[Taxacom] Felsenstein lecture available on-line

John Grehan jgrehan at sciencebuff.org
Fri Dec 5 08:22:16 CST 2008

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Karl Magnacca
> You should get out more.  Any molecular phylogeneticist will admit to
> far more than that.

Perhaps. I'm only dealing with the human origins molecular folk. Perhaps
they have their head in the sand more than others.
> > In practice the trouble with checking alignments by hand is that no
> > (at least of the papers I have seen) bothers to specify how they
> > their personal alignment decisions, just give the results. So there
> > no predictability to their hand method. Voodoo systematics rears its
> > head again.
> It's quite simple: it's the same way that you decide which
> characters are "good" and which are "clearly so homoplasious as to be
> worthless".  Voodoo systematics, indeed.  

That may be well and good, but it does not tell me anything specific. If
one matches by hand by creating gaps and substitutions one must make
decisions, and while homologies that can (or at least should) be
explained and illustrated in morphology, I have not seen any hand
alignments specified in a similar way so one may know how many possible
combinations of gaps and substitutions were present, and if more than
one, how the choice was made. 

Morphology is good and often
> better than molecular methods, but it suffers from its own limitations
> as well.  

Of course.

It's not the problems of molecular phylogenetics that bug me,
> because they can be noted if not always corrected; it's the
> self-righteous attitude of some of those who do only morphology and
> claim to be following the One True Way.

For example?

> Okay, enough of the mini-rant (a result of my traumatic upbringing :-)

No worries. I am interested in feedback. It helps identify gaps in my
thinking, or corroborates my assumptions. Either way it is interesting
for me (and hopefully for at least one other list member).

John Grehan
> Karl
> =====================
> Karl Magnacca
> Postdoctoral Researcher
> Department of Zoology
> Trinity College, Dublin 2
> Ireland
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