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Re: PAUP vs. MacClade



> Only a fool should beleive their analysis holds the
> truth, or an ounce of it.

Actually a cladogram is an hypothesis, an opinion based on evidence, and so 
only provides a different POV, perhaps one that should be entertained, 
enshrined or trashed. (And I before E except after C.)

And besides, why worry about finding "the truth"? This cladogram game is only a 
puzzle and you're given only so many pieces and so many years to solve it. The 
fun is in the journey.


> It is a product of a what you put into the
> analysis, how you treat characters, WAHT characters you're putting in,
> etc., not to mention how many species you put in. It doesn't matter if
> your analysis of any size always comes up with a single MPT, you need to
> analyze WHY the result appears as much as the input and the output, and
> reminding yourself of that long-understood axiom of GIGO would go a long
> way to solving this, as this is a cornerstone of scientific self-checking
> and hypothesis formation.
>
>   Similarly, NEVER a priori decide that you have "enough" taxa or
> characters. MORE data is better than LESS data, and the idea that if
> you're finding a single MPT means your analysis is good and you can stop
> adding characters is actually wrong on so many levels I wouldn't know
> where to begin but look back up to what I write and *hope* it makes some
> sort of sense.

Actually, you _do_ have to say "enough, it's time to publish" every so often, 
keeping the door open for new thoughts, new data and the next published 
analysis from your arch nemesis. If you stick to your hypothesis you'll never be
satisified with "your canvas" and no one will ever get to appreciate (or 
depreciate) your work.

>
>
> <One thing I have noticed is a vast emptiness in the literature when it
> comes to extant lizard skeletons.>
>
>   http://www.Digimorph.org/ houses an extensive (and expanding) collection
> of skeletal and cranial data on lizards and some snakes. I highly
> recommend this site as well as the sources otherwise listed.

Been there. It is great. Still, like you say, I need more.

Best,

David