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Re: [dinosaur] Dinosauria reclassification joins Ornithischia and Theropoda in Ornithoscelida



Gesendet: Freitag, 24. März 2017 um 00:23 Uhr
Von: "Ruben Safir" <ruben@mrbrklyn.com>

> On 03/23/2017 03:29 PM, David Marjanovic wrote:
>
> > Do tell. As a phylogeneticist, I'm all ears!
>
> Where were you 2 months ago when I was boning up on the computational
> math that is being used? The texts and articles that we have reviewed
> continued to have a lack of coherent methodology or theory, is often
> factually wrong (sometimes in critical areas, and sometimes later
> corrected) and play fast and loose with mathematical modeling.

"Modeling"?

What modeling?

The distinctive feature of the method called "parsimony" or "maximum parsimony" 
(a somewhat misleading name) is that it doesn't use a model of evolution at 
all, if that's what you mean. It's nonparametric. That's the method Baron et 
al. used; it's all TNT does, actually (unlike PAUP*, which can also use 
distance methods and maximum likelihood).

Would you like to talk about the advantages and disadvantages of "maximum 
parsimony" and model-based methods? There's an interesting conversation to be 
had there.

> I would personally start a Free Software project to create a
> standardized code base, and build an effort to pull in all the strings
> of research on the computational analysis, into a coherent body of
> knowledge that shares terminology, and models. and which can be broadly
> reviewed and embedded into the software design. I think some fellows at
> MIT would be interested in such a project.

Then ask them. They're probably not reading this.

BTW, why do you still send us your multi-kilobyte signature in every message? I 
think we know it all by heart now, including your quotes of yourself.