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Linc RNA–once believed useless–plays a role in the genome

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Here is a piece over at Phys.Org dealing with “long, intergenic non-coding” RNA.

“When we removed the specific lincRNA, we looked at the mouse brain and the progenitors were reduced. As a consequence probably, the population [of neurons] that sits on top of the cerebral cortex are reduced … It’s likely that in the future we’ll see a number of studies showing that other lincRNAs are involved in specific behaviors,” Arlotta said. “The brain likes this junk RNA.”

Rinn and his colleagues have generated 18 strains of mutant mice, removing from each a different piece of “junk” genome, or so-called long intergenic noncoding RNAs (lincRNAs). If the lincRNA truly had been “junk,” nothing should have happened.
What the researchers found was the opposite. Obvious defects were observed in seven of the 18 mutant strains. Three died shortly after birth, and there is reason to believe many others also are defective. The authors reported these and more findings in the new online journal eLife, initiated by the Howard Hughes Medical Institute, the Wellcome Trust, and the Max Planck Institute.

I would speculate that all this “junk-DNA” has a profound role in the embryonic development of the brain–here I mean not only the Linc-RNA, but also other types of ncRNA, and also “pseudogenes.” I suspect that the Linc-RNAs, because of their length, might have something to do with the overall length of neurons within the brain. Some clever experimentalist should follow this up.

Meanwhile, we’re seeing a complete repudiation of Darwinian/evolutionary(population genetics) expectations.

ID predicts something: it turns out to be right. Darwinists/geneticsits predict something: it turns out to be wrong.

So much for the scientific method.

However–drum roll, please….–
Another day; another bad day for Darwinism!!!

Semi OT: Excellent article up on ENV:
(Dual Coding) RNA Shows Design, Too - February 4, 2014 Excerpt: A paper in Nature describes how information is stored not only in RNA's base sequence, but in its folds. Because RNA has more degrees of freedom, it can take on a wide variety of forms not possible for DNA. "RNA has a dual role as an informational molecule and a direct effector of biological tasks. The latter function is enabled by RNA's ability to adopt complex secondary and tertiary folds and thus has motivated extensive computational and experimental efforts for determining RNA structures," the authors begin (emphasis added). In their conclusion, they say, "We identify hundreds of specific mRNA regions that are highly structured in vivo, and we show for three examples that these structures affect protein expression." In other words, the structure, not just the sequence, carries functional information. "Our studies provide an excellent set of candidate regions, among the truly enormous number of structured regions seen in vitro, for exploring the regulatory role of structured mRNAs.",,, If RNAs show design, why not design them ourselves? In an experimental twist, researchers at Carnegie Mellon invited the public to be their design lab. In a "crowdsourcing" experiment, they found that volunteers could create new RNA designs better than computers could. The starting pool of 37,000 citizen scientists has grown to 130,000 members exercising their intelligent design skills. "An enthusiastic group of non-experts, working through an online interface and receiving feedback from lab experiments, has produced designs for RNA molecules that are consistently more successful than those generated by the best computerized design algorithms, researchers at Carnegie Mellon University and Stanford University report." http://www.evolutionnews.org/2014/02/rna_shows_desig081841.html
Of related note: This following peer-reviewed paper holds that there is 'irreducible organizational complexity' between the genetic (digital) information and the epigenetic (analog/structural) information:
Refereed scientific article on DNA argues for irreducible complexity - October 2, 2013 Excerpt: This paper published online this summer is a true mind-blower showing the irreducible organizational complexity (author’s description) of DNA analog and digital information, that genes are not arbitrarily positioned on the chromosome etc.,, ,,,First, the digital information of individual genes (semantics) is dependent on the the intergenic regions (as we know) which is like analog information (syntax). Both types of information are co-dependent and self-referential but you can’t get syntax from semantics. As the authors state, “thus the holistic approach assumes self-referentiality (completeness of the contained information and full consistency of the different codes) as an irreducible organizational complexity of the genetic regulation system of any cell”. In short, the linear DNA sequence contains both types of information. Second, the paper links local DNA structure, to domains, to the overall chromosome configuration as a dynamic system keying off the metabolic signals of the cell. This implies that the position and organization of genes on the chromosome is not arbitrary,,, http://www.christianscientific.org/refereed-scientific-article-on-dna-argues-for-irreducibly-complexity/
To state what should be needless to say, these findings are not conducive to Darwinian presuppositions but are conducive to Intelligent Design presuppositions! bornagain77
I think you are conflating non-coding DNA, which is most of the genome, with long-noncoding RNAs which are products of a small subset of the non-coding DNA. wd400
I suspect your relatively new to the ID battles that have taken place online over the last 10 years, but I reassure you there have been prominent names in the business who have said, specifically, that lnc DNA= lnc RNA is almost 'proof' that the genome is mostly 'junk.' So just because you might see things differently, or you're unaware of what has or has not been said, doesn't make your declaration valid. For example, get your story right about lncRNA only representing 1% of the genome; evolutionists have been at this blog claiming that it is as high as 35% and more. PaV
Linc-RNA was, and is, the ’cause-celebre’ of those still convinced that the genome contains large portions of “junk-DNA” Really? I don't believe I've ever seen anyone claim the presence of lncRNAs was evidence for junkDNA. Hell, they combine to make less that one percent of our genome, so it wouldn't be much of an argument... wd400
Pav wondered
What will history have to say about all this?
Depends on who writes the history. -Q Querius
Eric: Linc-RNA was, and is, the 'cause-celebre' of those still convinced that the genome contains large portions of "junk-DNA". We aren't hearing from them now. Since what we call "natural selection" is mostly concerned with eliminating non-essential and harmful DNA, I don't think we'll end up with very much "junk-DNA" when all is said and done. What we're seeing is that most of what has been considered "junk-DNA" has a role in embryology. In 'adult' animals/organisms, this means that we won't see them at work in the living cell simply because their 'work' has already been done. What we'll continue to see is scientists zeroing in on ncRNA in the developmental phases of animals. The "junk-DNA" myth will be completely destroyed, and then the Darwinists will say with growing intensity: "Whoever said anything about "junk-DNA"? Why, if it didn't have function, it wouldn't be there! Of course we knew that the whole time." You know, Ptolomeic epicycles. What will destroy Darwinism completely--and I think it will only take about another 10-12 years (if there aren't any major wars)---because of whole genome analysis of more and more organisms, coupled with techniques for extracting genotypes from fossil remains. Unless, of course, Governor Cuomo becomes president and says that all who deny Darwinism don't deserve to live in this country, and he banishes us to Antarctica---which, of course, will be warm by then! Jonah Goldberg wrote a book, Liberal Fascism. What has become so much clearer under this present administration (and now spreading to the state level because the DoJ is so corrupt) is that liberals are, indeed, fascists. Definition of a fascist: someone who seeks to eliminate any dissenting political voices. Ah, yes, the great bastions of liberalism---the universities, where if you don't toe the ideological line--even in science--you will be destroyed. What will history have to say about all this? PaV
I think anyone who has had a glimpse at the mind blowing complexity being dealt with in DNA, who still thinks that the vast majority of DNA is junk just because we don't fully understand exactly what it all does, is a more than a few fries short of a happy meal,, Notes along that line: 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 DNA Packaging: Nucleosomes and Chromatin each of us has enough DNA to go from here to the Sun and back more than 300 times, or around Earth's equator 2.5 million times! How is this possible? http://www.nature.com/scitable/topicpage/DNA-Packaging-Nucleosomes-and-Chromatin-310 DNA - Replication, Wrapping & Mitosis - video https://vimeo.com/33882804 ‘How good would each typists have to be, in order to match the DNA’s performance? The answer is almost too ludicrous to express. For what it is worth, every typists would have to have an error rate of about one in a trillion (conservatively a billion);. Richard Dawkins - The Blind Watchmaker - Page 123-124 DNA: The Ultimate Hard Drive - Science Magazine, August-16-2012 Excerpt: "When it comes to storing information, hard drives don't hold a candle to DNA. Our genetic code packs billions of gigabytes into a single gram. A mere milligram of the molecule could encode the complete text of every book in the Library of Congress and have plenty of room to spare." http://news.sciencemag.org/sciencenow/2012/08/written-in-dna-code.html DNA Computer Excerpt: A DNA chip less than the size of a dime will have the capacity to perform 10 trillion parallel calculations at one time as well as hold ten terabytes of data. The capacity to perform parallel calculations, much more trillions of parallel calculations, is something silicon-based computers are not able to do. As such, a complex mathematical problem that could take silicon-based computers thousands of years to solve can be done by DNA computers in hours. http://www.tech-faq.com/dna-computer.html Cells Are Like Robust Computational Systems, - June 2009 Excerpt: Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. ,,,,"We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail." http://www.sciencedaily.com/releases/2009/06/090616103205.htm "Not only are there many different codes in the sequences, but they overlap, so that the same letters in a sequence may take part simultaneously in several different messages." Edward N. Trifonov - 2010 Systems biology: Untangling the protein web - July 2009 Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. "Combine all this and you can start to think that maybe some of the information flow can be captured," he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. "The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent," he says. "The simple pathway models are a gross oversimplification of what is actually happening." http://www.nature.com/nature/journal/v460/n7253/full/460415a.html "applying Darwinian principles to problems of this level of complexity is like putting a Band-Aid on a wound caused by an atomic weapon. It's just not going to work." - David Berlinski etc.. etc.. etc.. bornagain77
There might indeed be some junk DNA, but the notion that there are pervasive amounts of junk DNA is an idea based on a lack of information, coupled with a naive view of systems engineering, hampered with the trailing baggage of a nineteenth-century view of biology. Eric Anderson

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