# “Junk DNA” No More: Repetitive Elements as Vital Sources of Flatworm Variation
**URL:** https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352
**Category:** Conversation
**Tags:** Science
**Created:** [October 7, 2021, 1:15pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352 "2021-10-07T13:15:30Z")
**Posts on this page:** 20
**Page:** 1
### Author:  [@Spinosaurus-729](https://discourse.peacefulscience.org/u/Spinosaurus-729)
#### Post date: [October 7, 2021, 1:15pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/1 "2021-10-07T13:15:30Z")
> **[Highlight—“Junk DNA” No More: Repetitive Elements as Vital Sources of...](https://academic.oup.com/gbe/article/13/10/evab217/6380869?searchresult=1)**
>
> “The days of ‘junk DNA’ are over,” according to Christoph Grunau and Christoph Grevelding, the senior authors of a new research article in Genome Biology and Ev
> Blockquote “The days of ‘junk DNA’ are over,” according to Christoph Grunau and Christoph Grevelding, the senior authors of a new research article in _Genome Biology and Evolution._ Their study provides an in-depth look at an enigmatic superfamily of repetitive DNA sequences known as W elements in the genome of the human parasite _Schistosoma mansoni_ ([Stitz et al. 2021](javascript:;)). Titled “[Satellite-like W elements: repetitive, transcribed, and putative mobile genetic factors with potential roles for biology and evolution of Schistosoma mansoni](https://do.org/i10.1093/gbe/evab204),” the analysis reveals structural, functional, and evolutionary aspects of these elements and shows that, far from being “junk,” they may exert an enduring influence on the biology of _S. mansoni_ .
[Here is the actual paper](https://academic.oup.com/gbe/article/13/10/evab204/6361599'), the link seems to be broken. They say,
> Blockquote The days of “junk DNA” are over. When the senior authors of this article studied genetics at their respective universities, the common doctrine was that the nonprotein coding part of eukaryotic genomes consists of interspersed, “useless” sequences, often organized in repetitive elements such as satDNA
It seems to me that the study is conflating non-coding DNA with junk. Dan Graur [had a twitter exchange](https://twitter.com/DanGraur/status/1445404264872960004) with the author over it. What do you guys think?
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### Author:  [@Dan\_Eastwood](https://discourse.peacefulscience.org/u/Dan_Eastwood)
#### Post date: [October 7, 2021, 1:16pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/2 "2021-10-07T13:16:39Z")
I anticipate a spirited discussion. 😄
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### Author:  [@nwrickert](https://discourse.peacefulscience.org/u/nwrickert)
#### Post date: [October 7, 2021, 2:24pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/3 "2021-10-07T14:24:25Z")
> [@Spinosaurus-729](#):
>
> It seems to me that the study is conflating non-coding DNA with junk.
That’s very likely.
The reaction of creationists to the term “junk DNA” is a bit of a puzzle.
I long ago accepted that “junk DNA” is a technical term within biology, and should not be conflated with the ordinary meaning of “junk”.
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### Author:  [@Michael\_Okoko](https://discourse.peacefulscience.org/u/Michael_Okoko)
#### Post date: [October 7, 2021, 2:24pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/4 "2021-10-07T14:24:40Z")
> [@Spinosaurus-729](#):
>
> It seems to me that the study is conflating non-coding DNA with junk
You are right.
> [@](#):
>
> “When we studied genetics at university in the 1980s, **the common doctrine was that the non-protein coding parts of eukaryotic genomes consisted of interspersed, ‘useless’ sequences** , often organized in repetitive elements like satellite DNA,” note Grunau and Grevelding.
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### Author:  [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)
#### Post date: [October 7, 2021, 2:25pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/5 "2021-10-07T14:25:04Z")
> [@Spinosaurus-729](#):
>
> What do you guys think?
500mg of Larry Moran, stat, IV push.
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### Author:  [@dsterncardinale](https://discourse.peacefulscience.org/u/dsterncardinale)
#### Post date: [October 7, 2021, 4:59pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/6 "2021-10-07T16:59:49Z")
The overhyping of mediocre findings is outa control.
> Based on their findings, the authors hypothesize that W element presence, location, and copy number may change rapidly over time and across generations. Indeed, they note that variability and genome plasticity are hallmarks of parasite genomes, with different mechanisms giving rise to such variation in different lineages. This variability/plasticity may help parasites escape host surveillance and colonize new host environments. The authors hypothesize that W elements “not only influence the biology of _S. mansoni_ , but they might represent one of the sources of heritable variability, thus shaping the evolution of the family Schistosomatidae.”
> As Grevelding points out, one of the caveats of this study is that the functional predictions of W elements “are mainly based on bioinformatics analyses and have to be substantiated by functional analyses. This is also true for our hypothesis about the mobile character of W elements, which we concluded from genome and structural analysis, but for which we have no direct functional evidence yet.”
C’mon, people. Everyone involved should know better.
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### Author:  [@Michael\_Okoko](https://discourse.peacefulscience.org/u/Michael_Okoko)
#### Post date: [October 7, 2021, 4:59pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/7 "2021-10-07T16:59:58Z")
> [@John\_Harshman](#):
>
> > [@Spinosaurus-729](#):
> >
> > What do you guys think?
>
> 500mg of Larry Moran, stat, IV push.
I can see you are still traumatized by your recent hospital experience 😉
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### Author:  [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)
#### Post date: [October 7, 2021, 5:00pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/8 "2021-10-07T17:00:11Z")
Are they truly this ignorant, or just playing with sansationalism?
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### Author:  [@Joe\_Felsenstein](https://discourse.peacefulscience.org/u/Joe_Felsenstein)
#### Post date: [October 8, 2021, 12:55pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/9 "2021-10-08T12:55:01Z")
I’m embarrassed to say that I’m on the editorial board of _Genome Biology and Evolution_. Have been inactive in that role. It is possible that the Editor is trying to get a debate going in the journal’s pages. At least 95% of molecular evolutionists are on the pro-junk-DNA side of the argument.
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### Author:  [@dsterncardinale](https://discourse.peacefulscience.org/u/dsterncardinale)
#### Post date: [October 8, 2021, 7:36pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/10 "2021-10-08T19:36:08Z")
I’m repeatedly astonished at the pronouncements of NO MORE JUNK DNA and JUNK DNA IS DEAD. Is it not obvious to just about everyone that there’s at least SOME of the genome that’s just…there? But doesn’t do anything useful? With 40+ percent retrotransposons, 8 percent or whatever it is ERVs…putting aside how circumstantial this particular evidence is _according to the authors_, it would be completely unreasonable, just conceptually, to think all that stuff has acquired some secondary function since its incorporation. And that’s before the 2014 ENCODE study that found levels of transcription for many transcribed sequences so low as to be, like, countable number of RNAs per cell. Boggles the mind that we’re still getting headlines like this in 2021.
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### Author:  [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)
#### Post date: [October 9, 2021, 1:11am UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/11 "2021-10-09T01:11:24Z")
Fails the onion test, fails the fugu test, fails the smell test.
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### Author:  [@Joe\_Felsenstein](https://discourse.peacefulscience.org/u/Joe_Felsenstein)
#### Post date: [October 9, 2021, 2:20pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/12 "2021-10-09T14:20:00Z")
In 2012 when ENCODE announced the end of the idea of Junk DNA lots of molecular evolutionists were outraged. I used to go around saying that this was a huge setback, that it would take us a decade to convince molecular biologists and the outside world that there really was lots of junk DNA. At the time I was concerned that I was being too apocalyptic. Maybe I was exaggerating how bad the situation was.
Nearly a decade later, I can see I was understating how bad things would be.
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### Author:  [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)
#### Post date: [October 9, 2021, 2:20pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/13 "2021-10-09T14:20:14Z")
One has to wonder how something declared dead a hundred times over can die yet again. Just when are we finally going to run out of still living junk DNA?
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### Author:  [@Spinosaurus-729](https://discourse.peacefulscience.org/u/Spinosaurus-729)
#### Post date: [October 9, 2021, 2:20pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/14 "2021-10-09T14:20:15Z")
In the Twitter thread I linked, one of the authors seem to agree with Graur.
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### Author:  [@thoughtful](https://discourse.peacefulscience.org/u/thoughtful)
#### Post date: [October 9, 2021, 9:51pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/15 "2021-10-09T21:51:43Z")
> [@Rumraket](#):
>
> Just when are we finally going to run out of still living junk DNA?
That’s a good question. 🙂
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### Author:  [@Joe\_Felsenstein](https://discourse.peacefulscience.org/u/Joe_Felsenstein)
#### Post date: [October 10, 2021, 5:10pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/16 "2021-10-10T17:10:33Z")
Did they really agree? To me it seemed like he was trying to make Graur’s opposition go away by pretending that they agreed.
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### Author:  [@scd](https://discourse.peacefulscience.org/u/scd)
#### Post date: [October 10, 2021, 5:10pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/17 "2021-10-10T17:10:34Z")
> [@John\_Harshman](#):
>
> Fails the onion test, fails the fugu test, fails the smell test.
you are again ignoring the rule:
([A meta-analysis of the genomic and transcriptomic composition of complex life - PubMed](https://pubmed.ncbi.nlm.nih.gov/23759593/))
and we should also add this new study about ERVs:
[https://journals.asm.org/doi/full/10.1128/JVI.02299-20](https://journals.asm.org/doi/full/10.1128/JVI.02299-20)
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### Author:  [@Spinosaurus-729](https://discourse.peacefulscience.org/u/Spinosaurus-729)
#### Post date: [October 10, 2021, 5:10pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/18 "2021-10-10T17:10:35Z")
Yes, it is getting kind of ridiculous at this point.
I blame the pop sci writers. I mean, [check this out](https://phys.org/news/2021-10-human-overlooked-dna.html). It says all non-coding DNA was thought of as junk, and the actual paper doesn’t even mention anything about function…
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### Author:  [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)
#### Post date: [October 10, 2021, 10:50pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/19 "2021-10-10T22:50:16Z")
None of that addresses the Onion test.
And some ERVs are functional =/= all ERVs are functional.
You have done no work to deal with the case for junk DNA, you have just waved your hands in the direction of wild extrapolations from weak to non-existent data.
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### Author:  [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)
#### Post date: [October 10, 2021, 10:50pm UTC](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352/20 "2021-10-10T22:50:19Z")
> [@scd](#):
>
> you are again ignoring the rule:
That’s the dog’s ass plot, and the choice of genomes is oddly biased. The fact that humans are at the very top should make you at least slightly suspicious, though of course it won’t.
[Next page](https://discourse.peacefulscience.org/t/junk-dna-no-more-repetitive-elements-as-vital-sources-of-flatworm-variation/14352.md?page=2)