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Panned by Brenner

Jason E. Stewart jason at openinformatics.com
Sat Apr 6 07:02:16 PST 2002


"Jacob Koehler" <jacob.koehler at uni-bielefeld.de> writes:

> Erich Schwarz schrieb:
> > 
> > > http://www.the-scientist.com/yr2002/mar/opin_020318.html

You know, my mom taught me a couple of things when I was a kid:

* if you don't have anything positive to say, don't say it
* someone who focuses on the negative aspects of another says a lot
  more about themselves than they do about the person about whom
  they're speaking 

This article is a case in point, his article has no substance, merely
stating: 'biology is big and confusing, who do these people think
*they* can do anything to simplify it?'. It reads pretty lame inded


Here's a few catch phrases I picked up:
* 'the new science of Ontology' - new since when?
* 'These aims are laudable' - if so why isn't he praising you?
* 'I suspect that the best that [GO] will do is give us a common
  language to express our confusion'

The last one is the key. I wouldn't write a scathing reply to this,
merely an article from people who have used GO and site examples of
how useful a tool it's been. 

Help Sydney make his own opinionated view obsolete.

jas.

> 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,
> ways said, "My name is Sydney Brenner," and in old Mittel Europe I
> would probably clicked my heels, bowed, and merely said. "Brenner."
> But, then, what's in a ? I have always thought that there is a
> difference between who you are and what you 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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