Rosa Rubicondior: Creationism Refuted - The Theory of Evolution May Be Slightly Wrong

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A new theory of molecular evolution | University of Michigan News

A paper published in Nature Ecology & Evolution last november (2025) by four evolutionary biologists from the University of Michigan might have caused a stir of excitement in creationists cirles if any of them ever read a science paper because it appears on first sight to question the basis of the Theory of Evolution - what creationists call 'Dawinism'. However, that excitement would have been short-lived if they had read the details.

This is not the long-awaited collapse of the Theory of Evolution that creationists have been confidently predicting since at least the middle of the last century. It is nothing of the sort. It is a normal example of science doing what science does: testing a model against evidence, finding that the model is incomplete, and adjusting the explanation accordingly.

The theory being challenged here is not evolution itself, nor common descent, nor natural selection, nor mutation, nor population genetics. It is the neutral theory of molecular evolution, a theory developed in the 1960s to explain why many genetic changes appear to spread through populations without obvious adaptive advantage. The new paper argues that this appearance of neutrality may be misleading. What looks neutral in the long term may, in fact, be the result of short-term adaptation to changing environments.

The researchers found that beneficial mutations are more common than the classic neutral theory assumes. The problem, then, is why these apparently useful mutations do not become fixed at the rate one might expect. Their answer is beautifully evolutionary: environments change. A mutation that helps in one set of conditions may be useless, or even harmful, in another. So populations are not marching steadily towards some perfect design; they are continually tracking a moving target.

That is what the authors mean by adaptive tracking with antagonistic pleiotropy. “Pleiotropy” means that one mutation can have more than one effect. “Antagonistic” means that those effects can pull in opposite directions: helpful here, harmful there; useful now, costly later. This is not magic. It is not supernatural intervention. It is the ordinary interaction between genes, organisms and environments.

Creationists often pretend that science is an orthodoxy in which biologists merely defend Darwin at all costs. This paper shows the opposite. Scientists have examined one of their own long-standing theories, compared it with new evidence, and proposed a better explanation. No sacred text was protected. No dogma was shielded from scrutiny. No conclusion was declared immune from revision.

The result is not less evolution, but more evolutionary detail. Mutation still supplies variation. Selection still acts on differences in reproductive success. Genetic drift still matters. Environments still shape which variants succeed and which fail. What has changed is the understanding of how molecular change can appear neutral over deep time while still being shaped by episodes of adaptation in shifting environments.

So, far from helping creationism, this paper undercuts one of creationism’s favourite caricatures of science. It shows evolutionary biology as a living, self-correcting science, not a rigid ideology. It also shows why no supernatural designer is needed. The process described is entirely natural: mutations arise, their effects depend on circumstances, environments change, and populations respond as best they can, without foresight, plan or purpose.

Glossary^ Molecular Evolution Without Magic.

Theory of Evolution (TOE): The scientific explanation for how populations change over generations through natural processes such as mutation, natural selection, genetic drift, gene flow and common descent.
Molecular evolution: Evolution studied at the level of DNA, RNA and proteins, rather than at the level of whole bodies, fossils or visible traits.
Neutral theory: A theory of molecular evolution proposing that many genetic changes spread through populations not because they are useful, but because they are selectively neutral or nearly neutral.
Mutation: A change in genetic material. Mutations may be harmful, beneficial or neutral, depending on their effects and the environment in which they occur.
Amino acid: One of the building blocks of proteins. A change in DNA can sometimes alter an amino acid in a protein, which may affect how that protein works.
Beneficial mutation: A mutation that improves survival or reproduction in a particular environment. It is not necessarily beneficial in all environments.
Fitness: A measure of how well an organism’s traits help it survive and reproduce in its particular environment. Fitness is not absolute; it depends on circumstances.
Natural selection: The process by which inherited traits that improve survival or reproduction tend to become more common in a population.
Genetic drift: Random change in gene frequencies, especially in small populations. Drift can spread or eliminate mutations independently of whether they are useful.
Fixation: The point at which a genetic variant has spread through a population so that all individuals carry it.
Substitution: A genetic change that has become established in a population or species over evolutionary time.
Selective sweep: The spread of a beneficial mutation through a population because natural selection favours it.
Pleiotropy: The situation in which one gene or mutation affects more than one trait.
Antagonistic pleiotropy: A case where a mutation has mixed effects: helpful in one respect, harmful in another; or useful in one environment, but costly in another.
Adaptive tracking: The process by which a population follows changing environmental conditions through natural selection. Because environments change, today’s useful mutation may not remain useful tomorrow.
Adaptive Tracking with Antagonistic Pleiotropy: The idea proposed in the paper: populations may repeatedly begin adapting to changing environments, but mutations can have conflicting effects, so many changes may appear neutral over long periods even though selection has been involved.
Deep mutational scanning: A laboratory method used to test the effects of large numbers of mutations, often by measuring how different genetic changes affect protein function or organismal fitness.
Environment: The conditions in which organisms live. This includes temperature, food, competitors, predators, parasites, chemicals and many other factors. In evolution, the environment helps determine which mutations are helpful, harmful or neutral.

The paper in Nature Ecology & Evolution was accoumpanied by a news item from the University of Michigan:

A new theory of molecular evolution
For a long time, evolutionary biologists have thought that the genetic mutations that drive the evolution of genes and proteins are largely neutral: they’re neither good nor bad, but just ordinary enough to slip through the notice of selection.

Now, a University of Michigan study has flipped that theory on its head.
In the process of evolution, mutations occur which can then become fixed, meaning that every individual in the population carries that mutation. A longstanding theory, called the Neutral Theory of Molecular Evolution, posits that most genetic mutations that are fixed are neutral. Bad mutations will be quickly discarded by selection, according to the theory, which also assumes that good mutations are so rare that most fixations will be neutral, says evolutionary biologist Jianzhi Zhang.

The U-M study, led by Zhang, aimed to examine whether this was true. The researchers found that so many good mutations occurred that the Neutral Theory cannot hold. At the same time, they found that the rate of fixations is too low for the large number of beneficial mutations that Zhang’s team observed.

To resolve this, the researchers suggest that mutations that are beneficial in one environment may become harmful in another environment. These beneficial mutations may not become fixed because of frequent environmental changes. The study, supported by the U.S. National Institutes of Health, was published in Nature Ecology and Evolution.

We’re saying that the outcome was neutral, but the process was not neutra. Our model suggests that natural populations are not truly adapted to their environments because environments change very quickly, and populations are always chasing the environment.

Professor Jianzhi Zhang, senior author.
Department of Ecology and Evolutionary Biology
University of Michigan
Ann Arbor, MI, USA.

Zhang says their new theory, called Adaptive Tracking with Antagonistic Pleiotropy, tells us something about how well all living things are adapted to their environments.

I think this has broad implications. For example, humans. Our environment has changed so much, and our genes may not be the best for today’s environment because we went through a lot of other different environments. Some mutations may be beneficial in our old environments, but are mismatched to today. At any time when you observe a natural population, depending on when the last time the environment had a big change, the population may be very poorly adapted or it may be relatively well adapted. But we’re probably never going to see any population that is fully adapted to its environment, because a full adaptation would take longer than almost any natural environment can remain constant.

Professor Jianzhi Zhang.

The Neutral Theory of Molecular Evolution was first proposed in the 1960s. Previously, scientists studied evolution based on the morphology and physiology, or appearance, of organisms. But starting in the 1960s, scientists were able to start sequencing proteins, and later, genes. This prompted researchers to look at evolution at the molecular level.

To measure beneficial mutation rates, Zhang and colleagues investigated large deep mutational scanning datasets produced by his and other labs. In this kind of scanning, the scientists created many mutations on a specific gene or region of the genome in model organisms such as yeast and E. coli.

The researchers then followed the organism over many generations, comparing them against the wild type, or the most common version existing in nature, of the organisms. This allowed the researchers to measure their growth and compare their growth rate to the wild type, which is how they estimated the effect of the mutation.

They found that more than 1% of mutations are beneficial, orders of magnitude greater than what the Neutral Theory allows. This amount of beneficial mutations would lead to more than 99% of fixations being beneficial and a rate of gene evolution that is much higher than the rate that is observed in nature. The researchers realized they had made a mistake in assuming an organism’s environment remained constant.

To investigate the impacts of a changing environment, Zhang’s research team compared two groups of yeast. One group evolved in a constant environment for 800 generations (each generation lasted 3 hours), while the second group evolved in a changing environment, in this case composed of 10 different kinds of media, or solution, that the yeast grew in. The second yeast group grew in the first media for 80 generations, in the second media for another 80 generations, and so on, for a total of 800 generations as well.

The researchers found that there were far fewer beneficial mutations in the second group compared to the first. Although the beneficial mutations occurred, they didn’t have a chance to become fixed before the environment shifted.

This is where the inconsistency comes from. While we observe a lot of beneficial mutations in a given environment, those beneficial mutations do not have a chance to be fixed because as their frequency increases to a certain level, the environment changes. Those beneficial mutations in the old environment might become deleterious in the new environment.

Professor Jianzhi Zhang.

However, Zhang says there is a caveat: The data they used came from yeast and E. coli, two unicellular organisms in which it’s relatively easy to measure the fitness effects of mutations. Deep mutational scanning data collected from multicellular organisms would tell whether their findings from unicellular organisms apply to multicellular organisms such as humans. Next, the researchers are planning a study to understand why it takes so long for organisms to fully adapt to a constant environment.

Other authors of the study include former U-M graduate students Siliang Song and Xukang Shen and former U-M postdoctoral researcher Piaopiao Chen.

Publication:
Song, S., Chen, P., Shen, X. et al.
Adaptive tracking with antagonistic pleiotropy results in seemingly neutral molecular evolution.
Nat Ecol Evol 9, 2358–2373 (2025). https://doi.org/10.1038/s41559-025-02887-1

Abstract
The neutral theory of molecular evolution, positing that most amino acid substitutions in protein evolution are neutral, is supported by vast comparative genomic data. However, here we report that the key premise of the theory—beneficial mutations are extremely scarce—is violated. Deep mutational scanning data from 12,267 amino acid-altering mutations in 24 prokaryotic and eukaryotic genes reveal that > 1% of these mutations are beneficial, predicting that > 99% of amino acid substitutions would be adaptive. This observation demands a new theory that is compatible with both the high beneficial mutation rate and the comparative genomic data considered consistent with the neutral theory. We propose such a theory named adaptive tracking with antagonistic pleiotropy. In this theory, virtually all beneficial mutations observed are environment specific. Frequent environmental changes and mutational antagonistic pleiotropy across environments render most of the beneficial mutations seen at one time deleterious soon after and hence rarely fixed. Consequently, despite the occurrence of adaptive tracking—continuous adaptation to a changing environment fuelled by beneficial mutations—neutral substitutions prevail. We show that this theory is supported by population genetics simulation, empirical observations and experimental evolution and has implications for the adaptedness of natural populations and the tempo and mode of evolution.

Song, S., Chen, P., Shen, X. et al.
Adaptive tracking with antagonistic pleiotropy results in seemingly neutral molecular evolution.
Nat Ecol Evol 9, 2358–2373 (2025). https://doi.org/10.1038/s41559-025-02887-1

© 2025 Springer Nature Ltd.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

This paper is not an admission that evolution has failed, nor is it a retreat from Darwin, common descent, natural selection or any of the other foundations of modern biology. It is a refinement of one part of evolutionary theory at the molecular level — exactly the sort of refinement that happens when scientists compare ideas with evidence rather than forcing evidence to conform to dogma.

Creationists like to portray science as an orthodoxy, but this is projection. In real science, theories are examined, tested, challenged and modified when the evidence requires it. The neutral theory of molecular evolution was not a sacred doctrine; it was a model, and like all scientific models it remains useful only for as long as it explains the facts. If a better model explains more, science changes. That is not weakness. That is why science works.

What the researchers have shown is that mutations, selection and changing environments can interact in more subtle ways than previously appreciated. A mutation that is beneficial in one environment may become neutral or even harmful when conditions change. Populations therefore do not evolve towards perfection, nor according to a plan, but in response to immediate circumstances, local pressures and inherited constraints.

There is no hint here of magic, design or supernatural interference. There is only the familiar evolutionary picture: organisms living in changing environments, mutations arising without foresight, selection acting without purpose, and populations changing over time. Creationists have been waiting for more than half a century for scientists to abandon evolution. Instead, scientists continue to do what creationism cannot do — improve their explanations in the light of evidence.

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