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Panned by Brenner

LETOVSKY, STANLEY I [AG/2165] stanley.i.letovsky at cereon.com
Tue Apr 9 06:10:07 PDT 2002


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 
> > > > > ************************************************ 
> > > > > 
> > > > > -- 
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