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Keesey on a mathematical approach to defining clade names -- or -- Whatever Happened To Baby New Papers?



I'm delighted to announce that arrival of a new and potentially
important paper:

http://www.blackwell-synergy.com/doi/abs/10.1111/j.1463-6409.2007.00302.x

        Keesey, T. Michael.  2007.  A mathematical approach to
        defining clade names, with potential applications to
        computer storage and processing.  Zoologica Scripta,
        **, ***-***.

Although the page-numbers have not yet been allocated, the PDF is
online already.  Everyone know knows Mike will know that this paper
represents the culmination of several years' cogitation, and puts PN
on a much-needed firm mathematical basis by introducing a clade
calculus for AFAIK the first time.

Here's the abstract:

        Clade names may be objectively defined based on
        conditions of phylogeny.  Definitions usually take one
        of three forms -- node-, branch- or apomorphy-based --
        but other forms and complex permutations of these
        forms are also possible.  Some database projects have
        attempted to store definitions of clade names in a
        manner accessible to computer applications, but, so
        far, they have only provided ways of storing the most
        common types of definition.  To create a more
        extensible system, I have taken a mathematical
        approach to defining clade names.  To render
        definitions accessible to computer storage and
        analysis, I propose using Mathematical Markup Language
        (MathML) with extensions.  Since the mathematical
        approach is granular to the level of the organism, not
        to fuzzy higher levels such as population or species,
        it sheds light on some theoretical difficulties with
        defining clade names.  For example, some definitions
        do not resolve to a single organism as the ancestor,
        but to sets of organisms which are not ancestral to
        each other and share common descendants.  I term such
        sets 'cladogenetic sets'.

And for anyone who's wondering, yes he _does_ manage to express the
horrific phylogenetic definition of Ichyornis (Clarke 2004) not only
as a rigorous mathematical formula, but also (as an encore) in
MathXML!

 _/|_    ___________________________________________________________________
/o ) \/  Mike Taylor    <mike@indexdata.com>    http://www.miketaylor.org.uk
)_v__/\  "Machines take me by surprise with great frequency" -- Alan
         Turing.