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Re: Archaeopteryx



----- Original Message ----- 
From: "T. Michael Keesey" <mightyodinn@yahoo.com>
To: "Mailing List - Dinosaur" <dinosaur@usc.edu>
Sent: Monday, June 16, 2003 1:50 PM
Subject: Re: Archaeopteryx


 >
> > Well, without wanting to be facetious,  all organisms are believed to
share
> > a common ancestor.
>
> Not facetious at all -- that is the one underlying assumption of
phylogenetic
> taxonomy. If you accept this, I don't see how any phylogenetic definition
can
> be tautological.

I suppose.  Whether or not it remains useful is then a different
question....


> > The taxon thus becomes defined by what you leave out,
> > rather than what you include.
>
> It can be either way. A node-based clade is defined as all descendants of
the
> last common ancestor of a set of internal specifiers, and a stem-based
clade is
> defined as all descendants of the first ancestor of the internal
specifier(s)
> which is not also an ancestor of the external specifier(s).

With respect, this wasn't really the point I was trying to make.

> > At the moment, the _Archaeopteryx_ plus Neornithes definition is
acceptable
> > because it doesn't include any animals that most people would never
accept
> > to be birds.  But what if you found, in some future study, that
> > _Archaeopteryx_ is a highly convergent form derived from more basal
therapod
> > stock, so that to maintain this definition you would need to accept,
say,
> > ceratosaurs as birds.  This might make a few people choke on their
> > cornflakes.
>
> It isn't scientific to have "touchy-feely" taxa.

Again, I don't want to start gainsaying, but I think that Mike is
constructing a strawman of my argument here.  I'm not sure that I was
talking about 'touchy feely' taxa, and I'm not sure what he means by it.

>"Oh, I feel like this should
> be in _Aves_. No, this should not be in _Aves_." That's completely
subjective.

It's completely subjective to say that a reasonable definition of Aves
should not include crocodiles?  Snakes? Turtles?  Mike, where would you draw
the line?

The point is that, potentially, no matter how well you think you understand
a taxon and its place in the tree of life, it is theoretically possible for
even a well understoof organism to be shifted around the tree quite
radically in the light of new fossils and/or analyses.  It's happened
before, and it'll happen again.  If you think that, in 2003, we've finally
got the right topology of the tree, I think you're in for a rude surprise.

> The idea behind phylogenetic taxonomy is to have rigorous definitions
which can
> be objectively applied to a hypothesized tree.

Actually, one of the ideas behind taxonomy is to provide a stable
classification that can be used to enhance communication between natural
scientists of different disciplines, and between science and the general
public.  As far as I can see, phylogenetic taxonomy is a quasi-religious
tool used to beat about the head those who are not true-believing members of
the high priesthood.  I think it's missing the point by such a large margin
that it no longer has anything to do with traditional taxonomy.  Whoever
first said that taxonomy had to equal phylogeny was a fool who didn't
understand (a) taxonomy, (b) how the human brain perceives and recognises
patterns, and (c) phylogenetics.

> Personally, I really don't think we have to worry about ceratosaurs being
> avians. But if dromaeosaurids, troodontids, oviraptorosaurs,
therizinosaurs,
> etc. fall in Clade(_Archaeopteryx_ + _Neornithes_), then, yes, they should
be
> considered avians.

Excuse me, but this is bullshit.  If you found that any one of the taxa
currently included in Aves (Archaeopteryx + Neornithines) actually lay
outside of, say, the Tetanurae, you'd shift it without missing a beat and
keep Aves (in terms of included taxa) almost identical.  And so you should -
you're only moving one taxon out of maybe 10,000 in this group. Why should
it be any different if the one taxon you are forced to shift (as a result of
your new improved phylogeny) happens to be the one that (for reasons to do
with accidents of history and convenience) you had previously used to
bracket a higher taxon?  You are then completely changing the content and
practical definition of a major group for no better reason than it is
consistent with your ideology.  To me, this is throwing the baby out with
the bathwater.

> > The logical conclusion is that, even under the practice of cladistic
> > nomenclature, the _definition_ used for a higher taxon is not actually
the
> > ultimate conceptual definition of the group.  Rather, the group is
defined
> > (in the 'hearts and minds' of scientists and lay persons alike) in terms
of
> > the balance of included taxa, and the phenotypic description.
>
> This is exactly the old sort of archetypal thinking that PT is supposed to
free
> us from.
>
> Emotional attachment to older usages is something I think we all share.
The
> question is whether we really think it's the proper way to go about
things. A
> system ruled by opinion and authority, or by precedence and explicit
formulae?

I doubt that Nature has any preference for following formulae that we might
possibly be able to understand, at least in the context of this discussion.
As for 'opinion' and 'authority'?  Well, as I've argued before on this list,
I think they count.  I think that humans are a much more sophisticated
pattern recognition device than any algorithm that will be devised in our
life times.  I think that a human that knows its subject inside-out and
back-to-front is worth listening to - as do you, I'm sure, if you stop to
think about it.

Just because people such as Simpson did not explicitly frame ways of testing
their theories of phylogeny, doesn't mean the whole notion of 'prefered
phylogenetic hypothesis as influenced by expert opinion' is inherently
wrong.  You need to listen to everyone with a critical ear.  That includes
modern phylogeneticists as much as it does the old time 'experts'.  In fact,
your modern phylogenetic theories are still framed by the work of the
previous generation, even if they did not use 'explicit formulae'.  And the
opinion of the current generation of experts does counts for something in
today's world of 'rigorous' and 'explicit' methodologies.   And part of that
opinion will be formed by cognitive processes that lie outside of the strict
bounds of modern phylogenetic taxonomy methodologies.  What are you going to
do about that?

> We can have the latter, but only if we're able to see a clade in terms of
its
> definition, and not our preconceptions.

Taxonomy and phylogenetics will never be free from preconceptions.  I think
you're better off developing a theoretical framework that can accomodate
this, rather than dogmatically pursuing an unattainable ideology.

Don't agree?  Every time you make a list of taxa or specimens that you are
going to include in a phylogenetic analysis, you make a decision on what
taxa to leave out based upon your preconceptions, your intuitive
understanding of the pattern of nature, and the context of your immediate
question.  Why didn't you include _Sepia_ in your last analysis of the
Tetanurae?  Because you don't need to - every KNOWS that cephalopods aren't
anything to do with the evolutionary relationships of dinosaurs.  Yet every
outgroup taxon you omit has the potential to alter the results of your
analysis.  This is why any phylogenetic hypothesis can only be considered
valid within the context of the taxa included in the analysis.   It has no
larger truth in an absolute sense.

A dogmatic obsession with phylogenetic taxonomy assumes that the One True
Tree Of Life is discoverable.  It is not.  It can only be approximated, and
probably not all that well.  The level of accuracy with which we can
reconstruct the One True Tree Of Life is logically and philosophically
constrained by a large number of factors, some of which include the quality
of the fossil record and the vagarities of the methodologies used to
construct phylogenetic theories.

Additionally, one of the most important requirements of any taxonomic system
is that it should be stable enough to promote communication, not hinder.
The results of phylogenetic theories change with new fossils, new
algorithms, and new analyses.  I personally do not think that the taxonomy
that I use in communicating my work to other scientists, and the public,
should have to be revised every time some kid with a copy of PAUP updates
their character matrix.   Taxonomies should work for us, not the other way
around.

Besides which, my personal observation is that an desire to keep taxonomies
in line with the latest phylogenies can very quickly develop into an
obsession.  You will soon find that you have little time for considering
anything but phylogenies.  To suggest that any group, least of all one as
magnificent as the dinosaurs, is worthy only of phylogenetic analysis is, in
my opinion, a great shame.

An example of this?  Even on this list, most posts (especially in recent
times) are concerned with details of phylogenetic taxonomy.  I personally do
not think that this is a healthy situation.  I notice, with the posts I make
to the list, that most go largely ignored, but the few times I make a
comment (usually critical of the status quo) on cladistics or taxonomy there
is always a flurry of hurried, indignant responses.  I am not trying to
bellyache about this - it doesn't really bother me if my other stuff gets
little response, because my motive for writing it is usually to try and
clarify my own thoughts on a subject through the act of writing them down -
but I wonder if, for the large number of non-professional dinosaurologists
involved with this list, the emphasis upon phylogenetic systematics reflects
the focus of their interest in dinosaurs?

Anyway, before I get flamed again, I just want to make clear that I don't
mean anything personal against Mike (on the contrary, I have a great deal of
respect for his knowledge on dinosaurs), and I certainly don't regard
phylogenetics as a waste of time.  But I strongly disagree with the thrust
of his argument on this subject.

Cheers
Colin

Colin McHenry
56 Gaskill St
Canowindra NSW 2804
+61 2 6344 1009
0428 131 858
cmchenry@westserv.net.au