Larry Moran to write new book: Claims genome is 90% junk

_{Denyse O'Leary

April 13, 2021

'Junk DNA', Books of interest, Genetics}

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Readers will remember biochemist Larry Moran, now emeritus at the University of Toronto. He used to comment here a fair bit.

He is now publishing a book (probably 2022), called What’s in Your Genome: 90% of Your Genome Is Junk Some chapters include “The ENCODE Publicity Campaign” and “Zen and the Art of Coping with a Poorly-Designed Genome.”

In the comments, he tells us, “ I have a section in the last chapter titled “No comfort for intelligent design creationists” where I explain why they are wrong about junk DNA. I’m pretty sure that will silence any criticism. :-)”

Well, it’s sure not us here at UD he has to argue with really. We have 214 stories in the “junk DNA” category and most of them are about the uses found for DNA that was formerly thought to be junk.

If he wants to pick a fight with ENCODE, grab a seat.

Note: Today, he offered an explanation of his overall intentions.

See also: We are encouraged to celebrate ENCODE III and the demise of junk DNA.

and

Did beliefs about junk DNA hinder the Human Genome Project?

Comments

JVL:
why do you think the genome of a plant is orders of magnitude bigger than that of a human.
It needs to be. :)ET_{April 16, 2021
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Again, only a fool would think that histone octamers arose to spool and organize the junk so that the important sequences can be found and expressed. If you want to argue for a preponderance of junk DNA then you have to deal with the histone octamers and the fact that the junk is very well organized.ET_{April 16, 2021
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Moreover, (since Darwinists have now appealed to ‘chance’, all by its lonesome, to supposedly explain the ‘wonderful design’ we see in life), it is also worth pointing out that when Darwinists use the word ‘chance’ they are not appealing to a physical cause of anything but are, in reality, only using the word 'chance' as place holder for their ignorance of a known cause. 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’. And to make it even more interesting, 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 when 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 when they appeal to 'chance' than it is for Christians when they appeal to a 'miracle'. In the Christian’s appeal to a ‘miracle’ we are actually appealing to known cause to explain the information we see in life. i.e. We know for a fact that Intelligent minds can and do habitually create information whenever they want to do so. Whereas, on the other hand, in the Darwinist’s appeal to ‘chance’ to explain the information we see in life in life, the Darwinist is appealing to a completely unknown cause. That is to say, no one has EVER seen completely unguided material processes, (and/or completely ‘chance’ processes), EVER create any meaningful information. EVER! Again, when Darwinists use the word ‘chance’, they are not actually appealing to any known physical cause of anything, but are in fact appealing to their own ignorance of what caused the ‘wonderful design’ we see in life.
John 1:1-4 In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. In him was life, and that life was the light of all mankind.
bornagain77_{April 15, 2021
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JVL asks, "So, how do changes in genomes get ‘fixed’ or made dominant (if not by Natural Selection)? In other words: what causes a genome variant to become significant?" Well, the impotency of Natural Selection to fix beneficial mutations in a population seems like a pretty dog gone big problem for Darwinian presuppositions don't you think? And the impotency of Natural Selection is one of the main reasons that Darwinists (such as Graur and Moran,), were forced to adopt 'neutral theory'.
"many genomic features could not have emerged without a near-complete disengagement of the power of natural selection" Michael Lynch The Origins of Genome Architecture, intro "a relative lack of natural selection may be the prerequisite for major evolutionary advance" Mae Wan Ho Beyond neo-Darwinism Evolution by Absence of Selection "The publication in 1983 of Motoo Kimura’s The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura’s theories left the emergence of complex biological structures an enigma, but they played an important role in the local economy of belief. They allowed biologists to affirm that they welcomed responsible criticism. “A critique of neo-Darwinism,” the Dutch biologist Gert Korthof boasted, “can be incorporated into neo-Darwinism if there is evidence and a good theory, which contributes to the progress of science.” By this standard, if the Archangel Gabriel were to accept personal responsibility for the Cambrian explosion, his views would be widely described as neo-Darwinian." - David Berlinski
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 so the question becomes, "without natural selection as a driving force behind evolution, exactly where does this leave Darwinists?" Well, in the following article Larry Moran, (who denies even being a “Darwinist” anymore since he no longer believes Natural Selection to be 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
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 overwhelming ‘appearance of design’ that 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 with their new 'neutral theory', 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
bornagain77_{April 15, 2021
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Bornagain77: And the really good ones never get fixed in a population, So, how do changes in genomes get 'fixed' or made dominant? In other words: what causes a genome variant to become significant?JVL_{April 15, 2021
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And the really good ones never get fixed in a population,
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 waiting time problem in a model hominin population – 2015 Sep 17 John Sanford, Wesley Brewer, Franzine Smith, and John Baumgardner Excerpt: The program Mendel’s Accountant realistically simulates the mutation/selection process,,, Given optimal settings, what is the longest nucleotide string that can arise within a reasonable waiting time within a hominin population of 10,000? Arguably, 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]. This represents at least 75 million nucleotide changes in the human lineage, many of which must encode new information. 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. In this light, we suggest that a string of two specific mutations is a reasonable upper limit, in terms of the longest string length that is likely to evolve within a hominin population (at least in a way that is either timely or meaningful). 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. It is widely thought that a larger population size can eliminate the waiting time problem. If that were true, then the waiting time problem would only be meaningful within small populations. While our simulations show that larger populations do help reduce waiting time, we see that the benefit of larger population size produces rapidly diminishing returns (Table 4 and Fig. 4). 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/
bornagain77_{April 15, 2021
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Mohammadnursyamsu: In no way is it possible for all organisms to carry 4 billion years worth of random mutations with them. The really 'bad' ones kill the organism, sometimes before it's even 'born', and thus don't get passed on or 'stored'.JVL_{April 15, 2021
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Johnnyb: I think the ID perspective would be that a certain size is required for a certain amount of functionality/complexity, but that doesn’t equate to a certain size equalling that amount of functionality/complexity. A minimum size for a certain amount of 'complexity', sure, that makes sense.JVL_{April 15, 2021
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Bornagain77: Thanks for answering!JVL_{April 15, 2021
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JVL: I think the ID perspective would be that a certain size is required for a certain amount of functionality/complexity, but that doesn't equate to a certain size equalling that amount of functionality/complexity. I'm not really up on my biology of polyploidy, but it is my understanding that in the case of polyploidy, the function that the additional DNA is serving is largely structural. That is, you basically need more copies of the genes to support a larger cell size.johnnyb_{April 15, 2021
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In no way is it possible for all organisms to carry 4 billion years worth of random mutations with them. And natural selection is not efficient enough to weed out most all mutations, which mutations mostly do nothing much of anything. At least one must hypothesize some rational evaluation of the genome, like some mechanism that cuts away everything that was not activated up untill reproduction.mohammadnursyamsu_{April 15, 2021
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Of related interest as to what other functions that 'junk DNA' has now been found to have
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. As researchers deepened their analyses of what differentiates humans from other organisms at the DNA level, it became apparent that genes could not provide the explanation. In fact, only one genetic factor generally scaled with complexity. The only genomic features that increased in number as animals became more complicated were the regions of junk DNA. The more sophisticated an organism, the higher the percentage of junk DNA it contains. Only now are scientists really exploring the controversial idea that junk DNA may hold the key to (increasing) complexity. (p. 4),,," She goes on to spend the bulk of the book reviewing the numerous discoveries of function for non-coding "junk" DNA. Just a few of those include: * Structural roles such as packaging chromosomes and preventing DNA "from unravelling and becoming damaged," acting as "anchor points when chromosomes are shared equally between different daughter cells and during cell division," and serving as "insulation regions, restricting gene expression to specific regions of chromosomes." * Regulating gene expression, as "Thousands and thousands of regions of junk DNA are suspected to regulate networks of gene expression." * Introns are extremely important: The bits of gobbledygook between the parts of a gene that code for amino acids were originally considered to be nothing but nonsense or rubbish. They were referred to as junk or garbage DNA, and pretty much dismissed as irrelevant. ... But we now know that they can have a very big impact. (pp. 17-18) * Preventing mutations by separating out gene-coding DNA. * Controlling telomere length that can serve as a "molecular clock" that helps control aging. * Forming the loci for centromeres. * Activating X chromosomes in females. * Producing long non-coding RNAs which regulate Hox genes or regulating brain development, or serving as attachment points for histone-modifying enzymes helping to turn genes on and off. * Serving as promoters or enhancers for genes, or imprinting control elements for "the expression of the protein-coding genes." * Producing RNA which acts "as a kind of scaffold, directing the activity of proteins to particular regions of the genome." * Producing RNAs which can fold into three-dimensional shapes and perform functions inside cells, much like enzymes, changing the shapes of other molecules, or helping to build ribosomes. As she notes: "We've actually known about these peculiar RNA molecules for decades, making it yet more surprising that we have maintained such a protein-centric vision of our genomic landscape." (p. 146) * Serving as tRNA genes which produce tRNA molecules. These genes can also serve as insulators or spacers to stop transcription from spreading from gene to gene. * Development of the fingers and face; changing eye, skin, and hair color; affecting obesity. * Gene splicing and generating spliceosomes. * Producing small RNAs which also affect gene expression. http://www.evolutionnews.org/2015/04/a_new_book_on_j095611.html
Also of note,
Jonathan Wells Was Right: Non-coding DNA Continues to Show Function December 10, 2019 https://evolutionnews.org/2019/12/jonathan-wells-was-right-noncoding-dna-continues-to-show-function/
bornagain77_{April 15, 2021
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JVL asks, "So, are you saying you don’t know why Paris japonica’s genome is about 50 times the size of the human genome?" No, no one does, although some researchers may have better clues than others as to what those functional reasons are. i.e. There are functional considerations as to why a Designer may choose to have a genome that is that large. For instance, "Heterochromatin is not only essential for chromosome maintenance during cell division; it also poses specific threats to genome stability."
Nuclear membrane repairs the 'dark matter' of DNA - October 29, 2015 Excerpt: DNA exists inside of a cell's nucleus in two forms: euchromatin and heterochromatin. Euchromatin gets all of the attention because it encodes most of the genome, while heterochromatin, which is mostly composed of repeated DNA sequences, has long been ignored as "junk DNA." "Scientists are now starting to pay a lot of attention to this mysterious component of the genome," said Chiolo, assistant professor at the USC Dornsife College of Letters, Arts and Sciences. "Heterochromatin is not only essential for chromosome maintenance during cell division; it also poses specific threats to genome stability. Heterochromatin is potentially one of the most powerful driving forces for cancer formation, but it is the 'dark matter' of the genome. We are just beginning to unravel how repair works here." The reason why we don't experience thousands of cancers every day in our body is because we have incredibly efficient molecular mechanisms that repair the frequent damages occurring in our DNA. But those that work in heterochromatin are quite extraordinary.,,, Working with the fruit fly Drosophila melanogaster, the team observed that breaks in heterochromatin are repaired after damaged sequences move away from the rest of the chromosome to the inner wall of the nuclear membrane. There, a trio of proteins mends the break in a safe environment, where it cannot accidentally get tangled up with incorrect chromosomes. http://m.phys.org/news/2015-10-nuclear-membrane-dark-dna.html and, "for example, organisms with larger cell volumes (such as amoebas) tend to produce repetitive DNA, which serves structural purposes. As Thomas Cavalier-Smith explains, when cell size increases, “there is positive selection for a corresponding increase in nuclear volume; it is generally easier to achieve this by increasing the amount of DNA rather than by altering its folding parameters”
JVL then asks, "Do you think that most of the Paris japonica’s genome has some function?" Yes. JVL then asks, "Do you think that most of the Paris japonica’s genome is transcribed?" I don't know, but as with the structural considerations cited above, functionality is not limited a particular sequence being transcribed. In fact, what is termed 'poly-functionality', (John Sanford), is ubiquitous in and for DNA and is completely inexplicable on Darwinian presuppositions.
Multiple genetic codes Excerpt: Trifonov,, was also the first one to demonstrate[20] that there are multiple codes present in the DNA. He points out that even so called non-coding DNA has a function, i.e. contains codes, although different from the triplet code. Trifonov recognizes[19]:5–10 specific codes in the DNA, RNA and proteins:,, chromatin code (Trifonov 1980) RNA-to-protein translation code (triplet code) framing code (Trifonov 1987) translation pausing code (Makhoul & Trifonov 2002) protein folding code (Berezovsky, Grosberg & Trifonov 2000) fast adaptation codes (Trifonov 1989) binary code (Trifonov 2006) genome segmentation code (Kolker & Trifonov 1995) The codes can overlap[19]:10 each other so that up to 4 different codes can be identified in one DNA sequence (specifically a sequence involved in a nucleosome). According to Trifonov, other codes are yet to be discovered. http://en.wikipedia.org/wiki/Edward_Trifonov#Multiple_genetic_codes 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 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. 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
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Bornagain77: And wants to know the precise functions for the larger genomes when he knows well that nobody on the face of earth, due to the complexity being dealt with, can give an exact and concrete answer to that question. I wasn't looking for an exact and concrete answer; I just wondered what the ID perspective on the issue is. So, are you saying you don't know why Paris japonica's genome is about 50 times the size of the human genome? Do you think that most of the Paris japonica's genome has some function? Do you think that most of the Paris japonica's genome is transcribed?JVL_{April 15, 2021
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Johnnyb: Probably polyploidy. Why do you ask? To see if there is an ID perspective on the issue.JVL_{April 15, 2021
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JVL claims that "You didn’t actually answer my question" Yet, actually I did, I stated,
"it is fairly disingenuous for Darwinists to insist that most of the genome must be non-functional junk simply because genome sizes vary between species. Again, there are several functional considerations as to why it would be advantageous to have varying genome sizes. Given the fact that the coding in a genome of a living organism is, of necessity, orders of magnitude more complex than anything man has thus far programmed in computers, (after all computers don’t come close to reproducing themselves like living organisms do), and considering how little we actually know about the genome due to the sheer complexity we are dealing with, then I considered it fairly hubristic, and very premature, for any Darwinist to conclude that any DNA that they personally don’t know the function of must be non-functional junk. Indeed, besides hubris, it takes a certain amount of willful blindness on Moran’s part to overlook the extreme and staggering levels of complexity that we actually dealing with in life and say to everyone else, ‘90% of Human DNA must be junk I tell ya!”
Maybe JVL didn't like the answer? Maybe JVL is just playing games? And wants to know the precise functions for the larger genomes when he knows well that nobody on the face of earth, due to the complexity being dealt with, can give an exact and concrete answer to that question. But such lack of precise knowledge for genome sizes certainly does not mean that most of the genome must be junk, no matter how much JVL, and other Darwinists, may want to twist the argument in that direction! Again, it is severely disingenuous for them to suggest that it must be junk given the complexity being dealt with, and the multiple reasons that exist for why the genome sizes may be as as they are.. Moreover, since JVL is asking about a plant genome, it is interesting to note that both Dr. John Sanford, (who has done work that directly refutes Moran's Genetic Load argument), and Dr. Wolf-Ekkehard Lönnig, (who is no lightweight in the ID movement either), are both top of the class in regards to work done in plant genetics. Dr. Wolf-Ekkehard Lönnig is (retired) Senior Scientist (Biology) at the Max Planck Institute for Plant Breeding Research in Cologne, Germany, and has done extensive research on plant breeding. And here is Dr. John Sanford's resume once again,
Dr John Sanford, A Cornell University Professor for more than 25 years, John has been semi-retired since 1998. His Ph.D. was in plant breeding and plant genetics. While a professor at Cornell, John has trained graduate students and conducted genetic research at the New York State Agricultural Experiment Station in Geneva, NY. During this time, John bred new crop varieties using conventional breeding and then became heavily involved in the newly-emerging field of plant genetic engineering. John has published over 80 scientific publications and has been granted over 30 patents. His most significant scientific contributions involve three inventions, the biolistic (“gene gun”) process, pathogen-derived resistance, and genetic immunization. A large fraction of the transgenic crops (in terms of numbers and acreage) grown in the world today were genetically engineered using the gene gun technology developed by John and his collaborators. John also started two biotech enterprises derived from his research, Biolistics, Inc., and Sanford Scientific, Inc. John still holds a position at Cornell (Courtesy Associate Professor), but has largely retired from Cornell and has started a small non-profit organization, Feed My Sheep Foundation.
John Sanford, with his almost unmatched expertise in plant genetics, has been nothing less than a one man wrecking ball towards Darwinian claims. For instance he, fairly recently, overturned Fisher's Theorem in population genetics, (which is, IMHO, certainly not a minor thing for him to do, scientifically speaking)
Fisher’s Famous Theorem Has Been “Flipped” - January 2018 https://www.geneticentropy.org/latest-development
Dr. Wolf-Ekkehard Lönnig is no slouch either. For instance, from his expertise in plant genetics, he asks the following question, "Many of these researchers also raise the question (among others), why — even after inducing literally billions of induced mutations and (further) chromosome rearrangements — all the important mutation breeding programs have come to an end in the Western World instead of eliciting a revolution in plant breeding, either by successive rounds of selective “micromutations” (cumulative selection in the sense of the modern synthesis), or by “larger mutations” … and why the law of recurrent variation is endlessly corroborated by the almost infinite repetition of the spectra of mutant phenotypes in each and any new extensive mutagenesis experiment (as predicted) instead of regularly producing a range of new systematic species…"
Peer-Reviewed Research Paper on Plant Biology Favorably Cites Intelligent Design and Challenges Darwinian Evolution - Casey Luskin - December 29, 2010 Excerpt: Many of these researchers also raise the question (among others), why — even after inducing literally billions of induced mutations and (further) chromosome rearrangements — all the important mutation breeding programs have come to an end in the Western World instead of eliciting a revolution in plant breeding, either by successive rounds of selective “micromutations” (cumulative selection in the sense of the modern synthesis), or by “larger mutations” … and why the law of recurrent variation is endlessly corroborated by the almost infinite repetition of the spectra of mutant phenotypes in each and any new extensive mutagenesis experiment (as predicted) instead of regularly producing a range of new systematic species… (Wolf-Ekkehard Lönnig, “Mutagenesis in Physalis pubescens L. ssp. floridana: Some Further Research on Dollo’s Law and the Law of Recurrent Variation,” Floriculture and Ornamental Biotechnology Vol. 4 (Special Issue 1): 1-21 (December 2010).) https://evolutionnews.org/2010/12/peer-reviewed_research_paper_o/
Perhaps JVL would like to take a stab at honestly answering that honest question about the stunning lack of evidence for Darwinian claims, (after inducing literally billions of induced mutations and (further) chromosome rearrangements), rather than playing games with a question that he knows nobody can give a firm and honest answer to at the present moment in time,, due to the complexity involved and our present lack of knowledge?
Genesis 1:12 The land produced vegetation: plants bearing seed according to their kinds and trees bearing fruit with seed in it according to their kinds. And God saw that it was good.
bornagain77_{April 14, 2021
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JVL: Probably polyploidy. Why do you ask?johnnyb_{April 14, 2021
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Bornagain77: You didn't actually answer my question which was why do you think the genome of a plant is orders of magnitude bigger than that of a human. Is that because you can't answer that question or because you won't?JVL_{April 14, 2021
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JVL asks about the C-value argument for junk DNA. Which Moran stated as such
C-Value Paradox A comparison of genomes from closely related species shows that genome size can vary by a factor of ten or more. The only reasonable explanation is that most of the DNA in the larger genomes is junk.
Jonathan McLatchie addressed Larry Moran's argument and shows why there are many functional considerations as to why it would be advantageuous to have widely varying genome sizes. It is a lengthy article, so I will cite only the conclusion, but unbiased readers can dig into it and read it and judge for themselves whether Moran's argument survived McLatchie's critique.
Why the “Onion Test” Fails as an Argument for “Junk DNA” - Jonathan McLatchie - November 2, 2011 Conclusion The so-called onion test, or indeed the “C-value enigma,” is predicated on unsupportable assumptions about the physiological effects of — and/or requirements for — larger genomes, many of which are contradicted by the scientific evidence. As we learn ever more about the nature and functional inter-dependency of the genome, as the extent of genomic “dark matter” continues to shrink, those who continue to advocate the view that the preponderance of our genome is non-functional should find these facts disconcerting. https://evolutionnews.org/2011/11/why_the_onion_test_fails_as_an/
Jonathan McLatchie has a briefer article on the subject here:
Biologist John Mattick on Junk DNA, ENCODE, and Intelligent Design Jonathan McLatchie - August 9, 2013 Excerpt: There are a number of ways in which the C-value paradox could be resolved, however, and it is likely a combination of a number of factors. We now know that through RNA splicing after transcription, a single gene can produce more than one protein. Humans, for instance, produce around 100,000 proteins from 22,000 structural genes. Thus, an organism’s complexity cannot be viewed as a simple function of the number of genes it possesses. Second, there is in fact a relationship between biological complexity and the extent of gene regulation. Roughly 9% of genes in Homo sapiens encode transcription factors. In Drosophila melanogaster, only about 5.5% of genes code for transcription factors; 4.2% of the genes of Caenorhabditis elegans code for transcription factors; only 3.4% of genes code for transcription factors in the budding yeast Saccharomyces cerevisiae (see Table 2 of Messina et al., 2004). When coupled with an increased network of transcriptional enhancers and promoters, such a difference could result in a much larger set of gene expression patterns. This could lead to a non-linear increase in organismal complexity (e.g. see Levine and Tjian, 2003). There are other factors to consider as well — for example, organisms with larger cell volumes (such as amoebas) tend to produce repetitive DNA, which serves structural purposes. As Thomas Cavalier-Smith explains, when cell size increases, “there is positive selection for a corresponding increase in nuclear volume; it is generally easier to achieve this by increasing the amount of DNA rather than by altering its folding parameters” (Cavalier-Smith, 2005). Another thing to consider is that time taken to transcribe long stretches of non-coding DNA such as introns can be of functional consequence (e.g. see Swinburne and Silver, 2011). There are thus so many different factors needing to be taken into account that it is difficult to make a watertight argument for junk DNA based on the C-value paradox. https://evolutionnews.org/2013/08/john_mattick_on/
And Jonathan Well, author of "The Myth Of Junk DNA", weighs in on the 'onion test' here
The Onion Test Is a Red Herring - Jonathan Wells - March 11, 2015 Excerpt: In 2007, Canadian biologist T. Ryan Gregory wrote: "Some non-coding DNA is proving to be functional, but this is still a minority of the noncoding DNA, and there is always the issue of the onion test when considering all non-coding DNA to be functional."[22] The "onion test," according to Gregory, "is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?"[23] The difference between the DNA content of an onion cell and that of a human cell is one piece of a larger puzzle called the "C-value paradox" or "C-value enigma."[24-30] Biologists have long known that the DNA content (the "C-value") of eukaryotic cells varies by a factor of several thousand, with no apparent correlation to organismal complexity or to the number of protein-coding genes. There is a strong positive correlation, however, between the amount of DNA and the volume of a cell and its nucleus — which affects the rate of cell growth and division.[31-32] Furthermore, in mammals there is a negative correlation between genome size and the rate of metabolism.[33] Bats have very high metabolic rates and relatively small genomes.[34-35] In birds, there is a negative correlation between C-value and resting metabolic rate.[36-37] In salamanders, there is also a negative correlation between genome size and the rate of limb regeneration.[38] Gregory has written extensively on the C-value enigma,[39-42] and various hypotheses have been proposed to explain it.[43-48] One of those hypotheses attempts to explain the enigma by the accumulation of "junk DNA" or "selfish DNA," but — as Gregory himself has pointed out — that explanation cannot make sense of the correlations noted above.[49] "Under the traditional junk DNA and selfish DNA theories," Gregory wrote in 2005, "the relationship between genome size and cell size is considered purely coincidental." Since this approach is incapable of explaining the correlation between C-value and cell size, "the strictly coincidental interpretation has been rejected."[50] But if Gregory rejects the accumulation of "junk DNA" as an explanation for the C-value enigma, why does he use the "onion test" to defend the notion that most non-protein-coding DNA is nonfunctional? Something peculiar is going on here. Let’s take a closer look at his reasoning. First, Gregory directs his challenge to "anyone who thinks they have come up with a universal function for non-coding DNA." Yet there probably is no such person. As we have seen, scientists know of many functions for non-protein-coding DNA. Nobody claims that there is "a universal function" that applies both to mammals and to onions. Based on the evidence, scientists have proposed that non-protein-coding intronic DNA helps to regulate alternative splicing in brain cells, and that non-protein-coding repetitive DNA plays a role in placental development. Why should those scientists justify their proposals by referring to onions, which have neither brains nor placentas? Second, Gregory makes it clear that his true goal is to defend Darwinian evolution and attack intelligent design. One way he does this is by misrepresenting the latter. The same year he proposed the onion test he wrote that in order for ID to be considered scientific its proponents must "specify the basis for assuming that all non-coding DNA must be functional."[51] But ID proponents do not assume that all non-coding DNA must be functional. They infer that it is unlikely that most of our DNA would be nonfunctional; therefore, scientists should continue looking for functions.[52-53] Gregory misrepresents not only ID but also the logic of the argument. In 2007 he wrote: "It is commonly suggested by anti-evolutionists that recent discoveries of function in non-coding DNA support intelligent design and refute ‘Darwinism.’"[54] But Dawkins, Futuyma, Shermer, Collins, Kitcher, Miller, Coyne, and Avise argue exactly the opposite: They all claim that non-protein-coding DNA supports Darwinism and refutes intelligent design. It is THEIR claim that is the issue here — and "recent discoveries of function in non-coding DNA" refute it. Gregory stands the debate on its head. So the onion test is a red herring. Why onion cells have five times as much DNA as human cells is an interesting question, but it poses no challenge to the growing evidence against the myth of junk DNA. https://evolutionnews.org/2015/03/onion_expose_ca/
Thus it is fairly disingenuous for Darwinists to insist that most of genome must be non-functional junk simply because genome sizes vary between species. Again, there are several functional considerations as to why it would be advantageous to have varying genome sizes. Given the fact that the coding in a genome of a living organism is, of necessity, orders of magnitude more complex than anything man has thus far programmed in his computers, (after all computers don't come close to reproducing themselves like living organisms do), and considering how little we actually know about the genome due to the sheer complexity we are dealing with, then I considered it fairly hubristic, and very premature, for any Darwinist to conclude that any DNA that they personally don't know the function of must be non-functional junk. Indeed, besides hubris, it takes a certain amount of willful blindness on Moran's part to overlook the extreme and staggering levels of complexity that we actually dealing with in life and say to everyone else, '90% of Human DNA must be junk I tell ya!"bornagain77_{April 14, 2021
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There are some evolutionary biologists that argue without “junk” DNA there could be no evolution. It’s where over time new proteins are being born. I have not seen any evidence that this has actually happened but it is a hypothetical function of junk DNA for some. It was first put forth here by Allen MacNeill years ago. One way of testing this proposition it to compare genomes of similar species which are thought to have a common ancestor. Active proteins in one species should be present in the junk DNA of the so called cousin species but not fully developed. As far as I know there are no examples of almost protein generating gene sequences that are similar to functional genetic sequences in supposedly related species.jerry_{April 14, 2021
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Just curious: Why do y'all think Paris japonica's genome has 149 billion nucleotides whereas the human genome has only 3 billion? http://thatslifesci.com/2019-05-06-Biggest-genome-of-them-all-JBarnett/JVL_{April 14, 2021
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Moran starts with "Nothing in biology makes sense if you aren't using evolution as your baseline." Hogwash. Reality is a lot more complicated. Some changes are unquestionably caused by natural selection and variation, though the variation is usually epigenetic, not cosmic rays. Other kinds of changes and structures can't possibly be explained by variation and selection. Whenever the both-and pattern (irreducible complexity) appears, selection couldn't have caused it. Physically and logically impossible.polistra_{April 14, 2021
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Moreover, there are a couple of very good theoretical reasons why Darwinists will never ever be able to construct a realistic mathematical model for Darwin’s theory. Theoretical reason number 1 for why Darwinists will never construct a realistic mathematical model of evolution: Darwinian evolution is based on the framework of reductive materialism which holds the immaterial realm to be illusory, and/or a ‘epiphenomena’, of the material realm. Yet mathematics, which evolution absolutely needs if it is ever to be considered a real and proper scientific theory,, is profoundly immaterial in its foundational essence.
Naturalism and Self-Refutation – Michael Egnor – January 31, 2018 Excerpt: Mathematics is certainly something we do. Is mathematics “included in the space-time continuum [with] basic elements … described by physics”?,,, What is the physics behind the Pythagorean theorem? After all, no actual triangle is perfect, and thus no actual triangle in nature has sides such that the Pythagorean theorem holds. There is no real triangle in which the sum of the squares of the sides exactly equals the square of the hypotenuse. That holds true for all of geometry. Geometry is about concepts, not about anything in the natural world or about anything that can be described by physics. What is the “physics” of the fact that the area of a circle is pi multiplied by the square of the radius? And of course what is natural and physical about imaginary numbers, infinite series, irrational numbers, and the mathematics of more than three spatial dimensions? Mathematics is entirely about concepts, which have no precise instantiation in nature,,, https://evolutionnews.org/2018/01/naturalism-and-self-refutation/ What Does It Mean to Say That Science & Religion Conflict? – M. Anthony Mills – April 16, 2018 Excerpt: In fact, more problematic for the materialist than the non-existence of persons is the existence of mathematics. Why? Although a committed materialist might be perfectly willing to accept that you do not really exist, he will have a harder time accepting that numbers do not exist. The trouble is that numbers — along with other mathematical entities such as classes, sets, and functions — are indispensable for modern science. And yet — here’s the rub — these “abstract objects” are not material. Thus, one cannot take science as the only sure guide to reality and at the same time discount disbelief in all immaterial realities. https://www.realclearreligion.org/articles/2018/04/16/what_does_it_mean_to_say_that_science_and_religion_conflict.html
With their materialistic theory, Darwinists simply can't ever get to the 'upper story' of immaterial mathematics (see Nancy Pearcey's book "Total Truth"). As the old joke goes, 'you can't get there from here'! Theoretical reason number 2 for why Darwinists will never build a realistic mathematical model of evolution: Darwinists hold the randomness postulate as one of their primary presuppositions within their theory. Yet the randomness postulate itself is what prevents a realistic mathematical model from ever built for Darwinian evolution. In a paper entitled “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory, Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution”, Murray Eden stated that, “It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws-physical, physico-chemical, and biological.”
“It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws-physical, physico-chemical, and biological.” Murray Eden, “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory,” Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, editors Paul S. Moorhead and Martin M. Kaplan, June 1967, p. 109.
The reason why “the randomness postulate is highly implausible” towards Darwinists ever building a realistic mathematical model for evolution is simply because the amazing predictive power of all our mathematical equations in physics is based upon the fact that all our mathematical equations in physics are based on laws of nature. And it is exactly that unchanging regularity of the laws of nature that enable physicists to build realistic mathematical models that can accurately predict the future. Yet it is impossible, by definition, for a mathematical theory based primarily on the postulate of randomness, and not on a law of nature, to be able to accurately predict the future. In fact, unpredictability is literally the definition of randomness.
ran·dom·ness noun noun: randomness; plural noun: randomnesses 1. the quality or state of lacking a pattern or principle of organization; unpredictability.
Moreover, Darwinists simply have no known law of nature that they can appeal to in order to rescue them from this ‘unpredictable’ dilemma that their randomness postulate has forced them into. As Ernst Mayr himself conceded, “In biology, as several other people have shown, and I totally agree with them, there are no natural laws in biology corresponding to the natural laws of the physical sciences.”
The Evolution of Ernst: Interview with Ernst Mayr – 2004 (page 2 of 14) Excerpt: biology (Darwinian Evolution) differs from the physical sciences in that in the physical sciences, all theories, I don’t know exceptions so I think it’s probably a safe statement, all theories are based somehow or other on natural laws. In biology, as several other people have shown, and I totally agree with them, there are no natural laws in biology corresponding to the natural laws of the physical sciences. ,,, And so that’s what I do in this book. I show that the theoretical basis, you might call it, or I prefer to call it the philosophy of biology, has a totally different basis than the theories of physics. https://www.scientificamerican.com/media/pdf/0004D8E1-178C-10EB-978C83414B7F012C.pdf
In the following article, Roger Highfield makes much the same observation as Ernst Mayr and states, ,,, Whatever the case, those universal truths—’laws’—that physicists and chemists all rely upon appear relatively absent from biology.
WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT? Evolution is True – Roger Highfield – January 2014 Excerpt: If evolutionary biologists are really Seekers of the Truth, they need to focus more on finding the mathematical regularities of biology, following in the giant footsteps of Sewall Wright, JBS Haldane, Ronald Fisher and so on. ,,, Whatever the case, those universal truths—’laws’—that physicists and chemists all rely upon appear relatively absent from biology. Little seems to have changed from a decade ago when the late and great John Maynard Smith wrote a chapter on evolutionary game theory for a book on the most powerful equations of science: his contribution did not include a single equation. http://www.edge.org/response-detail/25468
Moreover, besides Evolutionists having no law of nature to appeal to so as to rescue them from the ‘unpredictability’ of their randomness postulate, the second law of thermodynamics, entropy, a law with great mathematical explanatory power in science directly, or almost directly, contradicts the primary Darwinian claim that greater and greater levels of functional complexity can easily be had and/or ‘naturally selected’ for over long periods of time. Indeed, entropy’s main claim is that, over long periods of time, everything in the universe will eventually decay into simpler and simpler states until what is termed thermodynamic equilibrium is finally reached. Thus, not only does evolution have no law of nature to appeal to so as to ever be able to build a realistic mathematical model upon, evolution is also strongly contradicted by one of our most powerful, most mathematical, laws in science. And as Eddington himself stated, “if your theory is found to be against the Second Law of Thermodynamics I can give you no hope; there is nothing for it (but) to collapse in deepest humiliation.”
“The law that entropy always increases holds, I think, the supreme position among the laws of Nature. If someone points out to you that your pet theory of the universe is in disagreement with Maxwell's equations - then so much the worse for Maxwell's equations. If it is found to be contradicted by observation - well, these experimentalists do bungle things sometimes. But if your theory is found to be against the Second Law of Thermodynamics I can give you no hope; there is nothing for it to collapse in deepest humiliation.” - Arthur Eddington, New Pathways in Science
Thus in conclusion, Dr. Moran has no empirical evidence that his genetic load argument is correct and that 90% of the genome must be junk. In fact, his argument is directly contradicted by ENCODE research and by subsequent research which consistently finds widespread functionality across the entire genome. Moreover, Dr. Moran’s theoretical reasons for considering the genetic load argument to be valid are theoretical reason that are more realistically used, (as Dr. John Sanford has done in his numerical simulations), as theoretical reasons for why we should consider Darwin’s theory to be invalid. And finally, the existence of immaterial mathematics itself, as well as the randomness postulate itself, are both VERY strong theoretical reasons for considering Darwin’s materialistic theory to forever be beyond the scope of ever being considered a true and rigid scientific theory that is based upon a rigid, (and ‘immaterial’ I might add), foundation of mathematics.
1 Thessalonians 5:21 but test everything; hold fast what is good.
Supplemental note:
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! https://uncommondescent.com/intelligent-design/discovery-of-useful-junk-dna-has-outstripped-the-discovery-of-protein-coding-genes-by-a-factor-of-five/#comment-727174
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Seversky, via Moran, claims that,
Genetic Load Every newborn human baby has about 100 mutations not found in either parent. If most of our genome contained functional sequence information, then this would be an intolerable genetic load. Only a small percentage of our genome can contain important sequence information suggesting strongly that most of our genome is junk.
And in the following article Moran claims that, because of Genetic Load, upwards to 90% of our genome 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
First off, it is important to note that Moran's claim that 90% of our genome must be junk is not derived from any direct empirical observation, but instead Moran's belief that 90% of the genome must be junk is forced upon Moran because of the mathematics of population genetics. Larry Moran’s claim for 90% Junk DNA, no matter how much Moran may act like it does not matter, is simply in direct conflict with the empirical evidence itself. Specifically, the trend in scientific research over the past several years, (after the ENCODE results in 2012 found widespread functionality across the entire genome), has certainly not been supportive of Moran’s claim that the vast majority of our genome must be Junk DNA.
“Discovery Of Useful “Junk DNA” “Has Outstripped The Discovery Of Protein-Coding Genes By A Factor Of Five” – March 2021 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/
Contrary to whatever Moran may believe, empirical evidence, (not theoretical posturing, via mathematics, as he is currently doing), has the final say in science. As Richard Feynman of quantum electrodynamics fame stated, “If it disagrees with experiment, it’s wrong. In that simple statement is the key to science. It doesn’t make any difference how beautiful your guess is, it doesn’t matter how smart you are who made the guess, or what his name is … If it disagrees with experiment, it’s wrong. That’s all there is to it.”
“Now I’m going to discuss how we would look for a new law. In general, we look for a new law by the following process. First, we guess it (audience laughter), no, don’t laugh, that’s the truth. Then we compute the consequences of the guess, to see what, if this is right, if this law we guess is right, to see what it would imply and then we compare the computation results to nature or we say compare to experiment or experience, compare it directly with observations to see if it works. If it disagrees with experiment, it’s wrong. In that simple statement is the key to science. It doesn’t make any difference how beautiful your guess is, it doesn’t matter how smart you are who made the guess, or what his name is … If it disagrees with experiment, it’s wrong. That’s all there is to it.” - Richard Feynman The Scientific Method-Richard Feynman https://www.youtube.com/watch?v=OL6-x0modwY
Thus, as far as the empirical evidence itself is concerned, Moran’s claim that 90% of the genome must be junk is simply wrong. And no amount of theoretical posturing on his part is ever going to eliminate his direct conflict with the empirical evidence itself. Only empirical evidence itself can possibly eliminate his conflict, and, as was pointed out, the trend in empirical evidence over the last several years gives no indication of ever giving Moran reprieve from his conflict with the empirical evidence. Moreover, Moran’s theoretical argument, (via Genetic Load and/or Neutral Theory), is simply not nearly as strong as Moran presupposes it to be. Dr. John Sanford, (who’s resume I would stack up against Larry Moran’s resume any day of the week),
Dr John Sanford, A Cornell University Professor for more than 25 years, John has been semi-retired since 1998. His Ph.D. was in plant breeding and plant genetics. While a professor at Cornell, John has trained graduate students and conducted genetic research at the New York State Agricultural Experiment Station in Geneva, NY. During this time, John bred new crop varieties using conventional breeding and then became heavily involved in the newly-emerging field of plant genetic engineering. John has published over 80 scientific publications and has been granted over 30 patents. His most significant scientific contributions involve three inventions, the biolistic (“gene gun”) process, pathogen-derived resistance, and genetic immunization. A large fraction of the transgenic crops (in terms of numbers and acreage) grown in the world today were genetically engineered using the gene gun technology developed by John and his collaborators. John also started two biotech enterprises derived from his research, Biolistics, Inc., and Sanford Scientific, Inc. John still holds a position at Cornell (Courtesy Associate Professor), but has largely retired from Cornell and has started a small non-profit organization, Feed My Sheep Foundation.
Dr. John Sanford, (who’s resume I would stack up against Larry Moran’s resume any day of the week), finds severe problems with Moran’s theoretical argument. As Dr. John Sanford stated in his book “Genetic Entropy", "Kimura apparently never considered his cost arguments (Genetic Load argument) 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 (Genetic Load argument) 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 Of note:
And in 2013, Dr. John Sanford and company, via numerous computer simulations which studied human mutation accumulation under a wide-range of circumstances, found that, “Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space. This appears to be primarily due to the predominance of nearly-neutral mutations. The problem of mutation accumulation becomes severe when mutation rates are high. Numerical simulations strongly support earlier theoretical and mathematical studies indicating that human mutation accumulation is a serious concern.”
Using Computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load John Sanford1, John Baumgardner2, Wes Brewer3, Paul Gibson4, and Walter ReMine5 Abstract. Long-standing theoretical concerns about mutation accumulation within the human population, (i.e. the problem of genetic load) can now be addressed with numerical simulation. We apply a biologically realistic forward-time population genetics program to study human mutation accumulation under a wide-range of circumstances. Using realistic estimates for the relevant biological parameters, we investigate the rate of mutation accumulation, the distribution of the fitness effects of the accumulating mutations, and the overall effect on mean genotypic fitness. Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space. This appears to be primarily due to the predominance of nearly-neutral mutations. The problem of mutation accumulation becomes severe when mutation rates are high. Numerical simulations strongly support earlier theoretical and mathematical studies indicating that human mutation accumulation is a serious concern. Our simulations indicate that reduction of mutation rate is the most effective means for addressing this problem. http://bioinformatics.cau.edu.cn/lecture/chinaproof.pdf
In their Genetic Load argument, Evolutionists unrealistically hold that, “As the load of deleterious mutations grows over time, the pool of possible beneficial mutations also grows with it. This eventually leads to an equilibrium, preventing fitness decline beyond a certain point.,,,,” Yet Darwinists have no rational basis for presupposing that. As Dr. John Sanford stated in 2020, ’This argument is: 1) merely dismissive, 2) categorically wrong, and 3) without a rational or data-driven basis. Obviously, rapidly accumulating deleterious mutations do not lead to more and more beneficial mutations. Rather, the much more abundant deleterious mutations effectively overwhelm and negate the fitness effects of the extremely rare beneficial mutations.” And Dr. John Sanford further states, “We have done thousands of numerical simulations showing this. Even given the most generous parameter settings, the near-neutral bad mutations consistently accumulate about 1000 times faster than the beneficial mutations.”
Responding to supposed refutations of genetic entropy from the ‘experts’ by Paul Price, Robert Carter and John Sanford - 1 December 2020 Excerpt: 1 Mutations & Equilibrium Claim: As the load of deleterious mutations grows over time, the pool of possible beneficial mutations also grows with it. This eventually leads to an equilibrium, preventing fitness decline beyond a certain point.,,,, Comments from Dr Sanford: This argument is: 1) merely dismissive, 2) categorically wrong, and 3) without a rational or data-driven basis. Obviously, rapidly accumulating deleterious mutations do not lead to more and more beneficial mutations. Rather, the much more abundant deleterious mutations effectively overwhelm and negate the fitness effects of the extremely rare beneficial mutations. The ratio of bad to good mutations is, minimally, 1000:1. With or without selection, bad mutations will always accumulate much more rapidly that beneficial mutations. We have done thousands of numerical simulations showing this. Even given the most generous parameter settings, the near-neutral bad mutations consistently accumulate about 1000 times faster than the beneficial mutations. https://creation.com/genetic-entropy-defense
Moreover Moran, nor any other Evolutionist, has ever constructed a realistic computer simulation that would tell us if Evolution, (much less the Genetic Load argument in particular), is correct, or even if it is feasible. As Robert Marks and company have found, (via extensive analysis of evolutionary algorithms), “there exists no model successfully describing undirected Darwinian evolution. According to our current understanding, there never will be.,,,”
Top Ten Questions and Objections to ‘Introduction to Evolutionary Informatics’ – Robert J. Marks II – June 12, 2017 Excerpt: “There exists no model successfully describing undirected Darwinian evolution. Hard sciences are built on foundations of mathematics or definitive simulations. Examples include electromagnetics, Newtonian mechanics, geophysics, relativity, thermodynamics, quantum mechanics, optics, and many areas in biology. Those hoping to establish Darwinian evolution as a hard science with a model have either failed or inadvertently cheated. These models contain guidance mechanisms to land the airplane squarely on the target runway despite stochastic wind gusts. Not only can the guiding assistance be specifically identified in each proposed evolution model, its contribution to the success can be measured, in bits, as active information.,,,”,,, “there exists no model successfully describing undirected Darwinian evolution. According to our current understanding, there never will be.,,,” https://evolutionnews.org/2017/06/top-ten-questions-and-objections-to-introduction-to-evolutionary-informatics/
bornagain77_{April 14, 2021
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5 replies to Seversky an Moron: 1. First off, a child is not a mutated parent. Second, you can be different than the parents yet like someone else. So absolutely new is not required. Third, nothing of the rest follows. 2. "The ONLY reasonable explanation... " is an illogical statement. You can't prove that even theoretically. Organisms differ - genomes differ. Period. 3. "Nothing in biology makes sense except..." is another illogical statement. It's your problem when many things don't make sense to you. In addition, "... evolution is perfectly consistent..." is just affirming the consequent, so another fallacy. 4. If there's so much junk as you claim, then" evolution " is false as it fails to optimize as it pretends in " natural selection of the fittest " and all the other nonsense . Second, the genome is already too small to be all and do all as claimed. If any part of it is junk, then this problem is even more acute. So "modern synthesis" fails too. 5. "Most of the genome is not conserved" presupposes "evolution". This is just awful circular logic. And more "consistent with..." is another fallacy as described.Nonlin.org_{April 13, 2021
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Five Things You Should Know if You Want to Participate in the Junk DNA Debate Here are five things you should know if you want to engage in a legitimate scientific discussion about the amount of junk DNA in a genome. Genetic Load Every newborn human baby has about 100 mutations not found in either parent. If most of our genome contained functional sequence information, then this would be an intolerable genetic load. Only a small percentage of our genome can contain important sequence information suggesting strongly that most of our genome is junk. C-Value Paradox A comparison of genomes from closely related species shows that genome size can vary by a factor of ten or more. The only reasonable explanation is that most of the DNA in the larger genomes is junk. Modern Evolutionary Theory Nothing in biology makes sense except in the light of population genetics. The modern understanding of evolution is perfectly consistent with the presence of large amounts of junk DNA in a genome. Pseudogenes and broken genes are junk More than half of our genomes consists of pseudogenes, including broken transposons and bits and pieces of transposons. A few may have secondarily acquired a function but, to a first approximation, broken genes are junk. Most of the genome is not conserved Most of the DNA sequences in large genomes is not conserved. These sequences diverge at a rate consistent with fixation of neutral alleles by random genetic drift. This strongly suggests that it does not have a function although one can't rule out some unknown function that doesn't depend on sequence. If you want to argue against junk DNA then you need to refute or rationalize all five of these observations. Posted by Laurence A. Moran at Thursday, July 04, 2013
Seversky_{April 13, 2021
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