More on the 'cladistics' of sequences

[John Grehan]

-----Original Message-----
From: Taxacom Discussion List [mailto:TAXACOM at LISTSERV.NHM.KU.EDU] On
Behalf Of Richard Jensen
Sent: Tuesday, June 08, 2004 8:23 AM
To: TAXACOM at LISTSERV.NHM.KU.EDU
Subject: Re: [TAXACOM] More on the 'cladistics' of sequences

Dear John,

It is becoming abundantly clear that (a) you have no desire to read the
comprehensive literature that explains how (from beginning to end;
including
being a competent systematist who understands that characters being
used)
cladistic analyses are performed 

Amazing how you know what I have or have not read. Amazing how the same
kind of accusations came up years ago when I favored panbiogeography
over dispersalism (i.e. I was obviously wrong and therefore did not know
what I was talking about since everyone else was a dispersalist).

or (b) you simply reject that notion that molecular data can provide
good hypotheses of phylogenetic relationships (fully testable, etc.; 

At the moment my concern is whether they have automatic priority over
morphology the way many appear to accept.

I know this is not the case, 

Glad to know you have your own certainties.

but your ignoring the extensive and informative comments provided by
members of this list certainly gives that impression)

Actually I am not aware of ignoring anything although I may not get to
respond to everything (not enough time and too much to do). And some of
the comments are rhetorical or repetitive.

, or (c) you are simply being a gadfly.

Whether or not I am is up to anyone to decide. No one has to respond to
anything I post. Just ignore it if it bothers you. I don't want to be a
burden.

The reference to uninformative characters is a classic example of your
not
paying attention

Just because you don't agree with me has nothing to do with my paying
attention or not. Perhaps it is really you who is not paying attention.
This does not seem to be a productive approach.

: any good cladistic algorithm can determine, as can any
competent systematist, whether or not a character is informative.

Only within the parameters of the recipe.

Uninformative characters are ignored because they don't provide any
information about sister-group relationships.  I don't have to be a
hominid
systematist to take a look at a data matrix and tell you whether or not
a
character is informative.  

Only in the context of the data matrix. Whether the characters are
really any good is another matter.

This is the "intelligent ignoramus" aspect of
analysis that was raised when numerical taxonomy was in its infancy.
Some
claimed that numerical taxonomy would reduce the science to a purely
algorithmic exercise that required no understanding of the organisms.
Well,
that's never been the case. 

I wonder. I have talked to a couple of molecular systematists who were
coming up with all sorts of phylogenetic revolutions without having any
clue about morphology of the group they were talking about. So perhaps
these things go both ways.

Morphological data are especially difficult to
evaluate and, in fact, are unlikely to provide "accurate" phylogenies
(see
Lamboy, 1994. Systematic Botany 19: 489-505). Yes, Lamboy's analyses
were
based on simulated data, but the data matrices generated were not unlike
real morphological data matrices.

One could make any kind of theoretical argument about this. If that
assertion is correct then Zander's reference to the general congruence
of molecular and morphological trees would be stupid. It would be like
saying that unlikely data is actually likely - if the molecular tree
were considered 'likely'

Respectfully,

Sure, but if you don't agree with me you don't have to comment or even
read the emails. Better than imputing what's going on in my mind.

John Grehan