“Phantom genes” turn out to be useful

_{Denyse O'Leary

February 6, 2020

'Junk DNA', Intelligent Design}

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It’s amazing how little junk there turns out to be in our systems, given that Darwinians boast that masses of junk supports their theory:

Unlike what we commonly refer to as ‘genes’, these phantom genes or ‘Long noncoding RNA’ (LncRNAs) do not lead to the production of proteins that our cells, and thus our entire bodies are made of.
Previously, it was believed that LncRNAs served no major purpose in cells, but new research now shows that one of these LncRNAs termed ‘LincIRS2’ is important for safeguarding our metabolism as LincIRS2 loss favors development of metabolic complications in mice.
University of Southern Denmark, “Phantom genes keep diabetes at bay” at Eurekalert

Paper. (open access)

But, of course, lack of masses of junk will likewise supports the Darwinians’ theory: Lack of junk proves how easy it is for complex, specified order to arise from disorder and something to arise from nothing.

See also: Nature Reviews Genetics Article Admits That Junk DNA Has Been “Prematurely Dismissed”

Comments

In fact, extensive repair mechanisms are completely incompatible with Darwinian evolution in principle.
The Darwinism contradiction of repair systems Excerpt: The bottom line is that repair mechanisms are incompatible with Darwinism in principle. Since sophisticated repair mechanisms do exist in the cell after all, then the thing to discard in the dilemma to avoid the contradiction necessarily is the Darwinist dogma. https://uncommondescent.com/intelligent-design/the-darwinism-contradiction-of-repair-systems/ Contradiction in evolutionary theory – video – (The contradiction between extensive DNA repair mechanisms and the necessity of ‘random mutations/errors’ for Darwinian evolution) http://www.youtube.com/watch?v=dzh6Ct5cg1o The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective – February 2011 Excerpt: “Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation.” http://www.benthamscience.com/open/toevolj/articles/V005/1TOEVOLJ.pdf
The burning question that extensive repair mechanisms presents for the Darwinist is, 'Why in blue blazes is the cell investing so much energy in protecting supposedly vast amounts of junk DNA in the genome?' On top of that, 'How is evolution even possible with these extensive repair mechanisms preventing the genome from randomly evolving in the first place? Of course, Bob, nor any other Darwinist, will ever honestly answer these questions because there is no honest answer he, nor any other Darwinist, can give save to honestly admit that this is yet another devastating falsification of foundational Darwinian presuppositions. Verse:
Luke 14:6 And they were unable to answer these questions.
bornagain77_{February 7, 2020
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For that matter, why is the cell wasting so much energy transcribing all these supposedly vast stretches of junk DNA in the genome into "highly non-random patterns of RNA production–patterns",,
"virtually the whole genome is transcribed" 4-7 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4671999/ Toppling Another Evolutionary Icon, ENCODE Suggests Endogenous Retroviruses Are Functional - Casey Luskin - September 7, 2015 Excerpt: ENCODE didn't merely study the genome to determine which DNA elements are biochemically active and making RNA. It also studied patterns of biochemical activity, uncovering highly non-random patterns of RNA production--patterns which indicate that these vast quantities of RNA transcripts aren't junk.... ENCODE's results suggest that a cell's type and functional role in an organism are critically influenced by complex and carefully orchestrated patterns of expression of RNAs inside that cell. As Stamatoyannopoulos observes, ENCODE found that "the majority of regulatory DNA regions are highly cell type-selective," and "the genomic landscape rapidly becomes crowded with regulatory DNA as the number of cell types" studied increases. Thus, as two pro-ENCODE biochemists explain, "Assertions that the observed transcription represents random noise . . . is more opinion than fact and difficult to reconcile with the exquisite precision of differential cell- and tissue-specific transcription in human cells." http://www.evolutionnews.org/2015/09/toppling_anothe099111.html Astonishing DNA complexity update Excerpt: Here are a few more exciting details from the ENCODE (Encyclopedia of DNA Elements) pilot project report,,, The untranslated regions (now called UTRs, rather than ‘junk’) are far more important than the translated regions (the genes), as measured by the number of DNA bases appearing in RNA transcripts. Genic regions are transcribed on average in five different overlapping and interleaved ways, while UTRs are transcribed on average in seven different overlapping and interleaved ways. Since there are about 33 times as many bases in UTRs than in genic regions, that makes the ‘junk’ about 50 times more active than the genes. https://creation.com/astonishing-dna-complexity-update Scientists go deeper into DNA (Video report) (Junk No More) - Sept. 2012 http://bcove.me/26vjjl5a Quote from preceding video: “It's just been an incredible surprise for me. You say, ‘I bet it's going to be complicated', and then you are faced with it and you are like 'My God, that is mind blowing.'” - Ewan Birney - senior scientist - ENCODE 2012 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."" http://www.evolutionnews.org/2012/09/junk_no_more_en_1064001.html
Moreover, if the cell were truly full of junk DNA and Junk RNA as Darwinists believe, then the cell should reflect that 'burden of junk' within the cell by being somewhat inefficient. Yet that is not what we find. Instead we find that, "A single cell in the human body is approximately 10,000 times more energy-efficient than any nanoscale digital transistor, the fundamental building block of electronic chips."
Cell-inspired electronics - February 25, 2010 Excerpt: "A single cell in the human body is approximately 10,000 times more energy-efficient than any nanoscale digital transistor, the fundamental building block of electronic chips. In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power." http://phys.org/news/2010-02-cell-inspired-electronics.html
Another way to infer virtually 100% functionality for the genome is to note that the entire genome, contrary to Darwinian presuppositions, is subject to multiple layers of extensive DNA repair:
A proofreading system that catches almost all errors A mismatch repair system to back up the proofreading system Photoreactivation (light repair) Removal of methyl or ethyl groups by O6 – methylguanine methyltransferase Base excision repair Nucleotide excision repair Double-strand DNA break repair Recombination repair Error-prone bypass http://www.newgeology.us/presentation32.html Quantum Dots Spotlight DNA-Repair Proteins in Motion - March 2010 Excerpt: "How this system works is an important unanswered question in this field," he said. "It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It's akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour." Dr. Bennett Van Houten - of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot. http://www.sciencedaily.com/releases/2010/03/100311123522.htm
bornagain77_{February 7, 2020
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In response to this comment by Truthfreedom,,,
According to evos, we could easily get rid of 99% of our genetic material because everything is “useless/junk” (until of course reality knocks on the door and they have to retract them-“selves”).
,,,, Bob O'Hara responds,,,
I don’t think the 99% figure is accurate, but the deletion of large chunks of DNA experiment has been done.
For evidence Bob cites this paper,,,
Megabase deletions of gene deserts result in viable mice - Edward M. Rubin - 21 October 2004 Excerpt: We deleted two large non-coding intervals, 1,511 kilobases and 845 kilobases in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis https://www.nature.com/articles/nature03022?proof=true
Unfortunately for Bob, and as is usual for all the evidence that is appealed to by Darwinists, upon closer inspection we find that Bob's evidence for junk DNA evaporates ,,,
Jonathan Wells on Darwinism, Science, and Junk DNA – November 2011 Excerpt: Mice without “junk” DNA. In 2004, Edward Rubin?] and a team of scientists at Lawrence Berkeley Laboratory in California reported that they had engineered mice missing over a million base pairs of non-protein-coding (“junk”) DNA—about 1% of the mouse genome—and that they could “see no effect in them.” But molecular biologist Barbara Knowles (who reported the same month that other regions of non-protein-coding mouse DNA were functional) cautioned that the Lawrence Berkeley study didn’t prove that non-protein-coding DNA has no function. “Those mice were alive, that’s what we know about them,” she said. “We don’t know if they have abnormalities that we don’t test for.”And University of California biomolecular engineer David Haussler? said that the deleted non-protein-coding DNA could have effects that the study missed. “Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years,” he argued. In 2010, Rubin was part of another team of scientists that engineered mice missing a 58,000-base stretch of so-called “junk” DNA. The team found that the DNA-deficient mice appeared normal until they (along with a control group of normal mice) were fed a high-fat, high-cholesterol diet for 20 weeks. By the end of the study, a substantially higher proportion of the DNA-deficient mice had died from heart disease. Clearly, removing so-called “junk” DNA can have effects that appear only later or under other circumstances. https://uncommondescent.com/intelligent-design/jonathan-wells-on-darwinism-science-and-junk-dna/
Here is the subsequent article by Rubin and company:
Targeted Deletion of the 9p21 Noncoding Coronary Artery Disease Risk Interval in Mice - 2010 Excerpt: Here we show that deletion of the orthologous 70kb noncoding interval on mouse chromosome4 affects cardiac expression of neighboring genes, as well as proliferation properties of vascular cells. Chr4?70kb/?70kb mice are viable, but show increased mortality both during development and as adults. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2938076/#__ffn_sectitle
As well there was this subsequent study:
Heart function is impaired by missing gene enhancers: Study - Oct. 5, 2016 Excerpt: According to other researchers, the study confirms that more elements of the genome are involved in gene expression than previously thought. “Prior to this work, no study had looked at what happens to heart function as a result of knocking out the heart enhancers in the genome,” said Dickel. “What was surprising to me was that outwardly, the knockout mice seemed fine. If you just looked at them, you wouldn’t necessarily see anything wrong.” Echocardiograms used to image the hearts from the two groups of mice confirmed that the heart tissue of mice with a disabled enhancer was pumping with less power than normal, consistent with the signs of human cardiomyopathy.,,, “The cardiac changes that we observed in knockout mice lacking these enhancers highlight the role of noncoding sequences in processes that are important in human disease,” http://www.upi.com/Health_News/2016/10/05/Heart-function-is-impaired-by-missing-gene-enhancers-Study/8511475675055/
Moreover, functionality for virtually 100% of the mouse genome was established by the following method:
Shoddy Engineering or Intelligent Design? Case of the Mouse’s Eye – Richard Sternberg - April 2009 Excerpt: — The (entire) nuclear genome is thus transformed into an optical device that is designed to assist in the capturing of photons. This chromatin-based convex (focusing) lens is so well constructed that it still works when lattices of rod cells are made to be disordered. Normal cell nuclei actually scatter light. — So the next time someone tells you that it “strains credulity” to think that more than a few pieces of “junk DNA” could be functional in the cell – remind them of the rod cell nuclei of the humble mouse. https://evolutionnews.org/2009/04/shoddy_engineering_or_intellig/
Moreover, another piece of evidence that argues very strongly for virtually 100% functionality of the genome is the "Fractal Globule Architecture" of the genome,,,
3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell - Oct. 2009 Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip -- while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication. http://www.sciencedaily.com/releases/2009/10/091008142957.htm Scientists' 3-D View of Genes-at-Work Is Paradigm Shift in Genetics - Dec. 2009 Excerpt: Highly coordinated chromosomal choreography leads genes and the sequences controlling them, which are often positioned huge distances apart on chromosomes, to these 'hot spots'. Once close together within the same transcription factory, genes get switched on (a process called transcription) at an appropriate level at the right time in a specific cell type. This is the first demonstration that genes encoding proteins with related physiological role visit the same factory. http://www.sciencedaily.com/releases/2009/12/091215160649.htm
As Stephen Talbott noted, "packing DNA into a typical cell nucleus is like packing about 24 miles of very thin, double-stranded string into a tennis ball,",,, "To locate a protein-coding gene of typical size within all that DNA is like homing in on a one-half-inch stretch within those 24 miles. Or, rather, two relevant half-inch stretches located on different pieces of string, since we typically have two copies of any given gene."
Genes and Organisms: Improvising the Dance of Life - Stephen L. Talbott - Nov. 10, 2015 Excerpt: You may recall from my earlier article, “Getting Over the Code Delusion” (Talbott 2010), that packing DNA into a typical cell nucleus is like packing about 24 miles of very thin, double-stranded string into a tennis ball, with the string cut up (in the normal human case) into 46 pieces, corresponding to our 46 chromosomes. To locate a protein-coding gene of typical size within all that DNA is like homing in on a one-half-inch stretch within those 24 miles. Or, rather, two relevant half-inch stretches located on different pieces of string, since we typically have two copies of any given gene. Except that sometimes one copy differs from the other and one version is not supposed to be expressed, or one version needs to be expressed more than the other, or the product of one needs to be modified relative to the other. So part of the job may be to distinguish one of those half-inch stretches from the other. “Decisions” everywhere, it seems. But no such decisions are made in a vacuum. As it happens, the chromosome does not consist of a naked DNA double helix. Our DNA, rather, is bound up with a massive, intricate, and dynamic protein-RNA-small molecule complex (called chromatin) that is as fully “informative” for the cell as the DNA sequence itself — and, you might say, much more active and directive.,,, the cell, by managing the shifting patterns of the chromatin infrastructure within which DNA is embedded, brings our chromosomes into movement on widely varying scales. These include large looping movements that put particular genes into connection with essential regulatory sequences and with other, related genes (that is, with other one-half inch stretches of our “24 miles of string in a tennis ball”).,,, http://www.natureinstitute.org/txt/st/org/comm/ar/2015/genes_29.htm
How the cell possibly knows how to find the precise 'secret hiding place' of that half inch of DNA within those 24 miles of 'tennis ball' DNA, no one has a clue. Such intricate choreography literally borders on the miraculous. And for Darwinists to presuppose that the rest of the genome is basically junk, just because they do not know the precise function of it, is simply an insane presupposition.bornagain77_{February 7, 2020
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@ BobO'H: "Megabase deletions of gene deserts result in viable mice" (2004)
Knowles cautions that the study doesn't prove that non-coding DNA has no function. "Those mice were alive, that's what we know about them," she says. "We don't know if they have abnormalities that we don't test for." "Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years," he argues. "Darwinian selection is a tougher test."
https://www.nature.com/articles/news041018-7Truthfreedom_{February 7, 2020
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The "evolutionary scenario" cannot account for the existence of DNA. The "evolutionary scenario" has to start with everything that needs an explanation in the first place.ET_{February 7, 2020
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@Bob O'H:
I don’t think the 99% figure is accurate,
Fine. Put your money where your mouth is. "Purify" ourselves please. Get rid of all the "human junk". Mmm. Hitler guy tried the "purification" strategy and look what happened. Per your link:
The functional importance of the roughly 98% of mammalian genomes not corresponding to protein coding sequences remains largely undetermined.
The quote says it all.
Here we show that some large-scale deletions of the non-coding DNA referred to as gene deserts2,3,4 can be well tolerated by an organism.
People can "tolerate" having their legs amputated. It does not mean that legs do not have a purpose . Enter link paywall. You evolutionists think most UD users are stupid "peasants"/ can not understand science. Big surprise surprise. Believing in a higher intelligence does not diminish ours. You clasist and despective morons.Truthfreedom_{February 7, 2020
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So what percent of DNA as junk would best support evolutionary theory? Same question for lncRNA: what percent of lncRNA being non-functional would best support evolution? Gimme a number now. No hedging of bets.
I'm afraid there's no simpler answer to that - it depends on the dynamics of the selfish DNA, and the effects it has on fitness. Give us the funding to estimate these and we can get back to you.
According to evos, we could easily get rid of 99% of our genetic material because everything is “useless/junk” (until of course reality knocks knocks on the door and they have to retract them-“selves”).
I don't think the 99% figure is accurate, but the deletion of large chunks of DNA experiment has been done. In addition the natural experiment has occurred - there is a lot of variation in the amount of junk DNA. If it was all necessary, why would wheat (say) have so much more junk DNA than rice?Bob O'H_{February 7, 2020
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"Long non-coding RNAs (lncRNAs) are diverse transcription products emanating from thousands of loci in mammalian genomes. Cis-acting lncRNAs, which constitute a substantial fraction of lncRNAs with an attributed function, regulate gene expression in a manner dependent on the location of their own sites of transcription, at varying distances from their targets in the linear genome... The emerging principles highlight lncRNAs as transcriptional units highly adept at contributing to gene regulatory networks and to the generation of fine-tuned spatial and temporal gene expression programmes." Evolutionist's delusions of 'randomness' and 'disorder' are nothing more than that, delusions. Welcome to reality. https://www.nature.com/articles/s41576-019-0184-5Truthfreedom_{February 7, 2020
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EDTA @ 2 So what percent of DNA as junk would best support evolutionary theory? According to Dan Graur at least 75% MUST be junk. Given the ever increasing amount that is known to be functional there probably isn't much room left to admit any is not junk. In the future evolutionists will sweep the junk DNA hypothesis under the carpet and pretend it never happened.aarceng_{February 6, 2020
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EDTA
Gimme a number now.
Mmm. Be careful. They do "magic" and can convert 0 into "every"-thing!
(Of course we know the answer will be, “Whatever the actual percent turns out to be.”)
Of course :) Their magical theory can accomodate "any"-thing. Is "some"-thing miraculous. It is sooo flexible!Truthfreedom_{February 6, 2020
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According to evos, we could easily get rid of 99% of our genetic material because everything is "useless/junk" (until of course reality knocks knocks on the door and they have to retract them-"selves"). Poor RNA is just an epiphenomenon. They have already gotten rid of the "self", human value, sanity, logic, maths...Truthfreedom_{February 6, 2020
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So what percent of DNA as junk would best support evolutionary theory? Same question for lncRNA: what percent of lncRNA being non-functional would best support evolution? Gimme a number now. No hedging of bets. (Of course we know the answer will be, "Whatever the actual percent turns out to be.")EDTA_{February 6, 2020
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lncRNA nonsense from Los Alamos Seversky_{February 6, 2020
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