Re: Taxon Search

["Jaime A. Headden" <qilongia@yahoo.com>]

David Marjanovic (david.marjanovic@gmx.at) wrote:

<It is quite interesting and makes several very good points, but I wouldn't
quite call it "excellent".>

  So it would need to be flawlessly perfect, or perhaps supportive of
PhyloCode, to be "excellent"?

<This starts with the (somewhat overblown) title -- there is no "phylogenetic
taxonomy", only phylogenetic nomenclature.>

  I beg to differ. Starting from a nomenclatural standpoint, we name things all
the time, essentially assigning labels. This is all nomenclature means, the
assignment for distinction of identifying terms. Taxonomy, on the other hand,
is related to phylogeny, and the nomenclature used by taxonomists either stems
from or leads to phylogeny. While it is correct as Mike observes David to say,
that taxonomy has relationships with ranks, this is only because of the
Linnaean taxonomic system that has dominated phylogenetic reconstruction and
nomenclature for the last 200+ years. Taxonomy in phylogenetic standings can
involve unranked names, such as names for species, and names for clades; it can
name types of clades distinctly, such as nomenclature prefixing "Pan-" to
total-content clade names, use of apomorphic allusion in nomenclature (e.g.,
*Opisthocoelicauda* for the shape of the caudal centra, rather than
*Stokesosaurus* for W. Stokes' dinosaur), and so forth. Thus, taxonomy and
nomenclature are both distinct, and the former need have nothing to do with
Linnaean taxonomy.
 
<(The term "taxonomy" was invented as "the theory of classifications".>

  The word evolution was originally used to imply that there is an ideal goal
in progression of organisms, originally to define man's imperialism above all
other creatures in the implied dominion of nature and the coincident "pure" and
"unclean" animals. Do we use the word in this way now? The original intent has,
for lack of a better word, evolved.

<People who apply phylogenetic nomenclature _do not classify_ -- they don't
hack the Tree of Life apart and try to shoehorn the pieces into a set of boxes
of predetermined sizes;>

  I beg to differ: a crown taxon specifically requires the content to be
living, and Sereno's (2005) criterion has appended this with an extinct
external specifier, meaning that two living groups whom are each other's sister
taxa cannot be crown taxa. Should be anchor "Pan-" to any total-content clade
names we coin, and to ensure this relationship, rename all taxa used or
definable as total-content clades to include "Pan-" as a prefix? Are these not
somehow predeterminate?

<Doesn't make any difference, except it allows somewhat more illustrative
terminology.>

  Linnaean systematics, aka, it's taxonomic system (often confused, perhaps,
with the phrase "Linnaean taxonomy" for shortness) also asserts, as Sereno
explains, that organisms belonged to certain groups only if they contained,
say, a majority of the predetermined features whatever author who named the
group considered diagnostic. Otherwise it was a different group. Systematist
use this ideology to ensure content-based clades likew many mammalian
suprageneric groups, and more prevalently and closer to dinosaurs, in Gerald
Mayr's naming of monotypic "families".

<(This is about apomorphy-based definitions -- so it's about defining taxa, not
just recognizing them.)>

  It was actually about the diagnosus, which amounted to a 1-10 part apomorphic
definition, but was essentially distinct from a single defining feature present
in an acestor. For example, a taxon who LOST a feature would often be excluded
from a group diagnosed on this feature solely due to that absence, but could be
diagnosed as a related group diagnosed by many of the same features only
without that one special feature. Thus, a diagnosis was not the same as an
apomorphy-based clade, which is as Sereno points out, a potential type of
stem-based clade.

<Better than the scheme currently used in the examples of the PhyloCode, but I
hear a paper is in press which will offer much better alternatives...>

  They are both useable, and as Sereno ALSO argues, systems should be run based
on concensus, which will with application give up an improving system for
recognizing and relating supraspecific clades. Nomenclature can even be put
aside when formulating definitions, for the sake of recognition without
imposing names, as study progresses.

<TaxonSearch is clearly a good thing (apart from the criteria for determining
"active" and "inactive" status, I'd say). I can't wait for it to grow!>

  I am told that this is not a fixed condition, and that it is certainly a very
flexible system for applying "active" versus "inactive". I also found out a
definitively inactive name that was applied to some sauropodomorphans,
Allophaga, a good while back. Since it is not used today, we can reject it
along with *Manospondylus gigas* which, in the system, may be a special
specimen-based stem excluding all other types, but is essentially inactive
through lack of validating use (i.e., "this taxon is considered distinct and
can be a senior synonym for other potential junior synonyms", and so forth).

  Cheers,

Jaime A. Headden

"Innocent, unbiased observation is a myth." --- P.B. Medawar (1969)

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