Wikipedia talk:WikiProject Tree of Life/Archive 8

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16	2005-09 – 2005-12	Paleontological ranges; Rosopsida; Taxobox redesign; identification
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MW 1.3 taxobox templates

Latest comment: 20 years ago4 comments2 people in discussion

Well folks, the time has come to build taxobox templates. Is there a clue somewhere to teach us all the bells and whistles of MW 1.3 templates? - UtherSRG 21:00, 29 May 2004 (UTC)Reply

Well I have started playing a little bit. See Template:Taxobox and User:Pcb21/Taxobox_test for a flavour of what we might do. This is not "production-ready" by any means. It is clear that they are major issues at the moment. Specifically

I am not sure if it is possible to use '|' as part of a parameter - that makes including things like [[Image:Image_name.jpg|Image_description]] very difficult
Images do not appear to interact well with templates more generally.

Will interested parties please meddle with the template page and the test page (which can be moved out of user name space if you like) to see what improvements can be made. But please don't include this in articles just yet - I think we will be changing template parameter names quite a lot in the first few days and it will be a bitch if we have 1,000 pages to update along with it. Pete/Pcb21 (talk) 23:48, 29 May 2004 (UTC)Reply

Crud.... I don't like 1.3 much then... and even worse when you want to sometimes have a field in a taxobox, and sometimes not. For instance, sometimes we'll want the suborder field as you have it. But if there is not suborder for the given family/genus/species/etc, you get an ugly line with {{{suborder}}}, or a blank, depending on if you provide a blank or don't list the field at all. Not good! I'v'e modified the taxobox template a little, adding an authority field.- UtherSRG 00:06, 30 May 2004 (UTC)Reply

I've had some further thoughts about the 1.3 templates. We need to be more flexible in setting them up, and they'll work better for us. Check out User:UtherSRG/Taxobox_test and Template:Taxobox 8fields status noimage authority norange. We'll need templates for 2-? fields, some with/without status, range, image, authority. - UtherSRG 02:19, 31 May 2004 (UTC)Reply

The problem is that with each optional field the number of templates necessary increases twofold. I guess we can make authoriy mandatory (leaving it empty gives just a mildly ugly empty line, and the authoriy is usually rather easy to find). To a lesser degree the same applies to the status. Yet noimage and nomap we definitely need, while I prefer to have the map in the article instead of in the taxobox which would make that field obsolete - but that's a different discussion. However I don't like the 8field-version - IMHO it's easier to use a template where one has to write "kingdom=animalia" instead of "level1=kingdom|level1_value=animalia". IMHO taxoboxes which include the sublevels like subclass or infrafamily are not the most standard one, so those can get a different template. And don't forget we need taxoboxes for the higher levels as well, not only for the species. Too bad the templates don't have a full programming language built in :-) andy 12:03, 1 Jun 2004 (UTC)

I can dig not having a "noauthority" bit although "noauthority" and "nostatus" make sense for the non-species level boxes. Take a look through the various pages. Many have "sub-" and "super-" level rank information. Do we want to remove that information for the sake of simplifying the template, or do we want a set of flexible templates that can handle whatever it is we think is needed for a particular article? I think we are much better off with the flexibility. At least the template is easier to read than the Wikitable format! *grins* And I'll second that request for a template programming language! *grins* - UtherSRG 13:12, 1 Jun 2004 (UTC)

BTW - I agree that my "unnamed fields" version is clunky. Let's look at this from the user perspective. There are two kinds of users - those knowledgable in why things are the way they are (because like you and me they are here in the discussions or following along) and those that don't understand but edit pages anyway. We will know that if we're adding a taxobox to a new article, that we'll need to match # of fields and template name. We'd also know (with the less flexible, precanned field names) that we'd need to match template name to article taxon level. Either way we know we need to match something. The unwashed masses? They'll copy a template from something, slap it in place, call it golden, and one of us will come by and clean it up - just as we do now anyway. - UtherSRG 13:12, 1 Jun 2004 (UTC)

Thing is though that if templates remain the preserve of advanced users, is it really worth bothering with them at all, particularly if we have to maintain a lot of templates. All we gain is the removal of ugly-looking table code from the edit screen.

I think it might be possible to minimize fields though. By omitting horizontal lines where possible (ie. using br instead of tr), the pages won't look too ugly if the authority, status and range fields are optional. If omitted, all we get is a little whitespace. Is this possible, especially given the '|' restriction? Pete/Pcb21 (talk) 13:31, 1 Jun 2004 (UTC)

(Outdenting for fun and profit....) I'm not saying that templates will be the balliwick of the advanced - at least no more than taxoboxes and taxotables are now - and to a certain degree they are. the more clueful editors figure it out. The less clueful ones slap in something they think is right, but needs to be fixed, or they don't bother. Same as now, same as it always will be. *grins* - UtherSRG 14:14, 1 Jun 2004 (UTC)

I suppose we could put the 'br' tag into the passed in value for status and authority, that would save the whitespace. Um... nowait... "authority" and "status" booleans would only be used for species level boxes, which would have at least 7 fields (KPCOFGS) and would always have a Binomial name section. So perhaps 7-12 fields for species level boxes, plus booleans for "authority", "range", "status", and "image". Non-species boxes would never have "authority", "status" or range, but would have a bottom section listing the next level down (class list for a phylum box, genus list for a family box, etc). Say 2-9 fields, plus a boolean for "image". 96 species level boxes and 16 non-species level boxes. (And I'm sure someone will chime in with a "What about the subspecies?"....) Once we get things settled, I'd be more than happy to do the grunt work to make the 112 templates... It'll mostly be copy-and-paste work. - UtherSRG 14:14, 1 Jun 2004 (UTC)

Ahem - the authority can also be present in the higher level taxons, it may only be less common to list it. But it principle it makes no difference if a taxonomist introduces a species or a genus or a family. andy 11:46, 3 Jun 2004 (UTC)

Oh certainly. However, Wikipedia_talk:WikiProject_Tree_of_Life/Archive4 we discussed putting it in the Binomial name section. It doesn't (or shouldn't) exist in the Genera section, or in the Families section, etc, where there is a list of items. When a taxobox contains an authority, it should only contain one, and it should be a species-level taxobox. Authority info can be added elsewhere in the articles about different taxa, although I find its addition tends to be "not-pretty". - UtherSRG 11:59, 3 Jun 2004 (UTC)

Urgh... I've editted my test template and taxobox again to get the Status working with our nice colorful Status msgs. Um... can someone take a look and see if it can be fixed? It would be very nice to get this to work.... then we can do similar for the taxon rank names, to make the non-EN folks happy and contented. - UtherSRG 14:14, 1 Jun 2004 (UTC)

Optional elements in taxobox templates

I happened on this site [[1]] in the Danish Wikipedia. There were some elements included in the taxobox that I had not seen before in the English Wikipedia, like height, flowering season, gardening instructions. What about including them as OPTIONAL elements in the botany taxobox template ? Opinions, anyone ? JoJan 16:12, 4 Jun 2004 (UTC)

Besides the fact that that isn't data we've decided to add to our taxoboxes (optional or not), the new 1.3 templates don't allow anything to be optional. *grumble* *grumble* *grumble*.... - UtherSRG 16:36, 4 Jun 2004 (UTC)

Does it look like optional elements are going to be added? If not, there's the possibility of a hack where different parts of the table are put in different templates:

{{Taxobox_begin | name = Rotifer | color = pink}}
{{Taxobox_section_image}}
[[Image:Rotifer.jpg]]
{{Taxobox_section_placement}}
{{Regnum | taxon = [[Animal]]ia}}
{{Phylum | taxon = '''Rotifera'''}}
{{Taxobox_section_subdivisions}}
[[Seison]]oidea<br>
[[Bdelloid]]ea<br>
[[Monogonont]]a
{{Taxobox_end}}

I wouldn't actually recommend it, but if templates are important to you, it would be better than creating dozens or hundreds of different templates - defeating the whole point, I think, of making them easy to use and update. It's not very pretty, but certainly not much harder than HTML once explained. - Josh 02:57, 14 Jul 2004 (UTC)

*blink* Wow. Now that's elegant! Duh! One of the primary rules of computer programing: divide and conquer! "Taxobox_begin" would setup the table? Brilliant! - UtherSRG 03:18, 14 Jul 2004 (UTC)

Well, I've started. Check out /taxobox_test. It needs some tweaking, but I think this is a workable idea! Need a way to get pipes to work (right now they lead to an edit. Also would be nice if they fixed the template in a template so we can use {{regnum}} and the Status templates. - UtherSRG 02:11, 16 Jul 2004 (UTC)

That's pretty bad, but I think that's inevitable, and it's nice enough within the limitations. A concern that I hadn't thought about. The placement section opens up a table. However, the subsequent section may be either binomial or subdivisions, and it's conceivable a taxobox may have both (or neither). I see two options:

Have begin and end tags for the sections, too. This is somewhat more flexible - we may have similar problems with </td>'s at some point - but is awfully close to just renaming table code.
Drop the nested table and make everything else span two columns. That involves no new template tags, but seems really brittle.

Also, if templates can't be nested, wouldn't it be better to have separate ones for different rank entries? The current set-up breaks the multi-language power. Although I suppose that can't be avoided unless we want to use taxobox_initium and taxobox_finis. Josh 05:18, 16 Jul 2004 (UTC)

I've tweaked it a little more. We can now include the Status templates. I really don't like that pipes don't work, *and* that you can't kluge around the breakage by using two parameters that are internally piped together in the template. This is just unacceptable. This feature is b0rken and needs addressing. I'm going to chat on MW again to see if a developer can put some attention to it. - UtherSRG 11:57, 16 Jul 2004 (UTC)

In response to Josh - yes, it would be better to havedo as you suggest. I was hoping that the nested templates had been fixed. Pipe dream, no pun intended. I'll make such things as {{Taxobox_regnum}}}, etc., so that the exiting {{regnum}}, etc., will continue to work while we get this form working.

For taxoboxes without a binomial/subdivision secion, or with both, I'll make a new template that just closes the taxonomy section. It's the only section that I think needs it. In general, we don't have to worry about </td> tags because the wiki processing adds them as needed. Also need a range_map template. - UtherSRG 21:19, 16 Jul 2004 (UTC)

More tweaking. Now it looks nearly identical to the taxobox on Bonobo. The only exception is where a pipe is used in Bonobo, an external link is used in the new taxobox. - UtherSRG 21:52, 16 Jul 2004 (UTC)

Well done. Looks fine to me. JoJan 22:05, 16 Jul 2004 (UTC)

To me, too. Maybe taxobox_section_placement should be renamed taxobox_placement_begin to make it clear it needs a closing tag. Otherwise, I don't see why it couldn't be used. I like how you did optional status. Josh 08:56, 17 Jul 2004 (UTC)

Good idea. Done. And thanks! :) - UtherSRG 20:01, 17 Jul 2004 (UTC)

So, are we ever going to use this? I said I wouldn't recommend the approach, but that was before people started worrying about HTML and wiki tables, which are really not that important and is rendered a technicality by these templates. Josh 04:26, 23 Jul 2004 (UTC)

I'll bite the bullet... i was hoping there'd be some positive response to my comment on meta and sourceforge about the pipe breakage within the template. the only response I got was to use the external link format.... which i don't like because you can't tell if the link will give you an article or an edit box.... i'll update Bonobo with the test taxobox and start working on converting the taxoboxes for primates and then on the project page. - UtherSRG 05:07, 23 Jul 2004 (UTC)

Hi Uther - just had a look at Bonobo. Is it right that the genus name and species author should appear as external links? - MPF 08:28, 23 Jul 2004 (UTC)

For now it is... you can't send a pipe into a template (taxon=[[Chimpanzee|Pan]]) and when constructing the pipe internally in the template, it always gives an edit link. The work aruond is to use an external link instead. - UtherSRG 16:33, 23 Jul 2004 (UTC)

Big Damn Heroes! Who? The developers, that's who. They fixed the pipe trick for templates. Now we can do things like {{Taxobox_genus_entry | taxon = '''''[[Chimpanzee|Pan]]'''''}} just like one would expect! Kudos to the BDH (and to all y'all who know where the phrase BDH comes from)! - UtherSRG 13:25, 2 Aug 2004 (UTC)

Distinguishing fossil and extinct species

Don't know if this has been discussed before or not . . . I'd like to suggest means for distinguishing non-extant taxa in taxon lists. There's two groups; those which became extinct naturally in prehistoric times (e.g. dinosaurs), and those that became extinct through human intervention. Can I suggest that the former be cited as 'fossil', and the latter as 'extinct' - or can anyone else suggest better naming? I'd also like to suggest adding a dagger † before taxa in lists to indicate they are not extant; I've done one example so far as an indication, at Cetacea; excerpt:

- - - - Southern Minke Whale, (Antarctic Minke Whale) Balaenoptera bonaerensis
        
        Balaenoptera omurai, discovery announced November 2003. No common name yet in usage
    - Subfamily Megapterinae
      - Genus Megaptera
        Humpback Whale, Megaptera novaeangliae
  - † Genus Eobalaenoptera
    - † Eobalaenoptera harrisoni, fossil species first discovered June 2004. No common name.
  - Family Eschrichtiidae
    - Genus Eschrichtius
      - Gray Whale, Eschrichtius robustus

Will hold fire on any others until consensus is reached. Anyone any thoughts? - MPF 08:45, 4 Jul 2004 (UTC)

Daggers are becoming extinct, and I'd like to help make it so. The dagger symbol is used in this manner because of the Christian overtones in connotes. As a non-Christian, I distinctly dislike this usage. An asterix is the currently accepted replacement for this usage. Otherwise, I'm fine with the notion. - UtherSRG 09:09, 4 Jul 2004 (UTC)

I'm irreligious so to me the dagger and the asterisk are just symbols. If the prevailing wind of scientific convention uses the asterisk we should go for that. However it is not particularly intuitive to the general reader so maybe we will need a key at the bottom.

Also if we are making a distinction in the in-article lists, shouldn't we also make a distinction in the status section of the taxobox - i.e. split out {{extinct}} into {{extinct}} and {{extinct-fossil}}. Pcb21| Pete 09:39, 4 Jul 2004 (UTC)

I've no problem with an asterisk (though an asterix will be real difficult to do! :-)), but won't an asterisk at the start of a line need <nowiki> markup - a bit tedious? I'm with Pete in being irreligious and regarding † as just a symbol, regardless of its origin. Also agreed on splitting {{extinct}} and {{extinct-fossil}} (or just {{fossil}}?), that seems very sensible. PS thanks for moving this to the talk page, I thought I was on it already! - MPF 11:07, 4 Jul 2004 (UTC)

We could put the asterisk at the end rather than the beginning thus alleviating the need for nowiki tags? Pcb21| Pete 11:35, 4 Jul 2004 (UTC)

Must admit, I think the symbol, whichever symbol is chosen, is better placed at the start to make it more obvious that it isn't just a footnote indicator. - MPF 16:56, 4 Jul 2004 (UTC)

Please don't use asterisks. I don't know how often the are used to mark extinct groups, but a terminal asterisk is becoming a standard way to mark paraphyletic groups, so it would be confusing. The dagger is common, and I don't think its origin should stop us from using it. Who knows where asterisks come from, and who thinks it is important to their use?

Incidentally, with the whales, I think it would be better not to point out when there is no common name, and in such cases just list the scientific name by itself. This goes double for extinct groups, among which common names are extremely rare. Josh 18:25, 4 Jul 2004 (UTC)

The asterisk, when used in conjunction with the dagger, becomes a religious symbol (Wikipedia_talk:WikiProject_Days_of_the_Year#Neutral_born/died_symbols?). I retract my suggestion because ofthis and because of the usage to indicate paraphyly. There are plenty of other symbols usable to indicate a fossil-only species. Let's brainstorm. What symbol would best represent a fossil? Something that looks like a bone? A skeleton? A rock? I'm in agreement to split {{fossil}} from {{extinct}} - UtherSRG 21:39, 4 Jul 2004 (UTC)

Daggers have the advantage that they are the recognizable standard, used in books, papers, and web pages. Something like a bone may not be, especially when applied to invertebrate groups. I find it hard to believe that they're on the way out, but that there is no generally used alternative, and I don't see why a word or symbol's origin should stop us from using it when it has acquired a separate and generally accepted meaning (there are reasons to associate daggers with death other than that they look like crosses). That seems to be the general opinion here. If we can't use a dagger, though, I think it would be better to write extinct or some such after the group in question than to invent our own symbol.

Also, if you do separate extinctions that happened in recent and prehistoric times, please give them different names! As far as I'm concerned, extinct doesn't carry the connotation that it happened recently, and I'm sure anyone who works with palaeontology will feel the same way. Also, you may want to define exactly what the splitting point is, at what point something stops being a fossil. Perhaps it would be better to record periods and dates - extinct, Creataceous or extinct, 1497 AD? Josh 21:56, 4 Jul 2004 (UTC)

Yes, and ToLWeb isn't a user edittable encyclopedia that is concerned with presenting a fully NPOV. The dagger (and in conjunction) the asterisk present a connotation that is user un-friendly to some users. Since the rock surrounding fossils is often called the matrix, how about using # to indicate a fossil species? For species that became extinct in the human era, how about ! or @ or ^ or anything else? I agree with indicating the (approximate) extinction year, but I think using fossil, Cretaceous or even fossil, Cretaceous (xx-yy mya) would be better for fossil species. - UtherSRG 22:08, 4 Jul 2004 (UTC)

Of dates, the IUCN use 1600 as a start date to separate modern, definitely human-caused extinctions from older extinctions (some of which may well be human-caused, but are mostly open to dispute, e.g. mammoth). I reckon that would be the date to use - MPF 22:58, 4 Jul 2004 (UTC)

ToLWeb is just an example - as said, most papers do the same thing, and if our goal is to convey information sticking to a standard is valuable. My preferences remain to use the dagger (which seems to be favored above) and if not to use text, but I'd like to offer another possibility. We already have colors that connote extant and extinct groups, in the status messages. Instead of putting random punctuation, we could use these same colors for groups in the lists, and that would at least have the advantage of always having explanations near at hand (in the status bar of the linked group). Josh 22:22, 4 Jul 2004 (UTC)

I'm agnostic with regard to the particular symbol used. Dagger, or something else. However I would object strongly to selecting AD1600 as the cut-off date. That might (or might not) work in a recently-settled place like Europe, but it's useless over here in Australia (which has been settled for 50-odd thousand years). A great many now-extinct Australian species were alive and well when humans first arrived and began making changes. It would be absurd to make a distinction between "extinct (white Australians)" and "extinct (black Australians). A parallel argument applies to North America, which also had a massive loss of species after human settlement began.

Differentiating between Extinct and Fossil, on the other hand, is an excellent idea, which I fully support.

Tannin 08:08, 5 Jul 2004 (UTC)

Hi Tannin - I agree that many animals became extinct due to man before 1600 (applies here too, Europe has been inhabited by Homo sapiens for as long as Australia, and longer by H. neanderthalensis). I think the difference is more related to whether written descriptions from life exist or not; obviously this doesn't always apply (e.g. moa), but that date does more-or-less divide species for which contemporary written accounts survive, from those which are only known from fossil or sub-fossil evidence. - MPF 13:31, 5 Jul 2004 (UTC)

It seems to me that there are two critical differences we might try to capture: (a) extinct due to "natural" processes vs extinct due to human action; (b) known only from fossils vs. known from contemporary accounts (MPF's suggestion above). Neither can be applied absolutely objectively, and there may be cases for blurring either line (there, are, after all, written accounts in natural history books of "Antipodeans", sensu strictu - i.e. people with their feet pointing backwards). But of the two, (b) seems to me by far the easier and less contentious to apply, so it would have my vote any time. It also seems to me to correspond to a more important distinction in the kind of knowledge we can have about a species.

While I'm on the air, my two-pennorth on symbols... Look, it's fine with me for everyone to exhibit their sensitivities (which I don't share) on religious symbolism, and I hope you're all going to get rid of the crosses, stars, etc on your national flags... But for goodness' sake let's not be actually perverse about it. To put a * to indicate disappearance rather than appearance would be to run in contradiction to about 3 million printed German-language obituaries, where (as someone referenced above), asterisk/dagger are used to indicate birth/death - for reasons that may be religious in origin but are now completely conventional. If I remember rightly the same is done in a number of other European countries, and the convention is certainly familiar to many people other than Germans (me for one). The reality is there are only a limited number of simple symbols, and they've probably all been used by some religious or political group somewhere; so while I wouldn't actually advocate using swastikas to indicate introduced species, we have to be a bit pragmatic about reusing things. Also it may not be sensible, or indeed scientific, to get into denial about a couple of thousand years of cultural history, or to ignore the way that cultural symbols of all sorts acquire layers of meaning that don't just obscure but replace their origins. Ah, for the times when anthropology was considered to be part of biological science.

seglea 18:13, 5 Jul 2004 (UTC)

As a matter of fact, it's just the one person who's been "exhibiting their sensitivities". The bulk of support seems to be in the "I'm not religious but am happy to use the religious symbol" camp. In fact if the literature tends to use the dagger, it would be more POV of us to use something else. It is not for Wikipedia to "make a stand". It is for Wikipedia to follow others. If that turns out to be the case, I have a bit of a hope that SRG will let this one go in turn for some brownie points when we try to close the categories debate :) Pcb21| Pete 18:33, 5 Jul 2004 (UTC)

Tempting. Very tempting. :) I'm willing to let it go, but I will point to Wikipedia_talk:WikiProject_Days_of_the_Year#Neutral_born/died_symbols? once again. :) They removed the dagger and asterisk in favor of the more neutral d. and b. respectively. - UtherSRG 01:01, 6 Jul 2004 (UTC)

For what is worth, books like Rails define recently extinct as after 1600 for the reasons given above relating to the existence of specimens or written descriptions. jimfbleak

IUCN uses 1500. Since our status system is based upon theirs, I suppose it makes sense to use 1500. I'd prefer the more nebulous "all of recorded history", but it does seem that that is pushing things too far. - UtherSRG 12:20, 12 Jul 2004 (UTC)

Hi Uther - do you have a reference for 1500? - 1600 is the date I've come across several places, e.g. Errol Fuller in the major introduction on fossil birds in Lynx HBW 7: 11-68 - "It has become traditional to regard 1600 as an approximate cut-off date from which to determine recently extinct bird species. Lionel Walter Rothschild's pioneering work of 1907 began this trend, since which time the date on 1600 has been adopted by several other writers, including the present one. The date is not quite as arbitarily chosen as it may seem. The year 1600 represents a date heralding a period at which relatively reliable records began to accumulate; before this time it is generally impossible to make realistic sense of the few records that exist" - MPF 22:15, 12 Jul 2004 (UTC)

Sure do: IUCN Redlist FAQ. - UtherSRG 22:52, 12 Jul 2004 (UTC)

implementation of templates

Ok... so I've got the energy and eagerness to create {{StatusFossil}} or a set of them, or a parameterized template. Do we want "fossil" to show up as "extinct" currently does? Do we want it parmeterized so that we can indicate what epoch/age/etc the fossil record link back to? Should it have the "Status" link? - UtherSRG 08:55, 11 Jul 2004 (UTC)

Likewise, should "extinct" be modified to allow a parameter for the (approximate) year of extinction? - UtherSRG 08:58, 11 Jul 2004 (UTC)

Hi Uther - excellent, go ahead! I don't know the workings of the system very well, but if it would need a seperate template for each year or period ({{StatusExtinct 1603}}, {{StatusExtinct 1604}}, {{StatusExtinct 1605}}; {{StatusFossil Triassic}}, {{StatusFossil Cretaceous}}, {{StatusFossil Eocene}}, etc) then I think we should go for just {{StatusExtinct}} and {{StatusFossil}}. For fossil, I'd go for black or very dark grey (the colour that most fossils are!). - MPF 14:35, 11 Jul 2004 (UTC)

No we wouldn't need separate templates like that - the new 1.3 templates allow parameters. Thus we could write something like {{StatusFossil|when=Creataceous}} or {{StatusExtinct|when=c1620}}. i.e. we only need two templates in total. The disadvantage of having parameters is that something has to be put in for the parameter every time the template is used, even if the answer isn't really known in a particular given article. If we include the status link, we should update the status article to also make the distinction between fossils and recently extinct too. Pcb21| Pete 14:50, 11 Jul 2004 (UTC)

Pete is correct. Take a look at Template:StatusExtinct to see how I've modified it and then check out the "What links here" for it to see it in use. I've left Template:StatusFossil with the old "Extinct" behavior for now. Its range of input parameters could be more varied - I can think of a few different ways parameters might be used. We may want {{StatusFossil plain}}, {{StatusFossil era|when=[[era]]}}, {{StatusFossil range|appear=[[era1]]|extinct=[[era2]]}}, or a few other possibilities. These variations *would* need different templates, hence the "plain", etc., epithets. - UtherSRG 14:18, 12 Jul 2004 (UTC)

a bit more on status templates

While on this, I notice that the colour for Lower Risk on Conservation status is different colour to the template; I originally chose orange to be intermediate between green Secure and brown Vulnerable but someone changed it on the template as the orange was hard to see in one of the taxobox colours - unfortunately the new colour (greeny-blue) isn't too easy to see on plant taxoboxes! (nor is green Secure). Should there be a check-out to make sure all combinations are easily readable, with amendments if necessary? - MPF 14:35, 11 Jul 2004 (UTC)

colors

Here's the previous "test pattern". "Darkgrey" is used for "Bacteria" - do we have any fossil-only bacterial species? I'll see about adding a "Lower Risk" entry to the test pattern. - UtherSRG 18:10, 11 Jul 2004 (UTC)

	Animalia	Plantae	Fungi	Protista	Bacteria	Archaea
Secure	Animalia	Plantae	Fungi	Protista	Bacteria	Archaea
Lower Risk	Animalia	Plantae	Fungi	Protista	Bacteria	Archaea
Vulnerable	Animalia	Plantae	Fungi	Protista	Bacteria	Archaea
Endangered	Animalia	Plantae	Fungi	Protista	Bacteria	Archaea
Critical	Animalia	Plantae	Fungi	Protista	Bacteria	Archaea
Extinct in the wild	Animalia	Plantae	Fungi	Protista	Bacteria	Archaea
Extinct	Animalia	Plantae	Fungi	Protista	Bacteria	Archaea
Fossil	Animalia	Plantae	Fungi	Protista	Bacteria	Archaea
Unclassified	Animalia	Plantae	Fungi	Protista	Bacteria	Archaea

Hi Uther - missed out {{StatusConcern}} ({{StatusConcern}}) :-) - MPF 20:12, 11 Jul 2004 (UTC)

Ooops - how did I miss seeing your introduction sentence . . . must get my eyes tested! - MPF 20:12, 11 Jul 2004 (UTC)

Oh, and yes - there's fossil bacteria, OK, from way back to near the start of the fossil record. No idea if any are cited on Wikipedia, but they might be, as examples of the oldest known life forms - MPF 20:12, 11 Jul 2004 (UTC)

Heh... Yes... an eye test indeed... and here's your color chart. *grins* Ok, it seems that the "Bacteria" "darkgrey" isn't so dark as it works well with the "darkslategrey" I picked for "Fossil", at least to my eyes on my monitor. I've added "Lower Risk" into the table, too, and it doesn't look bad to me. But I'm color blind. :) - UtherSRG 20:48, 11 Jul 2004 (UTC)

Hi Uther, thanks for doing the chart! Very strange, Fossil "darkslategrey" shows up bright red (same colour as Critical) on my computer. Even stranger, 'Extinct in the wild' and 'Extinct' are different on my computer, even though both are "darkslateblue" ('Extinct' being a paler shade of violet). - MPF 23:33, 11 Jul 2004 (UTC)

Actually, only the name for "Extinct" is "darkslateblue". The table's coloring is "slateblue". But you are right about "Fossil Red". I grabbed the name from a table elsewhere, and I suppose it isn't a standard HTML color name. I've fixed it by using the raw number: #25383c. - UtherSRG 00:06, 12 Jul 2004 (UTC)

Wiki vs HTML

User:Guanaco is in the process of converting various tables from HTML to Wiki, including this project's table. Personally, I prefer the HTML. It's shorter and easier to read and edit. I'm very tempted to revert his changes. Can I get a "Hell yes" or a "Hell no"? - UtherSRG 17:50, 15 Jul 2004 (UTC)

I'm using Wiki for my taxoboxes all the time. I find it easier and less troublesome than HTML. By the way, HTML is changing into XHTML (version 1.0). It will be a hell of a job converting all those taxoboxes into XHTML, when the time comes. Besides, the conversion from HTML to Wiki markup is very easy : there is an automatic converter on this site : [[2]]. Although, when I change someone else's taxoboxes, I'm rather loath converting them to the Wiki markup. I'm afraid that the original author would get confused. But, all in all, I'm pro Wiki markup. JoJan 18:35, 15 Jul 2004 (UTC)

That's fine for your usage. I'm asking about this project, and what is standard and all that. As I said, I personally prefer HTML. Like you, I use my preference when making my own articles. Rarely I'll convert a really bad wiki table to HTML. Yes, the convert from HTML to wiki is easy, but the reverse is not true. - UtherSRG 18:45, 15 Jul 2004 (UTC)

The use of Wiki markup is explained here : Using tables. If I remember correctly, originally Wiki markup was preferred to HTML. Now it is given on equal footing. So, that makes it confusing to decide which one to give preference. In other words, there is no standard. But since HTML will be replaced in time by XHTML, I put my all my eggs in the Wiki basket. Lets find out what others think about this. JoJan 18:55, 15 Jul 2004 (UTC)

If they are equal, then Guanaco shouldn't have gone and made the converts and I'll unconvert them. - UtherSRG 18:58, 15 Jul 2004 (UTC)

I use Wiki tables whenever possible, and even convert occasionally. I personally think the wiki syntax is easier, and less likely to create strange results - a missing </td> normally is fine, but some browsers might have a less optimal html table error fixing. And after the MediaWiki1.3 change some HTML table had strange behaviour, while the wiki table was fine. andy 19:06, 15 Jul 2004 (UTC)

My point is that none of the three tables in Using tables are given higher standing, so a convert for no other reason shouldn't be done. I convert to HTML when I find a fubared wiki table 'cos I haven't figured out how to tweak the alignment and auto-bolding on a line-by-line manner in the wiki code. I also don't care to learn yet-another-system of making tables. I can make an HTML table offline and view it to make sure it works, and then dump it into an article. I can make an HTML table for my own web page. Why should I have to learn wiki? I don't. That's why they are given equal standing. - UtherSRG 19:11, 15 Jul 2004 (UTC)

The argument for wiki tables runs the same way. I think we should just leave this stand, because it won't matter so much once we get decent templates. Josh 19:38, 15 Jul 2004 (UTC)

We should be preferring wiki tables, for the same reason we use tripled quotes for boldface instead of HTML - HTML is too low-level and finicky. I've spent far too much time debugging the seas of "<" and ">" trying to figure out why a taxobox is wrong; half the time I end up leaving it for somebody else to figure out. If there's something wrong with wiki tables, we have people we can bug to fix them. Stan 20:35, 15 Jul 2004 (UTC)

I can say the exact same thing, reversing wiki and HTML. I've spent far too much time wading therough the seas of "|", "||", "|-", trying to put in an 'align="center"' that I've just replaced a table outright with an HTML one. There are plenty of folks who you can ask to fix a messed up HTML table. - UtherSRG 21:31, 15 Jul 2004 (UTC)

HTML tables, like most HTML within MediaWiki, are deprecated. Please see the older revision of the help page on Meta. The only reason it now suggests HTML tables are allowed is because someone merged the page with the old help page from the English Wikipedia, which still included information about the old-style tables. I disagree with that edit as it just imposes one person's point of view that HTML tables are better. You can't specify one type of table as the standard for this WikiProject when the rest of the site is converting to proper wikitext. Yes, it takes a while to learn, but for newcomers with no knowledge of HTML, it is going to be highly confusing to come across pages that do not use the wikitext that is used everywhere but pages that are part of the Tree of Life project. Other Wikipedias are running bots to convert the old format, so you are also becoming increasingly inconsistent with them if you continue to revert changes back to the outdated HTML style. Angela . 03:27, 16 Jul 2004 (UTC)

Is there any way of making the wiki tables more compact? They require far too many carriage returns, which makes them nearly 3 times as long as a html table on the edit page. This makes for difficult editing with lots of scrolling up and down (and even worse if you want to move something, e.g. moving an image from the bottom of a table to near the top). If this could be fixed, then I'd be a lot happier to use the wiki tables. - MPF 21:29, 18 Jul 2004 (UTC)

I was an enthausiastic early adopter of the wiki table markup, but I've given up on it: it's just too darn difficult to read and understand. You can look at an HTML table and actually work out what it does - a wiki table is just an incomprehensible sea of |||| |||| symbols and new lines. We should convert to wiki syntax for tables after someone figurs out a way to make the wiki syntax readable and practical. (If that ever happens: it's a remarkably difficult task and it may eventuate that no practical solution ever emerges - I certainly can't think of one.)

BTW, in this context, the talk about HTML giving way to XML is a load of complete nonsense. Tables remain very much a part of the latest W3 specifications, for the simple reason that there is no other practical way to deal with tabular data. Tables are on the way out as page layout tools becausse divs are far superior. But tables remain a major part of the X/HTML world in their proper place: as a way of presenting tabular data. Tannin 22:15, 18 Jul 2004 (UTC)

Compacting Wiki Taxoboxes

I've just discovered that both of these formats work:

{| border=”1” cellspacing=”0” align="right" cellpadding=”2”
|- 
| align="center" bgcolor="lightgreen" | '''Common Hawthorn'''
|-
| align="center" | [[Image:Common hawthorn 800.jpg|200px|none|Common hawthorn]]<br>
<center><small>Common Hawthorn (''Crataegus monogyna'')</small></center>
|- 
| align="center" bgcolor="lightgreen" | {{Taxonomy}}
|-
|
{| align="center"
|-
| {{Regnum}}:
| [[Plantae]]
|-
| {{Divisio}}:
| [[Magnoliophyta]]
|-
| {{Classis}}:
| [[Magnoliopsida]]
|-
| {{Ordo}}:
| [[Rosales]]
|-
| {{Familia}}:
| [[Rosaceae]]
|-
| {{Genus}}:
| [[Crataegus]]
|-
| {{Species}}:
| '''''monogyna'''''
|}
|-
| align="center" bgcolor="lightgreen" | [[Binomial name]]
|-
| '''''Crataegus monogyna'''''
|}

and

{| border=”1” cellspacing=”0” align="right" cellpadding=”2”
|- 
| align="center" bgcolor="lightgreen" | '''Common Hawthorn'''
|-
| align="center" | [[Image:Common hawthorn 800.jpg|200px|none|Common hawthorn]]<br>
<center><small>Common Hawthorn (''Crataegus monogyna'')</small></center>
|- 
| align="center" bgcolor="lightgreen" | {{Taxonomy}}
|-
|
{| align="center"
|-
| {{Regnum}}:|| [[Plantae]]
|-
| {{Divisio}}:|| [[Magnoliophyta]]
|-
| {{Classis}}:|| [[Magnoliopsida]]
|-
| {{Ordo}}:|| [[Rosales]]
|-
| {{Familia}}:|| [[Rosaceae]]
|-
| {{Genus}}:|| [[Crataegus]]
|-
| {{Species}}:|| '''''monogyna'''''
|}
|-
| align="center" bgcolor="lightgreen" | [[Binomial name]]
|-
| '''''Crataegus monogyna'''''
|}

Obviously, the second is better, as it is more compact for editing, with fewer carriage returns, so less tedious scrolling up and down. But there's still far too many carriage returns there to make editing easy.

What can be done to make them even more compact, ideally with as few lines used as HTML taxoboxes? - MPF 11:33, 23 Jul 2004 (UTC)

Indeed, the double pipes make them more compact. Personally, I have no preference. Both are a lot easier to use than HTML. A really compact taxobox would be the taxobox templates, developed by UtherSRG. But he uses Html underneath the templates. If only, he would convert it to Wiki markup, this we would bring us into line with the rest of en.Wikipedia and indeed with many foreign Wikipedias.

Anyway, using the converter always gives Wiki markup of the first kind. If you want, you can edit them easily to the Wiki markup of the second kind, using double pipes. Furthermore, once a taxobox has been created, and there is no mistake to be found anymore, then editing of that taxobox becomes ipso facto unnecessary. That will be more the case in the future, but I realize that at this moment, we all are in the process of creating new articles and new taxoboxes. JoJan 17:08, 23 Jul 2004 (UTC)

Gee, and I thought that the move to template would make the underlying implementation of the template irrelevant. I created the templates the way I feel comfortable and confident about creting them. I don't understand Wiki code, I've tried to tweak wiki boxes and have given up. If other wikis want to use wiki code in their taxobox template, that's fine. If they make the sae named templates, they will be compatible with us. - UtherSRG 18:05, 24 Jul 2004 (UTC)

Well, taxobox templates are just a layer over the Html-code, as a macro is in Word. But we have to think a the future. I'm afraid that in the (far, or not so far ?) future, Html will become obsolete, just as Windows has replaced DOS. This would pose a serious problem for the thousands and thousands taxoboxes. Therefore a template, based on Wiki markup would be ideal and we would be conform to the rest of the Wikiworld. On the other hand, I know, there is the problem with the external link. You have done (more than) your best. We need a programmer to solve this problem. If I recall well, you have put this problem on the Meta Wiki. Until then, we will have to wait, unless someone else has a brighter idea ? JoJan 19:53, 24 Jul 2004 (UTC)

So, uh, I have a backlog of taxa I want to put in - what should I do? Can I use the templates? If so, then I don't care that much about what they expand into; changing later is easy, doesn't require touching articles. Stan 21:56, 24 Jul 2004 (UTC)

Chimpanzee naming

There's a current survey at Talk:Chimpanzee#Poll. Comments are very welcome. Mackerm 06:06, 19 Jul 2004 (UTC)

The poll is now closed, resulting in the articles in question staying as they are. - UtherSRG 13:08, 2 Aug 2004 (UTC)

Systematic vs common names

Well this [Chimp] poll didn't go my way, but what I was really hoping for were some comments, and sadly I didn't get many of those either. I had a second survey planned (whether Pan troglodytes should be described at Pan troglodytes or Common Chimpanzee), but before that I'd like some comments on the whole policy of listing species under common vs. scientific names. Birds are decided, and I have no problem with that, but everything else is a mess. Is everybody happy with a mix of common and scientific titles for the non-bird pages? Mackerm 06:18, 3 Aug 2004 (UTC)

Hi Mackerm - I'll admit not knowing much about chimps nor having a strong view on naming them, so never entered this poll/discussion. If wiki was starting over, my preference would (strongly) be to use scientific names for everything given that there is so much perverse and confusing naming of things in vernacular (and the perennial ding-dong over capitalisation!). But from what I've read, that would mean a major change of WPToL policy, as well as a huge number of articles to re-name. So generally, I've stuck with the English names except in the handful of most confusing English names. If a consensus for change to 100% scientific was achieved, I'd be happy to help do a deal of re-naming articles, though. - MPF 09:28, 3 Aug 2004 (UTC)

I agree with MPF, for the most part. If we were just getting started and ToL policy were to use scientific names, that would be peachy. But neither of those elements are true, and at this stage in the game, I believe keeping policy the way it is is better than changing the thousands of ToL articles we already have, and dealing with all the redirect issues this would create. - UtherSRG 11:46, 3 Aug 2004 (UTC)

As far as I can see, the current policy is so broad that it's functionally meaningless. In any case, we could specify that new pages should use the scientific name. Mackerm 02:10, 4 Aug 2004 (UTC)

I'd be against this. For those species that are familiar enough to have them, the scientific names of species are actually no more stable than common names - at present, rather less so if anything, with so much reclassification going on because of molecular systematics. But more to the point, who are species descriptions in wiki for? Are they for biological experts? Surely not - they will go to the original sources. They are (aren't they?) for the nonexpert - for whom the common names are much friendlier. Still, this discussion should probably go elsewhere, and has no doubt been had many times before... seglea 04:14, 4 Aug 2004 (UTC)

I skimmed the archives and didn't see any substantive discussion on this topic. I'll read it if someone points me there. I see no basis to say that scientific names are no more stable than common names; note the recent Wikipedia change to chimpanzee. My favorite garden book has all the plants described under their scientific names, and it's designed for the layman-- no problem there. And along with each plant description, it often gives several common names it goes by. I see no rational way to say which of the common names should be considered the "real" one.

Also note that common names don't necessarily match up to single species. I was going to say a little something about the tule, but I found this name is commonly applied to two different species. Then there are things like "Vinca" which means different things depending on if you are using a common name or scientific name. Mackerm 05:32, 4 Aug 2004 (UTC)

You get no better results when using scientific names. For instance, right now all the bird articles are classified using one system. There are at least two or three other classification systems of similar standing. Let's say next week someone publishes that all three are flawed and reclassifies all of the birds, including some reclassifications on the genus level. If all of our articles were name by scientific names, we'd have a whole big move fest. Instead, we'd just have to update the individual articles that are affected. These changes are happening all the time in large numbers of taxa as researchers use more sophisticated techniques to determine how the species are related. Common name changes, though, are much less affected by changes in (re-)classification, although it certainly does happen (as you've noticed). Also note, though, that common name changes take much longer to percolate from just the scientific literature to the broader usages.

The question then becomes 'At what point do we change from one to the other?' This question I think is best left to be answered on a case-by-case basis, and works in conjunction with many other questions: Should Wikipedia primarily reflect lay/common knowledge, professional/scientific knowledge, or some compromise between the two? Who will be looking for the information we have? Will they be able to find the information? Will they be best served by our articles being ahead of the change or lagging behind it? - UtherSRG 06:02, 4 Aug 2004 (UTC)

Deciding on a case-by-case basis is effectively having no policy, and I believe a policy is important here. As I said before, my favorite gardening book (for laymen) lists all plants under scientific names, with the various common names cross-referenced. Laymen use scientific names every day, and are comfortable with them.

I still see no basis for saying that scientific names for species are as likely to change as common names. As far as species having more than one scientific name, it doesn't seem to be a problem with Wikipedia's birds-- they picked one system for their taxoboxes without apparent problem.

But MY objections haven't been addressed. To restate: One common name may apply to several species. One species may have several common names. Mackerm 06:44, 4 Aug 2004 (UTC)

Mackerm's objections are important. But they don't convince me, because exactly that is true of scientific names, too. Look at all the cases of synonymy there are - all you have to do is run a genus search through ITIS or FishBase and you'll come up with typically twice as many scientific names as there are species to be named; conversely, as knowledge advances, species get split (e.g. what's recently been done with the African Elephant). Of course with scientific names this happens on a somewhat more principled basis than it does with common names, but the reasons are essentially the same - people in different places and at different times give the same name to different species, or different names to the same species, in good faith, and advancing knowledge shows we were wrong, so we change the names. There isn't any final knowledge out there that would give us an once and for all anchoring point (and, by the way, I don't think we should be giving the lay reader the misleading impression that scientific names have a finality they can never have). Normally, of course, one would hope that the scientific names would at least be more stable and justifiable than the common names - although revisions of taxa have always been the business of systematic biologists. But my point about stability is that, at present, this isn't so: we are in the middle of a particularly unstable couple of decades in scientific nomenclature, as the new molecular techniques overthrow a lot of the best conclusions that could be reached by more macro methods.

So I think the position we have reached is the best for the time being. It is, to summarise, that a good species article: (a) has as its main title the most common common name for the species, where one exists; (b) immediately mentions, in its introductory sentence, its currently best accepted systematic name; (c) early in the text (usually in the first sentence) mentions all other common names that are in widespread usage; (d) also early in the text, links to other species for which the same common name is used, explaining how different they are; (e) somewhere in the text mentions any significant reclassifications that have affected the systematic naming of the species. Probably we should add something that I know I don't always do: (f) it should have the systematic name as a redirect.

Of course, if we do all that, (a) is probably the least important matter. The great virtue of a computer encyclopedia rather than a printed one is that it can be searched on multiple bases with equal ease. But we do have to consider reader-friendliness, and (for better or worse) wiki does heavily privilege the main title of an article in serving it to the final user. I respect Mackerm's point that his favourite plant book titles by systematic names despite being written for lay people - that's evidence. But it's only a single case. I've just looked at my own collection of layperson's guides. I'm away from home, so I only have 6 on my shelves here... but every one of them titles entries by common names. I don't think we should lightly go out of step with what the market clearly suggests is preferred.

Sorry to go on at such length. I am now going to promise to write 3 new articles before I intervene in this debate again (so long as everyone else will promise to do the same).

seglea 07:19, 4 Aug 2004 (UTC)

Ha! No dice. But I will cut to the nitty-gritty. What do you do when two species have the same most common name, e.g. tule? (Fishbase appears to include spelling variants for species. I'll have to check further.) Mackerm 14:29, 4 Aug 2004 (UTC)

I think Seglea has a good point in his well-thought remarks. They could even be taken as a basis for a policy. Still we have to reflect a little more on practicalities. Like, what if the common name is different in American English and British English ? Take a look at Fireweed (Epilobium angustifolum), which is Rosebay Willowherb in British English. Which of the three names should we prefer in the title ? I'm in the process of rewriting and adding images to lots of botanical pages that are often little more than stubs. But they have already a title, which could be the scientific name or a common name (most of the time in American English). Should I then decide on a case-by-case basis or can these problems be described in a general policy ? I think others will experience the same problems in their fields. It worth debating. JoJan 15:06, 4 Aug 2004 (UTC)

And the bird organization here is following the British names. It's damn near impossible to have any policy that covers all of ToL on Wikipedia. - UtherSRG 16:00, 4 Aug 2004 (UTC)

My feeling on vernacular names is that preference should be given in the following order:
1. First choice to names that agree with accepted scientific classification - e.g. Manitoba maple takes precedence over Box elder, as the evidence for its classification in Sambucus is very poor;
2. Second preference should go to names used within the native range of the species concerned; in the same example, Manitoba maple (used in its native Canada) takes preference over Ash-leaved maple (used mainly in Britain, where it is not native);
3. Where two different, scientifically suitable names are used in different areas to both of which the species is native, the older name should be used, e.g. Horned Grebe (1785) should take precedence over Slavonian Grebe (1843);
4. other conflicts can be resolved by disambig pages, e.g. Black Vulture. Finally,
5. Objectionable names should definitely be avoided, e.g. "digger pine" for Gray Pine, "wellingtonia" for Giant Sequoia.
As an aside, on Epilobium angustifolium, the name Fireweed is widely used in Britain as well as the US, perhaps more by British gardeners trying to get rid of the stuff, than by British botanists. - MPF 18:27, 4 Aug 2004 (UTC)

Of scientific names, yes, there is some change going on, but not very much at the generic level, which is what would matter for article titles. Most of the changes are at species rank (e.g. one species being split into two), or at higher ranks (mainly which order various families belong to). There isn't a huge lot of changes from one genus to another. And moving pages isn't all that onerous a task. - MPF 18:27, 4 Aug 2004 (UTC)

Uther's note "Should Wikipedia primarily reflect lay/common knowledge, professional/scientific knowledge, or some compromise between the two? Who will be looking for the information we have? Will they be able to find the information?" - I find myself wondering, does anyone other than our small group at ToL read any of the stuff we write?!? :-) . . . but surely, with redirects, this won't matter anyway? If they type the one in the search, they'll get the other. And a google search will log both. - MPF 18:27, 4 Aug 2004 (UTC)

Ah, philosophy. Mine has been that WP is aimed primarily at lay people, with enough hooks to specialist material and literature that a motivated lay person can start from WP and learn enough to talk to a specialist productively. Another way to look at it is that most specialists are only expert in narrow areas - so for instance a tree expert might want to know more about the weevils eating on the tree, but finds the technical beetle literature rather daunting (60,000 species of weevil to choose from, oh goodie), and WP could be in the role of explaining the basics of weevils so the weevil literature is comprehensible.

As far as common vs taxonomic names goes, I don't think it's possible to have a single rule, you have to study usage among both experts and lay people. If there is any doubt about whether a common name is truly common, I go with taxonomic. FishBase is quite interesting to study actually, since they've accumulated hundreds of vernacular names; you can see patterns where some common names are stable and well-aligned with taxa, and others (like sardine), which are totally confused, and where WP's "value-add" is simply to provide signposts to all the possibilities. Stan 20:31, 4 Aug 2004 (UTC)

Does FishBase give any value judgements to the usage of the vernacular names it lists? - does it distinguish between real common names, used by thousands of people, and those which are (for want of a better term!) 'rare' names, where they found one 95-year old retired fisherman who could remember that name being used, once, by one person, in their childhood? - MPF 22:22, 4 Aug 2004 (UTC)

FishBase only distinguishes "Vernacular", "Market", "AFS", and "FAO" names, where the last two are name-assigning organizations, and "Market" is for names used in commerce (the can might say "sardines", but there are sprats inside). I think FishBase relies on local specialists to report vernacular names, don't know that they have any official criterion. Note that they don't necessarily want to discount that old fisherman, who may have once caught a megamouth shark, years before they became known to science - after all there were coelacanths being eaten routinely in Indonesia while the scientists were getting all excited about the ones off South Africa. Stan 04:41, 5 Aug 2004 (UTC)

I'm going to concede that it's impractical to change most articles to the scienific title. This means, though, that many common-name pages will potentially (and correctly) contain disambigtuation information. I think Stan has come up with a workable solution re. when to use scientific names. Mackerm 05:57, 5 Aug 2004 (UTC)

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