100 years of no change "Population Genetics" in crisis mode due to epigenetics.

"Population genetics is a field of biology that studies the genetic composition of biological populations and the changes in genetic composition that result from the operation of various factors, including natural selection."

Population genetics is intimately bound up with the study of evolution and natural selection and is regarded as the theoretical cornerstone of modern Darwinism."

From the early 1920s to a hundred years later, populational genetics has been a Cornerstone of evolutionary thinking.

It was the basis of neo-Darwinism, aka the modern synthesis. From this, the "gene-centric" point of view was formed.

When combined with the "central dogma theory" of Francis Crick in the early 1960s, it became even more codified.

Due to a quasi-religious following of this theory, many areas of contrasting studies were downplayed until the last two decades when the field of epigenetics was discovered.

The central dogma assumed that the DNA went to RNA and proteins went to you. On one level, this is correct, but only on 2% of the DNA. The vast majority of DNA had feedback loops, e.g., DNA might go to RNA, but that RNA might influence the DNA or even influence the proteins as well the proteins might affect the DNA might influence the RNA. The combinations appear endless.

Populational genetics is having a hard time adapting to the new epigenetic phenomenon.

Epigenetics raises questions for the last hundred years of research.

In this article, I will use "Google Scholar" to review current population genetics papers without the term epigenetics and population genetics with the term epigenetics. 

This contrast should help the reader see the difference between neo-Darwinism thinking and post-neo-Darwinian thinking.

First population genetics without epigenetics.

"An introduction to population genetics theory."

Kimura, M.

1970

"Many of the substitutions which have taken place in evolution may have been non-selective.

I suggest that this is because previous theory, at least in its more precise forms, has been too analytical and has concentrated too much on the evolution of the parts while forgetting that an organism functions as a whole.

We have at the moment only the rudiments of a theory of the evolution of the genotype as a unit or of the phenotype as a unit, bearing in mind now that any particular measurement may be affected by a great many genes.

And any satisfactory theory would, of course, have to deal with the environment as a whole."

In my sophomore year, I took my first course of evolution. On the first day, my teacher defiantly said she was not going to follow the then passed Florida law, which stated creationism should be taught as an alternative to evolution.

She then went on to say if we could all "evolve" together and drink hot chocolate and sing Kumbaya, everything would be okay.

I wasn't about to challenge her as I would get my A and then go to medical school. 

One day she handed me a rolled-up article by  Motto Kimura, the above author. I'm still not sure why. 

His theory was called the "Neutral Theory of Evolution." It was named this because when he studied the mutation rates in the DNA, he noticed that there were many more mutations in the so-called "junk DNA'' than in the parts of the DNA that code for protein.

This flew in the face of current evolutionary thinking, which stated that for a mutation to be fixed, it must be selected. But if it's occurring in the junk DNA, there are no proteins. How can these mutations become fixed? As I sat in the library poring over this paper, I realized this was a significant if not fatal challenge to the theory of evolution.

To get around these discoveries, evolutionists proposed mutations in the junk DNA moved by random drift to the portion of the DNA which could be selected for at which point natural selection would fix the mutation. However, Kimura pointed out that the differential equations of their population models were self-referential and, as such, were questionable.

Almost prophetically, Kimora pointed out that genetics alone was insufficient and that we must consider the whole organism. This is what epigenetics does. 

He was 40 years ahead of his time.

The following states:

"Tested building-loci pipelines for selection of SNP panels seem to have low influence on population genetics."

2021

"Two bivalves species (Manila clam and common edible cockle) and three fish species (brown trout, silver catfish, and small-spotted catshark) were studied. 

No remarkable differences were found on genetic diversity and differentiation within species with the SNP panels.."

Studying SNP (point mutations) is the basis of evolution for natural selection to work on. 

A mutation occurs, changing the genes resulting in a different phenotype (form) that natural selection acts on. In this way, a transformation is supposed to be fixed, making a "fitter" individual through natural selection.

But as this article shows studying five different species, there's little change for the SNP's raising the question of how they develop new character traits via natural selection?

Now we will introduce epigenetics to population genetics to see how things change. 

As a reminder, epigenetics does not alter the DNA sequence, so there are no mutations for natural selection to act on.

"Phenotypic, genetic, and epigenetic variation among diverse sweet cherry gene pools"

2021

"Recent studies have provided evidence that besides allelic variation, epi-allelic variation can establish new heritable phenotypes.

According to correlation analyses, our results provide evidence that epigenetic diversity in predefined populations of sweet cherry had a more substantial impact on phenotypic traits than their rich genetic diversity."

In this study of epigenetics versus genetics of sweet cherries, they noted that there were more changes in epigenetics than genetics. This is significant as it is, in essence, saying that Neo Darwinism is not providing the changes. Instead, Lamarckian epigenetics is.

Next:

"Epigenetic inheritance and evolution: a historian's perspective"

2021

"Epigenetic inheritance is a revival of (neo)Lamarckism.

Opposition to all forms of non-genetic inheritance that prevailed at the time of the rise of the Modern Synthesis helps to explain why the Baldwin effect was understood as an insignificant mechanism during the second half of the twentieth century.

Potentiate two neglected mechanisms: the Baldwin effect and genetic assimilation.

We tested building loci pipelines for selection of SNP panels that seem to have a low influence on population genetics."

Jean-Baptiste Lamarck preceded Darwin by 50 years and was the first to write out a full theory of evolution. However, unlike Darwin's theory, Lamarck envisioned the organism to have intrinsic properties which allowed it to adapt to its environment. The properties were teleological and not random, as per Darwin. This did not meet well with the atheism that was rising in the latter part of the 1800s. They did not like the teleological aspects of his theory. They favored the random materialistic scientism of Darwin's theory.

The Baldwin effect and genetic assimilation were two other theories that had similar Lamarckian aspects, and as well they were ignored.

Like the above study, they noticed that SNP's changes do not correlate well with the external forms, questioning Neo Darwin's mechanism.

Next:

"The irruption of Next-generation sequencing (NGS) and restriction site-associated DNA sequencing (RAD-seq) in the last decade have led to the idehavefication of thousands of molecular markers and their genotyping for refined genomic advances." 

2021

"Many building-loci pipelines have been developed to obtain robust single nucleotide polymorphism (SNPs)

No remarkable differences were found on genetic diversity and differentiation within species with the SNP panels obtained."

This reiterates the articles above.

Next:

"How does epigenetics influence the course of evolution?"

2021

"The MS view of evolution can be summarized by the statement that evolution proceeds by changes in allele frequencies within and between populations as a consequence of natural selection,

The significance of phenotypic plasticity to evolutionary processes is much debated, and a great deal of this debate hinges on divergent interpretations of its meaning.

There are growing calls for an extended evolutionary synthesis that incorporates all forms of inheritance, including epigenetics.

Such experiments support the thesis of phenotypic assimilation as a mechanism of rapid adaptation but do not prove it.

To do so needs a multilevel approach: identification (or better, practical intropracticalan environmental challenge, identification of a phenotypic response mediated by epigenetic changes, and then evidence of selection as demonstrated by non-synonymous changes in DNA that compe. Inte for or complement epigenetic changes."

In addition to reiterating the articles above, it raises whether epigenetics can blend into NeoDarwinism. They point out that so far, this has not happened. Again the problem is epigenetics does not change the DNA sequence, and for neo-Darwinism, it requires sequence changes.

This leaves us with an interesting question which is pointed out in this last article.

"Stories that can’t be told by SNPs; DNA methylation variation in plant populations"

2021

"A key question is whether there is novel information in the epigenome that is not captured by SNP-based genetic markers"

In essence, these authors recognize that SNP's and neo-Darwinism cannot tell the whole story, and they raised the question if there is a story to be told by epigenetics outside of NeoDarwinism.

Many believe that there is such a story.

Author

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