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Note from an interloper

Debra Hope dhope at cellomics.com
Tue Apr 9 09:27:42 PDT 2002


Way to get some free advertising Bill.

-----Original Message-----
From: Bill Andersen [mailto:andersen at ontologyworks.com]
Sent: Tuesday, April 09, 2002 12:16 PM
To: gofriends at geneontology.org
Subject: Note from an interloper



Hello, GO-ers..

A friend forwarded me the article by Sydney Brenner in "The Scientist" and
the subsequent thread that followed in this group.  This was fascinating
reading and the responses to it in this list even more interesting.  Here's
one I found particularly interesting (leaving out the author's name, but you
know who you are):

> Maybe you should respond to the editors, saying that printing these kinds
of
> diatribes discredits their publication. It is very obvious this guy
doesn't
> understand the aims or principles of GO. Specifically, that the sequence
is
> the object and the GO terms are a hierarchy of adjectives to describe it.
> As the journal editors didn't catch this by reading his article it's
> 'their bad'.
> 
> Taking these kinds of people too seriously only gives them encouragement.
The
> same thing happened last summer at ISMB (GO getting slammed) and GO has
> exploded in popularity since.

And YOU are talking about discrediting oneself?  Think about this:

  1) Professor Brenner does have a legitimate scientific claim to make
     about the adequacy of GO to do the representational task for which
     it is intended.  Just because you don't understand the meaning of
     his claim doesn't mean you get to call for his censure.

  2) So, last summer GO got slammed?  You mean in Copenhagen or La Jolla?
     Anyway, so what if it got slammed?  THIS IS SUPPOSED TO BE SCIENCE!
     Or do you all leave your scientific hats at the door when it comes to
     doing something outside of bioscience?  This isn't the only episode
     of such sensitivity I've seen and it's disgraceful.

  3) Finally, since this is MY area of science, one concrete comment on

       It is very obvious this guy doesn't understand the aims or
       principles of GO. Specifically, that the sequence is the object
       and the GO terms are a hierarchy of adjectives to describe it.
       As the journal editors didn't catch this by reading his article
       it's 'their bad'

    Well, I don't want to make the same mistake as the editor of "The
    Scientist" so let me edit YOUR post.  Tell me, what is an "object"?
    What are the referents of the terms in GO?  What are their identity
    conditions?  What are the underlying assumptions on existence?  On
    time?  Are properties real for GO?  It makes a difference, you know;
    you might need to quantify over them.  What?  No quantification?
    I could go on, but I won't.

    By this time you should be feeling one of two ways: (a) that you
    have no idea what you're talking about when you use the term
    "ontology"; or (b) that all of this is just a bunch of academic
    philosophical gibberish and thus irrelevant.  Since this is the road
    you took with Prof Brenner, I suspect you will choose (b).
    

Folks, you should be careful about such blanket denunciation of anyone who
dares direct any criticism at GO.  I've seen it before from some members of
the GO community, and it's shameful.  As scientists, we should all welcome
and learn from this criticism.  As real scientists (I'm just a computer
scientist, which doesn't really count) you should embrace this principle
even more closely.

  .bill

-- 
Bill Andersen
Chief Scientist, Ontology Works
1132 Annapolis Road, Suite 104
Odenton, Maryland, 21113
Mobile: 443-858-6444
Office: 410-674-7600
Web: http://www.ontologyworks.com



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This message is from the GOFriends moderated mailing list.  A list of public
announcements and discussion of the Gene Ontology (GO) project.
Problems with the list?           E-mail: owner-gofriends at geneontology.org
Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
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