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Researchers: Basic tenet of evolutionary theory “upended” by new find

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Darwinism
Epigenetics
Evolution
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Illustration of Cryptococcus neoformans (stock image). | Credit: (c) Kateryna_Kon / stock.adobe.com
Cryptococcus neoformans (stock image)/© Kateryna_Kon ,Adobe Stock

Looking past the tabloid prose, they say they found that selection can occur at the level of the epigenome:

The field of evolutionary biology has seen its share of spirited debates. But if there’s one principle that virtually every expert in the field agrees on, it’s that natural selection occurs at the level of the genome.

But now, a UC San Francisco-led research team has discovered the first conclusive evidence that selection may also occur at the level of the epigenome — a term that refers to an assortment of chemical “annotations” to the genome that determine whether, when and to what extent genes are activated — and has done so for tens of millions of years. This unprecedented finding subverts the widely accepted notion that over geologic timescales, natural selection acts exclusively on variation in the genome sequence itself.

In a study published Jan. 16, 2020 in the journal Cell, the researchers show that Cryptococcus neoformans — a pathogenic yeast that infects people with weakened immune systems and is responsible for about 20 percent of all HIV/AIDS-related deaths — contains a particular epigenetic “mark” on its DNA sequence, which, based on their lab experiments and statistical models, should have disappeared from the species sometime during the age of the dinosaurs.

University of California – San Francisco, “‘Living fossil’ may upend basic tenet of evolutionary theory: Natural selection’s reach extends beyond genome into epigenome, study suggests.” at ScienceDaily (January 16, 2020)

So what becomes of neo-Darwinism if selection isn’t tied to the all-powerful but accidental gene?

Paper. (paywall)

See also: Epigenetic change: Lamarck, wake up, you’re wanted in the conference room!

Comments
as to:
"The field of evolutionary biology has seen its share of spirited debates. But if there’s one principle that virtually every expert in the field agrees on, it’s that natural selection occurs at the level of the genome."
So natural selection occurs at the level of the genome.",,,, Really??? That's an interesting claim and it is a false claim because, After-the-fact differential survival and reproduction of already-living phenotypic organisms (ordinary natural selection) does not explain polynucleotide prescription and coding.
The GS Principle (The Genetic Selection Principle) - Abel - 2009 Excerpt: The GS (Genetic Selection) Principle states that biological selection must occur at the nucleotide-sequencing molecular-genetic level of 3'5' phosphodiester bond formation. (Yet) After-the-fact differential survival and reproduction of already-living phenotypic organisms (ordinary natural selection) does not explain polynucleotide prescription and coding. http://www.ncbi.nlm.nih.gov/pubmed/19273248
As Abel's PDF further elucidates,"Biological control requires selection of particular configurable switch-settings to achieve potential function. This occurs largely at the level of nucleotide selection, prior to the realization of any integrated biofunction. "
The GS (genetic selection) Principle - David L. Abel - 2009 Excerpt: The GS (Genetic Selection) Principle states that biological selection must occur at the nucleotide-sequencing molecular-genetic level of 3'5' phosphodiester bond formation. After-the-fact differential survival and reproduction of already-living phenotypic organisms (ordinary natural selection) does not explain polynucleotide prescription and coding. All life depends upon literal genetic algorithms. Even epigenetic and "genomic" factors such as regulation by DNA methylation, histone proteins and microRNAs are ultimately instructed by prior linear digital programming. Biological control requires selection of particular configurable switch-settings to achieve potential function. This occurs largely at the level of nucleotide selection, prior to the realization of any integrated biofunction. Each selection of a nucleotide corresponds to the setting of two formal binary logic gates. The setting of these switches only later determines folding and binding function through minimum-free-energy sinks. These sinks are determined by the primary structure of both the protein itself and the independently prescribed sequencing of chaperones. The GS Principle distinguishes selection of existing function (natural selection) from selection for potential function (formal selection at decision nodes, logic gates and configurable switch-settings). https://pdfs.semanticscholar.org/da07/424592a58fe76c6a0ac92e9b13729efff878.pdf
As to the fact that,,,
"After-the-fact differential survival and reproduction of already-living phenotypic organisms (ordinary natural selection) does not explain polynucleotide prescription and coding."
At the 8:15 minute mark of the following video, Dr John Sanford, with the "Princess and the Pea paradox" does a very good job of explaining exactly why Natural Selection is grossly inadequate for explaining the overlapping coding coding that must occur at the polynucleotide level.
Dr. John Sanford "Genetic Entropy and the Mystery of the Genome" 1/2 https://youtu.be/pJ-4umGkgos?t=495
Simply put, 'natural selection,' in so far as it can be said to operate at all, occurs at the whole organism level, which is far above the level of the 6 billion polynucleotides in the human genome. i.e. The Princess and the Pea paradox! Thus although "virtually every expert in the field (apparently) agrees that,,, natural selection occurs at the level of the genome."", (indeed it must occur at the level of the genome if it has any hope of explaining the multiple layers of overlapping coding within DNA), the fact of the matter is that those supposed experts have no empirical evidence whatsoever that their belief is true.
"There is no compelling empirical or theoretical evidence that complexity, modularity, redundancy or other features of genetic pathways are promoted by natural selection..." (Lynch, "The evolution of genetic networks by non-adaptive processes," Nature Rev. Gen., 8:803-13, (October, 2007)) Genome-wide analysis of a long-term evolution experiment with Drosophila – 2010 Excerpt of concluding paragraph: “Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments.” http://www.homepages.ed.ac.uk/aspiliop//2010_2011/Burke%20et%20al%202010.pdf “The Third Way” – James Shapiro, Denis Noble, and etc.. etc..,,, Excerpt: “some Neo-Darwinists have elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis.” http://www.thethirdwayofevolution.com/
I agree with the 'experts' that In order to adequately explain the coding within DNA, indeed, 'selection' must occur at the DNA level. Yet, natural selection is grossly inadequate to explain selection at the level of DNA. The only known cause within the universe that has the power within itself to 'select' at the level of DNA, so as to make the thousands, if not millions, of decisions that are necessary in order to produce overlapping coding and information within DNA, is an Intelligent Agent. And an exceedingly intelligent Intelligent Agent at that! And again, if Darwinian evolution were a normal science instead of basically being a unfalsifiable religion for atheists, this should count as yet another powerful falsification of a 'basic tenet' of Darwinian theory.
1 Thessalonians 5:21 but test them all; hold on to what is good,
bornagain77
January 19, 2020
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here we go again.... the almighty natural selection .... WHAT IS NATURAL SELECTION ??? Recently i came across a debate at researchgate.net (lots of mainstream scientists there) It was so funny to see how these mainstream scientists struggle to define the term NATURAL SELECTION :))))))))))) I would like to share with you, here is a very interesting post (from that debate) "What is Natural Selection? Accuracy is important in scientific language, then it is important to know what is natural selection: Please make your choice from the fourteen options indicated below . To help you taking a decission I may say: 1. Nature does not select. 2. The artificial process by which new varieties (not species) are obtained is not called selection, but breeding. 3. Most of the possibilities indicated below are incompatible with the others 1. A process, 2. A mechanism, 3. A theory, 4. An hypothesis, 5. A scientific law, 6. A natural law, 7. A fact, 8. A truth, 9. A principle, 10. An action, 11. An agent, 12. Survival of the fittest, 13. A semantic ghost, 14. A false expression,..... Please make your choice......." (the full debate is here: https://www.researchgate.net/post/What_is_Natural_Selection#share )martin_r
January 19, 2020
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Pw@5: I think I preferred pier review. You take the paper to the end of a convenient pier and throw it. The parts that the breeze blows back to you make it into the paper the parts that end up in the water didn't survive "pier" review. Darwinists are into random aren't they? This ought to work real well for them.Latemarch
January 19, 2020
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Basically the Evo 2.0 $10M prize remains frozen. No winning candidates yet. Not even applying contestants. Let’s keep waiting. Not there yet.pw
January 19, 2020
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AaronS1978, I know you meant “peer” not “pier” :)pw
January 19, 2020
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“based on their lab experiments and statistical models, should have disappeared from the species sometime during the age of the dinosaurs.” 1. Apparently their lab experiments and statistical models didn’t produce accurate results or were misinterpreted? 2. The paper doesn’t say how the genome or the epigenome appeared to begin with. It just seems to indicate that some epigenetic settings were altered and affected the survivability of the given organism? 3. This seems like another case of adaptation associated with adjustments in the system settings? 4. This seems like another example of microevolutionary adaptation. The yeast remained a yeast? 5. No macroevolutionary process seems to be described in this paper? 6. Another example of bacteria remain bacteria, birds remain birds, fish remain fish? 7. What else is new?pw
January 19, 2020
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So it was an epigenetic response that was passed on for millions of years and help the cell survive, this is their evidence. I don’t see how this is even a big deal, and I doubt this will survive pier review, in fact it almost seems like the really stretching their claim after reading it.AaronS1978
January 18, 2020
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Oooooooooooh natural selection naturally selected that epigenome work like that, naturally of course, You can extend natural selection into selecting standard particles over antimatter particles to and galaxies over galaxies, natural selection selection everything naturally. It really boils down to if it works it’ll survive!!!!!!! Holy cow novel right!? Now am I getting this right the conclusive evidence of this is that something that should’ve disappeared tens of millions of years ago is still there and that constitutes that natural selection selected that epigenome to continue to exist? I will read on for something seems silly about this and it is making a very loud claim PS I don’t see how this helps anything other than they keep trying to prove that natural selection is the key driver to all things evolution and life has nothing to do with it it has to be naturally selectedAaronS1978
January 18, 2020
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Darwin spoke of selection he didn't know anything about genes so why does it matter *where* the selection is occurring?es58
January 18, 2020
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