[Taxacom] dinosaurs and wolves

Kirk Fitzhugh kfitzhugh at nhm.org
Wed Oct 3 15:00:47 CDT 2012


Hi Pierre,

Cladograms are nothing more than abstract devices that imply very vague 
causal accounts of character origin/fixation in ancestral populations 
and subsequent population splitting events. We (abductively) infer these 
hypotheses as answers to questions regarding the occurrences of features 
among groups of individuals to which different species hypotheses refer 
(those hypotheses also abductively inferred, though separately from the 
phylogenetic hypotheses represented by cladograms). But prior to making 
such inferences, we decide whether or not the explanations of one set of 
observations have an effect on the explanations of another set of 
observations. Certainly in the context of cladograms the same sorts of 
causal events are applied and by default explaining one set of 
observations would be relevant to explaining another set of observations.

I think the greatest problem is that we don't specifically acknowledge 
the why-questions we're asking, for which we contend cladograms entail 
answers. Personally, I think answering a question of the form, "Why do 
these individuals have an A at position 546 in contrast to a G?", in the 
same causal context as "Why do these individuals have 15 skull bones in 
contrast to 18?" is very naive. But this means we need to stop thinking 
only in terms of tossing data into a computer and getting 'trees.' We 
need to think about the why-questions we ask, how best to infer causal 
explanations for our observations, and the extent to which relevance 
issues need to be considered. Simply continuing with the standard 
approach of 'partitioned analyses' and the empirically meaningless 
discussions of 'congruence' just don't work.

Kirk

On 10/3/2012 12:27 PM, Pierre Deleporte wrote:
> Hi Kirk,
>
> just a question :
> how do you propose to combine both classes of observations
> for an epistemically meaningful phylogenetic explanation?
> I mean the details of the procedure, and why so ...
>
> not a trap, a real interrogation -
> you know that I agree with your central point,
> I'm just questioning what's the way out
>
> in other words:
> beyond denegation, what positive perspective?
>
> Best,
> Pierre
>
>
>
> Le 03/10/2012 20:44, Kirk Fitzhugh a écrit :
>> It might have been some consolation to the authors had they acknowledged
>> that comparing 'molecular' and 'morphological' trees is epistemically
>> meaningless. Then it's a matter of deciding whether or not explaining
>> one class of observations is relevant to explaining another class of
>> observations.
>>
>> Kirk
>>
>> On 10/3/2012 11:06 AM, Wolfgang Wuster wrote:
>>> The paper itself ("Assembling the Squamate Tree of Life: Perspectives
>>> from the Phenotype and the Fossil Record") is well worth reading,
>>> containing a host of new morphological characters, and also discussing
>>> the extreme lack of congruence between molecular and morphological data,
>>> particularly in relation to the position of the Iguania in squamate
>>> phylogenies.
>>>
>>> Wolfgang
>>>
>>>
>>>> Hi Wolfgang,
>>>>
>>>>          I haven't seen the newest phylogeny (by Gauthier et al., 2012),
>>>> but I assume that it further solidifies the general consensus that
>>>> Pachyrhachis and relatives are macrostomatan snakes (not sister group
>>>> to all snakes).  However, even that would not necessarily mean that
>>>> they re-evolved legs.  Isn't there also a general consensus that it
>>>> only indicates that snakes lost their legs numerous times (in
>>>> different lineages)?
>>>>
>>>>                 -------------Ken
>>>>
>>>> ---------------------------------------------------------------------------------------------------------
>>>>> Date: Wed, 3 Oct 2012 07:47:21 +0100
>>>>> From: w.wuster at bangor.ac.uk
>>>>> To: taxacom at mailman.nhm.ku.edu
>>>>> Subject: Re: [Taxacom] dinosaurs and wolves
>>>>>
>>>>> On 03/10/2012 04:58, Ken Kinman wrote:
>>>>>> Stephen,
>>>>>> I didn't say anything about reversals requiring reactivation of
>>>> genes. I certainly know of no snakes or marine mammals reactivating
>>>> leg genes and the reinvention of legs.
>>>>> Actually, there is reasonable evidence that simoliophiid snakes
>>>>> (Pachyrhachis, Haasiophis) may have re-evolved hind limbs, based on
>>>>> their possession of these appendages and their nesting deep in the
>>>>> ophidian phylogeny. See Gauthier et al., Bulletin of the Peabody Museum
>>>>> of Natural History 53(1), April 2012.
>>>>>
>>>>> Wolfgang
>>>>>
>>>>>
>>>>> --
>>>>> Dr. Wolfgang Wüster - Lecturer
>>>>> School of Biological Sciences Bangor University
>>>>> Environment Centre Wales
>>>>> Bangor LL57 2UW Wales, UK
>>>>> Tel: +44 1248 382301 Fax: +44 1248 382569
>>>>> E-mail: w.wuster at bangor.ac.uk
>>>>> http://pages.bangor.ac.uk/~bss166/
>>>>>
>>>>>
>>>>>
>>>>>
>

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 at nhm.org
http://www.nhm.org/site/research-collections/polychaetous-annelids
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~




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