[Annelida] Swima the swimmer]

J. Kirk Fitzhugh via annelida%40net.bio.net (by kfitzhugh from nhm.org)
Sat Aug 22 18:41:43 EST 2009


Thanks Greg. No matter what method is used, be it 'parsimony,' 
quasi-Bayesianism, etc., I would never accept the results when I know 
there are other relevant data that need to be considered. In lieu of 
even publishing a cladogram using the sequence data, it would have been 
appropriate to wait on the formal phylogenetics until the relevant data 
are compiled. There is no such thing as 'total evidence' analyses - an 
inference either considers one's available relevant evidence for the 
sake of maximizing rationality of explanation, or they opt for accepting 
that the results are going to be more irrational.

But since you mention it, I'm also deeply concerned at the fact that 
systematists routinely publish phylogenetic hypotheses using a variety 
of different methods, often with contradictory results, regardless of 
what data are used. Why do it? We can't compare the results because 
they're inferred from very different assumptions regarding theories, and 
no one has ever provided any good empirical arguments for the practice. 
It seems we've lost sight (or maybe never had it) of why those trees are 
produced in the first place, and are too enamored with the fact that 
computers can produce branching diagrams whenever we want 'em.

I'm sorry for coming across so critically, but, we have to face the fact 
that a critical attitude toward phylogenetics is just plain absent. It's 
a dangerous situation when a field of science becomes so complacent that 
any sort of method is acceptable and in fact condoned.

Kirk

Greg Rouse wrote:
> Kirk,
> Please consult the Supplement for details on a maximum parsimony 
> analysis that I assume you would not find dubious. A total evidence 
> analysis (i.e., a "limited set of sequence data", plus what must also 
> be called a "limited set" of morphological data) will appear in due 
> course that may alleviate your other concern.
> greg
>
> On Aug 23, 2009, at 7:15 AM, J. Kirk Fitzhugh wrote:
>
>> The phylogenetic hypotheses are only 'solid' insofar as they explain 
>> a limited set of sequence data. Given that the authors must know they 
>> are actively avoiding considering all sorts of other relevant data 
>> that are in need of being explained in the same context, e.g. the 
>> setae as Jim Blake noted, and the use of Bayes Theorem is not meant 
>> for the inference of hypotheses, then Torsten's endorsement is 
>> ill-founded at best.
>>
>> But then, let's not quibble with the fine points of doing good 
>> science - it's more important to impose blind acceptance of methods 
>> by even more blind endorsement.
>>
>> Kirk
>>
>> Struck, Torsten wrote:
>>> Indeed, it is a nice discovery and very interesting. Moreover, the
>>> phylogenetic hypotheses are very solid (not at all "dubios at best") and
>>> good in comparison to several other analyses out there.
>>>
>>> Nice work Karen,
>>>
>>> Torsten.
>>>
>>>
>>> On 8/22/09 10:30 AM, "Kirk Fitzhugh" <kfitzhug from nhm.org> wrote:
>>>
>>>   
>>>> Nice discoveries indeed. It's unfortunate that the scientific merits of the
>>>> phylogenetic hypotheses are dubious at best. But then, it *is* published in
>>>> Science. ;-)
>>>>
>>>> Kirk
>>>>
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: annelida-bounces from oat.bio.indiana.edu on behalf of Geoff Read
>>>> Sent: Sat 8/22/2009 12:54 AM
>>>> To: <Annelida list
>>>> Subject: [Annelida] Swima the swimmer
>>>>
>>>> FYI
>>>>
>>>> Osborn KJ, Haddock SHD, Pleijel F, Madin LP, Rouse GW 2009. Deep-Sea, Swimming
>>>> Worms with Luminescent "Bombs". Science 325: 964 (and online 'supplement').
>>>>
>>>> http://www.sciencemag.org/cgi/citmgr?gca=sci;325/5943/964
>>>>
>>>> Swima bombiviridis named (new genus, new species of acrocirrid)
>>>>
>>>> Abstract: "By using remotely operated vehicles, we found seven previously
>>>> unknown species of swimming annelid worms below 1800 meters. Specimens were
>>>> large and bore a variety of elaborate head appendages. In addition, five
>>>> species have pairs of ellipsoidal organs homologous to branchiae that produce
>>>> brilliant green bioluminescence when autotomized. Five genes were used to
>>>> determine the evolutionary relationships of these worms within
>>>> Cirratuliformia. These species form a clade within Acrocirridae and were not
>>>> closely related to either of the two known pelagic cirratuliforms. Thus, this
>>>> clade represents a third invasion of the pelagic realm from Cirratuliformia.
>>>> This finding emphasizes the wealth of discoveries to be made in pelagic and
>>>> deep demersal habitats."
>>>>
>>>>
>>>> Nice discovery. I want to know what they feed on, and how.
>>>>
>>>> Geoff
>>>>
>>>>
>>>> --
>>>>
>>>>  Geoff Read <g.read from niwa.co.nz>
>>>>   http://www.annelida.net/
>>>>   http://www.niwa.co.nz/about-niwa
>>>>  ***************************
>>>>
>>>>
>>>> NIWA is the trading name of the National Institute of Water & Atmospheric
>>>> Research Ltd.
>>>>
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>>>>
>>>>
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>>>>     
>>>
>>>
>>> ------ CONTACT INFORMATION ------
>>> PD Dr. habil. Torsten H. Struck
>>> University of Osnabrück
>>> Department of Biology/Chemistry
>>> Zoology
>>> Barbarastrasse 11
>>> D-49069 Osnabrück
>>> Germany
>>>
>>> Phone: +49-541-9693450
>>> Fax: +49-541-9692587
>>> e-mail: struck from biologie.uni-osnabrueck.de
>>
>> <ATT00001.txt>
>
> Greg Rouse
> Scripps Institution of Oceanography, UCSD
> 9500 Gilman Drive
> La Jolla CA, 92093-0202
> USA
>
> http://spineless.ucsd.edu/
>
> e-mail: grouse from ucsd.edu <mailto:grouse from ucsd.edu>
> Office Ph:    +1 858 534 7973
> Lab Ph:        +1 858 534 9941
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>
> Courier delivery address:
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> USA
> .............................................................................
>
>
>
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-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
J. Kirk Fitzhugh, Ph.D.
Curator of Polychaetes
Invertebrate Zoology Section
Research & Collections Branch
Natural History Museum of Los Angeles County
900 Exposition Blvd
Los Angeles CA 90007
Phone: 213-763-3233
FAX: 213-746-2999
e-mail: kfitzhug from nhm.org
http://www.nhm.org/research/annelida/staff.html
http://www.nhm.org/research/annelida/index.html
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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