Talk:Phylogenetic nomenclature

message: 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)
replies: text: 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)
thread_title: All those tags

message: 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)
thread_title:  My latest edit 

message: 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)
thread_title:  Note to self 

message: 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)
replies: text: 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)
thread_title: Species problem

message: 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)
thread_title:  Editorializing 

message: 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)
replies: text: The article still reads to me, from the point of view of a serious but non-professional botanist, too much like an argument for PN and not a description/discussion of PN. There may not be papers arguing against PN in favour of rank-based approaches, but you also need to look at what is actually being done ("do what I do, not what I say"). So e.g. if you look at the field of angiosperm classification, dominated by the APG, you find that both clade-based and rank-based names are considered important. Circumscribing Linnean Families and Orders based on phylogenetic evidence is a major activity. Alongside this goes free use of informal clade names. (It's too early to tell, but I suspect that in most fields of biology, this kind of mix-and-match between formal Linnean ranks and informal clades is the likely outcome, rather than PN purity.) At least in botany, I can cite plenty of authors who by their actions obviously consider rank-based nomenclature worthwhile; they don't seem to bother to write papers which say so, they just do it.  Peter coxhead (talk) 00:30, 21 December 2010 (UTC)

text: Returning to the point, why is PN an "alternative" to rank-based nomenclature as the first sentence says? This seems to set up an opposition from the start. Perhaps it's really an "addition to" or a "complement to". Peter coxhead (talk) 00:35, 21 December 2010 (UTC)
thread_title:  Edit 7 June 2008 

message: According to the Philosophy section, "phylogenetic nomenclature follows the nomenclature in other sciences in trying to define its terms as precisely as possible. . ."  On the contrary, scientists require that terms be defined just well enough for the purposes of research, application, and communication within their fields, seldom as precisely as possible.  Economists, for example, use an admittedly imprecise concept of inflation, defining more exact measures only as the need arises.  In physics, the concept of energy is imprecise and has been repeatedly extended with an eye to preserving the conservation law.  Even the PN edifice rests on an ill-defined notion of species; if its supporters sought maximum precision, they would either formulate a definition or else adopt one  that has been proposed.  As David Marjanović notes above, the Phylocode allows you to use whatever species concept you like.   Peter M. Brown (talk) 17:09, 3 August 2011 (UTC)
replies: text: After I began this article, the PhyloCode gave up on species, at least for now. It will only regulate clade names. Clade names will not be defined with species as specifiers, but with specimens as specifiers. (It will be allowed to use species names as shorthand for their type specimens.) So, PN does not rest on any notion of species; it rests on the notion of "specimen in a collection", which is straightforward enough. David Marjanović (talk) 10:42, 22 September 2012 (UTC)
replies: text: I was unaware of the shift. The Phylocode article should be updated, not only by deleting the claim that species may be a specifier, but also by noting that an "ancestor" for PN purposes must be an organism or a breeding pair, not a species. Peter M. Brown (talk) 23:01, 24 September 2012 (UTC)

text: Letting individuals found clades means that the structure is no longer hierarchical, doesn't it. Clades can now overlap. Peter M. Brown (talk) 01:20, 25 September 2012 (UTC)
thread_title:  Philosophy 

message: There are several things in this section that might deserve modification:  —Preceding unsigned comment added by 160.111.254.11 (talk) 22:09, 11 June 2008 (UTC)
thread_title:  History 

message: While it's relevant, the diagram is almost completely disconnected from the text.  Its conventions are not explained and the terms that it is supposed to clarify are not used except that "branch-based" occurs once in passing, deep in the History section.  Without an explanation of the term, the latter occurrence is unhelpful. The sentence involved can easily be revised to eliminate it. 
The diagram's caption mentions "the apomorphy mentioned in the apomorphy-based definition" but there is no apomorphy-based definition in the article.
The diagram is used to excellent effect in the Phylogenetic definitions of a clade section of the Cladistics article.  I suggest that it be eliminated from Phylogenetic nomenclature and that a hatnote be added to Definitions:
::For types of phylogenetic definitions, see Phylogenetic definitions of a clade.
Things would be different if someone were prepared to enhance Phylogenetic nomenclature to make real use of the diagram.  As this is already done in Cladistics, though, that would be unnecessary effort. As things stand, the diagram is clutter.  Peter M. Brown (talk) 00:10, 22 August 2011 (UTC)
thread_title:  Should the Clade types diagram be here, in [[Phylogenetic nomenclature|Definitions]]? 

message: The Philosophy section needs work. There are important philosophical differences between rank-based and phylogenetic nomenclature, but only one small aspect appears here. I also think that the long Laurin quote is unhelpful. I suggest that to the general reader, the obvious analogy to the way that boundaries are fixed in determining geological time periods is not phylogenetic nomenclature but circumscription (e.g. specifying the precise boundaries of a taxon by specifying what organisms are included in it), which neither system uses. An analogy with PN might be to define a geological period on the basis of all strata which were affected by ("descended from") a particular geological event.
This points to a feature of PN which its proponents seem to play down and is weakly represented in the article: just as we wouldn't know for certain which strata were affected by a particular event, we don't know (can never know?) the precise phylogeny of organisms, so that the believed circumscription of a PN taxon is just as subject to change as is the circumscription of an RN taxon. To the lay person and to biologists generally, the "meaning" of a named taxon is partly to do with what organisms it is believed to contain and thus which appear in lists in reliable sources. PN has the "advantage" that an omniscient being knows the precise circumscription of every name, whereas the inherent fuzziness of RN makes this impossible. But to non-omniscient beings, there doesn't seem much difference; indeed the believed circumscription in PN is perhaps more likely to change, since it depends only on phylogenetic tree evidence, whereas, at least traditionally, in RN both characters and phylogeny are taken into account. Peter coxhead (talk) 09:55, 1 October 2012 (UTC)
replies: text: Responding to your second paragraph: good point, but it's not philosophy. I'm thinking of resurrecting Some criticisms of phylogenetic nomenclature from the old version of the Cladistics article in a new section of Phylogenetic nomenclature; your point, if it can be sourced, could perhaps go there. Nixon & Carpenter (2000), cited in that section, argue that PN is more likely to change than RN even without considering characters. (I am referring to their sand lizard discussion; while the paper is much cited, little attention seems to be paid to that argument.) Peter M. Brown (talk) 18:36, 1 October 2012 (UTC)
replies: text: I agree that the section title is also problematic, although phrases like the "philosophy of classification" do seem to be used in the literature with a meaning something like the "underlying principles of classification". Peter coxhead (talk) 09:45, 2 October 2012 (UTC)
replies: text: Using "philosophy" to refer to underlying principles seems unobjectionable, but I don't see your point as relevant to either. Stability of circumscription is seen by the PN crew as a virtue of their approach and can appropriately be considered in a section on philosophy. Stability of believed circumscription is something else; that the two are conflated is an objection, one that does not reflect an underlying principle but rather attacks the importance of such a principle. Peter M. Brown (talk) 15:05, 2 October 2012 (UTC)

text: The Laurin quote does need to be replaced. Specifying geological periods using type sections and specifying them by boundary stratotypes are equally objective, though the latter has proved more useful. Laurin does have a coherent POV, though his analogies are terrible (Mendeleev did not individuate elements by the number of protons, as the proton was not discovered until ten years after his death). I think that some of de Queiroz's work may be a better source for the view that terms should have a fixed circumscription, one that will not change under theory revision. For the opposing view, that the potential for such change is useful for scientific progress, I recommend Benton (2000). Peter M. Brown (talk) 16:01, 2 October 2012 (UTC)

text: I think you've made a very good case for removing this quote. The revised section seems to me a great improvement, presenting the issues very clearly and with appropriate support. Peter coxhead (talk) 08:32, 10 October 2012 (UTC)
replies: text: And I thank you for the reference to the ICZN definition of "taxon", which I surely would not have come across by myself. Peter M. Brown (talk) 21:38, 10 October 2012 (UTC)
thread_title:  Philosophy 

message: Among other matters,  presents analogies drawn from chemistry, stratigraphy, and geopolitics among his arguments for the superiority of phylogenetic over rank-based nomenclature. The stratigraphy analogy found its way into Phylogenetic nomenclature#Philosophy as a long quotation which I have now deleted on the grounds that the argument is not philosophical. Though this does not preclude the quotation from being restored to the article under a different heading, I urge that this not be done.
As I have made clear above, I regard these arguments as poor. This is, of course, merely my POV and provides no reason for excluding them. More to the point, they have been ignored in subsequent work by other PN advocates, writers like de Queiroz and Cantino, who I suspect agree with my evaluation. While other contentions in this paper have received attention in the literature, the chemistry/stratigraphy/geopolitics analogies have been cited only in one paper that Laurin himself wrote, , and in one that he coauthored, . In accordance with WP:UNDUE, a brief mention of these analogies would, at most, be appropriate. Since the arguments have gone nowhere, there is no justification for a 200-word quotation.
References
*
*
*
Peter M. Brown (talk) 15:36, 9 October 2012 (UTC)
replies: text: I think you've made a very good case for removing this quote. The revised section seems to me a great improvement, presenting the issues very clearly and with appropriate support. Peter coxhead (talk) 08:32, 10 October 2012 (UTC)
replies: text: And I thank you for the reference to the ICZN definition of "taxon", which I surely would not have come across by myself. Peter M. Brown (talk) 21:38, 10 October 2012 (UTC)
thread_title: Deleted quotation

message: Maybe it's just me, but :File:Clade names and phylogenetic hypotheses.svg seems confusing. In the right-hand figure, a line from the bottom goes up and apparently disappears behind a dotted triangle; it does not seem obvious how the line is related to the triangle that occludes it. The caption speaks of "the hypothesis that the relationships are as in the right tree"; are people going to understand what relationships the right tree shows? Peter M. Brown (talk) 22:44, 1 October 2012 (UTC)
replies: text: Good point; it would be better if the dotted triangle finishes lower down. I'll fix it. Peter coxhead (talk) 09:41, 2 October 2012 (UTC)
thread_title:  New diagram in [[Phylogenetic nomenclature#Definitions|Definitions]] 

message: The claim that the need for ranks limits names when only clades are named (which was removed) is basically true, although not clearly explained. I've tried to add something which is clearer without going into too much detail, which I don't think is relevant here. The key point is that if you name only clades then only so many "levels" or "depths" in a phylogenetic tree can be named otherwise you run out of ranks. If you allow paraphyletic taxa then it's easier, because such a taxon can span many levels in a tree. (Compare a classification which divides "cladistic reptiles" into "traditional reptiles" and birds, needing only two ranks, with say the diagram at Reptile#Phylogeny, which has names at seven levels without even reaching birds.) Peter coxhead (talk) 10:46, 2 October 2012 (UTC)
thread_title:  Ranks limit names 

message: The second sentence in the  History section implies that  John Hogg's 1860 introduction of Protoctista as a kingdom somehow reflects Darwin's influence. Can any support for this be provided from reliable sources? Indeed, is there any reason to suppose that Hogg subscribed to anyone's evolutionary theory in 1860? He did hold that Protoctista is older than Animalia or Plantae, but the fact that some taxa are older than others had already been well established by fossil studies; Hogg's extension of this notion to the kingdom level does not necessarily presuppose evolution. Peter Brown (talk) 17:36, 19 January 2013 (UTC)
thread_title:  Darwin and Hogg