[Taxacom] decline and fall of taxonomy

Kevin Richards RichardsK at landcareresearch.co.nz
Thu Jun 18 16:41:06 CDT 2009

This reminds me of my crazy brainwave of "Organism Concepts", where nomenclature and taxonomy are moved from the centre of defining an organism, to be only one of a set of "evidence" that support an "organism concept".

The idea is based on the fact that trying to "name" organisms, into definitive groups, is a fruitless/endless task.
So, we need to look at things from a "use case" / "end user" perspective and work out what is actually needed.

If we take an example, eg someone trying to identify a "specimen" that is being imported into a country, a possible pest - what we really want to know is "is this specimen closely enough related to another specimen that has been shown to be a pest"?  This has traditionally been done by "naming" the original pest specimen/organism, then attempting to identify/name the imported specimen and compare the 2 scientific names!  crazy!  What would be more accurate is to build up a set of "evidence" for the 2 specimens, then run some algorithms on the evidence to come up with a magic number to indicate a "degree of relationship" between those specimens (I have a computer science background you may notice).

The degree of relationship would be calculated differently depending on what the evidence was.  Evidence might include things like nomenclature, taxonomy, images, descriptions, genetic data, etc.  Some would be more accurate algorithms than others, eg comparing genetic/DNA data is fairly accurate, where as comparing images will be a bit fuzzy.

You could then build a graph of organism concepts, the distance between the nodes being calculated by the "degree of relationship".  Then, when identifying specimens, you could slot your specimen into the graph, sitting at the appropriate distance from each defined organism concept, to visualise where you specimen fits in the world.

An interesting approach I thought.
I would be interested in use cases where this approach is definitely not going to work.

Anyone want to poke me back into my corner? and I'll keep quiet again.

Kevin Richards

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Richard Pyle
Sent: Friday, 19 June 2009 6:25 a.m.
To: 'Peter DeVries'; 'Frederick W Schueler'
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] decline and fall of taxonomy

> Is there general agreement that a species description is a
> form of hypothesis driven science rather than a descriptive science?


Unless the hypothesis is, "defining this circumscription of organisms as a
single 'species' facilitates communication amongst biologists and others
better than this other circumscription definition".  But that hypothesis is
not a biological hypothesis; it would need to be tested by people expert in
the ways of human-human communication.

A biological hypothesis would be something like:

"the most recent common ancestor between one circumscribed set of organisms
and another circumscribed set of organisms lived more recently than the most
recent common ancestor between either set and a third circumscribed set of

...which is a convoluted (but more explicit) way of saying "organism 'A' and
organism 'B' are more closely-related to each other than either is to
organism 'C'".

In other words, the products of taxonomy are defined and labelled entities;
whereas assertions about phylogenies are [usually] testable hypotheses.

I say "usually" because I'm not even sure there is always a single clear-cut
answer to questions about phylogeny; in part because we don't necessarily
have a common undrstanding of what is meant by "related to" [see recent
exchange on "Human Origins" between Richard Zander and John Grehan], and in
part because certain pesky organisms don't always play by the rules
(introgression, reticulate patterns of evolution, etc.)

> Is there general agreement that we need to improve the
> documentation of these descriptions so it is clearer to other
> scientists why the authors came to the conclusions they did?

Absolutely; yes!

> *1) I don't think that there is anything wrong with
> descriptive science, but some scientists argue it is not science.
>   So, why fight that battle when you don't have to.

As long as we don't try to pretend that descriptive science is something
that it is not.

I wish I had more time to comment on many of the excellent concurrent
discussions happening on this and other lists, but I do not.


P.S. The answer to the taxon authorhip issue is straightforward:  we need
both sets of authors; one to disambuguate the name (and properly credit the
original proposer); and one to specify in what sense (i.e., which
circumscription, or taxon concept) is implied by the name.


Taxacom Mailing List
Taxacom at mailman.nhm.ku.edu

The Taxacom archive going back to 1992 may be searched with either of these methods:

(1) http://taxacom.markmail.org

Or (2) a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here

Please consider the environment before printing this email
Warning:  This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails.
The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz

More information about the Taxacom mailing list