Wikipedia talk:WikiProject Molecular Biology/Archive 2

Archive 1

Archive 2

Archive 3

Time for an overview?

Recently, a merger was made between the articles Prostaglandin-F synthase and Prostaglandin F synthase (a no-brainer as they clearly covered the same topic) by Reba16. I had noticed the proposal to merge and took an interest in the new article. This led me to discuss with Reba16 (see [1]) issues which are relevant to many articles on genes, enzymes and their reaction products. My perpective is that of an organic chemist but Reba16 (who is not) agreed with me. We now seek views from others and some guidance. I'll illustrate with specific examples but I suspect the problems are widespread.

• Why is the reaction in the lede of Prostaglandin F synthase written as if it was an oxidation, not a reduction? This enzyme converts a ketone to an alcohol, or (if PGH2 to PGF2) breaks an O-O bond. Answer: the IUBMB Enzyme database (at EC 1.1.1.188) often gets this "wrong". See "METACYC database entry". for details: it confirms the known physiological direction of the reaction. The original Wikipedia article seems to have been generated in semi-automatic fashion from the EC database.
• How does Prostaglandin F synthase differ from AKR1C3 for which there is another Wikipedia article, where some of the PDB id's are the same, for example 1RY0? Answer: one article is written to focus on the genetics, while the other focuses on the biochemistry but in fact they cover the same chemical reactions. (see "second METACYC database entry".).
• Why does the article on Prostaglandin H2 not describe the synthesis of PGF2α as one of the reactions from PGH2? Indeed, the diagram in that article (File:Eicosanoid_synthesis.svg which is very widely used in Wikipedia) would give the reader the impression that PGF2α is not formed directly but only through PGE2, which chemically is odd since E2 is more oxidised than either H2 or F2α. Answer: the article is "correct" but misleading. There is a pathway from PGH2 to PGE2, EC 5.3.99.3 and from PGE2 to PGF2α EC 1.1.1.189 but the direct one-step process also occurs, namely EC 1.1.1.188.
• Similarly, why does the article on Prostaglandin D2 not describe the synthesis of PGF2α from it? (Answer: no-one has written it yet.)

Conclusion: Many articles have been built up over the years without a sufficient overview. That seems to me to be one role Project Groups could usefully take.

• • I want to develop a proposal to handle these sorts of inconsistencies but before doing so it would be helpful to have comments from interested parties and (briefly!) other examples from non-prostaglandin pathways. Mike Turnbull (talk) 14:07, 24 March 2021 (UTC)

1. I agree it was a mistake to give the reactions of our automatized enzyme texts any direction. In Wikidata the reaction participants get a qualifier "part of" ---> "left/right side of reaction" without implying which is preferred as input. Your example in Wikidata: https://www.wikidata.org/wiki/Q21105043#P527. Note we put the reaction on the activity item not the enzyme. Why? Because enzymes can have multiple activities. Note also we use the physiologically correct ions not the neutral compounds.
2. articles like AKR1C3 are about genes, and the convention that such articles are named with the gene name is a good one. If you want to merge gene and protein, please separate these concepts in the new article as separate sections so they can be linked to.

Thanks. --SCIdude (talk) 16:30, 24 March 2021 (UTC)

Draft:SMIM19

Hey, this draft was submitted to AfC a few months ago: Draft:SMIM19. It's mostly greek to me, but I'm noticing that this protein is not the primary topic of any of the scientific sources listed. Should I accept or refuse this draft? Mottezen (talk) 07:01, 15 April 2021 (UTC)

This looks like primary bioinformatics research for the most part, which explains all the references to biological databases and online bioinfo tools. There are no secondary literature (or even primary research papers fitting the subject) in the references, so I think none of the references are usable. Actually there is nothing known about this except the sequence, and all you can say comes from bioinfo, so it's all hypothesis. --SCIdude (talk) 14:27, 15 April 2021 (UTC)

Thank you for your help. I just declined the draft. Mottezen (talk) 22:25, 15 April 2021 (UTC)

I've also added a belated comment to the draft. I agree with SCIdude that they've mixed in a load of original reserach in with the established information. It's a good example as to why we can't include that sort of primary research in the encyclopedia, as they've not stated their methodology for most of it and there are several significant flaws. T.Shafee(Evo&Evo)^talk 07:50, 16 April 2021 (UTC)

Now see, my impression was that genes like this one which is listed in NCBI are inherently notable and there are a lot of stubs of such genes. Jo-Jo Eumerus (talk) 08:44, 16 April 2021 (UTC)

Wikipedia:No_original_research. --SCIdude (talk) 05:04, 18 April 2021 (UTC)

Not what I am talking about. I was only discussing the existence of such articles, not whether these tables are suitable content. Jo-Jo Eumerus (talk) 09:06, 19 April 2021 (UTC)

You're both correct. Jo-Jo Eumerus is right that as human genes they're notable, so there should be articles on them. SCIdude is also right that they're peppered with high-risk original research that needs to be excised. T.Shafee(Evo&Evo)^talk 09:57, 19 April 2021 (UTC)

An alternative place for it would be an article that talks about all uncharacterized human proteins in general, maybe a list article. This needs a good reference, as well. --SCIdude (talk) 15:50, 19 April 2021 (UTC)

Draft:RNF227

I'd like the opinions of subject matter experts regarding whether Draft:RNF227, which has been languishing at Articles for creation for a few months, is a suitable topic for article space or not. When the same question was posed about another protein draft a couple threads ago, contributors were able to arrive at an answer quickly, so I hope this question isn't too burdensome. --Worldbruce (talk) 22:48, 18 April 2021 (UTC)

The draft ad the pages below have very similar issues with WP:original research in protein structure prediction and sometimes phylogenetics scattered amongst non-controversial info summarised out of databases:

• Draft:RNF227
• Draft:SMIM19
• FAM214B
• FAM180b
• FAM120AOS - also phylogeny diagram
• C11orf49
• TMED5
• TMEM81
• TMEM8B
• TMEM101
• TMEM128
• TMEM151A - also phylogeny diagram
• TMEM155
• TCAIM
• LSMEM2
• PRR32
• PROB1
• CCDC92
• CCDC142
• GOLGA8H
• SBK3
• GPATCH11 - also phylogeny diagram
• C7orf26 - also phylogeny diagram
• C13orf38
• C12orf60
• C10orf67
• C15orf39 - also phylogeny diagram
• C17orf53 - also phylogeny diagram
• I've just realised that there's dozens from this search so I'll stop here.

Given the very similar activities of the editors who created these, I have to assume they're part of a well-meaning class (though I can't find the course organiser). T.Shafee(Evo&Evo)^talk 03:20, 19 April 2021 (UTC)

This has been going on for quite a while, and due to the number, I suspect more than one University. While the subject is inherently notable, the problem with these bioinformatics exercises is that they are essentially WP:OR and therefore fundamentally in conflict with Wikipedia. Boghog (talk) 07:48, 19 April 2021 (UTC)

As per above, wouldn't this be a good start for a list article about uncharacterized proteins? --SCIdude (talk) 15:55, 19 April 2021 (UTC)

I've not got a good feel for how long such a list would be, but I wonder whether something more automated like a {{Wikidata list}} via User:ListeriaBot would work well. That way it'd encourage the info to be kept clean on and up-to-date on Wikidata. T.Shafee(Evo&Evo)^talk 23:42, 19 April 2021 (UTC)

Updating RCSB PDB search links

Hi, not sure where the best place is to put this (since it affects multiple templates), but the RCSB PDB search API has been updated (and the old API discontinued) and therefore most (all?) templates that link to it for a search currently fail. On an initial glance this at least includes Template:Infobox protein family, Template:Infobox protein, Template:Infobox gene, Template:Infobox enzyme and probably many more. (See also another talk page comment on this here). I'd love to fix this myself but don't see myself having the time to anytime soon, anyone else willing and able to take that on? Thanks! coiledcoil (talk) 05:32, 18 April 2021 (UTC)

At least the PDBe and PDBj searches still work. However it is not trivial to fix the RCSB PDB links. According to the "Search by UniProt Accession" example, a search for P69905 returns this JSON data string. For {{infobox gene}} which is written in Lua, parsing the retuned JSON for the PDB accession numbers should be possible (however I don't know much about Lua). For the other templates like {{infobox enzyme}}, {{infobox protein}}, {{infobox protein family}}, {{infobox nonhuman protein}}, I don't even know where to begin. It may require rewriting the whole template in Lua. Perhaps we should just comment out the RCSB links for now. Boghog (talk) 06:43, 18 April 2021 (UTC)

After digging around some more, I figured out that one can write a URL to query and return a list of PDB accession codes, although the URL is very messy. For example, after stripping out the session ID:

• {{Infobox gene}} – QUERY: Accession Code(s) = P69905 AND Database Name = "UniProt"
• {{Infobox enzyme}} – QUERY: Enzyme Classification Number = "2.7.1.153"
• {{Infobox protein}} – PDB link to specific accession number still works.
• {{Infobox protein family}} – QUERY: Identifier = "PF00104" AND Annotation Type = "Pfam"

but I am not certain these are persistent. This all seems very messy. Boghog (talk) 09:38, 18 April 2021 (UTC)

I don't think genes should have these links. And protein family should rather have a link to a human or model organism protein (which then links to PDB). --SCIdude (talk) 15:52, 19 April 2021 (UTC)

(edit conflict) What I meant by persistent is the link itself, not the target database. The target website (RCSB PBD) is continuously updated, and in fact, is where the bot via UniProt is getting the data. Now after stripping out the session ID, the links also appear to be persistent. My only remaining concern is how incredibly messy the links look in the template code. In Lua, this is not a problem since Lua has JSON html encoder function. But regular Wikipedia templates, as far as I know, do not. Boghog (talk) 16:11, 19 April 2021 (UTC)

{{Infobox gene}} template name is misleading. It encompasses both the gene and the protein encoded by that gene. So yes it should have a links to protein PDBs. A protein family is not limited to a single organism only related by primary sequence but also tertiary structure, therefore it is appropriate to have a link to a representative all PBDs from the family. Wikipedia ≠ Wikidata. Things are not so hierarchical in Wikipedia. Boghog (talk) 16:19, 19 April 2021 (UTC)

I tried to have a go at it, and yay, it works! I did my experiment on the Template:Infobox enzyme/sandbox (more useful link, the Template:Infobox enzyme/testcases). I coded the tentative Module:Sandbox/Bonob/RCBS PDB search with the idea that it could be used for other RCSB PDB searches by attribute. A number of remarks:

• This is my first encounter with Lua and Scribunto, and I expect I haven't a great sense of conventions.
• It's a fun approach, but that's just about preparing a complicated URL. Said URL can be reduced by a fair bit. I trimmed down the JSON object as much as I could, the ready-to-use URL is still long, but probably manageable with direct inclusion in the relevant templates (the two arguments that matter bolded):

https://www.rcsb.org/search?request=%7B%22request_options%22%3A%7B%22sort%22%3A%5B%7B%22sort_by%22%3A%22score%22%7D%5D%7D%2C%22return_type%22%3A%22entry%22%2C%22query%22%3A%7B%22type%22%3A%22terminal%22%2C%22service%22%3A%22text%22%2C%22parameters%22%3A%7B%22value%22%3A%222.7.1.153%22%2C%22attribute%22%3A%22rcsb_polymer_entity.rcsb_ec_lineage.id%22%2C%22operator%22%3A%22exact_match%22%7D%7D%7D

• (Furthermore, we don't really need to escape the curly brackets, at least that's the impression I'm under, and that would make a tremendous change in readability. I'm assuming that this would not be clean clean though.)
• To be fair, when a change is needed, manually dealing with the 'json-ifying' and the 'urlencoding-ing' is an absolute pain.. And as well for my reference since I keep getting lost in my tabs juggling with all that, a convenient URL encoder/decoder and JSON pretty printer (basically the first results in one's search engine of choice).
• About the JSON object, the RCSB PDB help has a splendid tool to play around, here it is with the parameters I ended up with: Query editor (click on "Run Query").
• Lastly, I've been wondering about this change of the RCSB PDB API. Their new API is powerful and clean, and it makes complete sense for its stated purpose, that is to be accessed by applications. It is also very well documented, but for a use case such as here, this doesn't make sense at all. I imagine others are in the same situation, other databases for example may want to embed links to specific searches to that database. On top of that, the documentation doesn't mention the web search service (from what I could find), hosted at www.rcsb.org/search, but only and explicitly enough the API endpoint search.rcsb.org/rcsbsearch/v1/query, which won't return a web search, but a formatted json output. They clearly use the same engine to power their web search tool, but I can't stop wondering if we're not missing something.
• Oh, after lastly, but very importantly, this really is a tentative, say a proof of concept; if there's some interest, there would be much to do to get that in a publishable condition (and I'd be very happy to give my best try).. bonob (talk) 23:14, 30 April 2021 (UTC)

Thanks Bonob for implementing a module to create a functional RCSB PDB link. A very impressive accomplishment for your first try. The module appears fully functional and looks close to publishable to me. The new RCSB API is very powerful, but it is way more complicated to create simple queries. Your Lau module seems like a good solution. Cheers. Boghog (talk) 04:13, 1 May 2021 (UTC)

So indeed we were missing something, and I found, serendipitously really, that a search may simply be done using https://www.rcsb.org/search?q=, there is no need to go through the API. (The idea popped up to copy two sequences to test a Rosalind exercise I did recently, and looking for a sequence related to the first EC 1.1.1.1 I picked -- oh, alcohol dehydrogenase, this one's full of surprises -- I saw such a link syntax under my mouse pointer o.O)

I don't know that the syntax here is documented, but I experimented a bit, it uses the same keywords as the API (e.g. rcsb_polymer_entity.rcsb_ec_lineage.id), associates keys and values with colon, multiple values separated by comma (key1:val1,val2) and combines them with space separated uppercase operators (key1:val1 AND key2:val2 OR key3:val3).

I checked the 7 templates I found using this search, only the 3 listed by Boghog were concerned:

• {{infobox protein family}} I updated,
• Module:infobox gene and {{infobox enzyme}} I fixed in the sandbox and sent edit requests. bonob (talk) 21:17, 1 May 2021 (UTC)

Thanks again Bonob for tracking down this alternative solution and for implementing it. As far as I can see, this syntax is not documented anywhere which made finding this solution way harder than it needed to be. Boghog (talk) 12:09, 2 May 2021 (UTC)

Ficain

Hi there. The article was inaccurate, I rewrote it. Synonymy problem. Ficain is a ficin, but ficin is not ficain. But it seems to me now that the title of the article should be ficin. 86.83.56.115 (talk) 20:07, 22 May 2021 (UTC)

It seems to me that the previous version was accurate, and that if you want an article about ficin, you should create a new article rather than overwriting and existing article. Boghog (talk) 20:31, 22 May 2021 (UTC) After looking at this a little more closely, it appears that some of the early publications referred to this enzyme as ficin, but the overwhelming name now used is ficain, including the Enzyme Commission name where ficin is listed as a synonym. Boghog (talk) 20:44, 22 May 2021 (UTC)

Ficin currently links to that article. Ficin is the purified mix of enzymes from ANY species of Ficus. "The term ficin must therefore be regarded as generic. In 1992 the International Union of Biochemistry and Molecular Biology (IUBMB) recommended the name ficain for the major proteolytic component of the latex of the fig, Ficus glabrata". The main two references to the article refer to ficin, the main reference is from 1987. The EU website on ficain says ficain is now sometimes called ficin. This isn't an inaccurate statement, but what Wikipedia is saying, that the 1980s uses of ficin pertain to ficain, is. 86.83.56.115 (talk) 20:57, 22 May 2021 (UTC)

For example, wikipedia now states "Commonly used fiCIN is a mixture of several isoforms from the latex of the common fig". That's true, but it's from the 1987 source, and fiCAIN is made from Ficus insipida (syn. F. glabrata). See EC 3.4.22.3. Or this. 86.83.56.115 (talk) 21:02, 22 May 2021 (UTC)

References

Other than PubChem which transliterated the name Ficin into the structure "F-I=CH-I=N-H" which is absolutely hilarious (was someone trying to make a joke?), all the databases list Ficain as the name and Fican as a synonym. The authority is the Enzyme Commission which list the name as Ficain. Boghog (talk) 21:14, 22 May 2021 (UTC)

Dry subject matter, needs jokes. Look, there are only two databases, and they are basically just copying each other. The sources I have added say there WERE originally two different things. We can have two articles, but then we need to remove all the sources which refer to the original ficin from this article -such as the uses in serology, that will leave an article of 2 sentence with none of the present sources. I say just keep everything in one place.86.83.56.115 (talk) 21:23, 22 May 2021 (UTC)

Having said that, let me switch around the text, maybe this is clearer now? You can always revert, but I'm just following the sources. 86.83.56.115 (talk) 21:33, 22 May 2021 (UTC)

According to the Enzyme Commission, EC 3.4.4.12 (ficin) was created 1961, and then transferred in 1972 to 3.4.22.3 (Ficain). So ficin was the original name and ficain is the currently accepted name. Ficain is identical to ficin and they are synonyms of each other. Boghog (talk) 21:55, 22 May 2021 (UTC)

Well, then sources are in dispute. Both should be given.... Wait up. Both sources are not contradictory, the definition of ficain has changed, is what's happened. This edit should make more sense. 86.83.56.115 (talk) 22:18, 22 May 2021 (UTC)

The definitions of both ficin and ficain has remained the same. They are identical and therefore are synonyms of each other. Boghog (talk) 22:53, 22 May 2021 (UTC)

Your assertion of synonymy is contrary to these sources. At this point, what are you basing this on? 86.83.56.115 (talk) 23:11, 22 May 2021 (UTC)

References

I do not see how the sources contradict synonymy. The enzymes, whether they are called ficin or ficain are extracted from the same fruit and have the same EC number. They are identical. I you want to convince me that they are different, you need to explain how they are different and quote specific passages in the sources that demonstrate that. Boghog (talk) 23:37, 22 May 2021 (UTC)

OK, after further reading, I now see that strictly speaking, the term ficain is restricted to the major proteolytic isoenzymes produced by F. glabrata. Nevertheless, ficain and fican are widely treated as synonyms. Many of the other ficans are also probably ficains, but they cannot be classified as such, since they have not yet been carefully characterized. I have made some additional edits which hopefully makes clear this distinction. Because of the fuzziness of the definitions, I do not think it would be appropriate to split the article into two. Furthermore I think we need to live with this ambiguity unless and until the Enzyme Commission revises the definition of EC 3.4.22.3. Boghog (talk) 09:23, 23 May 2021 (UTC)

That's what I've been saying! I see this chronologically:

• 1930 - 1972: ficin - defined as a mix of enzymes from any Ficus species
• 1972: renamed ficain; ficin & ficain are synonymous
• 1980s: mix used for antibody testing
• 1992: definition for ficain changed to a specific enzyme in a particular species; analogues of this enzyme also likely occur in other species (numerous similar enzymes occur in this one), but these are all likely slightly different; ficin & ficain are no longer synonymous, but no one bothered to update the old ficin info (that it's a synonym) in the database.
• 2000s: industrially, old-style ficin enzyme mix continues to be used, maybe also for antibody testing?

I think we've come to an understanding now. I'm largely good with article as you've left it now, and yes, splitting it never seemed useful to me. I edited it a bit more (see edit comments), think I'm good now. Odd how this article gets much more visitors than the plant, by the way. Cheers.86.83.56.115 (talk) 14:06, 23 May 2021 (UTC)

I apologize for being so dense, but the distinction between ficin vs. ficain was not immediately obvious to me. I appreciate your follow-up edits and now I think the article is in very good shape. Cheers. Boghog (talk) 16:23, 24 May 2021 (UTC)

.

One of your project's articles has been selected for improvement!

Hello, Please note that Savoriness, which is within this project's scope, has been selected as one of the Articles for improvement. The article is scheduled to appear on Wikipedia's Community portal in the "Articles for improvement" section for one week, beginning today. Everyone is encouraged to collaborate to improve the article. Thanks, and happy editing! Delivered by — MusikBot talk 00:05, 14 June 2021 (UTC) on behalf of the AFI team

Draft:Fluorescent Chemosensors for Ion and Molecule Recognition

Please, let me know if this book is valuable enough to be included on Wikipedia. https://en.wikipedia.org/wiki/Draft:Fluorescent_Chemosensors_for_Ion_and_Molecule_Recognition

--DrIlyaTsyrlov (talk) 23:36, 15 June 2021 (UTC)

Request for Comment Robert Lanza

There is a Request for Comment about Robert Lanza#Biocentrism that may be of interest to members of the WikiProject: Bibliographies/Science task force. Talk:Robert Lanza#Request For Comment Robert Lanza. I would encourage members of this project to consider participating to add diversity to the discussion. Sapphire41359 (talk) 17:33, 17 June 2021 (UTC)

Microtubule Catastrophe and Rescue

Greetings first. I'm new to Wikipedia editing so please correct me if I made any errors. While I was searching for cytoskeleton catastrophe and rescue I found out that there's no present articles about them. Should we add this as new article or we should add it in the microtubule post. Zlover0407 (talk) 14:21, 28 June 2021 (UTC)

Hi. Thanks for your question. As a general rule, I think it is probably better to create a new section in microtubule and see how long the section becomes. If the section grows to more than a few paragraphs, then at that point, it could be split from the parent. I see that there as least one review covering microtubule catastrophe and rescue (PMID 23092753), so I can see it has the potential to become a separate article. Cheers. Boghog (talk) 16:14, 28 June 2021 (UTC)

Draft:Minimizer

Will someone please look at this draft? It is too technical for a retired chemist and computer scientist to evaluate. Robert McClenon (talk) 22:45, 12 July 2021 (UTC)

• I've had a look and added some comments. T.Shafee(Evo&Evo)^talk 08:50, 13 July 2021 (UTC)

Job sites for hiring scientists for industry R&D roles

Hey everyone. Been a while.

Anyway, I'm currently hiring an R&D Scientist. I'm not linking the job description here because I'm not trying to recruit you; however, I figured you guys might have valuable insights on where I might be able to source bioscience job candidates that don't use mainstream job boards. I've already spent $1750 on Indeed, Monster, ZipRecruiter, and LinkedIn ads for our role, and I suppose we may budget up to $750 more for advertising if anyone has a useful suggestion. For context, our open position involves developing and validating a metagenomic nanopore sequencing pipeline using a series of standard and novel methods we've identified as a likely means of resolving the limitations of the pipeline employed in the INHALE trial.

To rephrase what I'm asking:

• Assuming you have a bioscience-related PhD, where would you go to look for a job?
• Are there any job sites that you suggest for recruiting scientists for industry/non-academic R&D roles?
• If anyone happens to know of a Wikipedia list article on science/R&D-related job sites, that'd be quite helpful too.

The only directly relevant recruiting service I'm aware of is Scismic, but it'd cost us $16,000-$18,000 to use their service to hire for our open position. Seppi333 (Insert 2¢) 19:20, 15 July 2021 (UTC)

Addendum: If questions like this on community talk pages are frowned upon, send me an email and I'll delete it. I've been away from Wikipedia for too long, so I don't really remember how the community would feel about me asking this question here. Seppi333 (Insert 2¢) 19:23, 15 July 2021 (UTC)

ISCB Wikipedia Hackathon today

Hi all, a heads up that as part of the ISCB Student Council Symposium, there will be a hackathon later today, 23 July 2021, with the main focus of connecting ISCB Communities of Special Interest to relevant articles within the Computational Biology subset of WP:MOLBIO and a stretch goal of reviewing the importance and quality ratings of these articles.

I expect actual Wiki editing to be minimal during this time but we might require some assistance with (1) implementing a system (possibly sub-taskforces??) where we can use the COSI classifications on-Wiki; and (2) making the actual updates to the importance/quality ratings sometime after the event.

Thanks! Amkilpatrick (talk) 08:04, 23 July 2021 (UTC)

Physiological modulator

The article is based on predatory sources (doi:10.11648/...) published by Science Publishing Group, and utterly fails WP:V and WP:MEDRS. A major cleanup is needed. Headbomb {t · c · p · b} 04:59, 4 August 2021 (UTC)

@Elmidae: since you've deal with this before at Wikipedia:Articles_for_deletion/Biodynamic_enzymology. Headbomb {t · c · p · b} 05:02, 4 August 2021 (UTC)

As far as I can tell, this is a recreation of Biodynamic enzymology, plus or minus a few curlicues - I recognize much of the phrasing, and entire sections register as straight copies to the mind's eye. G4'd. --Elmidae (talk · contribs) 13:13, 4 August 2021 (UTC)

Discussion at WP:RSN concerning a paper about COVID origins and bioengineering

There is a discussion at WP:RSN concerning this paper by Yuri Deigin and Rosana Segretto in Bioessays which may be of interest to the members of this WikiProject. See discussion here.

Segreto, R., & Deigin, Y. (2021). The genetic structure of SARS-CoV-2 does not rule out a laboratory origin. BioEssays, 43, e2000240. https://doi.org/10.1002/bies.202000240.

Thanks.— Shibbolethink ^{(♔ ♕)} 23:48, 9 September 2021 (UTC)

I've taken a look at the paper and those that cite it to give a summary of my thoughts over at the discussion there. T.Shafee(Evo&Evo)^talk 04:30, 10 September 2021 (UTC)

Merger discussion for PNPO

An article which may be of interest to members of this project—PNPO —has been proposed for merging with Pyridoxine 5′-phosphate oxidase. If you are interested, please follow the (Discuss) link at the top of the article to participate in the merger discussion. Thank you. DMacks (talk) 16:21, 12 September 2021 (UTC)

Portal:Biochemistry

There is a deletion discussion underway at Wikipedia:Miscellany for deletion/Portal:Biochemistry (2nd nomination). Robert McClenon (talk) 17:40, 24 September 2021 (UTC)

Gene vs encoded-protein article guideline?

Is there a guideline for whether there should be separate articles for a gene and the protein it encodes, vs a unified article? And if unified, whether the gene or the protein should be the actual article (vs redirect to it)? DMacks (talk) 21:26, 24 September 2021 (UTC)

We have MOS:MCB as a style guideline (at the essay-level) to gene and protein articles. For a combined article, it generally recommends using the protein name for the title. My two cents is that it is probably best to start a combined article. Then if there is sufficient sourcing and development that the article becomes unwieldy, a gene/protein split might be considered. --{{u|Mark viking}} {Talk} 00:11, 25 September 2021 (UTC)

Thanks! I didn't see that (or the parent Wikipedia:WikiProject Molecular Biology/Molecular and Cell Biology/Style guidelines) linked from Wikipedia:WikiProject Molecular Biology/Molecular and Cell Biology (is how I got here). Should it have a "Resources" section similar to the one at Wikipedia:WikiProject Molecular Biology? DMacks (talk) 07:08, 25 September 2021 (UTC)

The linking is a little indirect--Wikipedia:WikiProject_Molecular_Biology/Molecular_and_Cell_Biology has an advice & resources link to a resources page Wikipedia:WikiProject_Molecular_Biology/Molecular_and_Cell_Biology/Resources which has the MOS:MCB link. I'd be in favor of putting the resource links directly on the Wikipedia:WikiProject_Molecular_Biology/Molecular_and_Cell_Biology page.

Status of Nirenberg and Matthaei experiment page

Maybe my perspective is unusual, but to me the Nirenberg and Matthaei experiment is one of _the_ pivotal experiments that underpin our whole understanding of how molecular biology ties together genotype and phenotype.

Clicking to the article's Talk page, I see its status currently listed as Start-Class and Low-importance. That sounds .. odd. Who can change that? Are there specific complaints about the article as it stands? It looks pretty good to me.

I just reverted some vandalism there that had lasted for three months. I have trouble understanding the mind-set of someone who thinks that Wikipedia should present corrupted foundations of biology. But somehow this article has attracted at least three such actions in this past year. Does this rise to the level of needing semi-protection? Or would it be enough for a few members of this WikiProject pay a bit more attention to this article? Larry Doolittle (talk) 07:08, 3 October 2021 (UTC)

@Larry Doolittle: For the rating, it's not uncommon for them to get out of date, or sometimes to have been done in a rush. Anyone is allowed to update the rating so please feel free to take a quick look at this summary of the rating scale for similar pages and update the rating in the template at the top of the article's talk page! I'm not very knowledgeable about semi-protection on wp, so others will have to weigh in on that! T.Shafee(Evo&Evo)^talk 11:14, 3 October 2021 (UTC)

Call me paranoid if you want, but I see evidence of methodical biology article vandalism. Other articles affected are Poly(A)-binding protein and Translation (biology). Maybe someone else can step in there. Larry Doolittle (talk) 08:01, 3 October 2021 (UTC)

Y-DNA

Is Y-DNA a common scientific term? For me, latin character+DNA is associated exclusively with a A, B, and Z forms of double helix. Y-DNA as a synonym of Y-chromosomal DNA is found predominantly in amateur/recreational genetics websites which are not reliable sources. It does sometimes present in scientific papers, but most commonly just "Y-chromosome" or "Y-chromosomal DNA" are used instead. Y-chromosome page doesn't even mention "Y-DNA". Moreover, there is another meaning of Y-DNA, which is Y-shaped DNA (in self-assembled DNA structures, not about replication fork), and this abbreviation becomes increasingly more common. I propose to 1)convert Y-DNA to a disambiguation page (though Y-shaped DNA not created yet) 2)Change Y-DNA to "Y-chromosomal" etc. in titles of wikipedia articles like Y-DNA haplogroups by ethnic group --Hwem (talk) 01:48, 10 December 2021 (UTC)

IMO no, "Y-DNA" as shorthand for "Y-chromosome DNA" is fine in text if the context is clear but doesn't seem to be standard terminology. I agree with your suggestion to create a dab page. I also agree with retitling articles and categories that use "Y-DNA", though I feel less strongly about that. Opabinia regalis (talk) 22:36, 19 December 2021 (UTC)

Well, when I hear "Y-DNA" I think "Z-DNA" and not "Y-chromosome". So at least for me it's actively misleading. Jo-Jo Eumerus (talk) 09:38, 20 December 2021 (UTC)

AFD Drum RNA motif & hundreds of others

Hi folks, you may be interested in participating in discussions for pages relating to Rfam, see Wikipedia:Articles for deletion/Drum RNA motif and Wikipedia:Conflict of interest/Noticeboard#Hundreds of RNA motif pages --Amkilpatrick (talk) 08:26, 2 December 2021 (UTC)

Thank you for posting about this problem here! Here is a quick summary: several hundred of wiki articles describing RNA genes are nominated for deletion because supposedly they do not have a secondary source and do not meet the notability criteria, despite being linked to and updated by the team maintaining the Rfam database of RNA families. If these pages are deleted, Rfam would be forced to stop a decade-long collaboration with Wikipedia and move to a separate wiki, creating a barrier between scientists and the general public. As a result, the information about RNA genes will be harder to find and fewer people will maintain in the future. This would be a huge step backwards so I would like to bring this issue to the attention of a wider community of Wikipedians interested in Molecular Biology. Any input will be greatly appreciated! Antonipetrov (talk) 15:43, 2 December 2021 (UTC)

Thanks to both for flagging this here. I think it's highly relevant not only to RNA motif articles in particular, but also to some broader concepts:

• relationships between WP and external databases (e.g. the way Pfam & Rfam transclude content, vs the way that Cazypedia keeps all their summaries separate)
• inherent notability (relevant to motifs, genes, proteins etc)
• source use for scientific topics (in particular use of primary vs secondary sources and what type of source a database is)
• many stubs vs single lists

T.Shafee(Evo&Evo)^talk 00:38, 3 December 2021 (UTC)

Thanks a lot to everyone who contributed to the discussion! The AfD request has been closed as there was no consensus, so the articles are safe. We will aim to review these and other articles that correspond to Rfam families to avoid such situations in the future. Feel free to get in touch if anyone is interested in this effort. Thanks again! Antonipetrov (talk) 17:06, 8 December 2021 (UTC)

Notability guidelines for science/database topics?

User:Sandstein's close comment at WP:AfD/Drum RNA motif includes "There's no consensus to be found here, but our resident specialists should get together and try to resolve the question at which level we want to cover this kind of concept via a projectspace discussion or an RfC", which I think is a good idea. I suggest brainstorming here then drafting something short to list in WP:Molbio#Resources, or if it ends up more general, listing in Category:Wikipedia_notability_guidelines (thought I'm conscious of instruction creep).

Existing info

• The most relevant existing guidelines are for geographic_features, astronomical_objects, and numbers.
• The WP:Inherent notability guideline also uses microbial species as an example of de facto notability (living things are notable).
• Some prev discussions: [2] [3] [4] [5] [6] [7] [8] [9]

Guiding questions

1. Are there classes of molbio (or other) topics with inherent/De facto notability?
2. What are the principles / common features for which classes are notable?
3. If a database is a sufficient secondary source to support notability, what are the features of such a database?
4. Does the number of items of that class matter? Would the call on RNA motifs have differed if there were 100,000 observed motifs?
5. Does it make a difference if the class is naturally occurring vs man-made? (e.g. observed microbial species vs created cell lines)
6. Does it make a difference if the class is stable vs changes rapidly?

I've tried to collate my thoughts below as a starting point. T.Shafee(Evo&Evo)^talk 00:39, 9 December 2021 (UTC)

Starting suggestion

Class notability principles

When creating a set of pages of a given class (e.g. human genes), check that items in that class (e.g. BRCA1) are:

• Items are collated in a well-established, curated and reviewed database or review article (indicates notability to the relevant sci community)
• Databases don't significantly disagree on what is and isn't in that class (e.g. SCOP and CATH agree on most items, but there are some conflicting classifications)
• Items wouldn't be better listed within an existing wikipedia page (e.g. subspecies/strains/variants/cultivars could go within their parent species page)
• If most items in the class have only a small amount of information and don't require additional prose, consider a table (e.g. restriction enzyme cut sites)
• The class has a 'manageable' number of items in it (no idea how to define this). If there are too many items in a class to warrant individual pages, consider one hierarchical level above (e.g. 41 protein architectures is reasonable, 500,000 protein domains is probably not [10]).

Even if the whole set isn't inherently notable, individual members of the set may still be. E.g. many of them do has a WP page.

Class notability examples

• directly observed species: de facto notable
• indirectly observed organisms (e.g. metagenomics): may still be notable but probably not as a class
• subspecies/strains/variants/cultivars: usually within the organism's page
• cell lines: probably not inherently notable as a class?
• human genes: de facto notable?
• mutations: usually within the gene/protein
• protein families & superfamilies/clans: superfams de facto notable, families likely notable? (Pfam 33.1 lists 18259 families and 635 clans, SCOP 2 lists 5840 families and 2783 superfamilies, CATH 4.3 lists 6631 superfamilies and >30000 families)
• RNA families & superfamilies/clans: superfams de facto notable, families likely notable? Rfam 14 lists 4069 families and 127 clans.

• Note: I think clans are not created when there would only be one family in it. So, I think there would close to 4000 clans (as an analog to superfamily / class) if one-family clans where included. I agree with your point that our enthusiasm about including something in Wikipedia depends on his many there are, and whether that's practical to store in Wikipedia. (If a robot could be made that discovered there are actually millions of species on earth, maybe species would lose inherent notability.) Zashaw (talk) 09:04, 11 December 2021 (UTC)

• RNA motifs: de facto notable? Subject of the recent AfD. Closest equivalent are protein motifs, though no database currently collates an equivalent to Rfam's RNA motifs.
• Restriction enzyme cut sites: as a class, most items don't require a prose description and info is typically structured, so just the summary table is appropriate for most.

What do people think? T.Shafee(Evo&Evo)^talk 00:39, 9 December 2021 (UTC)

Based on the discussion below, I've drafted up a Wikipedia:Notability_(biology). I've tried to encompass all the feedback but please feel free to use it as a starting point and improve. T.Shafee(Evo&Evo)^talk 02:21, 31 December 2021 (UTC)

Discussion

Thanks for starting this discussion. I'd say that anatomical entities (including cell types) that are found in humans are inherently notable. Actually, I'd argue that any class identifiable in humans is inherently notable. I generally agree with the points raised so far; no objections. TiagoLubiana (talk) 13:21, 10 December 2021 (UTC)

On the subject of scale, the rule of thumb is that plant species are notable; there are possibly 500,000 (not all yet identified) plant species. Numbers of animal and fungal species are less certain, but animal species outnumber plant species, and fungal species may do. So 500,000 protein domains doesn't seem to preclude them from being inherently notable. I could see an argument being made that they are more remote from the concerns of the general audience, and thereby are less inherently notable as a class. Lavateraguy (talk) 00:28, 17 December 2021 (UTC)

• As a general procedural recommendation I suggest that unless the reliable sources support an immediate reasonably sized structured article, use a section in the article on the including group, with a redirect from the potential title (as a redirect to section with possibilities). If it gets too big it is probably sufficiently notable for an article, and can be split out. · · · Peter Southwood ^(talk): 06:41, 18 December 2021 (UTC)
• I don't think the numbers matter, but a smaller number of reasonably sized articles with appropriate redirects is in my opinion better than a mass of stubs. Also less likely to attract deletion proposals. · · · Peter Southwood ^(talk): 06:51, 18 December 2021 (UTC)
• I have to admit I don't think this is hugely important to settle for all such similar topics, just based on the RNA motif discussion - which I think would not have ended up at AfD at all if people with questions about specialized topics were more reliably directed to places they can get input from editors familiar with the topic instead of general noticeboards. My personal preferences have changed as more of my reading gets done on my phone or a tablet: I'd rather have many small articles than a few long ones that are a pain to navigate on a small screen, especially if the stub has good links to other sites (whatever classification system or database applies). I have no issue with 500,000 protein domain articles; likewise with 500,000 plant species or bacteria or anything else. As for sources, it seems obvious to me that an expert-curated database is just as good as a review article written by those same experts. Probably better, since it's more up-to-date. WP:SCIRS already mentions "standard reference guides", maybe it should also say "or expert-curated databases and reference material" or similar. Opabinia regalis (talk) 22:28, 19 December 2021 (UTC)
• Comments, One, some databases are pet projects of individuals, such as grad students or professors, others are massive federally-funded entities. There is a difference. Two, editors should make a distinction here between notability and the wisdom of creating a stub article where a list article, table in an article or just some prose in a bigger article would be better. Three, there is such a thing as primary source scientific literature, which is nearly all of it. See WP:MEDRS for an idea of how stringent it is possible to be on this. Four, there is a rough consensus on this topic already. Mass creation of stubs is frowned upon. All good species are notable. Subspecies, varieties, artificial hybrids, cultivars and so forth should be treated in the species article, and must meet the GNG if they are to have their own article. Well-studied genes of well-studied organisms (model organisms) are okay. But the lack of articles on the unimportant genes is quite telling. (So many open reading frames are uncharacterized.) Alleles, SNPs, homologous genes in other organisms, etc are probably not important, and even if they meet the GNG, should probably be treated in the main gene's article unless they need to be split off per WP:Article size. Monotypic taxa don't get an article for each rank, redirects are used. In general it is bad for the readers to have to flick back and forth between atomized stubs to find out what they need to know. A variety only makes sense in the context of the entity it varies from. Abductive (reasoning) 04:18, 20 December 2021 (UTC)

Computational and Statistical Genetics

I stumbled across Computational and Statistical Genetics and I'm not sure what to do with it.

• It seems to be a dupe of Bioinformatics, Computational biology, and/or Computational genomics.
• The latter two are the only mainspace articles that link to it.
• The text is virtually unchanged from its original writing in 2013 and requires considerable work.
• Even if re-written, I don't see benefit in preserving/merging/copying/reusing the text elsewhere.
• The talk page has one edit, where a reviewer appraised it as C-class.
• Both the author and reviewer are retired, so I have not attempted to reach them.

Should this be deleted? Redirected? Merged? --Xarm Endris (talk) 16:36, 6 January 2022 (UTC)

@Xarm Endris: Well spotted. Looks like it's had relatively little attention since it was made in 2013, and I suspect it's low viewcount is partly because few people will be searching for the compound page name and it has few inward links. Sadly, although the topics are relevant, the writing style and minimal referencing make it unlikely to be worth merging into computational genomics, so probably just a redirect (TBH, the computational genomics could probably do with an update & cleanup). T.Shafee(Evo&Evo)^talk 23:10, 6 January 2022 (UTC)

I'm not sure is a redirect is needed. We already have computational genetics (which appropriately redirects to computational genomics) and statistical genetics as separate articles, which makes sense because they are separate topics.

@Mark viking: What would you suggest instead of a redirect? --Xarm Endris (talk) 05:26, 7 January 2022 (UTC)

Sorry I was not clear--I'd suggest deletion because "Computational and Statistical Genetics" is an unlikely search term. But if others think it useful, a redirect to computational genomics would be fine, too. --{{u|Mark viking}} {Talk} 05:50, 7 January 2022 (UTC)

I would support deletion if we have a consensus. Thoughts, @T.Shafee(Evo&Evo)? --Xarm Endris (talk) 09:23, 7 January 2022 (UTC)

Certainly, fine by me. T.Shafee(Evo&Evo)^talk 10:18, 7 January 2022 (UTC)

I agree, likely delete IMO given the overlap with computational genomics. (In fact, computational genomics is one of the two articles that link in). Amkilpatrick (talk) 10:22, 7 January 2022 (UTC)

Help to revive an inactive Wikiproject on Biophysics

I would like to revive the inactive Wikiproject Biophysics and wonder if there are any editors that are interested in joining the Wikiproject on Biophysics. This research field is gaining continuously more importance in science, so I am convinced new subjects of research will come up regularly. Moreover, I noticed there are some really interesting Wikipedia pages in the category of Biophysics that could benefit from new edits and updates. I am a Biologist with strong interests in Biophysics, so I really need help from Physicists, Biophysicists and other Biologists to work together. Although this Wikiproject is inactive, any interested editor can still add his or her name to the list of participants on this page from where we might start to work and discuss the project. So I ask you to adhere to the project and revive it. Thank you - Phacelias (talk) 21:31, 9 January 2022 (UTC)

Disambiguation links to Cathepsin L

Could you help to disambiguate the links shown at Disambig fix list for Cathepsin L? I find these difficult and would not want to direct readers to the right one.— Rod ^talk 15:56, 20 January 2022 (UTC)

Cyclol Featured article review

I have nominated Cyclol for a featured article review here. Please join the discussion on whether this article meets featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Delist" the article's featured status. The instructions for the review process are here. SandyGeorgia (Talk) 20:55, 8 March 2022 (UTC)

Disagreement at Talk:Artemisinin

Hi all, we have a deadlocked disagreement at Talk:Artemisinin#Cell_differentiation that would benefit from others' opinions. Any thoughts shared would be much appreciated. Ajpolino (talk) 21:19, 24 March 2022 (UTC)

Enzyme inhibitor FAR

I have nominated Enzyme inhibitor for a featured article review here. Please join the discussion on whether this article meets featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Delist" the article's featured status. The instructions for the review process are here. GamerPro64 23:05, 25 March 2022 (UTC)

meiogenesis?

XRCC1 says that the protein "may play a role in DNA processing during meiogenesis and recombination in germ cells". That's great. Now what the #%&@ is "meiogenesis"? By the way, this exact phrase does appear in the source cited, so it's not a transcription error by the Wikipedia editor. BD2412 T 05:30, 25 March 2022 (UTC)

As far as I can see, the term derives from an analogy with 'mitogenesis' which is the process of triggering mitosis. Meiogenesis might therefore indicate triggering meiosis. The process of meiosis includes 'recombination in germ cells' so it is a weird sentence in any case. I get more than 800 hits on Google for meiogenesis always in the same context of the XRCC1 gene. The sentence you cite is right, but a short explanation might be added. Phacelias (talk) 06:49, 25 March 2022 (UTC)

How about "may play a role in DNA processing during meiogenesis, a process which includes recombination in germ cells"? BD2412 T 14:21, 25 March 2022 (UTC)

Meiosis includes 'recombination in germ cells'. Meiogenesis instead is the process of induction of meiosis. Probably it is better to add "may play a role in DNA processing during meiogenesis, i.e. during the induction of meiosis and recombination in germ cells". It probably is a new word/term in genetics and cell biology. Phacelias (talk) 21:21, 25 March 2022 (UTC)

 Done. Is it worth having an article on Meiogenesis? BD2412 T 22:35, 1 April 2022 (UTC)

Not a lot of sources to go on, seems like. Jo-Jo Eumerus (talk) 08:00, 2 April 2022 (UTC)

Junk DNA

The current Wikipedia pages are heavily biased against junk DNA and this needs to be fixed since the consensus view of the experts is that 90% of our genome is junk. At the very least, we need to introduce more balance into the relevant pages.

There's a discussion on the Non-coding DNA page about creating a new entry for Junk DNA. This is long overdue and I have begun working on it. Please let me know if you object to creating a separate entry for junk DNA and, if so, what are your scientific reasons for objecting? Genome42 (talk) 15:12, 19 May 2022 (UTC)

I totally agree with separating the two concepts out to create a new Junk DNA page. The topic shifted around a lot in popular science as science communicators tried to explain that there's more to genomes than just protein-coding ORFs, but ended up with this conflation between Junk and non-coding DNA in general (inc. RNA-coding regions, binding regions, structural regions etc). T.Shafee(Evo&Evo)^talk 02:28, 20 May 2022 (UTC)

User script to detect unreliable sources

Main page: User:Headbomb/unreliable

I have (with the help of others) made a small user script to detect and highlight various links to unreliable sources and predatory journals. Some of you may already be familiar with it, given it is currently the 39th most imported script on Wikipedia. The idea is that it takes something like

• John Smith "Article of things" Deprecated.com. Accessed 2020-02-14. (John Smith "[https://www.deprecated.com/article Article of things]" ''Deprecated.com''. Accessed 2020-02-14.)

and turns it into something like

• John Smith "Article of things" Deprecated.com. Accessed 2020-02-14.

It will work on a variety of links, including those from {{cite web}}, {{cite journal}} and {{doi}}.

The script is mostly based on WP:RSPSOURCES, WP:NPPSG and WP:CITEWATCH and a good dose of common sense. I'm always expanding coverage and tweaking the script's logic, so general feedback and suggestions to expand coverage to other unreliable sources are always welcomed.

Do note that this is not a script to be mindlessly used, and several caveats apply. Details and instructions are available at User:Headbomb/unreliable. Questions, comments and requests can be made at User talk:Headbomb/unreliable.

- Headbomb {t · c · p · b}

This is a one time notice and can't be unsubscribed from. Delivered by: MediaWiki message delivery (talk) 16:01, 29 April 2022 (UTC)

@Headbomb Great work on this - really useful. Eventually, it'd also be great to have something similar to detect predatory journals and retracted papers (with additional caveats for when it's approriate to cite such items anyway). Do you think it'd be possible to use some wikidata property to indicate wether a source is WP:RS? T.Shafee(Evo&Evo)^talk 03:09, 20 May 2022 (UTC)

This does detect predatory journals. If some aren't picked up, let me know and I'll add them. And I don't think there's anything to be done with Wikidata here. Headbomb {t · c · p · b} 03:11, 20 May 2022 (UTC)

Draft:Antigenic Essence

Hi, I'm reviewing this draft at AfD, and the sources seemed quite weak to me, so I was wondering if anyone who understands the subject matter could take a look and offer an opinion on how legit this topic is likely to be? Thanks, -- DoubleGrazing (talk) 07:23, 21 May 2022 (UTC)

@DoubleGrazing Thanks for flagging it here. I've added my comments over at the draft. In short, it may be wp:too soon and potentially wp:coi. The idea behind the technique is nice, but I can find almost no genuinely independent coverage of it, since it's research is pretty niche and its commercialisation is so pre-clinical. T.Shafee(Evo&Evo)^talk 05:12, 1 June 2022 (UTC)

Many thanks @Evolution and evolvability, appreciated. I'll go and look at your comments in more detail, but sounds like the draft might not be ready for publication yet. Thanks, -- DoubleGrazing (talk) 05:25, 1 June 2022 (UTC)

Acute myeloid leukemia FAR

I have nominated Acute myeloid leukemia for a featured article review here. Please join the discussion on whether this article meets featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Delist" the article's featured status. The instructions for the review process are here. Hog Farm _Talk 04:24, 18 June 2022 (UTC)

New computational biology workforce paper

Hi folks, just a heads up our new paper Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia, recently published in Bioinformatics and presented at ISMB may be of interest for some here.

We link WP articles from the computational biology workforce to relevant COSIs (dataset here) as a first step towards (1) characterizing the representation of computational biology on WP at the domain-level; (2) providing ISCB COSIs with an open educational resource specific to their domain/subfield; and (3) identifying domain experts who would have the knowledge to improve computational biology representation on WP.

Any comments welcomed, and if you've ideas for expanding upon this I'd be happy to collaborate. Thanks, Amkilpatrick (talk) 13:30, 15 July 2022 (UTC)

Do we need two templates for external links to EC number databases?

There are currently two templates in use which provide links to Enzyme Commission number databases. The original created in 2005 is {{EC number}} which as of today is transcluded in 4,859 places. The alternative {{EnzExplorer}} was created in 2021 and currently used in 324 places. In an article like adenosylcobinamide-phosphate synthase both versions appear: the former via the Infobox, where it appears as EC 6.3.1.10 and the latter in the first line of text as EC 6.3.1.10. The external links go to alternative databases, which may be confusing to readers and I wonder whether we should standardise on one or the other? Mike Turnbull (talk) 11:53, 7 July 2022 (UTC)

Getting a bit lost in the templates. The {{EnzExplorer}} one seems to me to be the right one as the main target (not that I know much about EC databases); the IUBMB seems to be authoritative on the topic of EC numbers, and their iubmb.org website in its "Resources" menu has a link to "Enzyme database" that points to ExplorEnz.

I got lost because I was comparing the first line of the {{Infobox enzyme}} to the {{EnzExplorer}} template. My impression is that the former (to iubmb.qmul.ac.uk) has been superseded by the latter (to enzyme-database.org). I then realized that the target of the {{EC number}} template is ExPASy.

My feeling is that the first line of the {{Infobox enzyme}} should point to ExplorerEnz rather than iubmb.qmul.ac.uk, and that the {{EC number}} template should also point ExplorerEnz, with the ExPASy Enzyme database remaining accessible through the Enzyme infobox only. bonob (talk) 19:42, 14 July 2022 (UTC)

I agree fully with what bonob says. I have been (before this) in discussion with Keith Tipton (chair of the IUBMB committee on enzymes), and he is in general in agreement with the proposed changes. I also wrote to all of the members of the committee a couple of weeks ago, but haven't had any replies except from Keith Tipton. Probably July wasn't the best moment to ask. My feeling is that the links to iubmb.qmul.ac.uk/enzyme/iubmb.qmul.ac.uk are obsolete now that ExplorEnz exists and should go, but for the moment that's just my opinion, and I haven't checked (yet) with IUBMB. Athel cb (talk) 08:13, 25 July 2022 (UTC)

One other point. No matter how good Expasy is (and it is good and well maintained) it doesn't represent the official view of the IUBMB, whereas ExplorEnz does. Athel cb (talk) 08:17, 25 July 2022 (UTC)

OK, so I assume that once the IUBMB have formally agreed Wikipedia should use ExplorEnz, we should update all such templates to use just that source. I have little expertise with templates but I assume that the current {{EC number}} template could readily be altered to point to the new URLs and we could "retire" the alternative, which, incidentally I don't know why Athel cb chose to call "EnzExplorer" rather than "ExplorerEnz"! Maybe Vanisaac would like to comment on the mechanics of updating templates, as the last person to edit the "EC number" documentation? Is there any reason to continue to keep links to ExPASy? Mike Turnbull (talk) 12:31, 25 July 2022 (UTC)

"I don't know why Athel cb chose to call "EnzExplorer": because I was confused! I didn't notice originally, but as it did what I wanted I left the name as it was. Athel cb (talk) 12:49, 25 July 2022 (UTC)

Featured Article Save Award for Enzyme inhibitor

There is a Featured Article Save Award nomination at Wikipedia talk:Featured article review/Enzyme inhibitor/archive1. Please join the discussion to recognize and celebrate editors who helped assure this article would retain its featured status. SandyGeorgia (Talk) 02:59, 6 August 2022 (UTC)

SME opinions requested at Talk:Intergenic region

It would be great if some subject matter experts could chime in at this discussion on the topic of describing intergenic regions — TheresNoTime (talk • she/her) 18:15, 19 August 2022 (UTC)

Requested move at Talk:Hook effect#Requested move 4 September 2022

There is a requested move discussion at Talk:Hook effect#Requested move 4 September 2022 that may be of interest to members of this WikiProject. – robertsky (talk) 05:01, 11 September 2022 (UTC)

Eran Elhaik and Jewish genetics

Please take a look at the discussion about citing Eran Elhaik in the Genetic studies on Jews article. Triggerhippie4 (talk) 23:56, 11 September 2022 (UTC)

Split Visual Cycle from Visual Phototransduction

If interested, please discuss a split of Visual cycle from Visual phototransduction. Discuss here. Curran919 (talk) 21:27, 7 October 2022 (UTC)

Help with updating article

I proposed a few updates to the article about neurologist Leslie B. Vosshall here: Talk:Leslie B. Vosshall#Proposals October 2022. I have a conflict of interest as a paid consultant but believe these changes are obvious improvements to address sourcing issues pointed out in a maintenance tag. A review by a project member would be very much appreciated. Thanks.W12SW77 (talk) 21:36, 12 October 2022 (UTC)

Same notice forum-shopped to Wikipedia talk:WikiProject Molecular Biology, Wikipedia talk:WikiProject Biography/Science and academia, Wikipedia talk:WikiProject Women scientists, Wikipedia talk:WikiProject Biography, Wikipedia talk:WikiProject Women in Red. —David Eppstein (talk) 22:45, 12 October 2022 (UTC)

Requested changes have been made. --Tagishsimon (talk) 23:02, 12 October 2022 (UTC)

LoD considerations when an analyte is a tested with a matrix type that differs from the sample matrix

Cross-posting here due to relevance. See WT:MED#LoD considerations when an analyte is a tested with a matrix type that differs from the sample matrix for details. Seppi333 (Insert 2¢) 10:40, 22 October 2022 (UTC)

New article in need of attention from this project

Hello! I just created the page Cortical alveolum and I think it belongs in this taskforce's scope. ☽ Snoteleks ☾ 17:28, 2 November 2022 (UTC)

Organ on a chip; MISLEADING (And for this reason inaccurate) INTRO; PLEASE CONSIDER MY SUGGESTION

Hello, Peace, I was reading the Organ on a Chip page and the introduction is soooo misleading. The basic concept is that OoCs are defined as ADVANCED IN VITRO MODELS and not (at all) as ARTIFICIAL ORGANS; these are two COMPLETELY DIFFERENT visions, and there could be misconceptions. Moreover OoCs are not only 3D, but also 2D, and they can also be single channel. The definition ARTIFICIAL ORGAN doesn't fit the OoC;

The problem is this source: Moyer MW (March 2011). "Organs-on-a-chip for faster drug development". Scientific American. 304 (3): 19. doi:10.1038/scientificamerican0311-19a. PMID 21438480. The part that refers to this article is conceptually misleading the idea of OoC

So I suggest instead of

An organ-on-a-chip (OOC) is a multi-channel 3-D microfluidic cell culture, integrated circuit (chip) that simulates the activities, mechanics and physiological response of an entire organ or an organ system, a type of artificial organ. !!!!!REF[1]!!!!!! It constitutes the subject matter of significant biomedical engineering research, more precisely in bio-MEMS. The convergence of labs-on-chips (LOCs) and cell biology has permitted the study of human physiology in an organ-specific context, introducing a novel model of in vitro multicellular human organisms. One day, they will perhaps abolish the need for animals in drug development and toxin testing.

To write something like that

An organ-on-a-chip (OOC) is an advanced in vitro model based on a microfluidic cell culture in an integrated circuit (chip) that simulates the activities, mechanics and physiological response of an organ or an organ system. It constitutes the subject matter of significant biomedical engineering research, more precisely in bio-MEMS. The convergence of labs-on-chips (LOCs) and cell biology has permitted the study of human physiology in an organ-specific context. One day, they will perhaps abolish the need for animals in drug development and toxin testing.

Moreover also instead of this:

"Nevertheless, building valid artificial organs requires not only a precise cellular manipulation, but a detailed understanding of the human body's fundamental intricate response to any event. A common concern with organs-on-chips lies in the isolation of organs during testing. The body is a complex network of physiological processes, making it challenging to simulate a single organ. Microfabrication, microelectronics and microfluidics offer the prospect of modeling sophisticated in vitro physiological responses under accurately simulated conditions."

I suggest this:

"A common concern with organs-on-chips lies in the isolation of organs during testing. The problem is in simulating the complex network of physiological processes that characterize the body. Microfabrication, microelectronics and microfluidics offer the prospect of modeling sophisticated in vitro physiological responses under accurately simulated conditions."

Instead of that source I would suggest these two, MORE VALID BY FAR

@article{zhang2018advances,

 title={Advances in organ-on-a-chip engineering},
 author={Zhang, Boyang and Korolj, Anastasia and Lai, Benjamin Fook Lun and Radisic, Milica},
 journal={Nature Reviews Materials},
 volume={3},
 number={8},
 pages={257--278},
 year={2018},
 publisher={Nature Publishing Group}

}

@article{bhatia2014microfluidic,

 title={Microfluidic organs-on-chips},
 author={Bhatia, Sangeeta N and Ingber, Donald E},
 journal={Nature biotechnology},
 volume={32},
 number={8},
 pages={760--772},
 year={2014},
 publisher={Nature Publishing Group}

}

PS: In this microfluidic field it is easy to get caught by hype and let us be drawn by the fantasy (and this is nice, for sure), there is plenty of possibility with this technology and this is why I like it. But the fantasy should never be misleading, and talking about artificial organs it is. Also the microchip section in the Artificial Organ Page

And also in the Italian Page Gio9797 (talk) 21:19, 23 January 2023 (UTC)

I've had a bit of a read through those sources and I think you're right, the emphasis isn't really accurate in the article lead as currently written. I'll implement the edits you suggested with a few minor modifications. To be honest, the applications sections of the article could also do with a bit of an update with the more modern research. T.Shafee(Evo&Evo)^talk 05:39, 25 January 2023 (UTC)

Flavin / flavoprotein enzymes

Hello. I wonder if Category:Flavin enzymes should be merged to Category:Flavoprotein enzymes or these two are separate groups? In addition, why not use simply Flavoproteins? --TadejM ^{my talk} 12:03, 31 January 2023 (UTC)

I've added a proposal to merge at Wikipedia:Categories for discussion/Log/2023 January 31#Category:Flavin enzymes and Category:Flavoprotein enzymes to Category:Flavoproteins. --TadejM ^{my talk} 17:35, 31 January 2023 (UTC)

Edit review requested

Hello. Consider this diff→https://en.wikipedia.org/w/index.php?title=PCSK9&diff=1135221926&oldid=1127977863&diffmode=source . This might or might not be a misrepresentation of content in the cited article. However, I do not have access to the article full text, which is in the journal Cardiology in Review. Request that someone a) more familiar with the topic and b) with access to the article full text evaluate to see if the edit is accurate or in error. Thanks for your help. User:Ceyockey (talk to me) 02:04, 25 January 2023 (UTC)

@Ceyockey: Well spotted! Those sorts of edits are notoriously difficult to identify. It turns out that the interaction is pretty complex. The original was not exactly correct but the edit was less-so. I've edited to try to capture a bit more of the complexity from figure 1 of the cited source. That figure is actually taken from this previous open access paper, so I'll insert the figure lower down as it's a pretty useful schematic. In case it is of interest in future, many such articles are illegally available on Sci-Hub, something that I certainly do not endorse or condone but merely mention as a point of interest. T.Shafee(Evo&Evo)^talk 08:51, 1 February 2023 (UTC)

Good article reassessment for X-ray crystallography

X-ray crystallography has been nominated for a good article reassessment. If you are interested in the discussion, please participate by adding your comments to the reassessment page. If concerns are not addressed during the review period, the good article status may be removed from the article. Onegreatjoke (talk) 21:31, 7 February 2023 (UTC)

Good article reassessment for Oligonucleotide synthesis

Oligonucleotide synthesis has been nominated for a good article reassessment. If you are interested in the discussion, please participate by adding your comments to the reassessment page. If concerns are not addressed during the review period, the good article status may be removed from the article. Onegreatjoke (talk) 22:17, 7 February 2023 (UTC)

Good article reassessment for Amino acid

Amino acid has been nominated for a good article reassessment. If you are interested in the discussion, please participate by adding your comments to the reassessment page. If concerns are not addressed during the review period, the good article status may be removed from the article. Onegreatjoke (talk) 22:17, 8 February 2023 (UTC)

Good article reassessment for Antibody

Antibody has been nominated for a good article reassessment. If you are interested in the discussion, please participate by adding your comments to the reassessment page. If concerns are not addressed during the review period, the good article status may be removed from the article. Onegreatjoke (talk) 21:09, 9 February 2023 (UTC)

Good article reassessment for Lipid

Lipid has been nominated for a good article reassessment. If you are interested in the discussion, please participate by adding your comments to the reassessment page. If concerns are not addressed during the review period, the good article status may be removed from the article. Onegreatjoke (talk) 21:27, 9 February 2023 (UTC)

Time to clean up some old GAs

Hi all, as you can see above, GAR is rumbling back to life after a very long quiescence. Expect there to be editors looking through some of our older GAs, and starting GARs to encourage us to bring these articles back up to the GA criteria. The first five up are the ones noticed above: X-ray crystallography, oligonucleotide synthesis, amino acid, antibody, and lipid. I'm happy to help out with cleaning these up, but I certainly won't have the bandwidth to do it alone. I know this is a sleepy project, but is anyone around with the time/interest/ability to put in some work on these? I will say that as I hinted at above, articles tend to degrade in the years following these review processes (GA/FA), so if you don't have time to help with this batch, fear not, I'm sure more opportunities to get involved will be coming down the pike. Thanks all. Ajpolino (talk) 07:33, 10 February 2023 (UTC)

Frontiers on the reliable sources noticeboard

An RSN discussion was recently opened about using Frontiers Media for genetic studies. Triggerhippie4 (talk) 04:17, 12 February 2023 (UTC)

Hayflick limit article

The "Hayflick limit" article seems a bit of a mess - it seems to equate the Hayflick limit (aka replicative senescence) with running out of telomere (aka cell crisis), but apparently they're not the same thing, see most recent entry on its talk page. Wombat140 (talk) 05:03, 24 February 2023 (UTC)

Definition of a Gene

A Definition section has been added to the gene article to try to clear up potential confusion around the molecular definition (around DNA, transcription-translation etc) and the Mendelian definition (unit of inheritance). It could do with a few extra eyes run over it for proofreading, and consensus on what it should emphasise over at the talkpage. - T.Shafee(Evo&Evo)^talk 04:13, 2 March 2023 (UTC)

Junk DNA

I'm working on a junk DNA article. Any advice would be appreciated, especially advice on how to get it accepted. Genome42 (talk) 21:45, 25 February 2023 (UTC)

I saw the article in your sandbox and it looks like a good start at splitting Non-coding DNA#Junk DNA into a separate article, I'm guessing you've seen that already. I wonder if, given it would be a new article, it might possibly be a candidate for a Topic Page at PLOS Genetics - what do you think @Evolution and evolvability? Amkilpatrick (talk) 10:19, 26 February 2023 (UTC)

@Genome42, Amkilpatrick, I've a few points that may be useful in this case.

Referencing: Broadly speaking, wikipedia articles should (ideally) be more dense in references than the average academic review on a topic - in the extreme every sentence having a ref so that if a paragraph is rearranged, the provenance of each statement is retained. You'll notice that not all wp pages actually adhere to this principle, but it's at least what it aspires to!

Balance: To satisfy the NPOV perspective, it'll need to give proportional due weight to competing positions. I actually think that an "arguments for/against Junk DNA" isn't really helpful since since more of the discussion in the literature is of how different exact definitions of 'junk' and associated measurement methods yield different estimates because they're looking at different facets of a complex, messy biological phenomenon. Where there is genuine disagreement between academics, then opposing viewpoints should still be steel-manned as much as possible, but the majority of the page can probably be written around the idea that it depends on what aspect of "Junk-ness" you're looking at. I've put some possible section organisation ideas below to be able to present that diversity.

Organisation/headings: It could be sensible to structure much of the page around an Estimation or Prevalence section, broken down in subsections for each major methodology, their results and their biological implications. Essentially "well, if by 'Junk' you mean expressed, then we use these method and it's about X% which means that this is happening in the organism, but if by 'junk' you mean it has no fitness effect, then these methods are used and yield Y% and shows that this is happening in its evolution". Obviously, it'll want a History section as well, along with probably Biological origins and maybe a separate Evolutionary consequences section.

Style: Generally specific names of researchers are rarely used, just their argument/position/discovery/formulation. For example it's not necessary to explicitly state in the text about the definition from Molecular and Genome Evolution that it was written by Dan Gaur - interested readers can see that in the refs. Similarly some phrases that are common in academic reviews are best avoided in wp, such as "Most of this article is about...", or "A recent review stated..." (I've listed a few to look out for in this presentation slide). Given the topic, it may be useful to list a few alternative definitions used if they capture different nuances. The other aspect is probably whether the language is clear (this is where it'll be important to lay out the differences between protein-coding vs RNA-coding vs binding site vs telomeres/centromeres vs selfish genetic element vs zero function of any sort).

Original research: Since Wikipedia can't contain any original thought (even synthesis of published ideas), e.g. I've removed "examination of Web of Science shows..." from Non-coding DNA#Junk DNA, since a published source would have to make that point.

Peer review & journal publication aspects: If you're interested in the external peer review option, the PLOS Genetics Topic pages format has the slight complication that it cannot accept CC-BY-SA licensed submissions. For wp pages written 100% by a single author this isn't a problem since that single author can decide to change the licence of their contributions to CC-BY. However, as soon as another person edits that page they also need to agree to a CC-BY license (so it can get complicated fast when there are lots of contributors). Sandbox space shouldn't have this problem, but it's worth bearing in mind. The alternative is to draft it in PLOS's on-wiki preprint drafting space where it's less likely to be spontaneously edited by other contributors. the other journal that is an option - WikiJSci - does accept CC-BY-SA so is fine to include material from multiple wikipedian authors.

I realise that's quite a bit of info, but hope at least some of it helps! T.Shafee(Evo&Evo)^talk 01:23, 27 February 2023 (UTC) (updated 05:49, 27 February 2023 (UTC))

I've done some more reading and have a couple of additional suggestions to the comment I made above and I've taken a stab at editing the Junk DNA section of Non-coding_DNA, though to be clear, I still think that Junk DNA should be a separate page. T.Shafee(Evo&Evo)^talk 05:21, 27 February 2023 (UTC)

Thank-you for posting that information.

I'm mostly interested in the process of getting a new article accepted. Assuming that I have drafted a good article on "junk DNA," what do I do next? Who decides whether it will be posted on Wikipedia? How long does that process take?

The original Junk DNA article was removed fifteen years ago because most editors thought, incorrectly, that there was no such thing as junk DNA. There are still many editors who are very skeptical of the term and I think it's well known that the majority of scientists believe (falsely) that most of the human genome is functional.

Given this opposition, I suspect that it will be difficult to get the article accepted so the most important question is how do we achieve this goal in the face of what's bound to be significant resistance? Can it be sponsored by a WikiProject?

Genome42 (talk) 15:07, 27 February 2023 (UTC)

Thank-you for taking an interest in the Junk DNA section of Non-coding_DNA. This should not be a major part of the Non-coding DNA article. I don't think it's the place to get into the nitty-gritty of the function wars, especially since that kind of focus is mostly a distraction propagated by people who oppose the idea of junk DNA. Let's just keep that sub-section simple and concentrate on a full Junk DNA article.

My goal is to inform the general Wikipedia readership that almost all the experts in molecular evolution support the idea that most of the human genome (up to 90%) is junk. That's not something that is widely known.

Genome42 (talk) 15:19, 27 February 2023 (UTC)

The Junk DNA article should not be an essay or personal take on a topic. The current draft in your sandbox looks more like it is making an argument for a particular POV, than being an neutral encyclopedic entry. One of your sections is "How much of the human genome is junk?" which is a very strange heading (loaded question). I agree with User:Evolution and evolvability that sections for "arguments for/against Junk DNA" isn't really helpful either. Using Wikipedia as some of competition ground or battlefield on the topic is problematic since the literature more mixed and subtle than some clear black-white camps. User:Evolution and evolvability explained it well. The way they split the Non-coding DNA#Junk DNA is more appropriate as it goes by sub-topic than questions.

Wikipedia articles should be encyclopedic with no particular goal except to inform of the diverse views found in the literature. Also, since as you said it's well known that the majority of scientists believe that most of the human genome is functional and only molecular evolutionists mainly think differently - prominent views should be clearly emphasized in the draft over minority views. In fact there is a policy on that WP:WEIGHT. It states "Neutrality requires that mainspace articles and pages fairly represent all significant viewpoints that have been published by reliable sources, in proportion to the prominence of each viewpoint in the published, reliable sources. Giving due weight and avoiding giving undue weight means articles should not give minority views or aspects as much of or as detailed a description as more widely held views or widely supported aspects."

Keep in mind that anything you write on the draft will not remain the same if the article gets its own mainspace either since other editors have the right to alter, change, and edit with sources as they see fit. There is no ownership for any wikipedia article. As time goes by, the articles do not resemble the original drafts. Just a few extra pointers. Ramos1990 (talk) 05:46, 28 February 2023 (UTC)

@Ramos1990: Thanks for helping. The Wikipedia articles in this field have been dominated by editors with a particular POV; namely, that most of the human genome is functional. They have been fiercely resisting all attempts to present a case for junk DNA ever since they succeeded in getting the Junk DNA article banned in 2007.

For them, the resurrection of a new Junk DNA article is a major threat because they don't want alternative POVs to be presented on Wikipedia. That's why getting approval for a separate article giving a balanced two-sided view of the controversy is going to be difficult.

I appreciate any help in drafting a new article that will be approved by the powers that be in spite of considerable opposition. I've been playing with a few things on my Sandbox but no decisions have been made. I don't expect to have a final draft for many weeks. This is not a good time to be critiquing my early outlines.

Clearly there has to be a section where the evidence for functional DNA and junk DNA is discussed. You don't like the subsection title "How much of the human genome is junk?" Can you suggest better subsections? Should I just have separate sections on pseudogenes and transposon fragments where I present the evidence that most of them are junk and the evidence that they are all functional? Do you know of any scientific papers making the case that all pseudogenes and all transposon fragments are functional? If so, I'll be sure to include them.

Introns are proving to be a challenging case. I have plenty of references to scientific papers showing that most intron sequences are nonfunctional (junk) but I can't find any that make an evidence-based argument that all these sequences have a biologically relevant function. Could you please send me any references that you might know about?

Genome42 (talk) 15:50, 28 February 2023 (UTC)

@Genome42: For your question on the process of getting a new article accepted, There are two potential routes within Wikipedia:

1. The Articles for Creation route (used for de novo article creation) just needs you to cllick the "Submit your draft for review" button at the top of your draft when your ready. That'll initiate their process (see workflow here for details and criteria) where editors mainly assess it for notability (not an issues), verifiability (references) and some suitability aspects (neutrality, depth, context etc) and would probably reach out to this page for feedback on content.
2. The second route is to revisit a WP:SPLIT discussion with the proposal of and A) migrating the current material at "Non-coding_DNA#Junk_DNA" over to "Junk_DNA" and use that as the seed of the page and editing it from there, and B) a suggested text and references for a summary paragraph or two that would be left at Non-coding_DNA#Junk_DNA.

Both will probably centre on consensus-building around the references, balance and style either at talk:Non-coding_DNA or here.

For a better title for the "How much of the human genome is junk?" section, I'd suggest Estimation, Prevalence or Measurement methods, with content summarising the main published estimates and how differences in each stem from exactly what is being measured. A summary table would possibly also be useful depending on how many there are. That should help to cut through some of the "for" and "against" framing. Then the semantics around definition and "is this junk DNA" can be gathered in a separate section - less about presenting evidence that they are all functional, and more about summarising what has previously been described as junk in certain contexts. T.Shafee(Evo&Evo)^talk 05:56, 2 March 2023 (UTC)

Suppose I create a new article and submit it. Who are the editors that decide whether to accept it and how long does it take? Genome42 (talk) 16:48, 2 March 2023 (UTC)

The most active editors at AfC are listed here, the queue of articles they're currently assessing is here. T.Shafee(Evo&Evo)^talk 23:52, 2 March 2023 (UTC)

There are 155 active editors on the list but there are only three of four who claim to have expertise in any biological science and none who claim to have expert knowledge of biochemistry, molecular biology, genetics, or evolution. In fact, there are only a small handful who seem to be interested in any science. That's a serious problem.

There are 2,847 draft submissions pending review. Of these, 46 are in the STEM/biology category and a quick glance suggests that almost of them are far too trivial to merit an encyclopedia entry.

People who submit drafts are warned that the process can take more than three months.

None of that information is particularly helpful since I still don't understand how the process works. How many editors does it take to reject a submission? How many to accept it and get it posted?

What about revisiting the original decision to delete the Junk DNA article (WP:SPLIT). What are the chances of success there? Genome42 (talk) 16:30, 3 March 2023 (UTC)

I agree that the paucity of AfC reviewers (also mentioned back in 2018 in this here), and scarcity of STEM reviewers is probably reflected in multiple other topic areas. I agree that WP:SPLIT is probably the likely more efficient route. I'll put my note of support over at Talk:Non-coding_DNA#Splitting_proposal_(Junk_DNA). T.Shafee(Evo&Evo)^talk 02:07, 9 March 2023 (UTC)

I'm a bit worried about all this. If you're going to have a separate article on "junk DNA", we need to sort out exactly what we're describing as "junk". Is it just pseudogenes, in which case why differentiate it from the existing article on pseudogenes? Or is it everything that's non-coding that we haven't labelled as something else? In which case, why not just deal with it at the article on non-coding DNA?

But on the other hand, the term clearly existed for a good while. It's dying out in most fields now, because geneticists have had the humility to recognise that apparently non-functional DNA might be of more evolutionary significance than the gung-ho molecular biologists of the early 1970's first thought - worthy of a name slightly less negative than 'junk'. Hence the tendency of modern authors to stick to a more generic "non-coding" or "pseudogene" depending on how recognisably gene-like it is. So you could write an article on junk-DNA subject to the risk that it will either become a historical article, or will have to be renamed, and then get threatened with a merge back into non-coding DNA. I'd go the historical way myself. Elemimele (talk) 10:21, 5 March 2023 (UTC)

The Junk DNA article will present the case for junk DNA as well as all the possible objections. A key part of the article will be to debunk the misconceptions that have propagated on Wikipedia and elsewhere.

History will be important, especially in this case because there’s so much false history out there. For example, most people don’t realize that 50 years ago some of the best scientists in the world supported junk DNA and they were fully aware of noncoding genes, regulatory sequences, and other functional DNA sequences other than coding regions.

A great many scientists think that nothing that’s been discovered in the past 50 years seriously threatens the concept that most of our genome is junk. It’s going to be difficult to explain that because it runs counter to what most people think. I hope you can help achieve the correct balance while making sure that the views of prominent molecular evolutionary biologist are presented fairly. Genome42 (talk) 00:45, 6 March 2023 (UTC)

I've now split the Junk DNA section of Non-coding DNA back out to its own page, reversing the merge that had been done back in 2012 per the discussion here and at Talk:Non-coding_DNA. See the talkpage of that new article for details. T.Shafee(Evo&Evo)^talk 06:12, 16 March 2023 (UTC)

Thank-you. I’ll start working on the new article right away. Genome42 (talk) 13:36, 16 March 2023 (UTC)

Nitrate reductase

I see that we have articles such as Nitrate reductase (NADH), Nitrate reductase (NADPH), Nitrate reductase (cytochrome) and Nitrate reductase (quinone) which aren't linked from Nitrate reductase. Are those four qualified titles commonly referred to simply as "Nitrate reductase" (in which case we need a dab at Nitrate reductase (disambiguation) and an {{Other uses}} hatnote) or is the suffix in parentheses an intrinsic part of the name? I found similar cases: Alcohol dehydrogenase, Aldehyde dehydrogenase and Saccharopine dehydrogenase; is action needed there too? Certes (talk) 20:20, 18 February 2023 (UTC)

I haven't been actively involved in science for 20 years - does that make me an expert? - but I would think that these all need disambiguation pages. The disambiguating terms are substrates or products, rather than being an inherent part of the enzyme's name. Leschnei (talk) 23:00, 14 March 2023 (UTC)

@Certes: I created these pages, as well as Nitrite reductase (disambiguation) as a bonus. And added {{other}} hatnotes. Leschnei (talk) 15:02, 16 March 2023 (UTC)

Similar enzyme lists are set index articles. Would this be a better choice? Leschnei (talk) 15:13, 16 March 2023 (UTC)

Thank you! They might work better as SIAs; I don't know. Do you have an example of a similar enzyme list? Certes (talk) 19:50, 16 March 2023 (UTC)

@Certes: there are apparently 253 enzyme set index articles. I haven't come up with good search parameters to identify other enzymer disambiguation pages similar to Nitrate reductase (disambiguation) Leschnei (talk) 23:01, 16 March 2023 (UTC)

Thanks again. That's the sort of insight I was looking for. A few pages (CCD8, NCED8 and Solanesyl diphosphate synthase) seem unsure whether to be SIAs or dabs – which is better? The ones I identified differ in that the base name holds an normal article rather than a list or dab, i.e. there is a primary topic. This search gives a rough list of dabs, including some false positives (general dabs mixing enzymes with other topics). Certes (talk) 11:15, 17 March 2023 (UTC)

Once we decide, I'll deal with Glucose 1-dehydrogenase, Glycine dehydrogenase, Pyruvate dehydrogenase and any others that crop up. Certes (talk) 17:55, 17 March 2023 (UTC)

Some of the enzyme set index pages contain entries that would not be appropriate for a DAB page, like on L-serine dehydratase or Laminaranase - at least it wouldn't be obvious to me that they might be put there. The enzymes that you listed at the beginning of this conversation were obvious candidates for disambiguation. It seems to me that we could create these obvious cases as DAB pages and if other editors, better versed in scientific vocabulary, think that they would be better as set index articles, they could change them. Leschnei (talk) 23:55, 17 March 2023 (UTC)

Old orphans

Dear members of the WikiProject Molecular Biology, this is to request your assistance in de-orphaning some articles that fall in the scope of your WikiProject and that are among the oldest orphans on Wikipedia. They are all tagged as orphans in January 2013. They are Restriction endonuclease BsobI/AvaI, PyrG leader, Lipopolysaccharide kinase (Kdo/WaaP) family, KSL cells, KduI/IolB isomerase family, IMPDH/GMPR family, Fic/DOC protein family and DLD/NP1. I am sure that it is much easier for you than for me to find the appropriate templates, lists, indexes, outlines and articles in general where a link can be included that directs towards these articles. Once you have created these incoming links, and the "What links here" shows valid incoming links to these articles, you may remove the Orphan tag from each article. Thanks for your help! Ruud Buitelaar (talk) 19:28, 19 March 2023 (UTC)

Chao1 index

Dear members of WikiProject Molecular Biology, we would like to ask for your consideration to include our article in Spanish about the Chao 1 index in the 12th ISCB Wikipedia competition. This is a newly created article which was previously missing in all languages.

Thanks in advance! SofiaZorrilla (talk) 21:38, 22 March 2023 (UTC)

Thanks @SofiaZorrilla - although I do not speak Spanish, there seems to be a lot of information there and a google of Chao1 has plenty results. Maybe it would be nice to have this article translated for English Wikipedia as well if you feel able? Also pinging @Tkarakulak & @NellySelem for visibility. Amkilpatrick (talk) 08:29, 23 March 2023 (UTC)

Dear all, Chao1 is an ecology index widely used in metagenomics and included in many R libraries, such as phyloseq. I think we can accept this article in the competition, and of course, if authors have the time it would be a significant contribution to have it translated into English NellySelem (talk) 13:34, 24 March 2023 (UTC)

I agree for sure we can accept it! Amkilpatrick (talk) 14:27, 24 March 2023 (UTC)

PMID 1 cleanup

As of writing, the following articles reference PMID 1, which is an article about some assay. These are mostly nonsense citations, but I'm not enough of an expert to know where and if any of these might be actually be appropriate.

1. Anaeromyxobacter dehalogenans
2. Biphasic calcium sulfate
3. C1orf27
4. CD40 (protein)
5. Caragana korshinskii
6. Childhood cancer
7. Chromium(III) boride
8. Clozapine
9. Cotylorhiza
10. Desmodium gangeticum
11. Diabetes in dogs
12. Eastern hognose snake
13. Environmental remediation
14. Espadarana prosoblepon
15. Formic acid
16. Huayllamarca
17. Human somatic variation
18. Lonicera sempervirens
19. Lumen (anatomy)
20. Mandevilla torosa
21. Maternal and child health in Tanzania
22. Melanocortin 4 receptor
23. Mohr–Tranebjærg syndrome
24. Nanomaterials
25. Pardosa milvina
26. Protein filament
27. Race and health in the United States
28. Rock squirrel
29. TRIP13
30. Thielaviopsis basicola

Headbomb {t · c · p · b} 13:42, 2 April 2023 (UTC)

As you might expect the only article in this list that uses this formate assay reference properly is the formic acid article. The Mandevilla torosa article incorrectly lists a PMID of 1 in its single reference. Finding the intended references would be a slog. I wonder how this even happens while writing. ― Synpath 16:58, 2 April 2023 (UTC)

Cleared them all.

There's still PMIDs 2 3 4 56 7 8 9 10 Headbomb {t · c · p · b} 01:33, 3 April 2023 (UTC)

I wonder if it's something to do with the journal citation tool that autocompletes the citation template based on a PMID or doi? Seems a bit strange otherwise. Just a thought. Amkilpatrick (talk) 13:59, 3 April 2023 (UTC)

I've checked two of the edits that added PMID 1 and they were done manually with the VisualEditor. Two isn't much evidence but it may be a VisualEditor problem. Jo-Jo Eumerus (talk) 15:18, 3 April 2023 (UTC)

It's very likely a VE issue where ref=1 becomes pmid=1. Either because of a VE bug, or because people who use VE don't know what to do with the pmid parameter and input nonsense in it. Headbomb {t · c · p · b} 01:19, 4 April 2023 (UTC)

Cleaned up PMIDs 1 through 4. 4+ need cleaning still. Headbomb {t · c · p · b} 01:28, 4 April 2023 (UTC)

Good article reassessment for Aquaporin

Aquaporin has been nominated for a good article reassessment. If you are interested in the discussion, please participate by adding your comments to the reassessment page. If concerns are not addressed during the review period, the good article status may be removed from the article. Onegreatjoke (talk) 14:46, 10 April 2023 (UTC)

I've also reached out to a couple of academics who work on the topic to see if they'd also weigh in with comments, though response rates when I've done so in the past have been variable! T.Shafee(Evo&Evo)^talk 12:51, 12 April 2023 (UTC)

Project-independent quality assessments

Quality assessments by Wikipedia editors rate articles in terms of completeness, organization, prose quality, sourcing, etc. Most wikiprojects follow the general guidelines at Wikipedia:Content assessment, but some have specialized assessment guidelines. A recent Village pump proposal was approved and has been implemented to add a |class= parameter to {{WikiProject banner shell}}, which can display a general quality assessment for an article, and to let project banner templates "inherit" this assessment.

No action is required if your wikiproject follows the standard assessment approach. Over time, quality assessments will be migrated up to {{WikiProject banner shell}}, and your project banner will automatically "inherit" any changes to the general assessments for the purpose of assigning categories.

However, if your project has decided to "opt out" and follow a non-standard quality assessment approach, all you have to do is modify your wikiproject banner template to pass {{WPBannerMeta}} a new |QUALITY_CRITERIA=custom parameter. If this is done, changes to the general quality assessment will be ignored, and your project-level assessment will be displayed and used to create categories, as at present. Aymatth2 (talk) 14:34, 12 April 2023 (UTC)

totally wrong history in this article

In https://en.wikipedia.org/wiki/Pulsed-field_gel_electrophoresis

the history seems to me totally totally wrong; I thought Schwartz and Cantor invented this, but the article gives an incorrect citation as the source

seems like a major error ? 2601:197:D00:3CA0:2168:4CC8:CDE2:A62C (talk) 02:35, 29 April 2023 (UTC)

Move request notification

There is a requested move discussion at Talk:Cytochrome P450 reductase#Requested move 3 May 2023 that may be of interest to members of this WikiProject. Natg 19 (talk) 01:44, 10 May 2023 (UTC)

Asking for expert help

Greetings - for article Prokaryotic acetaldehyde dehydrogenase dimerisation domain I tagged asking for an expert, for 1) it's an orphan article and 2) a stub article that can be expanded. This subject is way beyond me, so if another editor can help that would be great. Thanks.

Note: I had originaly posted at Talk:Molecular biology and was referred here. JoeNMLC (talk) 18:17, 17 May 2023 (UTC)

After looking for sources to expand the article, I don't think the topic meets WP:GNG. It isn't the topic of any direct coverage. Certainly there's some coverage of Acetaldehyde dehydrogenases in general, but not the dimerisation domain of the prokaryotic dehydrogenases. Is anyone opposed to redirecting the page to Acetaldehyde_dehydrogenase#Structure for now? At least that preserves the history visible for all. If anyone objects, we can bring it to AfD for broader discussion? Ajpolino (talk) 18:47, 17 May 2023 (UTC)

I'm not sure, but I think the page exists as it does because of the pfam website mirroring its info on Wikipedia or whatever that project was. With the pfam website becoming depreciated and the database now being hosted at InterPro there may not be a reason to keep any corresponding stubby Wikipedia articles around. But, the link to Wikiepdia can still be found on InterPro. Personally, I would merge the Prokaryotic acetaldehyde dehydrogenase dimerisation domain stub into the Acetaldehyde dehydrogenase structure section, but there might be a larger discussion to be had wrt these types of protein structure articles. ― Synpath 19:15, 17 May 2023 (UTC)

I thought about merging, but there is almost nothing to merge. My very best wishes (talk) 17:53, 18 May 2023 (UTC)

PKB and Akt1

There has long been a consensus that text at the Protein_kinase_B page referring specifically to Akt1 should be moved to AKT1, but not much has happened in the last 4 years to accomplish this. I would have helped, but I am not an expert, and it does require looking into the sources to see whether they use the plain Akt to refer to Akt1 specifically or to the family of Akt1, Akt2 and Akt3 as a whole. Any support would be very welcome! A brief discussion can be found at Talk:Protein_kinase_B#Merger_proposal. Felix QW (talk) 15:12, 27 May 2023 (UTC)

Alkaline Phosphatase

Hi I am a relative newby on writing for Wikipedia. I am teacher in moleculair biology and biochemistry and like to cooperate.

In our practicals we work with Alkaline Phosphatase and I would like to add some experiments about inhibition. Online I can find generic cocktails, but only a few papers. Can I add some of the generic inhibitors when I find papers to refer to? The best example why this is usefull is an experiment that was running before my time is purification involving imidazole, that is a known inhibitor since 1972 (paper). CloneALot (talk) 11:13, 27 June 2023 (UTC)

Hi there, welcome to editing. I'm also relatively new around here and mostly add structure diagrams of enzymes to pages that need them.

The alkaline phosphatase article seems like it could use some additions with respect to inhibitors and adding that would be great. Just note that Wikipedia prefers secondary sources, as they are something of a gold standard in assuring that the content is not original research and verified. So an academic review article on phosphatase inhibitors as used clinically or in lab settings is best. ― Synpath 00:40, 29 June 2023 (UTC)

Draft needs attention

I created the draft Draft:Chromosome scaffold some time ago, I think it deserves the attention of this WikiProject since it's been a while and nobody has reviewed it yet. Any input is greatly appreciated! —Snoteleks 🦠 10:32, 31 July 2023 (UTC)

Credibility bot

As this is a highly active WikiProject, I would like to introduce you to Credibility bot. This is a bot that makes it easier to track source usage across articles through automated reports and alerts. We piloted this approach at Wikipedia:Vaccine safety and we want to offer it to any subject area or domain. We need your support to demonstrate demand for this toolkit. If you have a desire for this functionality, or would like to leave other feedback, please endorse the tool or comment at WP:CREDBOT. Thanks! Harej (talk) 18:05, 5 August 2023 (UTC)

Articles for deletion/LeDock - molecular docking software designed for docking ligands with protein targets.

FYI, please see

• Articles for deletion/LeDock

It's molecular docking software designed for docking ligands with protein targets.

Please add your input as to what we should do with this article. Thanks,

--A. B. ^{(talk • contribs • global count)} 03:56, 8 August 2023 (UTC)

Expanding the list of human protein-coding genes

So, just for context, an AFD for a similar list on Draft:List of proteins in the human body recently closed and there was some discussion in expanding my bot's algorithm, which generates the current complete list of human protein coding genes, to include more useful data from gene/protein databases on the human gene and/or canonical encoded protein(s). Since the list is entirely within the scope of this Wikiproject and since I'd need support from other editors to gain approval for changes to the list, I was wondering what others thought about adding information like this to expand the lists.

More context can be found here: User talk:Boghog#HGNC-UNIPROT ID pairs in the HGNC database and Wikidata.

Seppi333 (Insert 2¢) 01:53, 22 August 2023 (UTC)

Article redlinks at Index of molecular biology articles

Greetings, Wondering if an expert could help clear/resolve a number of redlink-articles at this index? Way beyond me, and I do not want to just remove a link if there may be another article instead. Regards, JoeNMLC (talk) 15:36, 22 August 2023 (UTC)

FAR for Proteasome

I have nominated Proteasome for a featured article review here. Please join the discussion on whether this article meets the featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Delist" in regards to the article's featured status. The instructions for the review process are here. Z1720 (talk) 21:26, 26 August 2023 (UTC)

Requested move at Talk:Polyunsaturated fatty acid#Requested move 31 August 2023

There is a requested move discussion at Talk:Polyunsaturated fatty acid#Requested move 31 August 2023 that may be of interest to members of this WikiProject. —usernamekiran (talk) 03:35, 9 September 2023 (UTC)

Template:R from gene symbol use

I've noticed a lot of protein articles have redirects from the gene symbol, for example CTNNA1, which usually don't have any rcats, as well as redirects from the gene symbol with "(gene)" at the end, like CTNNA1 (gene), which usually includes the {{R from gene symbol}} rcat. It seems to me, that unless disambiguation is required, the versions with just the gene symbol should have the gene symbol template, and all the ones with the qualifier should instead be tagged as {{R from unnecessary disambiguation}} and {{R from avoided double redirect}} of the actual gene symbol. Any idea why the versions with "(gene)" at the end exist, and are categorized the way they are? Any opposition to fixing them as I suggest above as I come across them? Cheers, Mdewman6 (talk) 01:32, 26 September 2023 (UTC)

Requested move at Talk:Kinesin-like protein KIF11#Requested move 12 September 2023

There is a requested move discussion at Talk:Kinesin-like protein KIF11#Requested move 12 September 2023 that may be of interest to members of this WikiProject. ❯❯❯ Raydann^(Talk) 20:39, 27 September 2023 (UTC)

Talk:COVID-19 lab leak theory#Request_for_comment

An editor has started an RfC about whether the announcement by the FBI and the U.S. Department of Energy that they support the COVID-19 lab leak theory should be in the lede of the COVID-19 lab leak theory article. Editors are invited to contribute. TarnishedPath^talk 01:51, 4 October 2023 (UTC)

Request for Article Improvement : Common symbiosis signaling

Recently I have created an article on common symbiosis signaling pathway. It is just an initial version and needs a lot of improvement.

This article needs following improvements.

• 1. I have added some representational images. Need better quality images.
• 2. Needs to be scrutinized by more knowledgeable people in this specific topic, to check if there are any technical mistakes or wrong informations, and subsequently correcting them.
• 3. Needs to be add some sections in plain language to make the topic more sense to non-technical readers.
• 4. Needs a lot of minor edits regarding spelling, formatting, (italics, capitalization etc.) in context of scientific conventions.
• 5. If you or your institute is a part of research that is connected to Arbuscular mycorrhiza, Myc-factors, Symbiosis genes etc; then please feel free to enrich this article with photo and data files such as confocal fluorescence photomicrographs, calcium wave electrophysiology data, protein models, protein evolution and phylogeny, etc.

RIT RAJARSHI (talk) 15:00, 25 October 2023 (UTC)

Requesting the Molecular Cell Biology task force to look it up. RIT RAJARSHI (talk) 15:02, 25 October 2023 (UTC)

لدي طفلين توأم عمر عشر شهور مصابين باعتلال الجلايسين هل ممكن احد يهتم بالامر ويبلغني ب تطورات المرض او الامل في علاج للمرض ارجو الرد الطفلين مصابين والمرض غير مستقر وهناك تشنجات وحمي متكررة 105.196.72.31 (talk) 16:32, 29 October 2023 (UTC)

Nomination for deletion of Template:WikiProject Molecular Biology/doc

Template:WikiProject Molecular Biology/doc has been nominated for deletion. You are invited to comment on the discussion at the entry on the Templates for discussion page. -- 65.92.247.90 (talk) 13:18, 3 November 2023 (UTC)

Requested move at Talk:Mathematical modelling of infectious diseases#Requested move 30 October 2023

There is a requested move discussion at Talk:Mathematical modelling of infectious diseases#Requested move 30 October 2023 that may be of interest to members of this WikiProject. Polyamorph (talk) 08:08, 4 November 2023 (UTC)

Molecular biology / genetics review needed

Could you please review from the point of view of Molecular biology / genetics specialist the following texts:

• RCCX (whole page);
• Congenital adrenal hyperplasia due to 21-hydroxylase deficiency#Genetics (only the Genetics section).

Thank you!

--Maxim Masiutin (talk) 18:45, 14 November 2023 (UTC)

Infobox for all GPCRs, making it a standard to always include of what G-protein they are coupled to

There is a disturbing trend where articles on various GPCRs will wax lyrically on speculations on potential importance but fail to include the G-protein and signaling cascade they are coupled to. I was wondering if we could push for an initiative to set a standard to include downstream signaling in all GPCR articles in an infobox. For example, the Glucagon-like peptide-1 receptor contains no organized information about its Gs-coupled signaling cascade, but has lots of corporate marketing fluff. (Fixing this now.) Unfortunately this gives laypeople the impression that these receptors work by some woo-ey vitalistic mysticism. Let's try to push for ALL GPCR articles to always ensure that the proximal downstream signaling cascade is never buried outside the lede. Yanping Nora Soong (talk) 10:56, 19 November 2023 (UTC)

I kind of wonder how to source that. The number of known interactions of a protein is, in my experience by eyeballing academic publications, roughly proportional to how many scientists have worked on the protein. That implies that most proteins have a number of unknown interactions. Jo-Jo Eumerus (talk) 14:51, 19 November 2023 (UTC)

Sourcing primary G-proteins coupled for a GPCR on PubMed is not difficult. If there is functional selectivity or heterodimerization, etc. that could be addressed either in infobox or lede. Overall, this would make cell signaling articles more organized on Wikipedia. If there is no opposition, I intend to create an infobox for a generic GPCR, then roll it out to every GPCR (with citations). Yanping Nora Soong (talk) 19:00, 19 November 2023 (UTC)

Help with categorization

Hi all. I work on the backlog of uncategorized article and I'm stumped by a couple of articles. I was hoping someone from the project could help categorizing Foscenvivint and Acazicolcept. Thanks in advance, Pichpich (talk) 22:24, 27 November 2023 (UTC)

Template:Cytoskeletal_proteins

Hi all, this template is used on quite a few pages, but hasn't been updated for a long time and is missing some (I think) key proteins, specifically in the microtubule area.

I propose adding:

• Katanin
• Spastin
• Centrin
• PCM1
• Centrin 1
• Centrin 2
• Centrin 3
• CAMSAP1
• CAMSAP2
• CAMSAP3
• ACF7
• PLEKHA7

If others are happy, I'll go ahead and add them.

GraziePrego (talk) 00:17, 29 November 2023 (UTC)

Mmm, of these proteins, how many are PART of the cytoskeleton, rather than simply being proteins that interact with it? Jo-Jo Eumerus (talk) 09:57, 29 November 2023 (UTC)

Tricky distinction for some of them, I'll give a summary:

• Katanin and Spastin are both microtubule-severing enzymes, rather than direct components of the microtubules. This puts them more on the "cytoskeleton-associated" side, but they're still relevant to the cytoskeleton.
• Centrin, the other Centrins, PCM1 are all components of the centrosome, the main microtubule-organising centre across different animal cells. These proteins all are involved in providing the site for microtubule growth to begin- so I would argue they're part of the microtubule cytoskeleton? Debatable possibly.
• CAMSAP3 is a microtubule minus end protein, providing the site of microtubule growth, it also anchors and nucleates them- so it's also part of the cytoskeleton arguably. CAMSAP1 and CAMSAP2 assist in this process.
• ACF7 crosslinks Actin and microtubules, so it's less of a direct component of either.
• PLEKHA7 crosslinks E-cadherin and microtubules, so also less of a direct component.

Guess it depends how we define what gets included. The template gives the section header as "Microtubules and MAPs", which to me suggests it includes everything that can be considered a microtubule-associated protein. Weirdly, it bluelinks to MAPs but doesn't include the specific MAPs in the template list, like MAP2, MAP1A, MAP1B.

Additionally, if we're including MAPs, then there's an argument for including EB1, EB3, and other end-binding proteins.

I should also point out that all of the kinesins are included in the template- they're motor proteins that travel along microtubules, they're definitely not directly incorporated into the actual filaments.

GraziePrego (talk) 23:55, 29 November 2023 (UTC)

On looking at the template again, there's quite a few Tubulin types missing:

• TUBB
• TUBB1
• TUBB2A
• TUBB2B
• TUBB2C
• TUBB3
• TUBB4
• TUBB4Q
• TUBB6
• TUBB8
• TUBG1
• TUBG2
• TUBGCP2
• TUBGCP3
• TUBGCP4
• TUBGCP5
• TUBGCP6
• TUBD1
• TUBE1

GraziePrego (talk) 00:03, 30 November 2023 (UTC)

Tools to help fill in redlinked genes?

I see the Gene Wiki group has been quiet lately; but lately thanks to @Seppi333: we have an up-to-date list of human genes showing some of the remaining gaps. Is there a more recent overview than this of current tools for generating infoboxes and stubs? – SJ + 00:42, 8 December 2023 (UTC)

I believe the tool mentioned in that paper is the only one available for manually generating gene articles. It was automated at one point, but the bot started creating lots of redundant or erroneous articles if I recall correctly. Last time I ran a count of the red links in the gene list, there was somewhere around 6000-7000 of them for the indexed human protein-coding genes, so we only have articles on about 65%-70% of genes in the human exome. Correcting that seems like a massive undertaking if done individually and manually. Seppi333 (Insert 2¢) 22:09, 13 December 2023 (UTC)

@Sj: forgot to ping. Seppi333 (Insert 2¢) 22:10, 13 December 2023 (UTC)

I'm excited about the possibilities of this tool for generating lede paragraphs and stubs. It's not ready for longer articles, but could help a bit. – SJ + 05:45, 14 December 2023 (UTC)

Requested move at Talk:Citric acid cycle#Requested move 12 December 2023

There is a requested move discussion at Talk:Citric acid cycle#Requested move 12 December 2023 that may be of interest to members of this WikiProject. Bensci54 (talk) 17:43, 19 December 2023 (UTC)

One of your project's articles has been selected for improvement!

Hello, Please note that Carbon source (biology), which is within this project's scope, has been selected as one of the Articles for improvement. The article is scheduled to appear on Wikipedia's Community portal in the "Articles for improvement" section for one week, beginning today. Everyone is encouraged to collaborate to improve the article. Thanks, and happy editing! Delivered by — MusikBot talk 00:05, 25 December 2023 (UTC) on behalf of the AFI team