Wikipedia talk:WikiProject Molecular Biology/Archive 3

Archive 1

Archive 2

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 {{cs1 config|name-list-style=vanc}} 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 {{cs1 config|name-list-style=vanc}} 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)

@Boghog: - since the bot should already support {{cs1 config|name-list-style=vanc}}, 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#Regulation_of_eukaryotic_cell_cycle, as cell regulation is often discussed in the context of the cell cycle. --{{u|Mark viking}} {Talk} 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#Requested move 19 January 2024

There is a requested move discussion at Talk:NC ratio#Requested move 19 January 2024 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:

• Agouti (coloration)
• Agouti-signaling protein
• Agouti coloration genetics

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. Reconrabbit 00:25, 1 February 2024 (UTC)

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? Reconrabbit 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. ― 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. --{{u|Mark viking}} {Talk} 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. ― 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. ― 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 Wikipedia:Articles for deletion/Zoonotic origins of COVID-19. TarnishedPath^talk 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)

Mitochondrial fatty acid synthesis in lipid-related articles

Hello.

Mitochondrial fatty acid synthesis (mtFASII) is not yet well incorporated into the lipid-related articles or is completely missing in some of them. Therefore I ask for your help.

Could someone revise the introductory section of fatty acid synthesis? It should be clearer and earlier in the text that there are 2 different fatty acid syntheses in humans, cytosolic fatty acid synthesis (FASI) and mitochondrial fatty acid synthesis (mtFASII). The other sections of the article are also not quite coherent, you can simply see that the article was written with the knowledge that fatty acid synthesis only takes place in the cytosol.

In the articles on fatty acid and lipid metabolism, mitochondrial fatty acid synthesis is completely missing. Abvdj (talk) 12:45, 19 May 2024 (UTC)

Regarding fatty acyl-CoA esters

Hey there! I've been working on adding sources to the article fatty acyl-CoA esters, but since I haven't much expertise in the subject area, I'd like to get some clarification -- in particular, what's the relation between these esters and acyl-CoA itself? It seems the same process of beta-synthesis in mitochondrial metabolism is described in each. Thanks! DeemDeem52 (talk) 16:09, 28 May 2024 (UTC)

My impression is that they are the same thing, with Fatty acyl-CoA esters having a much more confusing name. Jo-Jo Eumerus (talk) 07:09, 29 May 2024 (UTC)

Hmm... if that's the case, then perhaps the page should be merged. I'll put in a merge proposal and see if it can't get consensus. Thanks! DeemDeem52 (talk) 14:53, 29 May 2024 (UTC)

Source evaluation requested at Promoter (genetics)

Over at WikiProject Mathematics, we ran into a citation-spamming issue, where references to a substandard book were inserted by a COI editor. The statements being spammed with these citations were, variously, summaries that didn't need to be cluttered with footnotes, already supported by other references, or not actually supported by the spam reference. The article Promoter (genetics) may also have been affected. It would greatly help if a subject-matter specialist could evaluate the two sources (cited a total of seven times between them) co-authored by P. Gagniuc. Are the claims accurate and worth the words spent on them? Should the statements in question be cited to textbooks instead? XOR'easter (talk) 23:14, 14 June 2024 (UTC)

Looking for some opinions

Please see Wikipedia:External links/Noticeboard#Human mitochondrial genetics. We are looking for opinions about whether some ==External links== would be valuable. WhatamIdoing (talk) 03:32, 19 June 2024 (UTC)

UK Biobank

Hi everybody. I have been hired by UK Biobank to improve the article. I have uploaded an edit request on the talk page which I think would benefit from some specialist knowledge as some of the updates relate to concepts within the scope of this project and COMPBIO. Any help or feedback would be appreciated! Burchrusks (talk) 10:50, 19 June 2024 (UTC)

ETS2

I've added a bit to the ETS2 article to reflect the latest paper in Nature linking ETS2 with a wide range of inflammatory diseases. Please amend, or even remove, this if what I've written is wrong. — The Anome (talk) 20:59, 22 June 2024 (UTC)

ETS2 is a fairly important transcription factor, and these often have multiple functions. I think this addition is WP:UNDUE as it emphasizes one function among many, but mostly b/c the article currently doesn't list any other function so I am not sure if it should be removed. Typical problem with well-studied proteins, really. Jo-Jo Eumerus (talk) 17:27, 23 June 2024 (UTC)

Do we really need to have separate Wikipedia articles for every human gene? I don't think so.

Is it a good idea to insert all the latest speculations about the function of a given gene before they are confirmed by additional experiments in other labs? I don't think so. Genome42 (talk) 19:54, 23 June 2024 (UTC)

Requested move at Talk:3α-Hydroxysteroid dehydrogenase#Requested_move_9_April_2024

There is a requested move discussion at Talk:3α-Hydroxysteroid dehydrogenase#Requested_move_9_April_2024 that may be of interest to members of this WikiProject. Natg 19 (talk) 23:23, 18 April 2024 (UTC)

See Talk:AKR1C4#Requested move 9 April 2024 for closed discussion with outcome of 'Move'. --User:Ceyockey (talk to me) 03:38, 16 July 2024 (UTC)

MID gene

Just a quick question is there any articles about a gene in particular? I’m talking about a gene called MID (minus dominance). There does seem to be a lot of sources about this gene from:

here

here

here

Just asking to make sure it doesn’t go by a different name or something. I’m also wondering if genes here on Wikipedia have a certain style or policies.

Also I am bringing this up to see what y’all think about there being an article on this gene. When researching the evolution of sexes and mating types I noticed a lot of sources keep mentioning this gene.CycoMa1 (talk) 04:52, 2 May 2024 (UTC)

Wikipedia is a popular encyclopedia intended for a diverse audience. There are 25,000 genes in the human genome and something close to one million different different genes in the biosphere. We do not need to have a separate Wikipedia article for each gene.

But there's another problem that just as important. Any article on an individual genes is certainly going to bring up the definition of a gene and important issues such as regulation, evolution, and alternative splicing. It is proving to be very difficult to get individual editors to stick to the definitions and descriptions of these features that have been thrashed out in the articles specific to those topics. This leads to a lot of confusion and conflict so we should be very cautious about creating any new molecular biology articles unless they are absolutely necessary. Genome42 (talk) 14:57, 2 May 2024 (UTC)

Does your response suggest that the "Gene Wiki Project" has been abandoned? --User:Ceyockey (talk to me) 03:43, 16 July 2024 (UTC)

Requested move at Talk:Ketone bodies#Requested move 25 May 2024

There is a requested move discussion at Talk:Ketone bodies#Requested move 25 May 2024 that may be of interest to members of this WikiProject. Safari Scribe^{Edits! Talk!} 00:15, 2 June 2024 (UTC)

The outcome of this request was "Not moved". --User:Ceyockey (talk to me) 03:45, 16 July 2024 (UTC)

RetractionBot

I posted this story from the Signpost last month. Things have evolved a bit and now Retraction bot handles {{Erratum}}, {{Expression of concern}}, and {{Retracted}}. These populate the following categories:

• Category:Articles citing retracted publications (129)

• Category:Articles citing publications with expressions of concern (76)

• Category:Articles citing publications with errata (65)

If the citation is no longer reliable, then the article needs to be updated, which could be as minor as the removal/replacement of the citation with a reliable one, to rewriting an entire section that was based on flawed premises. If the citation to a retracted paper was intentional, like in the context of a controversy noting that a paper was later retracted, you can replace {{retraction|...}} with {{retraction|...|intentional=yes}}/{{expression of concern|...}} with {{expression of concern|...|intentional=yes}}/{{Erratum|...}} with {{Erratum|...|checked=yes}}.

I put the list of articles within the scope of WP:MCB in collapsed sections. Any help you can give with those are greatly appreciated. Feel free to remove/strike through those you've dealt with. Headbomb {t · c · p · b} 20:27, 15 July 2024 (UTC)

This is great. Thank you. I've always wondered how we deal with retracted articles and now you've presented at least some alerting automation. --User:Ceyockey (talk to me) 03:48, 16 July 2024 (UTC)

PACSIN1

In 2019 an editor made some fairly substantial changes to PACSIN1. I removed some obvious vandalism and a partial reference, but this article needs the attention of a subject matter expert. 76.14.122.5 (talk) 19:55, 3 August 2024 (UTC)

Thanks for bringing this up, I've taken a moment to smooth it out. ― Synpath 17:05, 4 August 2024 (UTC)

Infobox genome is linking to incorrect genome lists on NCBI

Hi all,

As per the Infobox genome talk page, it appears a recent NCBI change has broken the links produced by the Infobox genome template. My talk page comment goes into more detail, but in summary: NCBI is removing the Genome resource, replacing it with the Datasets resource; the Infobox genome template links to the old Genome resource when given a taxId argument; the template now links to incorrect genome lists on some pages (e.g.: the box on Chimpanzee now incorrectly links to a genome listing for Impatiophila pipa). Not all pages are affected (e.g., NCBI automatically redirects the link on Bonobo to the correct genome list), but many are. I imagine there's a risk all the links could stop working if/when NCBI completely deprecates the Genome resource.

Note that the taxId field in the template actually expects a genome ID (and this is what articles have been using for this field). This is at the crux of the problem, as these genome IDs appear to no longer be used. When infobox links still work, it's because the NCBI silently redirects the link to one using the organism's taxonomy ID.

I can think of three ways to fix the problem; all would require updating each article using the Infobox with new IDs, so I wanted to talk about which solution is best before jumping in and making all those changes.

1. Change the infobox to link to the reference genome only; replace genome IDs on all articles with reference genome IDs. Right now, on pages where it's still working properly, the Infobox links to a list of all the genomes NCBI has available. E.g.: for Bonobo, the NCBI genome page lists 8 genomes, with the reference genome at the top. We could instead update the taxId on every organism's page by replacing the genome ID with the reference genome ID (for Bonobo, changing to taxId=NHGRI_mPanPan1-v2.0_pri) and change the URL the template uses to https://www.ncbi.nlm.nih.gov/datasets/genome/{{{taxId}}} (resulting in this link for Bonobo).
2. Keep the infobox behavior of linking to genome lists; replace genome IDs on all articles with taxonomy IDs. If we think it's valuable to link users to a list of all the available genomes rather than just the reference, we could instead replace the genome IDs on all pages with the taxonomy IDs (for Bonobo, we'd remove taxId=10729 and replace with taxId=9597). We'd change the URL the template uses to https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon={{{taxId}}} (resulting in this link for Bonobo).
3. Link to the NCBI Taxonomy page instead of directly linking to genome data; replace genome IDs on all articles with taxonomy IDs. We could instead link to the NCBI taxonomy pages, which give a short summary of the organism. This includes a link to the genome list & a link directly to the reference genome. This is technically not a link to a genome dataset anymore, but I believe this is the closest behavior to how our links worked before the NCBI change - and it does still provide easy access to the genome data (including a download button that directly links to the reference genome). We'd change the genome ID on all pages with the taxonomy ID (like option #2) and change the URL in the template to https://www.ncbi.nlm.nih.gov/datasets/taxonomy/{{{taxId}}} (resulting in this link for Bonobo).

Any thoughts on which option is best, or other options I haven't thought of? Of note, there are ~62 articles using this Infobox that would need to be updated to the new IDs no matter what option is picked; not an insurmountable number but not so few that changing them all would be quick & trivial. — nmael ^talk 14:38, 8 August 2024 (UTC)

A typical genome infobox contains a link to NCBI and at least three bits of information: ploidy, genome size, and number of chromosomes. I think that ploidy and the number of chromosomes are bits of information that should be in the main body of the article. The size of the genome is not a fixed number, it changes from year to year as more of a genome is sequenced and annotated. I would argue that putting this number in an infobox gives it too much credence.

I would also argue that the best link to sequenced genomes is the Ensembl site and not NCBI. For example, here's the Ensembl link to the chimpanzee genome. Note that it gives the genome size as 3,231 Mb and not 3,323 Mb as in the genome infobox. It also says that there are 23,534 protein-coding genes and 9,710 non-coding genes and this data conflicts with what's written in the article on chimpanzee.

I suggest a 4th solution, delete all genome infoboxes. Alternatively, someone could replace all the NCBI links with Ensembl links then review and update the genome sizes of all infoboxes every few months. Genome42 (talk) 16:38, 8 August 2024 (UTC)

While I think option 3 provides a more informative wrapping around links to genomes per taxon, option 1 actually would link to a genome as you would expect for the field NCBI genome ID. The field label should probably be updated to NCBI reference genome ID or similar. I also see no reason not to exclude linking to Ensembl or any other database as long as the statistics in the box are of the linked genome.

I think using an Infobox to pull out (or duplicate) common measures of genetic material from the body text is generally helpful and is especially useful for hosting external links to databases. I support keeping the infobox around.

Things like base counts would be accurate/stable as long as the genome is sequenced with complete coverage and high confidence. I'm more familiar with bacterial genomes where that kind of thing is more common, so I'm not sure how realistic that tends to be for eukaryotic reference genomes. Surely, cutting off those numbers at two significant figures would make the estimates close enough for general purposes and pretty stable over time. Same for coding vs. non-coding genes. ― Synpath 02:01, 13 August 2024 (UTC)