Larry Moran’s uphill battle convincing scientists that most of the genome is junk DNA

So Ed George, as usual, does not want to debate the empirical evidence. Telling and sad. My comments speak for themselves and I am more than happy to let unbiased readers judge for themselves who has been forthright with the evidence and who has not. bornagain77

BA77

But anyways Ed George, after you accusing me of being what Moran’s students observed Moran to be, namely of being prideful to the point of refusing to admit when I may be wrong, you also directly implied that I was wrong on Junk DNA and that Moran was right.

Nope. I didn’t imply any such thing. I was simply implying that “... perhaps being an arrogant, egotistical. know it all who refuses to listen to others might just hamper his ability to humbly admit when he was wrong..”. might describe you. Or are you honestly suggesting that comments written on ‘Rate My Teacher’ should be taken as gospel? Which, by the way, might explain the things that you do take as gospel. Ed George

Ed George, my comment as to Moran's overbearing and egotistical personality was taken directly from the evaluations of Moran's students themselves on Moran's teaching ability. I merely observed that such a prideful, egotistical, personality, if true, would go a very long way towards explaining why Moran refuses to admit when he is wrong on Junk DNA. But anyways Ed George, after you accusing me of being what Moran's students observed Moran to be, namely of being prideful to the point of refusing to admit when I may be wrong, you also directly implied that I was wrong on Junk DNA and that Moran was right. So, since you apparently agree with Moran, to the empirical evidence we will go. Moran believes that upwards of 90% DNA is 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

Yet, via empirical evidence, I hold that Moran’s 10% estimate for deleterious mutations, that he used in his own calculation in the preceding paper, to be far too conservative, and thus the percentage of junk DNA, according to his own calculation, should actually be much higher than his 90% estimate. Indeed it should be, when taking into account a far more realistic picture of 'slightly deleterious' mutations, for all practicle purposes, 100% junk DNA. As should be needless to say, for the mathematics of population genetics to predict that there should be 100% Junk DNA presents a rather insurmountable problem for Darwinists. As Michael Behe stated in the following paper, "we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent"

“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/

Moreover, as John Sanford showed in his book Genetic Entropy and the following paper, the unselectable ‘near neutral’ mutations, which Dr Moran apparently classified as being perfectly neutral, i.e. non-deleterious, in his calculation, should, in reality, all be classified as slightly deleterious mutations that will build up over time instead of being classified as perfectly neutral.,,,

Can Purifying Natural Selection Preserve Biological Information? – May 2013 – Paul Gibson, John R. Baumgardner, Wesley H. Brewer, John C. Sanford In conclusion, numerical simulation shows that realistic levels of biological noise result in a high selection threshold. This results in the ongoing accumulation of low-impact deleterious mutations, with deleterious mutation count per individual increasing linearly over time. Even in very long experiments (more than 100,000 generations), slightly deleterious alleles accumulate steadily, causing eventual extinction. These findings provide independent validation of previous analytical and simulation studies [2–13]. Previous concerns about the problem of accumulation of nearly neutral mutations are strongly supported by our analysis. Indeed, when numerical simulations incorporate realistic levels of biological noise, our analyses indicate that the problem is much more severe than has been acknowledged, and that the large majority of deleterious mutations become invisible to the selection process.,,, http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0010 Kimura’s Distribution of mutations http://dl0.creation.com/articles/p091/c09164/9164-diagram-3c-lge-white.jpg The Correct Distribution of mutations (via geneticist John Sanford) http://dl0.creation.com/articles/p091/c09164/9164-diagram-3d-lge-white.jpg

On top of that, even though Larry Moran used unrealistic estimates for deleterious mutations in his calculation, Moran was still, to repeat myself, only able to calculate that 10% of the genome may be functional and that 90% must be junk. That claim is simply ludicrous. The engineering parameters of DNA, just in terms information storage capacity and the efficiency of DNA translation, is enough. in and of itself, to show just how far detached from reality that claim is.

The thermodynamic efficiency of computations made in cells across the range of life. - 2017 Dec. Excerpt: Here we show that the computational efficiency of translation, defined as free energy expended per amino acid operation, outperforms the best supercomputers by several orders of magnitude, and is only about an order of magnitude worse than the Landauer bound. https://www.ncbi.nlm.nih.gov/pubmed/29133443/ Scientists Have Stored a Movie, a Computer OS, and an Amazon Gift Card in a Single Speck of DNA "The highest-density data-storage device ever created." - PETER DOCKRILL - 7 MAR 2017 Excerpt: In turn, Erlich and fellow researcher Dina Zielinski from the New York Genome Centre now say their own coding strategy is 100 times more efficient than the 2012 standard, and capable of recording 215 petabytes of data on a single gram of DNA. For context, just 1 petabyte is equivalent to 13.3 years' worth of high-definition video, so if you feel like glancing disdainfully at the external hard drive on your computer desk right now, we won't judge. http://www.sciencealert.com/scientists-have-stored-a-movie-a-computer-os-and-an-amazon-gift-card-in-a-single-speck-of-dna

Pray tell Ed George, how in blue blazes is a process that is incapable of removing the 90% of the genome that Moran holds to be junk, somehow able to build an astonishingly sophisticated information storage device, in the midst of all that junk, that puts to shame anything man has ever engineered in terms of information storage capacity and efficiency? Moreover, on top of the sheer ludicrousness of that proposition, Moran (and Graur) also insisted that most of the genome must be junk in spite of overwhelming empirical evidence to the contrary that came from ENCODE, and from many other sources.

Junk No More: ENCODE Project Nature Paper Finds “Biochemical Functions for 80% of the Genome” – Casey Luskin – September 5, 2012 Excerpt: The Discover Magazine article further explains that the rest of the 20% of the genome is likely to have function as well: “And what’s in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator and self-described “cat-herder-in-chief”. He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. “It’s likely that 80 percent will go to 100 percent,” says Birney. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.”” We will have more to say about this blockbuster paper from ENCODE researchers in coming days, but for now, let’s simply observe that it provides a stunning vindication of the prediction of intelligent design that the genome will turn out to have mass functionality for so-called “junk” DNA. ENCODE researchers use words like “surprising” or “unprecedented.” They talk about of how “human DNA is a lot more active than we expected.” But under an intelligent design paradigm, none of this is surprising. In fact, it is exactly what ID predicted. http://www.evolutionnews.org/2012/09/junk_no_more_en_1064001.html New Book on “Junk DNA” Surveys the Functions of Non-Coding DNA – April 29, 2015 Excerpt: Carey,, goes on to explain how today we now believe that, far from being irrelevant, it’s the “junk DNA” that is running the whole show: “The other shock from the sequencing of the human genome was the realisation that the extraordinary complexities of human anatomy, physiology, intelligence and behaviour cannot be explained by referring to the classical model of genes. In terms of numbers of genes that code for proteins, humans contain pretty much the same quantity (around 20,000) as simple microscopic worms. Even more remarkably, most of the genes in the worms have directly equivalent genes in humans. Per evolution news

In other words, in direct contradiction to how science is suppose to work, Moran (and Graur) ignored the results of empirical science itself when it conflicted with his preferred hypothesis of 90% junk DNA. Yet, empirical science itself could care less what Moran wants to believe beforehand. As Richard Feynman stated, "If it disagrees with experiment, it’s wrong. That’s all there is to it.”

"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

Moreover, although the prediction of massive ammounts of junk DNA followed directly from the mathematics of population genetics, and although ENCODE, and many other sources, empirically falsified that prediction of Darwinian evolution, Dan Graur and Larry Moran, to repeat myself, did not accept those empirical findings from ENCODE. In short, Dan Graur and Larry Moran refuse to accept empirical falsification as a criteria for their theory. In other words, since they refuse to adhere to the criteria of falsification, whatever Moran and Graur may be doing, they are certainly NOT doing science.

“In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality.” Karl Popper

To repeat what I quoted earlier in the thread, Junk DNA “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)

Verse:

Psalm 139:13-14 For you created my inmost being; you knit me together in my mother’s womb. I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well.

bornagain77

. circa 2011

UB: I would like to ask if you agree that there is information in DNA, or not? Is there a reason you call it information if you do? And if you don’t, then what is it about its existence that causes you decline to call it information? Does its existence have any observable physical qualities that would or would not sway your view in one direction or the other? Larry Moran: The specific order of nucleotides in DNA determines whether certain biochemical activities will occur at that site … In common parlance we refer to these sites as containing “information” in the form of specific nucleotide sequence. It’s a very useful analogy and I think everyone knows what we mean when we use it. Nobody expects it to conform to the meanings of “information” in other disciplines. Nobody, that is, except some IDiots who like to play semantic word games instead of addressing real science.

Larry, back in 2011 you were told that, indeed, the information recorded in the gene operated exactly like other forms of encoded information -- a fact that has been carefully and repeatedly documented in the physics literature for more than half a century. Your response in 2011 was to simply punt walk away from the conversation. Walking away from the presentation of documented physical evidence is a rather surprising choice for an otherwise confrontational and opinionated professor of biochemistry, don’t you think Larry? And (as I hope you would have already been aware) everything that I was presenting to you in 2011 was all famously predicted to be the case by none other than John Von Neumann. Isn’t that right? When Von Neumann laid out the organizational structure of autonomous open-ended self-replication (requiring a quiescent encoded description, a set of interpretive constraints, and a semantically closed coordination) was he “playing word games instead of addressing real science”? Was John Von Neumann one of those IDiots you speak of? Of course not. Far from being a situation where esteemed scientists (such as Turing or von Neumann) are misunderstood or misinterpreted, or that the microscopic physical descriptions of the gene system (such as that recorded by Pattee or Barbieri, for instance) are just plain wrong; the real problem here is you yourself, isn’t that right Larry? Larry Moran, as a scientist and an educator, why do you run from documented physical evidence? Why do you ignore the history of science? It is a question that answers itself, does it not? Upright BiPed

BA77

Let’s take a guess Seversky, perhaps being an arrogant, egotistical. know it all who refuses to listen to others might just hamper his ability to humbly admit when he was wrong on Junk DNA?

I couldn’t have said it better. Oh, wait, you weren’t referring to yourself? My mistake. Ed George

@13 Bornagain77: Haha. And the most important part: he was wrong. Truthfreedom

Seversky, "what does any of that have to do with his competence on the issue of “junk” DNA?" Let's take a guess Seversky, perhaps being an arrogant, egotistical. know it all who refuses to listen to others might just hamper his ability to humbly admit when he was wrong on Junk DNA? But hey, I am guessing here, others can add their two cents as to why they think Moran is so out of step on the issue of Junk DNA. bornagain77

Bornagain77 @ 13

Hmm, Moran would like teach us some things, Well, let’s see what Larry Moran’s own students say about him:

And what does any of that have to do with his competence on the issue of "junk" DNA? Seversky

Hmm, Moran would like teach us some things, Well, let's see what Larry Moran's own students say about him:

1.31 out of 5 rating Overall Quality Based on 27 ratings Larry Moran Professor in the Science department at University of Toronto - St. George Campus AWFUL For Credit: Yes Attendance: Not Mandatory Grade: B+ Textbook: No Molecular evolution. Dr. Moran ruined it for me. He doesn't listen to his students. When I would ask a question or make a comment, he would immediately disagree, and often proceed to show that I was in fact correct. He doesn't listen. Huge ego. Unfortunate. The course content is so interesting, but now no one is taking the course. AWFUL For Credit: Yes Textbook: No There are no words to describe this prof. If you wanna spare yourself post-traumatic stress disorder, 60 paged lab reports, his scary marking, and even scarier ego, don't take this course. he doesn't even deserve 15 on his evaluation. he deserves 05. Or less. The TA's were nice though. AWFUL OMG this guy needs to GROW UP. He acts like a spoiled brat playing king of the castle with his little throne in biochemistry. AWFUL instead of spending so much time on BIOME, i think mr. moran should use all that time improving his teaching abilities. he's certainly lacking in this respect, and he should either learn to design tests and exams properly, or leave to someone who can. AWFUL imagine the worst professor you've ever had. Moran probably taught him. etc,, etc... https://www.ratemyprofessors.com/ShowRatings.jsp?tid=39948

You get the idea. Don't be too discouraged Moran, you can always teach by being the bad example that other teachers will know to avoid. bornagain77

point them to some introductory textbooks.

How about some graduate texts on evolutionary biology which state they have no explanation for macro evolution (Please no discussion over the definition of macro evolution. Everybody knows what the term refers to). And the retort by an evolutionary biologist in a debate that his belief was based on his faith in deep time. I never saw a text book on evolutionary biology that could prove their models worked. I’ve read a lot of them. Do you have one? That would really help the debate along. jerry

@Larry A few times I’ve tried to at least point them to some introductory textbooks. No luck yet. Jim Thibodeau

@9 Larry Moran Hi distinguished Dr. Moran. Could it be possible that you did not succeed here because what you were trying to teach was garbage instead of science? Truthfreedom

Hi Denyse, It's true that I used to comment on this blog and try to answer legitimate scientific questions in order to inform your readers. It was a waste of time. Larry Moran

Apparently the CoViD-19 lockdown "stay-at-home" has brought visitors to some websites in the Alexa ranking list: Dr Moran's SandWalk has done remarkably well since last March 15. Now Peaceful Science has come back from the bottom (actually at some point they were out of the list) Perhaps more folks have found spare time to look at these websites lately? Dunno. TSZ still crawls down there at the bottom of the list. Any idea why? jawa

Alexa rankings EN……. 221,666........... 220,796 TO……. 447,175............ 459,635 UD……..587,622........... 543,442 SW…….763,618............ 763,932 PT…… 2,616,518...........1,908,454 PS…… 4,753,129..........4,753,952 TSZ….5,415,144........... 5,416,611 jawa

Fascinating how some scientists cling to their reductionist principles. Assuming that anything not coding for a protein or enzyme must be "junk" is so naively arrogant. Especially when recent research has revealed multiple purposes of much of that 99%, to cling to the "junk DNA" myth is just stupid. Here is an analogy that looks at possible additional purposes for the rest of the genome: https://thopid.blogspot.com/2019/02/a-junk-dna-functionality-analogy.html Fasteddious

In fact, because of the mathematics of population genetics, Dan Graur and Larry Moran insist that not only is some negligible amount of the genome to be considered junk but that upwards to 90% of DNA must be junk:

Revisiting the genetic load argument with Dan Graur – Larry Moran – July 14, 2017 Excerpt: I’ve discussed genetic load several times on this blog (e.g. Genetic Load, Neutral Theory, and Junk DNA) but a recent paper by Dan Graur provides a good opportunity to explain it once more. The basic idea of Genetic Load is that a population can only tolerate a finite number of deleterious mutations before going extinct. The theory is sound but many of the variables are not known with precision.,,, Let’s look at the first line in this table. The deleterious mutation rate is calculated using the lowest possible mutation rate and the smallest percentage of deleterious mutations (4%). Under these conditions, the human population could survive with a fertility value of 1.8 as long as less than 25% of the genome is functional (i.e. 75% junk) (red circle). That’s the UPPER LIMIT on the functional fraction of the human genome. But that limit is quite unreasonable. It’s more reasonable to assume about 100 new mutations per generation with about 10% deleterious. Using these assumptions, only 10% of the genome could be functional with a fertility value of 1.8 (green circle). Whatever the exact percentage of junk DNA it’s clear that the available data and population genetics point to a genome that’s mostly junk DNA. http://sandwalk.blogspot.com/2017/07/revisiting-genetic-load-argument-with.html

I hold Moran’s 10% estimate for deleterious mutations, that he used in his calculation in the preceding paper, to be far too conservative, and thus the percentage of junk DNA, according to his own calculation, should actually be much higher than his 90% estimate,,, As Michael Behe stated in the following paper,, we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent

“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/

Moreover, as John Sanford showed in his book Genetic Entropy and the following paper, the unselectable ‘near neutral’ mutations, which Dr Moran classified as perfectly neutral in his calculation, should, in reality, all be classified as slightly deleterious mutations that will build up over time instead of being classified as perfectly neutral.,,,

Can Purifying Natural Selection Preserve Biological Information? – May 2013 – Paul Gibson, John R. Baumgardner, Wesley H. Brewer, John C. Sanford In conclusion, numerical simulation shows that realistic levels of biological noise result in a high selection threshold. This results in the ongoing accumulation of low-impact deleterious mutations, with deleterious mutation count per individual increasing linearly over time. Even in very long experiments (more than 100,000 generations), slightly deleterious alleles accumulate steadily, causing eventual extinction. These findings provide independent validation of previous analytical and simulation studies [2–13]. Previous concerns about the problem of accumulation of nearly neutral mutations are strongly supported by our analysis. Indeed, when numerical simulations incorporate realistic levels of biological noise, our analyses indicate that the problem is much more severe than has been acknowledged, and that the large majority of deleterious mutations become invisible to the selection process.,,, http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0010 Kimura’s Distribution http://dl0.creation.com/articles/p091/c09164/9164-diagram-3c-lge-white.jpg Correct Distribution http://dl0.creation.com/articles/p091/c09164/9164-diagram-3d-lge-white.jpg

Thus, even though Larry Moran used unrealistic estimates for deleterious mutations in his calculation, Moran was still only able to calculate that 10% of the genome may be functional. The fact of the matter is that if realistic estimates are used in the calculations, and if Darwinian evolution is assumed to be true in the calculations, then ALL, i.e. 100%, of the genome should be functionless junk, instead of just 90%. Moreover, these leading Darwinists insisted that most of the genome must be junk in spite of overwhelming empirical evidence to the contrary from ENCODE, and from other sources

Junk No More: ENCODE Project Nature Paper Finds "Biochemical Functions for 80% of the Genome" - Casey Luskin - September 5, 2012 Excerpt: The Discover Magazine article further explains that the rest of the 20% of the genome is likely to have function as well: "And what's in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project's Lead Analysis Coordinator and self-described "cat-herder-in-chief". He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. "It's likely that 80 percent will go to 100 percent," says Birney. "We don't really have any large chunks of redundant DNA. This metaphor of junk isn't that useful."" We will have more to say about this blockbuster paper from ENCODE researchers in coming days, but for now, let's simply observe that it provides a stunning vindication of the prediction of intelligent design that the genome will turn out to have mass functionality for so-called "junk" DNA. ENCODE researchers use words like "surprising" or "unprecedented." They talk about of how "human DNA is a lot more active than we expected." But under an intelligent design paradigm, none of this is surprising. In fact, it is exactly what ID predicted. http://www.evolutionnews.org/2012/09/junk_no_more_en_1064001.html New Book on “Junk DNA” Surveys the Functions of Non-Coding DNA – April 29, 2015 Excerpt: Carey,, goes on to explain how today we now believe that, far from being irrelevant, it’s the “junk DNA” that is running the whole show: “The other shock from the sequencing of the human genome was the realisation that the extraordinary complexities of human anatomy, physiology, intelligence and behaviour cannot be explained by referring to the classical model of genes. In terms of numbers of genes that code for proteins, humans contain pretty much the same quantity (around 20,000) as simple microscopic worms. Even more remarkably, most of the genes in the worms have directly equivalent genes in humans. http://www.evolutionnews.org/2015/04/a_new_book_on_j095611.html

Thus in conclusion, although the prediction of junk DNA followed directly from the mathematics of population genetics, and although ENCODE. and many other sources, empirically falsified that prediction of Darwinian evolution, Evolutionists in general, and Dan Graur and Larry Moran in particular, did not accept those empirical finding from ENCODE. In short, Evolutionists in general, and Dan Graur and Larry Moran, refuse to accept empirical falsification of their theory. Yet, if your theory does not have a criteria for potential falsification via empirical testing, then it is not science

"In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality." Karl Popper

To repeat, Junk DNA "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)

Verse:

Psalm 139:13-14 For you created my inmost being; you knit me together in my mother’s womb. I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well.

bornagain77

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) https://uncommondesc.wpengine.com/books-of-interest/new-book-junk-dna-junked-in-favour-of-what/#comment-374475 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 as to why many Darwinists did everything they could to try to discredit the ENCODE findings of pervasive functionality for the genome:

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." But if most of our DNA is functional, as the ENCODE results suggest, then the "junk DNA" argument against ID collapses. So the four bloggers listed above are doing everything they can to discredit the ENCODE project's estimate of functional DNA. Yet whatever the estimate may currently be, it is certain to increase with further research. In 2007, the ENCODE pilot project reported on the basis of about 200 datasets that our DNA is "pervasively transcribed," suggesting functionality. The 2012 results, based on 1,640 datasets, documented that "the vast majority (80.4%) of the human genome" is biochemically functional in at least one cell type. But ENCODE has so far sampled only a fraction of the cell types in the human body. Clearly, we have a lot more to learn about our genome -- but not if we start by assuming that most of it is junk. 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? 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) http://www.evolutionnews.org/2007/06/will_darwinists_try_to_pull_a.html 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."

In 2003, John S. Mattick stated that the prediction of Junk DNA by Darwinists, "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)

In other words, Neutral theory, and the entire concept of junk DNA, was not developed because of any compelling empirical observation, but was actually developed because it was forced upon Darwinists by the mathematics of population genetics. In plain English, neutral theory, and the concept of junk DNA, is actually the result of a theoretical failure of Darwinian evolution, specifically the failure of natural selection, within the mathematics of population genetics! Because the prediction of Junk DNA is based in the mathematics population genetics, that is the primary reason why Dan Graur stated, after the results of ENCODE came out, (results that showed pervasive functionality across the entire genome), that “If ENCODE is right, evolution is wrong.”

"Dan Graur said ENCODE is “bonkers”[v] because “If ENCODE is right, evolution is wrong.”[vi]" https://crev.info/2018/07/keynote-speech-falsifies-darwinism/

In the following article Larry Moran quotes Austin Hughes who states, 'Darwinism asserts that natural selection is the driving force of evolutionary change. It is the claim of the neutral theory, on the other hand, that the majority of evolutionary change is due to chance.'

Austin Hughes and Neutral Theory - Laurence A. Moran - June 19, 2017 Excerpt: Originally proposed by Motoo Kimura, Jack King, and Thomas Jukes, the neutral theory of molecular evolution is inherently non-Darwinian. Darwinism asserts that natural selection is the driving force of evolutionary change. It is the claim of the neutral theory, on the other hand, that the majority of evolutionary change is due to chance. http://sandwalk.blogspot.com/2017/06/austin-hughes-and-neutral-theory.html

Thus, with Natural selection being tossed by the wayside by the mathematics of population genetics, (and by empirical evidence), 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 'appearance of design' that we see in 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 an understatement. bornagain77

Junk DNA is a shining example of the unfalsifiable, pseudoscientific, nature of Darwinian evolution. The prediction of Junk DNA was not just some common sense prediction that followed somewhat directly from the premises of RM and NS, (random mutation and natural selection), of Darwinian evolution, but is a prediction that was born out of the mathematics of population genetics itself. As Robert Carter states, "Junk DNA is not just a label that was tacked on to some DNA that seemed to have no function, but it is something that is required by evolutionary theory. Mathematically, there is too much variation, too much DNA to mutate, and too few generations in which to get it all done."

The slow, painful death of junk DNA - Robert W. Carter - 2009 Background Based on the work of J.B.S. Haldane5 and others, who showed that natural selection cannot possibly select for millions of new mutations over the course of human evolution, Kimura6 developed the idea of “neutral evolution”. If “Haldane’s Dilemma”7 were correct, then the majority of DNA must be non-functional. It should be free to mutate over time without needing to be shaped by natural selection. In this way, natural selection could act on the important bits and neutral evolution could act randomly on the rest. Since natural selection will not act on neutral traits, which do not affect survival or reproduction, neutral evolution can proceed through random drift without any inherent “cost of selection”.8 The term “junk DNA” originated with Ohno,9 who based his idea squarely on the idea of neutral evolution. To Ohno and other scientists of his time, the vast spaces (introns)between protein-coding genes were (exons) just useless DNA whose only function was to separate genes along a chromosome. Junk DNA is a necessary mathematical extrapolation. It was invented to solve a theoretical evolutionary dilemma. Without it, evolution runs into insurmountable mathematical difficulties. Junk DNA necessary for evolution Junk DNA is not just a label that was tacked on to some DNA that seemed to have no function, but it is something that is required by evolutionary theory. Mathematically, there is too much variation, too much DNA to mutate, and too few generations in which to get it all done. This was the essence of Haldane’s work. Without junk DNA, evolutionary theory cannot currently explain how everything works mathematically. https://creation.com/images/pdfs/tj/j23_3/j23_3_12-13.pdf

Here is a short history of the Junk DNA argument of Darwinists,

Haldane’s dilemma has not been solved Excerpt: The famous evolutionary geneticist J.B.S. Haldane (1892–1964) was one of the three founders of the field of study known as population genetics. Haldane articulated a serious problem for evolutionary theory in a seminal paper in 1957—the ‘cost of substitution’.1 When a beneficial mutation occurs in a population, it has to increase in the number of copies for the population to progress evolutionarily (if the mutation remained in one individual, then evolution cannot proceed; this is fairly obvious). In other words, it has to substitute for the non-mutated genes in the population. But the rate at which this can happen is limited. A major factor limiting the rate of substitution is the reproduction rate of the species. For a human-like creature with a generation time of about 20 years and low reproduction rate per individual, the rate of growth in numbers of a mutation in a population will be exceedingly slow. This is basically the ‘cost of substitution’. http://creation.com/haldanes-dilemma-has-not-been-solved Haldane’s Dilemma - Chase Nelson Excerpt: Haldane, one of the founders (along with Ronald Fisher and Sewall Wright) of mathematical population genetics, was the first to quantify such a limit on the speed of adaptive evolution.7 He concluded that the cost of selection “defines one of the factors, perhaps the main one, determining the speed of evolution.”8 Cost was the main reason Motoo Kimura proposed the neutral theory of molecular evolution.9 Many others cite its importance.10 The implications for mammalian evolution were considered so severe that the issue became known as Haldane’s dilemma.11 Despite Haldane’s work, a massive body of literature has accumulated asserting the primary role of natural selection in evolutionary change, often implying rates of adaptive evolution that exceed plausible limits. http://inference-review.com/article/haldanes-dilemma Haldane's Dilemma Excerpt: Haldane, (in a seminal paper in 1957—the ‘cost of substitution’), 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 Walter ReMine on Haldane's Dilemma - interview http://kgov.com/Walter-ReMine-on-Haldanes-Dilemma 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 "Kimura (1968) developed the idea of “Neutral Evolution”. If “Haldane’s Dilemma” is correct, the majority of DNA must be non-functional." – Sanford Austin L. Hughes - The Neutral Theory of Evolution - Chase Nelson - 2016 Excerpt: ORIGINALLY PROPOSED by Motoo Kimura, Jack King, and Thomas Jukes, the neutral theory of molecular evolution is inherently non-Darwinian.2 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://inference-review.com/article/the-neutral-theory-of-evolution/ "Although the term “junk DNA” was already in use as early as the 1960s [10]–[12], the term's origin is usually attributed to Susumu Ohno [13]" https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004351 So Much ‘Junk DNA' in our Genome - Susumu Ohno - 1972 http://www.junkdna.com/ohno.html

bornagain77

So they have to convince scientist that most of your dna is junk It’s a very telling thing AaronS1978

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