Message 2004-10-0054: Phylogenetic Notation (was: Panstems)

Mon, 13 Sep 2004 15:53:32 -0700 (PDT)

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Date: Mon, 13 Sep 2004 15:53:32 -0700 (PDT)
From: [unknown]
To: PML <>
Subject: Phylogenetic Notation (was: Panstems)

--- David Marjanovic <> wrote:

> > Which brings us to an interesting point. If definitions are consi=
dered to
> > be prose, and not rigorous formulae, we run into several problems=
. First of
> > all, wordings can be ambiguous. Secondly, reading prose requires =
> > comprehension of the language employed. Suppose somebody were to =
> > definitions in Russian, Portuguese, Hindi, Swahili, Classical Lat=
> > Classical Greek, etc.? Would the database then have to preserve t=
> > as THE definition, and wouldn't anyone who didn't know that langu=
age be
> > impeded from understanding it?
> This is why the PhyloCode currently rules to write definitions in E=
nglish or
> Latin (Art 9.4,

Whoops, missed that one.

> At this point in history, I don't think it's a noticeable exaggerat=
ion to
> claim that every scientist speaks English.

Yes, but what about Latin?
And will definitions written in either of these always be unambiguous=

> However, I think we should invent official
> abbreviations for at least the simpler and probably more common kin=
ds of
> definitions, like {A + B} for a node-based one -- this makes compre=
> even simpler and saves space (presumably even webspace and bandwidt=
h at the
> registration database).

Yes, in the next draft I wanted to add a section on abbreviated formu=
lae, in
accordance with Note 9.4.1:

clade(A and B) =3D nodeClade({A, B})

clade(A not Z) =3D stemClade({A}, {Z})

clade(M in A) =3D apomorphClade({M}, {A})

crown clade(A and [A not Z]) =3D nodeClade({x @ Organisms: "extant" @
characters(x) ^ x @ stemClade({A}, {Z})

crown clade(A and [M in A]) =3D nodeClade({x @ Organisms: "extant" @
characters(x) ^ x @ apomorphClade({M}, {A})

(substituting @ for the "is a member of" symbol, ^ for the "and" symb=

> >
> Impressive.

> The definition of "BreedingGroups" does make one scream, though...

And apomorph-based clades are even worse. This is why I presented pro=
descriptions along with every definition, although the porse should o=
f course,
be counted as secondary to the formula.

I was hoping someone whose experience with these notations was a bit =
fresher or
deeper could suggest ways to pare these down. (And I actually see som=
e ways
right now.)

> > Another benefit of using a rigorous notation for definitions is t=
hat they
> > are then capable of being parsed and understood by computer progr=
ams, which
> > could have useful applications.
> Sounds good...
> I'll try to retrieve the system I proposed a month or so ago (it's =
> uses non-ASCII characters but only such that occur in iso-8859-1 "W=
> European", and is not capable of expressing the more complex of you=
> examples), to see if I could find something about your system to qu=
> about... :-)

I'd be very interested to see that. Perhaps it can be instructive in =
making the
system more accessible.

=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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