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

[John Grehan]

Well one does wonder about one's sanity when everyone else says
something different.

By basis one might have a theory or principle by which the former state
of a base is determined (predicted). But then I am not trying to make
such a prediction myself so I don't know what basis one would use to do
so.

As for profitable topics, that will depend on one's individual
preferences.

John Grehan

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Jason Mate
Sent: Monday, May 09, 2011 2:45 PM
To: Taxacom
Subject: Re: [Taxacom] Molecular shared derived characters (was sine's
line's)


Dear John, nobody has claimed that you are insane and, judging by the
calm and highly informative postings of Pierre and Sergio, they are
taking a lot of troubleanswering your comments.
I will skip the clocl altogether and ask for a logical breakdown of the
statement: 
> 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.
Maybe if they understood the logic behind the statement it would be
possible to help or at least to steer the conversation towards more
profitable topics. In particular could you clarify what you mean,
exactly, by basis and prediction?
Best
Jason




















 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
> 
> 
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