[Taxacom] Pasimony and base alignment

[Richard Zander]

Ah, but what is Truth? Apropos of this is the case of the rechargeable
LED flashlight. 

Walgreens and other stores have been flooded with cheap flashlights with
a powerful LED, two disk batteries, a circuit board, a copper wire coil,
and a steel magnet, all exposed through the transparent case. By
vigorously shaking the flashlight, so the magnet bounces back and forth
through the coil, the batteries are recharged. Such a tough, dependable
light would be great for field trips when one needs to illumine the
flocking vampire bats on one's toes, or startle away the jaguar prowling
the night beyond one's tent. 

However, if you take the flashlight apart and look closely, the circuit
board has only one component (a resistor needed to reduce the current to
the sensitive LED), the copper coil is not connected to anything, and
the magnet is not magnetized. (I rejoice in five of these flashlights.)

By analogy, Fitzhugh is implying something like the coil is the data and
the magnet is the method. Thus, phylogenetists have been vigorously
shaking their flashlights for 30 years. As the cladistic set of
batteries fade, a new flashlight, parsimony, was taken up, then maximum
likelihood, then Bayesian methods, and so on. Fitzhugh, however, does
not detail the "mechanics" for properly testing phylogenetic hypotheses.

He asserts that "shared similarities can never serve as test evidence."
Why not? Surely the barnyard observation that like produces like, plus
the Darwinian theory allows a framework for testing, with simulations
providing confidence in the comparative method.

Perhaps the problem is in strict definitions of the words "confirmation"
and "truth," things never quite reached or expected in science or needed
in day-to-day decision-making, though well worn in philosophical
discussions.

******************************
Richard H. Zander 
NOTE: NEW PHONE NUMBER 314-577-0276
Missouri Botanical Garden
PO Box 299
St. Louis, MO 63166-0299 USA
richard.zander at mobot.org
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St. Louis, MO 63110
******************************
-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of J. Kirk
Fitzhugh
Sent: Friday, September 08, 2006 2:40 PM
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Pasimony and base alignment

If one carefully reads what I said, they will notice I was not 
'pooh-poohing' parsimony or posteriors, as Dr. Zander deftly contends.
I 
merely pointed out that the parsimony criterion as applied in the
inference 
of phylogenetic hypotheses provides no relation to truth.  This is not
idle 
philosophical double speak, but rather a reality of the mechanics of 
hypothesis inference. The 'middle ground' Dr. Zander seeks has existed
for 
quite some time, but is in fact no middle ground at all, but rather 
recognizing the proper testing of explanatory hypotheses, which has been

routinely misapplied in phylogenetics. Phylogenetic inference does not 
generate knowledge, but rather very vague, incomplete explanatory
accounts 
with modest potential to provide causal understanding. The issue is to 
correctly assess the explanatory veracity of hypotheses. For one to then

judge the truth, plausibility, or confidence in a given hypothesis
requires 
properly testing that hypothesis. Problem is, however, shared
similarities 
can never serve as test evidence. Ergo, Bayesian methods are irrelevant
for 
they deal not with the inference of hypotheses but with their subsequent

confirmation, and confirmation requires test evidence, which cannot be 
shared similarities.