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Tuesday, October 19, 2021

Society for Molecular Biology and Evolution (SMBE) spreads misinformation about junk DNA

The Society for Molecular Biology and Evolution (SMBE) is a pretigious society of workers in the field of molecular evolution. I am a member and I have attended many of their conferences. SMBE sponsors several journals incucluding Genome Biology and Evolution (GBE), which is published by Oxford Academic Press.

The latest issue of GBE has a paper by Stitz et al. (2021) that describes some repetitive elements in the platyhelminth Schistosoma mansoni. The authors conlcude that some of these elements might have a function and this prompts them to begin their discussion with the following sentences.

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. The latter might have accumulated during evolution, for example, as a consequence of gene duplication events to separate and individualize gene function (Britten and Kohne 1968; Comings 1972; Ohno 1999). This view has fundamentally changed (Biscotti, Canapa, et al. 2015), and our study is the first one addressing this issue with structural, functional, and evolutionary aspects for the genome of a multicellular parasite.

It is unfortunate that the senior authors didn't receive a good undergraduate education but one might think that they would rectify that problem by learning about genomes and junk DNA before publishing in a good journal devoted to genomes and evolution. Alas, they didn't and, even worse, the journal published their paper with those sentences intact.

As you might imagine, these statements were seized upon by Intelligent Design Creationists who wasted no time in posting on their creationist blog [Oxford Journal: “The Days of ‘Junk DNA’ Are Over ”].

But that's not the worst of it. The same issue contains an editorial written by Casey McGrath who self identifies as a employee of the Society for Molecular Biology and Evolution in Lawrence Kansus (USA). She is the Social Media Editor for Genome Biology and Evolution. The title of her editorial is "Highlight—“Junk DNA” No More: Repetitive Elements as Vital Sources of Flatworm Variation" (McGrath, 2021). She starts off by repeating and expanding upon the words of the senior authors of the study that I referred to above.

“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). Titled “Satellite-like W elements: repetitive, transcribed, and putative mobile genetic factors with potential roles for biology and evolution of Schistosoma mansoni,” 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.

“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. Since then, however, the common understanding of such sequences has fundamentally changed, revealing a plethora of regulatory sequences, noncoding RNAs, and sequences that play a role in chromosomal and nuclear structure. With their article, Grunau and Grevelding, along with their coauthors from Justus Liebig University Giessen, University of Montpellier, and Leipzig University, contribute further evidence to a growing consensus that such sequences play critical roles in evolution.

There's no rational excuse for publishing the Stitz et al. paper with those ridiculous statements and there's no rational excuse for compounding the error by highlighting them in an editorial comment. The Society for Molecular Biology and Evolution should be ashamed and embarrassed and they should issue a retraction and a clarification. They should state clearly that junk DNA is alive and well and supported by so much evidence that it would be perverse to deny it.


McGrath,C. (2012) Highlight—“Junk DNA” No More: Repetitive Elements as Vital Sources of Flatworm Variation. Genome Biology and Evolution 13: evab217 [doi: 10.1093/gbe/evab217]

Stitz, M., Chaparro, C., Lu, Z., Olzog, V.J., Weinberg, C.E., Blom, J., Goesmann, A., Grunau, C. and Grevelding, C.G. (2021) Satellite-Like W-Elements: Repetitive, Transcribed, and Putative Mobile Genetic Factors with Potential Roles for Biology and Evolution of Schistosoma mansoni. Genome Biology and Evolution 13:evab204. [doi: 10.1093/gbe/evab204]

12 comments :

  1. If things keep going like this, "Junk DNA Is Dead" headlines will become more common than "Darwin Was Wrong" headlines. It's a clickbait world.

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  2. As usual, I sent the authors a link to my blog post and invited them to reply. As usual, I got no response.

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  3. UNIVERSITY OF CHICAGO MOST MEMORABLE LECTURE

    Larry provides us with a link to a Discovery Institute article in Evolution News and Science Today. He might note recognition of macroevolution by Paul Nelson in another article (June 18) entitled "The Most Memorable Lecture I Ever Heard at the University of Chicago — Finally Published." I suspect that when there is a better general understood of the macroevolution/microevolution distinction, folk will begin to more clearly recognize the role(s) and evolution of DNA that some deem as "junk."

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    1. What do you mean when you say,

      "I suspect that when there is a better general understood of the macroevolution/microevolution distinction, folk will begin to more clearly recognize the role(s) and evolution of DNA that some deem as 'junk.'"

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  4. Despite his creationist leanings, Nelson recalls his attendance at the Chicago annual Conceptual Foundations of Science lecture series in 1989. After decades of "samisdat" circulation, the substance of that lecture has now publicly emerged. Hopefully, in future folk will look at problems in evolutionary biology, such as "junk DNA", with a deeper, more profound, conceptual understanding. [Thanks Larry for noting the typo: "I suspect that when there is a better general understanding of the macroevolution/microevolution distinction, folk will begin to more clearly recognize the role(s) and evolution of DNA regions that some deem as "junk".]

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  5. Despite his creationist leanings, Nelson ... His creationist "leanings"? I think he has leaned as far over as anyone could.

    Hopefully, in future folk will look at problems in evolutionary biology, such as "junk DNA", with a deeper, more profound, conceptual understanding. Do you expect that having a more detailed understanding of the disagreement between Yuri Filipchenko and Theodosius Dobzhansky on whether macroevolution was fundamentally different from microevolution will somehow greatly illuminate our own understanding of these issues? I would not expect that.

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  6. In the same sense questioning the existence of junk DNA, this article published in Quanta Magazine:
    https://www.quantamagazine.org/the-complex-truth-about-junk-dna-20210901/

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    1. We discussed this article on Facebook. It's interesting because the author actually covers the controversy very well but he's mainly interested in promoting an Australian scientist named Seth Cheetham.

      The author of the article references three experts on junk DNA: Alex Palazzo, Ryan Gregory, and Dan Gaur. Then he balances by quoting Seth Cheetam who says, "Cheetham thinks that dogma about “junk DNA” has weighed down inquiry into the question of how much of it deserves that description."

      I decided not to blog about that article because it's too complicated to explain where the author is going astray.

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    2. Do you have some news about the publication of your book?

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  7. But none of what you said was a refutation of what Stitz et. al. wrote. Merely stating that "junk DNA is alive and well" is not a refutation, how are Stitz et. al. wrong?

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    1. It was stupid to say that the "days of junk DNA are over." That reflects a profound misunderstanding of the structure of genomes.

      It was stupid to say that the noncoding part of the genome consists of useless sequences and it was stupid to say that such an idea was common doctrine. That just means that the authors were not only ignorant of the basic concepts of their field but ignorant of its history as well.

      The authors are just trying to hype their results by making them seem far more important than they really are. That's also wrong.

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