[CPN] Window for comments on proposal

[David Tank]

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/
>> 
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