Evolution is no longer a "Fact like Gravity"

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The neutral theory of molecular evolution, proposed by Motoo Kimura in 1968, is a theory that explains the rate and pattern of molecular evolution by the random accumulation of neutral mutations. Neutral mutations are mutations that have no effect or a very small effect on the fitness of the organism. Kimura argued that neutral mutations can become fixed in a population by genetic drift, which is the random change in allele frequencies over time.

Kimura's theory was controversial at the time, as it challenged the traditional view that all molecular evolution was driven by natural selection. However, the theory has since gained widespread acceptance, and is now one of the most important theories in molecular evolution.

When I was at FSU working on my degree in Biology I became a follower of Kimura's theory. I was struck with the fact Junk DNA had more mutations than exonic DNA. How could mutations get fixed there only natural selection fixes mutations? This was one reason neo darwinists overlooked Junk DNA; it wasn't explainable by their model. 

Kimira claimed Darwin only worked 5% of the time.

Kimura's method for estimating evolutionary rates of base substitutions

Motoo Kimura's 1980 paper "A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences" introduced a new method for estimating evolutionary rates of base substitutions in protein-coding genes. The method is based on the ratio of nonsynonymous (Ka) to synonymous (Ks) substitutions, which is also known as the ω ratio. Since then over 30,000 scientists used this to "calculate" natural selection in journal articles. "Natural selections did it" was the confident statement for 40 years furthering their belief that evolution was a "fact like gravity."

Nonsynonymous substitutions are those that change the amino acid sequence of a protein, while synonymous substitutions do not. Synonymous substitutions are generally assumed to be neutral, meaning that they do not have a significant effect on the fitness of the organism. Nonsynonymous substitutions, on the other hand, can be either beneficial or deleterious. It's based in the redundancy of the genetic code. Many synonymous codons code for the same amino acid.


Problem is even though several synonymous codons can code for the same amino acids these codons have a variety of affects on DNA transcription and translations. These findings are relatively new. I discuss this in more detail here.

Kimura's method for estimating evolutionary rates is based on the following principle: if the rate of evolution is constant, (and it's not,) then the ratio of nonsynonymous to synonymous substitutions will be equal to the ratio of the number of nonsynonymous to synonymous sites in the gene. This ratio can be calculated by comparing the nucleotide sequences of two orthologous genes, which are genes that have descended from a common ancestor.


If the ratio of nonsynonymous to synonymous substitutions is greater than 1, then this indicates that the gene has been under positive selection, which is when natural selection favors nonsynonymous substitutions. Positive selection is often associated with the evolution of new adaptations.

If the ratio of nonsynonymous to synonymous substitutions is less than 1, then this indicates that the gene has been under purifying selection, which is when natural selection favors the removal of deleterious nonsynonymous substitutions. Purifying selection is thought to be the dominant force shaping the evolution of most genes.

If the ratio of nonsynonymous to synonymous substitutions is equal to 1, then this indicates that the gene has evolved neutrally. This means that natural selection has not played a significant role in shaping the evolution of the gene.

Kimura's method for estimating evolutionary rates has been widely used in evolutionary biology to study the evolution of genes and genomes. It has been used to identify genes that have been under positive selection, such as genes that are involved in the immune system and resistance to pathogens. It has also been used to study the evolution of neutral mutations and the effects of genetic drift.

Limitations of Kimura's method

Kimura's method is a simple but powerful tool for estimating evolutionary rates. However, it is important to note that it has some limitations. For example, the method assumes that the rate of evolution is constant. This is not always the case, as the rate of evolution can vary depending on the gene and the environment.

Additionally, the method assumes that synonymous substitutions are neutral. However, this is also not always the case, as some synonymous substitutions can affect the expression or function of a gene. 

This assumption was just this year overturned as I explain here based on this source article. This has sent population genetics in a tailspin as their calculations are wrong. They are now forced to measure "fitness" at the nucleotide level using Cas9 CRISPR rather than natural selection at the population level.

Despite these limitations, Kimura's method remains a widely used tool in evolutionary biology. It is a valuable tool for any researcher who is interested in studying the evolution of genes and genomes.

Other methods for estimating evolutionary rates

In addition to Kimura's method, there are a number of other methods that can be used to estimate evolutionary rates. These methods include:

  • Molecular clocks: Molecular clocks are based on the assumption that the rate of evolution is constant for a particular gene or group of genes. This allows researchers to estimate the time since divergence between two species by comparing the sequences of their homologous genes. This has been proven wrong due to codon bias, gBGC and AT mutation bias to name a few factors.

  • Coalescent theory: Coalescent theory is a statistical approach to studying the evolution of populations. It can be used to estimate evolutionary rates by modeling the process of genealogical coalescence, which is the point in time at which two alleles coalesce, or come together in a population.

  • Phylogenomics: Phylogenomics is the study of the evolution of genomes. It can be used to estimate evolutionary rates by comparing the genomes of multiple species.

The best method for estimating evolutionary rates will be determined by the new incredibly accurate Cas9 CRISPR method as I explain here.

40 years of "natural selection did it" proclamations out the door. As well, evolution is now not a "fact like gravity." 

What's an evolutionist to do?

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