[Taxacom] Why Taxonomy does NOT matter‏

[Jason Mate]

Sorry for my long delay in replying. Here goes some midnight rambling.
My remarks were on how noise is data, but the ´´wrong´´ sort. A phylogenetic tree is just a hypothesis/guesstimate of relationships based on the data at hand. 
The assumption is that the data will, through adequate analysis, yield THE TREE. Now, THE TREE is at the level of interest of the researcher so any data that doesn´t
work at this level is useless. supposedly the researcher has selected the data adequate to the question.  In morphological studies characters are selected that are adequate 
(read variable but not too much). In molecular studies genes are a mixed bag and you can´t drop bases as you go so clever models are 
developed to do essentially the same. And that difference may be a problem to some.

In addition it is important to draw the distinction between what the phylogeny is and what it aims to be. It is, as you said, a representation of the shortest possible way to connect
bags of characters but it aims to represent the evolution of the group. Granted, it is based on a small subset of, mostly extant, specimens but other than sampling every specimen 
from all populations of all the species that have existed in a group, what else can you use to work out their history? 

Regarding the example of brown and polar bears, this is ´just´ a species concept issue. It reminds me of the blind men and the elephant, each describing a (true) part of the elephant 
and making the wrong inference. Hennig´s now (in)famous depiction of tokogenetic relationships and how the break (coveniently a wedge) of these causes the extinction 
of the stem species and the birth of two new ones is just one more blind man. I agree that the more men (kinds of information) you have the greater the chances to make the right choice.
But it is highly unlikely that we will ever have this kind of information for most species, and in any case we still lack a single convincing definition of species, if it even exists. In the mean time
I think that a bit of common sense and accepting that speciation is messy would go a long way.

Cheers

Jason