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Bacteria

I am not a member of this project, so wanted to enquire if there should be a page for each accepted species of Bacteria as listed in the LPSN? At present a large number of species are missing, at least half, my guess is that it is because it may be based on 20+yo Bergey's book (online though TOBA7.7 is more upto date). (If they should be there, I was thinking an automated bot-work to make the pages with taxonomy, authority reference and ethymology using LPSN repository, genome data from NCBI [1] and other data from Biocyc [2] if sequenced and a cladogram from ARB silva living tree [3] for higher ranks, hence the question) --Squidonius (talk) 02:01, 3 January 2011 (UTC)

Eventually, there should be a page on each bacterial "species". However in the past, bot-created species pages have often run into problems and been deleted, especially those created from some of the major on-line databases. These databases often have inconsistent high-level taxonomy, among other taxonomic problems, which results in poor pages. --EncycloPetey (talk) 02:17, 3 January 2011 (UTC)
Does it have to be all or nothing as far as bots are concerned? There does not seem to be a "work as community" attitude when it comes to bots. What about a bot that creates articles at the direction of a human? Single articles? For example, Squidonius checks LSPN, NCBI, Biocyc, and silva, sees we are missing an article on species x, then the bot creates the bones of the article in bot user space and Squidonius edits and moves it to article space? I often use adaptive aids for entering data on-line, and the bare-bones of a species article takes me hours. It's very handy having the deleted anybot articles moved into project space where I can edit and move them into main space. Can we consider this?
I don't see there being an article on every bacterial species, some will be reduced to participants in a list. Even recognized bacterial species are sometimes not so well defined. Wikipedia is missing some major prokaryote articles, though. --Kleopatra (talk) 04:30, 4 January 2011 (UTC)

Stock.xchng

The project page recommends this site for photo but when I checked the license information it seems incompatible with Wikipedia as redistribution of the images are forbidden. Regards, SunCreator (talk) 17:07, 12 January 2011 (UTC)

Tidying up references and footnotes

Many of the species pages use {{aut}} but is recommended that it should used sparingly. Also, some of the footnotes and references can be combined. The first random example I chanced on was Characidae#Footnotes. Other species pages are missing footnotes. I would like to see a list of species pages that use {{aut}} generated which can then be used to improve the refs. -- Alan Liefting (talk) - 22:29, 14 January 2011 (UTC)

Alternative taxonomical classification

Alternative taxonomical classification has been prodded for deletion. 65.93.14.196 (talk) 07:32, 16 January 2011 (UTC)

Categorization of species pages

There are some problems, in my view, with the current approach to the categorization of species articles when both Latin and common names occur as titles or redirects. There seem to be two approaches, often not consistently followed.

  • Categorize the species article only, regardless of whether there is a redirect page. Then in the category page the species occurs only once, either under its common name or under its Latin name, depending on which was used as the article title. See Category:Lathyrus as of 06:09, 22 December 2010, where "Sweet Pea" occurs under "S" and "Lathyrus odoratus" is absent. (I've linked to a specific version because categories seem to change quite often.)
  • Categorize the species article and also categorize any redirect from a common name or a Latin name. Then in the category page the species appears twice if it has a common name, under both its common and Latin names. This has mostly been done at Category:Pinus as of 16:26, 8 January 2011, where, e.g., "Pinus halepensis" and "Aleppo Pine" both appear. (However, look at the "s" [lower case] entries, which include "Siberian Pine" [expected under "S" if the cases are distinguished] and "Qiaojia Pine" [presumably because its Latin name is Pinus squamata, the next entry].)

There are also cases where the species article appears only once in the genus category page but in the wrong place, because the category declaration uses a different name from the article title. See Category: Phaseolus as of 21:09, 22 December 2010, where "Phaseolus vulgaris" appears under "C" (because, I assume, the common name is "Common bean").

The current position with many genus category pages is frankly a mess. However, tidying this up requires consensus on how the categorization should be done. My preference is the second of the two approaches described above: when there is a redirect, categorize both the article and the redirect page. Thus Sweet pea should be categorized [[Category:Lathyrus]] (as it indeed is), but also Lathyrus odoratus should be categorized as [[Category:Lathyrus|odoratus]], which it is not. Then both the common and Latin names will appear in the genus category page.

What do other people think? Peter coxhead (talk) 17:40, 24 January 2011 (UTC)

I prefer the second method mostly for completeness in the category. If there are a lot of common name redirects (for large genera), I prefer to split them off into their own category, e.g. Category:Banksia taxa by common name / Category:Banksia taxa by scientific name, and synonyms should have their own category, e.g. Category:Drosera by synonymy. I think all of the problems you identify above are the result of incorrect application of sortkeys or DEFAULTSORT. For example, the article titled at Siberian Pine currently has the following (incorrect) genus category syntax: [[Category:Pinus|sibirica]]. If the article remained titled at the common name, I would just remove the |sibirica. I believe this is the work of User:Look2See1 and I think we worked that out with him on his talk page; he'll be correcting those. Phaseolus vulgaris was recently moved as the result of a WP:RM from Common bean. The closing admin didn't clean up the page after the move. It had a {{DEFAULTSORT:Common Bean}} above [[Category:Phaseolus]]. Removing the defaultsort and adding the sortkey [[Category:Phaseolus|vulgaris]] fixed the problem diff. (I think a lot of closing admins on requested moves forget about DEFAULTSORT, which is one of the reasons I can't stand the use of it on species articles.) It'd be nice if we could come to consensus and write this down somewhere. Rkitko (talk) 16:38, 25 January 2011 (UTC)

Automatic taxoboxes

Just to let people know that Template:Automatic taxobox is now stable and suitable for use in articles. The template should be able to replicate any existing taxobox, although its documentation is still incomplete; if you can't work out how to do something, the best option is to ask at Template talk:Automatic taxobox. The template may not be appropriate for every article; please use your discretion when upgrading, and preview the taxobox before saving. In particular, please check that there is consensus for the taxonomy in the new taxobox!

The template provides the following benefits:

  • Automatic generation of many parameters, meaning:
    • Less code in the Wiki source
    • Consistency between articles
  • Reduction of duplicate data
    • Taxonomies are generated by reference to a series of templates within Wikipedia, meaning that all articles using the Automatic Taxobox will use the same taxonomy - this only needs updating in one place
  • Automatic generation of subdivision lists
    • Again, a change in classification can be reflected across Wikipedia in a single edit
    • Full taxonomy browsing: child taxa aren't "missed off" lists, and can be easily found

I've made a start automating some minor phyla (such as the Chytridiomycota). There are rudimentary instructions detailing how to perform the upgrade. Let me (or others at Template talk:Automatic taxobox) know if you need any help! Martin (Smith609 – Talk) 21:57, 24 January 2011 (UTC)

RfC

There's an RfC on a requested change to the way Appendix 1 conservation status in the CITES system is displayed in taxoboxes. Please stop by if you have any opinions on the subject. Bob the WikipediaN (talk • contribs) 16:31, 26 January 2011 (UTC)

Task force needed

Hi y'all. In light of the inconsistencies with the way unranked taxa are treated, we're trying to fix this so that unranked taxa always appear immediately prior to their ranked "equivalent". Unfortunately, however, the use of |unranked_familia= above the |superfamilia= has grown quite popular...so popular that tens of thousands of pages use it.

If the category Category:Taxoboxes employing both unranked familia and superfamilia can ever be emptied out, then we can update the taxobox code accordingly so that the unranked family is displayed below the superfamily instead of above it. Thanks for anything you can offer to this cause, be it a little bit of time or even a bot. Bob the WikipediaN (talk • contribs) 21:13, 30 January 2011 (UTC)

I'm finding the fastest manual way to correct this is to replace |unranked_familia= with |unranked_superfamilia=. Thanks to anyone willing to help out with this huge task. Bob the WikipediaN (talk • contribs) 22:55, 30 January 2011 (UTC)
This task needs a bot; it's too big to do manually. You need someone who knows how to write bots! (It's a beautiful illustration, by the way, of the need for automated taxoboxes...) Peter coxhead (talk) 14:52, 31 January 2011 (UTC)
Yeah... I tried to manually convert a genus from the list (instead of just replacing unranked familia with unranked_superfamilia) and it ended up taking a couple of hours for about 25 species, a tiny drop in the ocean of 25k remaining. As for the current infobox vs. automatic taxobox, with the old taxoboxes at least one species I came across was classified wrongly, another family had subfamilia that didn't match its members' classifications and necessitated additional research etc. but once converted, I didn't have to manually correct each member again, and adjusting them again in the future would be far easier.--Obsidi♠nSoul 15:08, 31 January 2011 (UTC)
Plastikspork has volunteered to work on this (using a bot, I believe). He's made a lot of headway already-- at this rate, it'll be done in under a week, I dare say. Bob the WikipediaN (talk • contribs) 23:14, 31 January 2011 (UTC)
And where is the bot request for approval for this task? Can you provide a link? --Kleopatra (talk) 05:16, 1 February 2011 (UTC)
Wikipedia:Bot requests/Archive 40#Taxobox maintenance, one-time - Bob the WikipediaN (talk • contribs) 06:33, 1 February 2011 (UTC)
That is not a bot approval. On the other hand, you didn't need consensus to edit fully protected templates, so what's a little lack of approval for 27,000 edits, when you made a dozen edits that impacted thousands of articles without approval? --Kleopatra (talk) 06:59, 1 February 2011 (UTC)

In light of the discussion, I've put up an RfC to make sure this series of cleanup actions isn't controversial. The bot owner has been notified of the RfC and is halting the process until an outcome is evident. Please post further comments at RfC. Bob the WikipediaN (talk • contribs) 07:12, 2 February 2011 (UTC)

Taxobox color RfC

There's an RfC at Template talk:Taxobox colour#In light of the luminosity increase. Please share your thoughts there. Bob the WikipediaN (talk • contribs) 15:54, 7 February 2011 (UTC)

Repeated classifications on the Human Taxonomy page

The Human Taxonomy page contains a comprehensive list of all the clades that humans can be said to belong to. However, between 'Phylum - Chordata' and 'Class - Mammalia', there are many classification names that are repeated elsewhere. For instance, we have 'Superclass - Osteichthyes' (bony fish) and 'Superclass - Tetrapoda [...and four limbs for terrestrial locomotion]'. Calling both of these 'superclasses' agrees with the individual 'taxoboxes' on the page for each clade; but when put together, it looks wrong. Similarly, we get 'Infraorder - Eucynodontia' (advanced 'dog tooth' therapsids, from which all mammals descend) and 'Infraorder - Simiiformes' (all monkey and apes) in the same list. Is there any way we can get this list to not repeat classifications in it, and yet be consistent with the uses elsewhere in Wikipedia, and in external sources? --Peace Makes Plenty (talk) 11:19, 9 February 2011 (UTC)

External sources aren't consistent on the ranks given to clades, so the page can't be consistent with all external sources.
The make can be made internally consistent by labelling every node from Osteichthyes to Mammaliformes as a clade.
The root problem is mixing cladistic and non-cladistic classifications. It turns up again at Synapsida which places class Synaspida as subordinate to class Amphibia. Lavateraguy (talk) 13:58, 9 February 2011 (UTC)
This problem is easily solved by removing the ranks in the list. I recommend making two lists, one for Linnaean classification and one for phylogenetic, similar to what has been done in the Vertebrata article. Petter Bøckman (talk) 12:43, 25 February 2011 (UTC)
I agree that mixing grade (Linnaean classification) and clade creates a problem in the taxoboxes. I think we need to clearly distinguish the two systems of classification in articles referring to or using evolutionary relationships. -- Donald Albury 13:02, 25 February 2011 (UTC)
The general consensus (see below) is to have Linnaean classification in the taxobox for ease og overview and navigation, and save the longer classification for the text. Petter Bøckman (talk) 08:08, 27 February 2011 (UTC)

Taxonomy/Reptilia

Considering Reptilia is paraphyletic group which shouldn't be used, I was about to replace Template:Taxonomy/Reptilia with Template:Taxonomy/Sauropsida, until I noticed that Sauropsida's taxonomy page was already deprecated in favour of Reptilia's page and started to wonder is there a point to this? Now for example Avialae shows class Reptilia even though it does not belong in it. --Sapeli (talk) 07:46, 24 February 2011 (UTC)

The problem lies in that the relational database requires a consistent parent for each taxon. Unfortunately, there's still a lot of debate around Wikipedia on whether to use the newer Sauropsida or the older Reptilia. Sauropsida is favored by the evolutionary editors, particularly the dinosaur articles, but Reptilia is favored by the editors of modern reptile articles. The decision to use Reptilia in the automatic taxobox was made per a discussion at Wikipedia talk:WikiProject Amphibians and_Reptiles/Archive 4#Reptilia or Sauropsida?. If you'd like, we can resurrect the discussion in a fresh topic at that WikiProject. Personally, I'm in favor of getting rid of Reptilia altogether, but that's just my opinion (and yours, it would appear). Bob the WikipediaN (talk • contribs) 09:33, 24 February 2011 (UTC)
One of the arguments forwarded was that the taxobox is an instrument for navigation, provided for the non-expert. Reptilia, still being by far better known and more commonly used than Sauropsida, is the most conductive to let the layman reader understand where in the tree of life he is. Notice that the discussion on paraphyly vs monophyly does not really enter into it, that discussion is one of how to word evolutionary relationship in fairly tight academic circles, and has no real impact on understanding of phylogeny (any phylogeny can be expressed perfectly well under bout systems). People wanting to let phylogenetic nomenclature have a prominent place has the whole of the article body to express themselves, the taxobox is reserved for classification (which is really not the same as cladification). Petter Bøckman (talk) 13:00, 24 February 2011 (UTC)
Monophyly isn't the end-all-be all - remember, the whole purpose of taxonomy is to communicate with other scientists, and sometimes the most meaningful groups in the context of a give field are defined by plesiomorphic traits, not synapomorphies. If you want to say something about the ecology or physiology of Sauropsida, you can't - they're too diverse. But you can about Reptilia, because you've excluded that one bothersome outlier clade. Seriously, plenty of scientists use terms like "fish" and "herp", both of which are about as far from monophyly as possible, because the terms are actually useful, especially for physiologists.
Additionally, I think WP runs the risk of stepping into the middle of an ongoing and contentious scientific debate on the topic, and as a result, changing dozens/hundreds of pages every time a new paper comes out. That's why WP:A&R uses the ITIS taxony - it's a single, unifying source that's slow to update, so we don't have to run around changing page names and moving things around every time someone publishes a paper, only to change it back 6 months later when a subsequent paper refutes it.
Most importantly, however, is that WP is not a technical journal - it's an encyclopedia, meant to be used by regular folks. If you drift too far into trying to make everything "cutting edge" while giving no consideration for communicating content to the vast majority of the public who use WP, you wind up with something like WP:Math, where 95% of the pages are completely incomprehensible, even if you just need a refresher, because it's all obscure proofs and notations. At the end of the day, using "Sauropsida" will make WP a less valueable and less useful resource to the vast majority of users.
As much as the "monophyly-only" crowd would love to believe otherwise, there are a variety of valid positions on this topic, both scientifically and within WP, and I for one favor stability and communicative efficacy over "cutting edge".Mokele (talk) 13:15, 24 February 2011 (UTC)
I think it's hard to say which we should use, but I definitely don't agree with some points: The similarities in physiology or appearance, or the use of terms that recognise this, don't mean that monophyly shouldn't be used in classifications.We probably should talk about the ecology and physiology of Sauropsida, whether or not we keep Reptilia in the taxoboxes—it is all the more remarkable for being diverse. Should A&R really use the ITIS? it was never even very complete. I am not convinced that we should be quite as conservative as you suggest, staying put for years even after the best new research, until a new website with a 'complete' taxonomy turns up. —innotata 18:56, 24 February 2011 (UTC)
Just to add an opinion...given that taxonomy is messed up as New York City hit by a hurricane, it's rather confusing. Reptilia is more classic, yet Sauropsida is (technically) a better organization. Personally I prefer Reptilia; like Petter Bøckman said, it's more familiar to the everyday reader. I could go on about this stuff...Crimsonraptor • (Contact me) Dumpster dive if you must 20:52, 24 February 2011 (UTC)
I think WP needs to recognise its role here. The discussion and acceptance of Sauropsida is far from over. It is not as yet accepted, particularly among workers on living species. The publications to date proposing these changes have not been adequately reviewed in the scientific literature. They have not been re-assessed on multiple taxa using multiple methodologies. It is not the role of WP to do this, nor to preempt change by jumping on a bandwagon too early. Personally I am all for major change to reptile nomenclature and have been since I started working as a taxonomist in 1993. However, it is a process, one that is far from complete. The process is still in the scientific literature. The taxobox is a two prong tool, it is a navigation tool and a representation of the accepted nomenclature. We here at WP should follow the most widely accepted nomenclature that has the bulk of the support from the scientific literature. Our role is not to discuss proofs of monophyly that is the role of the scientific journals. Our role is to present material that is encyclopedic, ie taken from the scientific literature, it is not original. Until it is widely accepted, the taxoboxes should remain with the consensus. Faendalimas (talk) 21:08, 24 February 2011 (UTC)
Just an addit, I do not agree with relying solely on ITIS, it is grossly out of date and not equally out of date, some sections are maintained better than others. Turtles for example are at least 20 years out of date on TIS, find and use the best source for your given taxonomic group. Faendalimas (talk) 21:10, 24 February 2011 (UTC)
I agree with several (though not all) of the arguments used here in favor of Reptilia. I find Faendalimas's remarks the most satisfying-- it's good to see that you're not letting the research you agree with bias the representation of the scientific majority. I actually wasn't aware Reptilia was still being used anywhere anymore, but I trust you all know what you're talking about. So...Sapeli, there you have it; this is why we've been using Reptilia. Further questions? Comments? Bob the WikipediaN (talk • contribs) 23:58, 24 February 2011 (UTC)
Faendalimas, is there really any remaining uncertainty about the science, as opposed to philosophical issues? As far as I'm aware, it's uncontroversial that birds fall somewhere within traditional Reptilia—even the few who do not accept that they are dinosaurs place them within Archosauria. The issue, then, is whether paraphyletic taxa have any place in taxonomy, and that is hardly a question of testable science. Ucucha 00:03, 25 February 2011 (UTC)
I dont think there is much, I think most have accepted, as you say, the placement of Aves within this group and other issues for a decade or more, there is also issues with anapsids etc, and your right it is a philosophical argument at most. Just one that needs to be completed and accepted. Cheers, Faendalimas (talk) 04:06, 25 February 2011 (UTC)
I didn't realize there was this much of disagreement over this. The main point I'm after here is that the current classification is incoherent, eg. Avialae is classified to belong in Reptilia, but in Reptilia article it is stated that birds do not belong in it. Currently Wikipedia's taxonomy is confusing and no wonder if only WP:A&R has agreement over how to proceed and the rest does whatever the editor happens to prefer. Above all there should be better agreement over which system to use and maybe make it clearer to the reader too. Personally as a non-expert I find monophyletic groups more useful, but I understand Faendalimas's view too, although I find it quite conservative, even biology textbooks nowadays don't bother with rank-based nomenclature, it's mostly mentioned in the marginal.
Also I disagree with Petter Böckman's rational about layman reader, we can't choose the content of encyclopedia on the basis of what is more appealing for some people. If we want to make taxobox friendlier for the layman, we should start with hiding all those "(unranked)" bits. --Sapeli (talk) 09:51, 25 February 2011 (UTC)
There's a couple of points I think we need to square away. First off, there is no real argument over phylogeny here. We all know where birds and mammals came from. The topography of the tree is fairly well established. Secondly, whether birds are dinosaurs or evolved from dinosaurs is entirely inconsequential. Bout statements express exactly the same phylogenetic topography. Thirdly, this debate has nothing to do with what we put into the Wikipedia as such. Indeed, we have room for bout views, see Vertebrata for a good example of an informative article explaining bout systems. Neither is this a philosophical debate over what system is "right" and what is "wrong". Bout systems are systems, with their own good and bad points. As systems they are bout artificial, there is nothing more inherently "right" about one or the other. This debate has nothing to do with these points, it is all about the role of the taxobox.
Im my view, the taxobox is a tool, and it's greatest virtue is utility. Non-hierarchical phylogenetic nomenclature may express the nuances of the phylogenetic topography better, but it is a very bad way of keeping overview. The Linnaean Hierarchy is nothing but an aid to the memory in keeping track of whom is whom. The classical systematic units (Like Reptilia) too is defined so as to be easy to keep track of. It is classification in the strict sense. Phylogenetic nomenclature is not classification, it is cladification and has a different use (details at the cost of overview). As far as I can understand, we are best served by having classic classification in the taxobox, and keep cladograms and phyologenetic discussions to the article texts.
Sapeli mentioned Avialae, and this is the result you get when mixing the two systems. Avialae is a purely phylogenetic unit, and from a purely phyleogenetic POW, birds are reptiles with feathers and wings. The problem is that we have two conflicting systems that does not mix well. I think the taxobox makes as good a show as it can of this strange little unit, though I can sympathize with Sapeli's wish for Sauropsida in this case.
Sapeli also mentioned that Faendalimas' argumens are very conservative. They are indeed, but then again the utility of Linnaean systematics (as opposed to phylogenetic nomenclature) is utility, and utility depend on stability. Taxonomic units that changes content every other year as new discoveries are made or preferred trend in cladograms changes are of no use as a classification tool. Yes, Reptilia is very much a paraphyletic unit, but the content of Reptilia has largely been stable since the basic phylogeny and physiology was mapped out by Huxley and Haeckel in the 1860's and -70's (Benton's move to make Synapsida a separate class nothwithstanding). By contrast, there are a number conflicting definitions of Sauropsida about (stem, node and crown definitions, anchored in a variety of taxa), a couple of whom even argue for dropping Sauropsida as a name and replace it with Reptilia. For the moment all these are equally valid, as PhyloCode isn't yet implemented, if it ever will be. As I hope is evident, Sauropsida is not useful as a unit of classification, It is useful as a tool for discussing phylogeny, but discussing phylogeny goes in the article text, not in the taxobox. Petter Bøckman (talk) 11:59, 25 February 2011 (UTC)
Strongly seconded about the uselessness of constantly changing taxa. I've actually had to resort to common names for communication with other scientists on several occasions specifically because the scientific names had changed so many times and so often that they'd become completely useless as a mean of communication.
Which brings me to the most important point: taxonomy is not real. There is no such thing as an order, a class, etc. Hell, the definition of species is a huge controversy. Taxaonomy is nothing more than a labeling system designed to make the diversity of nature easy to communicate, and as such, utility is the primary argument for or against any system. It is an entirely arbitrary human creation for the convenience of human minds. I strongly feel that paraphyletic taxa are *useful* in order to communicate with other scientists, and will continue to be used, even if informally. A system which is "phylogenetically correct" but cumbersome, unstable, and of inferior value for communication should be discarded - communication is the whole point.
Lastly, since there is currently no scientific consensus on "Sauropsida" vs "Reptilia", however much some may wish it, then by default the current system remains in place, and is therefor 100% accurate. Attempting to change it would be WP:OR - the purpose of WP is to show the current state of knowledge, not what we think it will be in 10 years or what we think is better than the current system. Once the debate is resolved, only then do we make the change. Mokele (talk) 12:32, 25 February 2011 (UTC)
I think that trying to shoehorn cladistic units into the Linnaean system is a problem. I'm just an interested non-specialist, and I find cladistics fascinating, but I think we need to be careful to avoid putting confusing mixes of grades and clades in taxoboxes. The article text offers ample opportunity to explain a taxon's place in different systems. Why can we not have two navigation systems for taxons, one based on the Linnaean system and the other on cladistics? -- Donald Albury 13:24, 25 February 2011 (UTC)
Actually we can. If you look at the taxobox for birds, if you click on the little (and somewhat cryptically labelled) "e" besides the words "Scientific classification", you'll get this page [[4]]. It gives the full cladistic listing. If Bob the Wikipedian would agree to give it some mind, we could potentially use this system to allow for a switch between classical and full cladistic taxonomy in the taxoboxes by the clicking on it. Petter Bøckman (talk) 14:37, 25 February 2011 (UTC)
Just another comment here if I may. But first I need to say where I am coming from so there is no confusion. First up I am a Linneaen Taxonomist, I do not agree with Phylogenetic Nomenclature and my reasons are not relevant here, second some of what I say here is purely prediction, not based on any published work and although happy for it to be used on a talk page, it is not for use anywhere else. Ok first up this is an issue between LN and PN systems. Which one is right or should be used is not relevant, reality though we currently recognise and use the LN system of Nomenclature, PN is only a proposal and has not been implemented. What will happen in the future there I do not know. As such we as WP's should be using the implemented system until that changes. Second and here is my prediction, the name Reptilia has been in use for 2 centuries, everyone on the planet has some concept of what it means, ask any 10 year old, try it. There idea may not be accurate but it is enough for most of them. If the name Sauropsida comes in any way in a position to replace Reptilia, I suspect a challenge to the rules will be made in favour of Reptilia. People just cannot stomach the loss of the name or its meaning, even the PN's specialists acknowledge that. Same has happened with Birds. I suggest we follow the wide usage here, not the conjecture of a very few that is only confusing. Faendalimas (talk) 22:44, 25 February 2011 (UTC)
Re Petter-- I value your faith in what I can do; unfortunately, that would tax the server significantly more than what it's already doing (we've added several seconds' server-end calculations by automating the taxobox). Not to mention that it's sometimes impossible to tell a phylo taxon from a Linnaean taxon-- and even then, how does one decide at what point a taxon becomes Linnaean? I believe we're in an age where new taxa are always described phylogenetically.
Re everyone-- Taxonomy is useless to me if it never gets corrected. In fact, the automatic taxobox was designed to make revisions (including this one) much simpler, although obviously many, such as this one, may be so controversial they may not ever happen.
Based on what's been said so far, it seems to me that Reptilia is still being commonly used in science and that Sauropsida has not been adopted by a majority of herpetologists yet. That having been said, it would appear that the debate must be resolved to a greater degree in the world of academe before we need to worry about it here.
Also-- the dilemma mentioned regarding Avialae is actually the solution agreed upon by the bird WikiProject folks per a discussion they were invited to participate in. I don't recall any objections to the current implementation from the bird folks.
So, seeing as how there's neither consensus in academe nor at Wikipedia, it would seem there's no ground for moving away from Reptilia here. Bob the WikipediaN (talk • contribs) 00:00, 26 February 2011 (UTC)

Maybe I am a bit late, but I think we have to start with some clarification. Phylogenetics is about relatedness. Taxonomy is about classification. Phylogenetics does not say ANYTHING about classification, it is a tool that shows us the relatedness between taxa, based on which taxonomists make subjective decisions to call specific groups of taxa something. The current trend towards blindly giving nodes in a tree names in order to enforce strict hierarchical monophyly is confusing and often devoid of a proper weighing of the total evidence. Having said that, Reptilia as a paraphyletic taxon is most likely to stay. Not just because it was how it was done, but because it makes the most sense. Both birds and mammals originated from reptilia, but evolution in those branches took them rapidly into a different direction. So, classifying them as a separate class makes perfect sense. Under the soon to be released phylocode, it would be perfectly accaptable as well. What we have now is a small group of taxonomists who try to force phylogenetic relationships onto the traditional method of classification, and that is where things go wrong. Anyway, I suggest we use traditional way of classification unless it becomes generally acceptable top do it different. Paraphyly or not. -- Kim van der Linde at venus 02:07, 26 February 2011 (UTC)

Kim: You mean PhyloCode is going to accept grades? Neat! Not sure I believe you until I see that coming from one of the PhyloCoders though. It seems to go against their very grain.
Bob: I really appreciated what you have done with the automatic taxoboxes. I fully understand if what I proposed is not doable. The skip-templates goes a long way towards ironing out the differences between the systems.
I've been having this discussion about Reptilia and to some extent Amphibia for some years now. To me, it seems dinosaur palaeontology is the stronghold of the phyolgenetic taxonomists, and I guess most of our palaeo-contributors (professionals and non-professionals) have come here via their dinosaur interests. I think that goes a long way towards explaining the apparent dominance of phylogenetic taxonomy (particularly the use of Sauropsida) you see among Wikipedia contributors. There are a few other areas where phyolgenetic nomenclature is strong, notably in the fields of early mammals (mammaliformes) and labyrinthodonts and in domain-level studies, though the hegemony in those areas aren't as strong as in dinosaur studies. If you go to zoology, Linnaean nomenclature is really dominant. The cladistic method is accepted and in use, just not for making classifications.
While my impression is that dinosaur studies are dominated by phyolgenetic taxonomists, there are exceptions. I work as an educator at the Natural History Museum at the University of Oslo, where Jørn Hurum is heading the vertebrate palaeontology department. I just went to listen to his students giving outlines of their work, and they actually used the Linnaean "class Reptilia", despite working in a phylogentically dominated field of big, extinct reptiles.
Working as an educator, I mostly deal with school classes. Of the many hundred classes I have toured over the last few years, most are able to identify and name Reptilia, but I have never ever heard anyone use the term "sauropsids". This may be a question of English versus Norwegian language, but to me the term appears to be restricted in use to a rather tight circle of academics. If Wikipedia is going to be a general encyclopaedia and not a specialist encyclopaedia for a secluded few, we would be doing it a disservice to switch to Sauropsida. Petter Bøckman (talk) 02:59, 26 February 2011 (UTC)
Your edit summary inquires "How common is Sauropsida?"-- I don't actually say "sauropsidan" myself ever, but mostly because I'm only referring to the reptilian members of the class. However, I did note that a textbook I used last year used replaced both Reptilia and Aves with Sauropsida (much to my surprise-- typically a class within a class means you disregard the parent class). And yes, you've got me pinned; I'm a paleo-enthusiast. Bob the WikipediaN (talk • contribs) 03:56, 26 February 2011 (UTC) Portion of comment retracted at 18:58, 27 February 2011 (UTC) by Bob the WikipediaN (talk • contribs)
Yeah, got one of those myself. Typically an "Atlas of Dinosaurs and other Prehistoric creatures". It's a bit older, so it has parareptilia and Eureptilia, but the idea is the same I guess. The only textbooks I've seen Sauropsida in are Benton's and the typical big, glossy dinosaur picture books. Actually, I'm just a palaeo-enthusiast myself, by education I'm a zoologist. I'm just lucky to work in a place where I can use bout my education and my side interests! Petter Bøckman (talk) 08:09, 26 February 2011 (UTC)
It was actually a book on zoology written by an ornithologist, which was why I was absolutely shocked he classified birds as Sauropsida. Bob the WikipediaN (talk • contribs) 19:39, 26 February 2011 (UTC) Comment retracted at 18:58, 27 February 2011 (UTC) by Bob the WikipediaN (talk • contribs)
No, not at all. It will be the same names as far as I can tell, and so we have the Linnean taxonomic names with grades that you can order independently ignoring the Linnean grade in phylocode. Over time, when the traditonalists keep changing names the match between the two will degrade but that will take some time. Drosophila comes in mid of a fun genus for the future. -- Kim van der Linde at venus 20:04, 26 February 2011 (UTC)

Taxa in disguise

While this long conversation is raging, I though I might just mention that I created a page Taxa in disguise (taxa which are phylogenetically nested in another but taxonomically they are not), with some bacterial examples as to avoid the reader thinking that the instance they meet one is the only one, to avoid repetition and increase interlinking. However, I have NO idea about Eukaryotes so if anyone has any paraphyletic genus/species they want to add please do! (thanks) --Squidonius (talk) 00:36, 27 February 2011 (UTC)
Whoops! I made a mistake above (and retracted the comments)-- I just now checked to make sure I hadn't misrepresented what I said yesterday, and it turns out I was very mistaken-- I mixed up two books and a bit of wording. The authors of the book included a marine biologist, a tropical biologist, and an invertebratologist, and they placed Aves as a subclass of Reptilia. The book I have by an ornithologist doesn't even mention classification at all. So suddenly that point I was putting forth vanishes in a puff of irrelevancy.
Also-- Squidonius, that sounds like fun! I'm aware of a few examples; I'll go see if you've added those already. Bob the WikipediaN (talk • contribs) 18:58, 27 February 2011 (UTC)
I am very tempted to nominate "taxa in disguise" for deletion. The term does not occur at all in scholarship as far as I can tell (zero Google Books or Scholar hits) and appears to be nothing more than a fancy term for either "paraphyletic taxon" or "taxon that should be included in a paraphyletic taxon in order to make that paraphyletic taxon monophyletic". Ucucha 19:14, 27 February 2011 (UTC)
If this term isn't used at all in the literature then we can't have an article on it. Simple as that. Incidentally, it should be "a taxon in disguise" - taxa is plural. mgiganteus1 (talk) 19:24, 27 February 2011 (UTC)
If you gents would care to have a look at the references, you'll see the very term used as an article title. Petter Bøckman (talk) 19:39, 27 February 2011 (UTC)
And in the title only. (Another example of such a usage is doi:10.1099/mic.0.27096-0.) If someone puts a nice phrase in an article title to make it sound better, that does not mean we should have an article on said phrase. Ucucha 19:47, 27 February 2011 (UTC)
Well, apparently the term is in use (in the title of one article, in the text of another), so an article on it seems OK to me. I'd agree with you on limiting it to bacteriology though, I haven't seen the expression used elsewhere, though in principle it can appear everywhere evolutionary taxonomy is in use. Petter Bøckman (talk) 20:14, 27 February 2011 (UTC)
Then is it notable, and if it is, would this, rather than something that doesn't sound as nice and untechnical, be the best name? —innotata 02:33, 28 February 2011 (UTC)
Thank you all for the unexpected enthusiasm (which is great), I chose the name "taxa in disguise" instead of "List of paraphyletic linnean taxa" as my aim was to create a gap-bridging hub-like page (but not an exhaustive list) to interlink various examples of paraphyletic taxa as to not confuse non-expert readers by slowly break in the technical jargon and, as mentioned, to avoid reader thinking that it is something unique that the members of the Shigella genus are actually strains of the Escherichia coli species and so forth. The point of the plural is a good one, as I suppose the article is a about the concept (so singular) not the group (plural) so will change to taxon in disguise. --Squidonius (talk) 01:55, 28 February 2011 (UTC)
We could call it...paraphyly...Bob the WikipediaN (talk • contribs) 03:07, 28 February 2011 (UTC)
While I do endorse accessibility (see above), I have 3 objections - 1) the term is far, far less widely used than 'paraphyletic taxa', 2) having a page called "Paraphyletic" or "paraphyletic taxon/taxa" would probably be *more* helpful, as it would be the first stop of people who've encountered the word and don't know what it means (I fully admit I use WP for that purpose quite frequently), and 3) it sounds like a biology-themed spin-off or parody of Transformers. Seriously, every time I see a new comment in this thread, the old Transformers theme from my childhood goes through my head. And while I give 'mad props' to the authors of those papers for managing to include such a geeky reference in their papers, I'm not sure it's used enough to warrant naming the page that. Mokele (talk) 03:14, 28 February 2011 (UTC)

Moved to paraphyletic taxon, for now (Note that Escherichia coli in the example above is a polyphyletic taxon and so is the B. cereus group, but that is being pedantic). However, in the process I saw paraphyly needs some TLC (it has a split into life science and linguistics, both uses of cladistics, ignores that one can have say gene trees and that a paraphyletic group can be anything not only a linnean taxon, such as thermophiles (=polyphyletic) or herbivorous animals, etc). Is there anything like List of phylogenetic terms in a similar fashion to Glossary_of_gene_expression_terms? --Squidonius (talk) 06:12, 28 February 2011 (UTC)

It's kind of an awkward situation. "Taxon in disguise" is about the groups that are removed from an evolutionary grade, while paraphyletic taxa is what remains when the "in disguise" taxa are removed. The two can certainly be treated under the same heading, but they are really at the opposite ends of the same phenomenon. We already have the articles paraphyly and evolutionary grade, if feel changing the focus from the excluded groups to the remain grade is adding yet another article to the rather well covered field of paraphyly. I suggest stripping the article down to it's bacterial content (since the two sources for the expression really is from bacteriology) and keep it as an "in disguise" article, and using the other content to spruce up the two other articles. Petter Bøckman (talk) 08:12, 28 February 2011 (UTC)

WP Viruses

Just a quick note to say, I am reviving WikiProject Viruses, and any help would be appreciated. Thomas888b (Say Hi) 19:58, 24 February 2011 (UTC)

Absurd example of phylogenetic classification in a Linean Context

Take Zaprionus indianus. Try this to get straight in a taxobox:

Kingdom: Animalia
Phylum: Arthropoda
Class: Insecta
Order: Diptera
Family: Drosophilidae
Tribe: Drosophilini
Subtribe: Drosophilina
Infratribe: Drosophiliti
Genus: Drosophila
Subgenus: Drosophila
Genus: Zaprionus
Subgenus: Zaprionus
Species group: vittiger
Species complex: indianus
Species: Zaprionus indianus

-- Kim van der Linde at venus 20:43, 26 February 2011 (UTC)

You omitted quite a few ranks. See the page for Drosophilidae on Wikispecies. They use a collapsible box at around the family level for taxa. --EncycloPetey (talk) 20:52, 26 February 2011 (UTC)
I believe the point she's trying to drive home is the genus>subgenus>genus>subgenus bit, which I agree is fairly awkward, and it reflects (I'm guessing) that Zaprionus diverged from Drosophila (Drosophila). Still, I've never seen (even in phylogenetic taxonomy) a genus within a subgenus. This sort of layering is what a cladistic tree is designed for, not a taxonomy. If we included every genus, then every taxonomy would look like this-- only on steroids with hundreds and thousands of genera. Is this the currently accepted taxonomy, and if so, where? Bob the WikipediaN (talk • contribs) 21:02, 26 February 2011 (UTC)
This is the kind of thing that makes systematicians (is there such a word?) cringe. I'd run this in a classical fashion, anchoring the genus Zaprionus directly in the family Drosophilidae, with a note that the genus has evolved from Drosophila. It's really the same as all us higher animals having evolved from the catenulid flatworms. This all brings us down to the basic question: Do "grades" exists in nature? The fundamental cladistic assumption (and thus the underlying assumption of phylogenetic nomenclature) is that each time a new species evolve, the ancestor species go extinct, so that you are left with two new species (the "old" one under a new name and the new one). My college, who have worked on speciation in caddisflies assure me that new species evolve easily, frequently leaving the more wide-ranging species as evolutionary grades relative to a handful of younger species.
For an absurd example, take humans. Imagine an Amazonian tribe developing a reproductive barrier toward the neighbouring tribes, not an unthinkable situation. By Mayr's species defintion, they'd be a new species ("Homo amazonica" for instance). If we are to follow phylogenetic nomenclature, Homo sapiens would go extinct, and all the side-branches leading up to the tribe would have to be designated as separate species. Quite a few of us would wake up to find we had married someone from another species, our children hybrids. Phylogenetic nomenclature is a model too, with it's own inconsistencies and limitations. Petter Bøckman (talk) 08:48, 27 February 2011 (UTC)
And just think what happens if you add all the higher level ranks which McKenna & Bell invented to squeeze a cladogram of the mammals into a rank-based classification (see Mammal#McKenna/Bell classification) – you'd probably need even more for insects. As Bob notes, supplying this level of detail is what a cladogram is for. A smallish number of key ranks are all that is needed for orientation or navigation; once you've reached these ranks a cladogram can provide detailed information about the phylogeny of that taxon. (However, the 'key ranks' are not the same across the TOL and usually not the same for extinct and extant groups.) Peter coxhead (talk) 11:27, 27 February 2011 (UTC)
What I tried to do here is make clear the absurdness classification can lead to, especially of we try to force phylogenetic thinking onto the Linnaen system. Because the example is what the phylogenetic classification would look like using the grade of the Linenan taxonomy. Some of the leading taxonomists in the Drosophilidae have effectively given up on Linnean taxonomy because changing the mess called Drosophila is going to piss of to many people (I agree that I am going to piss of a lot of people, but the experts of the ICZN thinks it is not a big deal). They advocate that we just accept this mess as is and do not try to revise it. The situation would may be acceptable if we had a clear example like bird evolving rapidly away from Reptiles and having clear traits that separate them, but that is not the case in this group. To the contrary, various genera are far more similar to for example species groups or radiations within the genus.
On another note, Petter Bøckman's example about humans misses one aspect, and that is that the group excluding "Homo amazonica" would get a new name as well, for example "Homo nerdius" or so (ducks and runs)....
Anyway, my point of this was to get the point across that Reptilia and Aves and Mamalia are perfect as they are and we should not try to force phylogenetic classification into those articles. Just as we are not going to do this with Zaprionus. -- Kim van der Linde at venus 03:07, 28 February 2011 (UTC)
I can see why ICZN want to stay out of this whole affair. I would personally sink the whole lot back into Drosophila and go for allowing superspecies epithets for the sunken genera, but then I'm not on the ICZN board. What a bloody mess!
As for my human example, not only would the immediate neighbours need a new species name, but the sister group of all Amazonian indians would need a new species name, and so would the sister group to all indians, and that would leave out all non-mongol humans which would also need a new name, and I shudder to think how the African population is to be divided up. So we would end up with (let's say) three or four African human species, Oceanians as a separate species, Caucasians in the wider sense as a separate species, a Mongol human species, an American native species, a South American native species, a jungle species and Homo amazonica itself, around 10 species, and that is a conservative estimate. I leave it to you to decide which one is Homo nerdius ;-) Seeing how some of my more spitting-happy colleagues go hunting for cryptic species to get their name in the "great book", I'm not exaggerating, it really is that ridiculous. My basal point though is that grades exist in nature. Petter Bøckman (talk) 08:39, 28 February 2011 (UTC)
Whow, you would opt for 100+ secondary homonyms, and introducing two more grades between genus and species? Zaprionus has to be sunk to the complete unspecified "radiation" or species group as it is within the subgenus Drosophila. To make the problem a bit more palatable, we can make the two subgenera species groups, the species groups we can make species subgroups, the species subgroups we can male species complexes and the species complex we make super species? 2500 species in a genus that is 60 million years old, has a lot of diversity and lacks a single synapomorphy. Nah. -- Kim van der Linde at venus 10:47, 28 February 2011 (UTC)
Ugh! Very happy I'm not in a position where I'm expected to make sense of that mess! I guess the current solution is the better one after all. Petter Bøckman (talk) 11:05, 28 February 2011 (UTC)
LOL, funny, this is the reaction that I get frequently once people start to see the mess. I think we just have to bite the bullet once and change Drosophila melanogaster to Sophophora melanogaster and after that, the rest is just normal uncontroversial splits and new names. BTW< the current genus does not have a synapomorphy either. -- Kim van der Linde at venus 11:20, 28 February 2011 (UTC)

Homo

If I recall correctly (and I definitely mean no racial slurs by it), recent research has pointed to a large percentage of living Homo sapiens as being a hybrid between H. sapiens and H. neanderthalensis-- so if the research continues to highlight this, we may very well see some revisions in the future of human taxonomy. Bob the WikipediaN (talk • contribs) 15:38, 28 February 2011 (UTC)
I'd guess it will extend sapiens backwards a bit, to include what is now "Archaic Homo". That was actually the taxonomy back when I was a lad. I will not be surprised if they find a bit more hybridisation. I think I've heard rumours of another "ancient" gene, this time from Asia, indicating H. erectus as the culprit. Petter Bøckman (talk) 18:23, 28 February 2011 (UTC)

Intreresting discussion! Do go on. Chrisrus (talk) 18:51, 28 February 2011 (UTC)

Alright then, just bear in mind that Wikipedia takes no action over this until the scientific community turns it mainstream.
So...what you're proposing, Petter, is that the revision might end up as something like this, with H.s. sapiens getting divided into infraspecies:
  • Homo sapiens sapiens caucus
  • Homo sapiens sapiens niger
  • Homo sapiens sapiens neanderthalensis
Have I interpreted your comment correctly? Bob the WikipediaN (talk • contribs) 22:15, 28 February 2011 (UTC)
  • If I've interpreted the evidence correctly, it's introgression; it's not as if modern humans were intermediate between African H. sapiens and Neandertals.
  • Coming from a background of flowering plant taxonomy, I'm always amused by the surprise occasioned by hybridization between species of tetrapods. If botanists took hybridization as de facto evidence of conspecificity, there would be a much smaller number of species, and they would be hyper-variable.--Curtis Clark (talk) 06:08, 1 March 2011 (UTC)
Bob: Nah, with the amount of crossing back and forth below subspecies level, I don't think anyone would dream of imposing taxonomy to that level anymore. I was rather thinking along the line of Homo sapiens sapiens (moderns), H. s. neanderthalensis (neanderthals), H. s. heidelbergensis etc, combining at least all non-erectus humans into one species. There's this one hyper robust finger bone from Altai that seems to combine Dali traits with possibly neanderthal nuclear DNA and mitochondrial DNA so divergent it must be Homo erectus, indicating hybridization may have happened in other branches of the human tree too (and why not, it's not like humans don't have sex a lot). (ref: [5] and [6]) The big problem here is that species boundaries vary form the abrupt to the very gradual (see [7] for a split that took several million years). Mixed in is probably unequal speciation rates in different lineages and the eternal problem of chronopspecies. I think it will be a decade or so before science comes around to the fact that human speciation appears to be messy and not the clear-cut Y-branching one often envisions.
Curtis: Indeed! We only seem to have picked up a selected few genes, the rest of the mix appears to have been bred out. The earliest Cro-Magnons looks kind of funny, I guess they still bore some of the more obvious archaic traits that we have later lost. Plants seem to be more prone to hybridization than animals though. I guess lower metabolic rate means less "fine mechanics" in the cell machinery can go wrong when mixing genes. My colleague with the caddisflies ended up using the botanical "superspecies" approach to speciation in his master thesis. Petter Bøckman (talk) 08:06, 1 March 2011 (UTC)
Animals are selective; this prevents hybridization and quite often either inbreeding or outbreeding as well. Plants (so far as I'm aware) don't choose whose pollen they get and just take whatever comes (an overgeneralization with obvious exceptions, of course). Bob the WikipediaN (talk • contribs) 08:18, 1 March 2011 (UTC)
That would only be a factor in animals with internal fertilization. Lots of marine animals just squirts things into the sea. Hybridization appears to be common in soft corrals (an aquarium enthusiast has told me), while almost unheard of in bivalves, yet bout spawn indiscriminately. I suspect there are several mechanisms at work here. Petter Bøckman (talk) 10:41, 1 March 2011 (UTC)
Annnnd that answers my question of why Curtis said "tetrapods"! Bob the WikipediaN (talk • contribs) 03:45, 2 March 2011 (UTC)
I might well have said amniotes for all that. Plants have other ways of dealing with hybridization, but the best and most effective mechanisms are in annual plants, where the cost of hybridization is much higher. Homo is politicized, but the general idea of combining species that have interbred doesn't serve systematics well in other organisms. Over most of their range in time and space, H. sapiens, H. neanderthalensis, and H. heidelbergensis are morphologically distinct. If one (a) lumps them, and (b) ignores subspecies, a lot of valuable and interesting biology is sidelined.--Curtis Clark (talk) 05:47, 2 March 2011 (UTC)
The current trend of lumping H. heidelbergensis, neanderthalensis, the Dali skull etc together informally as "Archaic Homo sapiens" seems to me to be a decent solution, and possibly as good as we can get it given the limitation of nomenclature to deal with species complexes. The groups you mention were morphologically distinct, but there's no denying the various groups of modern humans too (at least in the pre-industrial world) were very distinct, and yet we are one species as modern communication has amply proven. With the political aspects you mention on top, I don't think we'll ever see a good an honest classification. Whenever I need to explain this, I compare with the genus Canis: All or almost all species can easily interbreed, they just won't, unless domestic dogs enter the picture. Social species anyone? Petter Bøckman (talk) 08:07, 2 March 2011 (UTC)
And this is what happens when we mix politics with science. Bob the WikipediaN (talk • contribs) 06:37, 3 March 2011 (UTC)
Just a comment in regards to hybrids. During my work on Turtles I had to describe a new species called Chelodina canni the interesting issue with this species was the presence of a hybrid zone with another closely related species. This of course meant that because of a lot of peoples views on hybrids, at least in tetrapods, I had to explain the hybrid issue. Hence we studied it closely. In the end I felt that the capacity for two species to hybridise was more about their history as species than how closely they were related. Think of it in evolutionary terms, in particular micro-evolution. How do species evolve, well a number of ways. If they evolve in sympatry then there is evolutionary pressure to prevent hybridisation or they will not separate as species. They will continue to backcross preventing distinction. So the incapacity for two species to hybridise is when species split over time when they exist in the same place. Conversely, if they evolve separately, ie in allopatry, say after a vicariance event, there is no evolutionary pressure to ensure the gene pools are protected. Hence they will not become genetically incompatible by natural selection. This means if they come back together they may still be able to hybridise. Now apply that to humans, Homo sapiens and Homo neanderthalensis evolved in allopatry, they came back together in the western European area after they were separate species, so they could hybridise, so what. Their history is one of allopatry, there was no selection pressure to protect the gene pools of each species. In case anyone wonders there are species of vertebrates that don't even belong to the same genus that can and do hybridise, eg Emydura subglobosa and Chelodina longicollis can produce viable hybrids. Cheers Faendalimas (talk) 01:33, 19 March 2011 (UTC)
Very interesting point! Do you have any citeable sourses for speciation mechanisms and sympatry/allopatry? I'd really like to put this in the hybrid article. The neanderthal/modern hybridization event likely too place in the Middle East BTW. Petter Bøckman (talk) 09:11, 19 March 2011 (UTC)

Worms

Anybody with any knowledge of worms is invited to contribute to this discussion about the nervous system. --Anthonyhcole (talk) 16:21, 23 March 2011 (UTC)

Citing a page of an online database reported in a paper

For Prokaryotes there is a really good resource called LPSN, which is an online database, which was reported in a paper back in 1997. The website is:

Euzéby, J.P. "List of Prokaryotic names with Standing in Nomenclature". Retrieved 16 March 2011. {{cite web}}: Cite has empty unknown parameter: |1= (help)

while the paper is

Euzéby, J.P. (1997). "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet". Int J Syst Bacteriol. 47 (2): 590–2. ISSN 0020-7713. PMID 9103655..

If I were writing a paper I'd just reference the paper, but here I would like to direct the reader to the specific page, there may be two links in the same article and I am thinking of using this for many articles (=manual or automated).

Pseudomonas entry in LPSN [Euzéby, J.P. (1997). "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet". Int J Syst Bacteriol. 47 (2): 590–2. ISSN 0020-7713. PMID 9103655.]

So I was hoping to see how other editors would reference it... --Squidonius (talk) 07:49, 30 March 2011 (UTC)

Typically, when the source is taken from another source, you cite both. It's fairly simple to do, just do two {{cite}}s in a row like so. Since the author is the same, I left out the author when citing the website.

Euzéby, J.P. (1997). "List of bacterial names with standing in nomenclature: a folder available on the Internet". Int J Syst Bacteriol. 47 (2): 590–2. ISSN 0020-7713. PMID 9103655."List of prokaryotic names with standing in nomenclature LPSN". Retrieved 16 March 2011.

Bob the WikipediaN (talk • contribs) 15:20, 30 March 2011 (UTC)

Why would we cite the paper at all? The database is updated regularly (as far as I could tell from a quick browse of things like [8]) and the paper is just a three page description of the database as it existed in 1997. I don't see how "the source is taken from another source" would apply to this situation. Kingdon (talk) 01:14, 31 March 2011 (UTC)
It is simply a question of formalities: if I were to write a peer reviewed paper I'd cite the paper (as it is peer reviewed etc) —despite never having actually read it. It is not at all a big problem that it is cited in a different way in each page, but it is easily fixed. --Squidonius (talk) 21:12, 1 April 2011 (UTC)
Update — I gave template making a go...
classification of Cyanobacteria in LPSN; Parte, Aidan C.; Sardà Carbasse, Joaquim; Meier-Kolthoff, Jan P.; Reimer, Lorenz C.; Göker, Markus (1 November 2020). "List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ". International Journal of Systematic and Evolutionary Microbiology. 70 (11): 5607–5612. doi:10.1099/ijsem.0.004332. --Squidonius (talk) 23:26, 1 April 2011 (UTC)

Looking for a fulltext again

The following discussion is closed. Please do not modify it. Subsequent comments should be made in a new section. A summary of the conclusions reached follows.
received with thanks. Casliber (talk · contribs) 12:31, 22 April 2011 (UTC)

I am looking for this one which I can't get :( All help appreciated :) Casliber (talk · contribs) 22:10, 2 April 2011 (UTC)

On its way (well, almost). Ucucha 22:13, 2 April 2011 (UTC)
The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

Taxobox maintenance

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Noombot, owned by Noommos, will be performing a series of approximately 21,661 edits in order to clean up a syntactical error which causes a minor inconvenience at the implementation level of the {{taxobox}}. No visible change will take place in these articles; the series of edits has been carefully planned such that all the articles using the mis-sequenced parameters will retain the exact same output following the revisions. The advantage to these edits is that a syntactical error in the taxobox code concerning the sequence of two parameters can be fixed once these 21,661 edits are complete.

The bot is being programmed to replace the parameters |unranked_familia= and |unranked_familia_authority= with the parameters |unranked_superfamilia= and |unranked_superfamilia_authority=, respectively. Once this is complete, the |unranked_familia= parameter will be moved beneath the |superfamilia= in the {{taxobox/core}}, as it intuitively ought to be, making subsequent taxoboxes more intuitive to for editors to implement.

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The bot will also be correcting the taxoboxes of somewhere between 6K and 18K butterflies, moths, and skippers as described at WT:LEPID#RfC. Bob the WikipediaN (talk • contribs) 19:22, 23 April 2011 (UTC)

Disambiguation opinions

Hi. I'd be grateful if editors which an interest in disambiguation could take a look at Tristis and let me know their thoughts on its talk page. Thanks SP-KP (talk) 10:11, 29 April 2011 (UTC)

Kingdom Protista

In the past few weeks, User:J.H.McDonnell has been changing the taxoboxes of existing articles to Kingdom Protista[9][10][11][12] as well as creating new ones using this classification. My understanding was that we had stopped using Kingdom Prostista as it is effectively a wastebin taxon of evolutionarily disparate lineages. Thoughts? mgiganteus1 (talk) 22:37, 1 May 2011 (UTC)

I hsve noticed a couple of these changes but I do not know enough about the taxonomy to comment. I was concerned by the heavy usages of the 1988(?) paper over the new ones as the reason to us Protista. Have you asked him his reason for not using newer references?--Kevmin § 01:44, 2 May 2011 (UTC)
Protista is indeed a wastebin taxon, and has not been used in any peer-reviewed recently published classification schemes for the Eukaryotes. The edits under scrutiny also make claims about the ranks of some taxa (such as Foraminifera) that are not supportable by any mainstream sources I've ever seen. I suspect he's following the "Systema Naturae 2000" classification, which is a classification of all matter (not just life). --EncycloPetey (talk) 02:03, 2 May 2011 (UTC)
A few people convert Domain Bacteria to kingdom Bacteria or Monera. Luckly the taxobox synthax for kindom is regnum so the edits are hidden, I do not know if that was done on purpose but it is brilliant. --Squidonius (talk) 07:47, 2 May 2011 (UTC)
Using Protista as a kingdom gives a very orderly systematics, I guess that is his reason. As we all know, ranks as such are subjective, and partly a matter of taste. Besides, Protista is not a wastebasket taxon, it is an evolutionary grade, and has been understood as such from the beginning. Whether one wish to use it is a question of what aim one has with the classification. If the aim is to closely follow phylogenetic lines, then Protista is out of the question, if the aim is to have systematic overview, the Protista is possibly the best choice. Petter Bøckman (talk) 07:55, 2 May 2011 (UTC)
The problem is that there is no consensus classification of kingdoms at present. Several different classifications are in use in Wikipedia articles. Although I think there are good arguments not to use Protista as a kingdom, in the absence of a clearly agreed system, either from a consensus in the academic community or from within the Tree of Life Project, any editor seems free to use their own judgement. However, the system chosen should be sourced. Peter coxhead (talk) 13:33, 2 May 2011 (UTC)
We encountered this in the early implementation of the automatic taxobox, and Kleopatra had promised to do some research on this and get back with us. I seem to have scared her off, though. Any other qualified Wikipedians who would be willing to do some research on current taxonomies and report them here? Bob the WikipediaN (talk • contribs) 14:59, 2 May 2011 (UTC)
I make no claim to great expertise, but I did overhaul the Kingdom (biology) page last year and I try to keep up with research on 'deep phylogeny'. In summary, the situation appears to be (a) most researchers aren't interested in Linnean classification (b) even if they were, there is no consensus on deep phylogeny.
  • There was a classification in 2005, which seems to have been used as a basis for kingdoms, but the paper is explicit that its groups are not formal taxonomic ranks – it's a clade-based system. Furthermore, research post-2005 does not support the groups in the 2005 system. If you go to Eukaryote#Expanded_Chromalveolata and look at the two cladograms there and the one in the section below, all based on 2009 research, you'll see that it's not at all clear what the groups are within the eukaryotes, so there's no way of producing a kingdom-level classification consistent with the current state of research.
  • Only Cavalier-Smith seems interested in Linnean classification. His is the only recent attempt at a Linnean taxonomy at the domain/kingdom level I could find: see Kingdom_(biology)#Cavalier-Smith's_six_kingdoms. However, Cavalier-Smith doesn't believe in the importance of the Archaea-Eubacteria split, which he dates long after everyone else does, and there is no consensus in support of his views.
It's possible that there will never be a consensus Linnean system consistent with the phylogenetic evidence, since molecular phylogenetics researchers seem to be strongly oriented towards cladistics. I very much hope I'm wrong about this! Peter coxhead (talk) 16:30, 2 May 2011 (UTC)
For Bacteria and Archaea, taxa above class are not regulated (see [13]), despite there being substantial evidence of grouping above phylum level. I think authors are modestly not 100% sure of their results, not everyone speaks Latin, there is a stupid amount of red tape and one has to kind of publish in IJSEM paper. --Squidonius (talk) 19:55, 2 May 2011 (UTC)
From my limited knowledge of protist systematics, I think Peter Coxheads summary is fairly spot on. In my view this leaves us with two options: Either leave protists without a kingdom (as now), or put them in kingdom Protista, with all the varios groups between class and kingdom remain without rank (as now). If so, the difference between Protista and Eucaryota will be a semantic one ("descend from" or "are part of", the expressed tree topology is identical). Again, this is merely a question of prefference. Petter Bøckman (talk) 20:08, 2 May 2011 (UTC)
If it's a question of the first option or the second, I think you'll get far less opposition from the first option. Phylogeny is more useful (to me), anyway. Bob the WikipediaN (talk • contribs) 01:53, 3 May 2011 (UTC)
While there is not a universally accepted system that covers all the eukaryotes, there are clade-specific systems in use. These are often at odds with the use of "Protista" as a kingdom. The Chromista / Chromalveolata (for example) is a group typically given kingdom rank, in large part because workers have elevated all the member clades (no matter how small or poorly-known) to the rank of class. This produces 18 classes of heterokonts alone, and sanity argues for recognizing a kingdom other than Protista in which to place these. Workers in those groups seem to be doing so, but the choice of name and breadth of inclusiveness do vary. The monophyly of the Chromalveolata is disputed, but not that of the heterokonts. I don't have enough experience with the literature or recent work on other major eukaryote clades (other than Archaeplastida) to make any meaningful statements about them. --EncycloPetey (talk) 02:07, 3 May 2011 (UTC)
The "Chromista-as-kingdom" stance was known even when I was a student, though it was never taken seriously by anyone but the Chromista researchers. I don't know it that has changed much. The disentanglement of the protist tree is being actively worked on now, and there seems not to be a consensus tree yet. Thus I would suggest being inclusive rather than specific, and conservative rather than progressive, until things are a bit more sorted out (may take a decade or two though). The question is what to put in the taxo-boxes to get a neat system. I personally think Protista as kingdom and all the other units like Chromista as unranked below is as good as any system, but those working on protist articles must really decide for themselves. Petter Bøckman (talk) 07:13, 3 May 2011 (UTC)
An alternative is to leave out kingdom altogether, and go straight from domain Eukaryota to unranked clades which can be changed later. But I agree that ideally the editors working on protist articles should reach some agreement among themselves. Peter coxhead (talk) 08:20, 3 May 2011 (UTC)


Please give your opinion about disamb pages in the style of Tristis

User:SP-KP has created a novel type of disamb page, with a prototype article at Tristis.

Please comment on that article's Talk page - is this sort of disamb useful or not?

-- 189.122.29.43 (talk) 04:32, 5 May 2011 (UTC)

Very neat, very thorough, I like it! Petter Bøckman (talk) 06:30, 5 May 2011 (UTC)
It's far more useful than vulgaris, that's for sure! I feel sorry for the person trying to figure out the latest genus for a vulgaris species per that page! Bob the WikipediaN (talk • contribs) 16:11, 5 May 2011 (UTC)
As I said at Talk:Tristis, I don't like this one bit. They're all partial title matches, so they don't belong on a disambiguation page for the specific epithet. If anything, it reads more like a List of species with the specific epithet tristis or something like that, but this list would likely be deleted in an AfD. I don't foresee anyone actually using this kind of dab page (who would link to it?). Rkitko (talk) 21:46, 5 May 2011 (UTC)
*cough* I just linked to one in the comment proceeding yours. But you've got several very legitimate points. I still don't support that type of disambiguation. Bob the WikipediaN (talk • contribs) 00:24, 6 May 2011 (UTC)

Looking for fulltext....

The following discussion is closed. Please do not modify it. Subsequent comments should be made in a new section. A summary of the conclusions reached follows.
received with thanks. Casliber (talk · contribs) 05:22, 9 May 2011 (UTC)

I can't get this journal :( much appreciated if someone can....Casliber (talk · contribs) 01:14, 9 May 2011 (UTC)

Microsatellites for eastern Australian Banksia species Author(s): Usher AV, Ayre DJ, Whelan RJ Source: MOLECULAR ECOLOGY NOTES Volume: 5 Issue: 4 Pages: 821-823 Published: DEC 2005

Sent. Ucucha 01:30, 9 May 2011 (UTC)
The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

Bioinspired Robots

Anybody with any knowledge of bioinspired robots is invited to contribute to this discussion for taxonomy. —Preceding unsigned comment added by 109.108.161.182 (talk) 18:49, 13 May 2011 (UTC)

That's a vague topic. What aspect of them are you interested in? Bob the WikipediaN (talk • contribs) 19:32, 13 May 2011 (UTC)

English names of biological species

It seems to me that there's a rough consensus here in favour of the proposed moves to remove the capitalisation, but I'm relisting the moves to allow a little more time. Andrewa (talk) 19:13, 13 April 2011 (UTC)

The upper and lower case forms of one of these items -- Pygmy opossum (disambiguation) -- were inadvertently reversed in this list. —Preceding unsigned comment added by 96.251.199.55 (talk) 19:14, 14 April 2011 (UTC)

This does seem to be a perennial issue, see #Common names capitalization redux and #Article title capitalisation above. Andrewa (talk) 20:54, 14 April 2011 (UTC)

I have a slightly related problem. I am slowing writing Bacterial taxonomy (40% done, but has jargon issues and assumes the reader speaks Latin/Greek). In there I wrote a paragraph about trivial/vernacular names in Microbiology and wanted to ask if anyone is familiar with the trivialisation of latin names, which I know is common in Botony (e.g. bromeliads belong to the genus Bromelia) could give the section a double check or point me towards some references or a wikipedia article to {{main|...}}. Thanks --Squidonius (talk) 23:52, 16 April 2011 (UTC)
  • Support (2) sentence case. There are good arguments for title case when the name of a specific animal could also be a generic descriptor. However, there's seldom much chance of confusion in context, and that can be avoiding by (a) linking species and (b) rewording generics. So 'Nile crocodiles' could only be C. nilotici (or whatever the pl is), while 'crocodiles of the Nile' would be generic. Given how seldom we need such workarounds in articles which are already sentence case, I doubt this will be a problem. — kwami (talk) 01:27, 7 May 2011 (UTC)
  • Oppose sentence case. My basic reasons are that they are proper nouns for the most part, that there is an exception to this for birds seems a little ridiculous, since for example in reptiles, primary literature sources mostly use Scientific Names for these species, when common names are used they are utilised as proper nouns. I think the names should be used in their accepted formats for each species, not have an overall rule applied to them, in particular with a noted exception to that rule being one group of animals, the birds. I just don't see the value in this rule. Faendalimas (talk) 21:03, 17 April 2011 (UTC)
    Well, the argument for the birds exception is that in scientific/etc literature, the names tend to be capitalized more often than for, say, mammals. I'm a little surprised by your claim that when common names are used for reptiles in literature, the names are capitalized; that hasn't been my experience. I'm certainly no herpetologist though. The "proper noun" argument is tricky. Are cat or reptile proper nouns? Why not? The Chicago MOS seems to prefer lowercase, so I don't think it's so clear to say common names of species are proper nouns and therefore should be capitalized. I think instead we should focus, as Wikipedia always does, on what is done in reliable English language sources. ErikHaugen (talk | contribs) 04:07, 18 April 2011 (UTC)
    Following the sources is difficult, often because of regional differences. Databases and literature from Australia typically uses title case, which can make an article on a genus with species both native in Australia and beyond look like the authors are schizophrenic when it comes to common name capitalization. I'm not sure why a style guideline needs to follow the literature. We should simply weigh the pros and cons, consult some external style systems, and determine that we are going to apply a consistent system. And with all due respect to my WP:BIRD colleagues, I've never liked the exception for their organisms since it allows arguments like the above by Faendalimas. Rkitko (talk) 00:00, 19 April 2011 (UTC)
    I agree that following sources is difficult and undesirable, since they are certainly inconsistent between countries. The 'definitive' flora for the British Isles is Stace's New Flora of the British Isles (3rd ed.). Like the Australian literature quoted above, this uses title case for common names. Peter coxhead (talk) 10:08, 19 April 2011 (UTC)
    What if you search for those species on Google Scholar? What does the academic literature suggest? – VisionHolder « talk » 07:41, 23 April 2011 (UTC)
If there no consensus, e.i. both styles are acceptable, and one has to be picked for some reason (which cannot be consistency across articles as some articles are blatantly written in US english, which results in more difference than the case), I would urge out of practicality to use sentence case —where applicable— as mid-sentence uppercase words stand out, which is not a good thing given that this is an online work (poorer legibility) and there is a typographic circus going on with frequent hyperlinks in blue and latin words in italics. --Squidonius (talk) 20:42, 20 April 2011 (UTC)
I've long thought that we should make it a policy that if there really is no consensus possible, then it doesn't matter which way we go. Perhaps that's helpful here? Andrewa (talk) 20:03, 21 April 2011 (UTC)
With how I'm interpreting what you're suggesting, I would strongly disagree. That last thing we need is a bunch of mixed case articles about Bottlenose Dolphins, ring-tailed lemurs, Mountain Tapirs, and white-fronted capuchin monkeys. I can see an exception for birds, although I wish that wasn't the case. But otherwise, having no rules is tantamount to endorsing the current level of rampant inconsistency and confusion. As an encyclopedia that reflects our sources, we need to settle on a framework. – VisionHolder « talk » 20:20, 21 April 2011 (UTC)
An excellent statement of exactly what I'm suggesting Wikipedia is not. The one thing I agree with here is that it's a shame that the exception has been made for birds, but I don't think it seriously weakens Wikipedia. The three important things are content, content and content. That's what people come here for. What does weaken the project is wasting too much time on other issues. Andrewa (talk) 20:32, 21 April 2011 (UTC)
The primary feature of an encyclopedia, including Wikipedia, is content. However, it is not the only feature. If it were all about content, then we could just disband WP:GAN, WP:FAC, etc. Issues like standardization of formatting, copyright compliance, article layout, and many more issues are all important in their own right. It is certainly true that people come here for content, but inconsistencies and other non-content issues can and do stand out, as well as impact the perception of Wikipedia as a whole. – VisionHolder « talk » 20:45, 21 April 2011 (UTC)
Presentation certainly matters, and featured articles etc are a good thing, and one of the reasons is that these mechanisms promote good presentation. But standardisation is not an end in itself. Where it is helpful, and it often is, we should use it, and to this end we have policies, guidelines and the MOS. We should not be distracted by it, and to this end we have WP:IAR. The unfortunate lack of standardisation in the scholarly literature as to capitalisation of species names is something Wikipedia cannot fix and should not try to fix. Andrewa (talk) 21:36, 21 April 2011 (UTC)
Internal consistency is a virtue. The lack of it reflects badly upon Wikipedia. We need to just pick one and go with it. – VisionHolder « talk » 22:41, 21 April 2011 (UTC)
Agree that internal consistency is a virtue. Disagree that the lack of it reflects badly upon Wikipedia. Andrewa (talk) 08:28, 22 April 2011 (UTC)
(ec)I care a lot about the legitimacy of Wikipedia, and I think inconsistency can affect perception in that area, which is why I have been pushing for embracing one style project-wide. Wikipedia:Naming conventions (capitalization) says: "Because credibility is a primary objective in the creation of any reference work, and because Wikipedia strives to become a leading (if not the leading) reference work in its genre, formality and an adherence to conventions widely used in the genre are critically important to credibility." It's important to figure out the right style and to do it consistently. ErikHaugen (talk | contribs) 22:52, 21 April 2011 (UTC)
Agree with all of that, except the punch line of embracing one style project-wide. The point is, there is no convention(s) widely used in the genre. Or at least, there's one for birds, and another for other species. So Wikipedia is caught between competing authorities. Andrewa (talk) 08:28, 22 April 2011 (UTC)
Again, I don't believe style guidelines we generate need to follow usage in our sources. If we did exclusively, we'd also be starting to roll out italicization of botanical ranks higher than genus, too (ICBN and a few widely-read journals do this now). And as an encyclopedia, we're encouraged to consult external manuals of style, which mostly advocate for sentence case common names of organisms. Rkitko (talk) 12:06, 22 April 2011 (UTC)
I generally agree with this, but the battle was lost long ago. So far as our local conventions go, we're stuck with an inconsistency, and with a tendency away from the earlier ideals of Wikipedia and towards a more authoritative / prescriptive stance, which in the short and medium term doesn't lead to consistency and in the long term depends on consistency on the part of authorities, which isn't there. So far as WP:IAR goes, we're equally stuck with chaos. On this particular issue therefore, consistency is a windmill. Which brings me back to: Does it matter? Andrewa (talk) 19:30, 22 April 2011 (UTC)
I don't think things are quite this bleak. I think there's enough consistency on the part of authorities for us to come up with a guideline. Why do you say "in the short and medium term doesn't lead to consistency"? ErikHaugen (talk | contribs) 20:34, 22 April 2011 (UTC)
Good luck. In the short term, change in convention leads to inconsistency, as applying the change takes time. In the medium term, major change leads to inconsistency, as applying the change leads to other changes and they all take time. Andrewa (talk) 23:46, 22 April 2011 (UTC)
Please explain to me how WP:IAR even applies here? How does setting a guideline or policy about whether to consistently use upper or lower case prevent someone from improving Wikipedia? Anyway, yes, this topic has a long history of dispute, but that doesn't make it unresolvable. This isn't American politics. All we need to do is pick one and go with it. Dragging old disputes into this is a great way of stalling an issue, which I suspect is your objective. Personally, I'm about ready to close this discussion with 4 supports for sentence case and 2 opposes... using WP:IAR. Arguing for the sake of arguing impedes improving upon Wikipedia, and as you admitted, consistency does improve Wiki. Having white-tailed deer, Red Fox, skunk clownfish, Mongolian Wild Ass, and Siberian tiger vary in case is ridiculous. It causes confusion for readers and editors alike, leading to cases such as Nile crocodile, which doesn't even have internal consistency. If WP:BIRDS wants to be the sole exception (because of their sources), then fine. But we should at least be consistent everywhere else. And the simpler the rule (fewest exceptions possible), the easier it is to document and follow. Offering guidelines of "sometimes this", and "generally that" is detrimental. So unless you have something meaningful to add besides the (stereotypical) argument "this is a old issue, its never been resolved, and therefore can never be resolved, so let's drop it," then let's move forward. – VisionHolder « talk » 22:43, 22 April 2011 (UTC)

Replying to Andrewa: consistency between articles may or may not matter; consistency within articles does, surely? A common problem is that different sections of longish articles are edited independently of one another and if there are no clear policies for editors to follow they soon become inconsistent. It could be handled as, say, dialect of English is by having policies about the subject matter and then the preference of the article creator, but this leads to a lot of time-wasting discussions. Peter coxhead (talk) 21:45, 22 April 2011 (UTC)

Agree that we should be consistent within an article, I'd be surprised to see that questioned. Nile crocodile should be fixed if it's a case in point. Disagree that this is relevant to the choice of article title, as seems the inference here. Surely, this discussion is already convoluted enough? Andrewa (talk) 23:46, 22 April 2011 (UTC)
My argument is that the easiest way to be consistent within articles (now talking about the body of the article rather than the title) is to have clear consistent policies and not allow variation.
Nile crocodile is fixed I think; Diffs: changes to article, new section on its talk page. Andrewa (talk) 00:01, 23 April 2011 (UTC)

Replying to ErikHaugen: the evidence as far as the common names of plants are concerned is that although there may be consistency within (English speaking) countries, there is not consistency between countries, so this doesn't help us much as far as Wikipedia is concerned. Would anyone want a genus article which lists its species with their common names to have the case determined by which country they occur in? Peter coxhead (talk) 21:45, 22 April 2011 (UTC)

Why does it matter what they do in non-English speaking countries? This is the English Wikipedia. Those other countries/languages will have their own Wikipedia on which they can make their own guidelines. As for English-speaking countries, most of the literature I've seen varies more on year of publication. Old (roughly pre-1960's) literature uses uppercase while more recent literature uses lowercase. Yes, there are exceptions, but I would bet that other encyclopedias choose one or the other and stick with it. On Britannica, they use only lower case. See ring-tailed lemur and bald eagle. – VisionHolder « talk » 22:43, 22 April 2011 (UTC)
Sorry, I realize I wasn't as clear as I intended: there may be consistency within English speaking countries but there is not consistency between English speaking countries. For plants, there are countries where the current sentence case for titles, lower case for text (except for proper names of people, countries, etc.) is the norm. Equally there are countries (Australia, UK) where title case for titles and text is the norm. In the UK the most recent standard Flora published this year uses title case, so it is not a question of date of publication. Peter coxhead (talk) 06:56, 23 April 2011 (UTC)
Try this approach on the bird Wikiproject, if you can convince them it will save a lot of trouble. If not (as I suspect) then I'm not hopeful. Andrewa (talk) 23:46, 22 April 2011 (UTC)

Reply to post above the outdent, above: Please explain to me how WP:IAR even applies here? It applies everywhere. The points you raise questioning its applicability are begging the question on too many counts to list. Andrewa (talk) 23:46, 22 April 2011 (UTC)

  • Follow reliable sources, which vary in capitalization conventions across different taxonomic groups. Do not impose a consistency that does not exist in real-world usage. Hesperian 00:49, 23 April 2011 (UTC)
That has a lot to recommend it, but I'm curious... do you want to restrict this approach to the level of taxonomic groups? If reliable sources capitalise just one species of a group, why wouldn't you follow that usage too? Partial consistency is just inconsistency incognito. Andrewa (talk) 01:38, 23 April 2011 (UTC)
In particular, what taxonomic groups use uppercase, aside from birds? Because at this point, I think it's safe to close this discussion and state that WikiProject Tree of Life should use sentence case for all common names, except for birds. Then, once after a year of gradual conversions to across the various projects (such as the one currently underway at WP:PRIMATE), we can revisit the idea of a single standard for the entire project (much as other encyclopedias do). – VisionHolder « talk » 02:07, 23 April 2011 (UTC)
All Australian herbaria and journals capitalize common names of plants. Hesperian 02:26, 23 April 2011 (UTC)
Per Wikipedia:Naming conventions (flora), flora articles are generally to be named by the scientific name, unless the plant in question has a agricultural, horticultural, economic or cultural use. I would think the article text would follow from the title. Regardless, sampling the flora articles, there is a wide variety that I encountered that use scientific names, sentence case, and uppercase. Unlike the WikiProject Birds, there is no standard. Once again, though, other encyclopedias that use sentence case for all taxa also use sentence case for flora, including those from Australia. – VisionHolder « talk » 03:22, 23 April 2011 (UTC)
Checking my various tree guides and horticulture books, they use a mix: 2 upper case, 1 sentence case, and 1 an odd mix where the first word in the name is always capitalized, but the rest of the words aren't (e.g. Black oak), even in the text body. However, searching Google Scholar (ex. "Acer rubrum" or "Quercus alba"), the results seemingly unanimous for sentence case. – VisionHolder « talk » 05:44, 23 April 2011 (UTC)

Nothing new perhaps but...

As noted above I did some updates to the Nile crocodile article.

One in particularly interested me... Nile crocodile#Biology and appearance reads Nile crocodiles have a dark bronze colouration above..., or should it be Nile Crocodiles have a dark bronze colouration above...? The former could mean any crocodile that lives in the Nile regardless of species, the latter means any member of the species regardless of where they live.

The reason this might be very important is the question of precision and ambiguity, which are primary considerations when choosing article titles. Nile crocodile is unambiguous in practice as an article title, but other species are likely to be ambiguous if uncapitalised. Andrewa (talk) 04:37, 23 April 2011 (UTC)

Yes, this is one of the most commonly used arguments on Wikipedia for uppercase. In fact, this is the primary argument if you don't bother discussing what the sources use. In this specific case, I don't think there are any other crocodile species living in the Nile River. Let me make this clear: I'm not saying there aren't reasons for uppercase. I'm not even a major advocate of sentence case. If you want my honest opinion, I favor using scientific names and not common names, particularly for the article titles. I can give good reasons for why this should be done, but the fact remains that most sources for laypeople (including other encyclopedias) use common names when available. If you're trying to muddy the water, you're doing an excellent job, Andrewa. You stated quite clearly on that this issue doesn't matter in your opinion and that we shouldn't rock the boat and instead should focus our attention elsewhere. If you're trying to make a case for the pointlessness of this, you're failing. The fact remains that Wikipedia is horribly inconsistent, and this fact reflects poorly on it. If you can't help facilitate a solution to this problem, then please take your negativity and unproductive attitude elsewhere. I'm done debating this with you. – VisionHolder « talk » 05:01, 23 April 2011 (UTC)
Sorry I've offended you. Doing my best. Suggest you take a quiet read of WP:NPA and WP:AGF. I can take this rough stuff but I'd take a very dim view of such arguments being used against newbies, and it could be argued that it's equal unacceptable against seasoned campaigners as we have no idea who is watching and your outbursts can discourage others who are lurking, or worse, give them the idea that this is acceptable. It's not. Andrewa (talk) 15:57, 23 April 2011 (UTC)

PS Back on the issue, do you have an opinion on whether the phrase should be Nile crocodiles have a dark bronze colouration above... or Nile Crocodiles have a dark bronze colouration above..., assuming for now that the article title is Nile crocodile, uncapitalised? That's the question I find interesting. But it's very much a logician's question, and so may seem pointless to many I know. Andrewa (talk) 16:15, 23 April 2011 (UTC)

To answer your question, this is why we stick with one rule. Since the WikiProject Amphibians and Reptiles points to Wikipedia:Naming conventions (fauna), and that guideline is ambiguous, there is no clear-cut answer to your question, unless we assume to follow the convention used in the title of the article: sentence case. In which case, we stick with sentence case throughout the article, despite its limitations. (Likewise, if it went the other way we'd use uppercase throughout the article, despite any confusion it may cause or conflicts with sources.) But since Orinoco Crocodile uses uppercase, now we have inconsistency just within a single genus. So you have two choices: 1) Use your admin abilities to rename the article and make it all uppercase, or 2) just use sentence case throughout the article. Because this discussion is sufficiently confused, then there are no effective guidelines, and you can do whatever you want. – VisionHolder « talk » 21:50, 23 April 2011 (UTC)
But let's be practical [14]... What is the best way to write this article? Upper or lower jaw case Crocodile? That's what I was asking. I think we all agree the rules aren't all that helpful in what they do say. What should they say, on this very practical binary decision? Andrewa (talk) 11:19, 24 April 2011 (UTC)
Obviously, the article should use lowercase when the title is lowercase. Ucucha 11:31, 24 April 2011 (UTC)
OK... but even if that's true (and I think it is) it doesn't help very much, because the eventual goal of the whole discussion is to decide what to name articles such as this, so if we say we follow the article name we get a circular argument. Andrewa (talk) 11:59, 24 April 2011 (UTC)
Agree it would be good to rename either Nile crocodile or Orinoco Crocodile. It doesn't get much patchier than that. Andrewa (talk) 11:59, 24 April 2011 (UTC)
I'm on it. ErikHaugen (talk | contribs) 15:18, 24 April 2011 (UTC)
So I see [15] (with apologies for disturbing the chronology of the string, but I think it's more logical to put this post here above the earlier reply). Andrewa (talk) 05:44, 25 April 2011 (UTC)
That specific issue was just a single case, and not even the whole case. If you look at the genus article, Crocodylus, and follow the links, you'll see almost half of the crocodile species articles use sentence case while the other half use uppercase. Orinoco crocodile was just a specific example. If you zoom out further, I'm sure we'd discover similar inconsistencies throughout the entire family, order, class, and so on. At what point do we stop, and to which standard do we adhere? From my perspective, that was the point of this discussion. But the more I look at it and read the comments associated with explicit votes, this discussion lacked clear direction from the start. Was it truly a project-wide attempt to get a consensus, such that we might even overturn the rules at WP:BIRDS? Was it only for a specific case? Was it to clearly state which subprojects could continue using uppercase while the others standardize on sentence case? If anything, I think this discussion needs to be closed and a more planned-out proposal be made. – VisionHolder « talk » 16:57, 24 April 2011 (UTC)
Agree that it lacked clear direction, and it still does, and that last post is an excellent example of this lack IMO.
How do we get this clear direction? You refuse to focus on particular examples, such as the specific example which I had hoped would be the jumping of point for this new section, wanting to jump instead to a proposed convention. Both are valid ways of proceeding. You've suggested at User talk:Andrewa#Personal reply that we work together on that proposal. I'm still considering that. BTW, remembering that my user talk page like all pages belongs to the project and is a public part of the WWW, I'd welcome other users commenting there if anyone is interested. It's also possible that no other editor will even read this paragraph, let alone comment on it. Equally happy for it to remain a dialogue. Either way it helps to unclutter this page a (very) little, which I agree is a good thing.
Do you think we're ready for a proposed convention? Interested to see its form. And of course, however much sense it may make to you and I, we still need to gain a more general consensus for it. Andrewa (talk) 18:10, 24 April 2011 (UTC)
I thought I had addressed your specific example by outlining the two options and by acknowledging the limitations of one approach vs. the other. Are you asking if we go with sentence case, then how do we address wording issues like one one you raised above? In my opinion, it will boil down to a case of careful wording. In your specific example, maybe it could be worded: As a species, Nile crocodiles have a dark bronze colouration above... Alternatively, maybe this is a case where the scientific name should be used in one sentence for clarity. I'm sure there are other ways to word it. IMO, tere's no need to immediately jump off into WP:IAR (assuming there actually was a rule to ignore) for such a case... at least not until one or more editors tried to find a way to clearly word the information. I would suspect that 99% of all cases could be resolved this way. Does that adequately address your example? (And yes, I do hope others will participate in this discussion. I don't mean to monopolize it.) – VisionHolder « talk » 19:26, 24 April 2011 (UTC)
Just thought to mention (following one of posts above) small caps is the only option for some trivialised Latin names: with the exception of stuff like a bromeliad, a psuedomonad and an treponeme (from Bromeliaceae, Pseudomonadaceae and Treponema), all the trivialised names would just cause confusion with the official name. --Squidonius (talk) 20:32, 25 April 2011 (UTC)
I assume you mean "lowercase" when you say "small caps"? We don't need to call forsythias FORSYTHIAS, I hope. Ucucha 20:55, 25 April 2011 (UTC)
A clearer example is that of "geranium"/"Geranium", where the trivialized name and the Latin name do not apply to the same plants. That is the flowers commonly known as "geraniums" are in the genus Pelargonium, not in the genus Geranium. So, capitalization of trivialized names can lead to serious confusion in some situations. --EncycloPetey (talk) 21:20, 25 April 2011 (UTC)
Nasturtium is another example. Hesperian 00:29, 26 April 2011 (UTC)
Ah, but that's part of the point of italicizing genus names. For those who like to capitalize common names, the sentence "A Geranium can be any one of a number of species and hybrids of Pelargonium." is quite clear. (This isn't an argument in favour of capitalization, just a comment!) Peter coxhead (talk) 11:29, 26 April 2011 (UTC)
That's true, but which would be less confusing if discussed within the same sentence or in close proximity: Geranium and geranium, or Geranium and Geranium? Either way, I don't see this issue being a common concern because of the rarity of the event. Anyway, as long as an article is worded clearly, it should be obvious whether you're reading about a taxonomic genus or the common name. The same, in my opinion, goes for situations like brown bear/Brown Bear or Nile crocodile/Nile Crocodile. The situations will be rare, and as long as editors are careful with the wording, it would rarely be an issue. That's why I don't put much stock in arguments based around this. Instead, I prefer to debate either sources or whether species names qualify as proper names, not for clarity sake, but as a rule (by the definition of "proper name"). – VisionHolder « talk » 12:04, 26 April 2011 (UTC)
Debating rules in relation to the English language is fun (well, fun for some people, including me), but ultimately pointless. What is clear is that common names for species are capitonyms for those who capitalize them. For them, "the brown bear" refers to a specific individual brown bear presumed to be known to the reader/hearer; "the Brown Bear" refers to the entire species. But as others have noted, this distinction can be made (albeit usually in a more long-winded manner) by other techniques: "as a species, the brown bear ..." is unambiguous. The reality is, I think, that there are arguments on both sides, but none for inconsistency. Not capitalizing is an easier rule to follow, which I find a convincing argument in a multi-editor environment like Wikipedia. Peter coxhead (talk) 17:59, 26 April 2011 (UTC)
And something to consider when treating species' common names as proper names: there are a few cases were exceptions will undoubtedly be made for commonly used terms. For example, I doubt very many editors would support universal enforcement of an uppercase rule if they had to were forced to capitalize "Humans". The same can be said for some common domestic animals such as the "Domestic Cat" or the "Domestic Dog". Thefore, any proposal that aims for consistency needs to consider these far-reaching consequences. – VisionHolder « talk » 15:00, 26 April 2011 (UTC)
The retort is that none of those, strictly speaking, are species. ErikHaugen (talk | contribs) 15:41, 26 April 2011 (UTC)

The argument I was given for title case was that a "blue whale" could be any whale which is blue, but a "Blue Whale" is a specific species. Except of course that there are no whales which are blue. "Grey whale" makes the point better, but really, when does anyone ever say "grey whale" to mean a whale which is grey, as opposed to whales of other colours? And if we did want to say that, would the lack of capitalization really be enough to convey the point? Wouldn't we want to say "grey-coloured whales" or "whales which are grey" just to be safe? After all, that's what we have to do when speaking. There may be a greater chance of confusion in the case of birds, but even there I'm doubtful that in an encyclopedia we'd often find ourselves wanting to describe a bird in the same way that a species is named: Would we ever say "the Nilgiri wood pigeon is a short-billed pigeon" (potentially confusing the reader with the Short-billed Pigeon) rather than just "the Nilgiri wood pigeon has a short bill"? Or even "I saw a short-billed pigeon" (an unlikely sentence in an encyclopedia)—could that mean anything other than the species, or wouldn't we naturally say "I saw a pigeon with a short bill"? Even if birders insist title case is essential for clarity, beyond birds there's very little chance of confusion if an article is even halfway well written. — kwami (talk) 01:44, 7 May 2011 (UTC)

Relevant guidelines

These include:

  • Wikipedia:WikiProject Tree of Life#Common name capitalization, which reads in full Many of the WikiProjects listed above have defined standards for the capitalization of common names, which should be used when discussing the groups they focus on. There is currently no common standard, so no particular system should be enforced overall.
  • Wikipedia:WikiProject Birds#Bird names and article titles, which provides an excellent rationale for capitalisation, applicable to all species not just birds, but the scope of the guideline is of course restricted to bird article titles, and there's an explicit disclaimer to that effect in the guideline.

But that second bullet is only one of the many lower level guidelines referred to in the first bullet. Is there a list of some or all of the others somewhere, and if so can someone point me to it, and if not, can anyone able to, provide a wikilink to other relevant lower-level article title guidelines of which you are aware? I suppose otherwise I can wade through the list at Wikipedia:WikiProject Tree of Life#Scope and descendant projects to find them. Andrewa (talk) 13:44, 27 April 2011 (UTC)

I was actually planning to make time for this. It would be interesting to tally each of the many sub-projects, see who explicitly uses what case and see if they provide an explanation of why. If I do it, I was planning to walk the tree at Wikipedia:WikiProject Tree of Life#Scope and descendant projects. Anyway, out of time ... off to work. More later, if needed. – VisionHolder « talk » 15:11, 27 April 2011 (UTC)
I don't think any of them encourage caps other than birds, but I might have missed one. Moths, maybe? ErikHaugen (talk | contribs) 16:47, 27 April 2011 (UTC)
For a good example of inconsistency, look at Moth#Economic_significance_of_moths. If you follow the links to specific moth articles, they seem to match the section: e.g. "diamondback moth" has lower case in the section and article, "Chinese Oak Silkmoth" has upper case in the section and article (although there it has two different common names!). Peter coxhead (talk) 18:22, 27 April 2011 (UTC)
Examples of inconsistencies like this are very easy to find. ErikHaugen (talk | contribs) 18:55, 27 April 2011 (UTC)
Actually I've not often seen a single section of an article with such a mixture, but maybe I don't read widely enough on Wikipedia. I'm in favour of clear and simple guidelines: always lower case for common names in text with sentence case for titles (except for birds). Peter coxhead (talk) 19:42, 27 April 2011 (UTC)
There is a lot written here: I would think it a good idea if there were an unbiased summary of this debate section (linked-to from the guideline section), I would do it, but I have no free time. (Anyone think it a good idea and wants a barnstar?). Can we have a clear vote in a new section on the uc/lc on all projects bar birds without a discussion whether common names are proper nouns or not (e.g. I am sure they are not, but everyone had a different view), whether scientific names should be used more, whether birds should be included in the vote —that can be a separate one— or whether the plural of octopus should be octopi or octupusses. Please (this thread is dragging a bit)--Squidonius (talk) 21:44, 27 April 2011 (UTC)
Actually, Andrewa and I are pondering this very topic. Since he and I have been most at odds, we're trying to find some common, civil ground from which we can move forward. In summary, my current proposal is to hold a vote that will affect only sub-projects that do not have clear guidelines (excluding birds & primates, for example). Then, after a year of letting the dust settle, we could take up the challenge of conformity for the entire project. Of course the second vote runs the risk of 1) failing miserably, 2) undoing the previous vote, or 3) steam-rolling sub-projects that don't conform to the rule adopted in the first vote. Another idea is to first vote on whether we want conformity at all. Would both WP:BIRDS, WP:PRIMATES, and all other sub-projects with clearly defined guidelines be willing to submit to a general rule, even if it potentially goes against their existing guidelines? The problem here is how to balance it and prevent sub-projects from rallying members to swing the vote. What if members of WP:BIRDS (for example) shows up in strong numbers against the idea of a common guideline, but enough other members out-vote them? Needless to say, this raises questions about sub-project autonomy and the purpose of project hierarchies. IMO, we shouldn't back down from these obstacles. Not every democratic decision comes easily, and certainly democracies require a lot of blood, sweat, and tears to maintain. The question is: what is the best path forward. Rest assured that there are enough people here who care in order for this to continue forward. We just need a lot more clarity and direction this time. – VisionHolder « talk » 22:51, 27 April 2011 (UTC)
Just to point out that Wikipedia doesn't make decisions by votes but by consensus. My guess is that the only consensus is for consistency within (sub)projects. If the members of WP:BIRDS agree on capitalization and manage to be consistent on this, they will be (and should be) free to continue this policy whatever any other (sub)project members think. It is much more useful, in my view, to concentrate on removing inconsistency within articles and then within groups of organisms, than trying to pursue a non-existent global consensus. To put more clearly what I meant in my comment above: "The default policy should be lower case in text (sentence case in titles) except for groups of organisms where there is a clearly stated consensus policy to the contrary." Peter coxhead (talk) 07:51, 28 April 2011 (UTC)
I guess I'm so used to seeing polls treated as voting that I'm having a harder time than normal at taking this in. So you're right, per WP:Consensus. And I agree that the most important issue is to fix the inconsistency in articles and groups of articles that have no clear guidelines. I guess I'll have to do a little more searching to see if there is a Wikipedia policy or guideline for consistency for broader topics. So far, all of this discussion has focused on species and genus articles. A broader level of consistency is important for other types of articles, such as those about national parks or general biology/ecology/conservation. It can be really confusing when you're writing about primates (lower case), birds (upper case), butterflies (upper case), and other mammals (lower case), all in the same sentence. So the species articles may be more numerous and visible, but whatever consensus is reached has the potential make consensus impossible for these more general articles if everyone wants to have their own guidelines. That's a tough one... – VisionHolder « talk » 14:45, 28 April 2011 (UTC)

At the risk

At the risk of arguing from silence, reading the above suggests to me that Wikipedia:WikiProject Tree of Life#Common name capitalization may be in error when it says Many of the WikiProjects listed above have defined standards for the capitalization of common names.

So far, birds, primates (which says exactly nothing and is an obscure subpage) and breeds. So it's not a complete fiction, but many may be a stretch. Andrewa (talk) 00:10, 29 April 2011 (UTC)
Done all but plants and animals, ie the minor kingdoms. Nothing at all found in any of them. Andrewa (talk) 16:00, 3 May 2011 (UTC)
So where does this leave us? ErikHaugen (talk | contribs) 17:58, 3 May 2011 (UTC)
Thank you for pointing out that the primate pages need work. The edit I made following the vote was a quick fix. I will try to get to it, but right now I'm battling with a deadline for a research article I want to publish. If I have time tonight, I will help with the reviews of the various projects. Sorry I haven't been available to help this past week. – VisionHolder « talk » 19:02, 3 May 2011 (UTC)

It hadn't occurred to me before that this might be a fiction, but I think that's a question that now needs to be asked. Did any of these standards, apart from birds, ever exist? Where did they go? Why didn't the author of this bland and sweeping claim link to at least a few of them? Or did they? If so, when were these links removed and why?

I don't intend to delve into the page histories to answer these questions, but I'm interested in the results if somebody else wants to.

What I am going to do is walk the tree (rather than just talking about doing it) starting at the bottom and working up. If anyone else is interested in work rather than waffle, start at the top and work down, and post to this section saying you're doing that. If we get a third volunteer, start at the middle and work up, and again, tell us here what you're doing. Fourth starts at the same place as third and works down, fifth three quarters of the way down working up, and so on, sixth one quarter of the way down and work up...

Please don't volunteer unless you are prepared to do it well and soon. It will take time. Please do volunteer if you can and are interested. I don't care if I do it all myself, or if someone else does it all, just so long as it's done soon and well.

Report your results at User:Andrew/Tree of Life caps conventions, linking to sections found and reporting wikiprojects checked and found without conventions. Report work in progress below, to minimise duplication of effort. Andrewa (talk) 18:25, 28 April 2011 (UTC)

Primates used to require capitalizing. I'm not sure if others did. ErikHaugen (talk | contribs) 18:41, 28 April 2011 (UTC)
Whales used to require capitalization as well, as I found out when I tried moving some of them. — kwami (talk) 01:27, 7 May 2011 (UTC)
Interesting... I'll take a break from my upwards walk to look at it. Andrewa (talk) 19:11, 28 April 2011 (UTC)
Got it, Wikipedia:WikiProject Primates/Article format#Capitalization is the current guideline, but I'd never have found it from their project page. Sobering. Andrewa (talk) 19:18, 28 April 2011 (UTC)
"sobering" - ha! Yeah, that does make your current endeavor seem more challenging. ErikHaugen (talk | contribs) 19:34, 28 April 2011 (UTC)
I can tell you from my own experience researching it that the old upper case rule was not discussed on the project talk pages, and I never found any reasoning for its implementation. I think someone once suggested that one of their primary sources used uppercase, but as the more recent vote discusses the literature uses mostly lower case. I was the one who made the most recent edits to the guideline per the outcome of the discussion. If I missed something in the history, please let me know. – VisionHolder « talk » 19:43, 28 April 2011 (UTC)
For now I'm more interested in just finding the guidelines. Are there any others you've edited? Andrewa (talk) 23:58, 28 April 2011 (UTC)
No. – VisionHolder « talk » 00:25, 29 April 2011 (UTC)
Agree. And more important. Andrewa (talk) 18:09, 29 April 2011 (UTC)

So... what result?

What about these opossums, then? The closest thing we have to consensus seems to be that species names (except possibly birds and other special cases) should not be capitalized as proper nouns, and we should therefore rename the opossum articles - is this a reasonable assessment, given that discussion seems not to be going anywhere, and we need a decision?--Kotniski (talk) 12:41, 19 May 2011 (UTC)

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