Talk:Phylogenetic nomenclature

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[edit] All those tags

Phew… that's way exaggerated. Let's pick the first example: click on the link to the article on the PhyloCode, and you will find the PhyloCode website, which states in no uncertain terms that the PhyloCode is intended to regulate phylogenetic nomenclature. For some other things, like the growing number of biologists dissatisfied with traditional nomenclature, I could cite 100 papers if I took the time. David Marjanović 18:39, 2 June 2007 (UTC)

One or two would be just fine. But this is an encyclopedia. The sources need to be available in this article, not through links. That a grwoing number of biologists are dissatisfied should ideally have at least 2 or 3 refs, to give an example of a 'number' of biologists who hold this view. With no ref, statements like that can seem POV and unencyclopeadic, more like a web site about PhyloCode. Dinoguy2 03:07, 3 June 2007 (UTC)

[edit] My latest edit

As you have probably already seen, I left two incomplete sections. I will try to complete them over the next… say, weeks. I only tackled the most urgent problems. To wit:

  • Sorry, Stemonitis! I managed to overlook your edit. It is very important to remember that, contrary to your edit, names, not taxa, are defined. Clades exist, and we discover them. Names don't exist in nature; they are conventions that we get to define. I should have fixed this glaring error in the first sentence much earlier.
  • I must look up if Goodrich is Edwin. I think he is.
  • I removed "Category: Phylogenetics", because phylogenetic nomenclature only uses whatever the results of phylogenetics are; it is not part of phylogenetics.

David Marjanović 21:49, 22 August 2007 (UTC)

[edit] My even laterer edit

On the meaning of "some authors", I have a paper by Benton and probably someone else in mind. I'll look for it and cite it then. I'll also look up and cite the paper that describes the Phylogenetic Diversity Index.

On another note, the article looks unbalanced. I can't help it: I've never encountered anyone who demonstrably understands phylogenetic nomenclature but doesn't like it. Can someone else help…? David Marjanović 13:18, 26 August 2007 (UTC)

What do you mean by "demonstrably understands"? It seems pretty dodgy, not to mention unencyclopedic, to say the people opposed to total abandoment of taxonomy in favor of phylogenetics simply don't understand the latter.
That's why I didn't put that into the article, as you can guess. :-) David Marjanović 13:17, 15 September 2007 (UTC)
Juat typing "objections phylocode" into Google will give you a few hits from published literature.
I know – but all of them are, in my experience, misunderstandings. I have a paper in preparation on the latest few. David Marjanović 13:17, 15 September 2007 (UTC)
There is still too much subjective editorializing in th article: statements like "The problems is evident" (to who? The editor, obviously). The whole section "Perhaps most emportantly" (sic) consists of obviously biased interpretation based on papers by proponents of ranks.
I need to cite more. (Thanks for catching my typo!) David Marjanović 13:17, 15 September 2007 (UTC)
None of the papers cited (or currently, not cited) in this section object to the use of ranks, in fact they do the opposite,
An important point is the distinction between "use of ranks" and "obligatory use of ranks". That's what much of the article is about, and also what the references are about: they all argue strongly against the latter. For the fifth time: Ranks are allowed in phylogenetic nomenclature, but they are not part of the rules – they don't influence which names can be used, they don't influence which taxa get which names, and they don't influence the spelling of names. Here, read the thing again. David Marjanović 13:17, 15 September 2007 (UTC)
and the editor has used their positions to demonstrate why he or she finds the use of ranks problematic. This is unacceptable for an encyclopedia: i'm going to go ahead and revise some of this actually. Dinoguy2 00:37, 27 August 2007 (UTC)
In the process you introduced a few glaring mistakes, like deleting "obligatory" from one of the headlines, and rearranging a sentence so that it now seems to say that putting Aves into Reptilia requires Aves to be a genus, even though this is only the case if Reptilia is a class. (If Reptilia were in the process inflated to a domain or something, the problem wouldn't arise, at least not to this extent.) I'll try to fix them now. Thank you for several stylistic improvements and for changing "Advantages" to "Comparisons". David Marjanović 13:17, 15 September 2007 (UTC)
So, done.
I hope it is now clear that Goodrich did not coin the name Sauropsida. He didn't hide that fact: he cited Huxley.
I can't cite anyone for reasons why Goodrich's suggestion hasn't become mainstream because nobody seems to have written about the issue; as far as I know, only I have a paper on this in preparation.
I have some of the papers I cited as pdfs; if you want them, just tell me your e-mail address.
Also, if you can find someone who works on Mesozoic dinosaur phylogeny and doesn't use PN, please tell me. I follow that field and haven't found anyone in the last 10 years. Using ranks (as some Chinese workers on Mesozoic birds do) does not count, as I hope to have made clear. David Marjanović 15:52, 15 September 2007 (UTC)
I just added another reference and removed the "citation style" template because all citations now use the same style, as far as I can see. If you find a counterexample, tell me, or better yet, fix it. David Marjanović 22:20, 15 September 2007 (UTC)
Thanks to an anonymous editor for correcting "tenants" to "tenets"! That's something I, you know, "actually knew"… David Marjanović 23:11, 16 September 2007 (UTC)

[edit] PN vs PT vs Cladistic taxonomy, etc.

Is it possible to better sort out some of the overlap between these articles? This one obviously deals with phylo nomenclature, but phylogenetic taxonomy redirects to Cladistics (which, strictly speaking, is the method by which relationships are found using a computer program, not the classification system derived from that method. That article even contains a section of "Cladistic taxonomy". Doesn't CT=PT=PN, PN being the more correct name? Dinoguy2 00:37, 27 August 2007 (UTC)

Yes. Entirely correct.
(Except that a computer is not strictly necessary for cladistics; Hennig did his by hand. A computer only makes it possible to use reasonable numbers of taxa and reasonable numbers of characters and still find all most parsimonious trees in seconds to weeks rather than years.) David Marjanović 13:26, 15 September 2007 (UTC)
While I am at it, let me say that the Cladistics article is full of problems. It's so offputting that I don't dare lengthen its vast discussion page. The smallest is that it says "synapomorphy" when "autapomorphy" is meant – Hennig found it great fun to invent new technical terms, so he introduced "autapomorphy" (auto- = self) for any innovation of one taxon and "synapomorphy" (syn- = together) for the shared innovations of sister-groups. I'll give that article a lengthy treatment, perhaps next weekend, or the one after. David Marjanović 16:09, 15 September 2007 (UTC)
Now that i'm looking, all the cladistic/phylo articles are an absolute wreck. Check out the "See slao" sections--most of those are redundant with each other and could easily be merged to make one or two articles. Well, not "easily", that's one big project... Dinoguy2 09:31, 16 September 2007 (UTC)
Click the link in this article to "Linnaean nomenclature"! That's a redirect to an even more absolute wreck. Poor Linnaeus. He has really deserved better than that. David Marjanović 23:15, 16 September 2007 (UTC)

[edit] Note to self

The third paper on this page is online and freely accessible in its entirety, and even in HTML, so I should cite it at every occasion, and then some. If anyone else wants to do that to save some of my limited time, feel free… David Marjanović 23:08, 16 September 2007 (UTC)

[edit] Species problem

A more in-depth discussion of species under PN could be useful. Especially in taxa with good dispersal capabilities, evolution does not require species (if not defined under a phylogenetic species concept - which has nothing to do with PN however) to be monophyletic in any meaningful way, especially to molecular systematics.

Any allopatric and reproductively isolated population derived from a still-extant progenitor population that continues to evolve as a single entity presents a problem for PN. There exist various approaches to deal with this problem, but it is a major point of contention in PN. Discussing this in detail would underscore that PN (in the PhyloCode sense) is a brand-spanking-new topic (albeit with a long and dignified ancestry). At present the article seems too set and done, suggesting that there are two monolithic camps and that's that. But this is not correct; many taxonomists as of 2007/2008 seem to prefer to keep out of the debate and simply use a sort of "expanded" Linnean system allowing unranked and basal taxa and don't seem too unhappy with that (the ICZN permits that, as it only mandates a small set of ranks and leaves everything else to decision by consensus). Dysmorodrepanis (talk) 21:10, 3 February 2008 (UTC)

The PhyloCode will not regulate species names (at least not in its first edition). To name species, you have to use the rank-based codes, and you can use whatever species concept you like. The PhyloCode will only regulate clade names; under most species concepts species are not necessarily clades. David Marjanović (talk) 15:44, 7 June 2008 (UTC)

[edit] Editorializing

There is some really inappropriate commentary going on in this article. A few examples just gleaned from things added/removed in the most recent edits:

Perhaps most importantly, ranks encourage the misperception...

Who says this is most important? Who says the ranks encourage misperception? The cite is from a study that treated them as if they were meaningful. The editor is apparently disagreeing with peer-reviewed, published usage. If this isn't OR I don't know what is.

Note that this is probably not a particularly good example:

Again, says who? Obviously this is the opinion of the editor.

Explaining this stuff is one thing, but it should be done in a completely citable way. Any argument that has not been made in print, no matter how sound, should not be included. If these points have been argued in print, they should be phrased as "such and such argued, in the year x, that that this example (previously used by so and so) was faulty." I've half a mind to be bold and go in to decimate this thing myself, it's possibly my least favorite article after Prehistoric Park ;) Dinoguy2 (talk) 21:57, 3 February 2008 (UTC)

[edit] Edit 7 June 2008

It looks like someone tried to have a discussion with me in the article itself. Please let's have it here. That's what the discussion page is for.

I have changed too much to fit into an edit summary:

  • I have deleted the second paragraph of the introduction, because it lacks any context and is wrong anyway (as explained in the section "Extensions", PN can be used to define paraphyletic and even polyphyletic taxa – only the PhyloCode will forbid that).
  • I have changed "traditional" to "rank-based". This is more meaningful and avoids POV implications like ancient vs modern.
  • In the section "Lack of obligatory ranks" I deleted the paragraph after the quote, the one that began with "Note that this is probably not a particularly good example" because it is… well… wrong. Because they have different ranks, Homininae and Hominidae are never treated as synonyms by the ICZN, even if they have the exact same contents under a given classification, and don't compete for priority.
  • In the next paragraph, someone added a hidden comment "did any taxonomist really think this way since Darwin?" on the issue of ranks misleading people into believing ranks are somehow real at some level. Astonishingly enough, this happens all the time, as documented in the references later in that sentence. The most astonishing case is this paper by Benton (the APP website is currently down, so the Google cache is here), which says in the same sentence – in the abstract! – that ranks are not real and that ranks are "valuable surrogates" for actually quantifying biodiversity.
  • I have deleted the Nixon & Carpenter 2000 ref because it's not only way out of date, but also because it is chock full of misunderstandings that have been corrected again and again in more recent literature (much of which is cited). I hope this does not come across as POV. The latest papers on PN are de Queiroz (2007) and Laurin (2008), both of which argue strongly for it; there does not seem to be a paper that argues against it and is similarly recent. If one ever comes out, please add it. Benton (2007)… well, see above.
  • I have deleted the sentence "Taxa of the same rank can only be considered equivalent if they are placed in the same taxon one rank higher, and only if the taxonomic treatment is phylogenetically sound." That's because it's still wrong. "Equivalent" in what sense? In terms of contained number of species? No. In terms of included morphological or genetic diversity? No. In terms of age? No – sister-groups do fulfill that criterion, but being placed in the same taxon of the next higher rank is not the same. In terms of ecological dominance? No…
  • The same holds for the first half of the following paragraph. There isn't even such a thing as "phylogenetic taxonomy" – did you mean the principle of naming only monophyletic taxa except for species?
  • The second half does have a valid point: mandatory suffixes indicate nesting (although this works even better (Google cache) without mandatory ranks…), but this belongs in the PhyloCode article, which will set rules for PN, not in the PN article itself. So I deleted that, too.
  • I have reworked the introductory paragraph to the "History" section and removed the section-stub tag.
  • I have added lots of references.

David Marjanović (talk) 20:35, 7 June 2008 (UTC)