Message 2004-10-0051: Re: Panstems

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 <>
Cc: "Jonathan R. Wagner" <>, Mailing List - Dinosaur <>
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=
Follow-ups should probably be posted to the PhyloCode Mailing List, h=

--- "Jonathan R. Wagner" <> 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=
> 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=
> shorthand definition formats floating around); I believe this is th=
> 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=
> 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=
> abstract), and other kinds definitions are possible and indeed desi=

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=
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=
After one false start based on computer coding conventions, I came up=
 with a
system utilizing internationally accepted styles of mathematical nota=
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

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:

Here is a brief outline:

  SETS - set notation
  LOGIC AND CONDITIONS - Boolean notation
  FUNCTIONS - function notation
  ELEMENTS - original notation for dealing with characters, specimens=
, etc.

  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=
involving entities such as clades

  REALITY-BASED FUNCTIONS - pre-defined functions for dealing with ch=
possession, direct ancestry, etc.
  DEFINITION-BASED FUNCTIONS - functions for dealing with simple defi=
entities (species)
  SECONDARY FUNCTIONS - functions derived from reality- and definitio=
functions, dealing with ancestry, lineages, clade definitions, etc.

  FROM THE DRAFT PHYLOCODE - some prose definitions from the draft Ph=
rendered in phylogenetic notation
  OTHERS - various other samples

You can see that this notation would be universally appreciated, the =
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=
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 =
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=
appreciate feedback.


=3D=3D=3D=3D=3D> T. Michael Keesey <>
=3D=3D=3D=3D=3D> The Dinosauricon <>
=3D=3D=3D=3D=3D> Instant Messenger <Ric Blayze>

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