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Panned by Brenner

pdy951 at merle.it.northwestern.edu pdy951 at merle.it.northwestern.edu
Sat Apr 6 15:48:40 PST 2002


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 
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> > 
> > 
> > 
> > 
> > -- 
> > This message is from the GOFriends moderated mailing list.  A list of 
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> > announcements and discussion of the Gene Ontology (GO) project. 
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> > 
> 
> 
> 





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