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

Don.Colless at csiro.au Don.Colless at csiro.au
Mon Jul 27 01:10:36 CDT 2009

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)

> 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???


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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