Formerly thought “junk DNA,” lncRNA guides development of heart muscle cells

_{Denyse O'Leary

September 13, 2016

'Junk DNA', News}

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long noncoding RNA interacts with a cellular protein to control the development of heart muscle cells. / Jose-Luis Olivares,MIT

Several years ago, biologists discovered a new type of genetic material known as long noncoding RNA. This RNA does not code for proteins and is copied from sections of the genome once believed to be “junk DNA.”

Since then, scientists have found evidence that long noncoding RNA, or lncRNA, plays roles in many cellular processes, including guiding cell fate during embryonic development. However, it has been unknown exactly how lncRNA exerts this influence.

Inspired by historical work showing that structure plays a role in the function of other classes of RNA such as transfer RNA, MIT biologists have now deciphered the structure of one type of lncRNA and used that information to figure out how it interacts with a cellular protein to control the development of heart muscle cells. This is one of first studies to link the structure of lncRNAs to their function. More. Paper. (paywall) – Zhihong Xue et al. A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage. Molecular Cell, September 2016 DOI: 10.1016/j.molcel.2016.08.010

One doesn’t hear so much any more about how “junk DNA” is exactly what we should expect if Darwinism were a correct account of evolution. But finding out that it isn’t junk is, of course, a validation too, right? Some beliefs are just plain immune to the vagaries of evidence.

See also: The latest in functional junk DNA

and these for background:

New York Times science writer defends the myth of junk DNA

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

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

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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Comments

Larry Moran. It is evident that you have insight concerning biological processes and the "serious scientific debate", from your comments here and other information sources. I read your comments with inquisitiveness. Yet, not intending to diminish the previous acknowledgments, statements such as, "Unfortunately, nobody in the ID community is capable of participating in such a serious scientific debate.", are equally disingenuous to proponents of creation science making sweeping statements concerning counterfactual assumptions from evolutionary proponents. And the divisiveness between the fabricated groupings of physicalism-alone vs metaphysicalism-physicalism is too often a battle over unfortunate words (concepts) such as junk DNA, hidden variables, nothing, evolution and creation. This battle over unfortunate words could be traced to the continuing intercourse, made public, between specialists (scientists), quasi-specialists (journalists, hobbyists), and nonspecialists, though tracing the battle would be a daunting task even for the rare unbiased researcher. I would think, however naively, that a rare unbiased researcher could suspend even strongly held a priori assumptions during an empirical investigation to deduce a posteriori explanations for scientific data. We do not readily see a rare unbiased researcher standing in our midst ... not in the socio-political arena, not in religious pursuits, not in scientific inquiries, not in human experiencing. Possibly the obstinacy is a "natural" attribute of human experiencing ... for survival fitness, a drive (will) to power, a cognitive closure ... but are we not capable of "transcending" and "transforming" the results from evolutionary influences? "All I can do is to point to some excellent articles: Larry Moran has waged a longstanding effort to spread the true wisdom about junk DNA for years on his blog. Ed Yong exhaustively summarizes a long list of opinions, links and analysis. T. Ryan Gregory has some great posts dispelling the myth of the myth of junk DNA." http://blogs.scientificamerican.com/the-curious-wavefunction/three-reasons-to-like-junk-dna/ "Palazzo and Gregory, on the other hand, argue that evolution should produce junk. The reason has to do with the fact that natural selection can be quite weak in some situations. ... When non-functional DNA builds up in our genome, it’s harder for natural selection to strip it out than if we were bacteria. ... While junk is expected, a junk-free genome is not. Palazzo and Gregory based this claim on a concept with an awesome name: mutational meltdown." http://phenomena.nationalgeographic.com/2014/05/09/the-case-for-junk-dna/ "Genetic material derisively called “junk” DNA because it does not contain the instructions for protein-coding genes and appears to have little or no function is actually critically important to an organism’s evolutionary survival, according to a study conducted by a biologist at UCSD." https://www.sciencedaily.com/releases/2005/10/051020090946.htmredwave_{September 14, 2016
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as to:
Nevertheless, some scientists disagree (with 90% junk DNA) so there is a serious debate within the scientific community about the amount of junk DNA. Unfortunately, nobody in the ID community is capable of participating in such a serious scientific debate.
In order to have a 'serious' scientific debate about Darwinian evolution in the first place should not Darwinian evolution first qualify as a 'serious' science? Instead of being the unfalsifiable pseudo-science, filled with imaginary just-so stories, that it is?
Sociobiology: The Art of Story Telling – Stephen Jay Gould – 1978 – New Scientist Excerpt: Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers “Just So stories”. When evolutionists study individual adaptations, when they try to explain form and behaviour by reconstructing history and assessing current utility, they also tell just so stories – and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance. https://books.google.com/books?id=tRj7EyRFVqYC&pg=PA530 Dubitable Darwin? Why Some Smart, Nonreligious People Doubt the Theory of Evolution By John Horgan on July 6, 2010 Excerpt: Early in his career, the philosopher Karl Popper ,, called evolution via natural selection "almost a tautology" and "not a testable scientific theory but a metaphysical research program." Attacked for these criticisms, Popper took them back (in approx 1978). But when I interviewed him in 1992, he blurted out that he still found Darwin's theory dissatisfying. "One ought to look for alternatives!" Popper exclaimed, banging his kitchen table. http://blogs.scientificamerican.com/cross-check/dubitable-darwin-why-some-smart-nonreligious-people-doubt-the-theory-of-evolution/ Darwinian Evolution is a Unfalsifiable Pseudo-Science - Mathematics – video https://youtu.be/aKNHgQo2SSA
As to:
About. 90% of the human genome is junk.
That claim is a patently false claim. Moreover, it is a patently false claim that reveals the anti-scientific nature of the Darwinian core. Instead of fostering research, pseudo-scientific Darwinian dogmatism stifles research by sending researchers down blind alleys.
On Junk DNA Claim, Francis Collins Walks It Back, Admitting "Hubris" - July 20, 2016 Excerpt: (Francis) Collins claimed on page 136 that huge chunks of our genome are "littered" with ancient repetitive elements (AREs), so that "roughly 45 percent of the human genome [is] made up of such genetic flotsam and jetsam." In his talk he claimed the existence of "junk DNA" was proof that man and mice had a common ancestor, because God would not have created man with useless genes. Last year, though, speaking at the J.P. Morgan Healthcare Conference in San Francisco, Collins threw in the towel: "In terms of junk DNA, we don't use that term anymore because I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome, as if we knew enough to say it wasn't functional. ... Most of the genome that we used to think was there for spacer turns out to be doing stuff." http://www.evolutionnews.org/2016/07/on_junk_dna_fra103008.html
As to:
no knowledgeable scientist ever said any such thing. Junk DNA is inconsistent with strict Darwinism. That’s why most Darwinists opposed it.
Although corrected on this before, Moran just repeats the same false claim over and over again,
Jonathan Wells on his book, The Myth of Junk DNA – yes, it is a Darwinist myth and he nails it as such - March 2011 Excerpt: Some people revise history by claiming that no mainstream biologists ever regarded non-protein-coding DNA as “junk.” This claim is easily disproved: Francis Crick and Leslie Orgel published an article in Nature in 1980 (284: 604-607) arguing that such DNA “is little better than junk,” and “it would be folly in such cases to hunt obsessively” for functions in it. Since then, Brown University biologist Kenneth R. Miller, Oxford University biologist Richard Dawkins, University of Chicago biologist Jerry A. Coyne, and University of California–Irvine biologist John C. Avise have all argued that most of our DNA is junk, and that this provides evidence for Darwinian evolution and against intelligent design. National Institutes of Health director Francis Collins argued similarly in his widely read 2006 book The Language of God. It is true that some biologists (such as Thomas Cavalier-Smith and Gabriel Dover) have long been skeptical of “junk DNA” claims, but probably a majority of biologists since 1980 have gone along with the myth. The revisionists are misinformed (or misinforming). https://uncommondescent.com/junk-dna/jonathan-wells-on-his-book-the-myth-of-junk-dna-yes-it-is-a-darwinist-myth-and-he-nails-it-as-such/#more-18154 Susumu Ohno, 1972, Ford Doolittle, 1980, Francis Crick & Leslie Orgel, 1980, Carl Sagan, 1992 Kenneth Miller, 1994 Sydney Brenner, 1998 Francis Collins, 2006 Michael Shermer, 2006 PZ Myers, 2008 Richard Dawkins, 1979, 1998, 2009 John Avise, 2010 Dan Graur et al, 2012, 2013 Don Prothero, 2013 T. Ryan Gregory, & Alexander Palazzo, 2014 http://notascientist.d512.com/worldview/biology/evolution/junk-dna/
bornagain77_{September 14, 2016
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One doesn’t hear so much any more about how “junk DNA” is exactly what we should expect if Darwinism were a correct account of evolution.
That's because no knowledgeable scientist ever said any such thing. Junk DNA is inconsistent with strict Darwinism. That's why most Darwinists opposed it. Those of us who subscribe to a more pluralistic view of evolution know that junk DNA is consistent with that view but none of us ever said that junk DNA is what we "expect" if evolution were true. That would be ridiculous since there are millions of species that have very little junk DNA. I have explained this to Denyse and the other Intelligent Design Creationists many times over the past two decades. The fact that they still don't understand these basic facts tells me that they really aren't interested in facts. They are about 60,000 lncRNAs. If they were all biologically functional they would account for about 1% of the genome. However, it is certain that the vast majority are just spurious transcripts. There are about 200 known, biologically functional, lncRNAs in the human genome. There are probably a few hundred more strong candidates for functional lncRNAs and every now and then scientists succeed in finding a function for one of them. We don't hear about all the experiments that fail to find a function and end up showing that the lncRNA is just another accidental transcript or junk RNA. About. 90% of the human genome is junk. There is so much evidence to support this idea that it's very unlikely to be wrong. Nevertheless, some scientists disagree so there is a serious debate within the scientific community about the amount of junk DNA. Unfortunately, nobody in the ID community is capable of participating in such a serious scientific debate.Larry Moran_{September 14, 2016
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Are we posting these truths to upset Prof Moran?Andre_{September 14, 2016
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