[CPN] Fwd: Proposal to reorganize Note 9.3.1--COMMENTS DUE BY WEDNESDAY

    de Queiroz, Kevin deQueirozK at si.edu
    Wed Jul 24 11:18:12 EDT 2013 
    Brian et al.,

I agree with Phil that changes to the Companion Volume contributions
should be made by the editors--no need to trouble the authors to do this
(though the authors should check to make sure that the changes were done
correctly at the proofing stage).

In addition to the glossary, we would also presumably mention the change
(including the old terms) in the Preface under a heading such as "Changes
to Version 5."  

I want to point out that these changes in no way prohibit or even
discourage use of the older terms in publications, though their use
carries assumptions about the nature of certain ancestors (that those
specified by node-based definitions are only parts of species), and the
terms don't make much sense in the context of some types of trees (the
kind that I called "relationship trees," in which context the term
"branch-based" doesn't make sense).  The changes are being proposed for
inclusion in the PhyloCode to make it more general, thus avoiding the
issues just mentioned.

Kevin

On 7/23/13 8:24 PM, "Cantino, Philip" < cantino at ohio.edu 
> wrote:

> Brian, 
>  
> This is a good point.  My understanding is that we editors will be 
> responsible for changing all the terminology throughout the companion 
> volume before it is published, so it will not be a headache for the 
> authors and there will be no discrepancy between the companion volume and 
> the code.  (Kevin, please confirm whether this is your understanding as 
> well.) 
>  
> As for your suggestion that the old terms be mentioned in the new text 
> for the sake of continuity, since the old (current) terms are widely 
> known and used, I think the best place to do that might be the glossary. 
>  
> Phil 
>  
>  
> On Jul 23, 2013, at 6:08 PM, Brian Andres wrote: 
>  
>> Greetings all, 
>>  
>> I like how this section has been fleshed out commensurate to its 
>> importance. If the proposed changes are voted down, I would suggest 
>> keeping most of the new text with the old terminology. However, I do 
>> have one reservation for the proposed changes in terminology. If we 
>> excise all the node- and branch-based terms, are we going to ask all the 
>> authors for Companion Volume to rewrite their entries with these terms 
>> removed? Both the Examples_for_Authors and Instructions_for_Authors use 
>> these terms, and #5 under Format for Entries in the Instructions 
>> requires their use. I for one use these the old terms seven times in my 
>> entries. There is a tradition of using this terminology in the 
>> literature and previous versions of the Code, and I wonder if they 
>> should be at least mentioned in the discussion of minimum- and 
>> maximum-clade definitions for continuity and for this discrepancy 
>> between the Code and Companion Volume. 
>>  
>> Best, 
>> ? 
>>  
>> On Jul 23, 2013, at 1:47 PM, "Cantino, Philip" < cantino at ohio.edu 
> wrote: 
>>  
>>> David, 
>>>  
>>> Thank you for spotting the omitted quotation mark.  You raise a good 
>>> point about multiple apomorphies.  If I recall correctly, a definition 
>>> of this type was also used in one of the entries for the companion 
>>> volume (I was not the lead editor on that one, so I may be 
>>> mis-remembering).  The use of multiple apomorphies is not very 
>>> different from the use of a single complex apomorphy, which is 
>>> addressed in Art. 9.10 and Rec. 9E.   It may well be worth expanding 
>>> that article and recommendation to cover complex apomorphies as well, 
>>> or perhaps covering them separately but with wording parallel to that 
>>> of Art. 9.10 and Rec. 9E.  I also wonder whether that article and 
>>> recommendation should be moved up into the section of Article 9 that we 
>>> are now considering.  However, I'd prefer to delay considering these 
>>> questions  until we find out whether the proposal already on the table 
>>> is approved by the CPN.  I'll make a note to myself so I don't forget 
>>> to come back to this later. 
>>>  
>>> Phil 
>>>  
>>>  
>>> On Jul 22, 2013, at 3:21 PM, David Marjanovic wrote: 
>>>  
>>>> Good point in Note 9.5.2 about the use of external specifiers for 
>>>> minimum-clade definitions. 
>>>>  
>>>> In the explanation of apomorphy-modified crown clade definitions, the 
>>>> quotation mark after "the crown clade characterized by apomorphy M 
>>>> (relative to other crown clades) as inherited by A" is missing. 
>>>>  
>>>> Should we explicitly acknowledge the possibility of multiple 
>>>> apomorphies in an apomorphy-based definition? I've seen at least one 
>>>> in the literature, along the lines of "the first ancestor that had all 
>>>> of the following list of apomorphies inherited by A, plus all its 
>>>> descendants". 
>>>>  
>>>> That's all. :-) 
>>>> 
     
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