Here’s a lay-friendly explanation of the critical role “junk DNA” plays in mammalian development

_{Denyse O'Leary

October 19, 2021

'Junk DNA', Intelligent Design}

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The paper is paywalled but U Berkeley provides some background:

Nearly half of our DNA has been written off as junk, the discards of evolution: sidelined or broken genes, viruses that got stuck in our genome and were dismembered or silenced, none of it relevant to the human organism or human evolution …
A new study led by researchers at University of California, Berkeley, and Washington University explored the function of one component of this junk DNA, transposons, which are selfish DNA sequences able to invade their host genome. The study shows that at least one family of transposons — ancient viruses that have invaded our genome by the millions — plays a critical role in viability in the mouse, and perhaps in all mammals. When the researchers knocked out a specific transposon in mice, half their mouse pups died before birth.
This is the first example of a piece of “junk DNA” being critical to survival in mammals.
Robert Sanders, “So-called junk DNA plays critical role in mammalian development” at Berkeley News (October 18, 2021)

Odd, isn’t it, that ancient invading viruses would turn out to be critical for survival.

You may also wish to read: Term “junk DNA” critiqued at journal. But now remember the history! “The days of ‘junk DNA’ are over…”? So the house is clearly supporting this move away from the Darwinian position. Oh yes, let’s not forget that “junk DNA” was very much a Darwinian position. Most or all of the Darwinian Bigs signed onto junk DNA as part of their thesis about the unguided nature of life. The big question will doubtless be put off for now: Why does it only count if Darwinian predictions are right but never if they are wrong?

and

Casey Luskin reflects on the “official” demise of the term “junk DNA.” Luskin: “these authors remember a day when ‘the common doctrine was that the nonprotein coding part of eukaryotic genome’ consisted of ‘“useless sequences, often organized in repetitive elements.’” Good. Keep the history alive. It won’t be very long before Darwinians start claiming that they never thought it was junk. Then they will start insinuating that WE said it was junk. No, that doesn’t make any sense but if the history is forgotten, it doesn’t need to either.

Comments

Thanks for the references, Bornagain77. I didn't realize just how easily Dawkins pivots his adamant pronouncements without missing a beat. Unfortunately, he's been given a pass by the other Darwinists. After all, the narrative of "scientific" materialistic naturalism must be protected at all costs! I'm glad, that at least some researchers such as Haldane and Sternberg were honest. -QQuerius_{October 27, 2021
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Querius, Here is a short History of how the Junk DNA argument came about
Haldane’s Dilemma Excerpt: Haldane was the first to recognize there was a cost to selection which limited what it realistically could be expected to do. He did not fully realize that his thinking would create major problems for evolutionary theory. He calculated that in man it would take 6 million years to fix just 1,000 mutations (assuming 20 years per generation).,,, Man and chimp differ by at least 150 million nucleotides representing at least 40 million hypothetical mutations (Britten, 2002). So if man evolved from a chimp-like creature, then during that process there were at least 20 million mutations fixed within the human lineage (40 million divided by 2), yet natural selection could only have selected for 1,000 of those. All the rest would have had to been fixed by random drift – creating millions of nearly-neutral deleterious mutations. This would not just have made us inferior to our chimp-like ancestors – it surely would have killed us. Since Haldane’s dilemma there have been a number of efforts to sweep the problem under the rug, but the problem is still exactly the same. ReMine (1993, 2005) has extensively reviewed the problem, and has analyzed it using an entirely different mathematical formulation – but has obtained identical results. John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 159-160 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 Carter: Why Evolutionists Need Junk DNA – Robert W. Carter – 2009 Excerpt: 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. Think about it; in the evolutionary model there have only been 3-6 million years since humans and chimps diverged. With average human generation times of 20-30 years, this gives them only 100,000 to 300,000 generations to fix the millions of mutations that separate humans and chimps. This includes at least 35 million single letter differences, over 90 million base pairs of non-shared DNA, nearly 700 extra genes in humans (about 6% not shared with chimpanzees), and tens of thousands of chromosomal rearrangements. Also, the chimp genome is about 13% larger than that of humans, but mostly due to the heterochromatin that caps the chromosome telomeres. All this has to happen in a very short amount of evolutionary time. They don’t have enough time, even after discounting the functionality of over 95% of the genome–but their position becomes grave if junk DNA turns out to be functional. Every new function found for junk DNA makes the evolutionists’ case that much more difficult.,,, https://creation.com/images/pdfs/tj/j23_3/j23_3_12-13.pdf
Timeline of leading Darwinists claiming that the vast majority of DNA must be junk
Susumu Ohno, 1972, Ford Doolittle, 1980, Francis Crick & Leslie Orgel, 1980, Carl Sagan, 1992 Kenneth Miller, 1994 Sydney Brenner, 1998 Francis Collins, 2006 Michael Shermer, 2006 PZ Myers, 2008 Richard Dawkins, 1979, 1998, 2009 John Avise, 2010 Dan Graur et al, 2012, 2013 Don Prothero, 2013 T. Ryan Gregory, & Alexander Palazzo, 2014 Larry Moran - has a book coming out in 2022 arguing for Junk DNA
Richard Sternberg traces how the junk DNA argument developed through the mid 1970’s to the early 80’s and beyond in the following article:
How The Junk DNA Hypothesis Has Changed Since 1980 – Richard Sternberg – October 8, 2009 Excerpt: Two papers appeared back to back in the journal Nature in 1980: “Selfish Genes, the Phenotype Paradigm and Genome Evolution” by W. Ford Doolittle and Carmen Sapienza and “Selfish DNA: The Ultimate Parasite” by Leslie Orgel and Francis Crick. These laid the framework for thinking about nonprotein-coding regions of chromosomes, judging from how they are cited. What these authors effectively did was advance Dawkins’s 1976 selfish gene idea in such a way that all the genomic DNA evidence available up to that time could be accounted for by a plausible scenario. The thesis presented in both articles is that the only specific function of the vast bulk of “nonspecific” sequences, especially repetitive elements such as transposons, is to replicate themselves — this is the consequence of natural selection operating within genomes, beneath the radar of the cell. These junk sequences, it was postulated, can duplicate and disperse throughout chromosomes because they have little or no effect on the phenotype, save for the occasional mutation that results from their mobility. http://www.evolutionnews.org/2009/10/how_the_junk_dna_hypothesis_ha026421.html Biologists are racking their brains trying to think what useful task this apparently surplus DNA is doing. But from the point of view of the selfish genes themselves, there is no paradox. The true “purpose” of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA. …. “creationists…might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.” - Richard Dawkins – Selfish Gene (mid 1970’s) Selfish DNA: the ultimate parasite. Orgel LE, Crick FH. – 1980 The DNA of higher organisms usually falls into two classes, one specific and the other comparatively nonspecific. It seems plausible that most of the latter originates by the spreading of sequences which had little or no effect on the phenotype. http://www.ncbi.nlm.nih.gov/pubmed/7366731
Dr. Wells also gives some historical background of the Junk DNA argument
Why All the Fuss Over Some Junk? – Jonathan Wells – September 25, 2012 Excerpt: Some historical context might help. After James Watson and Francis Crick discovered the molecular structure of DNA in 1953, Crick announced that they had found “the secret of life,” a popular formulation of which became “DNA makes RNA makes protein makes us.” But biologists discovered that about 98% of our DNA does not code for protein, and in 1972 Susumu Ohno and David Comings independently used the term “junk” to refer to non-protein-coding DNA (though neither man excluded the possibility that some of it might turn out to be functional). Why didn’t biologists simply call non-protein-coding sequences “DNA of unknown function” rather than “junk DNA?” For some, it was because “junk DNA” seemed more suited to the defense of Darwinism and survival of the fittest. In 1976, Richard Dawkins wrote in The Selfish Gene that “the true ‘purpose’ of DNA is to survive, no more and no less. The simplest way to explain the surplus [i.e., non-protein-coding] DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.” In 1980, W. Ford Doolittle and Carmen Sapienza wrote in Nature (284:601) that many organisms contain “DNAs whose only ‘function’ is survival within genomes,” and that “the search for other explanations may prove, if not intellectually sterile, ultimately futile.” In the same issue of Nature (284:604), Leslie Orgel and Francis Crick wrote that “much DNA in higher organisms is little better than junk,” and its accumulation in the course of evolution “can be compared to the spread of a not-too-harmful parasite within its host.” Since it is unlikely that such DNA has a function, Orgel and Crick concluded, “it would be folly in such cases to hunt obsessively for one.” Two biologists then wrote to Nature (285:617,618) expressing their disagreement. Thomas Cavalier-Smith considered it “premature” to dismiss non-protein-coding DNA as junk, and Gabriel Dover wrote that “we should not abandon all hope of arriving at an understanding of the manner in which some sequences might affect the biology of organisms in completely novel and somewhat unconventional ways.” Cavalier-Smith and Dover were not criticizing evolutionary theory; they were merely questioning the claim that non-protein-coding DNA is non-functional. After the rise of intelligent design (ID) in the 1990s, “junk DNA” became a favorite weapon against ID in the hands of some Darwinists, including Richard Dawkins and the four bloggers mentioned above. According to ID, it is possible to infer from evidence in nature that some features of the world, including some features of living things, are explained better by an intelligent cause than by unguided natural processes. The Darwinists’ argument was that an intelligent designer would not have filled our genomes with so much junk, but that it could have accumulated as an accidental by-product of unguided evolution. In 2004, Dawkins wrote in A Devil’s Chaplain that much of our genome “consists of multiple copies of junk, ‘tandem repeats,’ and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself.” Dawkins suggested that creationists (among whom he included ID advocates) “might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.” Dawkins continued to rely on junk DNA in his 2009 book The Greatest Show on Earth: The Evidence for Evolution. “It is a remarkable fact,” he wrote, “that the greater part (95 per cent in the case of humans) of the genome might as well not be there, for all the difference it makes.” In particular, pseudogenes “are genes that once did something useful but have now been sidelined and are never transcribed or translated.” Dawkins concluded: “What pseudogenes are useful for is embarrassing creationists. It stretches even their creative ingenuity to make up a convincing reason why an intelligent designer should have created a pseudogene… unless he was deliberately setting out to fool us.” http://www.evolutionnews.org/2012/09/why_all_the_fus_1064721.html
In 1994, the authoritative textbook, Molecular Biology of the Cell, co-authored by National Academy of Sciences president Bruce Alberts, suggested (incorrectly!) that introns are “largely genetic ‘junk'”: Unlike the sequence of an exon, the exact nucleotide sequence of an intron seems to be unimportant. Thus introns have accumulated mutations rapidly during evolution, and it is often possible to alter most of an intron’s nucleotide sequence without greatly affecting gene function. This has led to the suggestion that intron sequences have no function at all and are largely genetic “junk”. Soon thereafter, the 1995 edition of Voet & Voet’s Biochemistry textbook explained that “a possibility that must be seriously entertained is that much repetitive DNA serves no useful purpose whatever for its host. Rather, it is selfish or junk DNA, a molecular parasite that, over many generations, has disseminated itself throughout the genome…”
Will Darwinists try to Rewrite the History of Junk-DNA? Excerpt: In 1996, leading origin of life theorist Christian de Duve wrote: “The simplest way to explain the surplus DNA is to suppose that it is a parasite or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.” (Richard Dawkins makes similar pronouncements that DNA is junk in an article after 1998) per ENV
Another leading biologist, Sydney Brenner argued in a biology journal in 1998 that:
“The excess DNA in our genomes is junk, and it is there because it is harmless, as well as being useless, and because the molecular processes generating extra DNA outpace those getting rid of it.”
A lonely voice of sanity, and a decade before the ENCODE results came out, John Mattick said the junk DNA argument “may well go down as one of the biggest mistakes in the history of molecular biology.”
“I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century,” Mattick says. “The failure to recognize the full implications of this—particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules—may well go down as one of the biggest mistakes in the history of molecular biology.” (John S. Mattick Scientific American (November, 2003)
Moreover, it is very interesting to note that Richard Dawkin's supposed ironclad 'prediction' for Junk DNA, via 'selfish genes', turned on a dime when the ENCODE results initially came out in 2012
Dawkins, 2009: on “junkDNA” “Junk DNA is just what a Darwinist would expect,” Dawkins, 2012: on non-junkDNA (after ENCODE)… “”junk DNA” isn’t junk at all but is instead “exactly what a Darwinist would hope for,” http://www.evolutionnews.org/2012/09/in_debate_brita_1064521.html
This insanity of Darwinists to label everything they don't understand about the genome as junk would all be very humorous save for the fact that many leading Darwinists, via their near monopoly control over the media and academia, are intent on continually pushing their Junk DNA falsehoods on the general public no matter how many careers they have to destroy along the way to do it.bornagain77_{October 22, 2021
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johnnyb @13, Good points! Imagine if someone examined some computer code and pronounced that 90% of it was non-functional "junk," all it would indicate was that the examiner was a clueless idiot. Same with DNA and epigenetic codes. The fact is that we're discovering function in more and more non-coding DNA even as Darwinists continue their desperately clinging to the idea that DNA is mostly junk for ideological reasons. As more discoveries are made, parsimony increasingly suggests an intelligent designer. And that's what they're fighting. -QQuerius_{October 21, 2021
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Yes, he was right about his mechanism. It just has nothing to do with the Evolution debate.
:) I guess we talk about different persons. I talk about that Darwin that talked about a bug that become a man if you give enough time and brought nonrandom/targeted adaptation as evidence (except he called directed adaptation as "random") All Darwin's points are off.Sandy_{October 21, 2021
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Here’s a link to Susumu Ohno’s 1972 paper, “SO MUCH “JUNK” DNA IN OUR GENOME”
I also highly recommend Jonathan Wells book, “The Myth of Junk DNA.”jerry_{October 21, 2021
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Junk DNA without function would prove evolution(random trial and error for “solving” the problems of evolution would mean a lot of junk must exist)
No, it would not prove naturalistic evolution. It would only show that the original design allowed variation to happen.
You said Darwin was right?Mention 1 point where Darwin was right. Actually was wrong on all counts.
Yes, he was right about his mechanism. It just has nothing to do with the Evolution debate. Darwin’s ideas (1) variation in germ cells happen. Darwin didn’t know how this happened but it has since been explained. Absolutely shown by science (2) the variation is inherited. Absolutely shown by science. (3) natural selection allows some of the variation to become part of the ongoing genome. Absolutely shown by science It’s called micro evolution or genetics and is an important science. But as I said is irrelevant to the Evolution debate.jerry_{October 21, 2021
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Jerry and all, Here's a link to Susumu Ohno's 1972 paper, "SO MUCH "JUNK" DNA IN OUR GENOME" http://junkdna.com/ohno.html It's short and brilliant. Only about 5 typewritten (!) pages long, it shows Dr. Ohno's deep thinking about why so much DNA doesn't have a protein coding function. I would fault him only for using the word "junk," although it could be argued that he wanted to be provocative rather than making a premature conclusion. However, he does provide interesting speculations for the purpose of what's now called non-coding DNA as well as suggesting that it might be a potential record of past mutational failures. After his paper was published, Darwinists unfortunately assumed that it was evidence for evolution, indeed evolutionary junk, and not worthy of further research. His paper is well worth the time to read carefully. Sandy, Good points all! -QQuerius_{October 21, 2021
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Whether what was called junk DNA Is divided into some that has function and some that doesn’t is irrelevant to the ID hypothesis. It could range from 0 to 100% either way and it would be irrelevant to the justification of ID.
1. Junk DNA without function would prove evolution(random trial and error for "solving" the problems of evolution would mean a lot of junk must exist) 2.Junk DNA with function is not "junk" actually it's the most exquisite part of DNA(while coding DNA it's the most simplistic type of DNA). Why evolutionists have missed this point that is so essential ? They had no idea about real function of a cell, because darwinism was dead wrong 3.You said Darwin was right?Mention 1 point where Darwin was right. Actually was wrong on all counts. Has nothing scientific in his theory that it was the base for the most bloodthirsty dictators and criminals that became presidents in Germany, Russia ,China.Sandy_{October 21, 2021
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Are you a special kind of troll?
Probably here longer than anybody current. Back to 2005 when Dembski ran blog.
Something is fishy in your ideas
If you don’t think what I am saying is logical and supported by evidence, challenge it. But with logic and evidence. Not ad hominems or vague accusations. I often propose ideas to see if there is any valid objection. Or challenge ideas that I believe are inconsistent. It’s a way of learning.jerry_{October 21, 2021
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@Jerry: You can't have the cake and eat it. Something is fishy in your ideas. Are you a special kind of troll?Sandy_{October 21, 2021
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First reference to Ohno's ideas at UD that I could find https://uncommondescent.com/intelligent-design/yet-another-feather-in-natural-selections-cap-what-hasnt-it-accomplished/#comment-29303 Comment by DaveScot who ran the blog then
“Predicted” sounds like a bit of revisionist history to me. I’ve been following this closely for over 30 years now. Junk really meant junk when the term was coined. It’s only in the last decade that the prevailing attitude has been changing. Here’s Nobel winning geneticist Walter Gilbert of Harvard talking about prevailing thought in this 1994 NYT article: Keys Emerge To Mystery Of ‘Junk’ DNA By NATALIE ANGIER Published: June 28, 1994
“I don’t believe in junk DNA,” said Dr. Walter Gilbert of Harvard University, a pre-eminent theoretician of the human genome. “I’ve long believed that the attitude that all information is contained in the coding regions is very shortsighted, reflecting a protein chemist’s bias of looking at DNA.” Coding regions may make the proteins that are dear to a chemist’s heart; but true biologists, he added, know that much of the exquisite control over these proteins is held offstage, nested within the noncoding junk.

jerry_{October 21, 2021
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Jerry @17,
We all know certain things that others don’t. I’m aware of the origin of the term junk DNA and have for several years.
Oh good. So what was the title of the paper? -QQuerius_{October 20, 2021
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seversky:
If 100% of genomes are fully functional then why does the humble onion have one five times the size of that of the much larger and more complex human being?
Layers, it's worth repeating.
If 100% of the genome is fully functional then how does the human genome survive around 100 mutations per generation without suffering catastrophic collapse?
Your strawman of "fully functional", is duly noted. Your concept of "functional" is very limited.ET_{October 20, 2021
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You would have more credibility on the assertions your standing by if you did your homework on the subject.
I stand by every thing I have said. We all know certain things that others don’t. I’m aware of the origin of the term junk DNA and have for several years. Whether what was called junk DNA Is divided into some that has function and some that doesn’t is irrelevant to the ID hypothesis. It could range from 0 to 100% either way and it would be irrelevant to the justification of ID. That’s the intelligent position. It should have always been the ID position. The higher the percentage that is functional the better for ID but it could have been zero and not change the ID position. I maintain ID supports better science and this position is better science. By the way there’s the position that junk DNA is there as a breeding ground for new proteins because it mutates away till it is exapted for a new function. It is proposed to be a way new proteins arise. Stephen Gould proposed this idea for his theory of evolution called punctuated equilibrium.jerry_{October 20, 2021
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Jerry,
A lot of what is/was called Junk DNA has function so is obviously not junk.
No, it's not obvious if you knew where the term "junk DNA" came from. Have you read Susumu Ohno's 1972 paper? You would have more credibility on the assertions your standing by if you did your homework on the subject. -QQuerius_{October 20, 2021
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I disagree with your assertion.
I stand by my assertion. A lot of what is/was called Junk DNA has function so is obviously not junk. Some junk DNA obviously exists. It is likely that some DNA has no function. That’s the position that should be taken and should have been taken since the beginning. But it also falls into the trap that DNA is paramount for the Evolution debate.jerry_{October 20, 2021
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Jerry @7,
Aside: Junk DNA was always a diversion and has nothing to do with the ID debate. But it creates lots of heat in discussions.
I disagree with your assertion. "Junk" DNA is an excellent example of the difference between the presumption of design (ID) and the presumption of random, usually useless mutations to be selected for or against (Darwinism). The presumption of junk stalled scientific advancement in non-coding DNA for almost 50 years. The presumption of design would have promoted rather than discouraged scientific inquiry. -QQuerius_{October 20, 2021
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"why does the humble onion have one five times the size of that of the much larger and more complex human being?" I've always thought this was an odd question. Why would physical size correlate to DNA? Why would you think that a human is more complex? That seems to just be prejudicial, unless you have a specific way of measuring human complexity. Additionally, it makes a common mistake that size is *equivalent* to complexity. Size is a *prerequisite* of complexity, but isn't its equivalent. "how does the human genome survive around 100 mutations per generation without suffering catastrophic collapse?" This question *assumes* Darwinism. This is an assumption that all of the mutations are accidental. However, more and more we are seeing that parts of the genome are actually essentially "tuning knobs" and that the mutations are focused there because they are *supposed* to be mutable. Your question also says, "if the genome is 100% functional" but nobody said that. What is said is that function should be a starting presumption in biology. In fact, it is, everywhere but genetics, simply because making it a presumption in genetics, too, looks bad for Darwin. To assign non-function in biology it has to be more than just an argument from ignorance. However, your questions are problematic for the reasons stated above whether or not assertion of the genome being 100% functional is on the table.johnnyb_{October 20, 2021
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Seversky , you missed the point (again) Think about this one:
Odd, isn’t it, that ancient invading viruses would turn out to be critical for survival.
Odd, isn’t it ? Do you even understand what this paper above claims? Does it make any sense to you?martin_r_{October 20, 2021
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If 100% of genomes are fully functional then why
The ignorance of evolutionary biologists was proven by their fall into the temptation of "junk DNA" idea. If an "expert " in computers tells you that for a computer to function is enough a processor you understand that "expert"understand NOTHING about computers. Same thing was happened with evolutionary biologists. They have NO CLUE.Sandy_{October 20, 2021
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If 100% of genomes are fully functional then why does the humble onion have one five times the size of that of the much larger and more complex human being?
Answer: not all of the genome is functional. Why should it be?
If 100% of the genome is fully functional then how does the human genome survive around 100 mutations per generation without suffering catastrophic collapse?
Answer: same as above. If a functioning part of the genome suffers a negative mutation, it won’t reproduce. So it’s not a problem. Have you heard about natural selection? You should look into it. It will take care of the negative mutations.jerry_{October 20, 2021
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If 100% of genomes are fully functional then why does the humble onion have one five times the size of that of the much larger and more complex human being? If 100% of the genome is fully functional then how does the human genome survive around 100 mutations per generation without suffering catastrophic collapse?Seversky_{October 20, 2021
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Odd, isn’t it, that ancient invading viruses would turn out to be critical for survival.
if this discovery is correct, it is not only odd, it is absurd ... it is as absurd as the whole Darwinian EVO-theory... Most probably, one day a paper or two will be published stating: " ...latest findings contradict the current dogma...." or " … it challenges a long-held theory… "martin_r_{October 20, 2021
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Welcome to biology. It’s a lot messier than physics.
Physics basically has two forces, electromagnetism and gravity. (I know there are four but the other two mainly operate to keep atoms stable) And the electromagnetic force (EM) is 10^26 times stronger. On a cosmological scale gravity plays a great role since there are so many particles and EM is neutralized by near equal positive and negative particles. But on a molecular level, EM dominates and especially in biology where there are zillions of positive/negative attractions affecting outcomes. This effect is not as much present in the physical world but definitely exists in lots of places. For example, water is bi-polar and this property causes all sorts of phenomena. Similarly the other forces play a role in the physical state of elements and compounds. But it is mainly the EM force that dominates in biology and life as polar ends of molecules are exposed and thus attract or repel. Aside: Junk DNA was always a diversion and has nothing to do with the ID debate. But it creates lots of heat in discussions.jerry_{October 20, 2021
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Junk DNA is an argument from ignorance.ET_{October 20, 2021
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Bob at 3:
News: "Odd, isn’t it, that ancient invading viruses would turn out to be critical for survival." Bob: "Welcome to biology. It’s a lot messier than physics."
Sorry Bob, but the only thing that is really 'messy' in understanding this present finding is the Darwinian 'just-so story' about how transposons supposedly randomly originated with no critical functionality whatsoever, and yet they now, 'unexpectedly', find that transposons play 'a critical role in viability'. If Darwinian evolution were a normal science, instead of being the supposedly unquestionable dogmatic assumption that Darwinists treat it as being, then this would count as yet another piece of evidence that falsifies Darwinian expectations and confirms the expectations of Intelligent Design. For instance, Richard Sternberg, who was driven out of his job at the Smithsonian Institution for daring to question the supposedly unquestionable assumption of Darwinian evolution, predicted functionality for repetitive DNA elements (REs) way back in 2003. In fact, Dr. Sternberg in the midst of predicting functionality for REs stated that, "the argument is presented that the selfish DNA "hypothesis" is actually a narrative scheme, that it serves to protect neo-Darwinian assumptions from criticism, and that this story is untestable and therefore not a hypothesis."
On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic-Epigenetic System January 2003 - Richard Von Sternberg Abstract: Repetitive DNA sequences comprise a substantial portion of most eukaryotic and some prokaryotic chromosomes. Despite nearly forty years of research, the functions of various sequence families as a whole and their monomer units remain largely unknown. The inability to map specific functional roles onto many repetitive DNA elements (REs), coupled with the taxon-specificity of sequence families, have led many to speculate that these genomic components are "selfish" replicators generating genomic "junk." The purpose of this paper is to critically examine the selfishness, evolutionary effects, and functionality of REs. First, a brief overview of the range of ideas pertaining to RE function is presented. Second, the argument is presented that the selfish DNA "hypothesis" is actually a narrative scheme, that it serves to protect neo-Darwinian assumptions from criticism, and that this story is untestable and therefore not a hypothesis. Third, attempts to synthesize the selfish DNA concept with complex systems models of the genome and RE functionality are critiqued. Fourth, the supposed connection between RE-induced mutations and macroevolutionary events are stated to be at variance with empirical evidence and theoretical considerations. Hypotheses that base phylogenetic transitions in repetitive sequence changes thus remain speculative. Fifth and finally, the case is made for viewing REs as integrally functional components of chromosomes, genomes, and cells. It is argued throughout that a new conceptual framework is needed for understanding the roles of repetitive DNA in genomic/epigenetic systems, and that neo-Darwinian "narratives" have been the primary obstacle to elucidating the effects of these enigmatic components of chromosomes. https://www.researchgate.net/publication/10933051_On_the_Roles_of_Repetitive_DNA_Elements_in_the_Context_of_a_Unified_Genomic-Epigenetic_System
As well, James Shapiro, who shuns both Neo-Darwinism and Intelligent Design, and who champions his theory of 'Natural Genetic Engineering' instead, joined Richard Sternberg in 2005 to 'predict' widespread functionality for repetitive elements, which was, and is, a prediction that is in direct contradiction to what Darwinists predict for REs
Why repetitive DNA is essential to genome function - James A Shapiro 1 , Richard von Sternberg - 2005 https://pubmed.ncbi.nlm.nih.gov/15921050/ Bob Dylan, ENCODE and Evolutionary Theory: The Times They Are A-Changin' - James Shapiro - Sept. 12, 2012 Excerpt: In 2005, I published two articles on the functional importance of repetitive DNA with Rick von Sternberg. The major article was entitled "Why repetitive DNA is essential to genome function." These articles with Rick are important to me (and to this blog) for two reasons. The first is that shortly after we submitted them, Rick became a momentary celebrity of the Intelligent Design movement. Critics have taken my co-authorship with Rick as an excuse for "guilt-by-association" claims that I have some ID or Creationist agenda, an allegation with no basis in anything I have written. The second reason the two articles with Rick are important is because they were, frankly, prescient, anticipating the recent ENCODE results. Our basic idea was that the genome is a highly sophisticated information storage organelle. Just like electronic data storage devices, the genome must be highly formatted by generic (i.e. repeated) signals that make it possible to access the stored information when and where it will be useful. http://www.huffingtonpost.com/james-a-shapiro/bob-dylan-encode-and-evol_b_1873935.html
So to repeat Bob, the only thing that is really 'messy' in understanding this present finding is the Darwinian 'just-so story' about how transposons supposedly randomly originated with no critical functionality whatsoever, and yet they now, 'unexpectedly', find that transposons play 'a critical role in viability'. Of supplemental note, this finding that transposons play 'a critical role in viability' reminds me of the time that Darwinists were very much surprised to learn that 'new' ORFan genes, 'unexpectedly', played an essential role in early embryonic development. As the following researcher remarked, "We were shocked."?
Age doesn't matter: New genes are as essential as ancient ones - December 2010 Excerpt: "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked."? http://www.sciencedaily.com/releases/2010/12/101216142523.htm?
And as the following researcher stated, “This goes against the textbooks, which say the genes encoding essential functions were created in ancient times.”
Darwin’s (Failed Predictions) - Similar species share similar genes - Cornelius Hunter PhD. Excerpt: As much as a third of the genes in a given species may be unique, and even different variants within the same species have large numbers of genes unique to each variant. Different variants of the Escherichia coli bacteria, for instance, each have hundreds of unique genes. (Daubin and Ochman) Significant genetic differences were also found between different fruit fly species. Thousands of genes showed up missing in many of the species, and some genes showed up in only a single species. (Levine et. al.) As one science writer put it, “an astonishing 12 per cent of recently evolved genes in fruit flies appear to have evolved from scratch.” (Le Page) These novel genes must have evolved over a few million years, a time period previously considered to allow only for minor genetic changes. (Begun et. al.; Chen et. al., 2007)? Initially some evolutionists thought these surprising results would be resolved when more genomes were analyzed. They predicted that similar copies of these genes would be found in other species. But instead each new genome has revealed yet more novel genes. (Curtis et. al.; Marsden et. al.; Pilcher)? Next evolutionists thought that these rapidly-evolving unique genes must not code for functional or important proteins. But again, many of the unique proteins were in fact found to play essential roles. (Chen, Zhang and Long 1010; Daubin and Ochman; Pilcher) As one researcher explained, “This goes against the textbooks, which say the genes encoding essential functions were created in ancient times.” (Pilcher) https://sites.google.com/site/darwinspredictions/similar-species-share-similar-genes
So again, if Darwinian evolution were a normal science, instead of being the supposedly unquestionable dogmatic assumption that Darwinists treat it as being, then this present finding would count as yet another piece of evidence that falsifies Darwinian expectations and confirms the expectations of Intelligent Design.
1 Thessalonians 5:21 but test everything; hold fast what is good.
bornagain77_{October 20, 2021
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Welcome to biology. It’s a lot messier than physics.
Messier you mean is too complex for human brain.Sandy_{October 20, 2021
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Odd, isn’t it, that ancient invading viruses would turn out to be critical for survival.
Welcome to biology. It's a lot messier than physics.Bob O'H_{October 20, 2021
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I always wonder what exactly a selfish DNA sequence is supposed to be and how exactly one would prove that a given DNA sequence is not part of the original design. Is there a good reason to assume that viruses invaded the genome rather than that viruses originated from highly mobile parts of the genome?Jonathan11_{October 20, 2021
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Excellent clear writing. University press offices have the best science writers. Another implication: We shouldn't be TORTURING AND KILLING THE ENTIRE FUCKING WORLD in a futile attempt to BLOCK a virus from spreading. Normal handling of viruses by the body is necessary for evolution, not just because it keeps the immune system alert and intelligent. Some viruses have been messengers of important information in the past, and we don't know which current viruses might be necessary for future survival.polistra_{October 19, 2021
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