User talk:Brya

Welcome!

Hello, Brya, and welcome to Wikipedia! Thank you for your contributions. I hope you like the place and decide to stay. Here are a few good links for newcomers:

I hope you enjoy editing here and being a Wikipedian! Please sign your name on talk pages using four tildes (~~~~); this will automatically produce your name and the date. If you need help, check out Wikipedia:Questions, ask me on my talk page, or place {{helpme}} on your talk page and someone will show up shortly to answer your questions. Again, welcome! 24 September 2005

Restarting

Archived Brya 08:42, 3 September 2006 (UTC)[reply]

Lebedev

I was looking through the Mikhail Lebedev page and it seems to be vanity and non-notable to me. First of all, there is hardly any information about him on Google. Then, none of the publications seem to be news-worthy and notable. Finally, the scientist does not have many 1st author publications and seems to be non-important in his field. If you agree with me, can you please help me nominate Mikhail Lebedev for deletion? --GoOdCoNtEnT 08:52, 3 September 2006 (UTC)[reply]

Contact

Brya,

you write As I have been de facto blocked from editing Wikipedia. Please contact me by email so I can help you work it out. I feel that as far as contents of the artcile go, you have at least one point, but it is hard for me to help you here. My english alas is insufficient to "hit the right tone".

TeunSpaans 04:18, 4 September 2006 (UTC)[reply]

ICBN Glossary

Where is the Glossary in the ICBN? I only have access to the on-line version, and I can't seem to find the glossary. Thanks, KP Botany 17:53, 3 October 2006 (UTC)[reply]

It is on page 484-491. I have no idea when it will be online. I expect they want to sell a reasonable amount of books before they do so. Best, Brya 17:57, 3 October 2006 (UTC)[reply]

Ah, so it's not in the on-line one. Well, there are good sites with the defintions. Still, it would be easier to use on-line with a glossary. Thanks, KP Botany 18:15, 3 October 2006 (UTC)[reply]

No, it is in the new one. Actually, I don't know of any good sites with definitions on botanical nomenclature. Best, Brya 20:10, 3 October 2006 (UTC)[reply]

Oh, the one newer than the St. Louis Code is out? It's not on the IAPT site links, yet. What is it called? There are actually a number of sites that include glossaries of all the various types and other bits of information for using botanical nomenclature. KP Botany 20:16, 3 October 2006 (UTC)[reply]

Yes it is out. It is called the Vienna Code. And I have never found a site that was anywhere near reliable on the matter of botanical nomenclature. Best, Brya 20:22, 3 October 2006 (UTC)[reply]

Oh, I've still been using the St. Louis Code. Thanks. Although I don't doubt you have personally never found a reliable site on botanical nomenclature I do doubt that you've seen them all. I've found quite a bit of useful and accurate and fun information on the web about botanical nomenclature. KP Botany 20:33, 3 October 2006 (UTC)[reply]

My user page

Thank you on corrections. I am very glad with your return to Wikipedia. Berton 15:45, 4 October 2006 (UTC)[reply]

About block

As you may have noticed, your account has been blocked and you can only edit this talk page. The issues which you had responded to on the WP:TOL talk page are a large part of this as there is some concern that you might be adding invalid and/or speculative material to articles. There also seems to be a considerable clash of personalities involved. If some of these issues can be resolved then I'm sure your account would be unblocked. Specifically, I think people are concerned about some of the APG information you have been using. For instance, you referenced an APG II 'paleodicots' classification, but users searching for such haven't been able to find one. Was this a mistake or do you have a reference? Likewise, various citations of 'APG III' are problematic because no such exists yet and thus any estimation of what one might eventually contain is inherently unverifiable. Hopefully it is still possible to set the past conflicts aside and try to work through these and similar disputes. People disagree... it is natural and inevitable. However, we should usually be able to find some sort of reasonable common ground between what is preferred and what is intolerable. --CBD 00:54, 18 October 2006 (UTC)[reply]

Block

For the record I should point out that my contributions are mostly strictly By-The-Book (solidly backed by references) and that this is why they are unpopular. There is a great deal of inaccurate information on botany in wikipedia (the result of quick google searches, sloppy reading and worse). A few editors hate to see their PoV challenged however indirectly and will attack any NPoV article. I have never 'pushed' anything except 1) NPoV, 2) putting in solid references and 3) internal consistency.

APG III

Occasionally I do use a more accessible turn of phrase such as in the case of "APG III" (likely to be published sometime in future). This looked like a useful device as lots of users mistook the APWebsite for the official APG classification (wikipedia is ful of such references). A distinction should be made between APG (1998), APG II (2003) and the APWebsite: these are three different things. Because the APwebsite is most easily accessible online it was most popular. This is not without its dangers as the site is kept up by a single person (very well read and well connected) and is without any official status: also as a webresource it changes very regularly. What is there today may be gone tomorrow. Any reference to it should be explicit and accompanied by the date of consulting it. Well, again as wikipedia was full of mix-ups between the three different systems I put in some work untangling the three. Besides putting in the APG (1998) and APG II pages this is also apparent in Nymphaeales, moving it to a carefully NPoV. Somewhat similar for Dilleniales. In doing this I used the image of "APG III" to reinforce the idea that any usage of these names in connection with APG is quite tentative. The "APG III" is there as a warning sign. Although it should be obvious to anybody who has kept up on plant taxonomy even in a minimal fashion, or even to anybody who reads carefully, that we are dealing with three different systems it is quite clear from the contents of wikipedia that there is a category of users who are neither botanist nor careful readers who would benefit by such an explicit warning sign.

Your thoughts on what APG III is likely to include in Nymphaeales and Dilleniales seem reasonable, but until it actually exists they remain inherently unverifiable. Often reasonable speculation is allowed to pass unchallenged so long as it is described as speculative, but it is technically not in conformity with Wikipedia practice and given the more general controversies is inevitably going to be challenged. If you could find references to someone saying these things in a reliable source then it would be verifiable that those speculations exist... but when you include your own estimations directly there is no 'third party verification' possible. I understand what you are saying about mentioning 'APG III' as a way of indicating that a classification is questionable under the specifics of APG and/or APG II, but may exist in 'general work along APG lines of reasoning' that might be included in a future standard. However, it would be better to attribute this to the website or a particular researcher who supports the classification while noting that it isn't part of a widely used published standard. Failing that any reference to such an informal usage in a citable text or article would do. --CBD 12:05, 19 October 2006 (UTC)[reply]

I felt I was being very clear about its speculative character. It was backed each and every time, the very prominent source the AP-Website (taken by the casual user as the gospel of what is in APG) was included explicitly, indicating where it departed from APG II (2003), sometimes also including APG (1998), thus sketching an ongoing development. Also note that these links to the AP-Website were removed by KPBotany so if there is sombebody guilty of removing useful information it is clear who it is. Brya 16:23, 19 October 2006 (UTC)[reply]

palaeodicots

I am afraid I don't quite see why palaeodicots is an issue. This was a page which existed as palaeodicotyledon. I moved this to its correct name and tried to put it in its correct context. It belongs somewhere in the APG universe and I phrased it sloppily when I used the phrase "In the APG system, ...", rather than as "In the APG universe, ...' or in "In molecular plant systematics, ...". However, do note that nobody challenged this sloppines, and I forgot to come back to it to readjust this. I never regarded this item as something which should be in wikipedia, but rather as something that was there and should not be allowed to run loose.

I think the objection raised was just to the appearance of this classification existing in the APG II standard. Your explanation of intending to say that it is sometimes used in conjunction with APG classifications, without being officially part of the standard, seems reasonable and I think there was even a citable instance of that mentioned on the ToL talk page. --CBD 12:05, 19 October 2006 (UTC)[reply]

I cannot find any trace of reasonableness on the ToL page. Even after I pointed out that KPBotany's assumption that I created was false, and even after MrDarwin confirmed this, KP Botany repeated his allegations here. Also note that Peta did not retract the wild accusation here, even now. Brya 16:34, 19 October 2006 (UTC)[reply]

APG II

I am not necessarily a fan of APG II, but if wikipedia is going to be using this as a reference, internal consistency is called for. It was clearly acknowledged (here) that the present taxoboxes for angiosperms are wrong (thus every wikipedia-page that uses such a taxobox is spreading misinformation). I do maintain that this wikipedia-only-system of Angiosperm plant taxonomy is original research.

The argument can be made, but I think it is more of a 'work in progress'. Wikipedia is not attempting to define a 'new' classification system, but rather cobbling together classifications from existing systems. If an 'APG III' system which extends AGP classifications to the higher taxa comes out Wikipedia would presumably adopt that and adjust the presentation of the information accordingly. In the meantime the plan seems to be to conform to APG II where possible and then pull in additional information from other systems. Obviously this is kludgy and leaves room for inconsistency and confusion but it does not seem an unreasonable approach under the circumstances. For the average lay person these discrepancies are minor... and any effort to adopt a 'perfect' system of classification would inherently be 'original research'. Wikipedia should never be 'leading the way' in having the most logical/consistent/accurate classifications, but rather 'following in the wake' as others do so. If we do as well as Brittanica that's 'good enough' for an encyclopedia. It wouldn't do for cutting edge research in the field, but it isn't supposed to. For that people should be looking to things like the APG website and the standards. Wikipedia is for 'Joe Bubblegum' who just wants a reasonable answer as to 'what this word means' and 'what type of weed that is'. --CBD 12:05, 19 October 2006 (UTC)[reply]

Well there are two options other than now used. 1) drop everything out of the taxobox above the level of order. This is more or less what the real taxonomy texts do. 2) Just follow APG II literally. It is quite doable. Brya 16:38, 19 October 2006 (UTC)[reply]

Standard system

Apparently there is also some confusion regarding a "standard system" for angiosperm taxonomy. It is a basic fact that every taxonomic classification (and for that matter every botanical name) is a PoV, by its very nature. It is a scientific PoV, published in a refereed journal, but a PoV. Thus in referring to any taxonomic placement it is necessary to indicate in what sense a name or classification is used. For example Malvaceae sensu Cronquist is something else as Malvaceae sensu APG, and using just Malvaceae is inadequate: it may be just vague or downright misleading. Thus in using a taxobox it is fundamental that there are two options only: 1) to indicate in each and every taxobox the reference this classification is taken from or 2) to agree on a standard that all taxoboxes follow (even if no more than as a default setting). Using a taxobox with just any old unreferenced taxonomy is downright misleading (and certainly unwikipedian). Thus it is almost inevitable that wikipedia adopts a standard system. It is true wikipedia picked APG II (2003) as its standard well before I came along, but I see no alternative, not until a new overview is published (in a printed source). Brya 12:27, 18 October 2006 (UTC)[reply]

The taxoboxes allow an 'authority' to be specified for each classification. Isn't that sufficient to clarify these issues? While 'APG II' may be the target, if a particular classification isn't covered in that system it can still be attributed to a source. --CBD 12:05, 19 October 2006 (UTC)[reply]

Basically yes (I personally made a few taxoboxes thus, not on this wikipedia). However, that is only so in theory as nobody actually does so. I have never seen anybody in this wikipedia indicate an authority in a taxobox. It seems very likely that any attempt to do so would be violently attacked (as being against consensus. Berton's Digital Maoisism is a stark image but it is not far off). Brya 16:04, 19 October 2006 (UTC)[reply]

Arbitration

You should be aware that this block is also being discussed on the requests for arbitration page with an eye towards determining some sort of 'official' position. You could probably be unblocked to comment there if you agreed to refrain from working on the disputed topic (pretty much anything to do with taxonomy) until this is resolved. --CBD 12:05, 19 October 2006 (UTC)[reply]

Arbitration looks like basically a good idea. Things are badly wrong in the "plant community" with a few users openly engaged in "vandalism, POV pushing, unrepentant editing" and worse, which is then called consensus.

The block, in a middle of a discussion, on a false (not to say fabricated) pretext, of a user who made some forty edits in the past six weeks (mostly on Talk pages) because he is such an immediate danger, is telling. Some people are very afraid of the facts, indeed. Brya 15:55, 19 October 2006 (UTC)[reply]

While I agree that the charges of 'vandalism' against you were unwarranted, the above also serves as an example of why you might wind up community banned anyway. Obviously, not everyone is familiar with botanical nomenclature and KP made a prima facie case for some of your contributions being questionable. Saying 'some people are very afraid of the facts' is unnecessarily combative and dismissive of legitimate concerns. You say above that you identified 'APG III' references as speculative, and I agree with that but it misses the point that speculation doesn't belong in Wikipedia at all unless it is properly referenced speculation by noted persons in the field. Likewise, while your explanation of 'paleodicots' existing as a term in the 'APG universe' is reasonable, but your text did originally attribute it to "the APG II system". Your mention that this was an 'informal' usage supports what you say above about that just being sloppy wording (something can't be both 'informal' and part of the official standard) and this is further demonstrated by your citation of the actual APG II monocot and eudicot classifications listed later in the article... but that would not be apparent to someone with no understanding of the field and thus the block was made based on seemingly reasonable claims of questionable edits rather than 'fear'. Likewise, you suggest that anyone trying to add 'authority' notes to a taxobox would be attacked... that's generally called assumption of bad faith around here. Try thinking that these people really are trying to build a useful reference work for people and just have different ideas on how to go about it than you do. Discuss without getting nasty and saying they do it wrong, don't make sense, and Wikipedia doesn't work right. Yes, nobody adheres to this all the time and it is frustrating, but you're definitely putting out alot of hostility and that is doing more to damage consideration of your views than the actual differences of opinion. I assure you that people can and do add authorities to entries without difficulty. There are even general standards for which taxa should list an authority and how to choose between competing nomenclatures. Everyone here IS trying to make things better rather than opposing your ideas because they are "afraid of the facts". --CBD 11:35, 20 October 2006 (UTC)[reply]

Thank you, I am glad to hear there is agreement that my edit of what is now paleodicots was sloppy. As I pointed out it was not challenged and I forgot about it. My concern at the time was to move eudicotyledons to the official wording in APG (i.e. A.P.G. (1998), APG II (2003) and the APWebsite). Palaeodicotyledon was just something I handled in parallel, for uniformity and my prime concern was to move it to palaeodicots (maybe paleodicots would have been better). The palaeodicotyledons that existed before I came along are shown by Google to be wikipedia-only.

Thank you, I am glad to hear there is agreement that my edit of what is now paleodicots was sloppy. As I pointed out it was not challenged and I forgot about it. If I may quote Brya, Clearly your "taking some steps in that direction" consists in creating the greatest tangle imaginable in order to pressure others in running after you to clean up your messes. I say this not to insult Brya, but to point out that Brya has made the same kinds of misleading, sloppy, and occasionally outright erroneous edits that s/he has excoriated other editors for making (and often in the rudest terms). Unfortunately we cannot follow each other around, cleaning up each other's messes, as there are not enough of us and we do not have enough time, especially when there is a very small number of editors making a very large number of edits, and particularly when those editors very firmly discourage anybody from challenging them. I have on occasion contributed to this poisonous atmosphere--which I greatly regret--but would also point out that I am far from the only editor who has had violent disagreements with Brya, yet Brya seems to think the responsibility lies entirely with the rest of us and none with him/her. While I do think Brya was blocked for quite the wrong immediate reason--an accusation of vandalism--I strongly suspect that, if Brya continues to maintain such a poor relationship with the other editors, s/he will end up being blocked anyway. MrDarwin 13:31, 20 October 2006 (UTC)[reply]

One more thing: I should point out that despite my disagreements and disputes with Brya I agree with Brya on many, many things. In particular I share Brya's skepticism about APG II and its wholesale adoption as the "official" system for Wikipedia (especially as it is already quite out of date, and there are now several competing systems floating around), and I agree that that Taxoboxes are a mess and bordering on original research as they are a peculiar hybrid of two or more quite different classification systems. MrDarwin 13:38, 20 October 2006 (UTC)[reply]

I have never claimed not to make any mistakes, all I have claimed is to do my utmost to be as careful as possible and try and reduce error to a minimum. I too have the feeling that there should be a great deal of agreement between us. As I see it there are two problems. Firstly, you talk a good Talk page but this does not translate into good edits on project pages (a prime factor here being that you appear to have started very few pages, but instead go looking for things in existing pages to get exited about). Secondly, you appear to be insufficiently self-aware especially as regards the ICBN. Being a professional anything requires being aware of what one does and does not know and how this compares to others in the field. It would appear that you have allowed the fact that you have been aware for a long time that there is such thing as the ICBN lull you into the belief that you know a lot about it. Instead the purely nomenclatural aspects are of a considerable complexity: also these are quite different from the taxonomic aspects of it. Brya 14:10, 21 October 2006 (UTC)[reply]

As to your example of an authority this is a confusion between nomenclature and taxonomy. The authority given is that for the name. An authority for the taxon would be called a reviser or monographer. An authority for the taxonomic placement would often be a taxonomic system, although it might also be called a reviser or monographer. Authorities for names are more or less accepted in wikipedia for the simple reason that there are lots of on-line nomenclatural databases which use authorities.

Caryophyllidae

Taxonomy according to Cronquist (1981)

regnum:	Plantae
division:	Magnoliophyta
classis:	Magnoliopsida

subclassis

Caryophyllidae Takht. (1967)

This would be a taxobox giving an authority for the taxonomic classification used. Here Takhtajan is the author of the name (no matter how the name is used) and Cronquist (1981) would be the authority for the taxonomic placement (the same name could be used in a different sense in the Takhtajan system). As you see this taxobox is something else entirely. And being new and, especially, different it would be attacked. But basically it would be a good idea to do it like this.

As to assuming good faith, yes of course I am assuming good faith, but there are limits, beyond which this is no longer possible. But I do agree that in such cases it is best to be quite specific, naming specifically the person concerned and especially the particular behaviour or habit. Someone who is regularly committing a particular atrocity may well be a model wikipedian in other respects. Nevertheless there are things in wikipedia which are badly wrong and have been so since before I came along Brya 13:29, 20 October 2006 (UTC)[reply]

I've said this before, and I guess I'll have to say it again, in reference to your example: It works fine for Caryophyllidae, but it would not work for Silene laciniata any better than the existing system. Admittedly I don't have Cronquist's work at hand, but I'm fairly certain that it doesn't include species, nor does it include all the genera known at that time, much less ones described since. To assume that Silene laciniata would be included by Cronquist on the basis of his 1981 work is as much original research as most of the taxoboxes that use APG II.

An even better example is Encelia nutans. I know that Cronquist would not place it in Encelia because he told me that; he supported Nelson's transfer to Enceliopsis. Circumscription is a slippery thing, but unless a reference or coordinated group of references provides a classification for all plant species, the only way to have a taxobox will be to engage at some level in "original research". Listing the source of the higher-level classification in the taxobox is a good idea, but it does not fully solve the issue you've raised elsewhere.--Curtis Clark 14:10, 20 October 2006 (UTC)[reply]

I agree that listing an authority for the classification will work only in the case of an exception. However the reason it will not work is that it is likely to mystify the majority of users.

As I pointed out before, presenting a complete classification from subspecies up to the level of the angiospermss can well be done without any original research. Both Cronquist and APG II present a solid framework from family to the level of angiosperm. The lower ranks are a little iffy, in the sense that only limited information is available in the systems. However, placement in a genus (or species) is never original research, provided an existing combination is used and no new combinations are published. Of course, any decision of exactly what existing taxa are to be placed in a genus (or species) may well be PoV (especially in the case of taxa with a complex taxonomic history), and when it is PoV it needs to be supported by argument (and references) for the article as a whole to be NPoV. Placement of genera in a family is a little more troublesome (I am a little unsure of how authoritative the list of genera by family in APG II on the internet is, but it won't be that badly off. It has been awhile since I last consulted a copy of the big book by Cronquist, but I assume that it contains plenty of clues as to what genera belong to what families (even if it only by the references which it accepts).

However, also as pointed out before, placing say the order Malpighiales in the class Magnoliopsida (when the latter, as circumscribed in wikipedia, can not exist in an APG II framework and the first definitely does not exist in Cronquist) is original research. Brya 14:45, 21 October 2006 (UTC)[reply]

Unblock

I am going to unblock you so that you may respond to the arbitration request. Please do not edit any pages except that one and this talk page for the time being. As I said, I agree that the claims of vandalism were unwarranted, but there are still alot of 'personality clash' issues which need to be dealt with and you will probably just be reblocked by someone if you resume editing before they are. I strongly suggest you stick to explaining that you were not vandalizing (as briefly as possible, the arbitrators are no more likely to be experts on taxonomy than admins are) and try to find some sort of common ground with the people you have been in dispute with to work together going forward. --CBD 11:35, 20 October 2006 (UTC)[reply]

You have been reblocked since you edited the Tree of Life page with more arguments when CBD specifically stated you should only edit your talk page and the arbitration page. pschemp | talk 14:21, 21 October 2006 (UTC)[reply]

Please do not post on my talk page

As to the post on the ToL-page I submit that this is a gray area. The conditions of an unblock were explained to me twice, namely

here: "You could probably be unblocked to comment there if you agreed to refrain from working on the disputed topic (pretty much anything to do with taxonomy) until this is resolved."
and here : "I am going to unblock you so that you may respond to the arbitration request. Please do not edit any pages except that one and this talk page for the time being."

Clearly I agree that the "Please do not post on my talk page" entry on the ToL page looks bad and does not belong there. As the post by KP Botany clearly addressed me repeatedly and made new and equally unfounded accusation I feel it is only right and natural that I should counter these in the same place that they were made. As to exact procedure in doing so I am still unsure. Presumably I should have asked an administrator to either delete KP Botany's entry (while simultaneously contacting KP Botany to explain this) or move it somewhere more discrete where I could answer it.

I think that user:SB_Johnny's suggestion to move the entire entry even now to a more discrete spot is well worth considering.

To contribute something positive: I think it is also a good suggestion to have all the plant articles marked by a warning that such plant articles are even more of a work in progress than other parts of wikipedia. Wikipedia does get an uncomfortable amount of exposure and any error is spread very widely over the web. It appears there is a widespread feeling that there are failings in probably the majority of the plant articles, even if there is no agreement on what these failings are. This will be somewhat unfair to those who put in work on extensive individual pages that as a result rise well above the average, but probably that cannot be helped.

As to bad language: there is a very uncomfortable habit by at least some contributors to plant articles to get angry first and make drastic (not to say brutal) edits first often accompanied by bad language, and to regard consultation and discussion as a last resort only. Personally I have long since abandoned making big edits in existing pages, without contacting the relevant contributors (when there clearly was an involved contributor). It is true that in defending against said brutal edits in pages where I was the involved contributor the tone of my comments has fallen well short of perfectly courteous behaviour. But I submit that it was made very hard for me to be perfectly courteous. Brya 08:23, 22 October 2006 (UTC)[reply]

APG I, II, III, etc.

Hi Brya,

I'm actually really interested in the APG system, but some is still unclear to me, and it strikes me that you might know the answers.

1. This is all based on 3 genes? Are they active genes, or "junk DNA"?

2. Is the reason for APG II's incompleteness a lack of data, or a lack of collation of the data that exists?

3. Is any account taken of viri and viroids that may be responsible for transporting genes between unrelated types?

4. If I understand a lot of the arguments being made against your approach (and regardless of whether these arguments and/or your approach are correct), how exactly would one venture reasonable guesses as to the contents of APG III? Or is it the overall structure (clades vs. higher taxa, etc.) that are the subject of conjecture?

--SB_Johnny|^talk|_books 19:36, 22 October 2006 (UTC)[reply]

APG I, II, III, etc

Hi SB_Johnny,

It may indeed be good to look at some facts. A lot of the stuff on APG is in the articles, but it may be good to review it. There are only the two official APG classifications, APG (1998) and APG II (2003), but there are more publications that belong in the APG universe (even leaving aside the research papers APG is based on).

A good start is the 1993 paper by Chase et al., referred to here, which was published jointly by some forty researchers. This was based on a single chloroplast gene rbcL which was inventoried across the angiosperms. At this stage a classification began to take shape (with names such as asterids and rosids being introduced). It is no coincidence that this was based on data from a chloroplast gene. Chloroplasts originated as prokaryotes, moving into plants, there performing a single important task. They retain their own DNA, which remains prokaryote in nature. Chloroplasts are passed in their entirety from parent to progeny, without recombination of DNA taking place. Not too many changes are possible in their genes, as that risks that they can no longer perform their function (and the 'host' plant dies). As chloroplast genes accept only few changes, and only slowly, they can be regarded as independent archives (of DNA sequences). This makes them a good source of information of evolution, at least at the higher level of plants groups.

The APG (1998) publication did propose a classification of the angiosperms, with formal names (conforming to the ICBN) at the levels of family and order only. Authorship of this paper was by a smaller group of researchers, but showing considerable overlap with the authorship of the 1993 paper. The 1998 APG does not mention anything on methods or genes in the text, although the research papers referred to tell their own story.

Following this, there is the introductory textbook of Judd et al., Plants Systematics, a phylogenetic approach (1999, with a second edition in 2002). This explains a "phylogenetic classification" in detail, although it is not officially linked to APG. Also, some placements of families are proposed different from APG. However, authorship overlaps with that of the APG paper (that is three of the four authors being members of APG), with other members of APG being acknowledged as having been consulted. The official APG system is included on CD-ROM. This book explictly presents the DNA sequences being used (the molecular data) as the chloroplast gene rbcL, the chloroplast gene atpB, and the 18S rDNA gene (a gene coding for ribosomes, but located in the cell nucleus).

In the APG II (2003) publication (available online) the caption of figure 1 summarizes what molecular data are used:

All except five of the clades are supported by the Soltis et al. (2000) analysis of 18S rDNA, rbcL, and atpB sequences from a wide sample of angiosperms. Three clades, Canellales+Piperales, Laurales+Magnoliales, and these four orders together, are supported by analyses of several different gene sequences of phylogenetically basal angiosperms (Qiu et al., 1999; Graham & Olmstead, 2000). One clade, that of all core eudicots except Gunnerales, is supported by analysis of rbcL sequences from a wide sample of eudicots (Savolainen et al., 2000). Another clade, that of all asterids except Cornales, is supported by a six-marker analysis of a wide sample of asterids (Bremer et al., 2002). Rosid and asterid families not classifed to order are not shown.

That is it basically uses the three genes mentioned above supplemented by other molecular data in some places.

As to what may be in APG III this is impossible to say as:

the various versions of APG are consensus systems, and consensus takes time to build
the group of scientists going by the name of Angiosperm Phylogeny Group is not constant. The three publications listed above (1993, 1998 and 2003) were written by three different groups that have the same core authors, but vary in exact composition.

I specifically used the phrase "APG III" to indicate clearly that such placements as Nymphaeaceae in Nymphaeales were quite speculative, instead of being part of the official APG, as Wikipedia stated before I came along as here and now again since this. There is an unfortunate tendency of people to take the APwebsite as the APG-system (merely because it is prominently available on the web), disregarding all evidence to the contrary. I put in as stark an image as possible to prevent. It looked (and looks) to me that connecting the APWebsite with wording such as "this suggests this order may be recognized in APG III" was as effective a way to erect the strongest warning sign possible to dissuade readers from making the assumption that the APWebsite is APG. I reinforced this by (upon occasion) referring to the APWebsite as the "APG Companion site", again a clear warning sign.

That is not say that there are no indication of where change is likely to occur, and in what direction.

APG II

APG II is not really incomplete. It does leave a few taxa entirely unplaced (on page 421) but this is a very modest list indeed. More disconcerting is that it leaves quite a few families unplaced as to order, which gets on some peoples nerves.

One of the other issues is the occurrence of "bracketed" families. That is, families that can be treated as separate or not, as in Asparagales. This looks good in theory, but may not be as good in practice.

The above does not trouble me. What troubles me is the taxonomic style (the style about what taxa to recognize), which to my taste is too easy about abolishing well-recognised families, on too little evidence (for example in transferring plants from Flacourtiaceae to Salicaceae APG II lost Samydaceae, and it did so on the basis of one single sample (with inconclusive results) for a prospective family with hundreds of species.

Virusses

Basically cladistics does not take account of horizontal gene transfers (either by virusses or the plants themselves), which is one of the big objections against cladistic methods. Brya 11:04, 23 October 2006 (UTC)[reply]

Thank you for the clarifications: this (and what MrDarwin put on my user talk) makes it a lot clearer than do the actual articles on the subject. I don't know how you feel about wikibooks, but the more I read from the conversations about these issues, the less satisfied I am about the articles on wp as they currently read. A more complete discussion of plant taxonomy issues would be a nice addition to the Botany book, and actually having a "verbose" discussion of this there would probably be helpful in copyediting and rewriting the related wikipedia articles (which of course are supposed to be kept brief). If you'd be interested in doing something like that, I can import the relevant articles for you (I'm an admin), so you wouldn't have to start from scratch. (This invitation also extends to Mr Darwin and Berton, of course).

My work with plants is actually more about growing them, caring for them, breeding them, and in some cases killing them. While the higher taxa aren't something that concerns me professionally, I do find it interesting. Perhaps more of interest to me is why all the species and genera keep getting broken up (which is rather contrary to what we were taught at the university: namely that the binomials were more important than the common names because they stay the same across time and national boundaries. Breaking up of families can be troublesome because of the horticultural and agricultural associations within families (pest & disease susceptibility, palatability to mammal pests, etc.), especially for rare plants for which there is otherwise little information to be found.

As far as the "OR conjectures" about what's coming next (i.e., making inferences from what's available now as to the eventual composition of the clades, orders, etc.), that kind of thing can be done on wikiversity, if it's a project you'd be interested in (wikiversity primarily just creates links to published papers and other "learning resources", and a certain amount of Original Research is permitted under the rules there). There's not much on wikiversity yet, but content could be added to School:Plant Sciences

BTW, I hope you don't think I'm just telling you to "just go find something else to do" (though for the time being that might be a good idea while things calm down), but rather that I suspect you'd like the atmosphere on these projects for the same reasons I do: namely that they aren't nearly as politicized or bureaucratic as wikipedia often becomes, and you have a bit more freedom to finish a thought and tie things together, rather than just relying on wikilinks to articles that often change several times a day. --SB_Johnny|^talk|_books 17:30, 23 October 2006 (UTC)[reply]

Thank you. I am glad this helped a little. However, how much of this belongs in wikipedia is a different matter. As you have noted the plant taxonomy articles attract a lot of edits; nobody can write in a vacuum (just look at the paleodicots, which as I pointed out I did not create, and I should emphasize existed in wikipedia before I touched it as a formally recognized plant group, taxobox and all, by its component groups defined as part of APG II. Look how much trouble I had to move it to the more proper "palaeodicots" and to emphasize its informal status). My experience is that anything beyond the basics does not survive (and even the basics need policing to resurrect them periodically).

Also, to write competently on a topic one really needs to know it in some depth. Writing is the art of knowing what to leave out. If I don't know enough about a topic to leave nine tenths of what I know out of the article, I don't feel I am justified in writing about it in the first place. Brya 06:49, 24 October 2006 (UTC)[reply]

Manual of Style

In here a willingness was acknowledged to consider Manual of Style aspects. The wikipedia Manual of Style emphasizes internal consistency, while allowing for more than one style (if appropriate to the topic). This is in line with style-manuals elsewhere in the real world.

As to the style of typesetting in botanical names, there are several different styles in use in the world at large. The most important of these (not a delimitive listing) will be:

No special typesetting. This is likely to be the most popular style (if all printed matter is considered, but is also found in some botanical publications).
Use italics for names at the level of genus (Quercus) and below (Quercus subgenus Quercus, Quercus sectio Quercus, etc. Quercus robur, Quercus falcata var. pagodaefolia, etc). A variation on this style is to use italics for names below the level of family (that is italicize names of subfamilies and neighbouring ranks, Caryophylloideae).
Use italics for all botanical names (Monocotyledones, Fagales, Campanulaceae, etc) . This is the style as exemplified by the International Code of Botanical Nomenclature, followed by a portion of scientific journals, with a marginal following in non-plant publications.

The Codes

The matter at hand is that of botanical names. Scientific names of organisms are regulated by Codes of Nomenclature of which there are three to eight, depending on viewpoint. The most important are the:

International Code of Zoological Nomenclature for names of animals. The current 1999 edition online here
International Code of Botanical Nomenclature for names of plants, fungi and algae (the 2000 edition online here. The 2006 edition is unchanged on these matters
International Code of Nomenclature of Bacteria for names of prokaryotes. The current, 1990 edition, online here

1) The style of typesetting followed in the ICZN is to use three different typefaces:

For scientific names not covered by the Code: no special typeface (Diptera)
For scientific names covered by the Code, above the rank of genus: small caps (BOVIDAE)
For scientific names covered by the Code, at the rank of genus and below: italics (Panthera, Panthera leo, Gorilla gorilla gorilla)

2) The style of typesetting followed in the ICBN is very simple: all scientific names (of plants, fungi and algae) are covered by the Code and they are all set in italics.

3) The style of typesetting followed in the ICNB is almost as simple: not all scientific names (of prokaryotes) are covered by the Code but they are all set in italics anyway.

Note that the three Codes do each have a different style for author citation so that often there are differences between such names anyway.

The style exemplified by the Codes is in no way binding, the well known guideline being that the Codes regulate nomenclature not typography. The ICBN in its preface (of the 2000 edition but very similarly in the 2006 edition) states:

"As in the previous edition, scientific names under the jurisdiction of the Code, irrespective of rank, are consistently printed in italic type. The Code sets no binding standard in this respect, as typography is a matter of editorial style and tradition not of nomenclature. Nevertheless, editors and authors, in the interest of international uniformity, may wish to consider adhering to the practice exemplified by the Code, which has been well received in general and is being followed in an increasing number of botanical and mycological journals. To set off scientific plant names even better, the use in the Code of italics for technical terms and other words in Latin, traditional but inconsistent in past editions, has now been abandoned."

Usage in practice

I am not all that familiar with usage in other groups than the higher plants. But note that this official list for prokaryotes does follow the example set by the Code.

Usage for the higher plants is varied. Botanical publications in general tend not to be dogmatic about it, rather going for internal consistency only. It is no exception to see different styles used in different parts of the same publication (a rather extreme example being the last few issues of the journal Taxon], which have included both all-italics and italics-at-the-level-of-genus-and-below articles, side-by-side, see August issue). Kew Gardens puts out both a scientific journal, Kew Bulletin (all italics) and a newsletter Kew Scientist (italics-at-the-level-of-genus-and-below). Quantification of the several styles in use is difficult and wil depend on what is taken into account (all printed material, only plant publications, only botanical publications) over what time frame, and in what languages. Yet, there is a clear general pattern: "all-italics" is correlated with nomenclatural (versus taxonomic), scientific (versus popular) and European-oriented (versus US-oriented) publications. Thus, it is easier to find a Russian botanical journal that uses all-italics than an American one. Still the arguably most prestigious US website dealing with plant taxonomy, that of the USDA (USDA Plants and GRIN) does use all-italics (another American site that does so is this.

Nor is all-italics restricted to botanical publications: I was pleasantly suprised to see a copy of the guinness book to use all-italics.

All in all, this all-italics style is not only the one preferred from the formal perspective, but that is in widespread active usage. It is not a majority style (likely not even close). But certainly it is appropriate in discussing botanical nomenclature, and higher level systematics. The more so with the rise of english names for clades (plant groups without a formal ranking or name according to the ICBN) In some cases all-italics greatly aids readability. Personally, I find this easier to proofread, to maintain, consult, etc than this. Also in the case when a taxobox includes both formal botanical names and informal, english, clade names (because the classificication followed does so) all-italics helps offset the difference, as here.

The objections

Applying this style when dealing with higher level plant taxonomy in pages on Wikipedia comes primarily from those dealing with animals, such as in the post by Dyanega of 21.13h, 6 Oct 2006 here (four fifths of the way down) :

Further, there is ample reason to avoid this practice, as can be demonstrated by the following example; consider the taxon names Aphelinoidea, Chalcidoidea, and Trichogrammatoidea versus Aphelinoidea, Chalcidoidea, and Trichogrammatoidea. Written the former way, one cannot determine, without recourse to external reference works, that two of these names are genera and the other a superfamily; written the conventional way, one CAN (and one can also see that an article exists for one of the names). This is precisely why the convention exists, and why names should be wikified.

Such objections fail to take into account that there was never any suggestion (that I am aware of) to introduce any kind of style of typesetting for pages on animals. Nor does it consider that if the analogous proposal (to follow the example set by the Code) for animals were to be made (which it was not) this would be to use small caps for names above the level of genus (up to superfamily) [this would presumably lead to Aphelinoidea, CHALCIDOIDEA, and Trichogrammatoidea]. In the same post Dyanega refers to the mandatory presence of ranks in the taxobox (notably that of class). This too is typical. Forcing plant taxoboxes that include classes, while these taxoboxes (putatively) represent a system of plant classification with which this is not compatible (not in the wikipedia circumscription of this class) does represent original research (a wikipedia-only system of plant taxonomy).

This of course complicates the issues, with contributors on animals not only dictating typesetting on pages of plant taxonomy, but at the same time making original research mandatory for pages on plants. All in all this creates an unpleasant political tangle. Brya 13:44, 24 October 2006 (UTC)[reply]

Comments

From a typographic perspective, foreign-language text in English text has consistently been italicized since at least the mid-1800s, so following a typographic tradition, nomen nudum, pax vobiscum, and Triticum aestivum would all be italicized. I've never seen a clear typographic explanation for families and above not being italicized, but I've speculated that, just as papaveracées and Papaveraceen are, respectively, French and German words (not Latin), Papaveraceae might well be an English word, spelled the same as the Latin.

It is not unusual for modern typography to go against typographic tradition, and an ICBN that recommends italicizing Papaveraceae and not nomen nudum is minor as such things go. But it's important to understand current usage in typographic terms. First, the Russian: I have seen Chinese books in which all scientific names are in roman (non-italic) type. If I were setting Russian prior to the last decade, I'd have to search around for an italic typeface (and if I were setting Serbian, the Russian one wouldn't do at all), and if I were setting Chinese, I might use a Japanese kanji face, not realizing that the differences are more than subtle to Chinese or Japanese readers. It is more parsimonious for all but the very most recent Unicode-encoded text to assume typographic ignorance of another script than to assume intentional usage.

Likewise, I have seen too many examples of things like "the rosaceae rosa rugosa plant" to assume that such things as Guiness are intentional rather than a "mistake-made-correct" by changing rules.

Although I would give the slightest preference to the "old style", I'd support either way, as long as it were a consensus and applied consistently.--Curtis Clark 14:21, 24 October 2006 (UTC)[reply]

I am pretty much agnostic on the italicization issue; I think it's a relatively trivial one and not one worth getting into edit wars over. My primary objections are that (1) the italicization advocated by Brya is a purely typographical practice not even recommended by the ICBN, it is only a matter of following their example; (2) this practice has been adopted by only a small minority of botanical journals and other publications (and outside of those three botanical journals I could find, I haven't found any textbooks or other publications using this practice although I don't doubt that there are at least one or two out there); (3) it's less confusing to the casual user or visitor to Wikipedia (i.e., somebody not already familiar with technical botanical or zoological matters) if articles, both plant- and animal-related, are relatively consistent in style and typography; (4) there is a clear consensus (except for Brya) among ToL participants for a particular typographical practice; (5) there is a clear consensus (again, except for Brya) among editors of plant articles to maintain a particular typographical practice; (6) Brya's choice to ignore an otherwise clear and overwhelming consensus has led to edit wars, acrimonious disputes, and a lot of bad blood. Like Curtis, I could swing the other way if there were a clear consensus, but there clearly is not. But since non-italicization is not violating any kind of rule or nomenclatural practice, has no bearing on nomenclature whatsoever, and has not even been adopted by most practicing botanists, I don't see any value in insisting upon it. (As an aside, I'm basically in agreement with all of Brya's comments about taxoboxes.) MrDarwin 14:57, 24 October 2006 (UTC)[reply]