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Re: Cladistics algorithm?



The question, really, is one of what algorithms are used.  I'm not interested in
whether it's done in J+++ or Cobol.

There is, as someone else pointed out, a GREAT DEAL of discussion about
cladistics here, and it's clear that there are assumptions behind the various
"positions" people take.

Clearly, now, not only the exact software, but the exact algorithm used within a
specific software colors the supposed "objective data output" that is used by a
paleontologist to draw a specific and deeply held conclusion.

In fact, it seems to me that the one of the addressable problems in paleontology
is the "fudge factor."

Which scientist uses which particular "fudge factor" in reference to which
particular algorithm in which particular piece of software.

In any other hard science (eg physics, chemistry) the variables and constants
must be clearly defined and the experiments designed with them in mind. Analysis
of medical effectiveness, for example, seems to have a much smaller range of
variance than what seems to be acceptable in paleontology.

It APPEARS to me that that the variables and constants here are having a lot of
smoke blown around them and the original question was to try to understand the
precise algorithms to begin with and to see if the variant algorithms are really
identical, equivalent, or have inherent differences that ought to be considered
in conversation.

So, for example, a paleontologist might need to specify not only his CONCLUSION,
but also
1) the name of the software used
2) the setting of the software
3) the version of the software (do they ever update them and the underlying
algorithms?  and are there proper names for these algorithms like, say "Fred's
Formula" or "Manny's Method?")
4) in what direction the data is "weighted" during input
5) how much post-analytical "blurring" is done.

All the opinions are all very well and good, I'd just like to understand what is
behind them in the same way that I'm able to get the sample size and the double
or triple blinding data on a good medical study.

ES

"Thomas R. Holtz, Jr." wrote:

> It was my impression that the question was essentially one of code: as in
> "what precisely is the computer code that runs the analysis?"  If I was
> wrong, please let me know.
> SNIPPED
> If the original poster wants more details on the exact nature of the various
> options, I again  recommend going to a particular software package and
> seeing the particular algorithm used.
>
> Hope this helps.
>
>                 Thomas R. Holtz, Jr.
>                 Vertebrate Paleontologist
> Department of Geology           Director, Earth, Life & Time Program
> University of Maryland          College Park Scholars
>                 College Park, MD  20742
> http://www.geol.umd.edu/~tholtz/tholtz.htm
> http://www.geol.umd.edu/~jmerck/eltsite
> Phone:  301-405-4084    Email:  tholtz@geol.umd.edu
> Fax (Geol):  301-314-9661       Fax (CPS-ELT): 301-405-0796

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