[Taxacom] Molecular shared derived characters (was sine's, line's)

[Sergio Vargas]

  ok...

 >In my opinion (seemingly alone and therefore insane) the outgroup is 
not informative unless one has a basis for predicting that the outgroup 
condition is >primitive. One cannot do that (at least one does not in 
practice) for individual bases because there is no way to know which 
base state proceeded the one present >(in effect each base in each taxon 
is a character, not a character state).

I think I see the problem now. This was clarified before already. The 
character is the position in the sequence of DNA/Protein data, the 
character states are the specific nucleotide/amino acid recorded for 
that position. We can trace in time the nucleotide changes for a given 
position, i.e. we can postulate the most likely/parsimonious series of 
changes leading to the observed nucleotide/amino acid at a given 
position in a sequence. If you want to define "primitive" conditions you 
can do it based on outgroup comparison the same way you do it with 
morphological characters, unless I just don't know how you do it with 
morphological characters... or better said, how do you do this with 
morphological characters? because I, sincerely, cannot see why DNA data 
is so different from morphological data, and I cannot see why you cannot 
take an alignment of your ingroup and your outgroup, find your uniquely 
shared derived characters, run a parsimony analysis with PAUP and find 
whether your orangutan-human clade is still present in the tree or not, 
for instance. I would really like to see something like this published 
with a clear explanation on how to do proper cladistics with molecular 
characters and a methodological account on why all previous molecular 
analysis were wrong pointing to a chimp-human clade. Perhaps you could 
point some papers on the matter?

 >Also problematic is the invocation of the molecular clock that seems 
to presuppose a clock line change in all bases overall, and the cladistic
 >model requiring bases in the outgroup to have retained their primitive 
condition.

well... retaining the primitive condition would be possible only if the 
rate of evolution (morphological or molecular) in the outgroup branch is 
low, independently of whether a clock holds or not. In most cases we 
don't know anything about the rate of morphological evolution so we can 
only hope or assume the rate was low enough so that the outgroup retains 
the "primitive" condition. I see most of the discrepancies may come from 
the way in which you argument characters which seems to be clique-like, 
as Pierre, said (i.e. excluding characters that doesn't fit the 
"uniquely derived" requirement). I'm not 100% sure though, I understand 
how you would build a matrix morphological or molecular characters for a 
"cladistic" analysis, so I'm hesitating to conclude that you, indeed, 
apply a clique method before any analysis... still don't know... perhaps 
it's me!

sergio