[Taxacom] quote of the week

Pierre Deleporte pierre.deleporte at univ-rennes1.fr
Thu Mar 20 13:01:53 CDT 2008

murrellze a écrit :
> Is a homology a concept or a hypothesis?
a hypothesis is a concept, not some material system out there
it is material as a phase of neuronal activity in your brain, during the 
time you are thinking it

it can be true

> If we polarize two characters states (using outgroup analysis), is 
> that polarization a hypothesis?
yes, in phylogeny inference it is a concept and a hypothesis, based on 
an explicit or implicit model of character evolution and homology 
criteria ('underlying theory', based on bakground knowledge...)
- roughly : these features are so similar that I consider them 'states' 
of a same 'character' descending from one another through evolutionary 
processes of "descent with modification" (transformation from generation 
to generation) and preserved in species descendant from the same 
ancestral population, at least putatively before the phylogenetic 
analysis, and until some new, relevant evidence would contradict this 

a considerable series of hypotheses in fact, and still nothing "material 
out there" - a concept (it can be true)

> Is the phylogenetic tree derived in a parsimony analysis a hypothesis, 
> a model, or a concept?
the phylogenetic tree is an explanatory hypothesis, a sketchy historical 
explanation of why such features (characters) are found on such taxa 
(you can read Fitzhugh on this);
it can be true... but still a concept
(explanatory phylogenetic trees are not walking by the roadside, 


> Thanks.
> Zack Murrell
> Pierre Deleporte wrote:
>> self-quotes of the week :
>> Sequences are not passing by 'pre-aligned' out there in nature;
>> but neither do squeletons and anatomies.
>> Morphologists do have 'alignment problems';
>> some mammals appear to have 12, 13, or 14 pairs of ribs...
>> and snakes can show many more
>> (they were likely paid by vicious molecularists for behaving such a 
>> tricky way).
>> Aligning bird and human squeletons was an enlighting biological 
>> conjecture,
>> despite the frustrating fact that squeletons themselves obstinately 
>> refused to align spontaneously
>> (such a lack of cooperative spirit is absolutely baffling ...).
>> Homologies are concepts, inferred properties,
>> they are not observable material systems or processes (= changes in 
>> systems).
>> Ears exist in  nature as things protruding on living beings, not 
>> 'homologies';
>> while homologies do not exist in themselves,
>> except as sequences of thought activities in human brains.
>> When nobody is thinking some homology, no homology is "existing" 
>> properly on Earth;
>> (which is not to say that the homology is erroneous when thought).
>> Confusing interpretative concepts with objectively 'observable' 
>> material objects
>> or processes has one name (at least): naive positivism (pleonasm).
>> Pierre
>> Hovenkamp, P. (Peter) wrote :
>>> John,
>>> >From your opponents you require the same infallibility that you claim
>>> for yourself. Both are unrealistic.
>>> They observe two sequences. They conjecture an alignment.
>>> You observe two ears. You conjecture homology.
>>> Same difference.
>>> Peter Hovenkamp
>>>> Subject: Re: [Taxacom] quote of the week
>>>> I guess it is radical, but then it's the molecularists who have pushed
>>>> the distinction (and superiority) of molecules.
>>>> I can observe or define an ear homology as something that exists in
>>>> nature. When alignment is involved, as it is so often, homologies are
>>>> created that do not exist in nature - they are the product of one or
>>>> more alignment programs. So the sequences are empirical, but the cross
>>>> species homologies of sequences are not when they are the product of
>>>> alignment.
>>>> John Grehan

Pierre Deleporte
Université de Rennes 1
CNRS UMR 6552 
Station Biologique de Paimpont
F-35380 Paimpont   FRANCE
Téléphone : 02 99 61 81 63
Télécopie : 02 99 61 81 88

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