[Taxacom] Phylogenetic classification? (and a masterpiece by Knox)

Mon Jul 27 07:52:25 CDT 2009

I agree with 'concrete' examples being important in arguing about
'cladistics' etc. I used conventional cladistic reasoning in arguing the
orangutan relationship. That resulted in some (on this list and other
sources) saying I did not understand cladistics and others saying I not
only did, but better than many. So one gets kicked at both ends. 

In the orangutan study I used 'cladistics' (have to put it in quotes as
there seems to be different 'cladistic' perspectives) as it provided me
with a formalized way of comparing characters and making explicit
statements about character relationships. On the other hand, I view
Croizat's recombination of characters model as having some reality in
the origin of species and other taxa. A cladogram may result in sister
species that are disjunct where the disjunction is occupied by more
distantly related taxa (this is called wing dispersal - as in the wings
of a stage). In this case additional spatial information is providing
additional information in the transformation of a cladogram into a
phylogeny.

John Grehan

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Stephen Thorpe
> Sent: Monday, July 27, 2009 2:38 AM
> To: Don.Colless at csiro.au; taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Phylogenetic classification? (and a masterpiece
by
> Knox)
> 
> The discussion is perhaps becoming a bit too abstract and divorced
> from concrete examples for some tastes. An example Don should know
> more than just a gnat's about is gnats (Nematocera). The true flies
> (Diptera) are traditionally divided into two suborders, Nematocera
> (paraphyletic) and Brachycera (monophyletic). The problem with the
> Nematocera is that there is little or no agreement over which of its
> component infraorders is sister to the Brachycera. So, given radically
> different competing hypotheses, what should we do? Is there anything
> wrong with maintaining a (paraphyletic) Nematocera? And are there in
> fact any non-vacuous other options? The following paper attempts to
> "solve the problem" in some preliminary way, by simply upgrading all
> the nematoceran infraorders to the rank of suborder! Gee, that helped!
> 
> Amorim, D.S.; Yeates, D. 2006: Pesky gnats: ridding dipteran
> classification of the Nematocera. Studia dipterologica, 13: 3-9.
> 
> So the real issue is what to do in terms of classification when there
> is more than one "live" hypothesis. You can keep testing and testing,
> but what if no conclusive answer is reached? What is the best way to
> classify Diptera NOW????
> 
> Stephen
> 
> 
> Quoting Don.Colless at csiro.au:
> 
> > On a point of order, philosophy of science does recognise a process
> > known as "Inference to the Best Explanation". The result may, of
> > course, be regarded as simply the best hypothesis around for
> > subsequent testing; but if you've used all your data already, you're
> > stuck with that inference as your best available "truth of the
> > matter". A cladogram can be regarded as such an inference; but,
> > unfortunately, it refers to a pretty restricted "matter".
> >
> > Donald H. Colless
> > CSIRO Div of Entomology
> > GPO Box 1700
> > Canberra 2601
> > don.colless at csiro.au
> > tuz li munz est miens envirun
> >
> > ________________________________________
> > From: taxacom-bounces at mailman.nhm.ku.edu
> > [taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Stephen Thorpe
> > [s.thorpe at auckland.ac.nz]
> > Sent: 27 July 2009 14:27
> > To: Kirk Fitzhugh
> > Cc: taxacom at mailman.nhm.ku.edu
> > Subject: Re: [Taxacom] Phylogenetic classification? (and a
> > masterpiece by Knox)
> >
> > Kirk:
> >> Cladistics is a process of inferring phylogenetic hypotheses, not
> >> assessing them. The latter lies in the realm of hypothesis testing
> >
> > If it were that simple, then I think that cladistics would be
somewhat
> > vacuous and trivial, for, as any intoductory philosophy of science
> > course would tell one, the hypothetico-deductive method of science
is
> > to come up with hypotheses by any old method (toss a coin, have it
> > come to you in a dream, read it on the back of a corn flakes packet,
> > ...) and then test it by testing it's predictions against known
truth,
> > preferably by trying to falsify it, and if it survives all such
> > attempts (up to the present), then it is a good theory. The more
> > predictions it gets right, the more confidence we can have in it,
> > provided that the tests weren't "selective" in the sense that you
> > choose only the tests that you know (or strongly suspect) will
confirm
> > the theory.
> >
> > If, as you seem to suggest, 'Cladistics is a process of inferring
> > phylogenetic hypotheses', then it has zero benefits over "good old
> > fashioned subjectivism" - both must be tested in exactly the same
way.
> > Maybe cladistics is for systematists without sufficient imagination
or
> > time to dream up hypotheses of their own???
> >
> > Stephen
> >
> > Quoting Kirk Fitzhugh <kfitzhug at nhm.org>:
> >
> >> Cladistics is a process of inferring phylogenetic hypotheses, not
> >> assessing them. The latter lies in the realm of hypothesis testing,
> >> which is wholly separate from the activity of inferring hypotheses
> >> and rarely ever correctly performed (testing, that is) when it
comes
> >> to phylogenetic hypotheses. As such, any desire for stability is a
> >> useless dream. Stability is a hallmark of the track record of
> >> testing. To wit, to invoke the notion of truth is contingent on two
> >> things: knowing what theory of truth (of which there are about six)
> >> you're applying and presenting the confirming test evidence that is
> >> the basis for asserting such (always ephemeral) truth.
> >>
> >> I'm always amused by the defenses and critiques of 'cladistics.'
> >> Most of them are founded on misunderstandings of how science
> >> actually operates.
> >>
> >> Kirk
> >>
> >> -----Original Message-----
> >> From: taxacom-bounces at mailman.nhm.ku.edu on behalf of Stephen
Thorpe
> >> Sent: Sun 7/26/2009 8:38 PM
> >> To: lammers at uwosh.edu
> >> Cc: taxacom at mailman.nhm.ku.edu
> >> Subject: Re: [Taxacom] Phylogenetic classification? (and a
> >> masterpiece by Knox)
> >>
> >> There is nothing intrinsically wrong with phylogenetic (cladistc)
> >> classification - it is just that although it solves some problems,
it
> >> creates others (cake and eat it syndrome!) It solves the problem of
> >> instability due to subjectivity, but instead creates instability
due
> >> to incompleteness of data. I guess the HOPE is that one day, data
will
> >> be complete, so it is temporary instability (that's the theory,
> >> anyway!) Furthermore, the really BIG evil of phylogenetics is that
it
> >> has become a bandwagon which has taken over and pushed taxonomy to
the
> >> sidelines, outcompeting it for funding (new toy syndrome!) Someone
of
> >> note in the taxonomic world recently told me that he turned his
back
> >> on phylogenetics for the reason that 90+% of all the species that
have
> >> ever lived are extinct and unlikely to be found as fossils (or if
> >> found as fossils, then unlikely to be informative enough to be
> >> useful). With so much missing information, data will never be even
> >> remotely complete. Also, my worry, though I'm not really up on the
> >> relevant details, is that I haven't seen a proof that cladistic
> >> methodology is even likely to uncover the evolutionary truth.
> >> Objectivity alone doesn't imply truth: let's all follow an
algorithm
> >> so that the outputs depend only on the inputs and not on who is
doing
> >> it. Great, we all get the same answer - but, er, is it the
truth????
> >>
> >> S
> >>
> >
> >
> >
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