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

[Philidor11@aol.com]

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.

<<...the number of [shared] characters, by itself, is not an arbiter of 
closeness of relationship... 
Definition and diagnosis are entirely different operations, regardless of 
whether an ancestor is inferred or documented.  Dinosauria is the last common 
ancestor of ornithischians and saurischians and all of its descendents.  
Whether we actually have that last common ancestor in hand is irrelevant - 
after all, we don't have all of the descendents, either.  The diagnosis is 
the set of characters at that node in a given
analysis - again, regardless of whether the state is actually known in all 
members; taxa for which the hip is unknown cannot be coded for the presence 
or absence of a perforate acetabulum, but other features support their 
placement in subgroups within Dinosauria.
Diagnoses are not stable - and we have no expectation that they should
be.  Any new discovery will change them.>> 

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?
Also, how does the incomplete record of descendants ('after all, we don't 
have all the descendants') justify the inability to document an ancestor 
('[w]hether we actually have that last common ancestor in hand iis 
irelevant')?  This seems instead to weaken the case for the ancestor because, 
as you point out, the better the fossil record the better the analysis.
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.  Further, the identification of the significant characters also 
seems subjective if proposed by the analyst, as discussed 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.

<<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?  This seems to 
argue that a hypothesis is correct because it is possible?  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.

<<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.
Anyway, I'm glad that I have the opportunity to clarify my confusions.  
Thanks!