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Saturday, May 14, 2022

Editing the Wikipedia article on non-coding DNA

I decided to edit the Wikipedia article on non-coding DNA by adding new sections on "Noncoding genes," "Promoters and regulatory sequences," "Centromeres," and "Origins of replication." That didn't go over very well with the Wikipedia police so they deleted the sections on "Noncoding genes" and "Origins of replication." (I'm trying to restore them so you may see them come back when you check the link.)

I also decided to re-write the introduction to make it more accurate but my version has been deleted three times in favor of the original version you see now on the website. I have been threatened with being reported to Wikipedia for disruptive edits.

The introduction has been restored to the version that talks about the ENCODE project and references Nessa Carey's book. I tried to move that paragraph to the section on the ENCODE project and I deleted the reference to Carey's book on the grounds that it is not scientifically accurate [see Nessa Carey doesn't understand junk DNA]. The Wikipedia police have restored the original version three times without explaining why they think we should mention the ENCODE results in the introduction to an article on non-coding DNA and without explaining why Nessa Carey's book needs to be referenced.

The group that's objecting includes Ramos1990, Qzd, and Trappist the monk. (I am Genome42.) They seem to be part of a group that is opposed to junk DNA and resists the creation of a separate article for junk DNA. They want junk DNA to be part of the article on non-coding DNA for reasons that they don't/won't explain.

The main problem is the confusion between "noncoding DNA" and "junk DNA." Some parts of the article are reasonably balanced but other parts imply that any function found in noncoding DNA is a blow against junk DNA. The best way to solve this problem is to have two separate articles; one on noncoding DNA and it's functions and another on junk DNA. There has been a lot of resistance to this among the current editors and I can only assume that this is because they don't see the distinction. I tried to explain it in the discussion thread on splitting by pointing out that we don't talk about non-regulatory DNA, non-centromeric DNA, non-telomeric DNA, or non-origin DNA and there's no confusion about the distinction between these parts of the genome and junk DNA. So why do we single out noncoding DNA and get confused?

It looks like it's going to be a challenge to fix the current Wikipedia page(s) and even more of a challenge to get a separate entry for junk DNA.

Here is the warning that I have received from Ramos1990.

Your recent editing history shows that you are currently engaged in an edit war; that means that you are repeatedly changing content back to how you think it should be, when you have seen that other editors disagree. To resolve the content dispute, please do not revert or change the edits of others when you are reverted. Instead of reverting, please use the talk page to work toward making a version that represents consensus among editors. The best practice at this stage is to discuss, not edit-war. See the bold, revert, discuss cycle for how this is done. If discussions reach an impasse, you can then post a request for help at a relevant noticeboard or seek dispute resolution. In some cases, you may wish to request temporary page protection.

Being involved in an edit war can result in you being blocked from editing—especially if you violate the three-revert rule, which states that an editor must not perform more than three reverts on a single page within a 24-hour period. Undoing another editor's work—whether in whole or in part, whether involving the same or different material each time—counts as a revert. Also keep in mind that while violating the three-revert rule often leads to a block, you can still be blocked for edit warring—even if you do not violate the three-revert rule—should your behavior indicate that you intend to continue reverting repeatedly.

I guess that's very clear. You can't correct content to the way you think it should be as long as other editors disagree. I explained the reason for all my changes in the "history" but none of the other editors have bothered to explain why they reverted to the old version. Strange.


21 comments :

  1. Behind each controversial Wikipedia page a group of friends (‘administrators’) form with a common view on the subject, the consensus view. They write the content and define the structure of the page. They defend the page against attacks of newcomers. They always support each other. They revert all edits disagreeing with the consensus and label the edits of the new-comers as 'edit-wars', disruption, or damage to Wikipedia. The friends don't need any arguments against edits of outsiders, because they have to power to define dissension. They interpret and apply the Wikipedia rules. They can ultimately block the newcomer-dissenter by blocking the user account and IP address. There is no point in searching for help higher in the Wikipedia hierarchy, because those people haven't got the time and expertise to investigate factual matters and fall back on the opinion of the group of friends of the page in question because they have contributed so much to the Wikipedia page and never were involved in edit-wars themselves.
    The only option is to start a completely new page with a different title and publish it as a completely worked out version with nearly every sentence backed up by references to the scientific literature.

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    1. I agree with all that Larry says, and have said so on the relevant Talk pages, but I've no great confidence that Ramos1990 will back down. Nonetheless, I think your analysis in terms of "groups of friends" is a bit exaggerated. Many administrators are open to cogent arguments.

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  2. The "corrections" at Wikipedia and the statement by the head of the NIHGR are certainly depressing. The both reflect the consensus among genomicists and molecular biologists. That in turn is based on their very limited grasp of molecular evolution. On the other side is the near-unanimous consensus among molecular evolutionists that there is lots of junk DNA. That is based on their actually understanding the processes of inserting junk and removing it. Unfortunately there are many more genomicists and molecular biologists, so the vote is still heavily against junk DNA. Wikipedia has the strength and the limitation that it is a dominant-consensus view, and we can see that in a case like this it serves to reinforce a wrong dominant consensus. Perhaps someday soon there will be a page on "Junk DNA controversy" in which the pro-junk side will get to edit the description of what we say. When the 2012 ENCODE disaster occurred, I predicted gloomily that it would take the field 10 years to get back to where it was. Those 10 years are nearly done, and things still look bad. I have more recently started telling people that it will take more like 20 years. Actually, 30 might be more like it.

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  3. Apparently I'm unable to comment today except as "Anonymous", but this is John Harshman.

    How is the field going to get back where it was? What processes are currently operating to educate moleculara biologists about junk DNA? Most of what I see just reinforces that position, and it seems like a closed system.

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    1. Seems like a Safari problem (the anonymous posting, not the molecular biologists). Chrome is fine.

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    2. John, you don't understand. Safari has features to screen for people who think there is lots of Junk DNA and block them from spreading that fake news.

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  4. Can someone enlighten me? In very brief/simple way what is the broad direction that evolutionary biology would advance given the opposite views on prevalence of non-coding DNA?

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    1. What views are you calling "opposite", and have you confused "non-coding" with "junk"? Everyone is more or less agreed that non-coding DNA is around 98% of the human genome. The argument is over how much of that non-coding DNA is junk and how much is functional in some way.

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  5. @Anonymous
    It's important to understand that the issue is not about the prevalence of noncoding DNA. There's basic agreement on the core amount of functional noncoding DNA elements such as noncoding genes, regulatory elements, centromeres, origins etc. There's also general agreement that junk DNA exists (e.g. pseudogenes, transposon fragments etc.) The controversy is over the amount of junk DNA.

    Advances in evolutionary biology will be stalled as long as scientists believe in and promote false ideas. Rejecting junk DNA is one of those false ideas and it's linked to a fundamental misunderstanding of evolution.

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  6. This is bad. I think you have to form a group. Why not just write the article on Junk DNA and make it good? Other articles are worse. All the wikipedia pages on historical schools of thought like neo-Darwinism, mutationism, orthogenesis, etc are full of nonsense and rely heavily on Ernst Mayr's Synthesis propaganda. One very active editor is taking the lead on all this badness. He will try to work with people but he just insists on putting crap on these pages, and much of it is "synthetic" thus contrary to wikipedia rules, e.g., all the pages have these maps of ideas with arrows and these diagrams are all generated by this one editor and do not come from sources.

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    1. It's even worse than I originally thought because, as you point out, all the Wikipedia pages are corrupted. I edited the section on introns and wanted to mention that introns are mostly junk so I linked to the Wikipedia intron article but of course there's no discussion there about junk in introns.

      It's not appropriate to discuss whether introns are junk in an article on noncoding DNA so I made the link anyway. Now I have to edit the intron article, which is just as bad. That article links to one on alternative splicing where there is no discussion of the controversy in that field.

      It's beginning to look hopeless.

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    2. I'm working on a stand-alone article on junk DNA but it will have to be approved by the Wikipedia police and I'm told that this can take several months with no guarantees.

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    3. I just looked at the Wikipedia article onmutationism.

      You must be tearing your hair out. Where to begin?

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    4. I felt like tearing my hair out when I first looked at the List of Biochemists a couple of years ago: Otto Warburg, Luis Leloir, William Jencks, Daniel Koshland, Fritz Lipmann and about 50 other distinguished people omitted, but people like Felisa Wolfe-Simon, Ernst Krebs, Anthony Kidman (famous for being the father of an actress) and Isaac Asimov included. This was one of the reasons for registering with Wikipedia, and I've tried to sort it out. That was quite an easy -- almost mechanical -- task, but fixing the very bad articles on various aspects of enzymology was more difficult, and I've only scratched the surface so far.

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    5. The "one very active editor" that Arlin refers to is probably Chiswick Chap, who in real life seems to be Ian Alexander -- not unusual enough as a name to make it easy to assess his contributions. I haven't found any of his publications on "neo-Darwinism, mutationism, orthogenesis, etc." but that doesn't mean there aren't any. I plan to work a bit on Convergent Evolution and Horizontal Gene Transfer in the next couple of days, but someone needs to work on the other articles that Arlin mentions.

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    6. How much is the anti-junk attitude interfering with progress in genetics and molecular biology?

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  7. I am one of those few souls that contributes to WIKIPEDIA so that it continues to appear on the internet. However, if they continue to delete correct information and add back incorrect information without trying to verify which information is correct, then I have donated my last penny. I don't want to read something that is wrong. I guess that leaves it up to the leaders at the website to give us all a proper answer.

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    1. I give Wikipedia $5 every month because I think it's one of the best things on the internet. It's not perfect but we can make it better with a little effort.

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    2. Stealing from Winston Churchill . . .

      Wikipedia is the worst aggregation of information on the internet, except for all the others.

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