[Taxacom] quote of the week

[murrellze]

Below are a few issues that have been difficult for me.  Any 
clarification would be helpful. 

Is a homology a concept or a hypothesis?

If we polarize two characters states (using outgroup analysis), is that 
polarization a hypothesis?

Is the phylogenetic tree derived in a parsimony analysis a hypothesis, a 
model, or a concept?

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
>>>
>>>     
>>>