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Is “dark genome” becoming the new name for junk DNA?


Well, a new book is called Junk DNA: A journey through the dark matter of the genome (Nessa Carey)

A New Scientist reviewer calls it “An encyclopaedic guide to the dark genome — junk DNA,” and sticks to “junk DNA” thereafter:

In fact, extra fingers and toes in both cats and humans result from alterations in junk DNA – the 98 per cent of the genome that has no genes, doesn’t code for proteins, and which was until recently dismissed as, well, junk. In the case of extra digits, a piece of regulatory DNA has mutated, “enhancing” the activity of a gene crucial to the development of hands and feet.

That’s not so different from the conventional explanation of how the genome works – more a small tweak in our understanding – but it’s just the start of junk DNA’s weird and intricate story. From “sleeper agents” that used to be viruses to reading genes backwards, Nessa Carey’s book, Junk DNA, guides us through this dark side of the genome. And it’s a side that is turning out to be full of strange twists and turns. More.

See, for example, “Researchers say junk DNA plays key role in brain development” and “Non-coding RNAs undermining the junk DNA concept?

But old concepts die hard, especially when they are value-laden as “junk DNA” has been—it has been a key argument for Darwinism. So even though “dark genome” makes more sense given all the functions now being identified, expect “junk DNA” to be defended in practice.

For an odd example of that, see “Nothing makes sense in evolution except in the light of junk DNA?”: “If ENCODE [a project that identifies functions] is right, then Evolution is wrong.” And more recently, Furore over no junk DNA?

For background, see Jonathan Wells on the junk DNA myth

Pod: Richard Sternberg on “junk DNA”

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Larry Moran considers Nessa Carey's book ridiculous
This is not looking good. Anyone who starts with the premise that noncoding DNA might all be junk is clearly way out of their depth in this debate. The claim that epigenetics might explain junk DNA is another dead giveaway. Looks like we're dealing with an amateur. ...This is 2015 and tons of stuff has been written about the definition of junk DNA and the history of the idea. It's pretty clear that Nassa Carey hasn't read any of it.
For the ten millionth time, no geneticist or molecular biologist ever said he thought non-coding DNA was equal to, or a subset of, Junk DNA. Jukes, King, Ohno etc. defined Junk DNA as a subset of non-coding DNA. Not the same thing. If you ID proponents don't know the difference draw some Venn diagrams in crayon and get back to me. Many journalists about 1993 starting writing that geneticists once thought non-coding DNA was equal to, or a subset of, Junk DNA-- their way of concocting a fake "paradigm shift" by lying about what Jukes, King, Ohno etc. actually said, so as to make them look dumb. It was journalistic malpractice, to use O'Leary's phrase. So from about 1993 on, you see dummy journalists writing crap like "Non-coding DNA, long dismissed as junk..." but never actually quoting, with references, any geneticist or molecular biologist saying he himself thought non-coding DNA was = or a subset of Junk. It was always using passive tense verbs, "Non-coding DNA was long dismissed..." Was dismissed? By whom? Passive tense pussies use passive tense to evade their responsibility to tell us who did the dismissing, and where. Give me some active tense verbs with a proper predicate including author's name and page number or piss off. ID proponents latched onto it later because they had to lie about what scientists said in order to make scientists look dumb, out of the belief that, if they could make scientists look dumb, that would make preachers, theologians and religious authorities look smart by comparison. No ID proponent-- not Casey Luskin or Jonathan Wells or anyone else-- have ever turned up a real quote from a geneticist or molecular biologist saying he himself thought non-coding DNA was = or a subset of Junk. No such quotes. Note that Casey Luskin esquire once tried to bury me under a pile of quotes proving that! Yeah, over at Evolution News & Views they made the mistake of opening up to comments until I started diogenizing them and they panicked the freak out. Luskin actually dumped on me a comment that he had actually written a year or so before and dumped on John Farrell at Forbes.com, so when Luskin used the second person pronouns, "You believe," "You think," "You say," the "You" was John Farrell and he was attributing to me what Luskin thought John Farrell had written a year before. It doesn't matter much, because Luskin esquire's too dumb to understand the English coming out of either of our mouths. At any rate I went through and debunked every one of Luskin's Junk DNA quote-mines and showed that NONE of his quotes were from a geneticist or molecular biologist saying that non-coding DNA was = or a subset of Junk. Some of the quotes said "non-coding" and "Junk" but the verbs were all wrong and Luskin was too dumb to understand the predicates or dependent clauses of the words he was copying. All of Luskin's Junk DNA gotcha quotes consisted of either: 1. Guys saying Junk DNA was a subset of non-coding DNA, and Luskin not knowing the difference, 2. Some guys describing what they thought OTHER GUYS believed, "Long dismissed as Junk..." with the "other guys" never being named, no journal name, no page number, no reference, just Passive Tense Pussying about unspecified anonymous Somebodys at at unknown time in an unknown place. So I diogenized his quotes, then Luskin quote-mined ME by chopping a dependent clause out of my sentence, totally lying about what I'd just written! I called Luskin a liar to his face, so the Evolution News & Views moderators panicked, insulted me, got in the last word and closed comments. Paul McBride and I kept hammering away at Luskin et al. so hard that eventually a few ID proponents had to deny what they had clearly previously said. For example, ID proponent Jonathan McLatchie started lying outright at Evolution News & Views, denying the false claims made by ID proponents like Jonathan Wells and Luskin had ever been made by them.
Jonathan McLatchie, 2012: As stated above, no credible scientist claims that all non-coding DNA is "junk." But there are plenty of scientists who claim that the majority of it is "junk." ...Notwithstanding what Paul McBride says, ID proponents are well aware of this literature and do not, as he claims, conflate "junk DNA" and "non-coding-DNA." -- [A Response to Paul McBride on Junk DNA. Jonathan M. ENV. August 3, 2012.]
Oh really Jonathan?
Casey Luskin, ~2003: Ever since scientists began to understand the working of genetics, it became apparent that only about 3% of our DNA is composed of genes that code for proteins. Many evolutionists have claimed that the rest of the DNA is “junk-DNA,"... [Design vs. Descent: A Contest of Predictions. Casey Luskin. IDEA Center. ~2003] Casey Luskin, 2008: Most studies that have claimed that humans and apes have nearly identical genomes have primarily looked at the gene-coding portions of the genome, not the non-coding DNA (formerly claimed to be "junk"). [Study Challenges Two Icons of Evolution. Casey Luskin. Evolution News blog. September 24, 2008.]
Stephen Meyer, 2009: Consider the case of so-called junk DNA—the DNA that does not code for proteins... [Stephen Meyer, Signature in the Cell, Ch. 18, p.406] Far from containing a preponderance of “junk” – nonprotein-coding regions that supposedly perform no function – the genome is dominated by sequences rich in functional information. [Stephen C. Meyer: Signature in the Cell, Epilogue, p. 461]
Casey Luskin, 2010: Examples of unknown DNA functions persist, but design encourages researchers to investigate functions, whereas Darwinism has caused some scientists to wrongly assume that non-coding DNA is junk. [How Do We Test Intelligent Design? Casey Luskin. ENV. March 15, 2010]
Right. So almost ALL ID advocates in fact conflated Junk DNA = non-coding DNA. Let's look again at what McLatchie wrote in 2012:
Jonathan McLatchie, 2012: As stated above, no credible scientist claims that all non-coding DNA is "junk." But there are plenty of scientists who claim that the majority of it is "junk." ...Notwithstanding what Paul McBride says, ID proponents are well aware of this literature and do not, as he claims, conflate "junk DNA" and "non-coding-DNA."
So, after McLatchie in 2012 trying to deny what IDologues had said about conflating non-coding DNA = Junk DNA, I guess IDologues from 2012 stopped promoting this obvious falsehood? Maybe?
Jonathan Wells, 2013: By 1970, however, biologists knew that the vast majority of our genome does not encode proteins, and the non-protein-coding fraction became known as “ junk DNA.” [Jonathan Wells, Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information. in Biological Information (2013)]
Guess not. "Was known as". Passive tense pussy! Who knew it and where, Jonathan?
Discovery Institute, 2013: The real science stopper is Darwinism. It focused only on protein-coding genes and dismissed everything else as “transcriptional noise” or “junk DNA” left behind by the blind tinkerer. -- [More Clues that Intergenic DNA Is Functional. Evolution News & Views. July 15, 2013.]
Doug Axe, 2013: They found out that a very small fraction of the genome actually encodes proteins --- that was the one aspect of genomes that we understood well, is that they encode proteins --- so they assumed all the rest of it is junk. [Biologist Doug Axe on Challenges to Darwinian Evolution. March 22, 2013.]
Can any creationist here tell the truth?
Michael Behe, 2007: But in fact, DNA isn't exactly like a blueprint. Only a fraction of its sections are directly involved in creating proteins and building life. Most of it seems to be excess DNA, where mutations can occur harmlessly." [Michael Behe, The Edge of Evolution (2007), p. 66]
Non-coding DNA was never = Junk DNA Diogenes
I did wonder what the evodelusionists were going to do about losing this sacred icon. Seems they intend to simply rename it and move on hoping nobody remembers the gigantic failure that was JunkDNA. humbled

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