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Panned by Brenner

Jacob Koehler jacob.koehler at uni-bielefeld.de
Sat Apr 6 00:47:08 PST 2002


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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