tag:blogger.com,1999:blog-5041663983772879899.post7710471567099493950..comments2023-11-08T02:17:24.211-08:00Comments on The Cellinese Lab: Species and Phylogenetic NomenclatureNico Cellinesehttp://www.blogger.com/profile/05502820618366076308noreply@blogger.comBlogger13125tag:blogger.com,1999:blog-5041663983772879899.post-66665910482253270252012-02-06T11:57:59.444-08:002012-02-06T11:57:59.444-08:00"I wouldn't mind so much if the Phylocode..."I wouldn't mind so much if the Phylocode used existing species names as specifiers *as a shortcut* to referring to their type specimen, as long as it was clear that the specifier legally is the type specimen rather than the species name."<br /><br />That's exactly what the current draft does:<br /><br />"Note 11.1.1. When a species is cited as a specifier, the implicit specifier is the type of that species name (if a type has been designated) under the appropriate rank-based code...."Mike Keeseyhttps://www.blogger.com/profile/00147156174467903264noreply@blogger.comtag:blogger.com,1999:blog-5041663983772879899.post-59980812426001771312012-01-18T16:14:50.580-08:002012-01-18T16:14:50.580-08:00I still think you are over-reacting on this issue....I still think you are over-reacting on this issue. We are not advocating anything here that is not in the current codes. When you name a species under the current codes you cite a type specimen including its number (read a species description). Just like we suggest for the PhyloCode.<br /><br />And as you point out, the PhyloCode already has note. 11.1.1. We just want to extend it a bit and remove the "if" clause to make it clear that the type specimen is the official, legal specifier, even if a taxonomic name is given for reference.Brent Mishlerhttp://ucjeps.berkeley.edu/people/mishler.htmlnoreply@blogger.comtag:blogger.com,1999:blog-5041663983772879899.post-26566224553911757302012-01-18T12:52:54.947-08:002012-01-18T12:52:54.947-08:00The problem isn't in using the name Titanosaur...The problem isn't in <i>using</i> the name Titanosauriformes, it's in defining it (and reading that definition). A definition based on numbers is less comprehensible than one based on names. We don't want to be erecting additional barriers to using the PhyloCode. Using a specifier such as <i>Brachiosaurus altithorax</i> is already totally unambiguous: however many species concepts might be floating around out there, the only only that matters for nomenclatural purposes is "whatever this species has been defined as under the ICZN". Which is why the existing Note 11.1.1 is perfectly adequate: "When a species is cited as a specifier, the implicit specifier is the type of that species name (if a type has been designated) under the appropriate rank-based code".Mike Taylorhttps://www.blogger.com/profile/06039663158335543317noreply@blogger.comtag:blogger.com,1999:blog-5041663983772879899.post-208661488338490622012-01-18T12:40:43.319-08:002012-01-18T12:40:43.319-08:00Hi Mike,
Yes, that is what it means. But in refe...Hi Mike,<br /><br />Yes, that is what it means. But in reference to your response to me (above), once we define Titanosauriformes under the PhyloCode using specimens, from then on we just refer to Titanosauriformes. The details about specifiers are available in RegNum, but you just use Titanosauriformes in everyday parlance. <br /><br />So this is just like the current codes, like you say, once someone names Brachiosaurus altithorax using a type, then the user doesn't need to mention the type every day. But the type still is behind the name in databases. So there is no difference here between the PhyloCode and the traditional codes, other than the Pylocode using multiple "types" rather than one. In many ways what we are suggesting is no major change for current practice. <br /><br />Traditionalists can see why one needs multiple "types" to specify a clade precisely, and many are starting to names clades, as you say.Brent Mishlerhttp://ucjeps.berkeley.edu/people/mishler.htmlnoreply@blogger.comtag:blogger.com,1999:blog-5041663983772879899.post-53592554471522661462012-01-18T06:53:21.826-08:002012-01-18T06:53:21.826-08:00"It seems to be that there is a fundamental m..."It seems to be that there is a fundamental misunderstanding of the issues. We are not even advocating to switch numbers in lieu of names, I am not sure where you see that."<br /><br />From your proposal, in the section on Articles 11.1-11.10: "All reference to species as specifiers should be removed from these articles and notes. Replace "species, specimens, or apomorphies" with "specimens or apomorphies" throughout. Remove Note 11.1.1, Article 11.3, and recommendation 11.B."<br /><br />Doesn't that mean I would have to define Titanosauriformes as (FMNH P25107 + PVL 4017-92) instead of (<i>Brachiosaurus altithorax</i> + <i>Saltasaurus loricatus</i>)?Mike Taylorhttps://www.blogger.com/profile/06039663158335543317noreply@blogger.comtag:blogger.com,1999:blog-5041663983772879899.post-14471188168642244412012-01-18T06:47:27.479-08:002012-01-18T06:47:27.479-08:00Mike, what you are saying doesn't make much se...Mike, what you are saying doesn't make much sense. We are trying to extend the Code to ALL clades including those that may correspond to traditional species. That does not mean that you can't use the Other Codes to name species, if you want to. All our proposal does is to allow us to name all clades including the most inclusives and make a reference to traditional names, just as you are doing it already at higher level. We are not even implying that those least inclusive clades are 'species' and that is why we want to term 'species' removed from the Code. In fact, we are trying to simplify the Code and make all clades equal. It seems to be that there is a fundamental misunderstanding of the issues. We are not even advocating to switch numbers in lieu of names, I am not sure where you see that.Nico Cellinesehttps://www.blogger.com/profile/05502820618366076308noreply@blogger.comtag:blogger.com,1999:blog-5041663983772879899.post-59655452755065316572012-01-17T16:35:54.287-08:002012-01-17T16:35:54.287-08:00Hi, Brent. My background is multilingual: I have ...Hi, Brent. My background is multilingual: I have a couple of published papers on aspects of PN, and a couple of others on rank-based zoological nomenclature. I also have a couple of chapters in press in the looong-awaited Phylonyms volume. So while I am very far from being expert in either form of nomenclature, I do have a reasonably balanced perspective.<br /><br />Yes, the current (i.e. rank-based) codes are anchored on specimens; but precisely so that we can then stop talking about individual specimens and start talking about names instead. You could say that the whole <i>point</i> of the ICZN is that I can say <i>Brachiosaurus altithorax</i> instead of FMNH P25107. To expect taxonomists to allow those specimen numbers to arise from their tombs for use in phylogenetic definitions is really not realistic.<br /><br />"There is a compromise position here, at least as far as I am concerned -- I wouldn't mind so much if the Phylocode used existing species names as specifiers *as a shortcut* to referring to their type specimen, as long as it was clear that the specifier legally is the type specimen rather than the species name." I guess that could fly. So long as it made no difference to what taxonomists had to actually <i>do</i> it shouldn't be too hard to sell. In fact, this is pretty much the status quo -- see Note 11.1.1 of the current draft PhyloCode: "When a species is cited as a specifier, the implicit specifier is the type of that species name (if a type has been designated) under the appropriate rank-based code."<br /><br />"You seem to be going off the deep end in arguing against the rational proposals we made." This is true, I admit it. Because I know exactly how this proposal will be met by mainstream taxonomists. And we need to win them over.<br /><br />Right now, we have a little bit of momentum with people like Mike Benton (my Head of Department at Bristol), who in the past has argued publicly against PN in general and the PhyloCode in general (e.g. Stems, nodes, crown clades, and rank-free lists: is Linnaeus dead? Biological Reviews 75:633-648). Despite his arguments in that paper and others, he is finding it expedient to include clade definitions in his work, which should be a cause for rejoicing. If the poor old PhyloCode ever makes it out of the door, I suspect Benton and other traditionalists will use it because they recognise that there is a need for PN, and it is better that it be regulated by a code -- any code -- than none. But if we throw that up in the air, we will lose what momentum we have with people like him.<br /><br />Finally, at the risk of repeating myself, let me say again I am truly sympathetic to what you're trying to do here. As science, I admire it. But as politics, it's a disaster. And I have been involved in too many scientifically admirable but politically disastrous standards efforts to stand idly by and watch another one die the same horrible death. Cruel to be kind.Mike Taylorhttps://www.blogger.com/profile/06039663158335543317noreply@blogger.comtag:blogger.com,1999:blog-5041663983772879899.post-79414018464627012102012-01-17T16:06:33.121-08:002012-01-17T16:06:33.121-08:00Hi Mike,
I'm not sure what your backgrou...Hi Mike,<br /><br /> I'm not sure what your background is, so I don't mean to be insulting, but you do know that names under the current codes are anchored on specimens. right? The only difference is that the PhyloCode insists on multiple specifiers (for good reason). But believe me, names under both the ICBN and ICZN are defined by type specimens.<br /> There is a compromise position here, at least as far as I am concerned -- I wouldn't mind so much if the Phylocode used existing species names as specifiers *as a shortcut* to referring to their type specimen, as long as it was clear that the specifier legally is the type specimen rather than the species name.<br /> You seem to be going off the deep end in arguing against the rational proposals we made (have you read the text of our proposal?) -- no one is arguing to replace names with numbers.Brent Mishlerhttp://ucjeps.berkeley.edu/people/mishler.htmlnoreply@blogger.comtag:blogger.com,1999:blog-5041663983772879899.post-64884813716124789562012-01-17T05:58:29.693-08:002012-01-17T05:58:29.693-08:00Well, that is a very appealing picture of the worl...Well, that is a very appealing picture of the world.<br /><br />I wish I could be a so sanguine. But I am not. Political realities are real, and the more the PhyloCode annoys taxonomists (e.g. by requiring definitions to be anchored on specimens rather than species), the fewer of them will come on board.<br /><br />I am truly sorry; but it's a non-starter. It just isn't going to happen that people will define Titanosauriformes as (FMNH P25107 + PVL 4017-92). Replacing names with numbers in the specifiers would be just as unhelpful as doing so in the clade-names, so that instead of defining Titanosauriformes, we defined Clade #5873-1235. No matter what you do, however theoretically pure your position, however compelling your argument, you will never persuade taxonomists to give up names for numbers.Mike Taylorhttps://www.blogger.com/profile/06039663158335543317noreply@blogger.comtag:blogger.com,1999:blog-5041663983772879899.post-33697259146565127712012-01-17T05:36:09.965-08:002012-01-17T05:36:09.965-08:00There are no opportunities lost in science. This ...There are no opportunities lost in science. This is not a business venture, and most of what we do now will stick with future generations, so it is very importan to do it right. This is not a matter of now or never. The Code will be published indeed but not tomorrow and hopefully by the end of the year, only hopefully. So, this is a good opportunity for refining it and make sure that it is widely accepted by a lage subset of the community. Proceeding otherwise may imply that many supporters won't use it. The brutal reality of anything at all is that changes are hard to embrace, new standards always hard to accept, but this should not imply that the implementation of new concepts should be impeded by the natural human reluctance for changes. If the PhyloCode is to make any dent at all, it needs to be flexible and inclusive and not bound by any particular philosophy. Living with something that is fundamentally wrong and a clear philosophical contradiction is not the way I like to do science. This is not a day job where compromises lead to a positive end of the day. Let's move on can only means let's do it right.Nico Cellinesehttps://www.blogger.com/profile/05502820618366076308noreply@blogger.comtag:blogger.com,1999:blog-5041663983772879899.post-36915461418037524542012-01-16T14:53:54.160-08:002012-01-16T14:53:54.160-08:00"We will get the Code implemented. I have all..."We will get the Code implemented. I have all interest in doing so."<br /><br />When? Sorry, but "this is not about saving time" is no longer the reasonable response that it was back in 2000. I don't want to be crude, but it's time for the Code to poop or get off the pot: the rest of the world already sees this effort as moribund. Re-tooling now will reinforce that perception. We long ago lost the opportunity to strike while the iron is hot; let's at least catch it while it's lukewarm.<br /><br />As for "making a difference between ranks is simply wrong, especially in a rank-free Code" -- I do have sympathy with this. In my day job over the years I have spent many hundreds of hours working on specification for data formats and interchange protocols, and I too know the longing to Do The Job right. Unfortunately, I also know the pain of releasing a perfect standard to a world too apathetic even to say "meh", and I am very much afraid that is where we're headed.<br /><br />The brutal reality of biological nomenclature is that everything is anchored on species, and specifically on Linnaean binomials. I'm sorry, I wish it weren't so -- I'm on record as hating binomials, I think they were a terrible mistake -- but that is the world we live in. If the PhyloCode is to make any dent at all in the way nomenclature is done, it simply has to live in that world. Make our own parallel universe, where everything is anchored on specimen numbers, and no-one will come.<br /><br />Again, I am truly sorry to be so discouraging, especially as I've been through much the same experience as you (in other fields) and know how dispiriting it is to run into nay-saywers. But that is the reality.Mike Taylorhttps://www.blogger.com/profile/06039663158335543317noreply@blogger.comtag:blogger.com,1999:blog-5041663983772879899.post-51116316663898614252012-01-16T13:47:27.797-08:002012-01-16T13:47:27.797-08:00This is not about saving time. This is about gett...This is not about saving time. This is about getting it right! We will get the Code implemented. I have all interest in doing so. But making a difference between ranks is simply wrong, especially in a rank-free Code. The species rank is not special and clades should be treated equally across the border. If you understand why we want to do this, then that should be the focus of the discussion.Nico Cellinesehttps://www.blogger.com/profile/05502820618366076308noreply@blogger.comtag:blogger.com,1999:blog-5041663983772879899.post-26381030370772958932012-01-16T13:28:18.681-08:002012-01-16T13:28:18.681-08:00Please no. Already ICZN taxonomists think that th...Please no. Already ICZN taxonomists think that the PhyloCode is dead, dying or mired in terminal indecision. If we now make a major change like this, which will entail completely redoing the Companion Volume, we won't get the code actually implemented for another decade, by which point every last iota of momentum will be gone.<br /><br />Sorry. I understand why you want to do this, and if it had come up ten years ago I would probably have supported it. But to do it now would be madness.Mike Taylorhttps://www.blogger.com/profile/06039663158335543317noreply@blogger.com