From ScienceDaily:
What used to be dismissed by many as “junk DNA” is back with a vengeance as growing data points to the importance of non-coding RNAs (ncRNAs) — genome’s messages that do not code for proteins — in development and disease. But our progress in understanding these molecules has been slow because of the lack of technologies that allow the systematic mapping of their functions.
Yes, that’s what they said.
ncRNAs come in multiple flavours: there’s rRNA, tRNA, snRNA, snoRNA, piRNA, miRNA, and lncRNA, to name a few, where prefixes reflect the RNA’s place in the cell or some aspect of its function. But the truth is that no one really knows the extent to which these ncRNAs control what goes on in the cell, nor how they do this. The new technology developed by Blencowe’s group has been able to pick up new interactions involving all classes of RNAs and has already revealed some unexpected findings.Paper. (paywall) – Eesha Sharma, Tim Sterne-Weiler, Dave O’Hanlon, Benjamin J. Blencowe. Global Mapping of Human RNA-RNA Interactions. Molecular Cell, 2016; DOI: 10.1016/j.molcel.2016.04.030 More.
It’s curious how blunt media releases are becoming, in dismissing the idea of “junk DNA.” But then Darwin didn’t predict junk DNA. Or junk RNA. Or that his stalwart followers would develop and promote the concept. So, leaving their interests aside, there isn’t a big investment in protecting the idea.
One result is that it’s probably not a great time to be Dan Graur. A better time, actually, to be Jonathan Wells
See also: “Inactive” gene helps prevent strokes A gene that “scientific dogma insists” is inactive in adults actually plays a vital role in preventing the underlying cause of most heart attacks and strokes, researchers have determined.
and
Jonathan Wells’s The Myth of Junk DNA
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source of study: University of Toronto
Isn’t Larry ‘neutral’ Moran, who teaches at the University of Toronto, also a big junk DNA proponent?
Ouch! Right in his own backyard! This certainly ain’t going to sit well with him. Maybe we ought to send him a box of Kleenex?
Moran even went so far as to argue with a ENCODE researcher on a science blog to try to change the ENCODE researcher’s mind back in 2012 when ENCODE research had found widespread functionality in the genome.
Supplemental note:
i.e. Neutral theory, and junk DNA, was not developed because of any empirical observation, but was developed primarily because it was forced upon Darwinism by the mathematics. In other words, neutral theory is actually the result of a theoretical failure of Darwinism within mathematics!
Here a cool video by Dr Carter that goes over some of the mind blowing complexity of the genome
It would appear that RNA is an informational molecule. But what conditions must obtain for that to even be the case?
Was the entire idea of “junk DNA” predicated on the belief that these areas of DNA were not being transcribed into RNA?
Would things have been different if the “junk DNA” advocates had been operating under an informational paradigm? If so, how so?
What do people think?
Larry Moran is writing a book on “junk DNA”.
http://sandwalk.blogspot.ca/20.....-book.html
IN IT, he is going to prove again that ENCODE deceived the public about their findings about “junk DNA” and despite ALL of the new evidence against “junk DNA”, Larry is going to continue to claim that human genome is still 90% junk.
You gotta love “true scientists” like Larry who hasn’t published one paper or performed one experiment to prove his point on “junk DNA” or other…
J-MAC,
Well, if you look at statements from the ENCODE researchers even they all but admit that.
Junk or functional DNA? ENCODE and the function controversy Pierre-Luc Germain, Emanuele Ratti, Federico Boem – 21 Mar 2014
Abstract: In its last round of publications in September 2012, the Encyclopedia Of DNA Elements (ENCODE) assigned a biochemical function to most of the human genome, which was taken up by the media as meaning the end of ‘Junk DNA’. This provoked a heated reaction from evolutionary biologists, who among other things claimed that ENCODE adopted a wrong and much too inclusive notion of function, making its dismissal of junk DNA merely rhetorical. We argue that this criticism rests on misunderstandings concerning the nature of the ENCODE project, the relevant notion of function and the claim that most of our genome is junk. We argue that evolutionary accounts of function presuppose functions as ‘causal roles’, and that selection is but a useful proxy for relevant functions, which might well be unsuitable to biomedical research. Taking a closer look at the discovery process in which ENCODE participates, we argue that ENCODE’s strategy of biochemical signatures successfully identified activities of DNA elements with an eye towards causal roles of interest to biomedical research. We argue that ENCODE’s controversial claim of functionality should be interpreted as saying that 80 % of the genome is engaging in relevant biochemical activities and is very likely to have a causal role in phenomena deemed relevant to biomedical research. Finally, we discuss ambiguities in the meaning of junk DNA and in one of the main arguments raised for its prevalence, and we evaluate the impact of ENCODE’s results on the claim that most of our genome is junk.
http://link.springer.com/artic.....014-9441-3
Protracted Unrest Between ENCODE Researchers and Junk-DNA Advocates Goes On – November 26, 2014
Excerpt: It’s not exactly Fergusson, Mo., but the battle between ENCODE researchers and junk-DNA holdouts goes on.,,,
,,,”Evolutionary conservation of primary sequence is typically considered synonymous with conserved function, but this finding suggests that this concept should be reinterpreted, because insertions of retrotransposon elements in new genomic regions are not conserved between species.”
In short, the Mouse ENCODE group takes direct aim at the arguments of Dan Graur and the other junk-DNA faithful, who say that everything evolution did not conserve is junk.,,,
,,,much of what Darwinian evolutionists had dismissed as junk appears functional. Non-coding regions of the mouse genome are transcribed, and appear to function in previously unimagined ways, such as regulation of gene expression, chromosomal stability, and maintenance of species identity. Carninci offers further thoughts:
,,,”we should rethink the relationship between genomic function and evolutionary conservation. Regulatory regions and long non-coding RNAs (lncRNAs) are not subject to the evolutionary constraints of protein-coding genes, which may help to explain the sequence drifts reported in these papers. However, it is striking that transcription-factor networks are conserved despite low conservation of their binding positions in the genome.”
http://www.evolutionnews.org/2.....91501.html
The ENCODE Embroilment, – part 3 – Summer 2015
Excerpt: Very Little DNA Is “Conserved”
After raising the C-value paradox, ENCODE critics often follow with a logical argument. “Only about 10 percent of our DNA is ‘conserved,’ or has a similar sequence, compared to the genomes of other mammals,” they point out. “This means that only about 10 percent of our genome is under selection to preserve the DNA sequence.” They then reason: “Since natural selection is the only force that creates and preserves functional elements in our genome, it’s impossible that more than about 10 percent of our genome is functional.”
This argument was on display in a 2014 paper claiming that only 8.2 percent of human DNA is functional because only that percentage of our genome is “conserved” between humans and other mammals like mice and pandas.7 But there’s a glaring problem with this thinking: it assumes that all DNA sequences are the result of undirected mutation and selection to begin with, and that biological function only comes from natural selection. Throw out the assumption of an evolutionary origin of species and there’s no reason to believe that only conserved DNA can be functional. After all, an intelligent agent could independently design functional genetic elements with widely divergent DNA sequences in the genomes of different species—no “conservation” required.
Only if we assume that strictly unguided evolutionary mechanisms produced our genome can we infer that such a small fraction of our genome is functional. Under this logic, when evolutionists cite the preponderance of junk DNA as evidence for evolution, they engage in circular reasoning.
Junk proponents seem blind to these flaws. A co-author of the 8.2-percent paper boasted, “our approach is largely free from assumptions or hypotheses.”8 Apparently he was forgetting about assumptions and hypotheses like evolution.
Even worse, ENCODE critic Dan Graur called it “‘idiotic’ to suggest that a part of the genome could be functional if it didn’t respond to pressure from natural selection.”9 He further charges that “what ENCODE researchers did not take into account . . . is that everything is shaped by evolution.”10 In Graur’s Darwinian world, the possibility that some important functional genetic element arose from a cause other than natural selection is simply inconceivable….
In any case, ENCODE provides a nice empirical test of the evolutionary assumption that only conserved DNA can be functional: It finds evidence of mass functionality in “non-conserved” (i.e., unique) DNA sequences. As one lead ENCODE researcher explains: “Most elements defined by biochemical signatures lacked strong evolutionary conservation.”12 Other ENCODE defenders argue that the research shows that “absence of conservation cannot be interpreted as evidence for the lack of function.”13 –
They conclude that ENCODE’s empirical evidence for functionality is the ultimate test: “differential expression (including extensive alternative splicing) of RNAs is a far more accurate guide to the functional content of the human genome than logically circular assessments of sequence conservation.”21 Bottom line: good evidence trumps bad theory.,,,
A Great Divorce
Critics like Dan Graur charge that ENCODE is guilty of “divorcing genomic analysis from its evolutionary context”22—and that’s exactly right. ENCODE’s empirically based finding that the vast majority of our genome is functional has withstood theoretical, evolution-based objections from critics. Maybe a divorce from evolutionary thinking is exactly what we need to liberate biology from bad evolutionary assumptions and explain what’s happening inside our cells.,,,
http://www.salvomag.com/new/ar.....rt-III.php
Why Are Biologists Lashing Out Against Empirically Verified Research Results? – Casey Luskin July 13, 2015
Excerpt: no publication shook this (ID vs Darwin) debate so much as a 2012 Nature paper that finally put junk DNA to rest–or so it seemed. This bombshell paper presented the results of the ENCODE (Encyclopedia of DNA Elements) Project, a years-long research consortium involving over 400 international scientists studying noncoding DNA in the human genome. Along with 30 other groundbreaking papers, the lead ENCODE article found that the “vast majority” of the human genome shows biochemical function: “These data enabled us to assign biochemical functions for 80 percent of the genome, in particular outside of the well-studied protein-coding regions.”3
Ewan Birney, ENCODE’s lead analyst, explained in Discover Magazine that since ENCODE studied 147 types of cells, and the human body has a few thousand cell types, “it’s likely that 80 percent will go to 100 percent.”4 Another senior ENCODE researcher noted that “almost every nucleotide is associated with a function.”5 A headline in Science declared, “ENCODE project writes eulogy for junk DNA.”6,,,
Evolutionists Strike Back
Darwin defenders weren’t going to take ENCODE’s data sitting down.,,,
How could they possibly oppose such empirically based conclusions? The same way they always defend their theory: by assuming an evolutionary viewpoint is correct and reinterpreting the data in light of their paradigm–and by personally attacking, (i.e. ad hominem), those who challenge their position.,,,
http://www.evolutionnews.org/2.....97561.html
goodusername,
Well, if you look at statements from the ENCODE researchers even they all but admit that.
All I know is that the main guys of the ENCODE are sticking to their guns even if they are regularly threatened by Darwinist or they had spoken conservatively about their findings. They know that eventually they are going to be exonerated and Darwinists will pretend that they knew it all and predicted it all along…
I have seen the denial first hand when Darwinists moved from 98% junk to 90% because they couldn’t deny it anymore. Larry Moran and the gang blamed the “not so knowledgeable Darwinists for making such claims”.
Who is going to stop the new generation of Darwinists blaming Larry and the gang for not being so knowledgeable?
They are not going to be alive or available to admit that they were wrong….
So, the scenario becomes increasingly clearer:
1) Non coding RNAs are mostly functional
2) They have mainly regulatory roles
3) Non coding DNA is much less conserved than coding DNA
4) The main reason for that is not that it is not functional, but that it has regulatory functions which differ from species to species. IOWs, non coding DNA is an important part of what makes species different. We can expect that a significant part of the procedures which control cellular differentiation are written there. IOWs, itr is an importanty example of “function which changes”
5) Those procedures in non coding DNA are obviously designed and, guess what?
“insertions of retrotransposon elements in new genomic regions are not conserved between species”
IOWs, transposons are important actors increasingly mentioned as a cause of functional and regulatory diversity. IOWs, tools of design.
Does that sound familiar? 🙂
Of related note to regulatory RNAs:
Jonathan Wells comments on the fallacious ‘Darwinian Logic’, within the preceding paper, that falsely tried to attribute the major differences that were found in INDEL variation to unguided Darwinian processes:
These following, more recent, papers also found that Alternative Splicing patterns are ‘species specific’:
Of related interest: The position and organization of elements on the chromosome is not arbitrary but is the “irreducible organizational complexity of the genetic regulation system of any cell”
Of related interest to species specific alternative splicing in tissues is the fact that there is also tissue-specific spatial organization of chromosomes :
As well, as Dr. Wells has pointed out, the 3-D spatial arrangement of parts in the cell is not reducible to DNA sequences:
BA:
“Extensive, large INDEL (Insertion, Deletion) variation exists between the human and chimpanzee genomes. This variation is primarily attributable to retrotransposon insertions within the human lineage. There is a significant correlation between differences in gene expression and large human-chimpanzee INDEL variation mapping in genes or in proximity to them.”
QED! 🙂
of related note, the disconnect between mutations to DNA and the ‘form’, i.e. the spatial organization, of an organism is fairly profound:
also of related note:
gpuccio:
You wrote above:
Indeed, it does sound familiar. Here’s a thread from 2007 on this very subject. If you look at my comments at #4,5, and 7, you’ll see that “design principles” lead you very quickly to proper conclusions; unlike evolutionists.