Wikipedia talk:WikiProject Tree of Life/Archive 10

message: We really should decide what to do about viruses - whether to include them in our phylogenetic system, or not.  Also, I'd appreciate comments on my proposed rewrite of our plant article, which I think focuses way to much on boundary cases and not enough on ordinary plants.  And, should anyone happen to be interested in protists, it would be neat if anyone had any insight on how to treat the heterokont/stramenopile/chromist group.
Please comment on Talk:Virus, perhaps Talk:Plant, and if you're feeling generous Talk:water mould.  Thanks, Josh 15:33, 17 Aug 2004 (UTC)
thread_title:  Requests for comment 

message: What's gone wrong with the taxobox at Cashew? - it should be:
Anacardium occidentale L.
but is actually showing:
Anacardium occidentale L.. {20 August 2004 (UTC)}
Can anyone solve it? - MPF 20:24, 20 Aug 2004 (UTC)
replies: text: Quite simple. You used the footer with authority, but that one requires both the authority and the date. However you omitted the date, so instead the standard template  is instead used. I added the standard Linnaeus 1761. andy 20:29, 20 Aug 2004 (UTC)
replies: text: Hi Andy - thanks; I didn't use the new taxobox, that was someone else put it in, I was just changing the citation of Linnaeus from spelled out to standard Botanical 'L.', and removing a question mark that had been there before. As botanical author citations (unlike zoological ones) don't cite dates, there should be no date there at all, just L. for Linnaeus. Can the relevant template be changed to one that doesn't require a date, please? - MPF 22:22, 20 Aug 2004 (UTC)

text: Thanks; I've copied across to Cashew. I've still not got round the new taxoboces yet, so won't be adding more, only editing any new-style that I run across MPF 09:46, 23 Aug 2004 (UTC)
thread_title: New style taxobox problem

message: According to IPNI the abbreviation Gray belongs to Samuel Frederick Gray, while quite a lot of the animals described by his son John Edward Gray also have the short reference Gray. If those are correct than we have to make Gray (taxonomist) to be a disambiguation (there was only one taxobox pointing there anyway, which I fixed now), or have to change to use something like Gray (botanist) and Gray (zoologist) instead. BTW: is there anything comparable to IPNI for zoologists? andy 11:55, 24 Aug 2004 (UTC)
replies: text: Hi Andy - I'd go for the Gray (botanist) and Gray (zoologist) option, or maybe for their full names (i.e., Gray and Gray respectively - MPF 14:19, 24 Aug 2004 (UTC)

text: And there is Asa Gray, George Robert Gray and there are a lot more. I suggest using the full name or the name plus all the initials, unless a link can be made to a biography, then you can use a link such as J.E. Gray. You can consult List of biologists, List of botanists or you can write a biography yourself, such as I have done a few times. JoJan 14:40, 24 Aug 2004 (UTC)
replies: text: Maybe you misunderstood - the other botanists Gray's have their own abbreviation, e.g. Asa Gray is A. Gray, so those are not the problem here. The problem is that apparently the Gray for flowers is a different Gray than the one fort animals. And of course once we have a full article about an author it should be at the full name, and only use a disambiguation if that one isn't unique. However for taxoboxes it's handy to insert something like Gray which then is a redirect to the plain author name, so not everyone who adds taxoboxes needs to know the translation table from short names to the full names. andy 15:21, 24 Aug 2004 (UTC)
replies: text: Gray (taxonomist) is no solution, since all the other Grays were also taxonomists. The University of Wisconsin offers this solution : "Citations of botanical authors are standardized and abbreviated as per Brummitt and Powell (1992), with one exception. British naturalist Samuel Frederick Gray, abbreviated simply as Gray in Brummitt and Powell, is abbreviated in this Checklist as S.F.Gray to distinguish him from the American botanist Asa Gray (A.Gray). " See here []. I suggest we do the the same. JoJan 16:07, 24 Aug 2004 (UTC)
replies: text:  I think, indicating the full reference would solve the problem. See Nymphaeaceae - the first reference gives enough information for any purpose. Iorsh 16:48, 6 Sep 2004 (UTC)
thread_title: References - short names not unique between botanists and zoologists? 

message: The image at http://en.wikipedia.org/wiki/Image:Common_clownfish.jpg is used in the article Clownfish, yet the way it does so (using a taxobox expansion) somehow precludes discovering that fact via the usual automated "What links here" mechanisms.  Apparently it is related to a known bug, see Bug #48. Is there a workaround? - Bevo 08:27, 26 Aug 2004 (UTC)
replies: text: I noticed the same thing on images I have uploaded and used on articles recently. Not really much of a workaround but I have been adding stuff like "This image is not an orphan. It is used on the article blah" to stop people from deleting it as an orphan. Pcb21| Pete 08:44, 26 Aug 2004 (UTC)
replies: text: I created Clownfish/images as a workaround to this bug. - Bevo 13:00, 26 Aug 2004 (UTC)
replies: text: Clownfish/images does not appear to exist at the moment.  nroose Talk 08:35, 1 Sep 2004 (UTC)
replies: text: Another option is to repeat the pic on the page's talk page; I've done this with :Image:Araucaria.columnaris1web.jpg which now shows up as being on Talk:Araucaria, even though its main appearance on Araucaria doesn't show - MPF 21:37, 4 Sep 2004 (UTC)
thread_title:  "What links here", [[Clownfish]] and [[:Image:Common clownfish.jpg]] 

message: The current page titmouse is a family page coveing the whole of the Paridae (tits & chickadees in Parus, titmice recently split off as Baeolophus, and a few monotypic genera) - I'd like to suggest (1) re-naming the current titmouse as Paridae (currently a redirect to titmouse), (2) re-model titmouse as a genus page for Baeolophus, (3) make a new page for Parus, and (4) the remaining genera names as redirects to their current sole species. Only problem is that the AOU split Parus up into several smaller genera (not followed by any other authorities, as far as I know). Anyone any thoughts? - MPF 18:37, 27 Aug 2004 (UTC)
replies: text: Sounds like a good plan. --Yath 21:53, 27 Aug 2004 (UTC)
thread_title: Titmouse

message: Is there a mammal expert around here who is able to answer a question about rats and especially rat kings? The question is, if rat kings do really exist or if they are just a product of forgery. See Talk:Rat king. Thanks for any answers. -- Baldhur 21:12, 28 Aug 2004 (UTC)
thread_title:  Rat kings 

message: I feel like we probably want to find some way to point editors to Taxobox_Usage right from the main article or edit page.  We can certainly make a template linking to the Taxobox_Usage page and add it to article talk pages, but I feel like for important help like this it's good to have something right on the article page too, in case notes on talk are overlooked.  I have some preliminary suggestions that I've prototyped here:
#We could just put a link to Taxobox_Usage in the main article.  This is not optimal, since we'd like to keep these details hidden from non-editors, but it's not unprecedented.  See the navigation box for Train.  Compare to the small note at the bottom of the taxobox.  The help message is in the table caption tag and I think pretty unobtrusive.  
#We could put a message for editors in HTML comments on the article page.  To standardize this a bit, we could agree on an HTML message like , for example, and put it in a template.  Using the  construction would put this message in the edit page where it might help some people.
I don't consider either solution optimal, but both are better than doing nothing, and maybe someone else will be inspired to a better idea.  --Chinasaur 17:31, 30 Aug 2004 (UTC)
thread_title:  Inline taxobox help 

message: Iv'e added several new pics to http://en.wikipedia.org/wiki/Plants_and_animals_of_Belize and as always I'm takeing request.
Belizian 17:58, 30 Aug 2004 (UTC)
thread_title: New pictures for you guys to use

message: This is what happens when people with no science background start writing about themselves. A fairly NPOV human article got hugely POVved.  this is just a heads up, folks. Dunc_Harris|☺ 21:00, 30 Aug 2004 (UTC)
thread_title:  yukkity yukkity yuk 

message: Azhyd added an orphan page on an interesting proteobacterium, Pelagibacter ubique.  However, strange to say, it looks like the formal name of the organism is actually Candidatus Pelagibacter ubique.  There is some information on this type of name at LSBN.  How do we want to handle it?  A new binomial name template can be made easily, but how should it show up in the placement (or subdivision boxes), and should the article be moved or kept where it is? Josh 22:41, 4 Sep 2004 (UTC)
replies: text: Candidatus isn't part of the name, it is a qualifier to indicate that the name has not (yet) been validly published. Since inclusion in wikipedia does not constitute formal publication, the page won't do any harm as it is, except possibly that it could alert others to the existence of this organism, who might then rush to print with their own formal valid publication and 'steal' the kudos of having described it. But I'd guess that anyone with the ability to do this will know about it from other sources anyway. The page needs a bit of cleaning (it's -> it is, etc). I'd also think the page might be better titled as the genus name only, not the full species binomial name (c.f. other monotypic genera). - MPF 23:13, 4 Sep 2004 (UTC)
thread_title:  Candidatus - a new naming code

message: Hi all - Several of us have been working on creating a Wikimedia Newsletter on Meta. Since ToL is by far the largest WikiProect in Wikipedia we would like one (or more) of you to write a quick summary of where the project stands for the newsletter. We are especially interested in how the different language versions interact and the possible use of the Wikimedia Commons to store taxoboxes. Anything you can add will be appreciated. :) --mav 04:51, 6 Sep 2004 (UTC)
thread_title:  Wikimedia Newsletter 

message: Shark articles have picked up a :Template:Sharks, which is incomplete, redundant with the category, and will be gigantic if all 368 shark species get included in it. Between taxoboxes and categories, I'm inclined to say that's plenty of navigational machinery, and the template on top of that is just extra noise. Any other opinions? Stan 15:31, 14 Sep 2004 (UTC)
thread_title: Use of templates

message: With some non-classification entries, Bagworm moth has a few lines in there that don't fit with the current taxobox. I'm sure there's a separate debate as to whether those things actually belong in the taxobox, but for now, I think we need a Template:Taxobox_foo_entry for them (Taxobox_unranked_entry is not it). Unfortunately, I cannot think of a good name for it. Help would be appreciated :-) -- Yath 07:14, 21 Sep 2004 (UTC)
thread_title:  General purpose placement template 

message: The current page is prosimian, but I think it would be best to split it into two articles. "Prosimian" is a polyphylogenic grouping that includes all strepsirrhines, plus the tarsiers and the extinct omomyids. Please follow up on talk:prosimian - UtherSRG 15:29, 27 Sep 2004 (UTC)
thread_title: Prosimian vs Strepsirrhini

message: The PloS is a new open-access organization whose mission is to make the world’s scientific and medical literature a public resource. They operate under the Creative Commons agreement , in other words within the copyright restraints of Wikipedia. I bring this to your attention, since PLoS Biology will contain articles which might be of interest to us.  JoJan 12:33, 12 Oct 2004 (UTC)
replies: text: Kewl! - UtherSRG 12:48, 12 Oct 2004 (UTC)
thread_title:  Public Library of Science 

message: 













































Species:C. esculenta(L.) Schott



I've moved the taxoboxes from above to here, and added two more (the current format and another possibility). I think we've all had a say and I don't expect there to be any change in positions. Which means it's getting close to time to lining up the options and coming to a concensus on which option to use. To facilitate that, voila. Let's see about doing this for a week. (Polling closes 16:00, 23 Oct 2004 (UTC)
thread_title: Taxobox Examples and vote

message: ====Support====
# UtherSRG 15:57, 16 Oct 2004 (UTC)
thread_title: Box 1

message: # UtherSRG 15:57, 16 Oct 2004 (UTC)
thread_title: Support

message: # Yath 18:05, 16 Oct 2004 (UTC)
thread_title: Oppose

message: # gadfium 17:58, 16 Oct 2004 (UTC)
thread_title: Neutral

message: ====Support====
# UtherSRG 15:57, 16 Oct 2004 (UTC)
thread_title: Box 2

message: # UtherSRG 15:57, 16 Oct 2004 (UTC)
thread_title: Support

message: # - Marshman 16:47, 16 Oct 2004 (UTC)
thread_title: Oppose

message: ====Support====
# UtherSRG 15:57, 16 Oct 2004 (UTC)
thread_title: Box 3

message: # UtherSRG 15:57, 16 Oct 2004 (UTC)
thread_title: Support

message: # - Marshman 16:47, 16 Oct 2004 (UTC)
thread_title: Oppose

message: # Josh 21:33, 16 Oct 2004 (UTC)
thread_title: Neutral

message: ====Support====
# - Marshman 16:47, 16 Oct 2004 (UTC)
thread_title: Box 4

message: # - Marshman 16:47, 16 Oct 2004 (UTC)
thread_title: Support

message: # UtherSRG 15:57, 16 Oct 2004 (UTC)
thread_title: Oppose

message: # Josh 21:33, 16 Oct 2004 (UTC)
thread_title: Neutral

message: The status quo is Box 2. It's my preference to keep status quo, and it's what we should do until we have concensus to change. My least favorite is Box 4. Of the others, I think I'm equally ambivalent about them, but can support using them. Box 1 would require a new template to be created (not a bad thing, just stating facts), or the existing genus entry template to be modified, and it wouldn't be difficult to do. - UtherSRG 15:57, 16 Oct 2004 (UTC)
replies: text: Quite so. Ain't that gonna be fun. - UtherSRG 22:28, 16 Oct 2004 (UTC)
thread_title: Comments

message: Well the poll isn't closed, but the results have been unchanged for some days, and it is clear the status quo doesn't enjoy support. Box 1 and box 3 look like being the only contenders worth thinking about (5/1/1 and 7/1/1 respectively). Yath is your opposition to box 1 strong? Marshman box 3? Pcb21| Pete 08:52, 22 Oct 2004 (UTC)
replies: text: No. :-) --Yath 00:02, 27 Oct 2004 (UTC)

text: No problem, I can accept box 3. I think it is redundant (since species name and binomial name are terms that refer to the same thing) but if it is felt it is in keeping with the taxobox form, I'll use it - Marshman 19:11, 26 Oct 2004 (UTC)
thread_title: The next step

message: Should an article like this be at the title Oleaceae which is now a redirect. Some of the species seem pretty far from the common understanding of an olive. Rmhermen 14:10, Nov 8, 2004 (UTC)
:I'd say yes. While it's good to have the article title be a common name, it's not good when that common name is misleading, as in this case. - UtherSRG 14:51, 8 Nov 2004 (UTC)
replies: text: ditto.  -- WormRunner | Talk 16:04, 8 Nov 2004 (UTC)

text: Technically, "olive family" is just as accurate as "Oleaceae" - note that a large number of botanical writeups write "olive family Oleaceae" at least on the first usage, which says two things; a) they're synonyms, and b) the "-aceae" names are still not quite second nature to everybody, what the computer nerds would call a "human interface"
problem. :-) But we've signed up with the Latin names. (Might not hurt to have redirs tho, "soapberry family" garners several thousand matches, 600 of them not mentioning Sapindaceae at all.) Stan 17:03, 12 Nov 2004 (UTC)
replies: text: I'd say "yes" to Oleaceae.  While I can understand the concern that common names are more familiar to most people, it is not the case that "olive family" should mean "all plants that look like an olive."  The terms are, in essence and as notedabove, synonyms; therefore olive family means: "plants related to and sharing specified morphological characteristics with the familiar olive plant." As cladistics advance this becomes "plants related to and sharing a specified genetic similarity with the familiar olive plant." - Marshman 17:40, 12 Nov 2004 (UTC)
thread_title: [[Olive family]]

message: When I come across a taxobox created with the table code rather than the new ToL template I update it. I'm not sure if people are of the opinion 'if it ain't broke -don't fix it', or if its better to update them to make any subsequent updates simpler. A list of entries with the 'old' template can be found here  .--nixie 02:48, 12 Nov 2004 (UTC)
replies: text: I think it's good to make the changes in an ad hoc manner. No need to rush out and change all the taxoboxes at once, but if one happens upon an article and it's got an old format, update it. If one is bored they could pick an article that needs an update taxobox and start there and work up and down the tree as appropriate. I've done that with Canidae and Felidae and with some other mammals. - UtherSRG 14:56, 12 Nov 2004 (UTC)
thread_title: 'Old' style taxoboxes

message: (Posted by new User:Fledgeling on my user page - can anyone help out? I'll have a look in HBW, but I suspect that's not up-to-date enough) - MPF 09:51, 21 Nov 2004 (UTC)
thread_title:  ! Important ! Kiwi page sorely out of date! 

message: There is something of an edit war starting with User:Mario and Dario on Anseriformes, Anatidae and the various whistling duck species' pages. I posted the following on their talk page:
::I noticed that you made changes to Penguin (new species) and Anseriformes. Usually we follow the taxonomy of Handbook of birds of the world (list available on-line). Where we want to show an alternative view, we normally make it as a comment in the next.
::I've done this with the whistling duck, since your change makes it inconsistent with related pages and with Wildfowl of the world. I've left the penguin species for now. On the relevant talk pages, could you please indicate the sources for the proposed changes? Many thanks, jimfbleak 06:31, 4 Dec 2004 (UTC)
replies: text: Hi again. The problem with ITIS is that it is a bit eccentric, and, as a USDA source, strongly linked to one country. Unfortunately, the USA taxonomy is also the one most out of step with the rest of the world, which is why we settled on HBW as the standard source. HBW
Wikipedia:WikiProject Tree of Life
Unfortunately, their only response has been to revert my changes, which I thought were a fair compromise. Any views? Should the relevant pages be protected pending resolution? jimfbleak 06:51, 6 Dec 2004 (UTC)

text: Hmm...unfortunately, my knowledge of ornithology is not strong enough to be able to offer factual support to either side. However, it looks like you have good evidence for your version. What I'd recommend is for each of the pages involved, explain on the article's talk page your reasoning, including documenting your sources if possible. Then go ahead and update the article in line with your ideas, including a statement about alternate views as you did before, if its appropriate (that is, if it's seriously a controversial topic). In your edit summary, I would very briefly explain the edit and make a note to discuss changes in the talk section before making them. If that doesn't work, or if this is too much or unfeasible, then protection may be necessary. Hopefully good documentation and explanation, along with vigilance, will suffice. Also—are there any other ornithologists who can help out here? — Knowledge Seeker দ (talk) 05:24, 7 Dec 2004 (UTC)
thread_title: [[Whistling duck]]

message: I haven't found any guidelines on this in the project page or in the talk archives, but if it's there just point me in the right direction, please! *grin*
There seems not to be consistency regarding the anglicization of names for higher taxa.  Since I'm working on fishes (see Wikipedia:WikiProject Fishes), I'm primarily concerned with them, where the family names are normally of the form Fooidae and the order names of the form Fooiformes, where both derive from the generic name Foous (or Fooa). It is common to anglicize the family name as "fooid", and (less so) the order name as "fooiform".  Should articles and categories be using Fooidae/Fooiformes or fooid/fooiform?  The Latin forms violate the singular and the English-language rules for article names, but in some cases the anglicized forms just look a bit odd.  The plural angicized order names in particular look strange, because they look like misspellings of the Latin forms (Fooiforms for Fooiformes).  In most cases, the anglicized systematic names are the only unambiguous English names available (how else, for example, to distinguish Perca, Percinae, Percidae, and Perciformes?). I'd like to do cleanup on this as I go through the taxa, but I'm not sure which to standardize on.  What does the ToL community think about this? 
One way to handle it might be to use (singular) anglicizations for article names and (plural) Latin forms for categories.
(On a related subject, can one anglicize a subfamily name of form Fooinae as "fooine"—e.g., can one refer to the "percine fishes" for fishes of subfamily Percinae?) —Tkinias 03:18, 13 Dec 2004 (UTC)
replies: text: I'm gonna take a whack at this. The preferred article title should be the common English language name for the group. Barring that, it should be the formal taxon name. The anglicized terms can be used casually through the article, and yes, "fooid" and "fooin" are perfectly acceptable casual terms for creatures classified in "Fooidae" and "Fooinae", with acceptible adjectival forms being "fooide" and "fooine". I'd guess the same could be said about "fooiform" and "Fooiformes", but since I primarily work with primates and cephalopods, I don't encounter the -iformes ending very often. Categories are less rigorous and generally less formal. For instance, look at the category tree starting at :Category:Primates. On the other hand, there's way many more fish taxa than there are primate taxa, so you'll want someting more than what I've got. lso, I'll probably want to add some finer granularity if all the primate artices are created. - UtherSRG 04:41, 13 Dec 2004 (UTC)
thread_title:  Category and article names 

message: I'd like to get a feeling for peoples like or dislkie for the 'always used common names' paradigm. I don't like is for a few reasons:
#Common names aren't universal, and it irks me when an article's name gets changed to the USDA PLANTS common name especially when that plants isn't from the US or a significant agricultural or horticultural species there.
#The same common name is applied to different species in different countries, like Mountain Ash or wood duck (there is also an Australian wood duck Chenonetta jubata).
I think a better system would be to have redirects to the species or disambiguation pages where a common name applies to many species. Since wikipedia isn't paper an integrated system of cross referencing shouldn't be a problem, nor should updating if name changes occurs. Let me know what you think, and I'll decide if I should take this on to the Village Pump--nixie 04:58, 13 Dec 2004 (UTC)
replies: text: I have been in favor of this for some time.  Go for it! -- WormRunner | Talk 06:03, 13 Dec 2004 (UTC)

text: I'd very much like to go with scientific names for the individual articles, certainly for plants. What Nixie points out is true; it'll also promote accuracy, and add A LOT to the reputation of wikipedia as a serious reference source. Just wishing I'd joined wikipedia before the 'use common names' was settled on! It'll be a huge task to move everything now, but I'll be happy to help do so. Birds, I'm not quite so sure; even some surprisingly high-powered ornithological journals use common names more than scientific names (typically a species is referred to by both common and scientific at the first mention, and thereafter only by the common) - MPF 13:48, 13 Dec 2004 (UTC)

text: Obviously, this is a never-ending story. We have agreed upon rules in the past, with  in the end as golden rule : use your common sense. I agree with MPF. I use the scientific name for the title, unless the common name is really commonly known and indicates univocally the taxon discussed. Anyway, when I use a scientific name as title, I put an eventual common name on top in the taxobox. Scientific names in titles also have the advantage of easily being found by bots, linking the diverse Wikipedias. BTW, have any of you noted that our Tree of Life-articles are being taken more and more seriously by the rest of the world ? For instance, the article on the orchid family Orchidaceae, where I and several others have worked on,  is mentioned as reference on On-line orchid references, in the company with the best, such as Kew, IUCN and several other great orchid sites. We have the eyes of the world upon us. Therefore we must have a correct and uniform standard for naming taxons. If the rules of the past don't agree with several of us, then the discussion is wide open again. But if we have to change the rules again, the task of changing the existing articles will be gargantuan. Better think twice. JoJan 14:40, 13 Dec 2004 (UTC)
thread_title: Common names