Cladistic hypotheses

[Edwards, G.B.]

Kirk,
In response to your earlier message:
To produce a cladogram, a computer finds a "solution" by "analyzing" the
input data to find the fewest steps to resolution of the involved taxa.
It does this by using an algorithm which the observer has given it,
regardless of the program.  Why is a computer algorithm used for this?
Because in most cases, the data is too extensive for a human mind to
analyze.  Therefore, a human creates an algorithm with certain rules of
analysis, in order to make some sense of the data.  The output may very
well become a working hypothesis, but the human (observer) has to
acknowledge it as such.  If you contend that the computer output is your
hypothesis by proxy, you make the assumptions that given the same data,
the same rules, and the same inferences, you would have come up with the
same result if you had been humanly capable of doing so.  This is not
necessarily true.  We know that the computer does not come up with all
possible solutions, or in some cases, even the most parsimonious
solutions, because our data input is not perfect and our algorithms are
not perfect.  We are getting a rough approximation of what we want (some
people tend to forget this).  So I still think there's a semantic
problem.

As for "data in the form of observation statements are themselves
hypotheses," this might be true only in its absurd extreme.  For
example, if your input data is something simple like "red head" vs.
"blue head," there is nothing hypothetical about it unless you want to
get into the limits of our observational powers.

In your later message, you seem to barely consider cladograms to be
hypotheses at all.  To paraphrase Richard, maybe we should call them
phylogenetic speculations?!

For all who celebrate it, have a Happy Thanksgiving and a safe holiday. 
-- 
G. B. Edwards 

-----Original Message-----
From: Taxacom Discussion List [mailto:TAXACOM at LISTSERV.NHM.KU.EDU] On
Behalf Of J. Kirk Fitzhugh
Sent: Wednesday, November 23, 2005 2:08 PM
To: TAXACOM at LISTSERV.NHM.KU.EDU
Subject: Re: [TAXACOM] Cladistic hypotheses

At 01:17 PM 11/23/2005 -0500, you wrote:
>This is basically a semantic problem, but I tend to agree with the
>reviewer.  A cladogram is produced by an algorithm which analyses
>observational data which is input to it and produces the most
>parsimonious solution it can find, i.e., it's a computer program which
>gives you a solution from the data you give to it.  Interpretation of
>the solution is up to the observer, including any hypotheses made based
>on the solution.  So I agree with Barry, and to lesser extent with
Karl,
>although I think you have to make too many assumptions to consider a
>cladogram to be a hypothesis per se.  Neither data, nor data analysis,
>is a hypothesis.

This is not a matter of semantics, and is not a matter blind acceptance
of
some diagram produced by a computer.  The matter here, contrary to the
reviewer, is one of producing hypotheses that might provide causal
understanding of observed effects.  In what way does a computer
"analyze"
data, and what does it mean to have a "solution?"  One cannot interpret
a
solution unless they know the intent of making the inference in the
first
place as the means to deal with a perceived problem.  There are not "too
many assumptions to consider a cladogram a hypothesis."  One of the most
fundamental activities in all fields of science, and everyday life for
that
matter, is that we hypothesize causes for observed effects.  Re "Neither
data, nor data analysis, is a hypothesis," data in the form of
observation
statements are themselves hypotheses; an analysis by a computer is
simply a
proxy for human inference that produces hypotheses.

Kirk

-----------------------------------------------------
J. Kirk Fitzhugh, Ph.D.
Curator of Polychaetes
Invertebrate Zoology Section
Research & Collections Branch
Los Angeles County Museum of Natural History
900 Exposition Blvd
Los Angeles CA 90007

Phone:   213-763-3233
FAX:     213-746-2999
e-mail:  kfitzhug at nhm.org
http://www.nhm.org/research/annelida/staff.html
http://www.nhm.org/research/annelida/index.html
----------------------------------------------------