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At Quanta: Cells need almost all of their genes, even the “junk DNA”

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File:DNA simple.svg From Veronique Greenwood at Quanta:

By knocking out genes three at a time, scientists have painstakingly deduced the web of genetic interactions that keeps a cell alive. Researchers long ago identified essential genes that yeast cells can’t live without, but new work, which appears today in Science, shows that looking only at those gives a skewed picture of what makes cells tick: Many genes that are inessential on their own become crucial as others disappear. The result implies that the true minimum number of genes that yeast — and perhaps, by extension, other complex organisms — need to survive and thrive may be surprisingly large.

“Perhaps what we’re sampling here,” Andrews said, “are some functional connections in the cell that we weren’t able to see before.”

One set of new connections, for example, was between genes involved in transporting proteins and genes involved in DNA repair. On the surface, it’s difficult to see what would connect these two functions. And in fact, the researchers still don’t have a mechanistic explanation. But they are sure there is one. “Our immediate reaction was, ‘Well, that’s kind of random,’” Andrews said. “But we’ve learned over the course of doing this project that it’s not random. We just don’t understand how the cell is connected.” More.

Note: One junk DNA defender just isn’t doing politeness anymore. In a less Darwinian science workplace, that could become more a problem for him than for his colleagues.

See also: “Junk” RNA helps regulate metabolism

Junk DNA defender just isn’t doing politeness any more.

Anyone remember ENCODE? Not much junk DNA? Still not much. (Paper is open access.)

Yes, Darwin’s followers did use junk DNA as an argument for their position.

Another response to Darwin’s followers’ attack on the “not-much-junk-DNA” ENCODE findings

Comments
I agree with rna @ 3. The Quanta paper does not mention junk DNA at all.aarceng
July 26, 2018
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goodusername,
Nothing in this article addresses junk dna.
Of course not. There's no such thing, contrary to Darwinist assertions. Just like vestigial organs.bb
May 26, 2018
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Eukaryotic cells require many things beside the genome. The functional complexity we are dealing with in biology is grossly underestimated by some pop-sci writers. The Darwinists behave like the famous guy who was still talking nonsense in the bunker under the Reichstag a few days before the end of WW2. In the days ahead new scientific discoveries will continue to bury their irrational ideas deeper in the mud of embarrassing pseudoscience under the weight of strong factual evidences. Now it's becoming obvious to many of us that they had lost the game right from the start, after they mistakenly extrapolated microevolutionary observations onto macroevolutionary wishful thinking. Sadly they haven't realized it yet.OLV
May 26, 2018
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Though not specifically about the misnamed "junk DNA" sequences, finding unexpected functionality within gene networks helps the now falsified Darwinian prediction of "junk DNA" how exactly? It seems a charitable reading of the headline would have conceded that this finding just taps the nail in that "junk DNA" coffin a little firmer. I particularly like these quotes:
And in fact, the researchers still don’t have a mechanistic explanation. But they are sure there is one. “Our immediate reaction was, ‘Well, that’s kind of random,’” Andrews said. “But we’ve learned over the course of doing this project that it’s not random. We just don’t understand how the cell is connected.”
Perhaps if they stopped trying to view life as a bottom up materialistic affair, and started viewing, correctly I might add, life as a top down information affair then the 'contextuality' of life would not puzzle them so much? Here is a simple example of the' contextuality of information' and how the characteristic of contexuality falsifies 'bottom up' Darwinian explanations:
Dawkin’s infamous Weasel phrase simply does not make sense without taking its proper context into consideration A Meaningful World: How the Arts and Sciences Reveal the Genius of Nature – Book Review Excerpt: They focus instead on what “Methinks it is like a weasel” really means. In isolation, in fact, it means almost nothing. Who said it? Why? What does the “it” refer to? What does it reveal about the characters? How does it advance the plot? In the context of the entire play, and of Elizabethan culture, this brief line takes on significance of surprising depth. The whole is required to give meaning to the part. http://www.thinkingchristian.net/C228303755/E20060821202417/ In fact, it is interesting to note what the specific context is for the “Methinks it is like a weasel” phrase that is used in the Hamlet play. Richard Dawkins's Weasel Program Is Bad in Ways You Never Dreamed - Jonathan Witt - September 23, 2016 Excerpt: "METHINKS IT IS LIKE A WEASEL.",,, The whole scene and the wider tension between the two men, in other words, actually involves Polonius's refusal to see intelligent design where it actually exists -- namely, in the designed death, the murder, of old King Hamlet. Polonius attributes the old king's death to purely blind, material causes when in fact the king's death was intelligently designed -- that is, foul play. Richard Dawkins Is Polonius One parallel to the origins science debate, then, is that Richard Dawkins is a modern day Polonius: He ignores the evidence of intelligent design that should be abundantly clear to him. And the moral, if we're willing to draw a line so far afield from the original play to our present context: Don't be Richard Dawkins. Don't mistake an intelligent cause for a natural one. Don't miss the wider context: http://www.evolutionnews.org/2016/09/dawkinss_weasel103162.html Moreover, the context, in which the phrase is used, is also used to illustrate the spineless nature of one of the characters of the play. i.e. To illustrate just how easily the spineless character in the play, i.e. Polonius, can be led around by the nose to say anything that Hamlet wants him to say: Ham. Do you see yonder cloud that ’s almost in shape of a camel? Pol. By the mass, and ’t is like a camel, indeed. Ham. Methinks it is like a weasel. Pol. It is backed like a weasel. Ham. Or like a whale? Pol. Very like a whale. http://www.bartleby.com/100/138.32.147.html I.e. The phrase, when taken into proper context, reveals deliberate, nuanced, deception and manipulation of another person. After realizing what the actual context of the ‘Methinks it is like a weasel’ phrase was, I remember thinking to myself that it was perhaps the worse possible phrase that Dawkins could have possibly chosen to use to try to illustrate his point. I’m sure deception and manipulation of other people is hardly the point that Dawkins was trying to convey with his infamous ‘Weasel’ program.
bornagain77
May 26, 2018
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Cells need almost all of their genes, even the “junk DNA”
Nothing in this article addresses junk dna. It's only about genes.goodusername
May 26, 2018
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anthropic #4 That concept is easy enough to understand. It is also a very popular research tool in molecular biology to find functionally interacting proteins and is teached in every basic molecular biology/genetics course worth its name. As you probably know yeast researchers call these combinations "synthetic sick" or "synthetic lethal". There can also be the opposite effect that a single protein coding gene knock-out is lethal but with a knock-out of a second protein coding gene the cells become viable again. The big breakthrough in the described work is that the scientists investigated essentially all ~ 36 million possible combinations pairwise knock-outs for the ~ 6000 protein coding genes in bakers yeast and a large number of all possible triple knockouts. What I do not understand is why the title of the post explicitly invokes "junk dna" when the actual work described in the quanta article explicitly deals only with protein coding genes. That is what I find misleading.rna
May 26, 2018
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rna 3 What part of "Many genes that are inessential on their own become crucial as others disappear. The result implies that the true minimum number of genes that yeast — and perhaps, by extension, other complex organisms — need to survive and thrive may be surprisingly large" did you not understand?anthropic
May 26, 2018
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So they find that "genes that are inessential on their own become crucial as others disappear." That finding makes the findings of this previous study of Yeast genes all the more devastating:
"According to a new study partly focused on yeast, the conflicting picture from individual genes is even broader than scientists suspected. “They report that every single one of the 1,070 genes conflicts somewhat,” said Michael Donoghue, an evolutionary biologist at Yale who was not involved in the study. “We are trying to figure out the phylogenetic relationships of 1.8 million species and can’t even sort out 20 [types of] yeast,” he said." A New Approach to Building the Tree of Life - June 2013 https://www.quantamagazine.org/a-new-approach-to-building-the-tree-of-life-20130604/
bornagain77
May 26, 2018
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Could someone at UD maybe make sure that "news" actually reads the articles or maybe even has at least a cursory glance at the papers she/he posts about? The "science" paper that is the basis for the quanta article deals exclusively with the protein coding genes of yeast and does not even mention non-protein coding dna. At quanta this is nicely explained but the headline here is very misleading. Or is this intentional?rna
May 26, 2018
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I know it's Quanta, i.e. science-lite written for whomever; but the way it's written, it sounds like they're relating their first time digging into a heavy duty codebase/software engine and witnessing the fact that you can't simply eyeball most dependencies/emergent functional contexts. Excellent work though. Keep it coming. To quote Dionisio: "They ain’t seen nothin’ yet."LocalMinimum
May 26, 2018
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Here's the ENCODE paper from 2014. The Conclusion of the paper:
In contrast to evolutionary and genetic evidence, biochemical data offer clues about both the molecular function served by underlying DNA elements and the cell types in which they act, thus providing a launching point to study differentiation and development, cellular circuitry, and human disease (14, 35, 69, 111, 112). The major contribution of ENCODE to date has been high-resolution, highly-reproducible maps of DNA segments with biochemical signatures associated with diverse molecular functions. We believe that this public resource is far more important than any interim estimate of the fraction of the human genome that is functional. . . . The data identify very large numbers of sequence elements of differing sizes and signal strengths. Emerging genome-editing methods (113, 114) should considerably increase the throughput and resolution with which these candidate elements can be evaluated by genetic criteria. Given the limitations of our current understanding of genome function, future work should seek to better define genome elements by integrating all three methods to gain insight into the roles they play in human biology and disease.
PaV
May 26, 2018
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