged hundreds of millions of years ago, rest in large part on this assumption of steady, neutral change.
The same thinking fed the idea of “junk DNA,” a phrase popularized by the geneticist Susumu Ohno in 1972. If most of the genome was simply accumulating neutral, useless changes, then most of the genome was presumably useless. That assumption was badly shaken in 2012, when the international ENCODE project reported biochemical activity across some 80 percent of the human genome.
Cracks in the Foundation
For decades the Neutral Theory was treated as the “null hypothesis,” the default assumption against which everything else was tested. But as whole genomes became available, evolutionists began finding the fingerprints of selection everywhere. In 2018 two evolutionary biologists, Andrew Kern and Matthew Hahn, published a paper in Molecular Biology and Evolution titled “The Neutral Theory in Light of Natural Selection.” They wrote that the theory “was supported by unreliable theoretical and empirical evidence from the beginning,” and that modern genomic data now allow scientists to “firmly reject its universality.” They even questioned Kimura’s original use of Haldane’s numbers.
Other scientists rushed to defend the theory, and the debate continues to this day. But consider what was being admitted. A theory that had underpinned evolutionary dating for half a century was described by evolutionists themselves as resting on “unreliable” evidence “from the beginning.”
The 2025 Discovery
In November 2025 a team at the University of Michigan led by evolutionary biologist Jianzhi Zhang published a study in Nature Ecology & Evolution that struck at the very heart of the Neutral Theory. Using a technique called deep mutational scanning, which measures the effect of thousands of individual mutations in a gene, the researchers examined data from yeast and from the bacterium E. coli.
The Neutral Theory depends on beneficial mutations being extremely rare. Zhang’s team found that more than 1 percent of the mutations that change a protein were beneficial, which the University of Michigan described as orders of magnitude more than the theory allows. And that created a new problem. If beneficial mutations were really that common, the team calculated, more than 99 percent of the changes that become fixed in genes should be adaptive, and genes should be changing far faster than they actually do in nature. They do not. So the beneficial mutations are there, but somehow they are not taking hold.
To find out why, the team ran an experiment with yeast for 800 generations. One population grew in an unchanging environment. Another was moved through ten different growth media, spending 80 generations in each. The yeast in the changing environment ended up with far fewer beneficial mutations spreading through the population.
| The Question | The Neutral Theory Said | The 2025 Study Found |
|---|---|---|
| How common are beneficial mutations? | So rare they hardly matter | More than 1% of protein-changing mutations |
| Why do most fixed changes look neutral? | Because they are neutral | “The outcome was neutral, but the process was not neutral” |
| Are populations well adapted? | Selection weeds out the harmful; drift handles the rest | “Natural populations are not truly adapted to their environments” |
“Seemingly Neutral”: A New Rescue
The Michigan team proposed a new explanation, which they call “Adaptive Tracking with Antagonistic Pleiotropy.” The idea is that a mutation which helps in one environment often harms in another. Because environments keep changing, a helpful mutation rarely has time to spread through a whole population before conditions shift and it becomes harmful. The result looks neutral, but it is not. As Professor Zhang put it, “We’re saying that the outcome was neutral, but the process was not neutral.” The paper’s title says the same: this process “results in seemingly neutral molecular evolution.”
Zhang drew a striking conclusion: “populations are always chasing the environment,” and “our model suggests that natural populations are not truly adapted to their environments.” He even suggested that some human genes “may be beneficial in our old environments, but are mismatched to today.”
To be fair to the researchers, they note that their data come from single-celled organisms, and that more data from complex, many-celled creatures will be needed before anyone knows whether the pattern holds for animals and people. The debate over the Neutral Theory is not finished. But the direction of the evidence is worth considering carefully.
What This Reveals
The foundations keep moving. First, natural selection was said to explain nearly everything. Then Kimura said that at the level of the genes, chance explains most of it. Then genome studies found selection everywhere, and the Neutral Theory was said to rest on unreliable evidence. Now a new theory says the changes are neither truly selected nor truly neutral, but only “seemingly” neutral. Each generation of evolutionary theory is presented with confidence, and each is revised by the next. “The grass withereth, the flower fadeth: but the word of our God shall stand for ever” (Isaiah 40:8).
Selection cannot keep up. Haldane’s dilemma asked how selection could pay for so many changes. Kimura answered that most changes did not need selection. The new study turns the problem around: beneficial mutations are common, but selection cannot hold on to them, because what helps today hurts tomorrow. A mutation that trades away fitness in one setting for gains in another is a trade-off, not a step upward. Shuffling back and forth between advantages, while never becoming “truly adapted,” is a very different picture from the steady climb from simple to complex that evolution requires.
The clock rests on an appearance. If the changes that look neutral are not actually neutral, then the assumption of steady, chance-driven change that underlies the molecular clock rests on an appearance rather than on the process itself. The dates assigned to evolutionary history are not observations. They are calculations built on assumptions, and one of the most important of those assumptions has now been called “seemingly” true.
Patches Upon Patches
The story of the Neutral Theory is not an isolated case. It follows a pattern that runs through the whole history of evolutionary thought. When a discovery conflicts with the theory, the theory is rarely abandoned. Instead, a new sub-theory, patch, or assumption is added to explain the problem away, and the core idea survives untouched.
Consider how often this has happened. When the fossil record failed to show the countless gradual transitions Darwin expected, Niles Eldredge and Stephen Jay Gould proposed “punctuated equilibrium” in 1972: evolution must happen in rapid bursts too quick to leave fossils. Gould himself admitted that “the extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology.” When the same complex features appeared in creatures that evolution says are unrelated, the answer was “convergent evolution”: the same design must have evolved more than once. When Haldane showed that selection was too slow to pay for the genetic differences between species, Kimura answered that most changes must be neutral. When the genome turned out to be far more active than “junk DNA” allowed, the junk became function. And now that beneficial mutations turn out to be common but are not taking hold, the changes are declared “seemingly neutral.”
A strong theory is one whose predictions are confirmed by new discoveries. A weak theory is one that must be patched after each new discovery to accommodate what it did not expect. The philosopher of science Imre Lakatos described exactly this. Every scientific “research programme” has a hard core that its followers will not give up, surrounded by a “protective belt” of auxiliary assumptions that can be adjusted to absorb contrary evidence. When the belt keeps growing only to explain away surprises, rather than predicting anything new, Lakatos called the programme degenerating. Each patch keeps the theory alive, but each one also concedes that the evidence did not turn out as the theory said it would. The discoveries are not making evolution stronger; they are making it weaker.
This is why evolutionary researchers tend to preserve the debate rather than overturn the idea. Notice how the Michigan study kept the Neutral Theory’s conclusion, that the outcome looks neutral, while denying its mechanism. To abandon neutrality outright would leave the molecular clock and the dates built on it without a foundation, and Haldane’s dilemma would return. Overturning a load-bearing pillar of evolution would threaten the whole structure, so the pillar is patched and the debate goes on. The hard core is never put to the test: that life arose and diversified by natural processes alone, without a Creator. That core is not a conclusion drawn from the evidence; it is the assumption through which all the evidence is read.
A Fallen World, Not an Upward Climb
The Bible gives a very different account of the living world. God created each creature “after his kind” (Genesis 1:24–25), fully formed and fitted for its place, and at the end of the sixth day “God saw every thing that he had made, and, behold, it was very good” (Genesis 1:31). Then sin entered, and the ground was cursed (Genesis 3:17–19). Since that day, “the whole creation groaneth and travaileth in pain together until now,” subject to “the bondage of corruption” (Romans 8:21–22).
A world of populations that are “always chasing the environment” and never quite catching it, where genes once suited to one setting are “mismatched” to another, and where mutations bring trade-offs rather than new design, looks far more like a good creation now groaning under the curse than like an upward march from molecules to man. The variation God built into living things allows them to adjust within their kinds. What it has never been shown to do is create the vast amounts of new, functional information that evolution needs.
Same Evidence, Different Starting Points
The yeast and bacteria in Professor Zhang’s laboratory are real, and the measurements are real. Christians have no quarrel with honest observation. The disagreement lies in the framework used to interpret the observations, and in the assumption, never proven, that the living world arose without a Creator. Paul warned Timothy to avoid “oppositions of science falsely so called” (1 Timothy 6:20), and the history of the Neutral Theory is a reminder of how quickly scientific certainties can become yesterday’s discarded ideas.
That is why creation makes far better sense of what scientists keep finding. Evolution must ultimately explain how matter, energy, information, and life came into being with no one to make them, as if the universe could make itself out of nothing. Every patch is a further attempt to explain how mindless processes could accomplish what only a mind could do. The Bible needs no such patches. It declares that God, who alone is eternal, spoke the universe into being: “In the beginning God created the heaven and the earth” (Genesis 1:1). “By the word of the LORD were the heavens made; and all the host of them by the breath of his mouth … For he spake, and it was done; he commanded, and it stood fast” (Psalm 33:6, 9). “Through faith we understand that the worlds were framed by the word of God, so that things which are seen were not made of things which do appear” (Hebrews 11:3). The universe did not make itself; it was made. A creation designed by an all-wise Creator, and then subjected to the curse, is exactly the kind of world in which we should expect finely engineered genes, abundant but limited variation, and populations that never quite keep pace with a fallen world.
The truth about the origin of life does not depend on the next study. “For by him were all things created, that are in heaven, and that are in earth … all things were created by him, and for him: And he is before all things, and by him all things consist” (Colossians 1:16–17). The same Lord Jesus Christ who holds every gene and every cell together is the Saviour of sinners. “For the invisible things of him from the creation of the world are clearly seen, being understood by the things that are made, even his eternal power and Godhead; so that they are without excuse” (Romans 1:20). The question is not whether science will finally settle the matter, but whether we will bow to the Creator who has already spoken.
Sources: S. Song, X. Shen, P. Chen and J. Zhang, “Adaptive tracking with antagonistic pleiotropy results in seemingly neutral molecular evolution,” Nature Ecology & Evolution 9 (2025), and the University of Michigan news release of November 14, 2025; ScienceDaily, May 29, 2026; A. D. Kern and M. W. Hahn, “The Neutral Theory in Light of Natural Selection,” Molecular Biology and Evolution 35 (2018); M. Kimura, “Evolutionary Rate at the Molecular Level,” Nature (1968); J. L. King and T. H. Jukes, “Non-Darwinian Evolution,” Science (1969); J. B. S. Haldane, “The Cost of Natural Selection” (1957); N. Eldredge and S. J. Gould, “Punctuated Equilibria” (1972); S. J. Gould, “Evolution’s Erratic Pace,” Natural History (1977); I. Lakatos, “Falsification and the Methodology of Scientific Research Programmes” (1970).