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Panned by Brenner

Gabriel Berriz gberriz at hms.harvard.edu
Mon Apr 8 07:42:48 PDT 2002


Jacob, thanks for posting the article.

IMO, Brenner's comments are far too glib and superficial to merit a 
response.  Or to put it differently, any response (at least any response I 
can imagine getting published) would elevate his comments from being a 
flippant elevator-ride comment to the being a serious, considered 
argument.  It just isn't.  He just doesn't like GO.  Fine, it's his 
prerrogative.  And some people don't like broccoli.  Big deal...

G.

At 10:47 AM 4/6/2002 +0200, you wrote:

>Erich Schwarz schrieb:
> >
> > > http://www.the-scientist.com/yr2002/mar/opin_020318.html
> >
> >     Is there somewhere I can actually read this?  the-scientist.com
> > has a brain-damaged "required login" system for its Web page, which
> > pretty much zaps 95% of the point of having a Web page.
>
>i could access it without problems. so i just copied and pasted it in
>case anybody else has problems to read it.
>
>jacob
>
>
>A few years ago, at a meeting at Dana Point in
>                            Southern California, I mistook the number of
>the
>                            room in which our breakfast was to be served
>and
>                            found myself in a room full of strangers. I
>can't
>                            remember whether they were the Veterinarians
>or
>                            the Veterans of Southern California (VSOC),
>but all
>                            were very large men wearing very large
>placards on
>                            their chests suspended around their necks
>with
>                            imitation gold chains and bearing the message
>"HI!
>                            I'M CHUCK" or BILL or HANK. With my failing
>                            eyesight, I appreciated the 2-inch-high
>lettering
>                            because I did not have to go close up to read
>the
>                            names with a monocle. Unfortunately, our own
>                            meeting supplied us with more modest tags,
>                            carrying our name and affiliation in small
>print, and I
>                            felt most embarrassed among the VSOC men not
>to
>     have a sign around my neck acknowledging "HI! I'M SYD."
>
>       This way of introducing oneself is typically American. In England,
>I always said, "My
>     name is Sydney Brenner," and in old Mittel Europe I would probably
>have clicked my
>     heels, bowed, and merely said. "Brenner." But, then, what's in a
>name? I have always
>     thought that there is a difference between who you are and what you
>are called, and
>     that objects are not the same as their names.
>
>       I was reminded of this a few months ago, when I met somebody who
>told me that
>     the coming thing in the post-genomic era is the new science of
>Ontology. When I
>     asked him what he meant by this, he said it had to do with how we
>name things in
>     biology and directed me to a paper, "Creating the Genome Ontology
>Resource:
>     Design and Implementation," written by a number of Web sites and
>printed in
>     Genome Research (11:1425, 2001). I urge everybody who has a lot of
>time to waste to
>     go and read it.
>
>       I discovered that an ontology is a structured vocabulary in the
>form of a directed
>     acyclic graph such that each term is descended from its parent by
>some defined
>     relationship such as "part of." It is a network where the children
>can have many
>     parents and, in turn, be parents themselves. The objectives of the
>Gene Ontology
>     Consortium are to define these structured hierarchical vocabularies,
>to describe
>     biological objects using these terms, and to provide computing tools
>to manipulate
>     these ontologies and connect them to databases.
>
>       These aims are laudable. Everybody should know what they are
>talking about and
>     should use the same language, and computers and databases need to be
>taught to
>     say the same thing. I doubt the paper's claims that this will solve
>the problems
>     generated by the endless growth of biological data and I suspect
>that the best that
>     gene ontology will do is give us a common language in which to
>express our
>     confusion. My aim is to get out of the Tower of Babel and go
>somewhere else, rather
>     than try to find a common language to govern it. The connection
>between Babel and
>     babble is more than a coincidence.
>
>       Going back to my VOSC friends' placards, we can now see they were
>a cheat. The
>     proclamation "I'M CHUCK" told me nothing about the immense
>biological object
>     carrying it, and it might just as well have said "MY NAME IS CHUCK"
>and, perhaps in
>     smaller print, "AND WHO I AM IS MY BUSINESS."
>
>       The great challenge in biological research today is how to turn
>data into
>     knowledge. I have met people who think data is knowledge but these
>people are then
>     striving for a means of turning knowledge into understanding.
>Knowledge and
>     science are related words and to know, I believe, is to understand.
>Before rushing to
>     convert genomics to 'genamics' and finding that it is another dead
>end, we should
>     consider evacuating the Tower of Babel. We need a theoretical
>framework in which to
>     embed biological data so that the endless stream of data, filled
>with the flotsam and
>     jetsam of evolution, can be sifted and abstracted.
>
>       Very simply, the network we should be interested is not the
>network of names but
>     the network of the objects themselves. The language of these objects
>is not the
>     Oxford Dictionary of Molecular Biology—the Ontology Consortium's
>main source—but
>     that of molecular recognition, the language of molecular biology
>itself. Objects carry
>     their own names in the form of the dispositions of nucleotides and
>amino acids in
>     chemical space, either as linear sequences or on the surfaces of
>three-dimensional
>     structures. The objects have their own names: they are chemical
>names written in the
>     language of DNA sequences and the arrangements of amino acids on
>protein
>     surfaces. It is the interactions between these objects that create
>the processes that
>     produce outcomes for cells, organs and organism.
>
>       This is the real vocabulary that we need to master. It is the
>language of molecular
>     biology—call it mobish if you like—where fluency needs to be
>achieved. The bard gave
>     us "What's in a name?" But who was the bard anyway? We know his name
>was
>     William Shakespeare but was he really William Shakespeare, or was he
>somebody
>     else whose name was Francis Bacon?
>
>       Sydney Brenner, PhD, is a Distinguished Professor at the Salk
>Institute for Biological Studies, La
>                                                         Jolla, Calif.
>
>
>
>     The Scientist 16[6]:12, Mar. 18, 2002
>
>--
>************************************************
>      Jacob Koehler
>      D5-117, AG Bioinformatik
>      Universität Bielfeld
>      PF 100131
>      D-33501 Bielefeld
>      jacob.koehler at uni-bielefeld.de
>************************************************
>
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