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

Stephen Thorpe s.thorpe at auckland.ac.nz
Mon Jul 27 01:38:27 CDT 2009

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????


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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