Wikipedia talk:WikiProject Molecular Biology

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WikiProject Molecular Biology Archives: 1, 2

Taskforce archives:

MCB: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11

Genetics: 1, 2, 3, 4
Computational Biology: 1, 2
Gene Wiki: 1, 2, 3, 4

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

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)Reply[reply]

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)Reply[reply]

@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)Reply[reply]

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

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)Reply[reply]

@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)Reply[reply]

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)Reply[reply]

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)Reply[reply]

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)Reply[reply]

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)Reply[reply]

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)Reply[reply]

@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

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))Reply[reply]

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)Reply[reply]

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)Reply[reply]

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)Reply[reply]

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)Reply[reply]

@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)Reply[reply]

@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)Reply[reply]

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)Reply[reply]

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)Reply[reply]

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)Reply[reply]

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)Reply[reply]

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)Reply[reply]

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)Reply[reply]

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)Reply[reply]

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

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)Reply[reply]

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)Reply[reply]

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)Reply[reply]

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)Reply[reply]

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

As of writing, the following articles reference

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)Reply[reply]

Cleared them all.

There's still PMIDs 2 3 4 56 7 8 9 10

b} 01:33, 3 April 2023 (UTC)Reply[reply

]

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)Reply[reply]

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)Reply[reply]

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.

b} 01:19, 4 April 2023 (UTC)Reply[reply

]

Cleaned up PMIDs 1 through 4. 4+ need cleaning still.

b} 01:28, 4 April 2023 (UTC)Reply[reply

]

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)Reply[reply]

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)Reply[reply]

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)Reply[reply]

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)Reply[reply]

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)Reply[reply

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

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)Reply[reply

]

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)Reply[reply

]

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

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)Reply[reply]