New findings challenge the “neutral” theory of evolution for 95% of human genome

_{Denyse O'Leary

October 26, 2018

Darwinism, Evolution, Intelligent Design, Natural selection}

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The neutral theory of evolution holds that “most variation at the molecular level does not affect fitness and, therefore, the evolutionary fate of genetic variation is best explained by stochastic [random] processes.”

From ScienceDaily:

However, what scientist Fanny Pouyet and colleagues from the Group of Laurent Excoffier at the SIB Swiss Institute of Bioinformatics and University of Bern recently discovered, is that 95% of our genome actually seems to be affected by selection and other genetic biases and that markers previously thought to be neutral appear to provide skewed estimates. Their study, published in eLife, calls for the re-examination of a plethora of results and provides the tools and recommendations to correct such issues in the future.

Models used to reconstruct the history of a species or to discover how populations are related to one another rely on a key assumption: that the genome regions under scrutiny are made of “neutral” snippets of DNA, i.e. parts that have evolved randomly rather than being selected for or against. But these regions might actually not be as neutral as previously thought, according to a recent finding by scientists at SIB and the University of Bern: “What we find is that less than 5% of the human genome can actually be considered as “neutral”,” says Fanny Pouyet, lead author of the study. “This is a striking finding: it means that 95% of the genome is indirectly influenced by functional sites, which themselves represent only 10% to 15% of the genome,” she concludes. These functional sites encompass both genes and regions involved in gene regulation. Paper. (open access) – Fanny Pouyet, Simon Aeschbacher, Alexandre Thiéry, Laurent Excoffier. Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences. eLife, 2018; 7 DOI: 10.7554/eLife.36317
More.

Perhaps the most reasonable conclusion is that all of Darwinism is in a mess similar to that of speciation.

Hat tip: Philip Cunningham
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See also: Heads up! Neutral theory of evolution

and

Commenter nails the problem with neutral theory of evolution

Comments

Awesomeness. I first saw this posted by Tomkins, nice follow up BA. So, is this the final, ten-thousandth nail in the mutation that is Darwinism? ;-) Or will Darwinism just mutate itself into another Dan Graur moment? Let the rants begin.DATCG_{October 28, 2018
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Darwinism lives again!Mung_{October 27, 2018
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While we're dashing expectations, how about this one: evolutionists thought the lower regions of the brain were older, inherited from more primitive species. So part of our brains were "reptilian". Turns out the cerebellum takes part in higher-level functions: https://www.npr.org/sections/health-shots/2018/10/25/660504533/the-underestimated-cerebellum-gains-new-respect-from-brain-scientistsEDTA_{October 26, 2018
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Implications: Does this rub out neutral theory somewhat???willh_{October 26, 2018
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Here is the paper:
Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences Fanny Pouyet, Simon Aeschbacher, Alexandre Thiéry, Laurent Excoffier, University of Bern, Switzerland; Swiss Institute of Bioinformatics, Switzerland; University of Zurich, Switzerland - Aug 20, 2018 Excerpt Results: As a measure of genomic diversity, we used the average derived allele frequency per individual (daf1),,, We have interpreted the striking linear relationship observed between derived allele frequency per individual (daf1) and recombination rate (Figure 1) as evidence for the pervasive effect of BGS (i.e. background selection). Excerpt Disussion: The exact proportion of the genome that is influenced by selection is still the source of an intense debate (Bernstein et al., 2012; Rands et al., 2014; Graur, 2017; Kern and Hahn, 2018). Here, we show that up to 80–85% of the human genome is probably affected by background selection (BGS), an effect that is not subtle (Reed et al., 2005) and that is visible from single individuals genomes (Figure 1—figure supplement 5A). Even though our estimate of the fraction of the human genome influenced by BGS matches relatively well with that reported to be biochemically functional by the ENCODE consortium (Bernstein et al., 2012), our results do not imply that 80–85% of the human genome is functional. They rather show that functional sites that are the direct target of purifying selection in both coding and non-coding regions (potentially representing 8–15% of the genome, Rands et al. (2014); Graur, 2017) have an important but indirect influence on most of the genome. https://elifesciences.org/articles/36317?fbclid=IwAR1zUaxRiaECggDS_eOIiJqsEPFNTnX1jQnSpWaRoZR_IH7KRG4dJioGMxA
Jeffrey Tomkins goes over the implications for ID here:
95% of Human Genome Can't Evolve - JEFFREY P. TOMKINS, PH.D. - OCTOBER 25, 2018 Excerpt: A new study just came out that analyzed vast amounts of data from human genome samples from all over the world.1 Based on the evolutionists’ own theoretical model of evolution, 95% of the human genome is “restrained”—it can’t evolve. According to the popular neutral model of evolutionary theory, much of the human genome is nothing but randomly evolving junk. All of this so-called neutral DNA that is allegedly not under any “selective restraint” only serves as fodder for functional new genes and traits to somehow magically arise and thus provide the engine of evolution. However, in 2012, a vast global consortium of biomedical geneticists working on the ENCODE project—scientists who are more interested in curing human disease than speculative and unproductive research about evolution—reported that at least 80% of the human genome had demonstrated biochemical function.2 Far more function than evolutionists’ models predict. Nevertheless, vocal theoretical evolutionists pushed back and published a variety of papers, essentially using evolution to prove evolution as an overall strategy. As a result of their theoretical calculations based on the premise of evolution, they claimed in one paper that the human genome could be no more than 8.2% functional despite the avalanche of hard empirical data that demonstrated otherwise.3 Renowned theoretical evolutionist Dan Graur, who has vociferously derided the ENCODE project results, has recently increased his estimate of this level of functionality to a range of 10 to 25%.4 Graur is famous for saying, “If ENCODE is right, then evolution is wrong.”5,,, Global data among diverse people groups for DNA sequence variability across the human genome was inputted into a statistical model of neutral evolution. It was discovered that, at most, only 5% of the human genome could randomly evolve and not be subject to the alleged forces of selection. Fanny Pouyet, the lead author of the published study stated, “What we find is that less than 5% of the human genome can actually be considered as ‘neutral.’”,, http://www.icr.org/article/10968/?fbclid=IwAR0A6IgyEdFG5dfDUol9sSlIamXIZsKQs6_GoxcEU33oEWt9BQNLrRuO-0U
Bottom line, they were not looking for functionality. They were only looking to see if the genomic data lined up with what neutral theory predicted. It did not. Dab Graur and Larry Moran, (who, because of 'neutral theory', both attacked the ENCODE findings of widespread functionality in the genome), will not be happy! My only gripes with the study are that they presupposed far less functionality than they should have and also presupposed that selection has far more explanatory power for the genetic sequences they observed than it actually does. Selection is shown both empirically and mathematically to be powerless as the supposed 'Designer substitute'. (Sanford, Behe, Axe, Sternberg) Moreover ENCODE, as well as numerous other studies into the staggering integrated complexity within DNA, have clearly shown that the default assumption should be the assumption of pervasive functionality instead of an assumption of pervasive non-functionality. Here is a small glimpse into the staggering integrated complexity within DNA
Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - published online May 2013 Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43]. 38. Sanford J (2008) Genetic Entropy and the Mystery of the Genome. FMS Publications, NY. Pages 131–142. 39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432. 40. Trifanov EN (1997) Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654. 41. Kapranov P, et al (2005) Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997. 42. Birney E, et al (2007) Encode Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816. 43. Itzkovitz S, Hodis E, Sega E (2010) Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006 Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - May 2013 Conclusions: Our analysis confirms mathematically what would seem intuitively obvious - multiple overlapping codes within the genome must radically change our expectations regarding the rate of beneficial mutations. As the number of overlapping codes increases, the rate of potential beneficial mutation decreases exponentially, quickly approaching zero. Therefore the new evidence for ubiquitous overlapping codes in higher genomes strongly indicates that beneficial mutations should be extremely rare. This evidence combined with increasing evidence that biological systems are highly optimized, and evidence that only relatively high-impact beneficial mutations can be effectively amplified by natural selection, lead us to conclude that mutations which are both selectable and unambiguously beneficial must be vanishingly rare. This conclusion raises serious questions. How might such vanishingly rare beneficial mutations ever be sufficient for genome building? How might genetic degeneration ever be averted, given the continuous accumulation of low impact deleterious mutations? http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006 Biological Information - Overlapping Codes 10-25-2014 by Paul Giem - video https://www.youtube.com/watch?v=OytcYD5791k&index=4&list=PLHDSWJBW3DNUUhiC9VwPnhl-ymuObyTWJ
If you believe that level of staggering integrated complexity can be the result of unintelligent processes, as Darwinists believe, then I have some swamp land to sell you.bornagain77_{October 26, 2018
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“This is a striking finding” Why?PeterA_{October 26, 2018
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“re-examination of a plethora of results” That phrase sounds familiar :)PeterA_{October 26, 2018
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