Wikipedia talk:WikiProject Tree of Life/Archive 21

Herrerasaurus
I've requested a scientific peer review of this article. The discussion is here, and all comments are greatly appreciated. Firsfron of Ronchester 06:58, 29 June 2007 (UTC)

Distribution maps
I have been working on some distribution maps for some species of birds and have been generating spot maps that are based on a number of sources (not all of them qualifying as equally reliable, but traceable and verifiable). I would just like to know if compilation of a map using data from multiple sources to generate a distribution map could in any way be construed as WP:OR (original research by synthesis). Thanks Shyamal 08:08, 29 June 2007 (UTC)


 * It's only OR if the synthesis is to advance a position, I can't see that a distribution map is likely to fall into that category. Assembling a taxobox is a synthesis of information, but it's just presentation, not polemics. Jimfbleak 12:05, 29 June 2007 (UTC)

Archive please
Can we archive please? The page is getting a bit long. Werothegreat 16:16, 29 June 2007 (UTC)


 * You may. I can't.  KP Botany 22:31, 30 June 2007 (UTC)


 * Consider it done. --Stemonitis 05:37, 1 July 2007 (UTC)

Input needed at WP:RFD
I have listed infraspecies and infrasubspecies at WP:RFD as confusing redirects. Editors from this wikiproject are invited to comment at Redirects for discussion/Log/2007 June 30. Thanks. Chick Bowen 22:01, 30 June 2007 (UTC)

confusion about what to do with eukaryotic higher level taxa flux
so i'm new here and i've started cleaning slime mould pages. i.e. the pages for Myxogastria: plasmodial or syncytial slime moulds, Protostelia: smaller plasmodial slime moulds, Dictyosteliida: cellular slime moulds, Acrasidae: similar life style to Dictyostelids, but of uncertain taxonomy

in particular. and the contradictory pages of higher level taxa they have been put in.

it's a tangled mess. so is there any consensus about this stuff? for instance there is: Dictyosteliida and dictyosteliomycota. there is slime mould and there is myxomycota. in each case one member of the pair sucks.

can someone sum up the discussion on these topics for me or do i have to read 20 archive files?

here's my ramblings on this tangle: User talk:Wikiskimmer/eukaryotic taxonomy, it's very confusing. i need a printer.

i cleaned up the slime mould page a fair bit. Wikiskimmer 21:38, 3 July 2007 (UTC)


 * YAY! I applaud your efforts.  We need more people like you and me who like slime moulds and other fun protists.  Werothegreat 02:08, 4 July 2007 (UTC)


 * O, I was just reading through some of your stuff... you should state that TRUE slime moulds belong to phylum/kingdom amoebozoa, and "pretend" slime moulds (slime nets, etc.) go elsewhere. Slime nets are chromalveolates.  And acrasids (or percolozoans) are excavates, and plasmodiophorids (the phytomyxea) are rhizarians.  Werothegreat 16:06, 9 July 2007 (UTC)

Bigfoot
Just to keep everything in perspective, I have written the following with our many excellent TOL editors in mind: User:Marskell/Think of the Children. Marskell 13:25, 4 July 2007 (UTC)

List of introduced fish in Australia
Hello. Would anybody in this WP be willing to help writing a lead section for this list? Thanks! A bbo tt 7 5 ☺ 01:01, 5 July 2007 (UTC)
 * ✅. Suggested format placed on talk page. Regards, AshLin 03:55, 9 August 2007 (UTC)

Anyone here
Posting contents of a mail below. Would hope that there is something Wikipedia related there. Shyamal 09:01, 12 July 2007 (UTC)

TDWG Annual Conference (http://www.tdwg.org/conference2007) Bratislava, Slovakia, 16-22 September 2007 Call for Abstracts to this call please contact me before then ** Symposium: Discovery, Integration and Use of Biodiversity Data Session: Building biodiversity data content (Friday 21 September) The idea of the session is to get away from the technical aspects of managing biodiversity data and to ask the wider community to tell us: 1) what is needed in terms of: - non-technical standards (standard lists, authorities, etc.)  - on-line services  - collection/specimen documentation standards  - other data content standards  - tools to help populate biodiversity, observational, ecological and conservation databases 2) what has already achieved (or is being worked on) towards these aims 3) how you can contribute The schedule for the 2007 Conference is very busy and we have space for only five or six verbal presentations. We do have ample space for poster presentations and computer demonstrations. My task is to ask the community for proposed presentations on the session theme, to integrate key verbal presentations into an interesting and thought-provoking session, and to encourage the submission of posters and computer demonstrations. If you think you have something to contribute, please contact me at A.Rissone@nhm.ac.uk with Subject line "TDWG 2007: Building biodiversity data content", indicating whether you are proposing a verbal presentation (remember these are very limited), a poster or a computer demonstration.
 * I will be away from my mail after 19 July. If you intend to respond

Another new article
I've been working on infanticide (zoology) for two or three days, and it will probably be coming up for did you know soon. I'd appreciate anyone looking over it or adding more themselves. It's clearly not complete yet, but a few more examples should do it (particularly of parents killing their own young). Richard001 08:41, 13 July 2007 (UTC)
 * How morbid of you. What does this have to do with this wikiproject?  This is about organisms and how they are classified...  this belongs in a crime or sociology wikiproject...  Werothegreat 17:34, 13 July 2007 (UTC)
 * Ah. I see after actually looking at the article.  Interesting.  Werothegreat 17:35, 13 July 2007 (UTC)
 * I've taken the liberty of removing the pipe to avoid similar future misunderstandings... Circeus 17:41, 13 July 2007 (UTC)
 * It would ideally be posted on an animal behavior project, but we don't have any animal project even so it's difficult to find the right project. This is the nearest parent project, though it's mainly concerned with taxonomy and classification. Biology could also be used but it has only recently been reopened and not that many people post there. Perhaps I should try rounding up some people from the various animal projects and see if we can put something together? Richard001 23:07, 13 July 2007 (UTC)
 * Go for it. Be bold.  Werothegreat 00:32, 14 July 2007 (UTC)
 * This was a good default place to start, though, Richard. I'll look at it in brief, while echoing Wero's comment, "how morbid of you."  I did study the topic in physical anthropology ages ago (for those unclear on the connection physical anthropologists also observe animal behaviour for clues to human behaviour, and to learn how to observe human behaviour), and in psychology--which is where I think you might post, as psychologists also study and observe animal behaviour.  KP Botany 17:52, 14 July 2007 (UTC)

Mitochondria - Cristae shapes
Can someone PLEASE (who knows what they're talking about) detail the various shapes that cristae take (discoid, flat, etc.), describing their differences, and possibly the purposes for different shaped cristae, either in the eukaryote, mitochondria, or cristae articles, or even create a new one. I would have done this by now, except the whole subject confuses me, and I don't have any sources that clearly explain them. Werothegreat 14:53, 13 July 2007 (UTC)
 * Perhaps this would get better results at WikiProject_Molecular_and_Cellular_Biology. AshLin 11:34, 30 July 2007 (UTC)

Ciliate article needs work
Ciliophora is one of the more important protistan phyla, and its article has no subsections. It contains a bunch of stuff about ciliates, a taxobox, and then a seperate section detailing classes and subclasses. And a bunch of thumbnails. I'm gonna need some help on this one. Werothegreat 16:07, 14 July 2007 (UTC)

conservation status in taxoboxes
Should the Taxoboxes section include how to use conservation status? I would appreciate some guidelines, and don't feel qualified to add it to the instructions myself. -- Donald Albury 13:05, 15 July 2007 (UTC)
 * WP:TX (the guideline/style guide covering them) links to it. That should be enough, shouldn't it? Circeus 16:04, 15 July 2007 (UTC)
 * Let's just say that things are not always obvious. I had looked for some guidance, but had not found that. -- Donald Albury 18:32, 15 July 2007 (UTC)

Template question
At least, I think it's a question about templates. I'm hoping someone here will either know the answer, or know where to find someone who can help. I've been busy with a series of articles on vipers, many of which use a template (?) that makes it easy to create external links to entries in a particular online database. An example would be the first link in this external links section, the markup language for which looks like this: These links used to be for records at the Reptile database at the European Molecular Biology Laboratory (EMBL). At one point late last year, the EMBL stopped hosting this database, upon which the man responsible for it, Dr. Peter Uetz, went looking for a new home for it. In the mean time, the code behind this template at Wikipedia was changed to work with the Species2000 database, even though that's only a subset of the original EMBL Reptile Database. Finally, about two months ago, Dr. Uetz's database went online again here, but it seems that the folks at Wikipedia who maintain the EMBL template have not yet discovered this. My question for you is therefore, how can I find out who maintains this template, or where can I find someone who can change it to query the Reptile database at its new location? Thanks! --Jwinius 22:04, 26 July 2007 (UTC)


 * Okay, it's been fixed, thanks to Shyamal. FYI, what needed to be changed was Template:EMBL species (and Template:EMBL genus). More information can be found at Help:Template and assistance can be sought at Wikipedia_talk:Requested_templates. --Jwinius 13:34, 1 August 2007 (UTC)

"Need taxobox" template
A new template, Template:Needtaxobox, is available for the purpose of tagging articles that do not yet have a taxobox. The "What links here" function can be used to comb through articles needing a taxobox. Badagnani 19:00, 31 July 2007 (UTC)

Chromalveolate Kingdom Color
Most high-level chromalveolate articles and many lower-level articles have had their taxoboxes changed to read Kingdom: Chromalveolata rather than (unranked): Chromalveolata. There have so far been no objections, and these changes have been standing for a while. I would like to take this one step further. I would like a unique taxobox color be chosen to represent the Chromalveolate kingdom, as Metazoa has pink, Plantae has Green, and Fungi has lightblue. Now, the last time I was bold and started changing taxobox colors right and left, there was an uproar and accusations of vandalism. I would like to avoid conflict this time by putting it to a poll. Post what color you feel it should be, and after a decent amount of time, say a week or two, or after we have sufficient nominations, we put it to a vote. Since this would take a lot of space, we could do this on the talk page of the chromalveolate article after we get started. Please remember, the following colors have been taken: pink, lightgreen, lightblue, khaki, brown (#e0d0b0), violet, lightgray, and darkgrey. Werothegreat 15:47, 2 August 2007 (UTC)
 * In the Catalan Wikipedia we did it time ago (see ca:Viquipèdia:Com entendre les taules taxonòmiques). If you choose the same colour, will be easier for us to move information from here to there :p Llull 19:15, 2 August 2007 (UTC)
 * Not that I have anything against lavendar, but if they've already chosen a color for those taxa on Catalan Wikipedia, I can't think of a good reason not to go with their color choice--nor am I going to try to. KP Botany 21:31, 2 August 2007 (UTC)
 * Not the color I would have chosen, but I have no objective objections. Implenting the change currently.  Werothegreat 21:02, 3 August 2007 (UTC)
 * Thanks.  KP Botany 21:05, 3 August 2007 (UTC)
 * I have changed all the higher taxa, and I have updated the eukaryote page and the taxobox usage page. Werothegreat 21:55, 3 August 2007 (UTC)
 * Thanks, I ran into one while looking something up, and it looks great to see these buggers discrimanted, even though no one but you and Cavalier-Smith know what they are. Oh, and apparently the Catalans.  KP Botany 17:59, 7 August 2007 (UTC)
 * We are more than seven million people. Don't forget it :) (we never used Protista kingdom) Llull 21:06, 7 August 2007 (UTC)
 * Why not use the colour "coral"?  It's easier to remember than six arbitrary hex characters, and much kinder to the eye as well... Verisimilus  T  11:56, 11 August 2007 (UTC)
 * Hmmm. Coral is a little more orange, (a little harder on the eyes, in my opinion).  Coral pink would be too close to the animal pink...  How about lightcoral?  It fits with the pastel scheme of the taxoboxes, and it is darker than the animal pink enough to be able to tell the difference.  Any objections?  Werothegreat 12:53, 11 August 2007 (UTC)
 * I think that they are colours too similar to the animal one. With the implementation of Taxobox colour template in the taxobox won't be the necessity of remember de colour code. Llull 13:44, 11 August 2007 (UTC)
 * Okay. What about: #F0b070

It's got a similar hue and saturation to the existing colours, but is easily discriminated. It's also less garish than the current option (which is my main argument against sticking with what we've got). Verisimilus  T  16:46, 11 August 2007 (UTC)
 * It's garrish, yet, but I think some unity around taxobox colors on the various Wikis is rather helpful, and it's just a color. I would really like to stick with  a choice already made by another group of Wikipedia editors, unless it is really necessary to change it.  It is readily distinguishable from other colors, it's already in use on another Wikipedia, it does not confuse with the other colors.  KP Botany 19:32, 11 August 2007 (UTC)
 * As much as I like the idea of using the Catalá color (anyone who both rejects Protista and keeps their language alive is to be commended and emulated), the Chromalveolate color, as well as some of their other colors, are not likely to pass text-to-background contrast tests that either are or eventually will be a part of web accessibility standards in many countries. In the case of the Chromalveolate color specifically, white text might pass muster, and the changes to Taxobox might allow that to be more or less automatic, but it is something we need to consider. When I have a chance later, I'll find the tool and test all the color combos.--Curtis Clark 22:54, 11 August 2007 (UTC)
 * Then please test, Curtis, as I hate to discuss something that someone else has already hashed out, and I have no reason to consider, if they've already debated choosing a color for the Chromalveolates, that we can pick better than the Catalans can. Then, if it turns out that there are issues with the color, we'll revisit the issue with everyone.  Or maybe they tested and that's how they wound up with this color.  Thanks.  KP Botany 23:03, 11 August 2007 (UTC)
 * Back to that taxobox color template, I really like the idea. Very nice.  However, what about Rhizaria, Excavata, and Amoebozoa?  Do they fall under the incertae sedis category?  Werothegreat 23:54, 11 August 2007 (UTC)
 * I think that the best is to put them in a generic Eukarya colour (Eukarya that is not in one of the other four kingdoms). The other clades are too revolutionary and I think that we should wait few years for change it, waiting for new reviews. And wait years seems still more important in bacterial clades of neomuran article. Llull 08:15, 12 August 2007 (UTC)

Here are the results of using Colour Contrast Analyser for Web Pages. According to the program, "Text or diagrams and their background must have a luminosity contrast ratio of at least 5:1 for level 2 conformance to guideline 1.4,and text or diagrams and their background must have a luminosity contrast ratio of at least 10:1 for level 3 conformance to guideline 1.4." I've added the contrast ratios to each of the color combinations used in ca:Wikipedia, with the standard blue link color (left column) and the redlink color (right column). Note that every combination except the last fails with redlinks. --Curtis Clark 00:26, 12 August 2007 (UTC)


 * But: when would redlinks appear? Surely the only thing that'll ever be wikilinked in the template is "Scientific classification"?
 * As I can't download the program, would you mind running it for #F0b070 too?
 * And at the hazard of broadening the debate, I did feel that the Virus colour was a bit dark, but didn't want to open that can of worms... Is it worth changing? It also appears very low classification with the purple "followed link" colour.Verisimilus  T  08:53, 12 August 2007 (UTC)
 * That's a good point about the redlinks. Viroide is a redlink here, but not on ca:Wikipedia (it is Viroid here) and Satèl·lits is a redlink in both places, but neither would be linked in an actual taxobox, since the name only appears in its own article. So it seems that the only text colors we need to worry about are black, the blue unfollowed link, and the purple followed link. I'll redo the table later today.--Curtis Clark 13:58, 12 August 2007 (UTC)
 * Satèl·lits refers to Satellite (biology) (used in (ca:virusoide article), genetic information that needs a helper virus for its own reproduction. There we use different colours for viruses, satellites and viroids tables (the last two very similar because of they are very similar), but here all these entities are classified with the same violet colour. Neomurans, Mycoplasma laboratorium, transposons and other unspecific elements use the lightyellow there, but here you don't use taxoboxes for mobile genetic elements and you haven't needed a standard colour for this purpose. Llull 14:57, 12 August 2007 (UTC)

Here's the new table with contrasts added. The program also tests contrasts for the three types of color blindness; we should check that as well on any candidate combinations.--Curtis Clark 16:22, 12 August 2007 (UTC)


 * So... not only do we need a different chromalveolate color, we also need a new archaea color?  This is becoming more trouble than it's worth.  How about a more yellow shade of green for c-als, and a reddish lighter gray for archaea?  I'm really reaching here.  Werothegreat 02:37, 13 August 2007 (UTC)
 * Something like this?
 * {| class="wikitable"

! style="background:GreenYellow" | Chromalveolata || GreenYellow ! style="background:#F3E0E0" | Archaea || #F3E0E0
 * }Werothegreat 02:40, 13 August 2007 (UTC)
 * }Werothegreat 02:40, 13 August 2007 (UTC)

Inasmuch as there will always be the possibility of visited links in the colored-background parts of a taxobox, we also need new colors for Virus and Viroid. There are all kinds of pastels in the RGB color space, so if we were inventing this from whole bits, it wouldn't be all that difficult. If we want to preserve colors already in use, we might check out taxoboxen in some of the other Wikipediae for colors with an adequate ratio. I guess what I'd like to know next is the consensus: Are we bound by existing colors, or do we want to go for optima?--Curtis Clark 03:17, 13 August 2007 (UTC)


 * I don't know. This might be something we want to coordinate more with other Wikis, as one reason for going with the Catalan's color choice is having some consensus across wikis in a multi-lingual world.  It's hand to be able to go to the Danish wiki and know I'm at least in the correct kingdom by the taxobox.  KP Botany 03:44, 13 August 2007 (UTC)
 * I tend to agree in principle, but it's my understanding that EU countries have stricter standards for web accessibility that the US (WAI vs Sect. 508, and the latter only applies to the US Federal govt plus a few states, such as California), so maybe we can help them out and come up with an adequate-contrast set of colors that takes from the best of all the Wikipediae.--Curtis Clark 03:52, 13 August 2007 (UTC)

Adding a subsection to make it easier to comment
Most of the wikipedias use pink/lightgreen/lightblue/khaki. The only real exception is the french wikipedia, which uses the khaki exclusively for alveolates for some reason, and uses teal for the rest. My assumption is that if we change our taxobox colors, the rest will most likely soon follow. Werothegreat 12:55, 13 August 2007 (UTC)
 * I'd rather do it with a little consultation internationally though, if it turns out it is problematic all over, that we want to change everything, and that it's likely the others will follow through, and that European countries have stricter requirements. KP Botany 16:32, 13 August 2007 (UTC)

Four kingdoms after all?
It's swings and roundabouts... These guys seem to think that Protista is a kingdom. How do we avoid POV in our Taxobox colours? Verisimilus  T  12:04, 24 August 2007 (UTC)
 * How quaint. Pananimalia and panplantae do make sense, but you can't really call a paramecium a plant, or a mushroom an animal.  It doesn't quite work.  And bacteria is paraphyletic.  Why can't we just accept that life isn't that simple, and is not going to fit into cookie-cutter groups?  Werothegreat 16:48, 24 August 2007 (UTC)
 * Because then all our taxoboxes would have to be the same colour, and what would we keep ourselves busy with then? { Verisimilus  T  18:39, 24 August 2007 (UTC)
 * I would rather have one color for everything (which the Germans do, coincidentally) than have a return of protista. Werothegreat 22:38, 24 August 2007 (UTC)
 * This does raise an interesting question which I suppose begs an answer: Is there really a purpose of having different colours at all, and if so, what precisely are we trying to achieve through them? Verisimilus  T  12:55, 25 August 2007 (UTC)
 * I was just reading through this: . It's like I'm reading a paper from the seventies.  He's grouping the cercozoans with the amoebozoans.  That doesn't work.  Werothegreat 16:55, 24 August 2007 (UTC)


 * Neither does your link! (-;
 * (Connection timed out) Verisimilus  T  18:43, 24 August 2007 (UTC)
 * It works for me. I'm using Mozilla Firefox.  What browser are you using?  Werothegreat 22:38, 24 August 2007 (UTC)
 * Firefox too. Still not working now - maybe you have different access permissions or something? If you give me the title I'll find it in Scholar... Cheers. Verisimilus  T  12:55, 25 August 2007 (UTC)
 * As for avoiding POV, this is a new development, just published. Whereas the six-supergroup system has lots of papers, Adl et al, Cavalier-Smith, lots of websites, etc.  No one in their right mind uses Vegetabilia anymore.  Werothegreat 22:41, 24 August 2007 (UTC)
 * It seems curious that Nature would publish something that's outdated... Classification isn't a subject I know much about, mainly because a cladistic approach renders it somewhat redundant on the phylum-scale. I'm interested to know more; is your principle objection with the paper mainly that it includes groupings which you consider paraphyletic?


 * I see no harm in including fungi in the same kingdom as the animals, as it does seem that fungi are a genuine stem-group to the animals. But then I'm a lumper, not a splitter. I have heard eminent scientists describe Paramecium as a plant (which has actually just led to a great deal of confusion, without my realising that you'd referred to it!). The level of diversity to be contained within a kingdom is always going to be a point of view issue, as it's entirely arbitrary.  But the argument of "they seem too different to be grouped together" doesn't hold water - as the platypus illustrates.
 * Regarding the paraphyly of bacteria, there's probably got to be a degree of that - simply as older lineages are more diverse. As I look at it, the two sister species today as as different as the two sister genera were X million years ago, and so on up the tree of life. (It'd be interesting to do some maths and see how consistent "x" actually is) If kingdoms are real entities representing a certain degree of evolutionary differentiation, then every organism at a given point back in time (corrected for varying rates of evolution) would have the potential to found a kingdom, and there were (surely?) many many more than 4 or 6 organisms back then that managed an unbroken line of descendants to the present day? I wonder whether they've formed the blanket "Bacteria" kingdom, with inverted commas, as it's more useful than naming the hundreds of kingdoms that probably exist, but we're not very good at discerning yet.  That's not the impression they give, but then there's very little discussion in the paper.


 * Whoops, I rambled a little there. The perils of becoming more and more interested in a subject...
 * Verisimilus  T  12:55, 25 August 2007 (UTC)


 * I'm just feeling very torn, because the panplantae etc. does make some sense, but then he goes and proposes vegatabilia etc., which isn't even trying to be monophyletic, and I'm like, "But, no!" No, no, no, no.  Linnaeus had some good ideas, but we've improved on them.  Just like Edison had good ideas, but we're using flourescent lightbulbs now.  Thanks for the start, but we've got it covered on our end.  You can't go backwards.  You have to go forwards.  And really, the four evolutionary kingdoms are basically the three-domain system, except he's split up the eukaryotes into basically unikonts and bikonts.  Don't make up new names!  We have names!  Unikonta, and bikonta!  And he describes the Apusozoa as incertae sedis, when Cavalier-Smith believes to be basal bikonts, putting them in "panplantae."  If ever I were to use the word "pananimalia," first, I would change it to "panzoa" to get lingual agreement (a latin root with a greek prefix?  Please.) and then I would clump the choanaflagellates in there.  The fungi would remain in Eumycota, which could be spread to "panmycota" to include the mesomycetozoa.  And the only sense in which I'd use "panplantae" would be for the archaeplastids, and, wait a minute, we already have a word for those!  This just gets better and better.  You're a lumper, you say?  Well, I've always been more of a splitter myself, if only to keep monophyletic groups.  Werothegreat 12:16, 26 August 2007 (UTC)
 * "Pananimalia" is perfectly good Latin; it means "animal bread". { --Curtis Clark 13:20, 26 August 2007 (UTC)
 * I don't see the linguistic problem with pananimalia. After all, the three greatest inventions of the last 150 years have mixed etymologies: auto (Greek), mobile (Latin); tele (Greek), vision (Latin); wiki (Hawaiian), pedia (Greek). Eugène van der Pijll 18:46, 26 August 2007 (UTC)

So... What should we do?
Well, I suppose it's become clear that there's little or no consensus in the scientific literature, on what to call the kingdoms, or even on what the kingdoms should be. Given the struggle one must go through to find consensus on anything in this place, it doesn't look like we stand much chance there. So: what do we do? The easiest way to avoid POV is to follow the Germans, and make everything the same unpleasant shade of wikipedia-blue. But I'm quite attached to the splashes of colour in articles, from a purely aesthetic perspective - and because I've nearly finished coding a bot to install my automater!

Emotional involvement aside, what do we aim to achieve with the colours? They're not adding information to an article, and in the vast majority of cases people don't need telling that something's a plant or an animal. In the event that it's not obvious, it often seems to be the case that the scientific jury is out.

So, much as it pains me, here's a suggestion for you to shoot down: Let's disable the colour parameter and make everything navbox-blue.

Verisimilus  T  20:43, 26 August 2007 (UTC)


 * A measure of whether people notice: A common newbie-vandalism that I see is to change the taxobox color, perhaps to something the newbie thinks would better fit the article.


 * The colour automator is a wondrous thing, and if there were better consensus on the Kingdoms, that would be the way to go. But I reluctantly agree with Verisimilus. I'm not familiar with how the automator works, but perhaps setting all the choices to #ccf or whatever would allow us to easily reward ourselves with color when the Kingdoms stabilize.--Curtis Clark 22:51, 26 August 2007 (UTC)

I don't see what all the fuss is about. Unless we're going to take down the kingdom information from all infoboxes, what difference does colour make? Richard001 23:37, 26 August 2007 (UTC)
 * Correct me if I'm wrong, but we're going to keep the Kingdom field in the taxobox, right? If so, each entry will still have a kingdom listed that the color can corespond to. As for what to list, why not just stick with the system we have now, or revert to the 'traditional' 5-kingdom system until such a time as the taxonomy is sorted out and some kind of consensus is reached? Dinoguy2 00:18, 27 August 2007 (UTC)


 * I agree with Dinoguy2; in most cases (in terms of number of articles), the kingdom is simple. I see no reason why we can't have Animalia set to pink, Plantae set to lightgreen and only lump the difficult cases together into a default colour (without that colour necessarily implying monophyly). --Stemonitis 05:39, 27 August 2007 (UTC)


 * I agree with you two. Just how many taxa (as in "taxa having articles on WP or being interesting enough to likely get them in the foreseeable future") are actually affected by this? And in any case, we still have #e0d0b0 (I think) for the "Problematica" (basically "Kingdom incerte sedis").
 * The concept of strict monphyly is flawed at the kingdom level in any case. This may sound harsh, but it's what you get at the levels of horizontal gene transfer that apparently were still nothing unusual when plant and metazoan ancestors diverged... if you pick the right (or wrong) sequences, metazoans come out paraphyletic with viruses. The "tree" they use at TOLweb (see here) probably gives a good impression of the real deal. Dysmorodrepanis 15:46, 27 August 2007 (UTC)
 * Although I don't discount horizontal gene transfer, metazoans are paraphyletic with respect to some viruses because the viruses are metazoans, phylogenetically speaking. It has long been theorized, and for some groups of viruses there is good evidence, that viruses are replicating pieces of the genomes of cellular organisms, such that, for example, mammalian retroviruses are descended from mammals.
 * The advantage of monophyly as a hypothesis is that it can be falsified. Horizontal gene transfer can't be, since it can be invoked for any phylogenetic pattern.--Curtis Clark 16:35, 27 August 2007 (UTC)


 * I don't really see what the colours add either. And I'd just like to say that I don't care if the colours stay, go, or are simplified. —Pengo 07:42, 27 August 2007 (UTC)


 * Except most eukaryote groups have settled out. Many biologists (even that russian nut) recognize the difference between unikonts and bikonts, and that they are the only two branches of eukaryotes, and many more recognize the six supergroups of opisthokonta, amoebozoa, rhizaria, excavata, chromalveolata, and archaeplastida.  All the incertae sedis fit into either bikonta or unikonta (most in bikonta).  Werothegreat 21:44, 27 August 2007 (UTC)

Let's follow Verisimilus's suggestion and make everything navbox-blue for now. We can change it when the taxonomy gets sorted out, hopefully soon though I think much of the current system will get scrapped. Calibas 03:31, 28 August 2007 (UTC)


 * Let's not make any decisions based upon one article that appears to draw conclusions one cannot possibly draw from the sources it cites, at least not without some serious debate in the scientific community. This usually takes more than 10 days. KP Botany 04:14, 28 August 2007 (UTC)


 * I don't think any decision will be based purely on that article; the article is just one of many that have viewpoints inconsistent with one another!
 * I am almost bought by the suggestion of keeping the colours for established monophyletic groups (plantæ, anamalia... I'm not the one to make this list), and complementing this with a paraphyletic "eukaryote" colour for non-stable "kingdoms" where debate still rages - e.g. the Chromalveolata - as well as incertae sedis. Verisimilus  T  09:06, 28 August 2007 (UTC)
 * Except debate isn't raging. Google rhizaria, excavata, or chromalveolata, and you will find many sites that recognize these clades.  Sure, you'll get a couple that still recognize chromista, and the few 5-kingdomers out there, but most of the 5ker's admit that protista is not a valid taxon, and use the 5 for simplicity rather than any sort of phylogenetic justification.  There is also the work of Adl et al, Cavalier-Smith, to name two.  I'm sure there are others, though I can't name them off the top of my head.  The only big incertae sedis I can think of are the apusozoa and the centrohelida, both of which are bikonts.  All the old incertae sedis, the nucleariids, the ebriids, all fit into one of the six groups now.  Nuclearida are choanozoans, and ebriids are cercozoans.  Debate hasn't been raging for a while.  Werothegreat 13:48, 28 August 2007 (UTC)
 * And is everyone agreed that the six groups are of equal ranking, i.e. kingdoms? If there is consensus for six groups, it does make a sound case for how to assign colours — if colours are deemed necessary.  The nature paper I linked to, however, suggests to me that such a consensus is absent, at the moment at least (even if the paper is founded on bogus science).
 * Cavalier-Smith has made a name for himself by refusing to be bound by convention, a practice that, whilst bold, has made many sceptical of his claims; Further, by all accounts, he's not fond of people who disagree with him in print — I've not had time to read his papers, less still to get the thorough familiarity with all the unfamiliarly-named groups, but my instinctive reaction is to want wider support than C-S and someone else I've not come across before believing something I've read on Wikipedia! I think I'm slowly coming round to your argument, though - don't give up bludgeoning me with more reasons to believe you! Verisimilus  T  16:26, 28 August 2007 (UTC)
 * The 6 groups being of equal rank is not the same as they being kingdoms. Merging fungi and animals into a kingdom Opisthokonta would be a big step from current practice. (It would also make taxobox colours by kingdom of little use, in that encylopedia users are not in general interested in the depths of eukaryote phylogeny - animal, fungus and plant are familar(ish) concepts to the man in the street, but opisthokont, chromalveotae and amoebozoan aren't.)
 * The evidence for the monophyly of each of the 6 groups is not unequivocal; in fact from the papers I've seen it appears weak. Lavateraguy 18:26, 28 August 2007 (UTC)
 * Verisimilus, we have hashed out the Cavalier-Smith issue with Wero, and he's aware of issues in the scientific community with C-S's organismal classifications, and is as mindful as possible of these concerns. Wero's a careful reader, and good at referencing.  The issues are complex, and it wouldn't hurt to have someone looking over what he writes, and reading the C-S articles, and others, also.  Wero deals more with articles that cite him than anyone else, so feel free to disagree specifically or elaborate any time you see an issue that requires this, as we are all aware of the need to handle citations by C-S with care and precision--it's a major, complex and very important issue in higher level classifications of organisms, and additional editors would be very useful--feel free to jump into the fire and the frying pan.
 * The issue isn't so much that people strongly disagree with C-S's conclusions, though, it's about the sweeping nature, overall, of the majority of conclusions. KP Botany 03:10, 29 August 2007 (UTC)

Cavalier-Smith
I'm meant to be reading a lot of other things at the moment, but if someone could post details of a couple of the more relevant references here, I'd be interested to cast my eye over them and see what I make of them! Cheers, Verisimilus  T  08:34, 29 August 2007 (UTC)
 * Here's the Adl et al. article, which outlines the six major groups. 
 * Cogent Cavalier-Smith articles -   Werothegreat 20:36, 29 August 2007 (UTC)
 * And please, don't anyone tell Verisimilus how long the average Cavalier-Smith paper is, until the hook is set. Thanks for posting links, Wero. KP Botany 05:01, 30 August 2007 (UTC)
 * Oh, I normally just skim through for important stuff, and focus on the diagrams. No one has the time to sit down and read an entire C-S paper in one sitting.  Though the C-S Stechmann one is only two pages.  Werothegreat 10:48, 30 August 2007 (UTC)

I love NCBI. This recent paper (from July!) gives further evidence for the monophyly of Rhizaria, Retaria (a clade within Rhizaria including the Radiolaria [sensus stricto] and Foraminifera), and Excavata. Also, the Nucleariids are found to be sisters to Fungi, so could be included in an expanded eumycetal kingdom, and all other choanozoa are sisters to Animals, which could be included in an expanded metazoan kingdom. Centrohelids (here called Heliozoa) and Apusozoa are still not including in one of the six supergroups, but Apusozoa are thought to be at the bottom of the bikont tree.  Werothegreat 22:11, 30 August 2007 (UTC)
 * p.s., this was done using LSU rRNA. I'm still reading through recent articles...  Werothegreat 22:12, 30 August 2007 (UTC)
 * Wow. Hear nothing for a couple years and ground-shaking work all within a year of each other (two were just published yesterday and last week!) Further evidence of mitochondrial endosymbiosis.  Suggesting the Apusozoa are sisters to either the Opisthokonts or Amoebozoa, suggesting that one or both unikont groups derived from a biflagellate ancestor.  Changes the definition of bikont and unikont.

  These papers, published within the last seven days, together suggest that Chromavleolata is a sister group to Rhizaria. This blows the whole corticata/cabozoa dichotomy of bikonts (if this is even a valid clade anymore) out of the water. Wow. This is much better science than that four-kingdom crap. Werothegreat 22:25, 30 August 2007 (UTC)


 * Please note, that even though these papers propose some radical changes to the six-supergroup system, that all six supergroups remain monophyletic, and more evidence is provided for this. The proposed Rhizaria-Chromalveolata group does not disprove the monophyly of either group, merely advocates their melding.

Werothegreat 22:29, 30 August 2007 (UTC)

Don't everyone comment at once... has this conversation sadly died? Werothegreat 20:18, 5 September 2007 (UTC)
 * Sorry, I've a lot on my plate, and haven't been able to catch up on the reading! I'll return shortly... Verisimilus  T  09:46, 6 September 2007 (UTC)

OK, not to be a topic necromancer, but we really can't just let this discussion die. This is an issue that needs to be settled. Werothegreat 20:55, 4 October 2007 (UTC)

Necromancy
Okay, so there seems to be ample evidence for many of the higher-level groups, eg. Rhizaria. But, this still begs the question, where do we go from here? If we do decide that colours are useful, keeping fungi separate from animals seems to make a lot of sense for most readers. The bacteria and archaea groups don't appear too contraversial, either. I suppose the debate must be what we include in "plants" - if we're keeping animals and fungi seperate, perhaps restricting it to algae + land plants would be best. What other groups would we need - would Chromalveolata suffice? Verisimilus  T  13:48, 27 October 2007 (UTC)
 * Recent evidence suggests that all of the choanozoa are split evenly on either side of the main branches of opisthokonta, i.e., animals and fungi. So, we can split all the unikonts into amoebozoa, "animals", and "fungi."  That leaves Rhizaria, Excavata, Chromalveolata, and "plants" (I prefer the term Archaeplastida, but whatever).  In this case, "plants" would mean land plants, green algae, and red algae, because they're all evolutionarily related.  Some research also suggests that Rhizaria and Chromalveolata are close, but the four mentioned, no matter what their relations to each other, are pretty much settled as monophyletic groups.  That gives us 7 major eukaryote groups (with some apusozoa and centrohelida on the side).  Archaea is fine, and Bacteria is fine, as long as it is acknowledged as a stem group to Neomura (archaea and eukarya).  As for colors, we have the green for "plants", the pink for "animals", the blue for "fungi", and the salmony-thing from the catalans for chromalveolata.  Some possibilities for the other three could be lavender, light orange, and keep the protists khaki for one.  Eukaryote brown can be used for apusozoa and centrohelida (which I believe is what they're colored now, anyway...)  Werothegreat 10:25, 30 October 2007 (UTC)
 * Or wait, the salmony-thing didn't pass the test - nor did archaea-grey... Or does it even matter?  Werothegreat 10:27, 30 October 2007 (UTC)
 * That sounds sensible. The salmony-thing (I assume you mean the bottom one on the final table) was close enough to passing (4.80 on a pass of 5.00) for common sense to permit its inclusion; I'm sure a slightly lighter version of Archaea grey could be suggested to make this compliant too, whilst we're making the changes.  Lavendar and light orange (which precise colour do you mean - lightsalmon?) seem sensible for excavata and rhizaria; is the protist khaki a little similar to the generic eukaryote #e0b0d0? Probably not. Verisimilus  T  13:09, 30 October 2007 (UTC)
 * Inasmuch as the foreground color is always black, they all pass.--Curtis Clark 14:01, 30 October 2007 (UTC)


 * The lighter pink color was meant for Archaea. The darker pink color (the one on the larger table) with the background word "Chromalveolata" is for Chromalveolata. I was thinking about #FFC8A0 for light orange, and that for Amoebozoa, and Khaki for Excavata, and Lavender for Rhizaria.  —Preceding unsigned comment added by Werothegreat (talk • contribs) 19:16, 30 October 2007 (UTC)
 * D'oh. Oops! Verisimilus  T  21:07, 30 October 2007 (UTC)

Well? The Archaea color change would have to be approved by the archaea group, so someone would have to post on the archaea wikigroup (if there is one, if not the archaea article) talkpage. As for amoebozoa and rhizaria, nobody really cares about them, so a vote here to change their colors would suffice. So, who's for changing amoebozoa to #FFC8A0 and rhizaria to lavender? Or against, if you like. Werothegreat 20:51, 2 November 2007 (UTC)


 * And the discussion dies again. *sigh*  Werothegreat (talk) 18:57, 18 November 2007 (UTC)


 * Well, no-one's objecting, so let's press ahead! I've left brief notes on Talk:Archaea and Wikipedia talk:WikiProject Microbiology requesting comments be left here; I'll submit a bot request to remove existing "colour" declarations from taxoboxes, and an edit request on Template:Taxobox colour, when consensus has been reached (or after waiting a while for someone to reply...)
 * I might get you to check out my suggested edits to check that automatic colour detection will work appropriately!


 * Verisimilus  T  20:27, 18 November 2007 (UTC)


 * Great! Let's sum up, shall we?
 * Animalia - pink
 * Archaeplastida - lightgreen
 * Fungi - lightblue
 * Chromalveolata - #FA7B62 (salmon-ish)
 * Amoebozoa - #FFC8A0 (a light orange)
 * Excavata - khaki
 * Rhizaria - lavender
 * Archaea - new color needed - possibly #F3E0E0 (a very pastel pink)?
 * Bacteria - lightgray
 * Virus - new color needed - Suggest #b9e
 * Incertae sedis/Eukarya - #e0d0b0 (a light brown)
 * Werothegreat (talk) 19:49, 19 November 2007 (UTC)


 * I still think the Chromalveolata colour is rather ugly. The suggestion of yellowgreen greenyellow seemed better, and also gives a nod to the close relationship of the group to the plants; I think that might be a more appropriate choice.
 * Verisimilus  T  09:40, 20 November 2007 (UTC)


 * Hmmm. Yellowgreen seems to be too dark.  I believe the color suggested was greenyellow ...  Werothegreat (talk) 21:00, 20 November 2007 (UTC)


 * Sorry - my misspelling; I thought it was a little dark, but blamed it on my laptop screen. Verisimilus  T  09:53, 21 November 2007 (UTC)

So... shall we start? With the changing of the colors? Werothegreat (talk) 01:28, 23 November 2007 (UTC)


 * I'm ridiculously busy until Sunday, and it would be nice to keep the transition period to a minimum; I'll put in a bot request today, and we'll go when someone's been good enough to code one for us! Verisimilus  T  10:16, 23 November 2007 (UTC)
 * So, any code yet? Werothegreat (talk) 16:52, 28 November 2007 (UTC)
 * No-one's shown much interest in my request yet. I hope I don't have to code it myself... Verisimilus  T  19:00, 28 November 2007 (UTC)

Subsection for ease
Don't they usually take a while to respond anyway? Werothegreat 02:28, 1 December 2007 (UTC)
 * * sigh* RIP discussion.  Whoa, deja vu!  Werothegreat (talk) 22:33, 4 December 2007 (UTC)


 * Well, they've now archived my bot request twice; I may have to make a bot myself, which will be very time consuming - I won't have any time to consume until mid-January. So unless anyone comes forwards - it may be a long wait, I'm afraid! Verisimilus  T  10:43, 5 December 2007 (UTC)


 * Very sad. Can we yell at anyone to make one for us?  PM them or something?  Werothegreat (talk) 00:38, 11 December 2007 (UTC)

Okay. In lieu of a bot, I'm going to start changing colors of higher level taxoboxes, in the hope that people will follow the trend and help out. Werothegreat (talk) 02:58, 20 December 2007 (UTC)


 * Okie dokie. I'll change guideline pages. Verisimilus  T  11:09, 20 December 2007 (UTC)

Ummm... the whole don't-give-a-color-and-it'll-give-the-right-one thing is working for chromalveolates, but not for rhizaria, amoebozoa, or excavata. Can this be fixed? Werothegreat (talk) 15:38, 21 December 2007 (UTC)


 * Remember that you need to wikilink the kingdom entry. This will have the effect of bolding the text anyway on the article pages. Verisimilus  T  16:02, 21 December 2007 (UTC)
 * Okay. But, the color for the excavates is the wrong color...  it's supposed to be khaki... that's more booger...  it should be the color that the protists used to be.  Werothegreat (talk) 16:04, 21 December 2007 (UTC)
 * I've already noticed that and requested an update. I think I misspelt the original colour to something horrible! Verisimilus  T  16:38, 21 December 2007 (UTC)


 * That's better. Lookin' good!  Werothegreat (talk) 20:07, 21 December 2007 (UTC)

Wanted categories?
I created several wanted categories this morning, some of which duplicate existing names such as Elepids and Bovids. The duplicates should be merged, and one should become a redirect to the other, but which is better? Your input is requested... -- Prove It (talk) 22:15, 3 August 2007 (UTC)

Request for opinions
Greetings. Polbot is a bot that reads information from the IUCN and creates new stubs on plant and animal species. There is currently a request for opinions here regarding the linking of biologists' names. Any comments on that page would be welcome. – Quadell (talk) (random) 17:17, 7 August 2007 (UTC)

Animals project
Despite having some very specific animal projects, we have no central one to tie them together and allow for animal specific guidelines, discussions and assessments. Many animal related articles have to be assessed under the tree of life or even biology assessment scheme, despite being specific to animals. There are also other projects that could emerge from it in the future, such as one on animal behavior for example. With the project the pathway to improving zoology related articles is much clearer. If you are interested in creating this project please register your support and ideas here. All projects that come under the potential parentage of this one have been contacted. Richard001 09:13, 8 August 2007 (UTC)


 * Regardless of whether or not an umbrella project is created (and I personally support a way to standardize bio/zoology pages), the idea that sticks out with me is the concept of a project on animal behavior. As of now, there are not even stub or cat tags for ethology, and I feel it is important that some sort of project concerning this should be started.  There are many species articles that inform the reader about an animal's name, habitat, size and shape, etc.--but that which intrigues and makes real the product of evolution and interests people not that concerned with systematics are the hows and whys of the way an organism interacts with its environment.  Wikipedia seems somewhat lacking with regard to information like this.  TeamZissou 09:41, 8 August 2007 (UTC)


 * I agree. Morphology, taxonomy, ethology & ecology of animals, amongt others, should be treated as centrally as possible with the inevitable forking/branching. Unfortunately instead of a Tree we have a weed approach with few articles being thrown up randomly by the WikiProjects. Snake scales has developed but Reptile scales has not. There is definitely a need for this WikiProject, not particularly from TOL pt of view, (WikiProjects are doing their bit, thank you very much) but to develop zoology in a general fashion. AshLin 11:45, 8 August 2007 (UTC)


 * I think this is a great idea, especially the animal behavior idea. I'd love to join such a project. Cheers, Corvus coronoides talk  01:40, 9 August 2007 (UTC)


 * I was wondering why there wasn't an animals project, nobody bothered to make one yet. I'll join. Calibas 02:23, 9 August 2007 (UTC)

I've started working on a draft at User:Richard001/Animals draft. Feel free to work on it - it's extremely skeletal at the moment and needs a lot of development. Richard001 01:44, 7 September 2007 (UTC)

Proposal Added
I think this is an excellent idea, so I've added the proposal to the WikiProject Council. If there is enough interest to handle a project of this size, I will start the skeleton and we can get working on it.  J. Hall  • ( Talk ) 18:10, 27 September 2007 (UTC)