[Taxacom] base alignment

Hovenkamp, P. (Peter) Hovenkamp at nhn.leidenuniv.nl
Tue Aug 29 09:15:00 CDT 2006


John Grehan wrote: 
> 
> I can't be bothered. Maybe you are right and there is no one else say
it
> like I do. I don't really care. The real issue is whether there is
more
> cladistic evidence for the human-orangutan relationship than the
> human-chimpanzee relationship. Everyone is free to analyze this
problem
> with whatever terminology and algorithm they prefer.
> 
> But for
> > everybody I know "phenetic" means classifying on the basis of
overall
> > similarity of taxa, not selecting compatible characters.
> 
> I agree with this definition. And according to that definition
cladistic
> analysis of molecular characters appears to be an analysis of
characters
> established through overall similarity of base substitutions and gaps.
> 
> Others who are computationally advanced might also find my positions
on
> cladistic theory to be algorithmically naive. Perhaps so. In the end
it
> is the empirical data that will have to be addressed, and for the
> orangutan question this has hardly begun. So far I have not had any
> responses to the Mona Lisa paper saying that the analysis of evidence
is
> garbage or that my observations about questions in molecular analysis
> are demonstrably wrong.

Maybe people just can't be bothered. Possibly they don't really care how
Schtroumpfs schtroumpf their characters or smurf their schtroumpfs (this
being the vocabulary I'm happy with as it is). 

Schtroumpf!


Peter Hovenkamp
Nationaal Herbarium Nederland, Leiden branch
www.nationaalherbarium.nl

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