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Date: Wed, 15 Sep 2004 08:34:12 -0700 (PDT)
From: [unknown]
To: Mailing List - PhyloCode <phylocode@ouvaxa.cats.ohiou.edu>
Cc: "Jaime A. Headden" <qilongia@yahoo.com>
Subject: Re: Phylogenetic Notation
--- "Jaime A. Headden" <qilongia@yahoo.com> wrote:
> Mike Keesey (mightyodinn@yahoo.com) wrote:
>=20
> <_Saurischia_ =3D clade(_Megalosaurus bucklandi_ von Meyer 1632 not
(1632?! Whoops. My mistake; it's 1832, of course.)
> _Iguanodon bernissartensis_ Boulenger in van Beneden 1881)>
>=20
> Highlighting this as an example. If the () or {} would enclose a
> definition, it is possible to use them to represent the term "clade=
,"
> without specifying otherwise:
As I said in my response to David Marjanovic, the problem here is tha=
t
parentheses or braces are then not available for any other type of us=
age.
(Remember, clades are not the only form of taxon, even if they are th=
e only
form to be covered by the first edition of the code.) This would proh=
ibit the
usage of parentheses for functional notation, or the usage of braces =
for set
notation, which I think would be detrimental to the system as a whole=
.
The notation used in the above definition of _Saurischia_ is a shorth=
and
notation pulled from Note 9.4.1. But while, in the current draft, it =
is meant
to be the shorthand for a textual definition, I proposed that it shou=
ld be the
shorthand for a mathematical definition:
_Saurischia_ =3D stemClade({_Megalosaurus bucklandi_ von Meyer 1832},=
{_Iguanodon
bernissartensis_ Boulenger in van Beneden 1881})
(That is, the application of function "stemClade" to two parameters, =
the sets
comprised solely of _M. bucklandi_ [internal] and _I. bernissartensis=
_
[external], respectively.)
Using parentheses or braces signify "clade" by default would complete=
ly undo
this more rigorous approach, as well as make it hard to define specie=
s,
lineages, what have you.
> *Saurischia*=3D{*Megalosaurus bucklandi* [von Meyer 1632] > [not]
> *Iguanodon bernissartensis* [Boulenger in van Beneden 1881]}
>=20
> Words in [] are not part of the set equation.
While I like the idea of being able to insert comments, brackets are =
already a
part of PhyloCode's citation format (see Article 20), signifying the =
authorship
of the name under another code. While this does apply in the above ex=
ample, it
may not always.
(Parentheses are also part of the citation format, but since they may=
only
occur inside brackets, this would not conflict terribly with using th=
em
mathematically, i.e., for containing function parameters and for sort=
ing order
of operations.)
> "not" may be problematic
> in intuitive notation, so perhaps using the "greater than" may be
> preferrable, as has been suggested before, and excluding use of the=
arrow
> as a signifier, since it performs the same function as "not."
As I've said before, I don't find using the "greater than" symbol to =
be
intuitive. But, if that were the preferred shorthand notation, it cou=
ld be
defined easily enough. I went with "not" because it's in Note 9.4.1.
> After all,
> intuitively, the first AND second names are part of the set, neithe=
r
> should be rejected, hence "not."
I must be misunderstanding you -- surely you do not mean that _I.
bernissartensis_ is a saurischian?! If you mean "part of the set of
specifiers", then I would argue that each one is really part of a dif=
ferent set
of specifiers (one internal, one external).
> "+" remains a valuable tool, and equates with "and" and "&" intui=
tively,
> though is not used in higher math, and may permit the shift from cu=
rrent
> definitions to the new formulae more easily, and still be simplisti=
c.
> There will be humans writing this, not robots ;).
Again, I just used "and" because it's in the current draft. Using plu=
s or
ampersand symbols (or Latin "et", for that matter) would be fine as w=
ell, since
they would not conflict with anything else. IIRC, earlier drafts did =
use "+"
for node-based definition shorthand, and it was changed after discus=
sion in
this forum.
=20
> Apomorphy-based clades can be written in simple language, otherwi=
se it
> will still be cumbersome to annotate, and reference using a note
> elsewhere.
>=20
> *Avialae*=3D{apomorph Gg in *Vultur gryphus* [Linnaeus]}
>=20
> APPENDIX 2. Apomorphies
>=20
> Gg, "wings adapted for use in powered flight" [or whatever].
I used a similar idea to this, except that the symbol is defined in t=
he
conditional clause.
_Avialae_ =3D clade(Character in _Vultur gryphus_ Linnaeus 1758)
<- Character =3D {"wings adapted for use in powered flight"}
I think it's important to keep the primary information for a definiti=
on
together, although it would certainly be useful to have further discu=
ssion (and
illustration, if applicable) of the character(s) in the text, whether=
in the
appendix or not.
=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
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