Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

Panned by Brenner

Jurg Bahler jurg at sanger.ac.uk
Tue Apr 9 07:08:32 PDT 2002


Brenner's comment has also been published by Genome Biology:

Life sentences: Ontology recapitulates philology
Sydney Brenner
http://genomebiology.com/2002/3/4/comment/1006/?etoc=0000035

> -----Original Message-----
> From: owner-gofriends at genome.Stanford.EDU
> [mailto:owner-gofriends at genome.Stanford.EDU]On Behalf Of LETOVSKY,
> STANLEY I [AG/2165]
> Sent: 09 April 2002 14:10
> To: Chervitz, Steve; 'p-dyck at northwestern.edu';
> gofriends at geneontology.org
> Cc: jason at openinformatics.com; 'Cathy Ball <ball at genome.stanford.edu>'
> Subject: RE: Panned by Brenner
>
>
> All,
> 	At the risk of prolonging unnecessarily: I believe "the
> Scientist"
> is the publication organ of the ISI
> citation index service. The "list of GO success stories"
> could perhaps be
> achieved simply by querying
> the citation database to find the number of citations of the GO Nature
> paper, and perhaps appending
> the query result to the response. I would think the list would be
> respectable and would speak for
> itself. ISI normally charges for such queries, but perhaps
> they could be
> persuaded to provide the query
> results for free, given that they were willing to publish Brenner's
> comments.
>
> 	A couple of Brenner's points (or possible readings of
> what he wrote)
> that may be worth conceding are:
> *"Ontologies" are by no means the "next big thing after
> genomics" -- Brenner
> is demolishing a staw man here.
> *The current GO embodiment of the ontology idea as term DAGs
> is -- by design
> -- not even a complete embodiment of a rich network representation of
> biological knowledge. More work is needed, and is being done,
> on richer
> representations which can support more elaborate
> computations. But the best
> should not be the enemy of the good.
>
> Cheers, -Stan
>
> -----Original Message-----
> From: Chervitz, Steve [mailto:Steve_Chervitz at affymetrix.com]
> Sent: Monday, April 08, 2002 7:45 PM
> To: 'p-dyck at northwestern.edu'; gofriends at geneontology.org
> Cc: jason at openinformatics.com; 'Cathy Ball <ball at genome.stanford.edu>'
> Subject: RE: Panned by Brenner
>
>
> Apologies for sparking such an extended thread and taking up
> the valuable
> time of GO workers everywhere!
>
> My initial take on Brenner's opine was that a lot of useful
> work by smart
> people was being trounced by an influential biologist who
> doesn't fully
> appreciate the computational difficulties faced by the field of
> bioinformatics.
>
> To wit, his statement that, "...computers and databases need
> to be taught to
> say the same thing...", seems to undervalue the years of
> effort it takes  to
> approach this problem, computationally, scientifically, and
> politically. His
> "computers should just work" attitude, to me, seems to
> classify efforts such
> as GO as uninteresting problems and a waste of time.
>
> Another flaw in his argument (as Cathy notes) is that he
> characterizes GO as
> an end to itself (and a "dead end" at that), and not as a
> means to achieve
> greater biological understanding.
>
> I also agree with many of the points he makes and respect his great
> understanding of biological problems. I think his insights
> are probably best
> kept in the laboratory and out of the computational arena.
>
> I might have written off the opinion as just another rant by a crusty
> biologist, but this isn't your average crusty biologist. The
> issue of The
> Scientist in which his opinion appeared features a special
> news story on the
> occasion Sydney's 75th birthday, containing glowing comments from 9
> distinguished scientist-colleagues.
>
> A listing of GO success stories would be a good way of
> letting the success
> and promise of GO speak for itself, but I fear it would be
> too lengthy to
> include in a response letter. Perhaps we could put together a
> GO success
> stories web page linked off of geneontology.org and just give the URL?
>
> Steve
>
>
> > -----Original Message-----
> > From: pdy951 at merle.it.northwestern.edu
> > [mailto:pdy951 at merle.it.northwestern.edu]
> > Sent: Saturday, April 06, 2002 3:49 PM
> > To: gofriends at geneontology.org
> > Cc: jason at openinformatics.com
> > Subject: Re: Panned by Brenner
> >
> >
> > In the last sentence of the first paragraph of my email, I
> > did say that the man
> > had a right to say whatever he did. I did agree with some of
> > his points, as
> > general and vague as they were. I do think that everybody has
> > a right to
> > question and critique (hence refine) other peoples ideas in
> science.
> >
> > Something integral to this is understanding what the other
> > person is doing so
> > that you can explicitly state what the other person is doing
> > wrong. Ultimately,
> > I just didn't believe from reading the article that he fully
> > understood what GO
> > was for. From his letter it appears that he thinks we are
> > trying to name the
> > gene "The objects have their own names: they are chemical
> > names written in the
> > language of DNA sequences" instead of use the same vocabulary
> > to define
> > process, compartment and function. I agree with you that
> > counterpoint is not
> > necessary only because he provides us with nothing to counter.
> >
> > A sad reality of being on the consortium is that you get each
> > and every of
> > these emails along with things more critical to your daily
> > job. I usually don't
> > respond to these things, much less on a weekend to
> > recapitulate high school
> > debating techniques. However, it's the price you pay for
> > getting valuable
> > feedback into how to make things better. Funny that he never
> > posted a comment
> > to it.
> >
> > Tricia
> >
> > Cathy Ball <ball at genome.stanford.edu> writes on Sat, 6 Apr
> > 2002 14:53:18 -0800
> > (PST):
> > >
> > >
> > > Hi all,
> > >
> > > Sydney Brenner is not exactly "these types of people."  I
> > would even go so
> > > far as to suggest that he's pretty darn bright.  There is
> > no need to
> > > respond to the editors to scold them for publishing a
> > diatribe.  It's not
> > > so much a diatribe against GO as a (insightful?) letter
> > expressing his
> > > concern that the generation and description of data is no
> > substitute for
> > > understanding biology.
> > >
> > > The real answer is that those of us involved in GO ARE molecular
> > > biologists, and we ARE dedicated to having the language of
> > molecular
> > > biology be revealed to us through experimentation and
> > research.  The truth
> > > is that we are NOT attempting to declare that GO is the
> > language.  GO is
> > > simply a tool we think will by useful to us in our attempts
> > to communicate
> > > about areas of research, things we think we understand and
> > things we have
> > > yet to understand.
> > >
> > > Read the letter again and maybe you'll see that there is a
> > lot with which
> > > we all agree.  We DO want to turn data into knowledge and
> > knowledge into
> > > understanding.  We think GO helps with that transformation.
> >  We are not
> > > creating GO to create a language, but because is helps us
> > in what I assume
> > > is our real mission in life -- understanding and appreciating the
> > > complexities and wonders of molecular biology.
> > >
> > > I don't think a counterpoint is necessary.
> > >
> > > Cheers,
> > >
> > > Cathy
> > >
> > > P.S. Next time I have a paper to write, I'm going to get my
> > website to do
> > > it for me.  Apparently I lack the necessary computational
> > skills, because
> > > I keep doing it myself.  Is there an O'Reilly book someone could
> > > recommend?
> > >
> > > On Sat, 6 Apr 2002 p-dyck at northwestern.edu wrote:
> > >
> > > > This wasn't a journal article or scientific report, it
> > was one man's
> > opinion.
> > > > This is clear from the format and the 'emotional'
> > language he used.
> > Listening
> > > > to opinions you don't like is the price you pay for
> free speech.
> > > >
> > > > Maybe you should repsond 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.
> > > >
> > > > Tricia
> > > >
> > > > jason at openinformatics.com (Jason E. Stewart) writes on 06
> > Apr 2002 08:02:16
> > > > -0700:
> > > > >
> > > > >
> > > > > "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
> > > > > > ************************************************
> > > > > >
> > > > > > --
> > > > > > 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
> > > > > > Unsubscribing send   "unsubscribe"  to
> > gofriends-request at geneontology.org
> > > > > > Web:          http://www.geneontology.org/
> > > > >
> > > > > --
> > > > > 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
> > > > > Unsubscribing send   "unsubscribe"  to
> > gofriends-request at geneontology.org
> > > > > Web:          http://www.geneontology.org/
> > > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > > 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
> > > > Unsubscribing send   "unsubscribe"  to
> > gofriends-request at geneontology.org
> > > > Web:          http://www.geneontology.org/
> > > >
> > >
> > >
> > >
> >
> >
> >
> >
> >
> > --
> > 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
> > Unsubscribing send   "unsubscribe"  to
> > gofriends-request at geneontology.org
> > Web:          http://www.geneontology.org/
> >
>
> --
> 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
> Unsubscribing send   "unsubscribe"  to
> gofriends-request at geneontology.org
> Web:          http://www.geneontology.org/
>
> --
> 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
> Unsubscribing send   "unsubscribe"  to
> gofriends-request at geneontology.org
> Web:          http://www.geneontology.org/


--
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
Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
Web:          http://www.geneontology.org/



More information about the go-friends mailing list