Re: Underlying basis of classification (Was: Re Dinobirds)

["Thomas R. Holtz, Jr." <th81@umail.umd.edu>]

At 08:22 PM 7/13/99 EDT, Philidor11@aol.com wrote:
>I've been reading what you wrote closely, and I'd appreciate your taking a 
>bit more time to clarify a few points for me: 
>
><< In principle, *all* relevant characters are considered.  I understand that 
>some analyses are more "selective" than others, but that's the fault of the 
>analysis, not the method.  >>
>
>My problem is the combination of 'all' and 'relevant'.  If characters are 
>pre-judged as relevant then the analysis would be selective.  Thinking of 
>this as a computer program, is your model a program that would look at all 
>characters, create a set of all possible trees consistent with the data, then 
>select the 'best' among them according to certain criteria?  These criteria 
>would presumably not consider one character to be a better indicator of 
>relationship than another.

Well, in terms of "relevant", there are two classes of data which can be
ignored for any given particular analysis.  One is the set of characters
shared among all members: for example, we don't need to code "has bones",
"has orbit", "has digits", etc. for a matrix in which we are comparing
different groups of dinosaurs.  (Note, however, that these characters ARE
relevant on higher order studies: the presence of orbits, bones, and digits
being diagnostic for different nodes within vertebrate history).  Characters
shared by all members do not help resolve relationships among these groups.

The second class of data which can be ignored for purposes of resolving
relationships are those found in only one member of the given study.  These
features are important in recognizing that member, but cannot help resolve
relationships as to what that member's closest relatives are.

These classes of data are called "symplesiomorphies" and "autapomorphies",
respectively.

>I wasn't arguing for a cumulative count of shared characters as decisive, but 
>I am curious about how a much less than complete connection can be diagnosed. 
> You mention other features, but they can't be directly associated with the 
>ornithiscian hip, which the non-bird-hipped ornithiscian does not have.  
>Aren't you therefore creating a second diagnosis of ornithiscia, arguably 
>better than the one based on the hip, because it includes at least a 
>substantial number of the animals you want to include, but who are left out 
>by the hip-based definition?

Ooog, you still don't seem to be distinguishing "definition" and
"diagnosis".  Diagnosis is a laundry list of descriptive characters;
definition is (in phylogenetic taxonomy) a statement of relationships.

The analogous case can be made from medicine: the definition of a particular
illness might be "an infection of the xxxxx bacterium", while the diagnosis
of the particular disease might be "high fever, profuse sweating, large
purple blotches on the skin, growth of an extra eye" (okay, a made up
disease...).

>You identify my core problem when you assert that '[d]efinition and diagnosis 
>are entirely different operations', because, absent an ancestor, the 
>definition is created, defined by the diagnosis of the significant 
>characters.

No; see above.

><<Proven?  Can't be done.  But as scientists, we're not in the business of
>proving anything - its disproof we're after.>>
>
>You mean that hypotheses can be refuted only by proving the negative?  That's 
>difficult to do, particularly if one of the problems is absence of data.

Chris is refering to a basic aspect of the scientific method: one cannot
prove an hypothesis, but we can falsify it.  (The classic example: how many
white swans do you need to see to prove the statement "all swans are white"?
In contrast, how many black swans do you have to see to falsify the
statement "all swans are white"?)

><<As far as phylogenetics is concerned, only two factors are important - that 
>the characters be heritable and independent.  If they're passed on from 
>parent to offspring, they can preserve a phylogenetic signal, regardless of 
>subjective assumptions of "importance.">>
>
>Aren't you dealing with characters which are heritable and are independent, 
>but which also might be coincidence in unrelated lineages?

It could well be, yes.

>I was asking if 
>one way to test for whether a shared character is significant might not be 
>whether the character helped the animal survive?  In fact, I was wondering 
>whether I should assume that a character must be part of the survival 
>strategy of an animal in order to use the character to identify a kinship 
>with another animal.

Although I like the sentiment, there are problems with this approach:
a) Much as I am a fan (and advocate) of functional morphology, the sad truth
of the matter that demonstration of the functional significance of any
character state is difficult and time consuming in living animals, and
multifold more in extinct forms.  Yes, a morphology might be *consistent*
with a particular behavior, but it is difficult to demonstrate that it is
actually used as such.  Nature has plenty of examples of potential forms not
utilized (e.g., the long legs of the maned wolf would suggest it is a very
cursorial predator, but it isn't); in fact, there is a large body of
literature on this problem (search under the name "Lauder" for a start).
b) Many people would argue the opposite (as I know from personal
experience!!): that if a character or character complex is functional, it is
MORE likely to be convergently acquired than an apparently non-functional
character.  "But Tom, the arctometatarus is such an obvious adaptation for
cursoriality, it is probably convergently acquired by many different
lineages of theropod...".

><<Detailed morphological analyses can highlight differences questioning 
>assumptions of homology.  Otherwise, we can't know two identical features are 
>nonhomologous without a phylogeny.>>
>
>I'm still working on this, but when you say 'we can't know two identical 
>features are nonhomologous without a phylogeny'  are you saying that only a 
>secure theory can prevent features from being considered homologous, in the 
>absence of decisive morphological analyses?  Sorry, I suppose I was thinking 
>back to (misapplying?) your point about needing a solid refutation to reject 
>(or not accept?) a theory.  Seems like a finding of homology absent disproof 
>positive.

Let's take the example of sabre-teeth in sabrecats and in the big nimravid
_Barbourofelis_.  All other things being equal, these teeth are so identical
in form (and distinct from typical carnivoran canines) that we can consider
them potentially synapomorphic.  It is only when the derived condition of
the rest of the anatomy is considered that we can test if this putative
synapomorphy is supported as such.  Convergence or reversals (together
called "homoplasy") should not be assumed at the beginning of an analysis,
but should be revealed as an analytical result.  The pre-analysis statement
should be "if they look the same, code them the same".  Otherwise you are
stacking the deck.

                        Thomas R. Holtz, Jr.
                        Vertebrate Paleontologist
Deptartment of Geology                  Director, Earth, Life & Time Program
University of Maryland                  College Park Scholars
College Park, MD  20742       
Webpage: http://www.geol.umd.edu        Phone:301-405-4084
Email:tholtz@geol.umd.edu               Fax:  301-314-9661