Message 2004-10-0096: Re: Phylogenetic Notation

Wed, 15 Sep 2004 08:34:12 -0700 (PDT)

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Date: Wed, 15 Sep 2004 08:34:12 -0700 (PDT)
From: [unknown]
To: Mailing List - PhyloCode <>
Cc: "Jaime A. Headden" <>
Subject: Re: Phylogenetic Notation

--- "Jaime A. Headden" <> wrote:

> Mike Keesey ( wrote:
> <_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)>
>   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=
parentheses or braces are then not available for any other type of us=
(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=
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},=
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=
lineages, what have you.

>   *Saurischia*=3D{*Megalosaurus bucklandi* [von Meyer 1632] > [not]
> *Iguanodon bernissartensis* [Boulenger in van Beneden 1881]}
>   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 =
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=
occur inside brackets, this would not conflict terribly with using th=
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=
> 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 =
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=
> 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=
> though is not used in higher math, and may permit the shift from cu=
> definitions to the new formulae more easily, and still be simplisti=
> 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.
>   Apomorphy-based clades can be written in simple language, otherwi=
se it
> will still be cumbersome to annotate, and reference using a note
> elsewhere.
>   *Avialae*=3D{apomorph Gg in *Vultur gryphus* [Linnaeus]}
>   APPENDIX 2. Apomorphies
>   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=
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=
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> T. Michael Keesey <>
=3D=3D=3D=3D=3D> The Dinosauricon <>
=3D=3D=3D=3D=3D> Instant Messenger <Ric Blayze>

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