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Note from an interloper (thanks)
pdy951 at merle.it.northwestern.edu
pdy951 at merle.it.northwestern.edu
Tue Apr 9 13:04:38 PDT 2002
Don't worry, you didn't hurt my feelings. Thanks for leaving my name out but
people can get that by following the thread back.
Thanks for the critique, I'll keep it in mind. Are you aware that GO is not an
ontology? I don't think that any of the computer scientists who is involved in
GO think that it is a real ontology (subject of ISMB meeting last summer), it's
a hierarchy of processes, components and functions (not gene names) ranging
from general to quite specific. The name has already caught on so changing it
to Gene Nontology or G!O is proabably not going to happen.
I was just as vague and opinionated as Sydney in my first post. I apologize.
Sydney used the analogy of our names and how they don't really define who we
are. We don't name the genes in GO we name the things they do based on
scientific evidence. So for Sydney, I have evidence that he is a molecular
biologist so I would call him that. Maybe if I had less evidence, I would call
him a biologist or a scientist. Calling him Sydney Brenner doesn't say anything
about who he is but trying to chraracterize what he does based on evidence has
merit. From his analogy I didn't think he understood that we were not trying to
name the genes.
Maybe we all need to work on our reading comprehension. Anyways, I have learned
never to check my email on a weekend.
Bill Andersen <andersen at ontologyworks.com> writes on Tue, 09 Apr 2002 11:15:57
> 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
> > 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.
> > 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 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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