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Let's say that in looking at available examples,
you knew about 1 definite situation that violated parsimony and 99 that
followed parsimony.
How could we know that?
Now, you can apply parsimony, believing
it is probably applicable to a specific past
situation. You will never have a definitive answer (distant past
evolution can be neither observed nor
rerun), but you can come up with a most likely
scenario.
Most parsimonious, yes.
That scenario is subject to change (being only
most likely) and to question
yep
in a way that [...] a 'theory' like evolution is
not.
The hypothesis remains the property of the
person who made it and those who agree with
it.
How do you mean "remains the
property"?
(I'm purposely leaving out what appear to be
logical flaws in the methodology
such as algorithms that can find a local
instead of the global minimum, the ability not to recognize long-branch
attraction...
[...] Someday, I'd enjoy hearing the comments of
a formal logician who has studied cladistics closely.)
So would I... good luck in finding any
formal logician that has any interest in biology :-)
In addition to the fact that the methodology a
priori cannot guarantee accuracy, there are also errors/subjective elements to
the data. Human beings are making these decisions about which animals to
include, what characters are present/absent, and how to code,
particularly relative codings like ratios above or below a certain
threshold.
Of course. Anyway, scientists are humans.
Cladistic analysis is just the least subjective of all methods for finding out
phylogeny invented so far. :-)
Relative codings are not so bad when there
is a morphological gap (such as "less than 20 % (0), more than 60 %
(1)").
Even with all the skills of the scientist
looking at sheets of computer paper, the preference for a result with 17
reversals, say, compared to 18 is not what you would want to call an
unarguable increase in credibility.
It is becoming more and more common
(appears to me) to publish both the MPT and an interesting different tree that
is slightly less parsimonious. The description of Rahona[vis]
is an example: the MPT has
Aves
|--+--Unenlagia
|
`--+--Archaeopteryx
|
`--Rahonavis
`--Metornithes
, while one tree that is one step longer
has
+--Unenlagia
`--Aves
|--Archaeopteryx
`--+--Rahonavis
`--Metornithes
-- the authors don't decide.
You concluded:
<So what if parsimony doesn't come up with the
tree you constructed in your head? What are you left with in the absence
or parsimony? Munificence makes science become impossible: there are so
many infinitely more complicated schemes why bother testing any of
them?>
Parsimony and the other problems all make the
results of the analysis less than totally reliable.
But still more reliable than all other
available methods (and the only one I can think of is using a lot of intuition,
the sort of thing that HP Ken Kinman is currently accused of).
[...] with no
guarantee of a successful result, and no certainty that we have made much
progress so far.
That's because we can't compare our results
to the truth and see how much progress we've made. I'm pretty sure that we have
made quite some progress, though.
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