Talk:Non-coding DNA

Junk DNA section

This section is merely a placeholder until the Wikipedia article on junk DNA is published. Meanwhile, Praxidicae has seen fit to remove my recent edits so I guess I need to explain why they were necessary.

The term "junk DNA" did not become popular in the 1960s. Most of us never heard of it until 1972. You have to look really hard to find any mention of junk DNA in the 1960s. That's why I said that the term "was used" in the 1960s instead of "became popular." I was there.

I deleted Ryan Gregory's reference to David Comings because it's extremely misleading and the source is obscure. (I've never seen it.) Also, we have already established that the term "junk DNA" predates his 1972 description so he does not get priority. But, most importantly, the idea that all non-coding DNA is junk is absurd. It was absurd in 1972 and it's even more absurd today. There's no benefit to be gained by referring to some person who said something stupid.

I don't think that Susumu Ohno "formalized" the term 'junk DNA' in 1972. That's why I deleted that phrase. (I'm not even sure what it means.)

What's the point of saying that Ohno's hypothesis "remains robust with the human genome containing approximately (protein-coding) 20,000 genes"? There are plenty of other places where the total number of genes can be discussed. The current estimates range from about 25,000 genes to about 45,000 genes.

I said that "most of the DNA" comes from transposon and other selfish DNA elements. The old version, now restored, said "the majority of non-coding DNA." There's no particular reason to single out noncoding DNA. We could also say that the majority of 'non-centromeric DNA' comes from selfish elements or 'non-regulatory DNA.' I'm trying to get away from the misleading connection between junk DNA and noncoding DNA.

The sentences beginning with "The term occurs mainly in popular science and in a colloquial way in scientific publications" are incorrect and that's why I removed them. Junk DNA is alive and well in scientific publications. (See above.)

I will re-post my corrections unless Praxidae can come up with a good reason for deleting them and restoring the old, out-of-date material.

Genome42 (talk) 22:45, 16 August 2022 (UTC)

I support Genome42's statements here and I think his edit gives a more correct view of the history and concept of junk DNA and it's relationship to non-coding DNA. Incidentally Genome42 (Professor Larry Moran) is also an actual expert in the topic. It's really bad style for Praxidicae to just drop in and edit the article back to previous form without even giving an explanation, and I have to wonder if this person even has any relevant expertise or familiarity with the topic. Perhaps Praxidicae would like to explain her/himself? Rumraket38 (talk) 12:33, 19 August 2022 (UTC)

I re-posted my edits a few minutes ago and Praxidicae removed them two minutes later with the comment "this was sourced just fine." Note that what's in dispute is the relevance of the sources and whether they represent the scientific consensus. I'm not disputing the fact that misleading sources exist. It's not clear to me whether Praxidicae is knowledgeable enough about the topic to recognize the issues. I strongly suspect she has not read this discussion.

What do I do now? Should I undo her revert and challenge her to break the 3-revert rule (3RR) so I can report her?

Genome42 (talk) 12:56, 19 August 2022 (UTC)

No need. I have done it. Praxidicae is a good illustration of why it's not a good idea to allow editing to be done anonymously by people with no identifiable qualifications. Praxidicae's user page says absolutely nothing beyond indicating an interest in Black Lives Matter. Athel cb (talk) 15:22, 19 August 2022 (UTC)

I've yet to see a single explanation as to how the source and content being removed are inadequate and incorrect, you've only been denigrating other editors without recognizing Wikipedia policies, including adding personal attacks. So please, explain so us pea-brain non-experts understand why you're right and everyone else is wrong. PRAXIDICAE🌈 15:38, 19 August 2022 (UTC)

Genome42 already provided those explanations above in his first post. Why do those explanations fail? At no point did Professor Moran's explanations involve denigrating or personally attacking anyone. On the contrary he provided rational justification for each edit in the form of explaining why, historically and logically, certain statements and their references are inappropriate and why the ones he gives instead are superior.

He explained the difference between popularity and mere usage concerning the term junk DNA.

He explained why Ryan Gregory's reference to Comings is misleading due to it's obscurity in the field, and that the term predates Comings.

He explains why factual knowledge in the field with a considerable history makes the conflation of non-coding with junk DNA absurd.

He explains that it does not make sense to mention Ohno's hypothesis of 20K genes in the human genome in the article.

He explains that it is a false statement that the term junk DNA occurs mainly in popular science nad in a colloquial way in publications.

These are actual explanations that justify his edits. Nothing personal or denigrating about this. Rumraket38 (talk) 21:56, 19 August 2022 (UTC)

He hasn't provided a single reliable source to support any statements he's made, nor any that contradict what is in the article. PRAXIDICAE🌈 22:37, 19 August 2022 (UTC)

Now you're moving the goalposts. You asked for explanations for why the source and content being removed were inadequate and incorrect, and you received them. It doesn't make sense to then turn around and say you want sources for the explanations.

Take the example of confusing popularity and mere usage. How does one "source" the statement that a term didn't become popular in the 1960's, but remained rather obscure until Ohno's 1972 paper? Well you'd have to go and look at all the various articles that use the term junk DNA and see what paper they reference (it's Ohnos 1972 paper btw). How many of such papers do you want? Here's one from 2020(DOI: 10.1016/j.cell.2020.09.047) There isn't going to be a review of "which junk DNA paper do people who use the term junk reference?".

How about the mistaken conflation of junk DNA with non coding DNA being absurd? Why would that even have to be sourced, it's a statement about logical entailment. It IS absurd to imply that use of the term junk DNA means all non-coding DNA is nonfunctional when that isn't what proponents of the concept think. It's like asking for a source that people who don't like pineapple in their pizzas don't like pineapple on their pizzas.

Many places in the whole non-coding DNA article actually gives many recent(within the last 5-10 years) references to the primary literature that use the term junk DNA to refer to DNA without a function. Rumraket38 (talk) 00:06, 20 August 2022 (UTC)

I'm not moving the goalposts. WP:V is a policy, it is not optional. Provide the sources or this entire discussion is pointless. PRAXIDICAE🌈 00:12, 20 August 2022 (UTC)

I checked the first two of the changes, and you are wrong in the first case.

• Version you reverted to: The term "junk DNA" became popular in the 1960s.
• Genome42's version: The term "junk DNA" was used in the 1960s

I cannot access one of the sources given, but it is from 1963. If it says that the term "junk DNA" became popular in the 1960s, that would be pretty weird. The other source [1] says, the term “junk DNA” was already in use as early as the 1960s. So, Genome's version is closer to the source than yours.

Second change:

• Version you reverted to: the nature of junk DNA was first discussed explicitly in 1972 by a genomic biologist, David Comings, who applied the term to all non-coding DNA.
• Genome42's version: No such sentence.

This time, the article does agree with the source, but the question is how relevant that is. For deleting a sentence, you do not need a source. Choosing which events in the history of the term to mention and which ones to omit is a matter of judgement and competence; guidelines cannot help a lot here. So, Comings has a short mention in some book. Genome42 says it is obscure. Is there anything telling us it is not? The source given is a hit from a Google search for not only is "junk dna" an inappropriate moniker, so, someone seems to have found the Comings sentence by accident while searching for something else. That says "obscure" to me.

This is not about providing sources, it is about reading the sources correctly and about selecting the right sources, and, judging from the first two items, it looks as if you are reverting good edits without any sound justification. Maybe it's different for the other items, but you'd need to show that. We do have WP:CIR, and resisting the edits of someone who is clearly competent without a good justification would be counterproductive. --Hob Gadling (talk) 08:49, 20 August 2022 (UTC)

Who do you mean by "someone who is clearly competent"? If you mean Genome42 then yes, definitely. If you mean Praxidicae, then where is the evidence? Athel cb (talk) 10:27, 20 August 2022 (UTC)

Genome42, obviously. --Hob Gadling (talk) 10:53, 20 August 2022 (UTC)

How does this policy apply to the paragraph that begins "The term occurs mainly in popular science and in a colloquial way in scientific publications..."? Where is the serious source to support this? All I can see is a popular article in a popular magazine (one that has fallen a long way since the 1970s: at that time every scientist read it; are there any who read it today?) by two people with no obvious qualifications in biochemistry. The first author has a grand total of six publications (of which this was the first), none of them indicating expertise in biochemistry. The other author has many publications, but I haven't found any that show expertise in biochemistry. Does this really outweigh Dan Graur's book? Or Sydney Brenner's various articles? Or Larry Moran's book? Athel cb (talk) 10:21, 20 August 2022 (UTC)

Who is "everyone else"? At the moment it seems to be just one person, you. Ramos1990 was quite vocal in May, but seems to have withdrawn from the fray. Athel cb (talk) 13:35, 20 August 2022 (UTC)

Do you really think that getting bbb23 to block Genome42 is the best way forward? It makes you look like someone who can't tolerate any disagreement with what you have decided is The Truth. How about addressing the arguments instead of just censoring them? Athel cb (talk) 17:34, 20 August 2022 (UTC)

I have reinstated the Scientific American article, but I've added two references to serious scientists to show that it is mistaken. Athel cb (talk) 13:27, 21 August 2022 (UTC)

Continued at Wikipedia talk:WikiProject Molecular Biology#Junk DNA - T.Shafee(Evo&Evo)^talk 04:33, 2 March 2023 (UTC)

Splitting proposal (Junk DNA)

Previous discussion Talk:Non-coding_DNA/Archive_1#Splitting_proposal

It looks like it's going to be very difficult to create a new Junk DNA page so a better option, with a more reasonable chance of success, is to split this article creating a separate article for the junk DNA section. This proposal appears to conform to the Wikipedia:Splitting criteria.

I think I have inserted the correct notification in the article. Please help by participating in the discussion and by informing everyone who might have an interest in this proposal. Genome42 (talk) 16:45, 4 March 2023 (UTC)

Sure. Looks like there are enough references on the history and modern debates to split it again to its own article. I am linking to the splitting proposal from last year for reference since that was pretty recent https://wiki.riteme.site/wiki/Talk:Non-coding_DNA/Archive_1#Splitting_proposal. Others were in agreement then. Ramos1990 (talk) 17:31, 4 March 2023 (UTC)

I'm glad you're on board with the split and a separate article on Junk DNA.

Judging from your previous comments, you will be very active in editing the new article. Genome42 (talk) 17:33, 5 March 2023 (UTC)

I also support the split proposal. Some further mention of the wide variation in vertebrate genome sizes is also warranted, as noted in the opening paragraph of Susumu's 1972 article. As is the C-value paradox in more detail + the onion test. I would vote for mention of the viscacha rat genomes too. --Paul (talk) 20:14, 6 March 2023 (UTC)

Also +1 on splitting. If consensus here is consistent with splitting over the next week, than I'll help implement that and split "Non-coding_DNA#Junk_DNA" → "Junk_DNA". The content can then be evolved and updated after the split where I think it'll make more sense. T.Shafee(Evo&Evo)^talk 02:15, 9 March 2023 (UTC)

@Evolution and evolvability Thanks. I can’t figure out how to split the article so any help would be greatly appreciated. I’ll work on a short paragraph that will be retained in Non-coding DNA. Genome42 (talk) 13:40, 9 March 2023 (UTC)

I've now implemented the split over to Junk DNA per WP:PROPERSPLIT (see the comment on that article's talkpage). I've left a short section behind on this page at Non-coding_DNA#Junk_DNA, trying to focus on the specific aspect of the term that is relevant on a page that is primarily about non-coding but functional DNA - i.e. not being protein-coding is one thing, but not having biological function is another. T.Shafee(Evo&Evo)^talk 05:57, 16 March 2023 (UTC)

Thank-you. I’ll work on fixing the stub in Non-coding DNA then get started on Junk DNA. Genome42 (talk) 13:39, 16 March 2023 (UTC)

Junk DNA stub

I created a short description of junk DNA in order to complete our list of all elements found in non-coding DNA. It's important to keep in mind that we now have (finally) a separate article on junk DNA so this is not the place to debate the topic. Let's try and keep that debate out of this article.

It's also important to remember that there's no debate over the EXISTENCE of junk DNA. The only controversy is over how much of it is present in some genomes. Finally, there's no real debate over the definition of function. Ever since the partial retraction by ENCODE (in 2014), everyone agrees that some form of selected effect function is what's important in the debate. There are no significant papers from the last ten years that try to make the scientific case that all TF binding sites are functional or that all transcripts are functional. The old "biochemical function" (causal role function) idea is dead. Genome42 (talk) 17:41, 16 March 2023 (UTC)

I think we should try really hard not to add unimportant bits of information to this short section. Genome42 (talk) 01:19, 17 March 2023 (UTC)

In line with my previous comments, we need to make sure that readers and Wikipedians know where to go to find the main articles on various topics. Our goal, IMHO, should be to clean up the molecular biology articles in order to reduce redundancy and reduce the number of conflicting views. This is one of the reasons for creating a separate article on Junk DNA. It's going to be the place where the issue is explained in great depth. Thus, all other mentions of junk DNA in other articles should be just (very) brief summaries and should direct readers to the main article.

That's why I put "Main article" at the top of the junk DNA stub. I think that's very different than "Further information." To me, the phrase "Further information" suggests that the following text contains a lot of information but you can get more by going to the link. The phrase "Main article," on the other hand, implies to me that the following text is just a brief summary of material that's covered elsewhere. Evolution and evolvability changed it to "Further information." What do the rest of you think?

The problem arises within articles as well. Take the issue of whether most intron sequences are junk as an example. It would be nice to keep that debate at a single location instead of having it spill over into several different articles where various Wikipedians can insert their views. But how do we alert readers and Wikipedians to the location where that discussion should take place? Here are two possible versions.

"In eukaryotic genomes nonfunctional DNA may also be found within introns."

"In eukaryotic genomes nonfunctional DNA may also be found within introns (see Introns)."

In my opinion, the second one is preferable since it tells readers and Wikipedians that they should go to the article on Introns for a discussion about how much junk DNA there is in introns. To me, the first one just says go to the Introns article if you don't know that an intron is.

I'd be willing to predict that it won't be long before some Wikipedian reads the first sentence and adds something like: "Most intron sequences are thought to be functional (Smith and Wong, 2004)." Then we will have an edit war over the credibility of the Smith and Wong (2004) reference. If we go with the second version, we can hopefully prevent such a war by directing all the debate to the Intron article where it belongs. I realize that using a cross-reference such as "see Introns" will be jarring to old Wikipedians (I am one) and that's probably why Evolution and evolvability edited it. But maybe it's time for a different way of cross-referencing in the interests of cleaning up some of the problems? What do you think? Genome42 (talk) 14:13, 17 March 2023 (UTC)

Just commenting on the further information stuff. If there is a main article for a section, we should always should use the template for "main" article so readers can redirect to it. Here is a helpful link Wikipedia:Template index/Links for the wikiscript for these templates. If there are related things in the section we can use the "See also" template or "Further" template to link to other articles. There are multiple options. If there is not a main article for a section then usually "See also" templates are used to best approximate a related article, if any.

There is a manual of style for wikipedia sections so we should follow that MOS:SO. I will fix this article to correspond to the MOS.

In terms of the Introns vs (see Introns), we should follow the manual of style on internal links MOS:LINKSTYLE because this is how wikipedia does internal referencing. This is common on the internet where people see blue text and understand they can click to get more info. Hope this helps. Ramos1990 (talk) 02:39, 18 March 2023 (UTC)

Thanks Ramos1990. I'm concerned about overlinking, which leads readers to ignore blue text. (See Junk DNA for examples.) Here's what the Manual of Style says about that.

An article is said to be overlinked if it contains an excessive number of links, making it difficult to identify those likely to aid a reader's understanding. A good question to ask yourself is whether reading the article you're about to link to would help someone understand the article you are linking from. Unless a term is particularly relevant to the context in the article, the following are usually not linked:

• Everyday words understood by most readers in context (e.g., education, violence, aircraft, river)

In the example we're discussing this means that "intron" is a word understood by most readers in context so it doesn't need a direct link. Readers will just ignore it because overlinking is ubiquitous. It would be better to follow the example in the Wikipedia:Manual of Style/Linking article: "see Fourier series for relevant background." We should use this style to direct readers to more complete articles with extensive discussions and references and avoid trivial links. Genome42 (talk) 15:38, 18 March 2023 (UTC)

Hi again. I hear you on the overlinking concerns. All of the linking in any article is optional so if you think some things should not be linked because they are more or less obvious, then go ahead and remove the wikilinks. It is also optional to add the main, see also, further redirects. Up to you if you want to remove some of those too for a more clean article. I think there is overlinking in this article, so feel free to clean it up.

To be honest, the "see Fourier series for relevant background." is an example of underlinking section of the MOS. Since a Fourier series is very specific, then it makes to sense to make a wikilink for it in that context. But I have not seen any articles use "(see Introns)" or do explicit internal referencing like "see X for relevant background." in it since the internal link does that automatically. Also, if you add numerous of these "see X for relevant background" it would look very cluttered when internal linking already does that. Look at the lead of this article, the relevant terms are already internally linked (you can internally link sections of the same article too using the "piped" links like "Riverside, California|Riverside" example here MOS:LINKSTYLE). The underlinked section of the MOS does say "If you feel that a link is relevant to the topic of the article but does not belong in the body of an article, consider moving it to a "See also" section." This "see also" section usually is at the very bottom of very article like it here for example [2] for the "Neutral theory of molecular evolution" article. More info on that can be found here in the navigation list MOS:NAVLIST.

I hope I did not confuse you. Ramos1990 (talk) 19:25, 18 March 2023 (UTC)

One minor addition to the discussion on how to wikilink intron, since you're aiming to direct editor debate to the Intron article, a possible solution is to include hidden comments, which only show up for editors. That way the style remains consistent for readers, but some lightweight commentary can be included for editors (e.g. directing them to more in-depth discussion on a talkpage, or notifying of existing consensus on an issue). They're not, super-common, but can be a useful option. T.Shafee(Evo&Evo)^talk 02:31, 20 March 2023 (UTC)