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Overhauling the tree of life

Quite frankly I don't particularly like the way you are characterizing my "mentality" either. If you think I base the separation of birds and mammals from reptiles on solely on their endothermy, you are totally mistaken. If you will recall, I criticized Eric for doing this even though he agrees with me on the recognition of a traditional Reptilia. I am not into one-character classifications and never have been. And as for being in "my right mind", if you had bothered to get my book on interlibrary loan, you would know that I classify Order Morganucodontiformes as mammals, not reptiles.
Yes, indeed you can only calibrate a motor by operating it. But you have to understand the whole motor, not to mention how it propels the vehicle. How many people do you know that have attempted to classify all organisms (living and extinct) to the extent that I did in 1994, much less try to propose new methodologies at the same time. I am the only person I know of who has attempted a recent "overhaul" of the entire tree of life (living and extinct) in such detail, and my conclusion was (and continues to be) that a cladisto-eclectic approach is what is most needed both in the short run, and most definitely for the long term. The only other person who has even come close to overhauling the entire tree of life in any detail is Thomas Cavalier-Smith, and he is an eclecticist and also a critic of strict cladism.
I define a strict cladist as one who automatically rejects all paraphyletic groups (many regarding them as bad and unnatural as are polyphletic groups). There are many such biologists. And Mayr and I are far from being alone in recognizing this. If you restrict yourself to dinosaur literature alone, you might get a false impression just how widely purely cladistic classifications are embraced. The exact opposite is true among most botanists.
And finally, I am not necessarily attacking the phylogenies of Holtz, Brochu, and others. We may agree perfectly on a given phylogeny and the cladistic analysis that gave rise to it, but still disagree on how that phylogeny is converted into a classification.
From: "Jaime A. Headden" <qilongia@yahoo.com>
To: dinosaur@usc.edu
CC: kinman@hotmail.com
Subject: Reptilia Again ....
Date: Fri, 29 Sep 2000 21:21:25 -0700 (PDT)

Ken Kinman wrote:

<The hope of strict cladists that paraphyletic groups
(NOT wastebaskets) like Reptilia are going to be
abandoned is probably a pipe dream.>

  Please don't characterize people you do not have the
mentality of to assume their thoughts. There is no
such thing as a strict cladist except as suggested by
Mayr. I've been reading up on Mayr's phylogenetic
opinion, and I'm not impressed.

<Vermes was a polyphyletic wastebasket, Reptilia is
not(it's paraphyletic).>

  Reptilia is only paraphyletic if you assume that
certain members included in the definition are not in
fact supportedly contained within that definition.
Remove a certain form, such as birds, on the sole
basis of their endothermy, and you enhance the
primitive view that the only real "Reptilia" is
composed of "cold-blooded" amniotes. On this matter, I
encourage analysis of giant tortoises and sea turtles
(gigantotherms [mass endotherms] and though
ectothermic, are not cold-blooded); similarly, tuna
active metabolizers, with a very interesting muscular
system. Avian metabolism differs strikingly from that
of mammals in application and respiration mechanics.
They are convergent in any phylogeny, even the

  Pointedly, if you have a disagreement with the
phylogenies as presented, and feel they are incorrect
as to reconstructing relations (as assumed) then
disprove them, don't attack the workers producing the
results. These phylogenies (ALL phylogenies) as Mickey
Rowe, Tom Holtz, and Chris Brochu have all said, are
theories; test, retest, etc., ad infinitum vel nauseum
(you be the judge). Even if they are based on
genetics, these may not be the most agreeable or even
plausible phylogeny (take Whippomorpha, for example,
first proposed by Nikaido et al. 1999 (PNAS 96:
10261-10266 -- http://www.pnas.org).

<...but Michael Benton's soon-to-be published
criticism of the PhyloCode will hopefully help to
prevent much of the confusion he also believes the
PhyloCode will cause.>

  Probably because it will require overhauling the
entire tree of life for the most part.

<Therefore I encourage those who continue to recognize
a traditional Reptilia,>

  ... to understand the point of the meaning, history,
and salvaging of an ancient name [I interject] ...

<although one needs to now indicate whether you are
using it in the traditional or cladistic sense.>

  Since the traditional sense is hardly a valid taxon
based as it is on an exclusion of a descent form, the
traditional sense is a historic usage only, and
shouldn't even be capitalized. The vulgar noun
"reptile" and adjective "reptilian" can be used to
refer to this, but to call that paraphyletic grouping
Reptilia would be to suggest the paraphyly has at all
any valid phylogenetic signal, and the last decade and
a half have strongly suggested it doesn't. Mammals are
not reptiles, since the basal stock of such are also
ancestral to the most recent common ansector of
turtles, lizards and crocs (which incidentally
includes birds in nearly EVERYONE's schema) but
ophiacodonts and therapsids have "mammalian"
specializations not shared by the long succession of
"reptilian" forms (especially in the jaw). This
suggests, nearly insists, exclusive ansectry, and
because no-one in their right mind still suggests
*Morganucodon* or *Thrinaxodon* are reptiles and might
have any similarity to *Procolophon*, it is at best
highly improbable reptiles includes mammals or
excludes birds. There is extensive literature, based
on pure morphological analysis (as well as, but not
primarily comprised by, cladistic analysis of both
molecular and morphological data).

<Perhaps someday we will all refer to a more
traditional (but semi-paraphyletic) Reptilia once

  Why? Does the taxonomic status of a paraphyletic
assemblage mean anything beyond the ability to
segregate birds from lizards and crocodiles and --
here's the pitch -- dinosaurs as if homeothermy was
anything special?

<but in the intervening years (or decades), confusion
will continue as long as the cladisto-eclectic war
continues, now well into its fourth decade.>

  Confusion persists (literature abounds for the last
entire millenium) where intuitive, "it feels right,"
and single character analyses or plots demonstrate an
opinion that are consistently (literature, again) at
odds with one another. Tools for analysis include our
analytical processes, logical systems and mathematics.
You can guess where this led.

  Do I think there are flaws with the system? Yes
there are flaws, and so is the opinion of many
systematists who operate through cladisitics in some
small ways; you can only calibrate a motor by
operating it, Ken.

  Fin d'Millionairre,

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