Wed, 15 Sep 2004 09:54:06 -0700 (PDT)

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Date: **Wed, 15 Sep 2004 09:54:06 -0700 (PDT)**

From: **[unknown]**

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

Cc: **David Marjanovic <david.marjanovic@gmx.at>**

Subject: **Re: Phylogenetic Notation**

--- David Marjanovic <david.marjanovic@gmx.at> wrote: > From: "T. Michael Keesey" <mightyodinn@yahoo.com> > > These (and node-based clades) are already provided with shorthand > > notations (which are also ASCII-friendly) in the current draft of PhyloCode. >=20 > Yes... I just like mine better. :o) I dunno, usage of "#" for "not" is pretty nonstandard. =20 > > Didn't know about that usage of the "backslash". >=20 > It's amazing how different school mathematics seems to be in differ= ent > countries. I've been taught to use it in expressions like "the irra= tional > numbers are the real numbers without the rational numbers", I =3D R= \ Q > (written with those broadened letters). A contraction for I =3D {x /member of/ R | x /not member of/ Q}? While I'm at it, backslashes aren't necessarily the best method for w= riting the non-ASCII symbols. It occurred to me that angle brackets or quotes mi= ght be more legible: I =3D {x <member of> R | x <not member of> Q} or I =3D {x =ABmember of=BB R | x =ABnot member of=BB Q} One problem with the first style is that angle brackets are used in c= itations (for original authorship of a supplanted homonym). I'd like to emphasize that this ASCII-friendly version would only be = intended for casual Internet discussion, *not* the actual definitions or in pa= pers. > > I don't think that's a problem, since there is clearly an operato= r > > bridging the two expressions. >=20 > ||*Lacerta agilis* + *Youngina capensis* \ *Crocodylus niloticus*|| > ||{*Lacerta agilis* + *Youngina capensis*} \ {*Crocodylus niloticus= *}|| "||" means "or" in C-based computer code. I see this symbol as redund= ant and potentially confusing, since there's no distinction between the begin= ning version and the ending version. > Problem solved, I think. Hmmm... perhaps the best way is: >=20 > ||{*Lacerta agilis* + *Youngina capensis*} \ *Crocodylus niloticus*= || >=20 > which avoids the impression of a set with only one element (the cro= c). Better, yes. > > > Ancestor-based definition (like "*Homo sapiens* and all its > > > descendants"): > > > {A} > > > A is the ancestor. The format is straightforward becaus= e a > > > species or specimen cannot by itself constitute a clade if it h= as any > > > descendants. > > > > Here's where I really dislike this notation, because it looks lik= e > > "the set of A". >=20 > OK... ||A||. And then what do we use for species definitions? For lineages? For ot= her types of taxa covered in future editions of the Code? =20 > > [snipped] > > > And now the big test: Can I manage to express the definition of > > > *Ichthyornis*? > > > {*Ichthyornis dispar* # *Struthio camelus*, *Tinamus major*, *V= ultur > > > gryphus* | amphicoelous cervical vertebrae, [rest of the list] = @ > > > *Ichthyornis dispar*} > > > I think this works. Does it? > > > > Nope. We know that the characters appear in _I. dispar_; the ques= tion is > > hwo far back they go. The actual prose definition is worded not s= o much as a > > definition with a qualifying clause, but as an intersection of tw= o clades. > > Rendering this is not really possible in your notation or the sho= rthand > > proposed in PhyloCode. >=20 > If my attempt is read as "those members of [the stem-based clade] f= or which > it is true that they have [all the apomorphies] homologous to those= in *I. > dispar*", "for which it is true that" symbolized by "|", then it wo= rks. The problem here is that, in your system, "M @ A" means "the apomorph= y-based clade stemming from the first ancestor of A to possess character M ho= mologous with that in A". I would read your expression as "the clade stemming = =66rom the first ancestor of _I. dispar_ which is not also ancestral to _Struthi= o camelus_, _Tinamus major_, and _Vultur gryphus_ such that the clade s= temming =66rom the first ancestor of _I. dispar_ to possess amphicoelous cerv= ical vertebrae, etc. homologous with those characters in _I. dispar_", whi= ch is a bit nonsensical. "Such that the clade stemming from ... homologous wi= th those characters in _I. dispar_" what? Such that it exists? Of course it do= es. But you haven't related it in any meaningful way to the first half of the expression. > The > question is now how to make the notation so unambiguous that people= would > read it the way it's supposed to be read. The "subset" symbol would= come in > handy here: >=20 > *Ichthyornis* =3D || [subset] {*I. dispar* # *S. camelus*, *T. majo= r*, *V. > gryphus*} | [apomorphies] @ *I. dispar*|| >=20 > Is this better? No, because the second half is still not related to the first, and th= e original definition is ambiguous as to which clade is more inclusive. It's not= a question of subsets, it's a question of set intersection. =20 > > Illegible? >=20 > Lengthy. True. > > More legible than the mathematic symbols? Equally difficult? >=20 > I think it's similar. It requires one to think around three more co= rners > than is probably necessary. This is why the shorthand definitions are incorporated. If all you wa= nt to do is discuss those types of definitions which have shorthand notations (ancestor-based, node-based, stem-based, apomorphy-based, modified cr= own clades), you don't need to use all the set and Boolean notations. But= if you want to go beyond that, there's a rigorous and powerful notation styl= e which the shorthand is defined by. > Besides, if it looks too mathematical, it > might drive some people away who might think we were all pattern cl= adists or > pheneticists (especially if they are already prejudiced and next to > uninformed). Yeah, using math in science? That's absurd! =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!? Yahoo! Mail - 50x more storage than other providers! http://promotions.yahoo.com/new_mail

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