WikiProject iconBiology Project‑class
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Wikimedia Discord has a Biology Channel! edit

It has recently come to my attention that not only is there a highly active Wikimedia Discord Server, it also has a #wpbiology channel! See Wikipedia:Discord for more details.

I hope to feature a link to this on the main page after the redesign is complete, but for the time being I wanted to advertise it here. I would love for more people to join, and I hope it will prove a major resource to us going forward as we improve WP:BIOL and it's subprojects. I cannot emphasize how refreshing it can be to talk in real time (or even in voice channels!) rather than in talk pages.

@Evolution and evolvability and Alexmar983: This also should serve us nicely for the user group discussions--they have a #meta channel as well.

Request for comment, deletion of dubious species edit

Should we, or should we not, delete articles about species that are not properly accepted?

The context for this RfC is a number of recent AfD debates on deletion of articles about species that have been described, but whose names have never been properly accepted, for example Stomopteryx splendens. WP:SPECIES advises that we should keep articles on valid species, but it doesn't give any advice on what to do about non-valid species. Elemimele (talk) 18:23, 9 November 2023 (UTC)Reply[reply]

To start the discussion: I believe we need to consider why we have articles on species. If they aim to help the reader establish the status of species names, whether they exist (or not) and who described them, then we should probably keep the non-valid names; readers still need to know that they're not valid. But if stubs on species with little information are kept because we hope they'll grow into more detailed articles, then we should probably delete those non-valid species that have never generated enough literature to create an article; they presumably never will. Obviously we should keep, or redirect articles about names that have created a decent quantity of literature. This RfC only applies to species names that aren't notable by GNG. Elemimele (talk) 18:24, 9 November 2023 (UTC)Reply[reply]
@Elemimele:, you're using some words that have a technical meaning in taxonomy that makes it difficult for me (with my awareness of the technical meanings) to understand exactly what is being proposed.
Valid name (zoology) basically means (in the context of WP:SPECIES) that a name isn't regarded as a synonym (taxonomy). If a name is regarded as a synonym (invalid), it typically doesn't get deleted because it can just be redirected to the accepted name. Articles on names regarded as synonyms get redirected all the time by taxonomy editors without them initiating a discussion. The redirect target should mention the synonym (which shows that the name exists). There is no need for articles about names that are definitely invalid (but redirects are appropriate).
A dubious name (nomen dubium) doesn't have a good type specimen; the type specimen may have be missing or destroyed, or may be a fragment (such as a single tooth) that lacks the characters needed to distinguish it from similar species. It can be possible to write a somewhat detailed article about a nomen dubium (e.g. Clasmodosaurus known from three teeth, or Pyxicephalus cordofanus with no known type specimen), although such an article is necessarily more about the name than an organism per se. Since nomina dubia can't be confidently identified, they can't be definitively synonymized with anything else, and thus there isn't a good place to redirect them if an article is unwarranted. I wouldn't encourage anybody to write articles about nomina dubia, and some of the articles Wikipedia has for nomina dubia might best be deleted.
Of the deletion discussions that prompted this, Wikipedia:Articles for deletion/Pyxicephalus cordofanus (a nomen dubium) was initiated by a taxonomy editor, with the delete/merge !votes coming from taxonomy editors. Wikipedia:Articles for deletion/Stomopteryx splendens was initiated by an editor who doesn't work on taxonomy articles and who started deletion discussions for some other species articles that were ultimately kept; several taxonomy editors commented without making a !vote. Stomopteryx splendens is valid (not a synonym) according to the source used in the article, although the nominator claimed it was not valid; it does appear that Stomopteryx splendens may be a synonym, but it not clear what the valid name is.
I think that "species with little information are kept because we hope they'll grow into more detailed articles". People who only want to "establish the status of species names, whether they exist (or not) and who described them" are better served by taxonomic databases than Wikipedia; Stomopteryx splendens is possibly something that may "have never generated enough literature to create an [detailed] article". Plantdrew (talk) 22:32, 9 November 2023 (UTC)Reply[reply]
I basically second Plantdrew here. We are largely writing articles about taxa (more or less natural groupings of organisms), which we conveniently label with names; in general, we should strive to title those articles with names consistent with the provisions of the relevant nomenclatural code, and with the taxonomic placement best supported by reliable authorities. When we have nomina dubia, names that we can't confidently attach to a taxon, there will rarely be material sufficient for an article, and we should usually be deleting or redirecting standalone articles on same. (Lsjbot did a great disservice by spewing nomina dubia, synonyms, misspellings, unpublished names, etc. from poorly-vetted datasets over the Wikipedias in which it operated, but I digress.)
I think it's reasonable, in a well-fleshed-out article on a higher taxon (genus, tribe, subfamily, etc.) to include in the taxonomy section a list of the nomina dubia that can be associated with this taxon but not with any lower one. (This could also be a section in "List of X species" articles.) That said, I would probably save that for nomina dubia that have explicitly been discussed in reliable sources. If there are 5,000 nomina dubia (to invent a number) about which the most we can say is that they belong to Geometridae, I'm not sure a giant list article enumerating them is terribly useful. Choess (talk) 00:05, 10 November 2023 (UTC)Reply[reply]
As stated by Plantdrew words such as valid, dubium and available have specific meanings in zoology and botany and unfortunately not necessarily the same meaning in both. So what is being asked here is a little confusing. However, if I am reading it right I will say the following.
If a species has a page that is now considered in the synonymy of another species yes that taxon should be removed, but not outright. Consideration should be given to merging. I would also argue that the synonym would serve well as a redirect to its current senior name if it was under the mainspace name of its scientific name. The current nomenclature of life is a dynamic situation. No species has to stay the same it can be recombined, synonymised or further split dependant on the current scientific knowledge which is forwever changing. No one should expect any species name to be immutable. That is even true of our own species with it being recombined, split and synonised in recent years.
I would suggest that you may want to use a tag on any species page that should be examined for its current nomenclature and if its still a used name, this way it can be discussed how best to take advantage of what information is on the page, ie maybe merge it, rather than delete maybe comment it all out and turn it into a redirect after all it may get resurrected again in the future and this preserves its page even if its not readily viewable. I think preserving information for potential use later is not unreasonable. I tried that once with several turtle species but the commented out info was later deleted by others.
The tag to me would serve well if it flagged the page, encouraged an rfc on its talk page, and notified relevant projects. Scott Thomson (Faendalimas) talk 03:13, 10 November 2023 (UTC)Reply[reply]
I was trying to avoid getting into the multitude of ways in which a species name can be less-than-perfect, and also to avoid the fact that zoologists, botanists and microbiologists all go about taxonomy in slightly different ways, each with their own meanings for technical terms.
To clarify what I was asking: WP:NSPECIES tells us we should keep anything that has a correct name (botany) or valid name (zoology) but periodically people turn up at AfDs with names that are (1) missing from whatever database/publication is considered definitive; (2) validly published but not formally accepted as "correct" (botany; which I think is equivalent of "available" in zoology?); (3) nomina dubia in various ways. I was trying to get clarity about whether these should be deleted.
I'm wondering whether it's too complicated to make a simple rule. For example, I think I'm right that palaeontology is riddled with nomina dubia because of the fragmentary nature of fossils, but many of these things are of interest to encyclopaedia readers, widely written-about, and there isn't actually a better name at the moment. Similarly bacteriology has ambiguous names, where the same name has been used for two different species, and it's really quite important that readers with an interest in bacteriology should know this has happened! Even worse, there are the cases where the ambiguity creates a hazard to health, something which an encyclopaedia might have to document. An ambiguous bacterial name might be a lot more significant than a botanical name validly-published in 1850 and never mentioned again! Not sure what to think... Elemimele (talk) 12:02, 10 November 2023 (UTC)Reply[reply]
Your point that "(2) validly published but not formally accepted as "correct" (botany; which I think is equivalent of "available" in zoology?)" not quite, a name in zoology that is meant to be in current usage ie the botanical correct name is a valid name. In zoology a synonomy is headed by the currently accepted valid name, all other names are available. Valid means must be used, available means could be used. In paleontology, yes many fossils are fragmentary and often you will see the term incertae cedis after a name. Of course fossils are rarely complete, it is the nature of this and just has to be dealt with. Nomina dubia technically refers to a species whose type specimen cannot be assigned to a taxon for some reason, it may be incomplete, it may be missing. If its missing researchers can set a Neotype and repair the situation, but if the type exists no matter how bad, only the Commission can set the neotype which tends to slow this down. If nomina dubia are old, ie more than 100 years, they tend to just be declared nomen oblitum and left as forgotten names. This is all up to the researchers working on the group though.
The reason I suggested using a tagging system was because of the complexities, sure some are simple and an outright decision can almost be made but some are far more complicated and probably warrant significant discussion to proceed. Scott Thomson (Faendalimas) talk 00:45, 11 November 2023 (UTC)Reply[reply]
Maybe this is my own hairsplitting, but I'd interpret that quotation from NSPECIES to mean that if you have a species (a group of organisms related in particularly close ways, cf. species concept), and there is a suitable name to apply to that species, you can presume notability. A nomen dubium is a name, not a species; definitionally, we don't know which species it applies to, if indeed to any. Names could wind up as parts of set index articles, as redirects to sections and in-article lists, or sometimes as standalone articles when sufficiently notorious that GNG applies. I'm not sure we have to try to craft a comprehensive rule for this as long as we understand NSPECIES protects articles about taxa, not about names. Choess (talk) 01:47, 11 November 2023 (UTC)Reply[reply]
I don't think this is hairsplitting at all. Articles are definitely about taxa, not about names. (Long ago, we had a plant editor who insisted on starting articles with text like "X y is the name of a species ..." This was firmly rejected.) If there is reliable evidence that a taxon is accepted, then we can have an article. What the title should be is a secondary question, given the general flux in taxonomy in the molecular phylogenetics era.
I'm more concerned about the quality of the evidence that a taxon is accepted. In almost all cases (all cases?), this requires at least one secondary reference, not just the paper that proposed the taxon. Peter coxhead (talk) 08:32, 11 November 2023 (UTC)Reply[reply]
To be honest, that approach fits very well with the concept that Wikipedia is an encyclopaedia, not an index, which means our traditional role is to take subjects on which many have written, and produce an overview summary. If there's only one document, no "overview" is necessary; the reader might as well just read the one document that exists.
Going a bit off-topic, it also fits with biomolecules and genes; new ones appear at a frenetic rate, but probably don't need an article until they get mentioned in reviews, or discussed outside the context of the primary paper that first described them.
The discussion above has cleared up a big question to me: we automatically accept articles about a species even if there isn't much to say about it yet, in recognition that they are likely to grow to be bigger articles in time. It's also helped me understand that the article is about the species, not the name, which is further reason not to have articles about names that shouldn't be used. We should have articles about the name only where the name itself is independently wiki-notable, perhaps widely used in popular culture, or the subject of a huge scientific bust-up, or whatever. Elemimele (talk) 11:26, 11 November 2023 (UTC)Reply[reply]
yes this is an encyclopedia, not a checklist. Wikispecies is about names and those who name them for the most part. Wikipedia has another purpose. I would prefer taxa were not accepted without some secondary review, however I recognise thats not always possible. But at least give the scientific literature time to respond to a new taxon. Cheers Scott Thomson (Faendalimas) talk 13:37, 11 November 2023 (UTC)Reply[reply]

Grant abstract as reference edit

I was cleaning up Reuben Shaw just now and noticed that there was an issue with a journal citation without a journal listed. It turned out to be a link to a grant abstract from grantome.com, and I couldn't remove it without leaving a substantial part of the article without a reference to a pretty specific claim. So:

1. How should a grant abstract be cited to not leave errors?
2. Should a grant abstract even be cited in an article? From my perspective it's a lot less useful than a primary source/journal article that draws the conclusions the grant author is relying upon. Only 70 articles on Wikipedia, the majority of them short biographies of scientists, cite this specific website.

Thanks. Reconrabbit (talk|edits) 15:51, 15 December 2023 (UTC)Reply[reply]

Grants are written for a specific purpose, to obtain money as such, although I won't say they are fiction, they have ulterior motives to the science being discussed. I do not think they should be a citation unless it is a page about the applicant for the grant or the granting body. Generally if you can get the grant proposal it should have in it any references they used, then if necessary those could be sout out and used instead. Or if an older grant application its possible it has since been published as finished work and this would be a better citation. Cheers Scott Thomson (Faendalimas) talk 23:45, 15 December 2023 (UTC)Reply[reply]

"rehabilitation" of Aristotle? edit

Hey all, there's a discussion about Aristotle's standing in current biological science going on here. I'm pretty sure this is wp:fringe or wp:undo, but I'm not trained as a scientist. Input from anyone who is would be most welcome! Cheers Patrick J. Welsh (talk) 22:59, 17 December 2023 (UTC)Reply[reply]

Fossorials! edit

Hello fellow Wikipedians! I have just created a new WikiProject, WikiProject Fossorials. If you can, please join, as we are in desperate need of members! Fossorials are animals that spend much of their time underground, so if you are interested, please join!

Thank you, UserMemer (chat) Tribs 00:33, 23 December 2023 (UTC)Reply[reply]

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

 

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 teamReply[reply]

Chronic wasting disease: clarification needed edit

Clarification needed (in-line template includes reason) from article Chronic wasting disease.

However, it is noted that as of 2013, although CWD prions were transmissible within the cervidae family, CWD was not considered transmissible to humans or to cattle.[1]

[...]

Recent research on Rocky Mountain elk found that with CWD-infected cows,[clarification needed] many subclinical, a high rate (80%) of maternal-to-offspring transmission of CWD prions occurred

Regards, Thinker78 (talk) 03:07, 29 December 2023 (UTC) Reply[reply]

References

  1. ^ Patrice N Klein, CWD Program Manager USDA/APHIS (5–6 February 2013). Chronic Wasting Disease - Review of Disease Transmission and Control (PDF). WHHCC Meeting. Archived from the original (PDF) on 26 September 2014.

How to handle human vs. Non-human? edit

I've been having some confusion with how to handle human and non-human components in anatomy/biology (and related) articles. Is there a rule of thumb for this?

I was making a plan to resolve visual system and visual perception and noticed ambiguity on whether information was human-specific or vertebrate-specific.

Looking through some similar articles:

  • Olfactory system is written generally, mostly human, but sense of smell is almost entirely general, not focusing on humans whatsoever, which is the opposite for visual system (some non-human content) and visual perception (entirely human).
  • Color vision is entirely general, mentioning humans specifically, when applicable.
  • Auditory system makes no mention of non-humans, but auditory perception (hearing) does.
  • Digestive system redirects to human digestive system, but then I don't know where to go for more general non-human digestive systems. It seems qualifying articles with human in the lead, but not in the title, and still including other animals as a subsection is an okay solution?
  • I see a perhaps useful example in trachea, but then would the vertebrate section just say "the vertebrate visual system generalizes well from the human case, with the following differences"? I have not seen an example of leads ever including human in the qualifiers, "The human trachea (pl.: tracheae or tracheas)...". I think I would prefer this, but I guess that has been discussed before somewhere.
  • Liver mentions only vertebrate in the lead instead of human, but then ignores this distinction until an #other animals section.

Ideas? Curran919 (talk) 13:29, 31 January 2024 (UTC)Reply[reply]

That's been handled lots of ways and Wikipedia is inconsistent. Of the descriptions above I like "entirely general, mentioning humans specifically, when applicable" and mentioning other species when applicable. There are many topics where so much work has been done on humans that article titles like Human sense of smell might be helpful, and there should be links to that from Sense of smell, but for an article about an aspect of biology to only or mostly talk about humans and ignore the rest of the tree of life is speciesist. SchreiberBike | ⌨  15:58, 31 January 2024 (UTC)Reply[reply]
This has come up repeatedly (see e.g. here), and the response from WikiProject Medicine editors is that somebody needs to write the content relevant to non-humans. Once sufficient content exists (in theory) an argument could be made to split the human content into a separate article.
In practice, previously separate articles on humans do get merged back into what were small articles that weren't focused on humans (e.g. human pelvis->pelvis), or a term that is primarily used in non-human contexts gets hijacked into a redirect to a human context (copulation->sexual intercourse, followed by a fork of copulation (zoology)). Recent successful splits are injury/injury in humans and kidney/kidney (vertebrates)/mammalian kidney.
My advice is to write the non-human content at what appears to be the appropriate title. If that gets reverted by an editor who wants the articles to stay focused on humans, bring it up here or at Wikipedia talk:WikiProject Tree of Life.
If a general title redirects to a human specific title (as with digestive system->human digestive system), you might consider making the general title a disambiguation page and creating a non-human article at a new title, or starting (or restoring) an article at the general title and see what happens. (For digestive system in particular digestion and gastrointestinal tract are apparently supposed to cover non-humans). Plantdrew (talk) 21:23, 31 January 2024 (UTC)Reply[reply]
Thanks for all the context. The template deletion thread was interesting, especially when poised as a wp:med vs. wp:biology conflict of interests! I agree is most cases it does not make sense to split into general and human articles, even once the non-human content is expanded. It also seems clear that a human centered article will often take priority over a name space (e.g. pelvis and pelvis (tetrapods) seems reader-friendlier than human pelvis and pelvis). However, I'm interested particularly in how best to get them to share the article and what language should be used in the article to clarify this organization. If the article defaults to human most of the time, should we isolate non-human content to the non-human section? Should the lead introduce the article as about the human aspect, even though the non-human part is represented in a section? Curran919 (talk) 22:54, 31 January 2024 (UTC)Reply[reply]
This. This is something that I agree on.
Its not just digestive system though. There's a few more articles that ONLY have human articles but no general article.
Voice and Back redirect to their human articles respectively, even when talking about them in other animals due to a lack of general articles for them. I still wish for a general Voice and Back article because there should be when you're referring to those topics in non-humans. LoverOfAllAnimalsActivist (talk) 07:08, 7 February 2024 (UTC)Reply[reply]
@LoverOfAllAnimalsActivist I think a concept like voice is inherently human-centric. A redirect to human voice, I think is a good design. There should probably be a headnote that directs to the non-human equivalent, but this doesn't seem to exist. Vocalization is a disambiguation page that references animal communication and subgroup vocalization (e.g. bird vocalization), so I think a generic non-human vocalization article would need to be synthesized before being worked into the mix. Back as well is such an inexact term that it leads to an inexact article (and wow, look at all those citations!). This would be ripe for a non-human animals section, but honestly, what information would you add here? If you have ideas, put it in a sandbox for review and we can talk about how to incorporate it, but I can't imagine what that would look like. Also, think about the type of user who is going to look up back on wikipedia instead of spine or something else more specific, and think of what kind of information would be useful to them. For example, I think redirecting back to a disambiguation page would probably be a mistake. Curran919 (talk) 10:03, 7 February 2024 (UTC)Reply[reply]
This and musculoskeletal system are the only systems that do not have general animal articles despite almost all animals having them in my knowledge. It BAFFLES me that digestive system has no general article whereas pretty much every other system aside from musculoskeletal have general articles. With this in mind, somehow there's a few animal info in human digestive system. So why don't we split that part into "Digestive System" that talks about animal digestive systems then? Other animals have them too (if gastropods have their own digestive system page, why can't a general digestive system article be made? Of all the major systems this is the odd one out and it baffles me.) LoverOfAllAnimalsActivist (talk) 11:28, 9 February 2024 (UTC)Reply[reply]
On digestion, I suggest you write an article that spans digestion of wood and cellulose by bacteria, fungi, and protozoa, mentioning their symbioses with herbivorous animals such as cattle, as well as digestion of oil and plastic by bacteria, digestion of insects by insectivorous plants, and for good measure digestion of meat by carnivores. This will be impossible to merge into an all-human article (and it won't be limited to animals, naturally). You will have a short subsection on digestion in omnivores, with a "further" link to Digestion in humans. Then we get the humans-only article renamed to that, and, Voila!, we'll have a proper representation of digestion for WikiProject Biology. Chiswick Chap (talk) 19:42, 13 February 2024 (UTC)Reply[reply]

Epicanthic Folds in other animals? edit

I looked on various places and there's literally only Quora that says these:

"Most animals have no whites of their eyes showing, as humans do, and so it is difficult to see the epicanthic folds. They seem to be in young animals like puppies and kittens."

"They have, but you did not know about them. Also, some have even evolved an extra transparent eye lid for even more protection and so forth."

But, there's no reliable info on this in animals, so I tried looking clearly into puppy and kitten eyes especially those of Asian breeds, and I think they have them? I'm not really sure, but I'm inclined to think they do?

If anyone is able to find more info please tell me. I desperately need to know. LoverOfAllAnimalsActivist (talk) 07:55, 7 February 2024 (UTC)Reply[reply]

Most mammals have the sclera of the eye showing, so I'm not sure how accurate any of that is (and the sclera isn't always white). In humans, epicanthic folds don't hide the sclera completely either. Either way, I believe the term "epicanthic fold" is exclusively used for the condition in humans, so there simply doesn't exist any such info on animals. FunkMonk (talk) 09:15, 7 February 2024 (UTC)Reply[reply]

Requested move at Talk:Hypoxia (environmental)#Requested move 10 February 2024 edit

 

There is a requested move discussion at Talk:Hypoxia (environmental)#Requested move 10 February 2024 that may be of interest to members of this WikiProject. ❯❯❯ Raydann(Talk) 02:17, 22 February 2024 (UTC)Reply[reply]