[Taxacom] quote of the week

Thu Mar 20 15:30:22 CDT 2008

That would be ok with me. Although someone else will have to make the case.

John Grehan

> -----Original Message-----
> From: Richard Zander [mailto:Richard.Zander at mobot.org]
> Sent: Thursday, March 20, 2008 4:05 PM
> To: Brian O'Meara; John Grehan
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: RE: [Taxacom] quote of the week
> 
> Why can't morphological evolution of taxa be decoupled from phylogenetic
> evolution of molecular traits? I think the slogan or maxim that ancestral
> taxa cannot be phylogenetically complex is in the way. Thus, molecular
> trees and trees of taxa could well be quite different yet no one is "bad."
> 
> *****************************
> Richard H. Zander
> Voice: 314-577-0276
> Missouri Botanical Garden
> PO Box 299
> St. Louis, MO 63166-0299 USA
> richard.zander at mobot.org
> Web sites: http://www.mobot.org/plantscience/resbot/
> and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
> 
> For FedEx and UPS use:
> Missouri Botanical Garden
> 4344 Shaw Blvd.
> St. Louis, MO 63110
> *****************************
> 
> 
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Brian O'Meara
> Sent: Thursday, March 20, 2008 2:13 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
> >>
> >>
> >>
> >> _______________________________________________
> >> Taxacom mailing list
> >> Taxacom at mailman.nhm.ku.edu
> >> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> >
> > _______________________________________________
> > Taxacom mailing list
> > Taxacom at mailman.nhm.ku.edu
> > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> 
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