[Taxacom] quote of the week

John Grehan jgrehan at sciencebuff.org
Fri Mar 21 07:37:27 CDT 2008

My statement "As in the orangutan case" was not that the alignment was
hard, but that it could lead to erroneous results.

John Grehan

> -----Original Message-----
> From: Brian O'Meara [mailto:omeara.brian at gmail.com]
> Sent: Thursday, March 20, 2008 5:34 PM
> To: John Grehan
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] quote of the week
> On Mar 20, 2008, at 3:19 PM, John Grehan wrote:
> >> -----Original Message-----
> >> From: Brian O'Meara [mailto:omeara.brian at gmail.com]
> > Sometimes
> >> alignment IS hard and leads to ambiguous or even erroneous results,
> >
> > As in the orangutan case.
> >
> > John Grehan
> The point of the dataset, which included orangutan sequence, was that
> alignment was NOT hard in that case. Try looking at it. If the
> results from a tree search with this dataset are different than your
> favorite tree (they were in a quick tree search), it is NOT due to
> difficulty in alignment. Thousands of characters recovered without a
> particular tree in mind reject a tree inferred from one particular,
> hand-crafted dataset; one could advance several arguments to justify
> the minority view, but it's a disservice to anyone who reads taxacom
> to continue to advance hand-waving arguments that are demonstrably
> not true.
> Just FYI for all: based on quickly grepping the archives, it appears
> that this human-orang discussion has appeared in 32 of the last 54
> months on taxacom. I don't think many minds have changed over that
> time, but I think it's at least worth checking that the arguments
> advanced are potentially valid.
> Brian O'Meara

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