Discovery of useful “junk DNA” “has outstripped the discovery of protein-coding genes by a factor of five…

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March 30, 2021

'Junk DNA', Intelligent Design

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… and shows no signs of slowing.”

Yes, more from that commentary at Nature on the 20th anniversary of the Human Genome Project:

[I]t is now appreciated that the majority of functional sequences in the human genome do not encode proteins. Rather, elements such as long non-coding RNAs, promoters, enhancers and countless gene-regulatory motifs work together to bring the genome to life. Variation in these regions does not alter proteins, but it can perturb the networks governing protein expression
With the HGP draft in hand, the discovery of non-protein-coding elements exploded. So far, that growth has outstripped the discovery of protein-coding genes by a factor of five, and shows no signs of slowing. Likewise, the number of publications about such elements also grew in the period covered by our data set. For example, there are thousands of papers on non-coding RNAs, which regulate gene expression.
Alexander J. Gates, Deisy Morselli Gysi, Manolis Kellis & Albert-László Barabási, “A wealth of discovery built on the Human Genome Project — by the numbers” at Nature

To see how significant a change this is, consider a blast from the past:

[…The late] Dr. Susumu Ohno [1928 – 2000], writing in the Brookhaven Symposium on Biology in 1972 in the article “So Much ‘Junk DNA’ in our Genome” is credited with originating the term. As anyone can read below, he tried to (mistakenly) construct a scientific argument that the human genome can not sustain more than a very limited number of “genes” and argued for “the importance of doing nothing” for the rest. Though his misnomer was doubted from the outset (see the first question after his presentation calling his arguments “suspect”), the misnomer lived for a generation, in spite of ample evidence that it was false. The reason is, that “facts don’t kill theories, only theories that exceed obsolete dogma can kill old theories. “The Principle of Recursive Genome Function”, heretofore the only concise interpretation how directly amino-acid-coding regions (formerly called “genes”) work together with intronic and intergenic sequences, carrying much auxiliary information that is perused in fractal recursive iteration, only appeared in 2008. There may be other mathematical algorithmic theories for genome function explaining why and how “Junk DNA” is anything but “Junk” – this author will be pleased to list them – Pellionisz_at_JunkDNA.com

It’s a good thing for the Darwinians that they have always been able to afford top spin doctors via the tax dollars of people who are sceptical. It’ll be interesting to see what they come up with to front this one.

See also: Did beliefs about junk DNA hinder the Human Genome Project? But wasn’t a vast pile of junk DNA supposed to be one of the Great Proofs of Darwinism in the DNA? Funny, no one suggests that the constant diminution of the pile is evidence against the theory that its presence was supposed to be evidence for. Now why do you think that might be?

Comments

The Bible also clearly says that we will get new and better bodies - if we believe! Humanity 2.0? For an analogical look at why cells need non-coding DNA, see: https://thopid.blogspot.com/2019/02/a-junk-dna-functionality-analogy.htmlFasteddious_{April 3, 2021
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Seversky asked:
Interesting. Sanford doesn’t exactly say exactly what Christ will do to fix all the mutations in our genome. Will He invert better DNA repair enzymes? What’s taking Him so long? And why weren’t we better designed to begin with?
Here are some answers. 1. That's because Sanford doesn't know. So unlike Darwinists, he doesn't write science fiction speculations about what we don't know. 2. That Yeshua/Jesus was God incarnate who designed the genetic code (and Information doesn't spontaneously generate itself), it seems plausible that He would also know how to repair it. 3. According to the scriptures, Yeshua, will return to save the world from complete destruction (Revelation 11:16-18). He will have rescued as many people as were willing have been saved from the judgment to come. 4. We were designed "good" and the entire universe together "very good" according to Genesis 1. Engineers know that design always involves priorities and tradeoffs. Then, in Colossians 1:17, we read "He is before all things, and in him all things hold together." Things are falling apart because mankind chose to reject God go their own way--just as you have. As Yeshua healed many people during His ministry, He will heal the earth from all the damage we've caused, directly and indirectly. On this Good Friday, disciples of Yeshua/Jesus remember that He willingly allowed Himself to be the ultimate sacrifice for our sins (and yours if you trust Him rather than in your own self-righteousness). -QQuerius_{April 2, 2021
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seversky's is an argument from ignorance. Entertainment at it's finest, though.ET_{April 1, 2021
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Seversky: What’s taking Him so long? He's got lots of prayers to listen to you know.JVL_{April 1, 2021
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“ Will He invert better DNA repair enzymes? What’s taking Him so long? And why weren’t we better designed to begin with?” You’re talking to yourself again, Sev.Belfast_{March 31, 2021
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Our genome is degenerating, but wait, someone is coming to help us According to plant geneticist, John Sanford, the human race is degenerating rapidly. It's one of the trade secrets of biology. Every population geneticists knows that it's true. Sanford has even written a book about this trade secret: Genetic Entropy and the Mystery of the Genome Now if humans are degenerating at the rate of 1% or so per year then this must mean that they were perfect only a short time ago—like maybe 6000 years? Are humans doomed just as described in scripture? Yes. Is there any hope for us? Our only hope is Christ. Interesting. Sanford doesn't exactly say exactly what Christ will do to fix all the mutations in our genome. Will He invert better DNA repair enzymes? What's taking Him so long? And why weren't we better designed to begin with?
Seversky_{March 31, 2021
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Moreover, because of the mathematics of population genetics,( i.e. the genetic load argument), Dan Graur and Larry Moran insist that not only is some negligible amount of the genome to be considered junk, but they instead argue that the vast majority, 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
Dr. Moran's belief that 90% of the human genome must be junk just strikes me as being a completely absurd claim right off the bat,,,, but anyways to continue on, I hold Moran’s calculation to be flawed in regards to empirical evidence we now have in hand. Specifically, 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 Moran's own calculation, should actually be much higher than the 90% estimate for Junk DNA that he derived. 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. – per uncommon descent
Moreover, as John Sanford explained in his book "Genetic Entropy" and as he elucidated in the following paper, the unselectable ‘near neutral’ mutations, which Dr Moran classified as being perfectly neutral in his calculation, should, in reality, all be classified as 'slightly deleterious mutations'. Slightly deleterious mutations that will build up over time, instead of being classified as perfectly neutral mutations as Dr. Moran erroneously classified them as being in his calculation.
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 Kimura’s Distribution http://dl0.creation.com/articles/p091/c09164/9164-diagram-3c-lge-white.jpg Correct Distribution http://dl0.creation.com/articles/p091/c09164/9164-diagram-3d-lge-white.jpg
Thus, to wind all this up, even though Dr. 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. Yet, the fact of the matter is that if realistic estimates are used for ‘slightly deleterious mutations’ in the calculations then ALL, i.e. 100%, of the genome should be considered functionless junk, instead of just 90%. My question for Darwinists is this, "Does even the 0% functionality predicted for the genome from population genetics falsify Darwinian evolution in your minds?" If not, what in the world would ever possibly falsify Darwinian evolution in your minds? if your theory does not have a specific criteria for potential falsification, via mathematics and empirical testing, then it is not a real science in any meaningful sense and, as Popper himself pointed out, “it does not speak about reality.”
“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
Moreover I remind people that these leading Darwinists (Moran and Graur) insisted that most of the genome must be junk in spite of overwhelming empirical evidence to the contrary from ENCODE, and from many 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 New Book on “Junk DNA” Surveys the Functions of Non-Coding DNA – April 29, 2015 Excerpt: Carey,, goes on to explain how today we now believe that, far from being irrelevant, it’s the “junk DNA” that is running the whole show: “The other shock from the sequencing of the human genome was the realisation that the extraordinary complexities of human anatomy, physiology, intelligence and behaviour cannot be explained by referring to the classical model of genes. In terms of numbers of genes that code for proteins, humans contain pretty much the same quantity (around 20,000) as simple microscopic worms. Even more remarkably, most of the genes in the worms have directly equivalent genes in humans. http://www.evolutionnews.org/2015/04/a_new_book_on_j095611.html
And as the article in the OP makes abundantly clear, the trend in scientific research over the last several years has certainly not been supportive of the Darwinist's claim, (in the face of the 2012 ENCODE results to the contrary), that the vast majority of non-protein-coding DNA must be Junk DNA.
“Discovery Of Useful “Junk DNA” “Has Outstripped The Discovery Of Protein-Coding Genes By A Factor Of Five” - Excerpt: “With the HGP (Human Genome Project) draft in hand, the discovery of non-protein-coding elements exploded. So far, that growth has outstripped the discovery of protein-coding genes by a factor of five, and shows no signs of slowing. Likewise, the number of publications about such elements also grew in the period covered by our data set. For example, there are thousands of papers on non-coding RNAs, which regulate gene expression.” – Nature – “A wealth of discovery built on the Human Genome Project — by the numbers” – Feb. 2021 – Alexander J. Gates, Deisy Morselli Gysi, Manolis Kellis & Albert-László Barabási, https://uncommondescent.com/intelligent-design/discovery-of-useful-junk-dna-has-outstripped-the-discovery-of-protein-coding-genes-by-a-factor-of-five/
Thus in conclusion, although Larry Moran and Dan Graur may personally find the genetic load argument to be a powerful argument for considering the vast majority of the human genome to be junk, the fact of the matter is that the genetic load argument is, when scrutinized, found to be much more effectively, and rationally, used as a argument against the validity of Darwinian evolution itself. As Dr. John Sanford stated, “Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom’s (neo-Darwinism’s) very validity.”
Kimura’s Quandary Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in response to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most ‘evolution’ must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom’s (neo-Darwinism’s) very validity. - John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 161 – 162 – 2005
Verse
1 Thessalonians 5:21 but test all things. Hold fast to what is good.
bornagain77_{March 31, 2021
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For crying out loud, the entire purpose of ‘Natural Selection’ in the first place was to supposedly “explain away” the overwhelming ‘appearance of design’ we see in life without any reference to a real Designer, i.e. without any reference to God. And as Ernst Mayr himself explained, "The theory of evolution by natural selection explains the adaptedness and diversity of the world solely materialistically. It no longer requires God as creator or designer,,, Every aspect of the “wonderful design” so admired by the natural theologians could be explained by natural selection."
"The theory of evolution by natural selection explains the adaptedness and diversity of the world solely materialistically. It no longer requires God as creator or designer (although one is certainly still free to believe in God even if one accepts evolution). Darwin pointed out that creation, as described in the Bible and the origin accounts of other cultures, was contradicted by almost any aspect of the natural world. Every aspect of the “wonderful design” so admired by the natural theologians could be explained by natural selection." - Ernst Mayr - “Darwin’s Influence on Modern Thought” in Scientific American, July, 2000 https://sciphilos.info/docs_pages/docs_Mayr_Dawin_css.html
And as Francisco J. Ayala put it, natural selection supposedly accounted for "Design without designer", i.e. "The adaptive features of organisms could now be explained,, as the result of natural processes, without recourse to an Intelligent Designer.,,,"
Darwin's greatest discovery: Design without designer - Francisco J. Ayala - May 15, 2007 Excerpt: With Darwin's discovery of natural selection, the origin and adaptations of organisms were brought into the realm of science. The adaptive features of organisms could now be explained, like the phenomena of the inanimate world, as the result of natural processes, without recourse to an Intelligent Designer.,,, Darwin's theory of natural selection accounts for the “design” of organisms, and for their wondrous diversity, as the result of natural processes, the gradual accumulation of spontaneously arisen variations (mutations) sorted out by natural selection. https://www.pnas.org/content/104/suppl_1/8567
And as Richard Dawkins himself staled in "The Blind Watchmaker", “Yet the living results of natural selection overwhelmingly impress us with the appearance of design as if by a master watchmaker, impress us with the illusion of design and planning.”
“Yet the living results of natural selection overwhelmingly impress us with the appearance of design as if by a master watchmaker, impress us with the illusion of design and planning.” - Richard Dawkins – “The Blind Watchmaker” – 1986 – page 21
Thus contrary to what Darwinists may believe, with the tossing of Natural Selection to the wayside as the explanation for the 'wonderful design' we see in life, the explanation for the ‘appearance of design’ we see in life does not all of the sudden become, ‘Well, golly gee whiz, chance, all by its lonesome, must have done it all by itself", as Darwinists are apparently intent on believing, but instead the explanation for the ‘wonderful design’ we see in life reverts back to what it originally was before Darwin came along with his theory of Natural Selection. As Richard Sternberg explains, “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.”
“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
Moreover, (since Darwinists have now appealed to 'chance', all by its lonesome, to supposedly explain the 'wonderful design' we see in life, minus any reference to natural selection), it is also worth pointing out that 'chance' is not the cause of anything but is only a place holder for ignorance. Charles Darwin himself admitted as much.
“I have hitherto sometimes spoken as if the variations—so common and multiform in organic beings under domestication, and in a lesser degree in those in a state of nature—had been due to chance. This, of course, is a wholly incorrect expression, but it serves to acknowledge plainly our ignorance of the cause of each particular variation.” Charles Darwin – Origin – Chapter V
The word ‘chance’, as it is used by Darwinists, is not an appeal to any known mathematical probability, or to any known cause in physics, but is, in reality, simply a placeholder for ignorance. Yet Darwinists when they appeal to chance, act as if ‘chance’ is a cause unto itself. As Robert C. Sproul explained: “By calling the unknown cause ‘chance’ for so long, people begin to forget that a substitution was made. . . . The assumption that ‘chance equals an unknown cause’ has come to mean for many that ‘chance equals cause.’
What Is Chance? – Nicholas Nurston Excerpt: “The vague word ‘chance’ is used as a substitute for a more precise word such as ’cause’. “To personify ‘chance’ as if we were talking about a causal agent,” notes biophysicist Donald M. MacKay, “is to make an illegitimate switch from a scientific to a quasi-religious mythological concept.” Similarly, Robert C. Sproul points out: “By calling the unknown cause ‘chance’ for so long, people begin to forget that a substitution was made. . . . The assumption that ‘chance equals an unknown cause’ has come to mean for many that ‘chance equals cause.’” Others who reasoned in this fashion, Nobel laureate Jacques Monod, for one, used this chance equals cause line of reasoning. “Pure chance, absolutely free but blind, (is) at the root of the stupendous edifice of evolution,”… https://books.google.com/books?id=bQ5OAAAAQBAJ&pg=PT25&lpg=PT25
Thus, for Darwinists, via neutral theory, to appeal to chance alone, (minus natural selection), as the supposed explanation for the ‘wonderful design’ that we see in life, it is, in reality, for them to appeal to their own ignorance of the known cause for that ‘wonderful design’. If fact, when Darwinists use the word 'chance' it is more of less synonymous with the word ‘miracle.’ As Wolfgang Pauli himself explained, “they (Darwinists) use the word ‘chance’, not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word ‘miracle.’
Pauli’s ideas on mind and matter in the context of contemporary science – Harald Atmanspacher Excerpt: “In discussions with biologists I met large difficulties when they apply the concept of ‘natural selection’ in a rather wide field, without being able to estimate the probability of the occurrence in a empirically given time of just those events, which have been important for the biological evolution. Treating the empirical time scale of the evolution theoretically as infinity they have then an easy game, apparently to avoid the concept of purposesiveness. While they pretend to stay in this way completely ‘scientific’ and ‘rational,’ they become actually very irrational, particularly because they use the word ‘chance’, not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word ‘miracle.’” Wolfgang Pauli (pp. 27-28) https://pdfs.semanticscholar.org/234f/4989e039089fed5ac47c7d1a19b656c602e2.pdf
The following article by Stephen Talbott is very good for illustrating just how synonymous the words 'chance' and 'miracle' actually are in the Darwinists appeal to 'chance' as a cause. Talbott, playing off the old cartoon which had the punchline of, “Then a miracle occurs”. states, "I picture Dennett and Dawkins filling the blackboard with their vivid descriptions of living, highly regulated, coordinated, integrated, and intensely meaningful biological processes, and then inserting a small, mysterious gap in the middle, along with the words, “Here something random occurs.”
Evolution and the Illusion of Randomness - Talbott - Fall 2011 Excerpt: The situation calls to mind a widely circulated cartoon by Sidney Harris, which shows two scientists in front of a blackboard on which a body of theory has been traced out with the usual tangle of symbols, arrows, equations, and so on. But there’s a gap in the reasoning at one point, filled by the words, “Then a miracle occurs.” And the one scientist is saying to the other, “I think you should be more explicit here in step two.” In the case of evolution, I picture Dennett and Dawkins filling the blackboard with their vivid descriptions of living, highly regulated, coordinated, integrated, and intensely meaningful biological processes, and then inserting a small, mysterious gap in the middle, along with the words, “Here something random occurs.” This “something random” looks every bit as wishful as the appeal to a miracle. It is the central miracle in a gospel of meaninglessness, a “Randomness of the gaps,” demanding an extraordinarily blind faith. At the very least, we have a right to ask, “Can you be a little more explicit here?” http://www.thenewatlantis.com/publications/evolution-and-the-illusion-of-randomness
Moreover, the situation is actually much worse for Darwinists than it is for Christians. In the Christian's appeal to a 'miracle' we are actually appealing to known cause to explain the information in life. i.e. We know for a fact that Intelligent minds can create information. Whereas on the other hand, in the Darwinist's appeal to 'chance' to explain the information in life, the Darwinist is appealing to an unknown cause. That is to say, no one has EVER seen completely unguided material processes, (i.e. completely 'chance' processes), EVER create any meaningful information. Again, when Darwinists use the word 'chance', they are not appealing to any known physical cause of anything, but are in fact appealing to their own ignorance of the known cause for the 'wonderful design’ we see in life.bornagain77_{March 31, 2021
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As to the headline: "Discovery Of Useful “Junk DNA” “Has Outstripped The Discovery Of Protein-Coding Genes By A Factor Of Five" And that headline is exactly the reason why this is a very good thread in which to reiterate what I stated last night on another thread, in regards to the Darwinian claim that the vast majority of non-protein-coding DNA must be junk. When the results of ENCODE first came out in 2012, showing that the genome was not full of junk, the backlash from many evolutionists was hostile and fierce.
Trash Be Gone: Why Are Biologists Lashing Out Against Empirically Verified Research Results (of ENCODE)? - Casey Luskin - July 13, 2015 Excerpt: How could they (Darwinists) possibly oppose such empirically based conclusions? The same way they always defend their theory: by assuming an evolutionary viewpoint is correct and reinterpreting the data in light of their paradigm–and by personally attacking those who challenge their position. For instance, multiple initial rebuttals from evolution defenders called ENCODE “hype”10 and castigated researchers and science journalists for acting “irresponsibly” in favorably reporting on its findings.11 In a post titled “The ENCODE Delusion,” PZ Myers dismissed ENCODE’s central claim that 80 percent of the genome has biochemical functions as “bull****,” maintaining that evidence of biochemical activity in DNA and RNA “isn’t function. That isn’t even close.” He called the ENCODE researchers themselves “fundamentally dishonest,” and scoffed at Evan Birney, saying, “I don’t think Birney has a clue about the -biology.”12 Another Darwin-defending biologist, Nick Matzke, allowed that the ENCODE researchers weren’t stupid, just ignorant: “I’m beginning to think that certain parts of molecular biology and bioinformatics are populated with people who are very smart, but who got through school with a lot of detailed technical training but without enough broad training in basic comparative [i.e., evolutionary] biology.”13 But University of Toronto biochemist and pro-evolution blogger Laurence Moran wouldn’t even grant that the ENCODE researchers were intelligent: “I guess I’ll just have to be content to point out that many scientists are as stupid as many Intelligent Design Creationists,”14 he ranted. Moran further lamented that “the creationists are going to love this,” and he feared that ENCODE’s results were “going to make my life very complicated,”15 since “it’s going to take a lot of effort to undo the damage caused by [ENCODE].”16,,, Clearly, some ID critics are embracing ENCODE’s results. But most remain steadfastly resistant, most likely because ENCODE threatens to overturn some of the most prominent scientific arguments for an unguided evolutionary origin of the human genome. What If ENCODE Is Right? Earlier in 2014, Science reported on the arguments made by another leading evolutionary critic of ENCODE, University of Houston biologist Dan Graur. According to Science, “Graur’s atheism inflamed his anger at ENCODE.”19 It’s not surprising that Graur would become emotional over ENCODE given his blunt framing of the issue in a talk he gave in 2013: If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome. If, on the other hand, organisms are designed, then all DNA, or as much as possible, is expected to exhibit function. If ENCODE is right, then Evolution is wrong.20 https://evolutionnews.org/2015/07/the_encode_embr/
The primary reason why Dan Graur and Larry Moran, in particular, believed that the vast majority of DNA must be junk was because of the genetic load argument from population genetics. So let's look at the genetic load argument. In laying this genetic load argument out, it is first important to note that the mathematics of population genetics has now falsified Natural Selection as being a major player in evolution.
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/
And with Natural Selection being cast to the wayside by the mathematics of populations genetics as being a major player in evolution, Darwinists were forced, (via the consequences of Natural selection being tossed to the wayside), to believe that the vast majority of the genome was junk. As Dr. Robert Carter explains, “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” (i.e. Kimura’s genetic load argument for the neutral theory), If “Haldane’s Dilemma”7 were correct, then the majority of DNA must be non-functional.”,,, “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
And here is Kimura's genetic load argument for neutral theory,
Molecular evolution and neutral theory - Summary Excerpt: Kimura argued that the high rate of evolution, and the high degree of variability of proteins, would, if caused by natural selection, impose a high genetic load. Neutral drift, (where evolution is decoupled from Natural Selection), however, can drive high rates of evolution, and maintain high levels of variability, without imposing a genetic load. https://www.blackwellpublishing.com/ridley/tutorials/Molecular_evolution_and_neutral_theory_Summary.asp
In other words, Neutral theory, and the entire concept of junk DNA, was not developed because of any compelling empirical observation, but was actually developed because it was forced upon Darwinists by the mathematics of population genetics. In plain English, neutral theory, and the entire concept of junk DNA, is actually the result of the theoretical failure of Darwinian evolution, specifically the theoretical failure of natural selection, within the mathematics of population genetics! Well, without natural selection, exactly where does this leave Darwinists? In the following article Larry Moran, (who denies even being a "Darwinist" anymore since he no longer believes Natural Selection is the driving force behind evolution), 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 by the wayside by the mathematics of population genetics, (and by empirical evidence I might add), as the supposed explanation for the ‘appearance of design’ that we see in life, Darwinists did not accept such a devastating finding from population genetics as an outright falsification for their theory, as they should have done, but are instead now reduced to arguing that the 'wonderful design’ that we see pervasively throughout 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 a severe understatement. Even Richard Dawkins himself finds the claim that chance alone, all by its lonesome, can explain the wonderful design we see in biology to be absolutely inconceivable. In the following video Dawkins states that it “cannot come about by chance. It’s absolutely inconceivable that you could get anything as complicated or well designed as a modern bird or a human or a hedgehog coming about by chance.’
4:30 minute mark: “It cannot come about by chance. It’s absolutely inconceivable that you could get anything as complicated or well designed as a modern bird or a human or a hedgehog coming about by chance. That’s absolutely out.,,, It’s out of the question.,,, So where (does the appearance of design)) it come from? The process of gradual evolution by natural selection.” Richard Dawkins – From a Frog to a Prince – video https://youtu.be/ClleN8ysimg?t=267
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SemiOT: Some biologists are fully on board with a more epigenetic view of "species" as tribes that don't get along, not as spontaneously generated entities. Good clear thinking in this piece. https://www.colorado.edu/asmagazine/2021/03/25/endangered-songbird-challenging-assumptions-about-evolutionpolistra_{March 31, 2021
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