[CPN] additions to proposed modifications

Tue Nov 12 11:25:48 EST 2013

Hi Phil, thanks for the updates which generally look good to me. I am on the road and so only read teh containing parts of the text. However, I also had some general and specific comments:

__

The code is very wordy in places. I know compex statements are often needed for precision, but this sometimes seems to come at the expense of clarity. I worry that this will be an additional barrier to an interested outsider to nomenclature/phylogenetics. I often feel the existing codes have become so stilted and ‘legalesy’ that they utterly impede understanding by non-taxonomists (do we want to start down that route…?). Here’s an example that I spent several minutes trying to unravel..

Original (p. 20):
“By contrast [Is this really a contrast? Isn’t “in contrast” more usual these days?] if the name were to be defined as applying to the largest crown clade containing Alca torda but not Alle alle, then the author would have to state explicitly that his or her concept of the named crown clade is based on species that were extant during the 19th Century if he or she intended for the name to apply to the same crown clade designated by the former definition (i.e., a clade that includes Pinguinus impennis†).”

Suggest change --
“If the name is instead to be defined as applying to the largest crown clade containing Alca torda but not Alle alle, which are two currently extant species, but the author still intends for the name to apply to a crown clade that included Pinguinus impennis†, they should state explicitly that their concept (of the named crown clade) includes this extinct species.”

I suggest we avoid the wordy “his or her” throughout the document and use the single-person neutral “their”, which seems to be where English is heading in terms of useage.

Changes to 9.16 (p. 20). What if some parts of these multiple, complex set of synapomorphies are subsequently shown to be homoplasies (and so not actually useful for defining a clade). Should we discourage too-complex definitions; aren’t simple, unambiguous ones be generally preferable? Or is this too prescriptive?

Rec. to 9E (p. 21). Similarly, I’m worried about the usual “fuzz” in reconstructions of where apomorphies fall, which the code in general tends to ignore (do we ever know the stepwise set of character with confidence? Does one have to be a cladist to use the phylocode for apomorphy-based definitions?).

Definition of branch (p. 60). I am not familiar with the definition in the last sentence, which sounds confusing and in conflict with the others (??). Should we specifically state this is a meaning we do not follow (or just exclude it?).

Also, branches *do* apply to unrooted trees, which I assume would not be a meaning considered acceptable under the phyloclade (because clades cannot be defined without a tree root/sense of time). So I would specifically exclude unrooted trees from the definition or note elsewhere that the phylocode relies on rooted trees (i.e., the branches are assumed to be time-directed).

Definition of “node” (p. 63) starts off too mathematical (I would prefer to start with the biological definition). Also, unless I’m mistaken, a vertex is a special point, or corner/intersection in a graph (aren’t branches made from an infinite series of connected points?).

Other things I have sometimes wondered about:

Should we be explicit in the document (as a practical aid) that the use of “phylogenetic tree” implies “species tree” or “gene tree being used as a proxy for species tree”?

Should we remind the reader somewhere in the rules that crowns vs. stems are only matters or persepctive (so, the base of one stem is the start of another crown)?

________________________________
From: cpn-bounces at listserv.ohio.edu [cpn-bounces at listserv.ohio.edu] on behalf of James Doyle [jadoyle at ucdavis.edu]
Sent: November-11-13 10:00 PM
To: Committee on Phylogenetic Nomenclature
Subject: Re: [CPN] additions to proposed modifications

Hello Phil (and other CPN members),

I've read over and approve of all these changes.  I think it is more prudent to remove plant fossil morphotaxa (called various things in earlier versions of the IBC, such as form and organ genera) from the discussion that now covers just ichnotaxa and ootaxa.  Morphotaxa seem to me several steps above ichnotaxa in being real parts of organisms.  Some morphotaxa (like pollen genera) may be analogous to ootaxa (I didn't know these existed), but a lot of others have been variously considered "form genera" and "natural" or "whole plant genera" by different authors, for instance starting out as form genera but later being used as names for whole plants.  I'm not an expert on the arcane history of these concepts, but it would indeed raise havoc to exclude all names of taxa that have been called morphotaxa from use as specifiers.

Jim

On Nov 12, 2013, at 3:03 AM, "Cantino, Philip" <cantino at ohio.edu<mailto:cantino at ohio.edu>> wrote:

Hi Jim,

... I would particularly like your opinion of the change in Rec. 11C, where we propose to delete some text referring to plant morphotaxa.

On Nov 7, 2013, at 3:07 AM, "Cantino, Philip" <cantino at ohio.edu<mailto:cantino at ohio.edu>> wrote:

Dear CPN members,

In the attached version of the code, Kevin and I have added several other changes that were not in the version I sent you on Nov. 1.  Some are in response to comments sent on Sept. 11 by David Marjanovic and the rest originated with us.

The newly proposed modifications are highlighted in yellow so that you can easily find them (the are in Principle 6, Note 6.1A.1, Note 9.14A.2 Example 1, Rec. 11C, Art. 17.1, Art. 17.5, Art. 20.4 Example 1, Note 20.4.1 Example 1, the Glossary entries for "branch" and "node", and Appendix C).  All are minor, so I don't anticipate it will take you long to check them.

I am surprised not to have received any comments on the changes I sent Nov. 1.  I hope this means that everyone is comfortable with the proposals.  On Friday, I will call for a vote unless there is discussion ongoing at that time.  The vote will be on the newly proposed changes (those highlighted in yellow) as well as those I sent on Nov. 1 (which are shown with Track Changes but without highlighting).

Regards,
Phil

Begin forwarded message:

From: "Cantino, Philip" <cantino at ohio.edu<mailto:cantino at ohio.edu>>
Date: November 1, 2013 10:03:31 AM EDT
To: Committee on Phylogenetic Nomenclature <cpn at listserv.ohio.edu<mailto:cpn at listserv.ohio.edu>>
Subject: Fwd: proposed modifications of PhyloCode

Dear CPN members,

Just a reminder: If you have comments, they should be sent to this listserv by next Friday (Nov. 8) so that there is an opportunity for discussion before I call for a vote.  No one has commented to date.

Regards,
Phil

Begin forwarded message:

From: "Cantino, Philip" <cantino at ohio.edu<mailto:cantino at ohio.edu>>
Date: October 25, 2013 1:10:46 PM EDT
To: Committee on Phylogenetic Nomenclature <cpn at listserv.ohio.edu<mailto:cpn at listserv.ohio.edu>>
Subject: proposed modifications of PhyloCode

Dear CPN members,

Over the past three-plus years since version 4c was posted online, Kevin and I have come to an agreement on a variety of modifications, some of them originating with one of us and some originating with other members of the CPN.  There is no central theme to the proposals, as there has been for other sets of modifications the CPN has considered in the past two years (e.g., rules dealing with species; expansion of the section describing the kinds of definitions).

The attached document consists of the most recently approved version of the code (i.e., including the modifications approved by the CPN last month), to which we have added the newly proposed changes using the Track Changes function of MS-Word.  If there is anyone who does not have MS-Word or an equivalent package that allows you to see the tracked changes, please let me know.  The Preface and Index are not included in this document.

The proposed changes occur in the Preamble, Articles 6, 7, 9 (beginning with 9.8), 10, 11, 12.2, 14, 15.11.1 Example 1, Rec. 17.3A, 19, 20.8, 21, 22, Glossary, Appendix A, and Appendix C.  Although there are many changes, the vast majority of them are minor (e.g., updating the abbreviation for the botanical code in umpteen places; clarifications that don't affect content, additional parenthetical references to other parts of the code).   There are a few more substantive changes proposed, but we anticipate that most and perhaps all of them will be uncontroversial.

Don't be concerned about formatting errors in this document (e.g., page breaks in inappropriate places; use of different fonts); these will be fixed later.

We don't anticipate that it will take you very long to review these proposed changes because most are not substantive.  Two weeks should be more than adequate unless some of you are traveling without email access during this period.  I suggest Friday, Nov. 8 as the target date for comments.  If this is difficult for some of you, or if discussion on some points is still ongoing on that date, we can extend the deadline.

Thank you, all.

Best regards,
Phil

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