Mon, 13 Sep 2004 13:19:12 -0700 (PDT)

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Date: **Mon, 13 Sep 2004 13:19:12 -0700 (PDT)**

From: **[unknown]**

To: **Mailing List - PhyloCode <phylocode@ouvaxa.cats.ohiou.edu>**

Cc: **"Jonathan R. Wagner" <jonathan.r.wagner@mail.utexas.edu>, Mailing List - Dinosaur <dinosaur@usc.edu>**

Subject: **Re: Panstems**

(Crossposted to the Dinosaur Mailing List, as some people on that for= um may be interested, since this deals with the definitions of dinosaurian clad= es. Follow-ups should probably be posted to the PhyloCode Mailing List, h= owever.) --- "Jonathan R. Wagner" <jonathan.r.wagner@mail.utexas.edu> wrote: > [...] I support not restricting definitional types, or the=20 > choice and application of names (other than for the sake of continu= ity). I=20 > am sympathetic to Dr. Padian's point (by the way, he favored two fo= rmats,=20 > node- and stem-, in his Paris talk), but I do not agree. I feel tha= t PN has=20 > moved past the idea that the wording of a definition somehow invoke= s a=20 > general case and the wording is irrelevant (as implied by the vario= us=20 > shorthand definition formats floating around); I believe this is th= e=20 > mindset that inspired Dr. Padian's suggestion. Instead, the wording= of the=20 > definition is paramount. As such, not all node- and stem-based defi= nitions=20 > are equal, the various classes of definition are just that, classes= (see my=20 > point about the so-called "stem-modified node-based definion" in my= =20 > abstract), and other kinds definitions are possible and indeed desi= reable. Which brings us to an interesting point. If definitions are considere= d to be prose, and not rigorous formulae, we run into several problems. First= of all, wordings can be ambiguous. Secondly, reading prose requires full comp= rehension of the language employed. Suppose somebody were to formulate definiti= ons in Russian, Portuguese, Hindi, Swahili, Classical Latin, Classical Greek= , etc.? Would the database then have to preserve that wording as THE definiti= on, and wouldn't anyone who didn't know that language be impeded from underst= anding it? While thinking about these issues over the past couple of days, I tri= ed to come up with a style of notation for internationally legible clade definit= ions. After one false start based on computer coding conventions, I came up= with a system utilizing internationally accepted styles of mathematical nota= tion, primarily notation dealing with sets, Boolean logic, and functions. T= his seemed to me far more concise and readily comprehensible than my initial att= empt with "pseudocode". Unfortunately, this system involves non-ASCII characters, so it canno= t be posted here. But I uploaded a Word document of the first draft detail= ing the system here: http://dino.lm.com/keesey/documents/PhylogeneticNotation= .doc Here is a brief outline: BASIC NOTATION SETS - set notation LOGIC AND CONDITIONS - Boolean notation FUNCTIONS - function notation ELEMENTS - original notation for dealing with characters, specimens= , etc. SETS REALITY-BASED SETS - pre-defined sets for dealing with entities suc= h as characters, specimens, etc. SECONDARY SETS - sets which may be derived from the reality-based s= ets, involving entities such as clades FUNCTIONS REALITY-BASED FUNCTIONS - pre-defined functions for dealing with ch= aracter possession, direct ancestry, etc. DEFINITION-BASED FUNCTIONS - functions for dealing with simple defi= ned entities (species) SECONDARY FUNCTIONS - functions derived from reality- and definitio= n-based functions, dealing with ancestry, lineages, clade definitions, etc. EXAMPLE DEFINITIONS FROM THE DRAFT PHYLOCODE - some prose definitions from the draft Ph= yloCode rendered in phylogenetic notation OTHERS - various other samples You can see that this notation would be universally appreciated, the = only exceptions being the prose descriptions of characters and of pre-defi= ned sets and functions, neither of which I can see a way around. The only othe= r case where a specific language enters into the matter is in the names of s= ets and functions, but this is not a real issue since they are all defined us= ing mathematical notation. These names could just as easily be derived fr= om another language, such as Classical Latin. Another benefit of using a rigorous notation for definitions is that = they are then capable of being parsed and understood by computer programs, whi= ch could have useful applications. What I would like to know is whether anyone else agrees that using a = rigorous system of notation would be a good idea, and, if so, what changes sho= uld be made to my draft (or if this draft should just be scrapped and someth= ing else created, and why). I encourage anyone who is interested to download t= he file and add notes (Tracking Changes is turned on in the file) and send it= back to me, or upload for the list to discuss. There are some parts I'm kind = of unsure about (e.g., the formula for apomorph-based clade definitions, the re= liance on "breeding groups", the reliance on non-ASCII characters), and I would= really appreciate feedback. Thanks, =3D=3D=3D=3D=3D =3D=3D=3D=3D=3D> T. Michael Keesey <http://dino.lm.com/contact> =3D=3D=3D=3D=3D> The Dinosauricon <http://dinosauricon.com> =3D=3D=3D=3D=3D> Instant Messenger <Ric Blayze> =3D=3D=3D=3D=3D =09=09 _______________________________ Do you Yahoo!? Declare Yourself - Register online to vote today! http://vote.yahoo.com

Feedback to
<mike@indexdata.com>
is welcome!