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

[James Doyle]

>Hmmm, Jim says that the reasons for the changes are exceedingly 
>abstruse, but then he admits that the new terms are theoretically 
>better, which was the reason for changing them.  :)  In addition, 
>these abstruse issues are considered very important by some critics 
>of the PhyloCode.

I meant abstruse to many less theoretical people who aren't closely 
involved in the PhyloCode but may eventually use it, and on first 
reading to people like me, before they spend an hour racking their 
brains trying to follow the arguments.  That said, I do agree that 
it's good to have terms that are more general and acceptable to 
people with different points of view on what trees mean.

>Finally, I'm not sure why some people are worried that other people 
>(who are not involved in phylogenetic nomenclature or the PhyloCode) 
>think that the project might be dead.  They're just wrong.  It 
>doesn't really matter what they think.

Hmm, I was starting to wonder if it was dead myself, and there may be 
others like me who are sympathetic to the PhyloCode and have done 
some work related to it but aren't (or weren't) in the inner circle. 
Such perceptions aren't entirely irrelevant.

>More importantly, I suppose we could deal with the continuity issue 
>by mentioning the older terms either in a Note or in footnotes.

I think whatever we say should be more conspicuous than that.

Jim

>From: "James A. Doyle" <jadoyle at ucdavis.edu<mailto:jadoyle at ucdavis.edu>>
>Date: Tuesday, July 23, 2013 9:10 PM
>To: "cpn at listserv.ohio.edu<mailto:cpn at listserv.ohio.edu>" 
><cpn at listserv.ohio.edu<mailto:cpn at listserv.ohio.edu>>
>Subject: Re: [CPN] Fwd: Proposal to reorganize Note 9.3.1--COMMENTS 
>DUE BY WEDNESDAY
>
>Hello Phil et al.,
>
>At the last minute I've finally gone through all the e-mails on 
>these issues since April.  The one thing that has bothered me all 
>along is Brian's point about continuity of old and new terms.  At 
>first the change in terminology struck me as one of those annoyances 
>that turn people off to nomenclature of all kinds - first we ask 
>people to adopt one new set of terms, like node- and branch-based, 
>and then just when they think they finally understand them we tell 
>them to forget all about it and adopt a new set, for reasons that 
>seem exceedingly abstruse (sorry, Kevin).  But now I'm coming around 
>to the notion that the new terms are theoretically better and 
>self-explanatory enough, actually more so than the old ones, and as 
>a neo/paleo person I'm relieved that the terms crown clade and total 
>clade maintain their conspicuous roles.  The idea that you'll change 
>the terminology throughout the companion volume is also a big relief.
>
>Nevertheless, I really would feel better if the old terms were 
>explicitly acknowledged in the text where the new terms are 
>introduced, not relegated to the glossary, since so many people have 
>seen the old terms in the literature on phylogenetic nomenclature 
>and have made efforts to understand them.  At the very least this 
>could be done parenthetically in terms such as "see Glossary for the 
>relations of these terms to the widely used terms node-based and 
>branch-based."
>
>Jim
>
>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

-- 
James A. Doyle
Department of Evolution and Ecology
University of California
Davis, CA 95616, USA
Telephone:  1-530-752-7591; fax:  1-530-752-1449