[Taxacom] quote of the week

Richard Jensen rjensen at saintmarys.edu
Thu Mar 20 08:39:17 CDT 2008 

John,

I can agree with some of what you write, but there is still the problem 
of homology. Just because you decide, based on empirical observations, 
that orang ears and human ears are homologous, that doesn't mean they 
really are homologous. That claim is based on a number of assumptions 
leading to an inference of homology. Can you provide a completely 
assumption-free argument for your claim that human and orang ears are 
homologous? What is the biological evidence for your claim?

Dick J

Richard Jensen, Professor
Department of Biology
Saint Mary’s College
Notre Dame, IN 46556
Tel: 574-284-4674



John Grehan wrote:
> I do not require infallibility as claimed by Peter. 
>
> The molecular alignment is not something that can be empirically
> observed in nature. It is created through one or more mathematical
> models. I can point to an ear on an orangutan and an ear on a human and
> say that a certain feature is the same. Anyone can look at those
> features as decided to agree or disagree with their empirical existence
> and homology.
>
> One may choose to say that all things are the same, and no doubt in the
> realm of philosophy once can invent such a proposition, but I do see a
> difference. If sequences matched up without alignment I would not have
> quite the same problem with homology claims, but when they have to be
> shifted around to make the alignment by selecting among multiple ways to
> manipulating theorized gaps and substitutions I find myself placing a
> little more confidence in a robust morphological (biological) pattern of
> character distribution. 
>
> I might be wrong, but at the moment the molecular world has its head in
> the sand when it comes to the orangutan evidence. Until they start to
> directly address the orangutan evidence and demonstrate (as opposed to
> rhetorical arguments such as the law of large numbers used in phenetic
> systematics) why their molecular answer has to be right, and the 30+
> (and growing) morphological (along with that of the fossil record)
> answer has to be wrong we have a major, major problem. This is not only
> for systematic theory, but in the basic foundation of evolutionary
> theory as well (the problem is so big that I am surprised creationists
> have not yet jumped on it).
>
> John Grehan 
>
>
>   
>> -----Original Message-----
>> From: Hovenkamp, P. (Peter) [mailto:Hovenkamp at nhn.leidenuniv.nl]
>> Sent: Thursday, March 20, 2008 8:53 AM
>> To: John Grehan
>> Cc: taxacom at mailman.nhm.ku.edu
>> Subject: RE: [Taxacom] quote of the week
>>
>> 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
>> Nationaal Herbarium Nederland, Leiden branch
>> www.nationaalherbarium.nl
>>
>>     
>>> -----Original Message-----
>>> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
>>> bounces at mailman.nhm.ku.edu] On Behalf Of John Grehan
>>> Sent: Wednesday, March 19, 2008 3:54 PM
>>> To: rjensen at saintmarys.edu
>>> Cc: taxacom at mailman.nhm.ku.edu
>>> 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
>>>
>>>       
>>>> -----Original Message-----
>>>> From: Richard Jensen [mailto:rjensen at saintmarys.edu]
>>>> Sent: Wednesday, March 19, 2008 10:27 AM
>>>> To: John Grehan
>>>> Cc: taxacom at mailman.nhm.ku.edu
>>>> Subject: Re: [Taxacom] quote of the week
>>>>
>>>> John,
>>>>
>>>> Are you suggesting that molecular sequences do not constitute
>>>>         
>>> biological
>>>       
>>>> evidence? This seems a radical point of view.
>>>>
>>>> And, why is an observation of the morphology of an ear more
>>>>         
>> empirical
>>     
>>>> than determining the sequence of a gene?
>>>>
>>>> Cheers,
>>>>
>>>> Dick J
>>>>
>>>> Richard Jensen, Professor
>>>> Department of Biology
>>>> Saint Mary's College
>>>> Notre Dame, IN 46556
>>>> Tel: 574-284-4674
>>>>
>>>>
>>>>
>>>> John Grehan wrote:
>>>>         
>>>>> As you all know, the chimpanzee theory of human origin is all
>>>>>           
> the
>   
>>> rage
>>>       
>>>>> because of their greater molecular similarity to humans than the
>>>>>           
>>> other
>>>       
>>>>> great apes, and that this theory of origin is contradicted by
>>>>>           
> the
>   
>>>>> biological evidence. For all the (usually blind) faith that is
>>>>>           
> put
>   
>>> in
>>>       
>>>>> the molecular theory, here is a footnote published in Scientific
>>>>> American, March 2008 (p. 21).
>>>>>
>>>>>
>>>>>
>>>>> "One thing everyone agrees on is that reading our history in our
>>>>>           
>>> genes
>>>       
>>>>> is fraught with pitfalls. Getting lots of data has become easy,
>>>>>           
>> but
>>     
>>>>> working out which sequences to use, whom to sample, and how to
>>>>>           
>>> identify
>>>       
>>>>> the genetic legacies of natural selection, migration and
>>>>>           
>> publication
>>     
>>>>> bottleneck is extremely touch. Even relatively simple analyses
>>>>>           
>>> involve
>>>       
>>>>> assumptions and educated guesswork and can take thousands of
>>>>>           
> hours
>   
>>> of
>>>       
>>>>> computer time."
>>>>>
>>>>>
>>>>>
>>>>> So you can chose a method fraught with pitfalls and educated
>>>>>           
>>> guesswork,
>>>       
>>>>> or  the biological evidence where the characters are empirical,
>>>>>           
>>> there is
>>>       
>>>>> no guesswork, and less in the way of computational assumptions
>>>>> (certainly no need to resort to a priori theoretical models of
>>>>>           
>> what
>>     
>>> the
>>>       
>>>>> phylogeny should be in the first place).
>>>>>
>>>>>
>>>>>
>>>>> John Grehan
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Dr. John R. Grehan
>>>>>
>>>>> Director of Science and Collections
>>>>>
>>>>> Buffalo Museum of Science1020 Humboldt Parkway
>>>>>
>>>>> Buffalo, NY 14211-1193
>>>>>
>>>>> email: jgrehan at sciencebuff.org
>>>>>
>>>>> Phone: (716) 896-5200 ext 372
>>>>>
>>>>>
>>>>>
>>>>> Panbiogeography
>>>>>
>>>>>
>>>>>           
>> http://www.sciencebuff.org/biogeography_and_evolutionary_biology.php
>>     
>>>>> Ghost moth research
>>>>>
>>>>>
>>>>>           
> http://www.sciencebuff.org/systematics_and_evolution_of_hepialdiae.php
>   
>>>>> Human evolution and the great apes
>>>>>
>>>>> http://www.sciencebuff.org/human_origin_and_the_great_apes.php
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Taxacom mailing list
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>>>>>
>>>>>           
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>
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