Wikipedia talk:WikiProject Molecular Biology

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WikiProject Molecular Biology Archives: 1, 2, 3

Taskforce archives:

MCB: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
Genetics: 1, 2, 3, 4
Computational Biology: 1, 2
Gene Wiki: 1, 2, 3, 4

Biophysics (inactive): 1, 2
Metabolic Pathways (inactive): 1
Cell Signaling (inactive): 1
RNA (inactive): 1

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)

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)

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)

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)

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 (287)

• Category:Articles citing publications with expressions of concern (60)

• Category:Articles citing publications with errata (74)

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)