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
11 Replies to “At Quanta: Cells need almost all of their genes, even the “junk DNA””
Here’s the ENCODE paper from 2014.
The Conclusion of the paper:
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.”
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?
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:
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?
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.
Nothing in this article addresses junk dna. It’s only about genes.
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:
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:
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.
Of course not. There’s no such thing, contrary to Darwinist assertions. Just like vestigial organs.
I agree with rna @ 3. The Quanta paper does not mention junk DNA at all.