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Re: future "taxonomy generally"

Using elephants and bacteria isn't the best of comparisons, since they are on opposite ends of the mutability spectrum. But having said that, I think you are overestimating the degree to which lateral gene transfer has affected bacterial evolution, and perhaps underestimating the degree to which lateral gene transfer affects the evolution of higher organisms (including elephants and ourselves). The differences are admittedly on different orders of magnitude, but they aren't astronomically different.
If one uncritically accepts a lot of what Carl Woese has been writing in the last several years, one would get the idea that lateral gene transfer is so rampant among bacteria that it wipes out most phylogenetic signals and makes prokaryotic trees almost a hopeless tangle of reticulation. However, I believe that the confusion that now plagues microbiology is more due to flawed reasoning (circular and otherwise). If you want to read more about my opinions on this, you can visit my homepage (URL given below). I threw this homepage together a few years ago rather haphazardly, so don't expect anything fancy. Just contains the texts of some of my papers on the subject.
As for lists and markers, I get the impression you think my classifications are a mere list of taxa. The coding sequence shows how the taxa are related (usually cladistically, but sometimes paraphyletically), thus replacing the branches of a cladogram in a more concise format. Take away the code and granted it's just a list of taxa, but the very same is true if you take the branches out of a cladogram (just a list of taxa).
And I'm still not sure exactly what you mean by ambiguity, but the markers and coding certainly do allow a lot more "flexibility" in updating classifications when new information warrants it (and in contrasting the views of those with different hypotheses on the phylogeny of a group. I prefer this approach to formally naming hundreds and thousands of new clades, many of which will be later be synonymized and/or discarded.
I don't know where you live, so I don't know if you have a copy of my 1994 book in your immediate area, so I will quote a paragraph from my Introduction:
"Since the basic categories (Kingdom, Phylum, Class, Order, Family) and the names filling them, are relatively stable, they have been retained, and the intermediate categories are replaced by a coding system described in Appendix I. This code can represent the relationships between taxa on any level in any classification, cladistic or otherwise, and can be easily modified to represent new and better classifications, but with little or no need to create new names or categories. Thus informational content (including anagenetic information) is preserved, while problems, such as the multiplicity of names and categories, hierarchical stability, etc., are minimized. Since the code will absorb most of the changes resulting from future knowledge, workers who only need to classify can ignore the code and be content with a simpler and more stable Linnean hierarchy. Those of us primarily interested in evolutionary relationships may continue our debates, and although our code sequences may vary dramatically, the basic classification will remain amazingly stable. Because the Kinman System synergistically unifies the best from cladistic and eclectic methods, stability and progress can successfully coexist!!!" To that I would only add that the Kinman System doesn't forbid the use of intermediate categories (they can be listed and coded as well), but it strives to make all such new categories (and the myriads of formal new names) unnecessary.
As promised, here is the URL to my homepage:
--------Ken Kinman
From: "Jaime A. Headden" <qilongia@yahoo.com>
Reply-To: qilongia@yahoo.com
To: dinosaur@usc.edu
CC: kinman@hotmail.com
Subject: Re: future "taxonomy generally"
Date: Thu, 7 Sep 2000 11:46:56 -0700 (PDT)

Ken Kinman wrote:

<The mutability of genes, bacteria, primitive
eukaryotes, and "higher organisms" is just one of the
virtually continuous facets of the complex
evolutionary continuity of life overall.>

  Let me put it this way ... if eukaryotes are basally
so mutable, the classificatory scheme as currently
used by cladistics, or by you, or other "eclectists"
(this is too _ad hominem_ for me) to described them
must be erroneously applied. A new scheme for them has
to be derived. Taking a group of elephants and
applying molecular or morphologic or purely intuitive
reasoning to their relationships to provide a
higher-order reasoning to the population (both living
and fossil), will produce a scheme of reasoning
generally represented as a tree. This can be visually
interpreted into a tree (most common) or as boxes
(historic) or as a list (faunal diversity). Depending
on whether the student (i.e., person who studies) is
deriving a descent, ancestry, in-group, or what-not
system from the group studied, different techniques
will be applied. This will in any case differ
substantially from the organization and descent and
mutation factors in bacteria.

  The two schemes will not be compatible. There must
be more than one scheme, else shoe-horning will derive
intrinsically erroneous conclusions. So trying to
apply a group of basal eukaryotes or more basal
organisms (as you have on the list before) to a
cladistic scheme will of course produce results that
will be, to say the least, screwy. Leaving the
higher-order organisms which do not present lateral
gene transfer, even mutation in a controlled, stable
ecosystem to a system that derives descent/ancestor
models will produce a more tree-based phylogeny.
Organisms, by observation, will have more common
ancestry will some than with others of similar mein.
This produces a tree, not a list. "Markers" argue for
an ambiguity, and I would like to hear your comments
on that.

  Of course, keeping in mind that _all_ taxonomies are
only hypotheses... :)

Jaime "James" A. Headden

  Dinosaurs are horrible, terrible creatures! Even the
  fluffy ones, the snuggle-up-at-night-with ones. You think
  they're fun and sweet, but watch out for that stray tail
  spike! Down, gaston, down, boy! No, not on top of Momma!

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