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Re: Cladistics algorithm?

I must admit that all this (Tom's various explanations) is very reassuring.

In the papers that I've had the opportunity to examine (and I'll freely
acknowledge that it's not many and mostly those that were set in front of me by
a specific individual), this sort of information is not present at all.

In addition, in the many "discussions" hereabouts on this list the "coloring
factors" by which I mean that little list of softwares and algorithms and post
analytic tinkering have not (to my recollection) ever been mentioned.

>From a journalist's viewpoint, it makes me yearn to understand where folks are
coming from sometimes and that was the origin of the original question.

Judging by a number of the responses I received both on and off list (some from
students, some from interested by standers and a surprising number from
professionals), there are others that share this concern.  Without meaning to, I
think that the original question struck a nerve.

Really, it's not that I think that casual conversation needs to be monitored and
referereed and it's not that I don't see the genuine value of simply
brainstorming parsimonious conclusions, it's that I'm left with an impression --
and, clearly, it's only an impression -- that some discussions jump from A to G
and ignore B,C,D,E and F. And that, further, opinion is a critical factor in the
end and much more so than in, for example, drug testing.


"Thomas R. Holtz, Jr." wrote:

> This is standard operating procedure, often listed in the Methods &
> Materials section of the paper.

> This is typically done (and when I review a paper, I require it!).
> I hate to use my tired old refrain, but your concerns would be much reduced
> if you read the papers in question to see if such is done or not.  It is
> true that some authors do not do such; their analyses should indeed be
> treated with caution.  On the other hand, in the field of systematics there
> are whole journals (Systematic Biology and Cladistics, in particular) which
> devote a majority of their pages to "methods papers".
> So, to turn this discussion to an informed one, could you bring up a
> particular paper or papers with a phylogenetic analysis, and we can discuss
> whether (and how effectively) the methods were documented.  For purposes of
> the list a dinosaur paper would be best, but any form of phylogenetic
> analysis (morphological or molecular; paleo or neontological) would suffice.
>                 Thomas R. Holtz, Jr.
>                 Vertebrate Paleontologist

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