Phylogeny continued

Buz Wilson - Australian Museum buz at EXTRO.UCC.SU.OZ.AU
Sat Jul 29 12:12:58 CDT 1995

At 15:27 28/7/95 -0400, Warren Lamboy wrote:
>My problem arises when they are presented as mathematical models of reality or
>of real historical processes.  It is one thing to create a model of reality and
>quite another to show that it is a good description of reality--the fact
that I can never test the model to see how well it "fits" is what really
makes me >pause.

But simulations and "real" phylogenies of microbes allow us to test the
*heuristic* performance of the tree building/estimation methods.  These
efforts indicate that we can get close to a hypothetical "real" tree.  Close
ain't bad, considering we can't calculate the paths of evolution in all of
its quirky ways.
>I agree that being close to the truth is better than being ignorant.  I would
>rather be ignorant, however, than to believe a falsehood.

We're not discussing  beliefs - I think you have a philosophical
misunderstanding about the practise of phylogeny estimation.  Falsehoods are
not mistaken as truths, because we employ neither; these are political
concepts where the assertion of supremacy is necessary.  Phylogenetists
attempt to find the hypotheses that have the highest likelihood. Hypotheses
are happily rejected when new data or new methods come to hand that suggest
more likely hypotheses. This approach is very different than asserting that
a tree gotten in some manner is the "true" path of evolution.  An aspect
(possibly unpleasant if you are a strict cladist) of phylogenies is that the
closer you look at the nodes in your trees, the harder they are to see. The
well-corroborated cladogram is only a generalisation of the processes that
generated the taxa being studied. At one level, it provides value as a
measure of relatedness, but at a finer level the tree is crude and
restrictive in its representation of reality.  The crude generalisation of a
map doesn't prevent us from using it to find our way. Similarly, the
cladogram is useful as a measure of relationship - as anything in science,
it usefulness depends on your aims.

BTW thanks for being the advocate of a differing opinion, this has been an
interesting debate.


Buz Wilson
Australian Museum

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