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Re: TETRAPODS, PHYLOGENETIC TAXONOMY, AND CLEAR DEFINITIONS



Peter,

I have a distinct feeling that you're not understanding what I'm saying, because
you appear to be attacking some positions I've never taken.

> There is a problem deliniating between "fish" and "tetrapod," there is no real
> difference between some taxa, and they do seem to show a continuum of
> creatures.  A similar thing happens with non-avian theropods and birds.
> ESPECIALLY with the new taxa coming to light?  Is Rahonavis a bird?  Is
> Unenlagia?  How about Protarchaeopteryx and Caudipteryx.

> We need to have clear definitions so that we won't have the ambiguity that can
> be involved.  How tetrapodish do you have to be to be a tetrapod?

Good question.  Do you have a good answer?  I don't.  That's my main objection 
to
what some people have done with phylogenetics -- it doesn't make any sense to 
me.
Or rather, it doesn't make any sense that people cling so rigidly to it when 
it's
so easy to envision a situation where the rules break down.

How is a taxon defined?  A crown-based taxon is defined as "the last common
ancestor of X and Y, and all descendants of that ancestor."  A node-based taxon 
is
defined as "X and everything closer to X than to Y."  In either case, you have 
the
_definition_ of the taxon, and as a separate matter you have the _diagnosis_ of
the taxon, or how you tell if organism A belongs to this taxon or not.  The
diagnosis has a list of features which are considered autapomorphies for the
taxon, and if A is

Now, what do you do if you get an organism that has every feature on your list,
but for some reason you can't tell if it's actually within the defined clade?
That is, for a crown group, you can't tell if it actually is a descendant of the
LCA; or for a node group, you can't tell if it's actually closer to X or to Y.


> So what?  If everyone agrees on what the name refers to, then there is no
> reason for it to mean anything.  Sometimes they are cute, sometimes they are
> neat (as in the case of Einiosaurus' etymology) but no where does it say, no
> where has it ever said, and no where has anyone ever suggested that the named
> NEED to mean something useful.

I'm a computer programmer by trade.  That's how I work; that's how I think.  In
computer code, names carry information, and naming conventions are at least the
second most important thing about program design.  It's a cardinal rule for me:
Don't Screw Around With Names.  Ever.  If a programmer doesn't use naming
conventions, it instantly tags them as a sloppy thinker and almost certainly
error-prone in other ways too.  And it makes the program a whole lot harder to
follow.

So, when names in other fields follow rules, I find them a whole lot easier to
understand.  And when names don't follow rules, I get annoyed.  Life is 
difficult
enough already -- why make it even more difficult?  Names don't _need_ to mean
anything useful, but if they _do_ mean something useful, then you've just
substantially cut the time and space required to communicate information.
"Tetrapoda" is a good name for the group made of all four-legged vertebrates and
their descendants, because it presupposes very little.  If you just know the 
Greek
translation of the word, you understand basically what the group is.  But
"Tetrapoda" is a very poor name, IMO, for "the last common ancestor of Man and
Bullfrog, and all descendants of that ancestor," because it presupposes much 
more
on the part of the reader.  You have to know what animals are and aren't
descendants of that LCA before you know what the group includes.  Does the
crown-group Tetrapoda include _Seymouria_? Anthracosaurs?  Microsaurs?
_Diadectes_?  _Edaphosaurus_?  All of those have four legs, a differentiated 
head
and neck, and a number of other traits that mark them as land-capable.  Is that
enough to call them a tetrapod?  Should it be enough?  What traits separate
members of this crown group from nonmembers?  Is there any way to tell that
_Hylonomus_ is a descendant of that LCA, but _Seymouria_ isn't?  I don't know.  
Do
you?

Or try an example from dinosaurs, since this is the Dinosaur List.  Somewhere 
not
long ago I read an analysis of early dinosaurs that said that since the
identifying autapomorphies for theropods were already present in _Eoraptor_ and
_Herrerasaurus_, and that therefore the sauropodomorphs and ornithischians must
have originated earlier than that.  But if I recall right, _Eoraptor_ itself is
barely a dinosaur, let alone a theropod.  It meets the diagnosis of a dinosaur,
but only by the skin of its teeth.  If it's the first _diagnosable_ dinosaur, 
how
do you tell that, say, _Plateosaurus_ is not a descendant of _Eoraptor_?

Do you see what I'm getting at?  In at least some circumstances, saying that "X 
is
not a member of group Y" requires you to prove a negative.


>  <<If the thing has all the diagnostic features for
>  the group, it should be included in the group.  What could be simpler?>>
>
> If it has all the diagnostic features of the group it has to be included
> within the group.
>
>  <<_Seymouria_ has all the diagnostic features for being a tetrapod, so how
> can it
>  not be in Tetrapoda?>>
>
> If Seymouria is not a tetrapod ss then it DOESN'T have all the diagnostic
> features of being a tetrapod.

What are the diagnostic features of a tetrapod, and how does _Seymouria_ not 
meet
them?

>  <<_Morganucodon_ has all the diagnostic features (all the
>  skeletal ones, at least) for being a mammal, so how can it not be in
> Mammalia?>>
>
> Because it doesn't have all the diagnostic features of being a mammal.  Is
> there something you are not getting here?

No, but there is apparently something that you aren't getting.  _Morganucodon_ 
is
a small, somewhat shrewlike fossil from the Early Jurassic.  It has 
differentiated
teeth, semi-erect posture, a dentary-squamosal jaw joint, evidence of 
endothermy,
a bunch of unusual specializations about the ear and braincase -- in short, it 
has
every feature I've ever seen or heard used to diagnose mammalness in fossils.
None of the authorities I've read can point to any trait or suite of traits that
distinguish crown-group mammals from morganucodonts.  Most are pretty 
unequivocal
in calling _Morganucodon_ a mammal, even though it clearly dates from before the
probable LCA of monotremes and therians.  So, how can you possibly tell that it
_isn't_ a descendant of that LCA and therefore a member of Mammalia?

>  <<> 2) there is no reason to have 'reason' applied to it, as long as everyone
>  > agrees to what something means, then that is what it means
>
>  I think that statement just might make my case all by itself, but no
> matter.>>
>
> Huh?  Weren't you the one who suggested we abandon Arctometatarsalia even
> though everyone agreed what it was because not all arctomets had an
> arctometatarsus?

Yup.  Because the name was misleading.  But I'm not sure what you're getting at
here -- how is that relevant to what I said in the bit you quoted?

>  <<The fact that it's widely accepted doesn't mean it's right.  Remember,
> thirty
>  years ago everybody thought dinosaurs were big, dumb, slow lizards and birds
>  descended from some other archosaur.>>
>
> Yes, yes, blah, blah.  I know things change.  The point is that almost
> EVERYONE has abandoned Linnean (subjective) clasification syestems in favor of
> Phylogenetic (objective) classification systems, or at least have started
> using cladistic analyses to aid in their quest for objectivity.

This is an interesting statement, for a couple of reasons.  First, what makes 
you
think cladistic analyses are any more objective than the old Linnaean methods?
The Linnaeans must have gotten most things right, because cladistic analyses
haven't really modified the whole Tree of Life all that much.  A lot of what's
being done nowadays is picking nits and trimming edge lines. The more I read 
about
the history of biology and paleontology, the more impressed I am at how much the
oldtimers got right, despite the fact that they didn't have any of the tools we
take for granted.

Second, I know a couple of modern biologist types, and they tell me, rather
vehemently, that Linnaean systematics is still being used quite a lot.  I made 
the
mistake of saying what you just did, in almost the same words, where one of 
these
guys could see it, and got my ears quite thoroughly charred for it.  That's not 
an
experience I'm likely to forget anytime soon.

Third, I don't object and never have objected to Phylogenetic Systematics being
used as a _tool_ for classification.  What I object to is the elevation of PS 
from
a tool to an end-in-itself.  I get the distinct feeling that too many people are
building too many cladograms and classifications based on a desire to get
everything into a slot, not a desire to better understand the evolution and
relationships of these animals.  Does it actually mean anything significant that
_T. rex_ is closer to _Ornithomimus_ than either is to _Velociraptor_?


>  <<"Most of the time" isn't all the time.  So why do people treat phylogenetic
>  taxonomy as being infallible, and either ignore or rationalize away the
>  exceptions?>>
>
> You still are not understanding the difference between phylogeneric taxonomy
> and cladistics.
>
> CLADISTICS has to do with entering data into a matrix and coming up with a
> tree.  When people make said trees, they can still apply Linnean ranks and
> have paraphyletic taxa etc just like in Linnean systematic.
>
> PHYLOGENETIC TAXONOMY is a different kind of taxonomy that does not rank taxa,
> has clear unambiguous definitions for taxa, and does not allow paraphyletic
> taxa.

This is a noble goal, but from where I sit, it ignores reality.  Paraphyletic 
taxa
are _inevitable_ in any system that tries to separate organisms into species and
genera -- because every species originates from a previous species, and every
genus originates from some species in an older genus.  All horses evolved from
_Hyracotherium_ -- so do we classify all the various horses of the past 
sixty-odd
million years as different species of _Hyracotherium_?

> <<So why do people treat phylogenetic taxonomy as being infallible,>>
>
> Why are you treating pick and choose Linnean systematics as infallible?  All
> anyone is saying is that the cladistic method is more objective than pick and
> choose.

Hold on a minute.  Where or when did I ever say I prefer "pick and choose"
Linnaean systematics, or think that it's infallible?

> Concerning crown clades, Woolf writes:
>  <<It makes them useless because they can't be relied on to do what they're
> supposed
>  to do: identify a _diagnosable_ monophyletic evolutionary group.>>
>
> Yes they can.  How is a crown clade different from any other node-based clade?
> You can see how Marasuchus and Psuedolagosuchus fall outside the node
> Dinosauria.  Why is it different for Morgonocudon falling outside the crown
> node Mammalia?

Because as far as I know, you can't tell just by looking at the fossil that
_Morganucodon_ falls outside the crown group Mammalia.

> <<If you can't tell what organisms belong to a group, then the group has no
> practical use.>>
>
> If the group is undiagnosible, it would never have been named.  It can't have
> been named in fact...

What if you find out that the group is undiagnosable _after_ it's been named?  A
certain group called Aves leaps to mind, as the autapomorphies once thought to
define Aves keep falling one after another.

-- Jon W.