[Taxacom] methodological plurality

Kipling (Kip) Will kipwill at berkeley.edu
Thu Nov 22 11:47:21 CST 2012


>> Ashley Nicholasa
>
> I agree with this statement and many of the others given below.
> However, this discussion has left me feeling somewhat unsettled and
> very conflicted. Say we use just one method, as advocated, what do we
> have in the end? A tree that may have good clade support but which
> hangs unconnected to anything else but itself.
>
> Purposeful use of a method appropriate to the data and question in a
> given study is not the same as saying we must have one method to rule
> them all. There isn’t just one statistical method, say the T-test,
> that all must use to look at difference in to populations. There are
> flavors of the T-test and out right alternatives. The reason one
> chooses one test or another has to do with the assumptions about the
> underlying sample (are they independent, normally distributed, etc.)
> and a single method is chosen that best deals with the sample and any
> possible violations of the assumption. Why do systematist not do this
> and is any other field as oddly eclectic in our methods as we are?

Like any good hypothesis it will explain much beyond itself, so I don’t
believe the resultant tree is unconnected at all. Consilience kicks in
when other data, which usually can’t be put into a phylogenetic method 
so readily is consistent with the pattern and we begin to see emergent 
and predictive results.

> Surely this end result will eventually have to be tested or retested? As
> pointed out, the chances are there will not be congruence when it is
> retested with a different method -- which means the result needs to be
> treated as highly uncertain from the start.

This would have made Popper happy,  I think. Maybe Fitzhugh not so much.

> The only way this uncertain tree can be tested is if it is tested using
> the same method. What is the solution to this dilemma? It would seem we
> only have two choices. Either systematists agree to use only one method
> and abandon all others. Or we explore the question/problem more widely
> with as many methods as possible and see what insight (if any) we gain
> from this. Albeit bearing in mind the flaws to this pluralist approach
> and the fact we are not comparing apples with apples (in a
> methodological sense).

Revisiting character coding and primary homology statements might be
appropriate, looking at sensitivity to parameters seems reasonable.
Otherwise, if the best formed justification of how to analyze those data
has been reached you need more/different data to be testing anything. I
think one has to be a bit schizo to serially take on different
epistemologies and call it a test.

> I would hesitate to abandon congruence and consilience because of the
> rich rewards it has already given us in terms of understanding our
> universe. E.g. Newton's connection of failing objects on earth and
> planets going around the sun actually being linked by the same cause.
> Which brings me to the comment: "If two people that view the same world
> (the data) differently, come to the same result they could just as well
> both be wrong or both be right." But isn't this why as scientists we
> test and explore further? In the case of Newton the movement of Mercury
> eventually falsified his hypothesis of gravity and lead the way to
> relativity.

Sorry, but you lost me here with the Newton example. Let me try this
made up example (someone will know a better real one). Lots of people
once viewed the way the world was and concluded the Earth was flat.
There were various methods that converged on this conclusion. They were
all very happy as long as they didn’t sail too far out. Others thought
that a flat Earth (on the back of a turtle maybe) was silly and applied
different methods and concluded the Earth was round-ish. The problem
wasn’t that the data were bad, nor was it solved by looking for
congruence across methods, ultimately it came down to one side was wrong
from the start (bogus ontology) and so consilience among their methods
(their epistemology) kept telling them the Earth was flat. The source of
conflict between them and round-ish Earthers was at this fundamental
level. Luckily we could do things like sail around the planet and go out
to space and look back to finally settle this. Unfortunately,
systematics is much harder than rocket-science and we are forced to do
the best we can to justify and be consistent in our historical science. 
That does mean that it is good that we have people with different views 
using different methods and discussing the virtues and pitfall of 
particular ontology-epistemology schemes. But the comparison must be at 
this fundamental level and not at the level where we run several methods 
and take shared elements as well supported.

> I am not a molecular systematist (my postgrads are co-supervised by
> someone more qualified) but I am now wondering what advice I should give
> them as we have tended to use a pluralist approach in the past. Will the
> examiners of PhD theses be happy with students using only one analytical
> method?
> Thanks for this interesting thread and the insights provided. I have
> really gained a lot from this discussion. Even if it has left me feeling
> conflicted.

Thanks for wading into the debate. I think any unsettled feeling you may 
have is healthy. We all need it, less we become entrenched. As for 
students, using one method to address a question is fine as long as 
there is a clear understanding of why that one and what are its 
advantages and disadvantages. A section that leads with “I selected this 
method because…” seems more important that just
doing them all.


-- 

Contact info:

Kipling W. Will
Associate Professor/Insect Systematist
Associate Director,Essig Museum of Entomology

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