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

[John Grehan]

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). 

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.

John Grehan

-----Original Message-----
From: Sergio Vargas [mailto:sevragorgia at gmail.com] 
Sent: Monday, May 09, 2011 2:09 PM
To: taxacom at mailman.nhm.ku.edu; John Grehan
Subject: Molecular shared derived characters (was sine's line's)

  I think I've asked this before.

> Yes they use clustering algorithms used by cladists, but it is my
contention hat this does not make their analysis cladistic because they
cannot (or have not so far) restrict the character data to shared
derived states.
why exactly is that "they" (us, I guess we are not there on the other 
side, whatever that means) cannot restrict the character data to shared 
derived states?

if I have both outgroup and ingroup and a bunch of molecular characters,

why exactly I (we/they) cannot do this? It seems I keep missing the 
point, could someone clarify? please please please.

sergio