Inadequacy of cladistics

[rjensen at SAINTMARYS.EDU]

Gosh, the "specter of phenetics" still haunts us.  In my simply view of taxonomy, OTU is a quite useful way to describe the entities that we are trying to classify - the operational taxonomic units.  In fact, early cladists used that terminology, along with HTUs, the hypothetical entities occupying the interior nodes of the cladogram.

And, I take exception with Jason's comment - any method that starts with a collection of objects and is used to group these into subsets can de described as cluster analysis.  When I look at a phylogenetic tree (cladogram) I see "clusters" of OTUs that share particular sets of characters.

Cheers,

Dick

----- Original Message -----
From: "A.P. Jason de Koning" <apjdk at ALBANY.EDU>
Date: Friday, January 23, 2004 3:24 pm
Subject: Re: Inadequacy of cladistics

> I think the discrepancies in what everyone actually considers to
> be "the" cladistic methodology is interesting.  For my part as a
> statistical molecular evolutionist / phylogeneticist, I am
> accustomed to referring to all methods of phylogenetic inference
> which involve functions of inferred character state changes as
> "cladistic" (i.e., maximum likelihood, bayesian likelihood, and
> parsimony).  Whereas maximum parsimony is a logical generalization
> of the classical cladistic approach, likelihood modelling with
> Markov models is a logical generalization of parsimony.  Indeed,
> maximum parsimony can be formally shown to be a special case of a
> full likelihood treatment using equal rates, equal equilibrium
> frequencies of states, and no branch lengths...
>
> So with respect to your comments, Richard: 1) I disagree that
> 'cladistics' is a clustering approach (since methodologically,
> "clustering" usually implies a phenetic approach); and 2) I argue
> that the strict cladistic approach does indeed seek to reconstruct
> a process--it just does so more badly than other approaches which
> have generalized and improved upon it..
>
> Cheers,
> - Jason
>
> __________________________________________________________________________
> A.P. Jason de Koning, Doctoral Candidate    Email: apjdk at albany.edu
> Department of Biological Sciences            Lab: (518) 442-4347
> University at Albany, SUNY                   FAX: (518) 442-4767
> 1400 Washington Ave., Albany NY 12222, USA Mobil: (518) 210-4504
> __________________________________________________________________________
> "Not ignorance, but ignorance of ignorance is the death of
> knowledge." - Whitehead
>
> ----- Original Message -----
> From: <Richard.Zander at MOBOT.ORG>
> To: <TAXACOM at LISTSERV.NHM.KU.EDU>
> Sent: Friday, January 23, 2004 1:37 PM
> Subject: Re: Inadequacy of cladistics
>
>
> > I think I agree. Cladistics is essentially a cluster analysis
> that groups
> > taxa. The theory is simplistic, and details of process are
> ignored. Of
> > course, we don't know details of process for most taxa, so as
> long as
> > cladists state we are using a simple model to cluster OTUs, and
> are not
> > reconstructing a process, that's okay. The problem, is, as you
> say, that
> > there is a confusion between such.
> >
> > In molecular terms, finding similarities between introns shows
> > relationships, finding dissimilarities between exons shows
> process. I think.
> >
> > ______________________
> > Richard H. Zander
> > Bryology Group
> > Missouri Botanical Garden
> > PO Box 299
> > St. Louis, MO 63166-0299
> > richard.zander at mobot.org <')" >mailto:richard.zander at mobot.org>
> > Voice: 314-577-5180
> > Fax: 314-577-9595
> > Websites
> > Bryophyte Volumes of Flora of North America:
> > http://ridgwaydb.mobot.org/bfna/bfnamenu.htm
> > Res Botanica:
> > http://ridgwaydb.mobot.org/resbot/index.htm
> >
> >
> >
> >
> > -----Original Message-----
> > From: Thomas G. Lammers [mailto:lammers at vaxa.cis.uwosh.edu]
> > Sent: Friday, January 23, 2004 12:07 PM
> > To: Richard.Zander at MOBOT.ORG; TAXACOM at LISTSERV.NHM.KU.EDU
> > Subject: Re: Inadequacy of cladistics
> >
> >
> > At 11:55 AM 1/23/04, Richard.Zander at MOBOT.ORG wrote:
> > >Excellent thought. What is this fundamental inadequacy?
> >
> > Your points are valid, but my criticism has always been the poor
> > correlation between cladistic methodology and biological reality.
> >
> > Evolution is NOT perpetually dichotomous.  In plants at least,
> there is a
> > great deal of reticulation.  Paraphyly is real; a parental
> population does
> > not speciate when it gives rise to a daughter species.  Etc.
> >
> > Since the early years of the 20th century, we have learned a
> great deal
> > about the complex array of diverse biological phenomena by which
> species> come into existence.  With cladistics, we have chucked
> all that out the
> > window and chosen to represent it by a gross oversimplification
> of the
> > process.  Those pretty stick figures are utterly detached from
> the complex
> > reality they purport to represent.
> >
> > Cladograms may be objective, testable, and repeatable, but if
> the procedure
> > by which they are created IGNORES underlying biological reality,
> they are
> > (pardon the horribly mixed metaphor) a house of cards with feet
> of clay,
> > built on sand.
>