[CPN] next set of CBM-related proposals

[Cantino, Philip]

Dear CPN members,

It has taken a couple of weeks, but Kevin and I have finally worked through David's suggestions, some of which we have led to changes in the attached revision of the proposals I initially sent you on Sept. 24.  I have inserted our responses below after each of David's comments.

I would like to take a vote on this set of changes soon (i.e., the set of proposals I sent you on Sept. 24 plus the modifications contained here).  If David or anyone else has further comments, please send them to the listserv by the end of the end of the day on Sunday (Oct. 28).  If there is no further discussion calling for more changes, I think we could go ahead and vote on these starting on Monday.  If anyone feels this is not sufficient time to review the changes, please let me know and we can delay the vote by a few days.

I am attaching two files: one uses Track Changes to show the changes that resulted from David's comments; the other has saved all the changes to make the document easier to read.

Regards,
Phil


On Sep 29, 2012, at 12:38 PM, David Marjanovic wrote:

> Everything not mentioned below is fine with me.
>
> Glossary entry for "species": shouldn't "population lineage" be
> "population lineage segment"?

We agree and have made that change in the attached version.


> And Note 11.1.1 makes it debatable whether
> taxa are ever used as specifiers, because it states: "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."

David's insightful comment led to a major rethinking and complete rewrite of Note 11.1.1 and the addition of a new Note 11.4.1 in the attached version.


>
> Preamble Item 1: perhaps use "taxon names" instead of "scientific
> names". Nomenclature isn't science, biology isn't the only science, and
> the extant codes don't cover anatomical nomenclature...
>

The term "scientific name" is widely understood to mean a formal taxon name and is defined as such in the PhyloCode glossary, so we have not adopted David's suggestion.  However, we do propose a minor wording change in the glossary definition of "scientific name": changing "a name" at the beginning of the definition to "a taxon name".


> Article 3.1 and Note 3.1.2: I prefer "taxonomic rank" over "categorical
> rank". The former is clearer; the latter will become confusing if Alain
> Dubois' proposal to use "category" and "rank" for different things ever
> spreads. He wants to use "category" for the kind of taxon that e. g. any
> particular species concept describes. This proposal has been largely
> ignored, probably because Dubois is the kind of person that loves
> inventing new terminology just for the fun of it, but it makes enough
> sense that it might be more widely adopted at some point. Interestingly,
> it is compatible with the proposed wording for the glossary entry for
> "categorical rank".
>

Oddly enough, we prefer the term "categorical rank" for the same reason that David prefers "taxonomic rank"; we think it is clearer and that "taxonomic rank" is ambiguous.  Some criticisms of PN argue that PN cannot be independent of taxonomic or hierarchical ranks because phylogeny is inherently ranked.  In other words, the term "taxonomic rank" can be used to refer to relative position alone (e.g., higher versus lower) rather than to the rank categories that we're talking about.  In addition, the meaning in Art. 3.1 should be clear from the the example provided.  We also feel that the fact that Dubois uses "category" differently is irrelevant.  The term is a very general one, but that fact does not argue against its narrower use in systematics--either as Dubois uses it or as we do in the code.  Finally, the use of "category" in the sense that we are using it is well established, going back to the distinction between taxa (the groups themselves) and categories (the ranked classes to which they are assigned).  For example, see Mayr (1969 Principles of Systematic Zoology pp. 4-5, where he defines both "taxon" and "category" in this way).



> Art. 9.7: What if there is no species or subclade to which a particular
> specimen that one wants to use as a specifier can be referred? I'm
> thinking about the current practice of the people who work on Mesozoic
> dinosaurs: they use species names as a pure formality and treat the
> monospecific genus as the unit of biodiversity. (Almost all genera
> contain just one species.) What if people want to give a branch-based
> definition to a new name of that kind? As Art. 11 says (most clearly
> spelled out in Rec. 11.4A), they shouldn't be forced to name a pro-forma
> species for their single new specimen.
>
> I suggest adding "Whenever possible," in front of the proposed new
> sentence. Alternatively, turn that sentence into a Recommendation.
>


The last part of the new sentence in Art. 9.7 says "...unless the clade whose composition is being described does not contain any named species of clades."  Doesn't this cover the situation David is concerned about?



> Glossary entry for "taxon": The first sentence sounds very good at
> first, but it would mean that different codes consider different groups
> to be taxa. "Paraphyletic taxon" would then become a contradiction in
> terms under the PhyloCode. But isn't this entry redundant with Art. 1
> anyway?... Oh. I just noticed that the two sentences of Art. 1
> contradict each other on this. The first implies that only clades are
> taxa, the second states that clades and species are taxa. I'll try to
> come up with a solution later.

We agree some changes are needed here, but (as I said in my Oct. 8 message, to which Michel and David agreed), we'd rather delay dealing with this until after we finish with the changes directly related to the CBM proposal.




-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://listserv.ohio.edu/pipermail/cpn/attachments/20121024/50b41e4e/attachment-0001.html 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: CBM-related changes_3.doc
Type: application/msword
Size: 55808 bytes
Desc: CBM-related changes_3.doc
Url : http://listserv.ohio.edu/pipermail/cpn/attachments/20121024/50b41e4e/attachment-0002.doc 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: CBM-related changes-saved_3.doc
Type: application/msword
Size: 52224 bytes
Desc: CBM-related changes-saved_3.doc
Url : http://listserv.ohio.edu/pipermail/cpn/attachments/20121024/50b41e4e/attachment-0003.doc