[CPN] Window for comments on proposal

• Previous message: [CPN] Window for comments on proposal
• Next message: [CPN] Window for comments on proposal
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

David, thanks for this.

Could I ask a naive question:  instead of deciding between "organism"
(which can be an individual) or "taxonomic unit" (which seems to be
something that people name), is there a problem with the general word
"lineage," which seems to represent what we're all about, that is,
genealogical entities?  Thx for any clarification.  -- kp


> Hi all, 
>  
> 2 things. 
>  
> First, yes, I think that we (CPN) should get this discussion going now. 
> If you haven't taken the time to read the proposal yet, now is a good time 
> - if you have, and would like to comment, great.  A couple folks have 
> already - I've pasted that thread below. 
>  
> Second, Mike K. wrote: 
>> I'd like to send out a link once the date on that page is changed. 
> This is a great idea.  I've cc'd Torsten here, so that he can update the 
> comment window on the web to Jan. 31.  Thanks, Torsten. 
>  
> Mike, will you please send a note to the society to make them aware of 
> this. 
>  
> Best, 
> Dave 
>  
>  
> Mike Keesey: Oct 5. 
>>  
>>  
>> I like the idea of removing the dependency on species from the code, 
>> thus avoiding the "species problem". In the past I've advocated a 
>> similar approach, where we deal in organisms rather than species. 
>> However, since then I've realized there is also an "organism problem"! 
>> That is, it's not always clear in biology what constitutes an 
>> individual organism (think of slime molds, lichens, etc.). 
>>  
>> Now I think perhaps it is preferable to think of phylogeny in terms of 
>> taxonomic units. A phylogeny is a directed, acyclic graph wherein the 
>> nodes are taxonomic units and the [directed] edges are [immediate] 
>> ancestor-descendant relationships. How units and relationships are 
>> determined is beyond the purview of the code (just as taxonomy is 
>> beyond the purview of the rank-based codes), but the code requires 
>> them in order to be applied. 
>>  
>> So I would suggest that perhaps we use the phrase "taxonomic units" 
>> (or, where clear, just "units") instead of "organisms", "populations", 
>> "species", etc. 
>>  
>> I've written a document explaining this approach in nauseating detail: 
>>  http://namesonnodes.org/ns/math/2009/index.html 
 
>>  
>>> Art. 2.1: I agree with the proposal, though I like Keesey's "ancestral 
>>> set" 
>>> even better. 
>>  
>> More recently I've been using the term "cladogen": 
>>  http://namesonnodes.org/ns/math/2009/index.html#section-Cladogens 
 
>> -- 
>> T. Michael Keesey 
>>  http://tmkeesey.net/ 
 
>  
> David M., Oct 6: 
>  
>>>> I'll offer some preliminary thoughts as well. 
>>>>  
>>>> I like the idea of removing the dependency on species from the 
>>>> code, thus avoiding the "species problem". In the past I've 
>>>> advocated a similar approach, where we deal in organisms rather 
>>>> than species. However, since then I've realized there is also an 
>>>> "organism problem"! That is, it's not always clear in biology what 
>>>> constitutes an individual organism (think of slime molds, lichens, 
>>>> etc.). 
>>  
>> That's true, but the organism problem is much, much smaller than the 
>> species problem! Cases where it could lead to actual trouble will be, at 
>> most, so rare that we (the CPN) could easily deal with them on a 
>> case-to-case basis. 
>>  
>>>> Now I think perhaps it is preferable to think of phylogeny in terms 
>>>> of taxonomic units. A phylogeny is a directed, acyclic graph 
>>>> wherein the nodes are taxonomic units and the [directed] edges are 
>>>> [immediate] ancestor-descendant relationships. How units and 
>>>> relationships are determined is beyond the purview of the code 
>>>> (just as taxonomy is beyond the purview of the rank-based codes), 
>>>> but the code requires them in order to be applied. 
>>>>  
>>>> So I would suggest that perhaps we use the phrase "taxonomic 
>>>> units" (or, where clear, just "units") instead of "organisms", 
>>>> "populations", "species", etc. 
>>  
>> This will be misunderstood to include "higher taxa". 
>>  
>>>> I've written a document explaining this approach in nauseating 
>>>> detail: http://namesonnodes.org/ns/math/2009/index.html 
 
>>  
>> I'll try to read it sometime... :-] 
>>  
>>>>> Art. 2.1: I agree with the proposal, though I like Keesey's 
>>>>> "ancestral set" even better. 
>>>>  
>>>> More recently I've been using the term "cladogen": 
>>>>  http://namesonnodes.org/ns/math/2009/index.html#section-Cladogens 
 
>>  
>> That's a nice word! 
>  
> Oct 6: Mike Keesey: 
>> In response to the proposed revisions, I wrote: 
>>  
>>> I'll offer some preliminary thoughts as well. 
>>>  
>>> I like the idea of removing the dependency on species from the code, 
>>> thus avoiding the "species problem". In the past I've advocated a 
>>> similar approach, where we deal in organisms rather than species. 
>>> However, since then I've realized there is also an "organism problem"! 
>>> That is, it's not always clear in biology what constitutes an 
>>> individual organism (think of slime molds, lichens, etc.). 
>>>  
>>> Now I think perhaps it is preferable to think of phylogeny in terms of 
>>> taxonomic units. A phylogeny is a directed, acyclic graph wherein the 
>>> nodes are taxonomic units and the [directed] edges are [immediate] 
>>> ancestor-descendant relationships. How units and relationships are 
>>> determined is beyond the purview of the code (just as taxonomy is 
>>> beyond the purview of the rank-based codes), but the code requires 
>>> them in order to be applied. 
>>>  
>>> So I would suggest that perhaps we use the phrase "taxonomic units" 
>>> (or, where clear, just "units") instead of "organisms", "populations", 
>>> "species", etc. 
>>>  
>>> I've written a document explaining this approach in nauseating detail: 
>>>  http://namesonnodes.org/ns/math/2009/index.html 
 
>>  
>> In response, David Marjanović wrote: 
>>  
>>> That's true, but the organism problem is much, much smaller than the 
>>> species problem! Cases where it could lead to actual trouble will be, 
>>> at 
>>> most, so rare that we (the CPN) could easily deal with them on a 
>>> case-to-case basis. 
>>  
>> Likely true, and, to be clear, I would definitely favor using 
>> "organisms" over "species", even if my ultimate preference is 
>> "[taxonomic] units". 
>>  
>>> This will be misunderstood to include "higher taxa". 
>>  
>> If a taxonomic unit in a phylogenetic hypothesis is a "higher taxon" 
>> then that is actually what I mean! 
>>  
>> I see the process of phylogenetic nomenclature this way: 
>>  
>> 1) A researcher, using whatever criteria they desire, organizes the 
>> relevant life forms into units. 
>>  
>> 2) The researcher, again using whatever criteria they desire, 
>> hypothesizes ancestor-descendant relationships between the units. We 
>> now have a phylogenetic hypothesis, which is a directed, acyclic graph 
>> where the taxonomic units are the nodes (or vertices) and the 
>> immediate ancestor-descendant relationships are the directed edges (or 
>> arcs). 
>>  
>> 3) The researcher consults RegNum for definitions which are applicable 
>> to the phylogenetic hypothesis. Definitions are applicable if their 
>> specifiers indicate units or unions of units in the hypothesis. (A 
>> specimen should generally indicate a single unit, a species is just a 
>> proxy for its type specimen, and an apomorphy may indicate a union of 
>> any number of units, as may the term "extant".) 
>>  
>> 4) The researcher applies these definitions. Definitions indicate 
>> operations which yield either the empty set, an individual unit, or a 
>> union of units, depending on the phylogenetic hypothesis. 
>>  
>> 5) The names associated with these definitions, under the PhyloCode, 
>> may now be used to refer to the appropriate taxa yielded by the 
>> definitions (under the phylogenetic hypothesis). 
>>  
>> So, for example, suppose we have a phylogenetic hypothesis where one 
>> of the units is "Aves", and we seek to apply a definition which uses 
>> the type specimen of _Vultur gryphus_ as a specifier. (Note that, per 
>> 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.") Then, in that 
>> context, the taxonomic unit "Aves" is indicated by that specifier 
>> (never mind that it's a "higher taxon"). 
>>  
>> You may ask, what happens if another specifier indicates the same 
>> unit? E.g., how do we apply the definition of _Neognathae_ (the 
>> branch-modified node-based clade stemming from the last common 
>> ancestor of all extant members of the branch-based clade stemming from 
>> the first ancestor of _Vultur gryphus_ not also ancestral to _Tinamus 
>> major_ or _Struthio camelus_)? All three of the specifiers indicate 
>> the same unit ("Aves"), so doesn't that definition yield the empty 
>> set? The answer is, yes, *under that context*, _Neognathae_ is empty! 
>> But the conclusion to be drawn from this isn't that there are no 
>> neognathes *under any context*, rather that this particular context is 
>> too coarse for a useful application of the definition. 
>>  
>> -- 
>> T. Michael Keesey 
>>  http://tmkeesey.net/ 
 
>  
> 
 
> David C. Tank 
> Assistant Professor & Director, Stillinger Herbarium 
> University of Idaho 
> 208.885.7033 
>  dtank at uidaho.edu 
 
>  http://www.phylodiversity.net/dtank/ 
 
>  
> On Jan 10, 2012, at 6:18 AM, Cantino, Philip wrote: 
>  
>> The end of the month is fine with me.  Does anyone have any thoughts on 
>> the question I sent the listserv Jan. 5?  My question was whether CPN 
>> members are expected to comment by the end of the public comment period 
>> or save our comments for the CPN discussion. 
>>  
>> Phil 
>>  
>>  
>> On Jan 9, 2012, at 5:14 PM, Mike Keesey wrote: 
>>  
>>> On Thu, Jan 5, 2012 at 1:15 PM, Kevin Padian < kpadian at berkeley.edu 
> 
>>> wrote: 
>>>> I agree with Michel, and I think that the end of the month is a good 
>>>> deadline.  How does the Committee propose to proceed at that point? 
>>>> -- kp 
>>>  
>>> I agree that the deadline for comments should be extended at least 
>>> until the end of this month. (I wouldn't mind an even later date, as 
>>> long as it doesn't delay our own discussion on this list.) 
>>>  
>>> Does anyone disagree? I'd like to send out a link once the date on 
>>> that page is changed. 
>>>  
>>> -- 
>>> T. Michael Keesey 
>>>  http://tmkeesey.net/ 
 
>>>  
>>> 
 
>>> CPN mailing list 
>>>  CPN at listserv.ohio.edu 
 
>>>  http://listserv.ohio.edu/mailman/listinfo/cpn 
 
>>  
>>  
>> 
 
>> CPN mailing list 
>>  CPN at listserv.ohio.edu 
 
>>  http://listserv.ohio.edu/mailman/listinfo/cpn 
 
>  
> 
 
> CPN mailing list 
>  CPN at listserv.ohio.edu 
 
>  http://listserv.ohio.edu/mailman/listinfo/cpn 
 
>  
-- 
Kevin Padian
Department of Integrative Biology &
Museum of Paleontology
University of California, Berkeley CA 94720-3140
510-642-7434 http://www.ucmp.berkeley.edu/people/padian/home.php 

• Previous message: [CPN] Window for comments on proposal
• Next message: [CPN] Window for comments on proposal
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]