Wikipedia talk:WikiProject Molecular Biology/Archive 3

Specify name list style for new entries for the Citations Bot
@Boghog, can you please comment on a discussion with the authors of the Citations Bot on configurable format of the name list style based on the template.

https://github.com/ms609/citation-bot/pull/4236#issuecomment-1842928339 Maxim Masiutin (talk) 14:12, 6 December 2023 (UTC)


 * @Boghog The citations bot is developed in such a way that where issues require consensus on Wikipedia policy, they are discussed on the [Citation Bot Talk Page](https://en.wikipedia.org/wiki/User_talk:Citation_bot). According to the discussion here, there was a consensus that the bot should use existing template that was introduced in August 2023 to avoid creating any new template. I modified the pull request to support this template, and the maintainers of the citation bot on Github accepted the change. If you take the citations bot from Github, it will insert "vauthors" rather than "first1/last1" for the pages where it sees the "name-list-style=vanc" parameter for the "cs1 config" template. JFYI. Please consider updating your citation tool to always insert  if a page does not contain it. If you get the bot from github, you will see what regexp can be easily used to detect such template. Therefore, with that template the bot will insert vauthors and you will no longer need to patrol pages to replace first/last to vauthors, it will be done by the citations bot. Maxim Masiutin (talk) 04:39, 15 December 2023 (UTC)
 * - since the bot should already support, I'm running a custom version of the bot to add this template to all the pages which have "vauthors" in at least one citation. Therefore, in such pages, the bot in the future should add this kind of list of authors. Maxim Masiutin (talk) 20:54, 27 December 2023 (UTC)

Requested move at Talk:3"-deamino-3"-oxonicotianamine reductase
The question posed in the RM at Talk:3"-deamino-3"-oxonicotianamine reductase is what symbol should be used in similar titles. Currently, that article and several other articles are using a quote mark after the numeral. I suspect this should be a double prime or two single primes or two apostrophes instead. You are invited to participate in that discussion, which should take place there, not here. —⁠ ⁠BarrelProof (talk) 21:43, 30 December 2023 (UTC)

Cell regulation
Seems like we ought to have a topic for cell regulation, or at least redirect to someplace relevant, since people are misusing the redirect for the journal Cell Regulation. Dicklyon (talk) 02:29, 2 January 2024 (UTC)


 * It probably needs a disambiguation page for the journal and for the concept. One possible redirect for the concept would be to Cell_cycle, as cell regulation is often discussed in the context of the cell cycle. -- 04:19, 2 January 2024 (UTC)
 * OK, I stubbed that in at Cell regulation. Dicklyon (talk) 19:21, 2 January 2024 (UTC)

Requested move at Talk:NC ratio
There is a requested move discussion at Talk:NC ratio that may be of interest to members of this WikiProject. – robertsky (talk) 07:15, 31 January 2024 (UTC)

Agouti
I was trying to make sense of Agouti (coloration) when I realized that the following articles exist: My confusion here comes from the overlap and vague scope between all of these articles. Agouti-related peptide also exists but I see no problem with it, it just gets lumped in with the rest due to the name. Agouti-signaling protein and Agouti coloration genetics seem to have a lot of overlap, only that the latter is a list of all the genes related to agouti coloration and the former is a more useful, if somewhat technical, overview of the gene. What I'd like to know is if a merge is possible or if there's some better approach that I don't see because I'm not familiar enough with molecular biology to say. Also, would like to figure out the scope of Agouti (coloration) because it's not in a good spot right now, but there isn't much room for it to grow without getting into genetics. Recon rabbit  00:25, 1 February 2024 (UTC)
 * Agouti (coloration)
 * Agouti-signaling protein
 * Agouti coloration genetics


 * I'd probably have one article for the gene and another for the colouration. We don't need 2 articles for the colouration. Jo-Jo Eumerus (talk) 12:51, 1 February 2024 (UTC)
 * A bit ago the article on coloration was merged with coloration genetics, presumably very poorly as it was un-merged later. I could try to do it again after putting it up for comment? Recon  rabbit  13:21, 1 February 2024 (UTC)

Request to create a new article
Good day Computational Biology taskforce, I am writing to request the creation of a new article. I need your help, because I want to participate in (Wikipedia:WikiProject Molecular Biology/Computational Biology/13th ISCB Student Wikipedia competition announcement) https://en.wikipedia.org/wiki/Wikipedia:WikiProject_Molecular_Biology/Computational_Biology/13th_ISCB_Student_Wikipedia_competition_announcement. Is possible ???? The title of new article is "El espacio químico de la vida" because I want to participe in OTHER LANGUAGES. Thank you very much for time and help me.https://es.wikipedia.org/wiki/El_espacio_qu%C3%ADmico_de_la_vida

Excellent day, Haikluum (talk) 23:09, 2 February 2024 (UTC)


 * Pinging @Tkarakulak, @NellySelem.
 * Haikluum, I don't speak Spanish but it seems the page https://es.wikipedia.org/wiki/El_espacio_qu%C3%ADmico_de_la_vida was deleted due to a copyright violation - not sure if this was a draft you started? Please note the competition rules on plagiarism and copyright; these are Wikipedia guidelines as well. Amkilpatrick (talk) 10:35, 3 February 2024 (UTC)
 * Hello I'm not sure about the copy-right violation, grammarly says its original text. Perhaps, you need to ask the user Saloca about why he considers that this is infringes copyright. NellySelem (talk) 05:31, 5 February 2024 (UTC)

Irrelevant section in certain article - what's your opinion?
Im reading a section "Research areas/P53 mutations in Apoptosis" in apoptosome over and over, but it seems to me, this section is completely unrelated to the subject of the article, apoptosome itself. I don't want to delete it right of the bat though. It looks like, with two preceding sections, like an informal introduction to the fourth one, hence this little thread in Wikiproject. InternetowyGołąb (talk) 02:13, 15 February 2024 (UTC)


 * Oy, yeah, that section is about p53 or apoptosis, not the apoptosome. Jo-Jo Eumerus (talk) 07:34, 15 February 2024 (UTC)

APETx1 article - Infobox error
Greetings, For article APETx1, at top it shows error line in red, Unknown parameter SequenceUnknown parameter Amino Acid Sequence. Asking for help here as I know almost nothing of the topic. Regards, JoeNMLC (talk) 20:01, 15 February 2024 (UTC)


 * The infobox parameters have been corrected, thank you. &#8213; Synpath 20:40, 18 February 2024 (UTC)

Delete "Gene expression" article
I propose that we delete the article on Gene expression and replace it with redirects to relevant material found elsewhere such as Transcription, Translation, and Regulation of gene expression.

It's a bad idea to have multiple articles covering the same topic, especially when they conflict. Also, the Gene expression article is far too big and full of extraneous technical information that's way beyond the level we should be aiming at.Genome42 (talk) 21:47, 17 February 2024 (UTC)


 * Gene expression is a fundamental topic in molecular biology; we need an article on the topic. I agree there are many facets to this broad and deep topic. The current organization, which introduces the topic, provides summaries and links to other more specialized topics, seems a good structure to reflect these facets. If there are sections that are too technical, those would be good candidates for a rewrite, but not a deletion. Let's not delete the forest to get at the trees. -- 00:23, 18 February 2024 (UTC)
 * Gene expression is represented as a whole process in biology textbooks. With the use of "Main article" templates, more interested reader shoudn't face any problems with finding more information. InternetowyGołąb (talk) 03:06, 18 February 2024 (UTC)
 * As a textbook writer and teacher I'm quite familiar with how the topic of gene expression is covered in molecular biology. We usually cover transcription and translation in some detail then we cover the basics of regulation of gene expression. All three of those topics are presented in separate articles on Wikipedia.
 * There's nothing in the article on gene expression that's not found elsewhere. The problem isn't just redundancy. It's that various editors insert their own biases and (possibly) misinformation into the various articles so that the more articles we have the greater the chance that they will conflict. There aren't very many of us working on these articles so let's concentrate on getting a few articles correct. Genome42 (talk) 21:09, 18 February 2024 (UTC)


 * Check out the Gene expression article to see examples extraneous information. There are sections on "Folding," "Translocation," and "Protein transport." Are those really relevant topics in an article on gene expression?


 * The section on "Regulation of gene expression" only talks about the complex mechanisms in eukaryotes. There's nothing about the lac operon or the other fundamental examples in bacteria. There's nothing about how a transcription factor finds the right gene. Some of the material that's in that section is either incomplete or misleading. There's a section on methylation that doesn't even mention chromatin and doesn't explain why some CpGs are demethylated.


 * There's an entire section on "Transcriptional regulation in learning and memory" and another on "Transcriptional regulation in cancer." Really? There's a lengthy section on "Measurement" that's far too detailed, boring, and doesn't cite any sources. Does anybody really want to waste time cleaning up this article?Genome42 (talk) 21:34, 18 February 2024 (UTC)
 * Gene expression is a solid example of a WP:BROAD concept. I don't think you could redirect the term to a single article and have that be satisfactory. I don't think it would be possible to build it into a disambiguation either. The current organization of a set of summarized subtopics linking to main articles is likely the best way of handling the term. Though I do agree that the article has bloat. &#8213; Synpath 21:36, 18 February 2024 (UTC)

"Random sequencing"
On our Mycoplasma genitalium article, it says:


 * They performed an initial study of the genome using random sequencing in 1993

where "random sequencing" links to Random sequence (the mathematical concept). What should it link to instead? Marnanel (talk) 13:39, 2 March 2024 (UTC)
 * It should link to DNA sequencing where you can find descriptions of early sequencing techniques. Randomness is a core part of several techniques, but there's no dedicated section describing its use in that article. I don't think that the word 'random' should be part of the wikilink. &#8213; Synpath 16:17, 2 March 2024 (UTC)
 * Done— thank you. I note that "random" was in the title and abstract of the linked paper, which is presumably where the previous editor found it. Marnanel (talk) 21:04, 2 March 2024 (UTC)

Zoonotic origins of COVID-19
Zoonotic origins of COVID-19 has been nominated at Articles for Deletion. Interested editors may participate at Articles for deletion/Zoonotic origins of COVID-19. TarnishedPathtalk 09:47, 9 March 2024 (UTC)

Unused PDB Gallery templates
Hey everyone, the following PDB Gallery templates are not used anywhere. If you know where they should be used, please use them in the relevant articles. If they aren't needed please let me know.


 * Template:PDB Gallery/10228
 * Template:PDB Gallery/10484
 * Template:PDB Gallery/11073
 * Template:PDB Gallery/2109
 * Template:PDB Gallery/2217
 * Template:PDB Gallery/26227
 * Template:PDB Gallery/51128
 * Template:PDB Gallery/51684
 * Template:PDB Gallery/59272
 * Template:PDB Gallery/8473

Thanks! Gonnym (talk) 15:39, 13 March 2024 (UTC)

Atavism: Real or psuedoscience?
Folks - quick question because I'm not a biologist or scientist by any stretch of the imagination. Is Atavism real or is this a psuedoscience article that has evaded detection? There appears to be a lot of synthesis or original research.--57.140.108.63 (talk) 03:12, 8 April 2024 (UTC)


 * Atavism seems to be a legitimate concept but it wouldn't surprise me if it's sometimes used by fringe claims. Jo-Jo Eumerus (talk) 07:07, 8 April 2024 (UTC)
 * Since it is tagged with Original research, it does look like the article needs to be bolstered with citations. Peaceray (talk) 07:40, 8 April 2024 (UTC)
 * Possibly a bit of both. A Google Scholar search for "atavism" in article titles gives over 100 hits since the year 2010, of which this article is a reasonable review. Mike Turnbull (talk) 11:50, 8 April 2024 (UTC)

Appropriate template for gene/protein synonyms
Recently I made some protein or gene (article about protein with title being gene descriptor) synonymous names redirects, and I wonder what would be the appropriate "R from..." tracking category template. InternetowyGołąb (talk) 13:15, 23 March 2024 (UTC)


 * @InternetowyGołąb We have alternatives like R from acronym and R from initialism as well as the tracking Category R from alternative name I see you have used for NAXE. The template pages give guidance on which to use: in some cases more than one is appropriate. Mike Turnbull (talk) 12:08, 8 April 2024 (UTC)