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Yay! Cladobabble! :-)

Part of the problem in this discussion ("Re: Archaeopteryx") seems to be
that it isn't one discussion. I can discern here

- Is cladistics a good thing? (The cladistic method to find phylogenetic
trees, I mean.)

- Is phylogenetic nomenclature a good thing? (The young art of defining
names. It seems to be true that all followers of PN are cladists, but by no
means vice versa.)

- How, if at all, should Aves be defined? (An extra complicated example of
the above. -- Because it _means_ "birds", no way around this, _I_'d like a
complicated stem-based definition, one so complicated that it'll survive
several decades with hardly changed contents: e. g. "everything more closely
related to *Passer domesticus* [or perhaps *Turdus merula*... or both... and
adding *Struthio camelus* wouldn't hurt either...] than [to] *Velociraptor
mongoliensis*, *Adasaurus mongoliensis*, *Microraptor zhaoianus*, *Troodon
formosus*, *Sinovenator changii*, *Ornithomimus velox*, *Tyrannosaurus rex*,
*Ornitholestes hermanni*, *Beipiaosaurus inexpectus*, *Oviraptor
philoceratops*, *Caudipteryx zoui*, *Protarchaeopteryx robusta*,
*Sinosauropteryx prima*, *Scansoriopteryx heilmanni*, *Crocodylus
niloticus*, *Euparkeria capensis*, *Longisquama insignis* and
*Megalancosaurus preonensis*". Add a bat if you like to prevent
Haem[at]othermia. Don't add Archie or an alvarezsaur, I wouldn't like that.
:-) )

- How can we integrate Feduccia's finding of fingers II-III-IV in birds with
the hypothesis of their theropod ancestry? (Mind you, I think this is _not_
a finding, but a _misinterpretation_, that the fingers Feduccia found are
not I -- V, but the prepollex and I -- IV [plus a very small V that he
overlooked, proximal to IV]; but I'm currently discussing this with Feduccia
himself, so we'll see, perhaps.)

- Are frameshifts, as suggested by Wagner & Gauthier, going to happen? (I'm
somewhat confused by this question. Firstly, "frameshift" is used in
genetics in a totally different way, namely that, when reading mRNA, the
ribosome hops and reads the rest differently than how it should be read
judging from the sequence, e. g. reading AUGGGTAGUCGAAGATTA instead of as
AUG GGT AGU CGA AGA TTA as AUG GGT TAG UCG AAG ATT, you'll find the place
where it jumped backwards for a base. Secondly, it assumes _a priori_ that
digit identity is fixed by genes. _This may not be the case!_ Instead it may
well be produced by, say, the amount of a signal molecule that's produced at
one side of the limb bud [cranial or caudal] and diffuses to the other -- 
producing a gradient --, or who knows. If a gradient, threshold values etc.
instead of direct genes are involved, then of course digit "identity" will
change on all occasions.)

- Is anything real, and should we care about this? (IMHO some species are
real, while others, as shown by ring species, allospecies and so on, are
not; some organisms are real, while others, e. g. few-cell vertebrate
embryos and adult sponges, are not.)

- Are organisms comparable to a continuum like geological time? (IMHO not.
Instead of being a simple continuum, organisms are a _branched_ continuum,
with a very interesting branching pattern that should be used for -- or
instead of -- classification.)

- Is phylogenetic nomenclature useful, how useful should a classification
be, and is Linnaean classification more useful than phylogenetic
nomenclature? (Note the constant confusion of nomenclature and
classification. Also note that Benton's famous critique of the PhyloCode is
IMHO not worth much, because it attacks partly a very old version of the
draft PhyloCode, partly a strawman. See
http://dino.eu.tc/Benton-Phylocode.htm [case-sensitive!] for details. [The
cladograms there are all outdated.])

Most of these 8 should be separate discussions. They should not be confused.
More (but probably not much more) tomorrow...