[Taxacom] quote of the week

Fri Mar 21 17:31:51 CDT 2008

Here's where I will probably show even more ignorance than usual. If one only has to align five taxa (orang, chimp, bonobo, gorilla, human) is suggested below what is the point if there is no outgroup for analysis? I have seen quite a few analyses that treat the orangutan as the outgroup which means, of course, that the analysis contributes nothing to the orangutan question. In other analyses only one or two species of gibbon or monkey are used. If that were done in morphology one would be laughed out of the room (I take that back, evidently that is no longer the case). 

One of the robust aspects of the orangutan evidence is that if one uses an outgroup to refer to ALL species of monkey and all the lesser apes, any demonstration of absence of the derived state in all these representatives is pretty good corroboration of the derived state for great apes and humans. It will be interesting if the same can be said of sequences where complete outgroup comparison is made, and not just for a few species.

John Grehan

-----Original Message-----
From: Brian O'Meara [mailto:omeara.brian at gmail.com] 
Sent: Thursday, March 20, 2008 3:13 PM
To: John Grehan
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] quote of the week

On Mar 20, 2008, at 9:49 AM, John Grehan wrote:
> I acknowledge that some may argue that all things may be the same.  
> In the case of the ear I can point to a positional homology - what 
> appears to be an ear is postionally in the same place as another 
> apparent ear. Anyone can go and see that. With positional sequence 
> homology one cannot do that. One has to put one's faith in a 
> theoretical mathematical model of how molecular evolution is believed 
> to have worked.
>
> John Grehan

This sort of discussion periodically flares on taxacom (and often with the same participants). Actually looking at the maligned molecular data might be a useful approach to the issue. I've included a small fasta file of hominidae sequences for cytochrome oxidase II.  
I downloaded it from phylota ( http://loco.biosci.arizona.edu/cgi-bin/
sql_getcluster.cgi?ti=9604&cl=61&ntype=1&db=GB159 ), added taxon names to the annotations, and trimmed off the regions of DNA present in only a subset of the taxa (and if this is a controversial step, feel free to get the original data from the above URL and play with it directly). One can load this file in a favorite sequence alignment program that allows manual alignment (MacClade and Mesquite are popular), or even just print out the sequences and truly manually align them, and "go and see that" the reasonable alignment is one with no indels, even though the sequence data are rather divergent (up to 16% pairwise differences) and thus potentially difficult to align. For a mitochondrial protein-coding gene, the lack of indels and thus trivial alignment is what you'd expect. One can also try various "theoretical mathematical models" (Clustal, Muscle, etc.) using reasonable parameter values (such as the program default
values) and verify that these algorithmic approaches return the same results as the gold standard eyeball analysis. Of course, one can set bizarre parameter values to get wacky results, just as one could assert that ears in elephants are homologous with fins in sharks, but barring this, in many cases molecular homology statements will be reasonable and uncontroversial.

Perhaps the morphological characters are giving the correct answer while the molecular data are consistently misleading about hominidae relationships, but if so, the explanation has to come from somewhere other than some innate arbitrariness of alignment. Sometimes alignment IS hard and leads to ambiguous or even erroneous results, but often, especially with exons of protein-coding genes, it's just not that bad. See for yourself.

Best regards,
Brian O'Meara

 >'gi51104787_ti9601_Pongo_pygmaeus_abelii'
ACTCACCAACACCAGCATCTCAGACGCCCAAGAGATAGAGACTATTTGAACTATCCTACCGGCCATCATCCT
AATTCTAATCGCCCTCCCATCCCTACGCATCCTCTACTTAACAGACGAGATCAACGACCCTTCCTTCACCAT
CAAATCAATCGGTCATCAATGATACTGAACCTACGAGTACACTGACTACGGTGGATTGATCTTCAACTCTTA
CATGCTCCCACCACTATTCCTAGAACCAGGCGACCTTCGACTCCTCGACGTCGACAACCGAGTAGTCCTCCC
AGTCGAAGCTCCCGTTCGCATAATAATCACATCCCAAGACGTCTTACACTCATGAACTGTACCCTCACTAGG
CCTGAAAACGGACGCAATCCCCGGACGCCTAAACCAAACCACATTCACTGCCACGCGACCAGGAGTGTACTA
TGGCCAATGCTCAGAAATCTGTGGAGCTAACCACAGCTTTATGCCTATCGTCCTAGAACTAATCCCCC
 >'gi51104761_ti91950_Pan_troglodytes_vellerosus'
ACTAACTAATACTAGTATTTCAGACGCCCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCT
AGTCCTTATTGCCCTACCATCCCTCCGTATCCTTTACATAACAGACGAGGTCAACGACCCCTCCTTTACTAT
TAAATCAATCGGCCATCAATGATATTGAACCTACGAATACACCGACTACGGCGGGCTAATCTTCAACTCCTA
CATACTCCCCCCATTATTTCTAGAACCAGGTGATCTACGACTCCTTGACGTTGATAACCGAGTGGTCCTCCC
AGTTGAAGCCCCCGTTCGTATAATAATTACATCACAAGATGTTCTACACTCATGAGCTGTTCCCACATTAGG
CCTAAAAACAGACGCAATTCCCGGACGCCTAAACCAAACCACTTTCACCGCCACACGACCAGGAGTATACTA
CGGCCAATGCTCAGAAATCTGTGGAGCAAACCACAGTTTTATACCCATCGTCCTAGAATTAATCCCTC
 >'gi1743318_ti9602_Pongo_pygmaeus_pygmaeus'
ACTCACCAACACTAACATCTCAGATGCCCAAGAGATAGAAACTATTTGAACTATCCTACCAGCCATCATCCT
AATTCTAATCGCCCTCCCATCTCTACGCATCCTCTACTTAACAGACGAAATCAACGACCCTTCCTTCACCAT
TAAATCAATCGGCCATCAATGATACTGAACCTACGAGTATACTGACTATGGCGGATTGATCTTCAACTCTTA
CATGCTCCCACCACTATTCCTAGAACCAGGCGACCTTCGACTCCTAGACGTCGACAATCGAGTAGTCCTCCC
AGTCGAAGCCCCCGTTCGCATAATAATCACATCCCAGGACGTCTTGCACTCATGAACCGTCCCCTCACTAGG
CCTGAAAACAGACGCAATCCCCGGACGCCTAAACCAAACCACATTCACTGCCACACGACCAGGAGTATATTA
TGGCCAATGCTCAGAAATCTGTGGAGCTAACCACAGCTTTATGCCTATCGTCCTAGAACTAATCCCCC
 >'gi51104763_ti37010_Pan_troglodytes_schweinfurthii'
ACTAACTAATACTAGTATTTCAGACGCCCAGGAAATAGAGACCGTCTGAACTATCCTGCCCGCCATCATCCT
AGTCCTTATTGCCCTACCATCCCTGCGTATCCTTTACATAACAGACGAGGTCAACGACCCCTCCTTTACTAT
TAAATCAATCGGCCATCAATGATATTGAACCTACGAATACACCGACTACGGCGGGCTAATCTTCAACTCCTA
CATACTCCCCCCATTATTTCTAGAACCAGGTGATCTACGACTCCTTGACGTTGATAACCGAGTGGTCCTTCC
AGTTGAAGCCCCCGTTCGTATAATAATTACATCACAAGATGTTCTACACTCATGGGCTGTTCCCACATTAGG
CCTAAAAACAGACGCAATTCCCGGACGCCTAAACCAAACCACTTTCACCGCCACACGACCAGGAGTATACTA
CGGCCAATGCTCAGAAATCTGTGGAGCAAACCACAGTTTTATACCCATCGTCCTAGAATTAATCCCTC
 >'gi1743320_ti9602_Pongo_pygmaeus_pygmaeus'
ACTCACCAACACTAACATCTCAGATGCCCAAGAGATAGAAACTATTTGAACTATCCTACCAGCCATCATCCT
AATTCTAATCGCCCTCCCATCTCTACGCATCCTCTACTTAACAGACGAAATCAACGACCCTTCCTTCACCAT
TAAATCAATCGGCCATCAATGATACTGAACCTACGAATATACTGACTATGGCGGATTGATCTTCAACTCTTA
CATGCTCCCACCACTATTCCTAGAACCAGGCGACCTTCGACTCCTAGACGTCGACAATCGAGTAGTCCTCCC
AGTCGAAGCCCCCGTTCGCATAATAATCACATCCCAGGACGTCTTGCACTCATGAACCGTCCCCTCACTAGG
CCTGAAAACAGACGCAATCCCCGGACGCCTAAACCAAACCACATTCACTGCCACACGACCAGGAGTATATTA
TGGCCAATGCTCAGAAATCTGTGGAGCTAACCACAGCTTTATGCCTATCGTCCTAGAACTAATCCCCC
 >'gi51104791_ti9601_Pongo_pygmaeus_abelii'
ACTCACCAACACCAGCATCTCAGACGCCCAAGAAATGGAGACTATTTGAACTATCCTACCGGCCATCATCCT
AATTCTAATCGCCCTCCCATCTCTACGCATCCTCTACTTAACAGACGAGATCAACAACCCTTCCTTCACCAT
CAAATCAATCGGTCATCAATGATACTGAACCTACGAGTACACTGACTACGGTGGATTGATCTTCAACTCTTA
CATGCTCCCACCACTATTCCTAGAACCAGGCGACCTTCGACTCCTCGACGTCGACAACCGAGTAGTCCTCCC
AGTCGAAGCTCCCGTTCGCATAATAATCACATCCCAAGACGTCTTACACTCATGAACTGTACCCTCACTAGG
CCTAAAAACGGACGCAATCCCCGGACGCCTAAACCAAACCACATTCACTGCCACGCGACCAGGAGTGTACTA
TGGCCAATGCTCAGAAATCTGTGGAGCTAACCACAGCTTTATGCCTATCGTCCTAGAATTAATCCCCC
 >'gi51104789_ti9601_Pongo_pygmaeus_abelii'
ACTCACCAACACCAGCATCTCAGACGCCCAAGAGATAGAGACTATTTGAACTATCCTACCGGCCATCATCCT
AATTCTAATCGCCCTCCCATCCCTACGCATCCTCTACTTAACAGACGAGATCAACGACCCTTCCTTCACCAT
CAAATCAATCGGTCATCAATGATACTGAACCTACGAGTACACTGACTACGGTGGATTGATCTTCAACTCTTA
CATGCTCCCACCACTATTCCTAGAACCAGGCGACCTTCGACTCCTCGACGTCGACAACCGAGTAGTCCTCCC
AGTCGAAGCTCCCGTTCGCATAATAATCACATCCCAAGACGTCTTACACTCATGAACTGTACCCTCACTAGG
CCTGAAAACGGACGCAATCCCCGGACGCCTAAACCAAACCACATTCACTGCCACGCGACCAGGAGTGTACTA
TGGCCAATGCTCAGAAATCTGTGGAGCTAACCACAGCTTTATGCCTATCGTCCTAGAACTAATCCCCC
 >'gi549964_ti9600_Pongo_pygmaeus'
ACTCACCAACACTAACATCTCAGATGCCCAAGAGATAGAAACTATTTGAACTACCCTACCAGCCATCATCCT
AATTCTAATCGCCCTCCCATCTCTACGCATCCTCTACTTAACAGACGAAATCAACGACCCTTCCTTCACCAT
TAAATCAATCGGCCATCAATGGTACTGAACCTACGAGTATACTGACTATGGCGGATTGATCTTCAACTCTTA
CATGCTCCCACCACTATTCCTAGAACCAGGCGACCTTCGACTCCTAGACGTCGACAATCGAGTAGTCCTCCC
AGTCGAAGCCCCCGTTCGCATAATAATCACATCCCAAGACGTCTTGCACTCATGAACCGTCCCCTCACTAGG
CCTGAAAACAGACGCAATCCCCGGACGCCTAAACCAAACCACATTCACTGCCACACGACCAGGAGTATATTA
TGGCCAATGCTCAGAAATCTGTGGAGCTAACCACAGCTTTATGCCTATCGTCCTAGAACTAATCCCCC
 >'gi549966_ti9600_Pongo_pygmaeus'
ACTCACCAACACCAGCATCTCAGACGCCCAAGAAATGGAGACTATTTGAACTATCCTACCGGCCATCATCCT
AATTCTAATCGCCCTCCCATCTCTACGCATCCTCTACTTAACAGACGAGATCAACGACCCTTCCTTCACCAT
CAAATCAATCGGTCATCAATGATACTGAACCTACGAGTACACTGACTACGGTGGATTGATCTTCAACTCTTA
CATGCTCCCACCACTATTCCTAGAACCAGGCGACCTTCGACTCCTCGACGTCGACAACCGAGTAGTCCTCCC
AGTCGAAGCTCCCGTTCGCATAATAATCACATCCCAAGACGTCTTACACTCATGAACTGTACCCTCACTAGG
CCTAAAAACGGACGCAATCCCCGGACGCCTAAACCAAACCACATTGACTGCCACGCGACCAGGAGTGTACTA
TGGCCAATGCTCAGAAATCTGTGGAGCCAACCACAGCTTTATGCCTATCGTCCTAGAATTAATCCCCC
 >'gi51104783_ti9600_Pongo_pygmaeus'
ACTCACCAACACTAACATCTCAGATGCCCAAGAGATAGAAACTATTTGAACTATCCTACCAGCCATCATCCT
AATTCTAATCGCCCTCCCATCTCTACGCATCCTCTACTTAACAGACGAAATCAACGACCCTTCCTTCACCAT
TAAATCAATCGGCCATCAATGATACTGAACCTACGAGTATACTGACTATGGCGGATTGATCTTCAACTCTTA
CATGCTCCCACCACTATTCCTAGAACCAGGCGACCTTCGACTCCTAGACGTCGACAATCGAGTAGTCCTCCC
AGTCGAAGCCCCCGTTCGCATAATAATCACATCCCAGGACGTCTTGCACTCATGAACCGTCCCCTCACTAGG
CCTGAAAACAGACGCAATCCCCGGACGCCTAAACCAAACCACATTCACTGCCACACGACCAGGAGTATATTA
TGGCCAATGCTCAGAAATCTGTGGAGCTAACCACAGCTTTATGCCTATCGTCCTAGAACTAATCCCCC
 >'gi51104785_ti9600_Pongo_pygmaeus'
ACTCACCAACACTAACATCTCAGATGCCCAAGAGATAGAAACTATTTGAACTATCCTACCAGCCATTATCCT
AATTCTAATCGCCCTCCCATCTCTACGCATCCTCTACTTAACAGACGAAATCAACGACCCTTCCTTCACCAT
TAAATCAATCGGCCATCAATGATACTGAACCTACGAGTATACTGACTATGGCGGATTGATCTTCAACTCTTA
CATGCTCCCACCACTATTCCTAGAACCAGGCGACCTTCGACTCCTAGACGTCGACAATCGAGTAGTCCTCCC
AGTCGAAGCCCCCGTTCGCATAATAATCACATCCCAGGACGTCTTGCACTCATGAACCGTCCCCTCACTAGG
CCTGAAAACAGACGCAATCCCCGGACGCCTAAACCAAACCACATTCACTGCCACACGACCAGGAGTATATTA
TGGCCAATGCTCAGAAATCTGTGGAGCTAACCACAGCTTTATGCCTATCGTCCTAGAACTAATCCCCC
 >'gi51104755_ti9593_Gorilla_gorilla'
GCTAACTAACACCAACATCTCAGACGCCCAAGAAATAGAGACCATCTGAACCATCCTGCCCGCTATTATCTT
AGTCCTGATCGCCCTCCCATCTCTACGAATCCTCTATATGACAGATGAAATCAATGACCCCTCCTTCACTAT
CAAATCAATCGGTCACCAATGATACTGAACCTACGAATACACCGACTATGGTGGATTGATCTTTAACTCCTA
TATACTCCCCCCATTATTCCTAGAACCAGGTGACCTACGACTCCTTGACGTCGACAACCGAGTAGTCCTTCC
AGTTGAAGCCCCCGTCCGTATAATAATTACATCCCAAGATGTCTTACACTCATGAGCTGTTCCCACATTAGG
CCTAAAAACAGACGCAATCCCCGGACGCCTGAACCAAACCACATTCACCGCCACACGACCAGGAGTATACTA
CGGCCAGTGCTCAGAAATCTGTGGAGCCAACCACAGTTTTATGCCCATTGTTCTAGAGCTAATCCCCC
 >'gi51104753_ti9593_Gorilla_gorilla'
GCTAACTAACACCAACATCTCAGACGCCCAAGAAATAGAGACCATCTGAACCATCCTGCCCGCTATTATCTT
AGTCCTGATCGCCCTCCCATCTCTACGAATCCTCTATATGACAGATGAAATCAATGACCCCTCCTTCACTAT
CAAATCAATCGGTCACCAATGATACTGAACCTACGAATACACCGACTATGGTGGATTGATCTTTAACTCCTA
TATACTCCCCCCATTATTCCTAGAACCAGGTGACCTACGACTCCTTGACGTCGACAACCGAGTAGTCCTTCC
AGTTGAAGCCCCCGTCCGTATAATAATTACATCCCAAGATGTCTTACACTCATGAGCTGTTCCCACATTAGG
CCTAAAAACAGACGCAATCCCCGGACGCCTGAACCAAACCACATTCACCGCCACACGACCAGGAGTATACTA
CGGCCAGTGCTCAGAAATCTGTGGAGCCAACCACAGTTTTATGCCCATTGTTCTAGAGCTAATCCCCC
 >'gi51104751_ti9593_Gorilla_gorilla'
GCTAACTAACACCAACATCTCAGACGCCCAAGAAATAGAGACCATCTGAACCATCCTGCCCGCTATTATCTT
AGTCCTGATCGCCCTCCCATCTCTACGAATCCTCTATATGACAGATGAAATCAATGACCCCTCCTTCACTAT
CAAATCAATCGGTCACCAATGATACTGAACCTACGAATACACCGACTATGGTGGATTGATCTTTAACTCCTA
TATACTCCCCCCATTATTCCTAGAACCAGGTGACCTACGACTCCTTGACGTCGACAACCGAGTAGTCCTTCC
AGTTGAAGCCCCCGTCCGTATAATAATTACATCCCAAGATGTCTTACACTCATGAGCTGTTCCCACATTAGG
CCTAAAAACAGACGCAATCCCCGGACGCCTGAACCAAACCACATTCACCGCCACACGACCAGGAGTATACTA
CGGCCAGTGCTCAGAAATCTGTGGAGCCAACCACAGTTTTATGCCCATTGTTCTAGAGCTAATCCCCC
 >'gi51104749_ti9593_Gorilla_gorilla'
GCTAACTAACACCAACATCTCAGACGCCCAAGAAATAGAGACCATCTGAACCATCCTGCCCGCTATTATCTT
AGTCCTGATCGCCCTCCCATCTCTACGAATCCTCTATATGACAGATGAAATCAATGACCCCTCCTTCACTAT
CAAATCAATCGGTCACCAATGATACTGAACCTACGAATACACCGACTATGGTGGATTGATCTTTAACTCCTA
TATACTCCCCCCATTATTCCTAGAACCAGGTGACCTACGACTCCTTGACGTCGACAACCGAGTAGTCCTTCC
AGTTGAAGCCCCCGTCCGTATAATAATTACATCCCAAGATGTCTTACACTCATGAGCTGTTCCCACATTAGG
CCTAAAAACAGACGCAATCCCCGGACGCCTGAACCAAACCACATTCACCGCCACACGACCAGGAGTATACTA
CGGCCAGTGCTCAGAAATCTGTGGAGCCAACCACAGTTTTATGCCCATTGTTCTAGAGCTAATCCCCC
 >'gi549956_ti9593_Gorilla_gorilla'
GCTAACTAACACCAACATCTCAGACGCCCAAGAAATAGAGACCATCTGAACCATCCTGCCCGCTATTATCTT
AGTCCTGATCGCCCTCCCATCTCTACGAATCCTCTATATGACAGATGAAATCAATGACCCCTCCTTCACTAT
CAAATCAATCGGTCACCAATGATACTGAACCTACGAATACACCGACTATGGTGGATTGATCTTTAACTCCTA
TATACTCCCCCCATTATTCCTAGAACCAGGTGACCTACGACTCCTTGACGTCGACAACCGAGTAGTCCTTCC
AGTTGAAGCCCCCGTCCGTATAATAATTACATCCCAAGATGTCTTACACTCATGAGCTGTTCCCACATTAGG
CCTAAAAACACACGCAATCCCCGGACGCCTGAACCAAACCACATTCACCGCCACACGACCAGGAGTATACTA
CGGCCAGTGCTCAGAAATCTGTGGAGCCAACCACAGTTTTATGCCCATTGTTCTAGAGCTAATCCCCC
 >'gi549954_ti9593_Gorilla_gorilla'
GCTAACTAGCACCAACATCTCAGACGCCCAAGAAATAGAGACCATCTGAACCATCCTACCCGCTATTATCTT
AGTCCTGATCGCCCTCCCATCTCTACGAATCCTCTATATGACAGATGAAATCAATGACCCCTCCTTCACTAT
CAAATCAATCGGTCACCAATGATACTGAACCTACGAATACACCGACTATGGTGGATTGATCTTTAACTCCTA
TATACTCCCCCCATTATTCCTAGAACCAGGTGACCTACGACTCCTTGACGTCGACAACCGAGTAGTCCTTCC
AGTTGAAGCCCCCGTCCGTATAATAATTACATCCCAAGATGTCTTACACTCATGAGCTGTTCCCACATTAGG
CCTAAAAACAGACGCAATCCCCGGACGCCTGAACCAAACCACATTCACCGCCACACGACCAGGAGTATACTA
CGGCCAGTGCTCAGAAATCTGTGGAGCCAACCACAGTTTTATGCCCATTGTTCTAGAGCTAATCCCCC
 >'gi337100_ti9593_Gorilla_gorilla'
GCTAACTAGCACCAACATCTCAGACGCCCAAGAAATAGAGACCATCTGAACCATCCTACCCGCTATTATCTT
AGTCCTGATCGCCCTCCCATCTCTACGAATCCTCTATATGACAGATGAAATCAATGACCCCTCCTTCACTAT
CAAATCAATCGGTCACCAATGATACTGAACCTACGAATACACCGACTATGGTGGATTGATCTTTAACTCCTA
TATACTCCCCCCATTATTCCTAGAACCAGGTGACCTACGACTCCTTGACGTCGACAACCGAGTAGTCCTTCC
AGTTGAAGCCCCCGTCCGTATAATAATTACATCCCAAGATGTCTTACACTCATGAGCTGTTCCCACATTAGG
CCTAAAAACAGACGCAATCCCCGGACGCCTGAACCAAACCACATTCACCGCCACACGACCAGGAGTATACTA
CGGCCAGTGCTCAGAAATCTGTGGAGCCAACCACAGTTTTATGCCCATTGTTCTAGAGCTAATCCCCC
 >'gi549960_ti9593_Gorilla_gorilla'
GCTAACTAGCACCAACATCTCAGACGCCCAAGAAATAGAGACCGTCTGAACCATCCTACCAGCTATTATCTT
AGTCCTGATCGCCCTCCCATCCCTACGAATCCTCTATATGACAGATGAAATCAACGACCCCTCCTTTACTAT
CAAATCAATCGGTCACCAATGATACTGAACCTACGAATACACCGACTATGGTGGATTGATCTTTAACTCTTA
CATACTCCCTCCATTATTCCTAGAACCAGGTGACCTACGACTCCTTGACGTCGACAACCGAGTAGTCCTTCC
AGTTGAAGCCCCCGTCCGTATAATAATTACATCCCAAGATGTCTTACACTCATGAGCTGTTCCCACATTAGG
CCTAAAAACAGACGCAATCCCCGGGCGCCTGAACCAAACCACATTTACCGCCACACGACCAGGGCTATACTA
CGGCCAGTGCTCAGAAATCTGTGGAGCCAACCACAGTTTTATGCCCATTGTCCTAGAGCTAATCCCCC
 >'gi549958_ti9593_Gorilla_gorilla'
GCTAACTAGCACCAACATCTCAGACGCCCAAGAAATAGAGACCGTCTGAACCATCCTACCAGCTATTATCTT
AGTCCTGATCGCCCTCCCATCCCTACGAATCCTCTATATGACAGATGAAATCAACGATCCCTCCTTTACTAT
CAAATCAATCGGTCACCAATGATACTGAACCTACGAATACACCGACTATGGTGGATTGGTCTTTAACTCTTA
CATACTCCCTCCATTATTCCTAGAACCAGGTGACCTACGACTCCTTGACGTCGACAACCGAGTAGTCCTTCC
AGTTGAAGCCCCCGTCCGTATAATAATTACATCCCAAGATGTCTTACACTCATGAGCTGTTCCCACATTAGG
CCTAAAAACAGACGCAATCCCCGGGCGCCTGAACCAAACCACATTTACCGCCACACGACCAGGGGTATACTA
CGGCCAGTGCTCAGAAATCTGTGGAGCCAACCACAGTTTTATGCCCATTGTCCTAGAACTAATCCCCC
 >'gi530080_ti9597_Pan_paniscus'
ACTAACTAATACTAGTATTTCAGACGCCCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCT
AGTCCTTATTGCCCTTCCATCTCTACGTATCCTTTATATAACAGACGAGGTCAACGACCCCTCCTTTACTAT
TAAATCAATCGGCCATCAATGATATTGAACCTACGAATACACCGACTACGGCGGACTAATCTTCAACTCCTA
CATACTCCCCCCATTATTTCTAGAACCAGGCGACCTACGACTCCTTGACGTTGATAACCGGGTGGTCCTCCC
AGTTGAAGCCCCCGTTCGTATAATAATTACATCACAAGATGTTCTACACTCATGAGCTGTTCCCACATTAGG
CCTAAAAACAGACGCAATTCCCGGACGCCTAAACCAAACCACTTTCACCGCCACACGACCAGGAGTATACTA
CGGCCAATGCTCAGAAATCTGTGGAGCAAACCACAGTTTTATACCCATCGTCCTAGAGTTAATCCCCC
 >'gi51104757_ti9597_Pan_paniscus'
ACTAACTAATACTAGTATTTCAGACGCCCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCT
AGTCCTTATTGCCCTTCCATCTCTACGTATCCTTTATATAACAGACGAGGTCAACGACCCCTCCTTTACTAT
TAAATCAATCGGCCATCAATGATATTGAACCTACGAATACACCGACTACGGCGGACTAATCTTCAACTCCTA
CATACTCCCCCCATTATTTCTAGAACCAGGCGACCTACGACTCCTTGACGTTGATAACCGGGTGGTCCTCCC
AGTTGAAGCCCCCGTTCGTATAATAATTACATCACAAGATGTTCTACACTCATGAGCTGTCCCCACATTAGG
CCTAAAAACAGACGCAATTCCCGGACGCCTAAACCAAACCACTTTCACCGCCACACGACCAGGAGTATACTA
CGGCCAATGCTCAGAAATCTGTGGAGCAAACCACAGTTTTATACCCATCGTCCTAGAGTTAATCCCCC
 >'gi549962_ti9597_Pan_paniscus'
ACTAACTAATACTAGTATTTCAGACGCCCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCT
AGTCCTTATTGCCCTTCCATCTCTACGTATCCTTTATATAACAGACGAGGTCAACGACCCCTCCTTTACTAT
TAAATCAATCGGCCATCAATGATATTGAACCTACGAATACACCGACTACGGCGGACTAATCTTCAACTCCTA
CATACTCCCCCCATTATTTCTAGAACCAGGCGACCTACGACTCCTTGACGTTGATAACCGGGTGGTACTCCC
AGTTGAAGCCCCCGTTCGTATAATAATTACATCACAAGATGTTCTACACTCATGAGCTGTCCCCACATTAGG
CCTAAAAACAGACGCAATTCCCGGACGCCTAAACCAAACCACTTTCACCGCCACACGACCAGGAGTATACTA
CGGCCAATGCTCAGAAATCTGTGGAGCAAACCACAGTTTTATACCCATCGTCCTAGAGTTAATCCCCC
 >'gi530078_ti9597_Pan_paniscus'
ACTAACTAATACTAGTATTTCAGACGCCCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCT
AGTCCTTATTGCCCTTCCATCTCTACGTATCCTTTATATAACAGACGAGGTCAACGACCCCTCCTTTACTAT
TAAATCAATCGGCCATCAATGATATTGAACCTACGAATACACCGACTACGGCGGACTAATCTTCAACTCCTA
CATACTCCCCCCATTATTTCTAGAACCAGGCGACCTACGACTCCTTGACGTTGATAACCGGGTGGTCCTCCC
AGTTGAAGCCCCCGTTCGTATAATAATTACATCACAAGATGTTCTACACTCATGAGCTATCCCCACATTAGG
CCTAAAAACAGACGCAATTCCCGGACGCCTAAACCAAACCACTTTCACCGCCACACGACCAGGAGTATACTA
TGGCCAATGCTCAGAAATCTGTGGAGCAAACCACAGTTTTATACCCATCGTCCTAGAGTTAATCCCCC
 >'gi51104759_ti37011_Pan_troglodytes_troglodytes'
ACTAACTAATACTAGTATTTCAGACGCCCAGGAAATAGAGACCGTCTGAACTATCCTGCCCGCCATCATCCT
AGTCCTTATTGCCCTACCATCCCTGCGTATCCTTTACATAACAGACGAGGTCAACGACCCCTCCTTTACTAT
TAAATCAATCGGCCATCAATGATATTGAACCTACGAATACACCGACTACGGCGGGCTAATCTTCAACTCCTA
CATACTCCCCCCATTATTTCTAGAACCAGGTGATCTACGACTCCTTGACGTTGATAACCGAGTGGTCCTCCC
AGTTGAAGCCCCCGTTCGTATAATAATTACATCACAAGATGTTCTACACTCATGGGCTGTACCCACATTAGG
CCTAAAAACAGACGCAATTCCCGGACGCCTAAACCAAACCACTTTCACCGCCACACGACCAGGAGTATACTA
CGGCCAATGCTCAGAAATCTGTGGAGCAAACCACAGTTTTATACCCATCGTCCTAGAGTTAATCCCTC
 >'gi51104765_ti37012_Pan_troglodytes_verus'
ACTAACTAATACTAGTATTTCAGACGCCCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCT
AGTCCTTATTGCCCTACCATCCCTGCGTATCCTTTACATAACAGACGAGGTCAACGACCCCTCCTTTACTAT
TAAATCAATCGGCCATCAATGATATTGAACCTACGAATACACCGACTACGGCGGGCTAATCTTCAACTCCTA
CATACTCCCCCCATTATTTCTAGAACCAGGTGATCTACGACTCCTTGACGTTGATAACCGAGTGGTCCTCCC
AGTTGAAGCCCCCGTTCGTATAATAATTACATCACAAGATGTTCTACACTCATGAGCTGTTCCCACATTAGG
CCTAAAAACAGACGCAATTCCCGGACGCCTAAACCAAACCACTTTCACCGCCACACGACCAGGAGTATACTA
CGGCCAATGCTCAGAAATCTGTGGAGCAAACCACAGTTTTATACCCATCGTCCTAGAATTAATCCCTC
 >'gi530082_ti9598_Pan_troglodytes'
ACTAACTAATACTAGTATTTCAGACGCCCAGGAAATAGAGACCGTCTGAACTATCCTACCCGCCATCATCCT
AGTCCTTATTGCCCTACCATCCCTGCGTATCCTTTACATAACAGACGAGGTCAACGACCCCTCCTTTACTAT
TAAATCAATCGGCCATCAATGATATTGAACCTACGAATACACCGACTACGGCGGGCTAATCTTCAACTCCTA
CATACTCCCCCCATTATTTCTAGAACCAGGTGATCTACGACTCCTTGACGTTGATAACCGAGTGGTCCTTCC
AGTTGAAGCCCCCGTTCGTATAATAATTACATCACAAGATGTTCTACACTCATGGGCTGTTCCCACATTAGG
CCTAAAAACAGACGCAATTCCCGGACGCCTAAACCAAACCACTTTCACCGCCACACGACCAGGAGTATACTA
CGGCCAATGCTCAGAAATCTGTGGAGCAAACCACAGTTTTATACCCATCGTCCTAGAATTAATCCCTC
 >'gi549968_ti9598_Pan_troglodytes'
ACTAACTAATACTAGTATTTCAGACGCCCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCT
AGTCCTTATTGCCCTACCATCCCTGCGTATCCTTTACATAACAGACGAGGTCAACGACCCCTCCTTTACTAT
TAAATCAATCGGCCATCAATGATATTGAACCTACGAATACACCGACTACGGCGGGCTAATCTTCAACTCCTA
CATACTCCCCCCATTATTTCTAGAACCAGGTGATCTACGACTCCTTGACGTTGATAACCGAGTGGTCCTCCC
AGTTGAAGCCCCCGTTCGTATAATAATTACATCACAAGATGTTCTACACTCATGAGCTGTTCCCACATTAGG
CCTAAAAACAGACGCAATTCCCGGACGCCTAAACCAAACCACTTTCACCGCCACACGACCAGGAGTATACTA
CGGCCAATGCTCAGAAATCTGTGGAGCAAACCACAGTTTTATACCCATCGTCCTAGAATTAATCCCTC
 >'gi549970_ti9598_Pan_troglodytes'
ACTAACTAATACTAGTATTTCAGACGCCCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCT
AGTCCTTATTGCCCTACCATCCCTCCGTATCCTTTACATAACAGACGAGGTCAACGACCCCTCCTTTACTAT
TAAATCAATCGGCCATCAATGATATTGAACCTACGAATACACCGACTACGGCGGGCTAATCTTCAACTCCTA
CATACTCCCCCCATTATTTCTAGAACCAGGTGATCTACGACTCCTTGACGTTGATAACCGAGTGGTCCTCCC
AGTTGAAGCCCCCGTTCGTATAATAATTACATCACAAGATGTTCTACACTCATGAGCTGTTCCCACATTAGG
TCTAAAAACAGACGCAATTCCCGGACGCCTAAACCAAACCACTTTCACCGCCACACGACCAGGAGTATACTA
CGGCCAATGCTCAGAAATCTGTGGAGCAAACCACAGTTTTATACCCATCGTCCTAGAATTAATCCCTC
 >'gi336513_ti9598_Pan_troglodytes'
ACTAACTAATACTAGTATTTCAGACGCCCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCT
AGTCCTTATTGCCCTACCATCCCTGCGTATCCTTTACATAACAGACGAGGTCAACGACCCCTCCTTTACTAT
TAAATCAATCGGCCATCAATGATATTGAACCTACGAATACACCGACTACGGCGGGCTAATCTTCAACTCCTA
CATACTCCCCCCATTATTTCTAGAACCAGGTGATCTACGACTCCTTGACGTTGATAACCGACTGGTCCTCCC
AGTTGAAGCCCCCGTTCGTATAATAATTACATCACAAGATGTTCTACACTCATGAGCTGTTCCCACATTAGG
CCTAAAAACAGACGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCCACACGACCAGGAGTATACTA
CGGCCAATGCTCAGAAATCTGTGGAGCAAACCACAGTTTTATACCCATCGTCCTAGAATTAATCCCTC
 >'gi530076_ti9606_Homo_sapiens'
ACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCT
AGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCAT
CAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTA
CATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCC
GATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGG
CTTAAAAACAGATGCAATTCCAGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCAGGGGTATACTA
CGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCC

>> -----Original Message-----
>> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom- 
>> bounces at mailman.nhm.ku.edu] On Behalf Of Pierre Deleporte
>> Sent: Thursday, March 20, 2008 9:45 AM
>> To: taxacom at mailman.nhm.ku.edu
>> Subject: Re: [Taxacom] quote of the week
>>
>>
>> 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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