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Template for deletion discussion for Virusbox 2018 November 27

Template:Virusbox (edit | talk | history | links | watch | logs) is being discussed at Wikipedia:Templates for discussion/Log/2018 November 27#Template:Virusbox, if anyone would like to chime in. --Nessie (talk) 20:10, 27 November 2018 (UTC)

Facto Post – Issue 18 – 30 November 2018

Facto Post – Issue 18 – 30 November 2018 The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page. To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see the footer. Back numbers are here. WikiCite issue GLAM ♥ data — what is a gallery, library, archive or museum without a catalogue? It follows that Wikidata must love librarians. Bibliography supports students and researchers in any topic, but open and machine-readable bibliographic data even more so, outside the silo. Cue the WikiCite initiative, which was meeting in conference this week, in the Bay Area of California. Wikidata training for librarians at WikiCite 2018 In fact there is a broad scope: "Open Knowledge Maps via SPARQL" and the "Sum of All Welsh Literature", identification of research outputs, Library.Link Network and Bibframe 2.0, OSCAR and LUCINDA (who they?), OCLC and Scholia, all these co-exist on the agenda. Certainly more library science is coming Wikidata's way. That poses the question about the other direction: is more Wikimedia technology advancing on libraries? Good point. Wikimedians generally are not aware of the tech background that can be assumed, unless they are close to current training for librarians. A baseline definition is useful here: "bash, git and OpenRefine". Compare and contrast with pywikibot, GitHub and mix'n'match. Translation: scripting for automation, version control, data set matching and wrangling in the large, are on the agenda also for contemporary library work. Certainly there is some possible common ground here. Time to understand rather more about the motivations that operate in the library sector. Links Wikidata and Libraries: Facilitating Open Knowledge, book chapter by Mairelys Lemus-Rojas, metadata librarian and Lydia Pintscher, Wikidata Product Manager, from Leveraging Wikipedia: Connecting Communities of Knowledge (2018) LD4P and WikiCite: Opportunities for collaboration, WikiCite 2018 program abstract, Christine Fernsebner Eslao of Harvard Library Information and Technical Services and Michelle Futornick, Linked Data for Production Program Manager at Stanford University Shell Lessons for Librarians, Library Carpentry lesson At-risk content on Flickr, blogpost 3 November 2018, Andrew Gray Toward an Abstract Wikipedia, recent white paper by Wikidata founder Denny Vrandečić (Google) Account creation is now open on the ScienceSource wiki, where you can see SPARQL visualisations of text mining. If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 11:20, 30 November 2018 (UTC)

Hybrids?

Hi, possibly a dumb question about hybrids, but are they inherently notable in the same way that valid species are inherently notable? Ie, is Graellsia isabellae × Actias selene a necessary article (given the fact that it's only got two sources it doesn't seem to meet GNG), or should there just be a note in each respective species that they can interbreed? ♠PMC♠ (talk) 07:27, 27 November 2018 (UTC)

I would say no. In fact, it seems such examples are usually covered in overview articles, such as Gamebird hybrids or Panthera hybrid. FunkMonk (talk) 11:37, 27 November 2018 (UTC)

Notable, but not an article at a glance. It should redirect to … I don't know, turns out to be a good question. Maybe collapse to a disambiguation or redirect to a section of one of the species article, in principle, frustrating that the article doesn't explain the hybridisation between separate genera, and the only link I can find is to archived offers to sell from the trade. cygnis insignis 14:33, 27 November 2018 (UTC)

Perhaps cover it in a section of a higher level taxon article. FunkMonk (talk) 14:52, 27 November 2018 (UTC)

FunkMonk, that would work, I should have read your comment more closely. cygnis insignis 15:27, 27 November 2018 (UTC)

When in doubt, use WP:GNG – if there is significant coverage in RS and you want to write an article, go for it. ErikHaugen (talk | contribs) 17:37, 27 November 2018 (UTC)

I don't think hybrids are inherently notable. I don't read French, but I gather that this moth hybrid was facilitated by humans raising the insects and isn't something that naturally occurs in the wild? There are tons of human created plant hybrids and they don't all need articles. It's fairly easy to hybridize many plants bytreating with colchicine. And potential orchid hybrids number in the millions; orchid species are maintained largely by allopatry and pollinator specificity. Bring two orchids together in one place and have a human transfer the pollen? Boom, new hybrid. SPECIESOUTCOMES should not apply to human created hybrids; notability standards for human created hybrids should probably follow the standards for other works of humans (e.g., books, artworks, etc.). As for naturally ocurring hybrids, I think the bar should be higher than that they are simply documented to exist (i.e. SPECIESOUTCOMES), but I'm not sure quite what it should be. Plantdrew (talk) 20:39, 27 November 2018 (UTC)

At best, create an article about moth hybrids and dump them all there. FunkMonk (talk) 20:46, 27 November 2018 (UTC)

Hi, sorry about my lack of response over the past couple days. I appreciate the input - one suggestion over at Wikipedia talk:WikiProject Lepidoptera was to document the information at the articles of each species, then delete the hybrid article as non-notable. I think I might do that, but instead of deletion, redirect to G. isabellae, as that seems to have been the focus of the research. ♠PMC♠ (talk) 22:55, 30 November 2018 (UTC)

Capitalization of names of standardized breeds

FYI

 – Pointer to relevant discussion elsewhere.

Please see Wikipedia:Village pump (policy)#RfC on capitalization of the names of standardized breeds.

This is a neutral RfC on a question left unanswered by MOS:LIFE (on purpose in 2012–2014, pending "later discussion"). It is now later, and lack of resolution of the question has held up MOS:ORGANISMS in draft proposal state for 6 years.  — SMcCandlish ☏ ¢ 😼  22:03, 9 December 2018 (UTC)

Template:Hybrid and Category:Scientific name templates

Something I meant to do a long time ago but keep not getting around to has finally been done:

• Template:Hybrid has been feature-expanded to handle all kinds of cases (including their italicization, no italics on the "×", capitalization, spaces that should be non-breaking and/thin, etc.). Examples:
  • {{hybrid|[[Felis silvestris catus]]|[[Prionailurus bengalensis bengalensis]]}} gives: Felis silvestris catus × Prionailurus bengalensis bengalensis
  • {{hybrid|[[Felis silvestris catus]]|x}} ''[[Prionailurus bengalensis bengalensis]]'' gives: Felis silvestris catus × Prionailurus bengalensis bengalensis
  • {{hybrid|Amarcrinum}} gives: × Amarcrinum
  • ''Citrus'' {{hybrid|sinensis|lc=y}} gives: Citrus × sinensis
  • The original use, just {{hybrid}}, of course still gives: × (forcibly de-italicized, to deal with infobox parameters that are pre-italicizing).
• Template:Chimera has been created, to format graft chimera names (I don't know how many are notable or are mentioned in our text, but it's at least easy now):
  • {{chimera|Crataegomespilus}} gives: + Crataegomespilus
• Category:Scientific name templates has been created for these, along with:
  • Template:Trade designation ({{tdes}}), which we've had for several years.
  • {{tdes|Foo Bar}} gives: Foo Bar (changed font style).
  • Are there any other pre-existing templates that need to be in this category?
  • Is there any other such thing you wish you had a template for?

I've beaten on the overhauled {{hybrid}} in every way I can think of, and it's accounting for all that I can throw at it (like different ways to wrap italics around it, the need to be able to insert material, like an infraspecific term, that is not italicized, and so on). Even had to create a new {{yesitalics}} meta-template (opposite of {{noitalics}}) to make it all work.
 — SMcCandlish ☏ ¢ 😼  05:24, 5 December 2018 (UTC)

{{Taxon italics}} is Lua-based – the Lua function is used directly by all the automated taxobox templates. Thus {{Taxon italics|Felis silvestris catus}} gives Felis silvestris catus; {{Taxon italics|×Amacrinum}} gives ×Amacrinum; {{Taxon italics|Citrus × sinensis}} gives Citrus × sinensis; {{Taxon italics|Citrus {{hybrid}} sinensis}} gives Citrus × sinensis. It also handles botanical connecting forms, thus {{Taxon italics|Acer series Arguta}} gives Acer ser. Arguta. It won't handle "Felis silvestris catus × Prionailurus bengalensis bengalensis", but could be extended to do so. Peter coxhead (talk) 09:19, 5 December 2018 (UTC)

Nifty. It actually seemed to work okay when I fed it such a hybrid name, though I suggested some tweaks at Template talk:Taxon italics.  — SMcCandlish ☏ ¢ 😼  08:22, 10 December 2018 (UTC)

Stub vs. Start class for taxon pages

FYI

 – Pointer to relevant discussion elsewhere.

Please see this discussion at WikiProject Arthopods on clarifying the distinction between stubs and starts for articles about species and other taxa. I looked at the assessment pages for TOL and WPPLANTS recently and since there is a basic template for these types of pages, I think it would be helpful if we had a bit clearer guidelines to distinguish the class categories. Thanks! —Hyperik ⌜talk⌟ 20:01, 12 December 2018 (UTC)

Large number of taxoboxes messed up

This edit and this one, both by Sarsath3, had messed up almost 600 taxonomy templates and corresponding articles by the time I caught up with it. Null edits should fix any that still show up. Peter coxhead (talk) 08:06, 17 December 2018 (UTC)

I am so sorry. it was a simple honest mistake. Sarsath3 (talk) 04:26, 17 December 2018 (CTZ) — Preceding unsigned comment added by Sarsath3 (talk • contribs)

FWIW, I null edited the ~2000 direct transclusions of the 2 above templates, but I know of no easy way to obtain a list of their cascading uses.   ~ Tom.Reding (talk ⋅dgaf)  14:04, 17 December 2018 (UTC)

@Tom.Reding: thanks, that was very helpful – a couple of different errors were hidden in the error-tracking categories by these ones. Peter coxhead (talk) 17:25, 17 December 2018 (UTC)

Out of interest, how does that propagation work? Is it instantiated once when an article containing an affected box is accessed and a template change is found, and then it sticks for repeat viewings until the underlying template receives the next change (here, null edit)? --Elmidae (talk · contribs) 14:27, 17 December 2018 (UTC)

Every time a page is edited (or null edited), all templates/modules/etc. are fully recursed (there is a recursion limit, but it's relatively high) and resolve to their final text, which is actually way messier than what you see in the editor (you can see for yourself by playing around with Special:ExpandTemplates). If server load is low enough, this can be done by just refreshing/navigating to the page. Editing a page forces this though, regardless of server load.   ~ Tom.Reding (talk ⋅dgaf)  14:46, 17 December 2018 (UTC)

Does that must mean visitors to a page are served a cache of the rendered page rather than a new version using all the templates and modules?   Jts1882 | talk  15:39, 17 December 2018 (UTC)

That is server load dependent.   ~ Tom.Reding (talk ⋅dgaf)  16:05, 17 December 2018 (UTC)

@Jts1882: my experience is that, at least in recent months, the server load is sufficiently high that null edits, rather than just visiting a page, are necessary to force full expansion of templates. A particular issue is the presence of a page in an error-tracking category added by a template – viewing the page can show it to be ok, but the cache still has it in the category, until you perform a null edit. Peter coxhead (talk) 17:25, 17 December 2018 (UTC)

{{Wikispecies}} templates on taxon articles

Do we need three links to Wikispecies on each taxon page: lefthand sidebar, taxonbar, and a separate template? Because of the redundancy with the sidebar and taxonbar, I've been removing the {{Wikispecies}} templates, usually as part of other edits, but sometimes other editors replace them. Thoughts? —Hyperik ⌜talk⌟ 20:10, 17 December 2018 (UTC)

It seems to me clear that the answer is "no, we don't" and I strongly favour removing them. (A similar argument applies when a taxonomic database is in the taxonbar and also in the "External links" section.) Peter coxhead (talk) 22:55, 17 December 2018 (UTC)

I'm not in favor of including a Wikispecies template, and when editing a page for other reasons, I usually remove the template. The template is sometimes added willy-nilly without regard for whether Wikispecies actually has an article on the taxon (perhaps a bot could be employed to find and remove Wikispecies templates on en.wiki when Wikispecies doesn't have a corresponding article?). There are a fair number of stubs with the template where there isn't enough text to keep the template from extending the article vertically; ({{Wikispecies-inline}} should be used in these case if a templated Wikispecies link is provided at all).

However, mobile view doesn't include Wikispecies in the list of interwiki links, and taxonbar isn't displayed in mobile view either. Perhaps consideration of mobile view is sufficient reason to include the template (playing devil's advocate here)? Plantdrew (talk) 04:11, 18 December 2018 (UTC)

I'd forgotten about mobile view. The best answer, I think, would be to alter mobile view, so that the taxonbar can be expanded from some small icon.

@Tom.Reding: do you know why the taxonbar is suppressed in mobile view? Is it part of the general policy on nav templates? Peter coxhead (talk) 07:16, 18 December 2018 (UTC)

@Peter coxhead: yes, navbars (full-width) in general are suppressed in mobile view. Partial-width navbox contents are shown though (example), but with most formatting elements removed.   ~ Tom.Reding (talk ⋅dgaf)  16:00, 18 December 2018 (UTC)

Hmm, yeah, if the Taxonbar is supposed to help replace long External links sections, it should definitely be visible on mobile. —Hyperik ⌜talk⌟ 14:49, 18 December 2018 (UTC)

Roosmalens' dwarf marmoset

so i'm not liking the title of this article. The IUCN calls this the black-crowned dwarf marmoset which we use as an alternate name. We could go scientific name as title, but may be still under dispute? We can keep as is, but we are not usi g apostrophe at end per manual of style. The current english name is a reference to 2 close relatives named Roosmalen, not a single person named Roosmalens. I know I'm getting pretty detailed, but I thought I'd deal with it now, now that I'm here....Do we use Roosmalen's, Roosmalens's, or Roosmalens?....Pvmoutside (talk) 23:37, 17 December 2018 (UTC)

What do you mean per manual of style? If it's named after two people named Roosmalen, then Roosmalens' is fine, no? Though I guess it really depends on what current, reliable sources say. Umimmak (talk) 21:46, 18 December 2018 (UTC)

Wikipedia has been staying away from the apostrophe at the end....Pvmoutside (talk) 23:13, 18 December 2018 (UTC)

And would anything be wrong with just moving the article to the IUCN name (black-crowned dwarf marmoset)? Loopy30 (talk) 21:56, 18 December 2018 (UTC)

nothing, just waiting for a few more responses....more sources use Rossmalen (and variations thereof) as a common name however....Pvmoutside (talk) 23:13, 18 December 2018 (UTC)

What do you mean by Wikipedia has been staying away from the apostrophe at the end? Where do you see Wikipedia refer to it as Roosmalens ... not Roosmalens' ...? That would just be wrong, no? Umimmak (talk) 00:45, 19 December 2018 (UTC)

Small changes to the criteria for the display of a taxon in a taxobox

Please see Wikipedia talk:Automated taxobox system/Archive 13#Criteria for display of a taxon in a taxobox. The changes should affect very few taxoboxes (if any). Peter coxhead (talk) 15:30, 22 December 2018 (UTC)

Indo-Pacific humpbacked dolphin - subspecies?

Could someone with an overview have a look at what's going on at Indo-Pacific humpbacked dolphin? I'm confused as to why the article talks about two subspecies but styles them as species (Sousa chinensis, Sousa plumbea) throughout. The usual online sources do not appear to follow the subspecies interpretation. - Then there is Chinese white dolphin (Sousa chinensis), linked nowhere from that page, and treated as a "variety" in that standalone article.

To muddy the waters further, someone has just switched the primary species name (box) in Indo-Pacific humpbacked dolphin from chinensis to plumbea and shuffled a number of redirects around [1]. I have no idea at that point whether that cleared things some up or made them worse. --Elmidae (talk · contribs) 10:40, 21 December 2018 (UTC)

The IUCN recognises two species: Sousa chinensis (Indo-Pacific humpbacked dolphin) and Sousa plumbea (Indian Ocean humpbacked dolphin). The taxonomic notes of the latter say that they have "been recognized as a species since taxonomic revision of the genus Sousa in 2014 (Committee on Taxonomy 2014, Jefferson and Rosenbaum 2014)". The Australian humpback dolphin (Sousa sahulensis), which also seems another species carved out of the Indo-Pacific species, has its own article.

I assume someone tried to update the information in a simple way, which left inconsistencies in the taxobox and elsewhere. There is already an article on the Chinese white dolphin (S. chinensis) so it makes sense that this article gets converted to S. plumbea, but it needs someone with some knowledge of dolphins to separate the relevant material.   Jts1882 | talk  13:19, 21 December 2018 (UTC)

Bryde's whale is also combined in 2 species (albeit disputed), but is in better shape....Pvmoutside (talk) 18:11, 22 December 2018 (UTC)

Facto Post – Issue 19 – 27 December 2018

Facto Post – Issue 19 – 27 December 2018 The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page. To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see the footer. Back numbers are here. Learning from Zotero Zotero is free software for reference management by the Center for History and New Media: see Wikipedia:Citing sources with Zotero. It is also an active user community, and has broad-based language support. Zotero logo Besides the handiness of Zotero's warehousing of personal citation collections, the Zotero translator underlies the citoid service, at work behind the VisualEditor. Metadata from Wikidata can be imported into Zotero; and in the other direction the zotkat tool from the University of Mannheim allows Zotero bibliographies to be exported to Wikidata, by item creation. With an extra feature to add statements, that route could lead to much development of the focus list (P5008) tagging on Wikidata, by WikiProjects. Zotero demo video There is also a large-scale encyclopedic dimension here. The construction of Zotero translators is one facet of Web scraping that has a strong community and open source basis. In that it resembles the less formal mix'n'match import community, and growing networks around other approaches that can integrate datasets into Wikidata, such as the use of OpenRefine. Looking ahead, the thirtieth birthday of the World Wide Web falls in 2019, and yet the ambition to make webpages routinely readable by machines can still seem an ever-retreating mirage. Wikidata should not only be helping Wikimedia integrate its projects, an ongoing process represented by Structured Data on Commons and lexemes. It should also be acting as a catalyst to bring scraping in from the cold, with institutional strengths as well as resourceful code. Links Zotero Comes to Google Docs, Zotero blogpost by Dan Stillman, 19 October 2018. Category:Wikipedians who use Zotero T115158 Write a Zotero translator and document process for creating new Zotero translator and getting it live in production, long Phabricator thread 2015–17. Zotero Translators, documentation from zotero.org. Home page on GitHub for Zotero translator Javascript Example translator, for Wikisource. m:Structured Data on Commons/Newsletter/2018-12-07 Diversitech, the latest ContentMine grant application to the Wikimedia Foundation, is in its community review stage until January 2. If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 19:08, 27 December 2018 (UTC)

Cleaning up unaccepted taxa with {{cleanup taxon}}

FYI

 – Pointer to relevant discussion elsewhere.

A pilot project at WP:Gastropods for systematically identifying and cleaning up unaccepted ("invalid") taxon articles, see discussion: Wikipedia talk:WikiProject Gastropods#Cleanup template for Invalid (unaccepted) taxon, new template {{Cleanup taxon}}, and Category:Taxa that may be invalid —Hyperik ⌜talk⌟ 15:34, 3 January 2019 (UTC)

RfC: Are disease names common names for organisms?

This probably affects Wikipedia:WikiProject Microbiology, Wikipedia:WikiProject Viruses, Wikipedia:WikiProject Fungi, Wikipedia:WikiProject Medicine, and Wikipedia:WikiProject Veterinary medicine, but I thought this would be a goob place to centralize a discussion.

I know this may be considered a bend by some, but if you really boil it down, the name of a disease, for example Raspberry spur blight, is just a common name for the organism, in this case Didymella applanata. I know not all diseases are caused by onle a single organism, but not all common names apply to a single species either. Also many diseases are significant enough to need their own article (like HIV and HIV/AIDS). But I run across many instances where one or both of the disease/cause articles are stubs and run into a bit of resistance on proposed mergers solely on the assumption that a disease name is totally different from the organism name. Similarly, sometimes even when there is only one article, under the disease name, people reject the addition of a taxobox on the basis of it being a 'disease' and not a 'fungus' or whatever the taxon is.

So to sum up, in instances where the following are all true:

• A disease is caused by a single organism and the organism only causes that single disease
• The disease article, organism article, or both are stubs and likely to remain that way, or one is non-existant.

The general guideline should be to merge the articles and include a {{speciesbox}} and {{taxonbar}}.

So what do you all think? --Nessie (talk) 03:45, 5 January 2019 (UTC)

I agree that one article makes more sense than two when the organism and disease are so interrelated. However, I'm not convinced that the disease name is necessarily a common name for the organism. In the Raspberry spur blight article it looked odd to me that the taxobox title was the disease name rather than the organism name. The taxobox is about the organism, not the disease, so this seems a case where the taxobox shouldn't follow the page title.   Jts1882 | talk  07:51, 5 January 2019 (UTC)

Can you explain why more? Where’s the line?--Nessie (talk) 22:25, 5 January 2019 (UTC)

I think the point is that the article begins "Raspberry spur blight is caused by the fungus Didymella applanata" not "Raspberry spur blight is the English name of the fungus Didymella applanata". Peter coxhead (talk) 22:36, 5 January 2019 (UTC)

But my point is that the two statements you made are essentially the same. If there is a one to one mapping of disease and causative organism, especially to the point that two articles could not be supported. If the fungus were called Didymella raspberryensis and the disease were "Raspberry Didymella blight" would that be okay for a single article? Would two stubs be preferable? I'm trying to understand the reasoning, i'm not trying to be annoying. --Nessie (talk) 02:05, 6 January 2019 (UTC)

In the example of raspberry spur blight there are already several taxa involved. The condition is the result of the pathogenic taxon and an infected taxon. A condition or disease is the product of the interaction of two or more organisms, the cause [blame] in the name may be the vector, or its parasite, or the fungal or viral thingamajig that lives on the parasite. I think that keeping them separate is the solution, adding a note or expanding stubs is simpler than untangling forks or knotty lumps. That is not to say that a taxon or disease article ought not to be expanded with the related info instead of creating the stub, but I don't think the reader would gain more by merging two stubs with a different scope. cygnis insignis 03:02, 6 January 2019 (UTC) P.S. I think the same points are already given at the outset, I just fancy I am looking at this from a different angle. 03:05, 6 January 2019 (UTC)

As Peter Coxhead pointed out, the article begins "Raspberry spur blight is caused by the fungus Didymella applanata". If we follow the wikipedia conventions on using common names, this really should be written "Raspberry spur blight is caused by the fungus raspberry spur blight (Didymella applanata)". One article might still make sense, but the writing has to reflect the use of raspberry spur blight as the common name for both the disease and the organism (which are not the same thing logically as something can't cause itself). It would need an opening sentence like "Raspberry spur blight is the common name of the fungus Didymella applanata and the name of the disease caused by infection of certain plants by this fungus". If this sentence cannot be written clearly and unambiguously, it could be taken as a sign that merging to articles is not such a good idea.   Jts1882 | talk  08:36, 6 January 2019 (UTC)

Ok, so what about Rickettsia aeschlimannii infection? I just added a taxobox. Rickettsia aeschlimannii is just a redirect to it. --Nessie (talk) 20:18, 8 January 2019 (UTC)

The article is on the disease, the taxobox is titled after the organism causing the disease. That seems to be the appropriate combination unless the disease and organism are notably enough for separate articles.   Jts1882 | talk  20:35, 8 January 2019 (UTC)

It seems to me that following the convention, the sentence would be "Raspberry spur blight is caused by raspberry spur blight fungus (Didymella applanata)". But there are counter examples in stenophagic lepidoptera, in that people sometimes talk about the horse chestnut, rather the horse chestnut moth, etc. But in general the name of the disease is not the same as the name of the causative agent. Lavateraguy (talk) 23:20, 8 January 2019 (UTC)

Renaming Chimpanzee

Some strongly held opinions are currently being expressed about whether to rename the genus article Chimpanzee to "Chimpanzee (genus)" or "Pan (genus)" (or leave as is). Some comments at Talk:Chimpanzee#Misleading!_Either_make_this_a_"chimp_&_bonobo"_page,_or_disentangle would be appreciated; there seem to be good arguments either way. Cheers --Elmidae (talk · contribs) 09:08, 5 January 2019 (UTC)

Hmmm, but has anyone demonstrated that the term "chimpanzee" doesn't include both the common chimpanzee and the bonobo/pygmy chimpanzee? If not, I see no point in a move. FunkMonk (talk) 09:38, 5 January 2019 (UTC)

• This is a now a formalised requested move Talk:Chimpanzee#Requested_move_6_January_2019: chimpanzee -> Pan (genus) Another separate discussion is contingent on the outcome, the title of chimpazzz … erm, that other article on the species Pan troglodytes ^{[Homo (Pan) troglodytes?]}. cygnis insignis 07:53, 9 January 2019 (UTC)

Adding infra-specific ranks to Virusbox

I have been working on adding infra-specific ranks to {{Virusbox}}, and would like some views on the questions I've posed at Template talk:Virusbox#Ranks below species from anyone interested in virus taxonomy. Peter coxhead (talk) 12:19, 15 January 2019 (UTC)

Invasive species?

Hi, WikiProject Tree of Life,

I do a lot of work with categories and right now we are seeing many categories involving "invasive species" that are empty. Is there a recategorization going on or deletion of articles involving invasive species? Right now there are 14 invasive categories that have been tagged for deletion as empty categories (see Category:Empty categories awaiting deletion) and I see more coming my way. Because some categories are emptied out of process, categories sit in the empty category for 7 days before they are deleted.

Typically empty categories appear randomly about different topics and this happens when 1) a category has only one article and that article gets deleted or 2) recategorization occurs and a new category system replaces an older one or there is renaming going on. It's unusual to have 14 categories on one subject to appear unless it's an intention editing project. So, I thought I'd post here in case anything funny is going on because I hope members of WikiProject Tree of Life would know about this.

Thanks. Liz ^{Read! Talk!} 02:14, 17 January 2019 (UTC)

Ongoing post-Caftaric clean-up to reduce over-categorization. See additional discussion here. Loopy30 (talk) 02:25, 17 January 2019 (UTC)

See also later on in my talk page. Also just added: Wikipedia:Categories for discussion/Log/2019 January 17#Category:Invasive plant species, started this for one of the bigger categories (currently 622 articles). —Hyperik ⌜talk⌟ 17:15, 17 January 2019 (UTC)

Category:Sponges vs. Category:Poriferans

All organism groups under the purview of {{Category described in year}} have a corresponding one-word category parent at their top. For example,

• Category:Animals by year of formal description → Category:Animals
• Category:Birds by year of formal description → Category:Birds
• Category:Bivalves by year of formal description → Category:Bivalves
• Category:Fungi by year of formal description → Category:Fungi
• Category:Plants by year of formal description → Category:Plants
• etc.

The only outlier to this structure is:

• Category:Sponges by year of formal description → Category:Poriferans

which has stood for ~12 years, and the Category:Sponges redirect has stood uncontested for ~10 years.

So I would like to propose that this situation be standardized by either:

1. the contents of Category:Poriferans be transferred to Category:Sponges, and Category:Poriferans redirected to Category:Sponges, or
2. all of the categories starting with 'Sponges' be made to start with 'Poriferans' (e.g. Category:Sponges described in 1864, Category:Sponges described in the 19th century, Category:Sponges by year of formal description, Category:Sponges of New Zealand, etc.).

I prefer #1 since it's the easiest and the least disruptive, but I can help with #2 if there's consensus for it.   ~ Tom.Reding (talk ⋅dgaf)  15:33, 21 January 2019 (UTC)

There is also the issue of monophyly of Porifera, although last I looked it is considered monophyletic again. Sponges will be appropriate regardles of any changes.   Jts1882 | talk  15:47, 21 January 2019 (UTC)

 Done.   ~ Tom.Reding (talk ⋅dgaf)  16:21, 24 January 2019 (UTC)

Facto Post – Issue 20 – 31 January 2019

Facto Post – Issue 20 – 31 January 2019 The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page. To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see the footer. Back numbers are here. Everything flows (and certainly data does) Recently Jimmy Wales has made the point that computer home assistants take much of their data from Wikipedia, one way or another. So as well as getting Spotify to play Frosty the Snowman for you, they may be able to answer the question "is the Pope Catholic?" Possibly by asking for disambiguation (Coptic?). Amazon Echo device using the Amazon Alexa service in voice search showdown with the Google rival on an Android phone Headlines about data breaches are now familiar, but the unannounced circulation of information raises other issues. One of those is Gresham's law stated as "bad data drives out good". Wikipedia and now Wikidata have been criticised on related grounds: what if their content, unattributed, is taken to have a higher standing than Wikimedians themselves would grant it? See Wikiquote on a misattribution to Bismarck for the usual quip about "law and sausages", and why one shouldn't watch them in the making. Wikipedia has now turned 18, so should act like as adult, as well as being treated like one. The Web itself turns 30 some time between March and November this year, per Tim Berners-Lee. If the Knowledge Graph by Google exemplifies Heraclitean Web technology gaining authority, contra GIGO, Wikimedians still have a role in its critique. But not just with the teenage skill of detecting phoniness. There is more to beating Gresham than exposing the factoid and urban myth, where WP:V does do a great job. Placeholders must be detected, and working with Wikidata is a good way to understand how having one statement as data can blind us to replacing it by a more accurate one. An example that is important to open access is that, firstly, the term itself needs considerable unpacking, because just being able to read material online is a poor relation of "open"; and secondly, trying to get Creative Commons license information into Wikidata shows up issues with classes of license (such as CC-BY) standing for the actual license in major repositories. Detailed investigation shows that "everything flows" exacerbates the issue. But Wikidata can solve it. Links Wikipedia:Wikipedia Day for 18th birthday celebrations WMUK video page, with "fake news", Jimmy Wales, Wikidata and more (health warning for those with tune allergy) Why Wikipedia’s Medical Content Is Superior, Stephen Harrison, 28 January 2019, Slate Olivia Colman reveals struggle with Wikipedia over age, Naomi Gordon, 28 January 2019, harpersbazaar.com Making Wikidata visible, Martin Poulter blogpost, 24 January 2019, Bodleian Digital Library Inventory, Magnus Manske blogpost, 24 January 2019, on Wikidata tech support for an image donation by Cleveland Museum of Art If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 10:53, 31 January 2019 (UTC)

Request for comment: new classification scheme for eukaryotes

Adl et al. (2019) proposes a revised classication scheme for eukaryotes, updating their 2012 system, among others. Jmv2009 began to implement some of this in taxonomy templates used by the automated taxobox system, but this caused many such templates and article taxoboxes that use them to have inconsistent ranks, so I have reverted the changes, pending discussion.

If there is consensus to use the ranks in the Adl et al. (2019) system, then radical changes will be needed in many places. In particular, this system places the rank of kingdom much higher up, so that none of Plantae s.l./Archaeplastida, Animalia and Fungi are kingdoms, and if implemented full in taxonomy templates, all articles currently showing a kingdom for these taxa would have changed taxoboxes and many would need changes to the text.

Comments, please. Peter coxhead (talk) 09:44, 3 February 2019 (UTC)

(Multiple Wikiprojects under this one have been notified.)

References

• Too soon My personal view is that eventually we will have to accept that the traditional classification schemes place many Linnaean ranks far too low down, but that we should not change until multiple reliable secondary sources do so (i.e. we should follow WP:RS). It's just about possible to create parallel systems, as we do for birds = Class Aves, and ornithischians = Order Ornithischia, with no Class but Superclass Tetrapoda, but it becomes increasingly difficult. Peter coxhead (talk) 09:44, 3 February 2019 (UTC)

• Too soon per WP:PRIMARY. This is one suggestion among many. It is evident that taxonomy at kingdom level (and above) is in turmoil and will eventually result in a quite different tree of life. Policy is to wait until the situation stabilises and there is sufficient agreement for the way ahead to be clear, as summarised in reliable secondary sources like review articles. Chiswick Chap (talk) 09:56, 3 February 2019 (UTC)

• "under consideration, then development, then implementation"? So interesting, I'm looking forward to the part that references Saint‐Exupéry, A. 1943. cygnis insignis 10:33, 3 February 2019 (UTC)

Encyclopedias aren't research papers. There's no reason why we shouldn't have some vaguely sensible process, either. A. St-E. relied for his safety on first servicing his plane, then refuelling it, then doing his heroic bit of solo flying. Wouldn't have worked too well in any other order. Chiswick Chap (talk) 11:50, 3 February 2019 (UTC)

All comments here appear to presume that the taxonomic ranking needs to be "resolved" before it can be committed into wikipedia. However, the scientific literature continues to use these inconsistent ranks regardless. The most prescient examples currently are kingdom Embryophyta in class Phragmoplastophyta and genus Homo in genus Australopithecus. These are not recent problems either, which will imminently be resolved. For the record: E.g. Australopithecus/Australopithecus is recognized as paraphyletic since 2001. E.g. Embryophytes/Embryophyceae in green algae since Lewis & McCourt 2004.

Rugierro et al, 2015 had Embryophyta as a superphylum. I guess the main argument here is that we need multiple sources. Jmv2009 (talk) 11:55, 3 February 2019 (UTC)

This is the comment of Peter Coxhead on my talk page about his view on the status of this synthesis paper "On the other hand, I'm very aware that deep phylogeny remains a fast moving subject, and by the time good secondary articles appear they tend to be out of date. However, the Adl et al. (2018) paper at doi:10.1111/jeu.12691 is a synthesis of primary research with a wide range of authorship and so, I believe, presents a system we can legitimately use. Personally, I'm still digesting it. There are two different issues: what are the main clades that should be recognized, e.g. in taxoboxes, and what names should be used for these clades." Jmv2009 (talk) 11:59, 3 February 2019 (UTC)

"the scientific literature continues to use these inconsistent ranks regardless." --- It has no choice but to use what there is, and where appropriate to object to it, add to it, point out inconsistencies, propose resolutions, adduce new evidence, and so on. All of these are strategies which we can't, shouldn't, or (WP:OR) must not use: an encyclopedia is at most a description of science (etc), not science itself. Chiswick Chap (talk) 12:16, 3 February 2019 (UTC)

Just proposing here to follow the literature: Removing ranks just because it is inconsistent is not following the reliable sources. Jmv2009 (talk) 12:26, 3 February 2019 (UTC)

If "follow[ing] the literature" means making changes to tens or hundreds of thousands of articles, only for the changes to be reversed or reworked a few months later, then we should resolutely oppose. Chiswick Chap (talk) 12:36, 3 February 2019 (UTC)

Not proposing anything like that here. Just proposing to allow wikipedia to reflect longstanding inconsistencies. Two issues are being conflated: inconsistency and reliability of the sources. Jmv2009 (talk) 12:48, 3 February 2019 (UTC)

How are we doing it for order Apterygiformes in order Saurischia? It looks like it results in skipping vasts swaths of (extinct) phylogeny. This is also the tendency in homo, not being put taxonomically in Australopithecus. Just for taxonomic level-naming consistency sake which is not even anything tangible? Jmv2009 (talk) 12:56, 3 February 2019 (UTC)

• Comment. I've never been convinced that the distinction between primary and secondary references works well in science, especially within taxonomy. Some of the best reviews of taxonomy are included in papers making taxonomic proposals, so the papers have elements of both primary and secondary sources. The overall eukaryote divisions included in Adl et al (2019) seem to represent a good review of the current status, reasonably consistent with other proposals, which makes it a good secondary source. The specific proposal to use "system of hierarchical nameless ranks" is more controversial and is likely to remain so. They also go on to include some ranks in Table 1 "to help orient the student", including just two kingdoms: Bilateria and Embryophyta. Given they propose to use nameless ranks, I don't think they should be used as a source for ranks.   Jts1882 | talk  13:37, 3 February 2019 (UTC)

• Waaaay too soon - we should never implement radical new schemes the very moment they are proposed. At best, we should wait years to see if they catch on among other researchers first. FunkMonk (talk) 13:47, 3 February 2019 (UTC)

Please bear in mind that "nameless" only appears to refers to the endings of the names, not necessarily completely rankless. The above comments appear to assume ranklessness. Jmv2009 (talk) 13:57, 3 February 2019 (UTC)

In proper English "nameless ranks" can only mean ranks with no name. Their system also "ignores endings of clade names", but that is another feature. That said, the article is poorly written and in some places its hard to decypher what they are trying to say. My reading is that their system doesn't use formal ranks and the ranks they give are for comparative purposes and not part of their proposal.   Jts1882 | talk  14:44, 3 February 2019 (UTC)

This is the phrasing they use: "We assembled the classification according to the principles outlined elsewhere, and we refer the reader to the introductions of both Adl et al. 2005 and 2012 for background information, and to Adl et al. 2007 for a discussion. Briefly, we adopted a hierarchical system without formal rank designations. The hierarchy is represented by indented paragraphs. The nomenclatural priority is given to the oldest name (and its authority) that correctly assembled genera or higher groups together into a clade, except where its composition was substantially modified. In these cases, we have used a newer term and its appropriate authorship. In cases where ranks were created to include a single lower rank, the higher ranks were eliminated as superfluous. In this scheme, monotypic taxa are represented by the genus only. Nested clades represent monophyletic lineages as best we know and para- or polyphyletic groups are so indicated. This system of hierarchical nameless ranks, that ignores endings of clade names," So indeed nameless appears to refer to more than just the ending of the names, as is their long standing practice, going back to e.g. 2007. Jmv2009 (talk) 14:54, 3 February 2019 (UTC)

Take my comment as a blanket statement. We were also cautious when the new Ornithoscelida scheme of dinosaur taxonomy was proposed a few years ago, and it hasn't yet been implemented in taxoboxes, simply because there is no scientific consensus yet. That should be the general approach here. FunkMonk (talk) 14:24, 3 February 2019 (UTC)

Please specify what you mean by radical then. Just proposing to allow wikipedia to reflect longstanding practice, without editors hawking at every inevitable inconsistency. I have seen many papers where authors acknowledge the inconsistency, and consent to leave it in place. The lesson is that despite the inconsistency, there can be consensus about it. Jmv2009 (talk) 14:33, 3 February 2019 (UTC)

Radical as in new and not widely known or used. Yes, there is inconsistency, this has been known for decades, but any proposed solution is what's radical, until it gains acceptance. And we only implement it when that happens, Wikipedia follows sources, it doesn't lead. FunkMonk (talk) 15:37, 3 February 2019 (UTC)

Not proposing a solution. Just proposing to follow the sources, not resolving the inconsistencies. However, wikipedia seems to be at odds with these inconsistencies, as they are consistently flagged and removed, even the ones over which there is consensus over keeping the inconsistencies. Jmv2009 (talk) 16:14, 3 February 2019 (UTC)

• Too soon. I echo the caution expressed by the editors above. Of all the higher level taxonomic ranks, changing that of Kingdom is bound to be the most problematic. The terms "Animal Kingdom" and "plant kingdom" are just too ingrained in most readers understanding and will be a major hurdle for the scientific community at large before they adopt such a "radical" change in papers and text books. It could be a generation before this one is settled enough to reflect in the taxoboxes of an encyclopedia. Loopy30 (talk) 15:04, 3 February 2019 (UTC)

To avoid misunderstanding: not proposing here to change animal kingdom and plant kingdom. Just proposing keeping the long standing taxon names of the higher up clades, leading to inconsistencies, acknowledging the inconsistencies. Not clear where you think the Plant kingdom should be (Embryophyta or Archaeplastida or Viridiplantae) Jmv2009 (talk) 15:14, 3 February 2019 (UTC)

Changing the taxon names of the higher up clades based is one thing, although we should discuss it first. Changing the ranks is another; you simply can't change the ranks without affecting all the taxonomy templates below the changed ones, and hence all the articles that use those taxonomy templates. Peter coxhead (talk) 18:13, 3 February 2019 (UTC)

Please describe "affecting". Specifically, what goes wrong in the wikipedia automatic taxonomy system for an inconsistent taxonomy, other than being flagged? Jmv2009 (talk) 18:54, 3 February 2019 (UTC)

The ranks largely determine what is displayed. Remove the "classic" ranks and the taxobox classification will be emptied (no family, order, class, phylum, etc). This means changing the ranks in the taxonomy templates will change what is displayed in a large number of articles (thousands if a higher taxon). This behaviour of the system could be changed if there was consensus, but as things are currently set up, taxon ranks matter. That is why such changes need to be discussed first.   Jts1882 | talk  20:23, 3 February 2019 (UTC)

• Question - If Adl is not to be our source of higher taxonomy for eukaryotes, what is? There seems a lack of consistency in general. --Nessie (talk) 17:10, 3 February 2019 (UTC)

Yes, there is a lack of consistency, but this reflects the literature. The best example is probably birds. If Class Aves is demoted, then the orders, superfamilies, even families used by ornithologists would need to be lowered in rank (and their endings changed accordingly). There are no reliable sources for this that I am aware of, nor any sign that ornithologists are likely to take this route. So we just have to cope with different systems. Hopefully not more than one per WikiProject! Peter coxhead (talk) 18:13, 3 February 2019 (UTC)

Again, how do we incorporate consensus inconsistent phylogenies? Let's have a discussion about consensus later to avoid conflation of issues. Jmv2009 (talk) 19:25, 3 February 2019 (UTC)

I'm not sure what you mean by Let's have a discussion about consensus later. I believe the consensus is clear:

• We should always discuss all alternative classification systems that are appropriately sourced in the text of the relevant articles.
• Taxoboxes cannot properly show alternative systems, so they should use the established consensus for the group.
• Taxoboxes should not show inconsistent Linnaean ranks, like two kingdoms, or a family above an order.

Up to a point, it is possible to use taxonomy templates to support alternative systems, via skip and variant taxonomy templates, and we currently manage to do this – as I noted above – for dinosaurs and birds. (I have some ideas on how the system could better support alternatives, but that's something to discuss separately.) If it were agreed, we might be able to use Adl et al. (2019) complete with ranks for, say, "protists", while using more traditional systems for multicellular organisms, although I haven't yet worked out how this might be set up. Peter coxhead (talk) 20:20, 3 February 2019 (UTC)

I meant consensus about particular phylogenies. In this discussion there appears to be a conflation about the discussion about whether there is consensus about particular inconsistent taxonomies and whether inconsistent taxonomies are "admissible" on wikipedia at all. The other possible conflation is the confusion between inconsistency and consensus. Proposing here to make clear which of these three issues is being addressed in each comment. In any case, the comments make it clear that this is not just about Adl et al, but about many more phylogenies (Birds in Dinosaurs, genus Homo in genus Australopithecus, just to start...) Jmv2009 (talk) 04:48, 5 February 2019 (UTC)

• Too soon - Adl et al suggest a reordering of Eukaryotes, but they also note that their research is still incomplete, and that further data from other sources (such as deep oceans) could cause them to reclassify or reorder even further. I think we need to wait until the scientific community figures out the ramifications of the study and more literature is published. This would be an absolutely massive undertaking for us, and that energy shouldn't be wasted if in a few months time another paper refutes Adl, or Adl refines their findings. And furthermore, Adl is still a primary source! We need a reliable secondary source here. Captain Eek ^{Edits Ho Cap'n!} 20:50, 3 February 2019 (UTC)

• Too soon: we should not make radical, drastic changes on the basis of bleeding edge science. Wikipedia shouldn't be the de facto proponent and popularizer of new taxonomic schemes or clades that are absent in virtually every other authoritative source. We shouldn't jump the gun, nor automatically accept the newest scheme as true (or 'best') simply because it's newest (or in an open-access journal, creating a cognitive bias), which can result in a WP:NPOV violation by lending one hypothesis undue weight. Let's at least wait until the scheme is more widely adopted. --Animalparty! (talk) 21:16, 3 February 2019 (UTC)

• Question. What exactly is so radical about the Adl et al 2019 proposal? This paper is the third in a series of papers (Adl et al, 2005, 2012, 2019) proposing a revised taxonomy of eukaryotes based on an ongoing review of the literature. It is generally conservative with the groupings and the major supergroups have been stable since 2007 or 2012. The position of a number of taxa that fall outside the main supergroups is left incertae sedis, even though a number of recent papers have suggested clearer relationships (Burki et al 2016, Brown et al 2018, Lax et al 2018, Cavalier-Smith 2018, etc). It doesn't contain primary research so I don't think the proposed taxonomy should be rejected because it is a primary source.

What might be radical is changes to the automatic taxonomy system that could result from implementing their rejection of traditional named rank names. This proposal is hardly new as that was part of their 2005 proposal and has long been advocated by others. It would have radical effects on how taxoboxes are displayed. There also seems some confusion about the Linnean ranks they indicate in Table 1, which seems to advocate kingdoms Bilateria and Embryophta, but this is not part of their formal proposal in Table 2.   Jts1882 | talk  12:03, 4 February 2019 (UTC)

That one author (and his group) has published several papers over many years doesn't create a consensus; it needs to be accepted by other researchers which are not affiliated with them. That is why it is radical, it is not widely accepted consensus, but something proposed by a specific research group. We need to establish that these ideas have gotten wide acceptance before we can do anything other than just mention their ideas in articles. If a consensus hasn't emerged since 2005, I don't see why we have to rush here. FunkMonk (talk) 12:06, 4 February 2019 (UTC)

You haven't answered the question about what is so radical. People seem to be rejecting it as radical without saying which part they consider radical. The Adl et al taxonomic hierarchy is conservative and based on extensive review of the literature over a long period; their supergroups are largely adopted by others (i.e there is consensus). This makes is a good potential secondary source for the overall topology of the eukaryote taxonomy. Whether to abandon named ranks is a secondary question that can be decided independently. Here I agree there will be no consensus and unlikely to be so for a long time.   Jts1882 | talk  12:52, 4 February 2019 (UTC)

Well, I think it has been explained multiple times now; even if the "solution" is a synthesis of older ideas, the synthesis itself is new and needs to be generally accepted. Otherwise, the implementation of it itself is "radical". Per the dictionary definition: "thoroughgoing or extreme, especially as regards change from accepted or traditional forms: a radical change in the policy of a company". FunkMonk (talk) 14:18, 4 February 2019 (UTC)

• Oppose? Maybe I'm not understanding... It seems like people are responding to two totally unrelated questions (or more likely, I'm not understanding the discussion). Question 1 is "should we depart from Linnaean taxonomy ranks in infoboxes in order to display more precise and evolutionarily relevant taxa?" To that question, I currently answer no. I think infoboxes should display very brief snippets of information that can be interpreted at a glance. Adding taxa beyond the classic Linnaean ranks seems to me to be clutter that will confuse the average reader (though it certainly adds precision, which the average reader will likely not notice). Question 2 is "should we believe and write about a recently published summation and revision of eukaryotic taxonomy?" On that question, I'm a yes. We've known for a long time that Linnaean ranks aren't going to accurately capture divergence of groups. Unranked taxa have been widespread for a long time and are largely uncontroversial. It's great that this group is going through and synthesizing phylogenetic data to give a larger view of eukaryote phylogeny. I'd feel comfortable writing about it in the relevant section of an article. I just don't think it's beneficial to expand the taxoboxes to include non-Linnaean ranks (and I think that's what prompted Peter coxhead to start this discussion?). Ajpolino (talk) 00:46, 6 February 2019 (UTC)

The problem is not using unranked taxa per se - they are already used in the taxoboxes for flowering plants (there's no consensus ranked classification above the rank of order for flowering plants) and for a variety of fossil groups. The immediate problem was inconsistent use of ranked taxa. Lavateraguy (talk) 16:09, 7 February 2019 (UTC)

Clarification of the issue

Apologies if I'm wrong, but some comments above suggest that the issue isn't entirely clear to everyone. Suppose the hierarchy [Life → ... → Clade B → ... → Kingdom A → ...] has been set up in taxonomy templates. Then suppose it's changed to [Life → ... → Kingdom B → ... → Kingdom A → ...]. Then, since kingdom is a rank always displayed, every single article about any taxon in Kingdom A that uses an automated taxobox – likely tens of thousands of articles about subspecies, species, genera, families, etc. (Template:Taxonomy/Animalia has 173,545 transclusions) – will have a taxobox containing two kingdoms. There's absolutely no consensus for this! Peter coxhead (talk) 20:38, 3 February 2019 (UTC)

Thank you, this is most usefull. Anything else? (Because this particular issue, for this particular rank, appears to be easily addressable) Jmv2009 (talk) 23:56, 3 February 2019 (UTC)

doesn't this type of situation throw errors? As in, when a template is published that has out of order ranks, does it pop up in a cleanup category or something? --Nessie (talk) 04:15, 4 February 2019 (UTC)

I agree it does appear to be flagged somewhere. Also in the templates themselves sometimes are reddish flagging shows up. The question then is whether it should always be acted upon. Jmv2009 (talk) 06:21, 4 February 2019 (UTC)

@NessieVL: as well as showing the offending ranks shaded in red when you view a twxonomy template, it puts the taxonomy template in Category:Taxonomy templates showing anomalous ranks, which is monitored, generally daily, by a number of editors, and the offending template rapidly fixed.

@Jmv2009: how is it easily addressable? Of course it should always be acted on, given that the alternative is masses of taxoboxes with inconsistent ranks, which will certainly puzzle readers and lead to attempts to fix them.

Peter coxhead (talk) 09:16, 4 February 2019 (UTC)

So there is no way yet on wikipedia to systematically reflect the inconsistencies pointed out in the literature is what you are basically saying here. There should be no shield to protect wikipedia from the scientific literature. Jmv2009 (talk) 05:04, 5 February 2019 (UTC)

@Jmv2009: where has anyone said that we want a shield to protect wikipedia from the scientific literature? Sorry, but it's just ridiculous to suggest that. Everyone agrees that all appropriately sourced views must be discussed. Appropriate sourcing is clearly defined in WP:RS, including WP:RSPRIMARY – we don't have to reflect the very latest view expressed in a primary source like a journal, but can wait to see if other sources pick it up. I would certainly discuss Adl et al. (2019) in articles, just as I added text discussing the earlier Adl et al. system. It's just a fact that a taxobox can only show one of the possible views, and the consensus has been that this view should not have inconsistent ranks. Peter coxhead (talk) 09:16, 5 February 2019 (UTC)

For example, plant describes 4 different concepts of the kingdom Plantae. Lavateraguy (talk) 10:08, 5 February 2019 (UTC)

Protecting from literature may sound ridiculous, but is it though?: e.g., once again, I can't put the tree of fig.1 of [2] in the taxoboxes because of the genus in genus situation. Try it, you will fail! This is almost literally a textbook example. Jmv2009 (talk) 17:56, 5 February 2019 (UTC)

This gets complicated, but solutions might posssible. First there are some semantic issues to consider.

If genus Australopithecus is the evolutionary group from which Homo arose, then Australopithecus is paraphyletic. That means Homo isn't part of the parapheyletic genus Australopithecus. The parent includes both Australopithecus and Homo but not in a sister relationship. Australopithecus as a genus is not the parent of Homo, making Genus Australopithecus inappropriate for the parent in the taxobox. However, Australopithecus sensu lato as a broader group would be the parent, say, if considered a tribe. There must be some taxonomies treating Australopithecus inclusive of Homo as a higher rank.   Jts1882 | talk  20:12, 5 February 2019 (UTC)

Fig. 1 doesn't present a taxonomy. That aside, Hominini sensu strictu is available (as are Hominina sensu lato and Australopithecina sensu lato).

However, you don't have to name every node in a cladogram, and you don't have to show every named node in a taxobox.

Also, with fossils, there's the problem of unresolveable early taxa - diverse and distinct group B might be nested in group A, but you can't tell exactly where. Lavateraguy (talk) 22:12, 5 February 2019 (UTC)

You realize how many arguments you just made, which you wouldn't necessarily have made if Australopithecus already had e.g. a tribe status? "It's paraphyletic", " It's not really a genus", "It doesn't present a taxonomy" "Hominini sensu strictu is available" "You don't have to show every node" "It's not resolved" To me these arguments sound very contortionist, where showing the true consensus direct phylogenetic status is inhibited by the consensus of the naming convention. To me it is clear showing the phylogenetic status is more important than following the naming, especially when everyone is already making cases that the naming is not consistent. Jmv2009 (talk) 02:27, 6 February 2019 (UTC)

The difficulty of separating Homo from Australopithecus is discussed in From Australopithecus to Homo: the transition that wasn't. The monophyly of the genus may not be a useful concept in talking about descent. - Donald Albury 15:24, 6 February 2019 (UTC)

Of course, "But it's a chronogenus" was still the missing contortionist argument, which also would not have been made if Australopithecus had already been at the tribe level. And how do you put chrono-XXX in the taxoboxes again? Ironically, historically they were assigned separate genuses because they were regarded as significantly distinct, while now they are being argued to be virtually the same. Sorry, not buying it. If it was not assigned to a above genus level because of lack of diversity, it's the wrong argument also, as as soon as it has a descendent, it has to go all the way to above the descendent's level without consideration of diversity for it to work in a modern, phylogenetically determined taxonomy. Jmv2009 (talk) 17:24, 6 February 2019 (UTC)

@Jmv2009: we're not going to get anywhere, because you are defending your personal view as to what a modern, phylogenetically determined taxonomy should be, whereas all that matters is what the consensus is in reliable secondary sources. No more here from me. Peter coxhead (talk) 21:44, 6 February 2019 (UTC)

Once again conflating the issues of sources and the issues of permissibility of inconsistent taxonomy. And just trying to follow e.g. [3] and see chapter 20 of amounting to textbook examples. By the way, in this case textbooks may actually be ahead of scientific publications, because I read that in anthropology scientists are especially careful due to the sensitive nature of the subject. Jmv2009 (talk) 18:09, 7 February 2019 (UTC)

Would I be right in thinking that the problem isn't in using the hierarchy in Adl et al per se, but in assigning Linnaean ranks to their clades?

Yes, that is what I have been trying to argue above. The hierarchy and use of named ranks are two separate qustions.   Jts1882 | talk  12:54, 4 February 2019 (UTC)

@Jts1882: well, it certainly wasn't clear to me that this is what you were trying to argue above. So can we now agree that is wrong to use the ranks in Adl et al. (2019) because of their effects on taxoboxes throughout many articles, and you won't change the ranks in the relevant taxonomy templates again without prior discussion and consensus?

I don't remember making changes to the ranks in any Eukaryote taxonomy templates. I've changed a few parents, but none based on Adl et al (2019), which I hadn't seen until this weekend.   Jts1882 | talk  15:10, 4 February 2019 (UTC)

Peter might, like I did a couple of times, have been confused by you having an, at a glance, similar username to Jmv2009. FunkMonk (talk) 15:21, 4 February 2019 (UTC)

Yes, absolutely right. My abject apologies! Peter coxhead (talk) 15:25, 4 February 2019 (UTC)

Ignoring ranks, others have noted above (and below) that there are other hierarchies. However, the one in question does have the considerable merit of being proposed by multiple authors (unlike Cavalier-Smith's). So if it is taken up by other reliable sources, then in, say, a year's time, we can revisit the question of whether to use its names and hierarchy. Peter coxhead (talk) 14:30, 4 February 2019 (UTC)

Ignoring ranks, there are three different questions remaining - the hierarchy, for which Adl et al may well be as good a synthesis of the current state as knowledge as we can find, their nomenclature (e.g., they use Chloroplastida, where Viridiplantae seems to be the consensus usage), and the stability of the data (I have the impression that protist trees haven't stabilised to the degree that say angiosperms or pteridophytes have). Lavateraguy (talk) 19:31, 4 February 2019 (UTC)

Further comments

The other source of protist (and in this case prokaryote as well) classifications is Cavalier-Smith (et al).

With regards to stability, the monophyly of Archaeoplastida remains an open question. Lavateraguy (talk) 11:43, 4 February 2019 (UTC)

Is it the monophyly or its contents? Archaeoplastida could be expanded to include Cryptista and Picozoa.

read the above as "Archaeoplastida as currently understood" Lavateraguy (talk) 19:25, 4 February 2019 (UTC)

Any thoughts on the Handbook of the Protists as a secondary source for Eukaryote phylogeny? The introduction by Simpson et al (2017) has a reasonable consensus phylogeny.   Jts1882 | talk  17:12, 4 February 2019 (UTC)

@Jts1882: is it available online? Researchgate only has an abstract. Peter coxhead (talk) 21:47, 6 February 2019 (UTC)

Yes and no. Handbook of the Protists is available online but only the chapter abstracts are free. The latter undermines its goal of providing a "community resource". When I made the suggestion I was under the impression that the introductory chapter by Simpson et al (2017) was freely available.

Against that major disadvantage, the advantages are that is clearly passes the reliable secondary source test, has chapters written by a wide selection of experts, and it provides a combination of being relatively up to date and conservative. The phylogenies in Simpson et al (2017) show polytomies where there is doubt, wheras another potential source (Silar 2016) is much bolder at presenting detailed trees. Incidentally, there are a number of Wikipedia articles with phylogenies attributed to Silar (2016) that bear little resemblance to them (e.g. in Hacrobia).  Jts1882 | talk  13:53, 7 February 2019 (UTC)

Possible alternatives At Wikipedia talk:Automated taxobox system/Archive 1#Fixing inconsistent ranks in taxonomy templates I've suggested some alternative ways of fixing inconsistent ranks in taxonomy templates that might make it easier to deal with part of the issue being discussed here. Peter coxhead (talk) 15:37, 8 February 2019 (UTC)

References

Fixing inconsistent ranks in taxonomy templates

Input sought At Wikipedia talk:Automated taxobox system/Archive 1#Fixing inconsistent ranks in taxonomy templates I've suggested some alternative ways of fixing inconsistent ranks in taxonomy templates. They could make it easier to deal with the problem of inconsistent classification systems, e.g. the ones used for birds and dinosaurs, or the ones used for mammals and dinosaurs. Be warned that it's a long post, but it very much needs input, particularly from "old hands" at using the automated taxobox system. Peter coxhead (talk) 15:42, 8 February 2019 (UTC)

use of nav boxes

Can I request some comments on nav boxes for 'groups' of animals, in general, but especially those that provide a link to every other article in a family, for example, by one taxonomic classification of that group. I already have an opinion, but want to know how others view their presence in our articles. cygnis insignis 07:55, 8 February 2019 (UTC)

Some examples I notice recently Template:Chiroptera, Template:Molossidae (display title "Extant species of family Molossidae") and the configurable Template:Vespertilioninae nav. The array of templates may be contained by Category:Mammal species templates, where I just notice more chiropteran navigation as regional Template:Madagascar bats nav. TY for the interest so far. I would argue they are a net negative, beyond matters of taste (which is why they are hidden?). cygnis insignis 14:51, 8 February 2019 (UTC)

Reason for your redlink in Template:Molossidae: it has a couple of invisible characters. You can see them as red dots in edit mode.   Jts1882 | talk  15:27, 8 February 2019 (UTC)

The alarming thing is that I can not see them, but I see it seems to be spat out as a "zero-width non-breaking space". Thanks for the reality check. cygnis insignis 20:07, 8 February 2019 (UTC)

Can you give an example?--Nessie (talk) 12:35, 8 February 2019 (UTC)

Navboxes are like marmite. Some people can't get enough of them and other hate them.   Jts1882 | talk  13:23, 8 February 2019 (UTC)

I'm more of a durian fan, myself. In any event, I don't have objections with navboxes per se, but those examples have a few problems, in my mind. First, they are gigantic and so are then less useful. Second, they basically replicate much of what's in a Taxobox. But they are typically collapsed and way at the bottom, so not so much of a negative. Personally I'd like them to include links to related topics not found in taxoboxes, like {{banana}}. --Nessie (talk) 15:30, 8 February 2019 (UTC)

That is the first navbox that I did not hate on sight, I like it in fact—like durian—if I hold my nose; but now I have that banana phone song in my head! The chiropteran navs are redundant to categories, lists, and articles, but are also pov without citations (which the taxo-nav-box does have). The creators see an opportunities for yet another mechanical assemblage of boxified content,they do not tend to be maintainers of their creations, that falls to those concerned with uncited and contradictory data in our articles. For me, the biggest objection is the mess it makes of incoming links, which is why categories and some lists can be useful, I place a high value on the cross-referencing of properly cited content. Still, the banana box is lovely, ring ring ring … cygnis insignis 16:09, 8 February 2019 (UTC)

I've noticed the inflation of incoming links by nav boxes before - bit of an irritation if you're trying to disambiguate incoming links. Lavateraguy (talk) 16:26, 8 February 2019 (UTC)

I'm not a fan of them. I hate the mess they make of incoming links (although that is only a problem for editors, not readers). They impose a maintenance burden; they are yet another place that needs to be edited to keep taxonomy up to date (and in practice they are NOT being maintained). Navboxes for higher ranks (e.g {{Lepidoptera}}, which covers families) get placed willy nilly on species articles that aren't included in the navbox. For organisms other than birds and mammals, our coverage of species is far from complete, so a navbox would mostly be a sea of redlinks (although mammals are the only group where navboxes are widespread anyway). As a reader, the only navboxes I've ever really clicked on are geographic (e.g. cities in a US county) or chronological (earlier/later holders of a political office or winners of an award). I've never used an organismal navbox to browse related topics. Plantdrew (talk) 16:34, 8 February 2019 (UTC)

I endorse all of Plantdrew's comments above, except that I would put it more strongly than "I'm not a fan of them". At best they are useless clutter in organism articles, and I would strongly support their removal in almost all cases. Peter coxhead (talk) 17:46, 8 February 2019 (UTC)

I only edit a couple (animals, Template/eukaryotes, plants), and try to keep them consistent with the articles. If it's hard to keep limited trees in articles properly reffed, for the navboxes it is probably impossible; They are never based on a single or just a few articles, which is a problem. No room for alternative phylogenies. It is also not clear whether the grouping should be phylogenetically based, which incidentally leads to conflicts. What I am trying to do is when I make a change, is to refer to the scientific article to which the change was made. When following the links in the taxoboxes, one invariably gets to wikipedia pages with different cladogram or taxoboxes, e.g. cnidaria. Also missing the option to generate empty, unnamed groups. Anyway, does wikipedia have any click-through rate about these boxes? Jmv2009 (talk) 20:10, 8 February 2019 (UTC)

what Plantdrew and Peter coxhead said....Pvmoutside (talk) 23:10, 8 February 2019 (UTC)

~700 conflicting Wikidata items

@ User:Tom.Reding/Wikidata conflicting items

While adding missing descriptions to various biota in Wikidata, I came across these (on the surface) duplication errors. Wikidata does not allow 2 QIDs to possess identical labels AND descriptions, so these have to either get merged OR relabeled in some combination (either QID_1, or QID_2, or both), then have the appropriate descriptions applied. I don't have the time/patience/knowledge to fix all of these accurately nor quickly, so I'm leaving it here for more capable editors to fix!   ~ Tom.Reding (talk ⋅dgaf)  15:12, 22 February 2019 (UTC)

@Tom.Reding: I've commented on the page you've wikilinked above, but these are not all duplicates. Peter coxhead (talk) 15:57, 22 February 2019 (UTC)

Ah, thank you! This is exactly why I didn't venture into this group of items, except only for the obvious cases, of which I guess there are few.   ~ Tom.Reding (talk ⋅dgaf)  16:28, 22 February 2019 (UTC)

@Tom.Reding: I think the fungus examples are duplicates which should be merged. I will try to look into it sooner or later. Strobilomyces (talk) 20:45, 23 February 2019 (UTC)

The more TOL eyeballs the better - they might not all be true duplicates, but they all need something fixed.   ~ Tom.Reding (talk ⋅dgaf)  21:08, 23 February 2019 (UTC)

Yes to the comment above. After looking a bit more closely, I am wrong - although some should be merged, others just need the English label to be changed. This is because the items represent names and unfortunately there is no way of identifying organisms (which can each have many names). So every case needs to be examined separately. Strobilomyces (talk) 21:27, 23 February 2019 (UTC)