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This is an old revision of this page, as edited by Genome42 (talk | contribs) at 16:31, 22 February 2023 (→Karyotype image). The present address (URL) is a permanent link to this revision, which may differ significantly from the current revision.

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Untranslated regions

I'm trying to cover all of the non-coding DNA so I added a short section on 5'-UTRs and 3'-UTRs. This is standard textbook stuff so I don't think it requires a lot of citations. This is an encyclopedia entry and the authors are expected to be authorities on the subject matter.

Nevertheless, I added citations to three textbooks. Unfortunately my most recent copy of the Alberts text is from 1994 and my latest copy of Genes is from 2004. I threw out all my old biochemistry textbooks when I retired but I kept a copy of my own book from 2012 so I cited it. If anyone has more recent copies of textbooks please check to see if they cover UTRs and cite them. Genome42 (talk) 14:11, 5 June 2022 (UTC)[reply]

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)[reply]

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

Karyotype image

Mikael Häggström has created a pretty image showing the G-band pattern of human chromosomes. He has inserted this image into a large number of articles including this one. The chromosome icons are from the Ensemble website (see Human karyogram).

This is an article about non-coding DNA. It is not restricted to non-coding DNA in humans even though the topic is relevant to discussions about the human genome. I don't think this karyotype image should be prominently displayed on the top page of this article because it has nothing to do with noncoding DNA or noncoding genes. Genome42 (talk) 21:23, 21 February 2023 (UTC)[reply]

Thanks for the input. I've now moved the image to a subsection, and better explained its relationship to non-coding DNA. Mikael Häggström (talk) 23:55, 21 February 2023 (UTC)[reply]
@Mikael Häggström. Thank-you for moving the karyotype image. I would still prefer to delete it but if we are going to keep it then I suggest we improve the caption. I suggest the following: "The images are a cartoon version of the G-banding patterns seen when human metaphase chromosomes are stained. Other published representations of these patterns differ from the ones show here. The G-bands have no particular significance with respect to non-coding DNA since 99% of the DNA in these chromosomes is non-coding."
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