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Re: TETRAPODS, PHYLOGENETIC TAXONOMY, AND CLEAR DEFINITIONS



>chris brochu wrote:
>
>>  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
>>
>> This really was no different in the Linnean system.  We can consider a
>> taxon to have several properties:  name definition, diagnosis, group
>> membership, timing of origin.  The Linnean system effectively tried to
>> maximize the stability of the diagnosis, but diagnoses were still labile:
>> were we to diagnose Dinosauria on the basis of a perforate acetabulum and
>> inturned femoral head, and then discover some new fossil with one but not
>> the other, the diagnosis would still require modification.
>
>Would it?

Absolutely.



If the diagnosis of Dinosauria is as you state, then an animal must have
>both those features to be a dinosaur.   Remember, I'm a programmer.
>Boolean logic:
>(A AND B) is true if and only if A is true and B is also true.  (I'm sure you
>already know that, but an awful lot of stuff I've said lately has been badly
>misconstrued, and I want to avoid any more of that.)  If taxon M is
>diagnosed by 22
>characteristics, and organism X has 21 of those characteristics, then X
>isn't a
>member of M.


Try to think like a systematist, please.

In principle, a diagnosis is not just a guide to identification - it should
also indicate something phylogenetic.  As such, if we state "inturned
femoral head and perforate acetabulum diagnose Dinosauria", we're stating
that these features were present in the last common ancestor of Dinosauria.
At this point, it's not a simple matter of set theory - you have to think
of classification as reflecting evolutionary history.  By discovering that
the features thought to diagnose a clade did not arise at the same node, we
are forced to make a decision about which characters to retain in our
definition.

The problem grows more severe if the characters in question evolved more
than once.  Crocodylians have perforate acetabulums - not normally a
problem, since very few would confuse a croc with a dinosaur, but what if
crocs were much more closely related to dinosaurs, AND still evolved their
perforate acetabulums independently?  The defining characters are no longer
unique.

For more on this, I recommend:
Rowe, T.  1986.  Definition and diagnosis in the phylogenetic system.
Systematic Zoology, 36:208-211

[shortened]

>> Taxon names are not like computer code.  They are more like personal names.
>> Philosophically, a taxon is an individual.  This is why it is inappropriate
>> to refer to The Dinosauria - it should be Dinosauria, just as it's Jon
>> Woolf, not The Jon Woolf.
>
>A taxon is an individual entity, yes.  So is a variable.  And a field, and a
>record, and a file.

Actually, I would not regard variables or fields as individuals.
Philosophically,  they are classes defined by essential possessed
properties.



In the programming paradigm called Object-Oriented Programming
>(OOP), objects can be organized into "classes," where each class is either
>a root
>class or a subclass of another class.

Like I said.



Each subclass has all the features of its
>parent class, and at least one additional characteristic that makes it unique.
>Sounds a lot like a typical nested-tree of taxa to me.

Hierarchical arrangements are not the sine qua non of an individual.  My
own family tree is not strictly hierarchical, as there have been marriages
- and yet my wife and I are still individuals.

An individual is defined by process rather than by some sort of
identifiable physical property.  I am defined, in this sense, by my
conception.  I could change any of my physical properties - shave my head,
get lots of tattoos, more piercings, stop wearing clothes, but I have not
changed who I am.  My father had part of his leg amputated a few years ago,
but he's still the same individual, even though one of his physical
properties is no longer applicable.




>
>>  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.
>>
>> Again, I don't think computer code is a valid model for taxonomy.  The
>> goals and underlying philosophies are very different.
>
>Are they?  My goal when I write a program is twofold.  First, it has to do
>what
>it's supposed to do.  Second, it has to be readable by another programmer --
>because I know that someday, some other programmer will have to follow my
>footsteps
>and understand my logic.


The primary goal of systematics is to describe biological diversity.  It
has no specific stated "function," as computer code would have.  The
readability is true for both, but the stated goals - description rather
than a set task - are entirely different.



  To that end, names, and comments, and code structure all
>need to be carefully constructed to communicate information efficiently.
>Maximum
>information in minimum time and space.  I honestly don't see why taxon
>names should
>be any different.

Because they describe biological diversity, which is evolutionarily fluid,
and are not meant to solve any problems by themselves.




 Knowledge is useless if it can't be communicated to others,
>right?  So who's a better communicator: somebody who uses simple, clear,
>easily
>understood names, or somebody who uses obscure tongue-tangling names that
>force you
>to consult six other papers in four different journals published over the
>last ten
>years in order to figure out what they're talking about?


I think you're confusing two different issues here.  The central issue of
importance is explicitness.  It doesn't matter how long or convoluted the
names are.  That some do not like taxonomic names is irrelevant - what
counts is that they have an explicit definition.

Ugliness or inappropriateness have never, ever, been a valid basis for
ditching a name.  Even the Linnean code specifies this.

[shortened]

>
>Incidentally, and jerking this grimly back to the list's ostensible topic
><g>, it
>appears that Dinosauria has a similar problem, though not as extreme.  Current
>taxonomy as given in _The Complete Dinosaur_ says that by the time they
>appear in
>the fossil record, the three major groups of dinosaurs (Theropoda,
>Sauropodomorpha,
>and Ornithischia) are already separate, and there is no known animal
>that's a good
>candidate for their LCA.  So how do you tell what's a dinosaur and what isn't?

Actually holding the last common ancestor in your hand has never been a
requirement for identifying a member of Dinosauria.  However, in a
phylogenetic analysis, several characters fall out as uniquely derived for
the clade - these are recognized as diagnostic.

Bear in mind, there's a big difference between what an organism IS
(definition) and how we recognize it for what it is (diagnosis).  This is a
major difference between systematics and computer programming.





>
>
>> >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?
>>
>> I'm not sure "objective" is the right word here.  But, phylogenetic methods
>> do have two big, big plusses:
>>
>> 1.  When presented properly (and I know they're not always so presented),
>> they're explicit.  They come with a matrix.  You don't like my codings?
>> Here's the data - have at it.  Redo it, rerun it yourself.  And to the
>> criticism that no one really goes through those big matrices - I know of
>> two people doing just that with mine, and I've done it with the matrices of
>> several others, both on theropods and crocs.
>
>Using the same datapoints and characteristics, or different ones?

Same taxa and characters - not necessarily same "data points," however.




 One great virtue
>of computer-based analyses is that they're 100% reproducible: given the
>same input
>and the same program, you get the same output every time.  But if the input is
>wrong, the output will also be wrong -- the same way, every time.  And if the
>program is flawed, the output will be flawed -- the same way, every time.
>Been
>there, seen that, got the battle-scars.  I don't place blind faith in computer
>analyses, and I get skeptical whenever anyone else does.  A computer's only as
>smart as its program, and only as accurate as its input.
>

I don't think I ever advocated blind acceptance of computer output, and
neither has anyone else.  That's why I, as an editor, would immediately
reject for publication any cladogram that did not either publish or refer
to a matrix.


chris

-=--=--=--=--=--=--=--=--=--=
Christopher Brochu

Postdoctoral Research Scientist
Department of Geology
Field Museum of Natural History
Lake Shore Drive at Roosevelt Road
Chicago, IL  60605  USA

phone:  312-922-9410, ext. 469
fax:  312-922-9566

cbrochu@fmppr.fmnh.org