OOS Ch 1 fails but Lamarck to the rescue.

Darwin started his Origin of Species with chapter 1 - "the variation of domestication". 

Dog domestication figured prominently in this chapter. Darwin used this model to develope his signature "natural selection".

In the 1900's the modern synthesis incorporated natural selection and population genetics with the study of alleles (genes) with random mutations to explain evolution.

This gene-centric point of view has unfortunately led neo-Darwinists down the wrong path. They did not realize other factors were sitting on top of genes (epigenetics) that cause the expression of the organism into different phenotypes (forms).

Their strong commitment to this view caused them to ignore such pioneers as Barbara  McClintock and Conrad Waddington as well as other information coming out of the Botanical fields. Theirs was a quasi-religious commitment to Darwin.

Jean-Baptist Lamarck lived 50 years before Darwin and proposed the organisms had "agency" and responded to its environment as a form of evolution. There are many parallels to the recent field of epigenetics.

Conrad Waddington coined the word "epigenetics" for the first time but it was sixty years before we flushed out its mechanisms.

In this blog, I'm going to show a progression of our understanding of the domestication process and dogs genetically and finally epigenetically. 

You will notice that there is a commitment to neo-Darwinism even though it is far from explaining domestication.

In the last decade, with epigenetics being more fully utilized, you will see a definite change away from neo-Darwinism and the gene-centric point of view towards the organisms as having "agency" and not just being a slave to the "selfish gene."

We start with this journal:

2006

"Dogs are the most phenotypically diverse mammal. The difference in cranial and skeletal proportions among dog breeds exceeds that among wild canids.

Therefore, an essential question is whether phenotypic diversity reflects a diverse ancestral gene pool.

The origin of this diversity is uncertain. Does phenotypic diversity reflect a genetically diverse founding pool?"

The authors recognize there's a large number of phenotypic differences and to fit with neo-Darwinism it would require a large gene pool. However, they admit that avenue is not yielding results. 

Paradoxically there are more phenotypic changes with the domesticated canine than the wild-type canine. Looking back forty thousand years before modern domestication you might think there would be more changes to their outward appearances or phenotypes and yet you find the greatest change in appearance or phenotypes is in the modern domesticated canine. 

We will discuss it later as epigenetics can take a smaller gene pool and produce many different phenotypes (breeds).

Next:

2010

"We conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs.

The evolution of modern dog breeds seems to have.. a limited genetic toolkit to create remarkable phenotypic diversity."

SNP are single nucleotide polymorphisms, in essence, mutations of nucleotides at different places on the DNA

It's "random" mutations like these that are needed for neo-Darwinism to work.  Mutations occur and then according to neo darwinism, a better phenotype is made which natural selection acts on to preserve the new gene. So 50,000 SNP's and a limited genetic toolkit. 

Further:

2012

"This transfer of mutations across the dog evolutionary tree leads to the appearance of high phenotypic diversity that in actuality reflects a small number of.. genes."

Again they note a lot of difference however a small number of gene changes How can this be?

Continuing:

2012

"We analyzed 49,024 autosomal SNPs in 1,375 dogs.

We conclude by assessing the limitations of past studies and how next-generation sequencing of modern and ancient individuals may unravel the history of dog domestication."

Another 50,000 SNP's mutations and little results. They make the "appeal to the future" fallacy where X is possible, therefore, X is probably true. Darwin did this a lot. Most notably with the Cambrian explosion where he said if X is not true it would be "fatal" to his theory. Well X was not true.

Then the first epigenetic study.

2017

"Is dog domestication due to epigenetic modulation in the brain?"

"Domestication means decreased aggression and decreased flight distance concerning humans and canines.

It suggests it is an epigenetic based process that changes the interactions of the HPA axis between canines and humans."

The HPA is the Hypothalamus, Pituitary gland, and Adrenal gland, and all the hormones that they modulate. Examples include "fight or flight" or pleasure. The system is being discovered to be under epigenetic control and the authors suggest that humans and dogs through these mechanisms can get in sync with each other to lower each other's stress.

Neo Darwinism didn't see that one coming. How do different species get their HPA axis in sync to their mutual benefit? Survival of the fittest trods this over in favor of the "fit" over the "unfit". Per NeoDarwinism they would have to have similar "random" mutations to cause different phenotypes bringing their HPA system in sync. Ain't gonna happen.

And finally: 

2021

"Research on the genetics of domestication most often focuses on the protein-coding exons. However, exons cover only a minor part (1–2%) of the canine genome, whereas functional mutations may be located also in regions beyond the exome, in regulatory regions.

Therefore, a large proportion of phenotypical differences between dogs and wolves may remain genetically unexplained."

The results highlight the importance of regulatory mutations during dog domestication and motivate the functional annotation of the noncoding part of the canine genome"

They start by pointing that past research has focused on the Exon portion of the DNA. They also point out that it only constitutes about 2% of the total DNA. This is in large part due to the central dogma theory of Francis Crick which claims that DNA goes to RNA goes to protein goes to you. Crick famously said that 98% of DNA was "junk DNA" and that it was worthless to study.  This all changed with the ENCODE project in 2013 when they discovered that this "junk DNA" was 80% functional. 

This article points out that we need to study the noncoding DNA (junk DNA) as this is all considered to be part of epigenetic mechanisms. 

This is difficult for neo-Darwinism to recognize. 

To explain dog domestication it's been necessary to move away from Neo Darwinism to epigenetics.

We are finally coming to an explanation of Darwin's first chapter of the OOS to the modern field of Lamarckian epigenetics.

Just think if Darwin had HG Wells' time machine and he jumped to today.  A couple of hours on Pubmed and he would have ditched chapter 1. And yet that formed a cornerstone for natural selection and his WHOLE book.

I wonder what he'd say today to his faithful followers?

They'd probably ignore him as a "mad man" after all evolution (Neo-Darwinism) is a "fact" like gravity.

bibliography ;)