Genomics Shows Evolutionary Theory Is Baseless
New Study Reveals Evolution Does Not Have a Weak Foundation: It Has NO Foundation.
by Jerry Bergman, PhD
A new review article by Vivian Callier in Quanta Magazine reveals that evolution does not have a weak foundation: It has no foundation. The subtitle summarizes the dilemma evolutionists are in: “For 50 years, evolutionary theory has emphasized the importance of neutral mutations over adaptive ones in DNA. Real genomic data challenge that assumption.”
Classical Darwinian or “Adaptationist” Evolutionism
In a nutshell, evolution theory has historically postulated that the source of genetic variety is created by genetic mutations which in turn are selected by natural selection. Improvements in a life-form that enable it to out-compete other life forms are more likely to survive and out-produce its competitors, thus maintaining or improving its position in its ecological niche. Those life-forms that are less able to compete are more apt to go extinct. This is the source of the expression, ‘survival of the fittest.’ As explained by Darwin, whose
core insight was that organisms with disadvantageous traits would slowly be weeded out through negative (or purifying) selection, while those with advantageous features would reproduce more often and pass those features on to the next generation (positive selection). Selection would help to spread and refine those valuable traits. For most of the first half of the 20th century, population geneticists largely attributed genetic differences between populations and species to adaptation through positive selection.
Then, as more research was completed, it was realized this straightforward core of evolution was contradicted by much contrary evidence. One problem has always been the fact that the vast majority of mutations are deleterious, or nearly neutral. Mildly-deleterious or near-neutral mutations individually cause only minor or no problems, but they add up, in time producing genetic meltdown, causing death and eventually extinction.
Neutral Theory to the Rescue
One major proposed solution was neutral mutation theory. This proposed that evolution is caused by mutations that are not deleterious, nor are they near neutral, but fully neutral, meaning they have no effect on the organism. When enough mutations have occurred to provide a beneficial effect, then and only then are they selected. The idea was first proposed by the eminent Japanese population geneticist Motoo Kimura in 1968. He concluded that most mutations were “neutral in effect rather than beneficial or harmful, and that shifts in the frequency of these neutral mutations dominated evolutionary change at the genomic level…. [and] an ‘appreciable fraction’ of the genetic variation within and between species is the result of genetic drift — that is, the effects of randomness in a finite population — rather than natural selection, and that most of these differences have no functional consequences for survival and reproduction.” This four-fold conclusion was based on the assumption that most DNA was useless junk as was widely believed then.
a more comprehensive theory of molecular evolution must be sought.
Genetic drift, according to the Kimura model, is the change in the frequency of an existing gene variant (an allele) in a population due to random factors. In a diagram comparing the competing models of evolution, genetic drift is described as being caused by the mutation number which “rises or falls in frequency through chance alone.” The result is that genetic drift may cause some gene variants to disappear completely, reducing genetic variation, or genetic drift can also cause rare alleles to become much more common, even fixed, in the genome. The alleles in the offspring are a sample of those in the parents, and chance has a major role in determining whether a given individual survives and reproduces.
Neutral Theory vs Genomics
A review of the literature illustrates some of the many problems with this idea. The most obvious is how importantly the theory relies on chance in the evolutionary process. Classical evolution theory at least appears plausible because it is not evolution by chance, but if a genetic change improves survivability—even if only slightly—it will improve the likelihood that the organism can better compete in the natural world. In short, as described in Darwinian terms, fitness increases by natural selection. The problems with genetic drift are the natural-world factors of order, design, and constraints. Deviation from these constraints, even slightly, causes disease or problems. Randomness plays a part in Darwinism, but a very small part. As Callier noted
When Charles Darwin articulated his theory of evolution by natural selection in On the Origin of Species in 1859, he focused on adaptations — the changes that enable organisms to survive in new or changing environments. Selection for favorable adaptations, he suggested, allowed ancient ancestral forms to gradually diversify into countless species.
Callier adds the adaptation concept was so powerful that it was easy to conclude
evolution is all about adaptation. So … for half a century, a prevailing view in scholarly circles has been that it’s not…. [how] most evolutionary changes appear at the level of the genome and are essentially random and neutral. Adaptive changes groomed by natural selection might indeed sculpt a fin into a primitive foot, they said, but those changes make only a small contribution to the evolutionary process, in which the composition of DNA varies most often without any real consequences.
They were judged as essentially neutral because many of an organism’s traits are not critical for survival, but are part of the enormous variety existing in the natural world which do not appear to confer a clear survival advantage to the organism, such the enormous coloration variety and intricate detail of many insects.
Problems with Genetic Drift
The many major problems with neutral theory and random drift soon became very obvious. These include (1) chance is centrally based on a non-negotiable belief in evolution, and (2) the theory is unconstrained by solid evidence but rather is the result of an attempt to reason out how life could possibly have evolved based on a few firmly established facts such as the enormous amount of variety existing in life. Another problem (3) was, we now know that most all of the genes in humans, and other life-forms as well, had some function, often regulation, as indicated by the Encyclopedia of DNA Elements (ENCODE) Project. This project determined that more than 80 percent of this non-coding component of the genome, which was once considered “junk DNA,” actually has important roles in regulating the activity of particular genes. Therefore, many, if not most, mutations are not neutral, but at the least slightly deleterious.
Callier explains that some evolutionists recognize the serious problem of giving chance a central role in neutral theory, noting that
genomes show much more evidence of evolved adaptation than the theory would dictate. This debate is important because it affects our understanding of the mechanisms that generate biodiversity, our inferences about how the sizes of natural populations have changed over time and our ability to reconstruct the evolutionary history of species (including our own). What lies in the future might be a new era that draws from the best of neutral theory while also recognizing the real, empirically supported influence of selection.
Professor Rebekah Rogers, an evolutionary geneticist at the University of North Carolina, Charlotte, explained the situation among evolutionists this way: “Any time you have limited data, the arguments get really fierce.” Until recently, no way existed to broadly prove or disprove neutral theory and genetic drift except on theoretical grounds. Now that sequencing technology and polymerase chain reaction (PCR) have become widely available, gene sequence data has overflowed from our genetic labs. The result of inexpensive genome sequencing is the “explanatory power of the neutral theory looks even worse.” Because of its simplistic explanation, researchers used the neutral model as a convenient default explanation for the patterns of genetic variation that they observed in the natural world, but it can only explain trivial details like eye color, but not the evolution of body organs. It is inconceivable that a heart or lung, each requiring scores of complex genes, could ever evolve by genetic drift.
As a result of the problems with genetic drift, many evolutionists are returning to adaptationist theory they had rejected for good reasons. Problems with adaptationism had motivated the development and acceptance of neutral theory because
affordable genomic sequencing and sophisticated statistical methods are allowing evolutionary theorists to make headway on quantifying the contribution of adaptive variation and neutral evolution to species differences. In species like humans and fruit flies, the data have revealed extensive selection and adaptation, which has led to strong pushback against Kimura’s original idea.
As Kern and Hahn wrote in their recent article “The ubiquity of adaptive variation both within and between species means that a more comprehensive theory of molecular evolution must be sought.” In short, Darwinists don’t have a foundational theory of evolution.
One fruitful area of mutational study is cancer. Cancer cells are rife with mutations, and although only a small subset of those mutations are important in causing cancer, they do help us to understand mutations, and especially the commonality of patterns such as hot spots and trends, such as the conversion of the genetic base G to T is a far more common mutation than T to G. This information will, the evidence so far indicates, destroy both neutral theory as well as evolution based on mutations according to the fact that mutations as a whole tend to degrade the genome and not improve it.
 Viviane Callier, 2019. Quanta Magazine. Theorists Debate How ‘Neutral’ Evolution Really Is. https://www.quantamagazine.org/neutral-theory-of-evolution-challenged-by-evidence-for-dna-selection-20181108/
 Callier, 2019.
 John Sanford, 2014. Genetic Entropy, 4th Edition. New York, NY: FMS Publications.
 Jerry Bergman, 2019. Neutral Theory of Evolution Debunked. Elaborating on Michael Behe’s refutation of “neutral evolution,” March 2. https://crev.info/2019/03/neutral-theory-of-evolution-debunked/
 Callier, 2019.
 Callier, 2019. Chart by Lucy Reading, titled Competing Models of Molecular Evolution.
 B. Star and H. Spencer, 2013. “Effects of genetic drift and gene flow on the selective maintenance of genetic variation.” Genetics, 194 (1): 235–244, May.
 Jeffrey P. Tomkins and Jerry Bergman, 2017. Neutral Model, genetic drift and the Third Way—A Synopsis of the self-inflicted demise of the evolutionary paradigm. Journal of Creation, 31(3):94-102.
 Callier, 2019.
 Callier, 2019.
 E. A. Feingold, et al., 2004. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306(5696): 636-640. October 22.
 Callier, 2019.
 The Evolutionary Importance of Neutral vs. Adaptive Genes. https://www.wired.com/story/quanta-neutral-vs-adaptive-evolution/
 Callier, 2019.
 Heather Rowe and Sudhir Kumar (Editors), 2018. Celebrating 50 years of the Neutral Theory. Molecular Biology and Evolution. https://academic.oup.com/mbe/pages/neutral_theory.
 Vincent L. Cannataro, Stephen G. Gaffney, and Jeffrey P. Townsend, 2018. Effect Sizes of Somatic Mutations in Cancer. Journal of the National Cancer Institute, 110(11): 1171–1177, November.
 John Sanford, 2014.
Dr. Jerry Bergman has taught biology, genetics, chemistry, biochemistry, anthropology, geology, and microbiology at several colleges and universities including for over 40 years at Bowling Green State University, Medical College of Ohio where he was a research associate in experimental pathology, and The University of Toledo. He is a graduate of the Medical College of Ohio, Wayne State University in Detroit, the University of Toledo, and Bowling Green State University. He has over 1,300 publications in 12 languages and 40 books and monographs. His books and textbooks that include chapters that he authored, are in over 1,500 college libraries in 27 countries. So far over 80,000 copies of the 40 books and monographs that he has authored or co-authored are in print. For more articles by Dr Bergman, see his Author Profile.