ENCODE produces a genomic encyclopedia

_{Denyse O'Leary

July 31, 2020

'Junk DNA', Intelligent Design}

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Explained in nine papers in Nature

Less than 2% of the human genome encodes proteins1. A grand challenge for genomic sciences has been mapping the functional elements — the regions that determine the extent to which genes are expressed — in the remaining 98% of our DNA. The Encyclopedia of DNA Elements (ENCODE) project, among other large collaborative efforts2–4, was established in 2003 to create a catalogue of these functional elements and to outline their roles in regulating gene expression. In nine papers in Nature5–13, the ENCODE consortium delivers the third phase of its valuable project…
This yet-to-be-completed encyclopedia has already become a quintessential tool for understanding gene regulation and genetic predisposition to disease. In the upcoming fourth phase of the ENCODE project, we would be excited to see a systematic assessment of whether the catalogued CREs actually performed the functions inferred on the basis of histone modifications and bound proteins; this could be achieved using high-throughput functional-genomic technologies. The continued expansion of ENCODE to wider biological contexts (such as disease samples and rare cell types) at single-cell resolution would help researchers to use genomic information to diagnose and prevent diseases.
Chung-Chau Hon & Piero Carninci, “Expanded ENCODE delivers invaluable genomic encyclopedia” at Nature

Readers may also remember ENCODE from a flap a few years ago when Darwinian Dan Graur announced that the ENCODE team had to be wrong in saying that there wasn’t nearly as much junk DNA as had been thought. After a while, Graur just wasn’t doing politeness any more.

Now that ENCODE has so much information to offer, maybe Graur should do politeness again and try listening.

See also:

Junk DNA: Dan Graur (Junk!), ENCODE Team (Not Junk!), And the Science Media

Is Nature needlessly annoying Dan Graur, the champion of junk DNA?

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At Quanta: Cells need almost all of their genes, even the “junk DNA”

“Junk” RNA helps regulate metabolism

Junk DNA defender just isn’t doing politeness any more.

Anyone remember ENCODE? Not much junk DNA? Still not much. (Paper is open access.)

Yes, Darwin’s followers did use junk DNA as an argument for their position.

Another response to Darwin’s followers’ attack on the “not-much-junk-DNA” ENCODE findings

Comments

How does junk DNA imply common descent?ET_{August 3, 2020
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John_a_designer: Several prominent ID’ists (Denton and Behe, for example) accept common descent. But even if you accept CD that doesn’t prove or even imply that the neo-Darwinian mechanism is the cause of evolutionary change. Okay, but can you still call it common descent if a designer intervened. That's not how I understand common descent. That's more like partial common descent surely.JVL_{August 3, 2020
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At best all junk DNA implies is common descent. It doesn’t make the case for neo-Darwinian evolution (NS + RV) any stronger. It certainly doesn’t weaken the case for ID. Several prominent ID’ists (Denton and Behe, for example) accept common descent. But even if you accept CD that doesn’t prove or even imply that the neo-Darwinian mechanism is the cause of evolutionary change. Of course, some of the so-called junk has turned out to have some function and nobody really knows how much of the junk is really junk.john_a_designer_{August 3, 2020
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In fact, because of the mathematics of population genetics, Dan Graur and Larry Moran insist that upwards to 90% of DNA must be junk:
Revisiting the genetic load argument with Dan Graur – Larry Moran – July 14, 2017 Excerpt: I’ve discussed genetic load several times on this blog (e.g. Genetic Load, Neutral Theory, and Junk DNA) but a recent paper by Dan Graur provides a good opportunity to explain it once more. The basic idea of Genetic Load is that a population can only tolerate a finite number of deleterious mutations before going extinct. The theory is sound but many of the variables are not known with precision.,,, Let’s look at the first line in this table. The deleterious mutation rate is calculated using the lowest possible mutation rate and the smallest percentage of deleterious mutations (4%). Under these conditions, the human population could survive with a fertility value of 1.8 as long as less than 25% of the genome is functional (i.e. 75% junk) (red circle). That’s the UPPER LIMIT on the functional fraction of the human genome. But that limit is quite unreasonable. It’s more reasonable to assume about 100 new mutations per generation with about 10% deleterious. Using these assumptions, only 10% of the genome could be functional with a fertility value of 1.8 (green circle). Whatever the exact percentage of junk DNA it’s clear that the available data and population genetics point to a genome that’s mostly junk DNA. http://sandwalk.blogspot.com/2017/07/revisiting-genetic-load-argument-with.html
I hold Moran’s 10% estimate for deleterious mutations, that he used in his calculation in the preceding paper, to be far too conservative, and thus the percentage of junk DNA, according to his own calculation, should actually be much higher than his 90% estimate,,, As Michael Behe stated in the following paper,, we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent
“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/
Moreover, as John Sanford showed in his book Genetic Entropy and the following paper, the unselectable ‘near neutral’ mutations, which Dr Moran classified as perfectly neutral in his calculation, should, in reality, all be classified as slightly deleterious mutations that will build up over time instead of being classified as perfectly neutral.,,,
Can Purifying Natural Selection Preserve Biological Information? – May 2013 – Paul Gibson, John R. Baumgardner, Wesley H. Brewer, John C. Sanford In conclusion, numerical simulation shows that realistic levels of biological noise result in a high selection threshold. This results in the ongoing accumulation of low-impact deleterious mutations, with deleterious mutation count per individual increasing linearly over time. Even in very long experiments (more than 100,000 generations), slightly deleterious alleles accumulate steadily, causing eventual extinction. These findings provide independent validation of previous analytical and simulation studies [2–13]. Previous concerns about the problem of accumulation of nearly neutral mutations are strongly supported by our analysis. Indeed, when numerical simulations incorporate realistic levels of biological noise, our analyses indicate that the problem is much more severe than has been acknowledged, and that the large majority of deleterious mutations become invisible to the selection process.,,, http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0010
Thus, even though Larry Moran used unrealistic estimates for deleterious mutations in his calculation, Moran was still only able to calculate that 10% of the genome may be functional. The fact of the matter is that if realistic estimates are used in the calculations, and if Darwinian evolution is assumed to be true in the calculations, then ALL, i.e. 100%, of the genome should be functionless junk, instead of just 90%. Moreover, these leading Darwinists insisted that most of the genome must be junk in spite of overwhelming empirical evidence to the contrary from ENCODE, and from other sources
Junk No More: ENCODE Project Nature Paper Finds “Biochemical Functions for 80% of the Genome” – Casey Luskin – September 5, 2012 Excerpt: The Discover Magazine article further explains that the rest of the 20% of the genome is likely to have function as well: “And what’s in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator and self-described “cat-herder-in-chief”. He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. “It’s likely that 80 percent will go to 100 percent,” says Birney. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.”” We will have more to say about this blockbuster paper from ENCODE researchers in coming days, but for now, let’s simply observe that it provides a stunning vindication of the prediction of intelligent design that the genome will turn out to have mass functionality for so-called “junk” DNA. ENCODE researchers use words like “surprising” or “unprecedented.” They talk about of how “human DNA is a lot more active than we expected.” But under an intelligent design paradigm, none of this is surprising. In fact, it is exactly what ID predicted. http://www.evolutionnews.org/2012/09/junk_no_more_en_1064001.html
Thus in conclusion, although the prediction of junk DNA followed directly from the mathematics of population genetics, and although ENCODE. and many other sources, empirically falsified that mathematical prediction of Darwinian evolution, Evolutionists in general, and Dan Graur and Larry Moran in particular, refused to accept those empirical finding from ENCODE. Yet, if your theory does not have a criteria for potential falsification via empirical testing, then it is not science
“In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality.” Karl Popper
In short, Darwinian evolution, at least how Darwinists treat it, is NOT a science. Verse:
Psalm 139:13-14 For you created my inmost being; you knit me together in my mother’s womb. I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well.
bornagain77_{August 1, 2020
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Of related note, it has now been found that when modern day population geneticists apply the 'miracle' of mathematics, (Einstein, Wigner), to Darwin's theory of natural selection, then the mathematics of population genetics itself falsifies natural selection as the supposed 'designer substitute'.
The waiting time problem in a model hominin population – 2015 Sep 17 John Sanford, Wesley Brewer, Franzine Smith, and John Baumgardner Excerpt: the waiting time for the fixation of a “string-of-one” is by itself problematic (Table 2). Waiting a minimum of 1.5 million years (realistically, much longer), for a single point mutation is not timely adaptation in the face of any type of pressing evolutionary challenge. This is especially problematic when we consider that it is estimated that it only took six million years for the chimp and human genomes to diverge by over 5 % [1]. ,,, While fixing one point mutation is problematic, our simulations show that the fixation of two co-dependent mutations is extremely problematic – requiring at least 84 million years (Table 2). This is ten-fold longer than the estimated time required for ape-to-man evolution.,,, Certainly the creation and fixation of a string of three (requiring at least 380 million years) would be extremely untimely (and trivial in effect), in terms of the evolution of modern man. ,,, When we increase the hominin population from 10,000 to 1 million (our current upper limit for these types of experiments), the waiting time for creating a string of five is only reduced from two billion to 482 million years. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573302/
As Richard Sternberg stated,
“Darwinism provided an explanation for the appearance of design, and argued that there is no Designer -- or, if you will, the designer is natural selection. If that's out of the way -- if that (natural selection) just does not explain the evidence -- then the flip side of that is, well, things appear designed because they are designed.” Richard Sternberg - Living Waters documentary Whale Evolution vs. Population Genetics - Richard Sternberg and Paul Nelson - (excerpt from Living Waters video) https://www.youtube.com/watch?v=0csd3M4bc0Q
Many leading Darwinists, such as Dan Graur and Larry Moran, who are familiar with the failings of natural selection within the mathematics of population genetics now champion what is termed the neutral theory of molecular evolution which holds that at the molecular level most evolutionary changes and most of the variation within and between species is not caused by natural selection but by genetic drift of mutant alleles that are neutral.'.
Neutral theory of molecular evolution The neutral theory of molecular evolution holds that at the molecular level most evolutionary changes and most of the variation within and between species is not caused by natural selection but by genetic drift of mutant alleles that are neutral. https://en.wikipedia.org/wiki/Neutral_theory_of_molecular_evolution
In the following article Larry Moran quotes Austin Hughes who states, 'Darwinism asserts that natural selection is the driving force of evolutionary change. It is the claim of the neutral theory, on the other hand, that the majority of evolutionary change is due to chance.'
Austin Hughes and Neutral Theory - Laurence A. Moran - June 19, 2017 Excerpt: Originally proposed by Motoo Kimura, Jack King, and Thomas Jukes, the neutral theory of molecular evolution is inherently non-Darwinian. Darwinism asserts that natural selection is the driving force of evolutionary change. It is the claim of the neutral theory, on the other hand, that the majority of evolutionary change is due to chance. http://sandwalk.blogspot.com/2017/06/austin-hughes-and-neutral-theory.html
Thus, with Natural selection being tossed to the wayside by the mathematics of population genetics, (and also by empirical evidence itself), as the explanation for the 'appearance of design' that we see in life, Darwinists did not accept such a devastating finding from mathematics as an outright falsification for their theory, as they should have done, but are instead now reduced to arguing that the 'appearance of design' that we see in life is, basically, the result of pure chance with natural selection now playing a very negligible role if any role at all. To call such a move on the part of Darwinists disingenuous would be an understatement. As William Murray commented on this development within Darwin's theory,
"One wonders what would have become of evolution had Darwin originally claimed that it was simply the accumulation of random, neutral variations that generated all of the deeply complex, organized, interdependent structures we find in biology? Would we even know his name today? What exactly is Darwin really famous for now? Advancing a really popular, disproven idea (of Natural Selection), along the lines of Luminiferous Aether? Without the erroneous but powerful meme of “survival of the fittest” to act as an opiate for the Victorian intelligentsia and as a rationale for 20th century fascism, how might history have proceeded under the influence of the less vitriolic maxim, “Survival of the Happenstance”?" - William J Murray
Moreover, the 'prediction' of Junk DNA was born out of the mathematics of population genetics itself. As Robert Carter states, “Junk DNA is not just a label that was tacked on to some DNA that seemed to have no function, but it is something that is required by evolutionary theory. Mathematically, there is too much variation, too much DNA to mutate, and too few generations in which to get it all done.”
The slow, painful death of junk DNA – Robert W. Carter – 2009 Background Based on the work of J.B.S. Haldane5 and others, who showed that natural selection cannot possibly select for millions of new mutations over the course of human evolution, Kimura6 developed the idea of “neutral evolution”. If “Haldane’s Dilemma”7 were correct, then the majority of DNA must be non-functional. It should be free to mutate over time without needing to be shaped by natural selection. In this way, natural selection could act on the important bits and neutral evolution could act randomly on the rest. Since natural selection will not act on neutral traits, which do not affect survival or reproduction, neutral evolution can proceed through random drift without any inherent “cost of selection”.8 The term “junk DNA” originated with Ohno,9 who based his idea squarely on the idea of neutral evolution. To Ohno and other scientists of his time, the vast spaces (introns)between protein-coding genes were (exons) just useless DNA whose only function was to separate genes along a chromosome. Junk DNA is a necessary mathematical extrapolation. It was invented to solve a theoretical evolutionary dilemma. Without it, evolution runs into insurmountable mathematical difficulties. Junk DNA necessary for evolution Junk DNA is not just a label that was tacked on to some DNA that seemed to have no function, but it is something that is required by evolutionary theory. Mathematically, there is too much variation, too much DNA to mutate, and too few generations in which to get it all done. This was the essence of Haldane’s work. Without junk DNA, evolutionary theory cannot currently explain how everything works mathematically. https://creation.com/images/pdfs/tj/j23_3/j23_3_12-13.pdf
Because the prediction of Junk DNA is based in the mathematics population genetics, that is the primary reason why Dan Graur stated, after the results of ENCODE came out, (results that showed pervasive functionality across the entire genome), that “If ENCODE is right, evolution is wrong.”
“Dan Graur said ENCODE is “bonkers”[v] because “If ENCODE is right, evolution is wrong.”[vi]” https://crev.info/2018/07/keynote-speech-falsifies-darwinism/
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