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

Mon Jul 27 02:15:37 CDT 2009

not "old-fashioned" Don, just "experienced"! Oh, and not hopelessly!

taxonomy that was built to last, as opposed to throwaway plastic  
cladistics ...

Quoting Don.Colless at csiro.au:

> I'm hopelessly old-fashioned, I know, and I hate to oppose my  
> colleague and friend David Yeates; BUT I still think of and refer to  
> Nematocera without any qualms about confused reference. I have my  
> own opinion about the sister-group to the Brachycera, too; but it's  
> not for publication!!
>
> Donald H. Colless
> CSIRO Div of Entomology
> GPO Box 1700
> Canberra 2601
> don.colless at csiro.au
> tuz li munz est miens envirun
>
> ________________________________________
> From: Stephen Thorpe [s.thorpe at auckland.ac.nz]
> Sent: 27 July 2009 16:38
> To: Colless, Donald (Entomology, Black Mountain); 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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