Revisit: Unified theory of evolution, 2016

_{Denyse O'Leary

April 19, 2020

Culture, Darwinism, Epigenetics, Intelligent Design}

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Aeon is recycling this article from 2016:

Unified theory of evolution Darwin’s theory that natural selection drives evolution is incomplete without input from evolution’s anti-hero: Lamarck
The unifying theme for much of modern biology is based on Charles Darwin’s theory of evolution, the process of natural selection by which nature selects the fittest, best-adapted organisms to reproduce, multiply and survive. The process is also called adaptation, and traits most likely to help an individual survive are considered adaptive. As organisms change and new variants thrive, species emerge and evolve. In the 1850s, when Darwin described this engine of natural selection, the underlying molecular mechanisms were unknown. But over the past century, advances in genetics and molecular biology have outlined a modern, neo-Darwinian theory of how evolution works: DNA sequences randomly mutate, and organisms with the specific sequences best adapted to the environment multiply and prevail. Those are the species that dominate a niche, until the environment changes and the engine of evolution fires up again.
But this explanation for evolution turns out to be incomplete, suggesting that other molecular mechanisms also play a role in how species evolve. One problem with Darwin’s theory is that, while species do evolve more adaptive traits (called phenotypes by biologists), the rate of random DNA sequence mutation turns out to be too slow to explain many of the changes observed. Scientists, well-aware of the issue, have proposed a variety of genetic mechanisms to compensate: genetic drift, in which small groups of individuals undergo dramatic genetic change; or epistasis, in which one set of genes suppress another, to name just two.

Michael Skinner, “Unified theory of evolution” at Aeon (09 November, 2016)

Of course. Michael Skinner, a Washington State U biology prof, makes good sense. But no, nothing happens. Too many fossils in Darwin world now. They just want dusting off now and then. And, in a world of change, they also expect things to continue that way…

By the way, why is Lamarck an “antihero”? His basic idea (we would now call it “epigenetics”) was sound. And Darwin went along with it. But any idea other than Darwin’s is inconvenient to the cult that has come to dominate biology, with unhealthful results.

Evolution is a history of life, involving many factors. The study of history does not need cults. It comes down to Darwinism vs. the history of life.

See also: Conclusions: What the fossils told us in their own words.

Comments

Perhaps a much simpler way to answer the question of why epi-genetics is incompatible with Darwinian materialism is the way that Jonathan Wells stated it, "I now know as an embryologist,,, It's the organism controlling the DNA, not the DNA controlling the organism."
Ask an Embryologist: Genomic Mosaicism - Jonathan Wells - February 23, 2015 Excerpt: humans have a "few thousand" different cell types. Here is my simple question: Does the DNA sequence in one cell type differ from the sequence in another cell type in the same person?,,, The simple answer is: We now know that there is considerable variation in DNA sequences among tissues, and even among cells in the same tissue. It's called genomic mosaicism. In the early days of developmental genetics, some people thought that parts of the embryo became different from each other because they acquired different pieces of the DNA from the fertilized egg. That theory was abandoned,,, ,,,(then) "genomic equivalence" -- the idea that all the cells of an organism (with a few exceptions, such as cells of the immune system) contain the same DNA -- became the accepted view. I taught genomic equivalence for many years. A few years ago, however, everything changed. With the development of more sophisticated techniques and the sampling of more tissues and cells, it became clear that genetic mosaicism is common. I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It's the organism controlling the DNA, not the DNA controlling the organism. http://www.evolutionnews.org/2015/02/ask_an_embryolo093851.html
Further note as to rapid adaptations to differing environments:
A. L. Hughes's New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago - Wolf-Ekkehard Lönnig - December 2011 Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species' particular environment....By mutative reduction of the genetic potential, modifications became "heritable". -- As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The "remainder" has been lost by mutations (accumulation of slightly disadvantageous alleles) -- in the formation of secondary species. http://www.evolutionnews.org/2011/12/a_l_hughess_new053881.html
bornagain77_{April 19, 2020
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As to:
why is Lamarck an “antihero”? His basic idea (we would now call it “epigenetics”) was sound. And Darwin went along with it.
Simply put, the main reason why “Larmarckism” and/or epigenetics is incompatible with Darwinian materialism is that it strongly implies 'top down' control instead of 'bottom up' emergence.
,, In the following video, Dr Denis Noble states that around 1900 there was the integration of Mendelian (discrete) inheritance with evolutionary theory, and about the same time Weismann established what was called the Weismann barrier, which is the idea that germ cells and their genetic materials are not in anyway influenced by the organism itself or by the environment. And then about 40 years later, circa 1940, a variety of people, Julian Huxley, R.A. Fisher, J.B.S. Haldane, and Sewell Wright, put things together to call it ‘The Modern Synthesis’. So what exactly is the ‘The Modern Synthesis’? It is sometimes called neo-Darwinism, and it was popularized in the book by Richard Dawkins, ‘The Selfish Gene’ in 1976. It’s main assumptions are, first of all, is that it is a gene centered view of natural selection. The process of evolution can therefore be characterized entirely by what is happening to the genome. It would be a process in which there would be accumulation of random mutations, followed by selection. (Now an important point to make here is that if that process is genuinely random, then there is nothing that physiology, or physiologists, can say about that process. That is a very important point.) The second aspect of neo-Darwinism was the impossibility of acquired characteristics (mis-called “Larmarckism”). And there is a very important distinction in Dawkins’ book ‘The Selfish Gene’ between the replicator, that is the genes, and the vehicle that carries the replicator, that is the organism or phenotype. And of course that idea was not only buttressed and supported by the Weissman barrier idea, but later on by the ‘Central Dogma’ of molecular biology. Then Dr. Nobel pauses to emphasize his point and states “All these rules have been broken!”. Professor Denis Noble is President of the International Union of Physiological Sciences. Denis Noble - Rocking the foundations of biology - video http://www.voicesfromoxford.org/video/physiology-and-the-revolution-in-evolutionary-biology/184 "Physiology Is Rocking the Foundations of Evolutionary Biology": Another Peer-Reviewed Paper Takes Aim at Neo-Darwinism - Casey Luskin March 31, 2015 Excerpt: Noble doesn't mince words: "It is not only the standard 20th century views of molecular genetics that are in question. Evolutionary theory itself is already in a state of flux (Jablonka & Lamb, 2005; Noble, 2006, 2011; Beurton et al. 2008; Pigliucci & Muller, 2010; Gissis & Jablonka, 2011; Shapiro, 2011). In this article, I will show that all the central assumptions of the Modern Synthesis (often also called Neo-Darwinism) have been disproved." Noble then recounts those assumptions: (1) that "genetic change is random," (2) that "genetic change is gradual," (3) that "following genetic change, natural selection leads to particular gene variants (alleles) increasing in frequency within the population," and (4) that "inheritance of acquired characteristics is impossible." He then cites examples that refute each of those assumptions,,, He then proposes a new and radical model of biology called the "Integrative Synthesis," where genes don't run the show and all parts of an organism -- the genome, the cell, the body plan, everything -- is integrated. http://www.evolutionnews.org/2015/03/physiology_is_r094821.html
For example, here is a direct experimental falsification of one of the central assumptions of the modern synthesis, i.e. of neo-Darwinism
Genome research shows that the body controls the integrity of heritable genomes - University of Cologne - July 24, 2019 Scientists,,, have discovered that body cells which are in direct contact with the germ cells in the nematode Caenorhabditis elegans are responsible for controlling the stability of the genome in primordial germ cells (PGCs).,,, For more than a hundred years, inheritance of genetic information was thought to be autonomously controlled by the germ cells, explaining why acquired traits cannot be genetically inherited. Scientists believed that mutations occurring only in germ cells were responsible for any heritable genetic changes—be it during evolution or as cause of genetic disorders. Schumacher and his team now challenge this assertion. The DNA of an organism constantly gets damaged. Not only environmental influences, but also by-products of the body's energy metabolism damage the molecular structure of the genome in every cell. The scientists investigated how the genome integrity of PGCs is controlled. PGCs need to survey their genomes particularly rigorously because they give rise to all sperm or eggs of the organism. Damaged PGCs are particularly dangerous because they are hereditary and can lead to serious genetic disorders. PGCs thus need to stop dividing when their genomes are damaged until the DNA is repaired. Special niche cells are responsible for signalling to the PGCs that they need to stop dividing and repair before generating further germ cells. If they fail to do so, the PGCs might pass on dangerous mutations to the next generation. To fulfil this important function, the niche cells are in intimate contact with the PGCs and instruct them whether to divide and generate germ cells or whether to stay inactive. "This means that the body is responsible for controlling the integrity of heritable genomes," Schumacher remarked. "The parental body thus has somatic control over the integrity of PGC genomes, controlling the quality of the heritable genetic information." Since studying PGCs in mammals is a complicated endeavour, Schumacher's team used C. elegans as a simple animal model to shed new light on to how PGCs control the integrity of the genomes they will pass on to their offspring. https://phys.org/news/2019-07-genome-body-heritable-genomes.html
bornagain77_{April 19, 2020
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What about chromatin remodeling, TFs binding site codes, TADs, etc? How did all that evolve?jawa_{April 19, 2020
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