Saturday, June 28, 2008

decoded - first few chapters

Recently a friend lent me Craig Venter's autobiography "A Life Decoded". The first few chapters have been pretty interesting, particularly the part about his time in VietNam. Knowing quite a few people that have struggled to get into and out of medical school, its amazing to think of all the people that, like Venter, were conducting major life saving operations without the benefit of even an undergraduate education - talk about learning by doing... In relation to my last post, I found some solace in the fact that he apparently often feels very much the same way I do about the relationship between his visions and their ultimate reality:

"The sweetest moment of any project is not when it is finished but when the end is in sight [...] Today, ... I still find that the final version often falls short of the one glimpsed in my head during construction."
J.C Venter (2007) "A Life Decoded" page 14
That being said, the chapters describing his early scientific career are positively humbling - it seems that he went quite a ways before he really guessed wrong. One aspect of his career that he highlights is that, aside from his own drive and cleverness, he always had the benefit of being surrounded be truly world class mentors and collaborators - he lists one nobel prize winning colleague after another and he's barely out of grad school..

Another aspect of the book that is a bit jealousy inducing (as most of the book is likely to be for any scientifically motivated person) is the very clear, step by step progress of his brand of science (currently biochemistry). It reminds me of one of Duncan Hull's best remarks
"Nobody is going to win a Nobel prize for creating a standard schema, ontology or whatever".
This might be the essence of the bioinformatician's lament. Though we know intuitively that the work we are doing is important, many of us feel that it is just plain not as scientific an endeavor as establishing the reasons why a certain drug has a certain effect on a certain kind of cell. Despite knowing that our work is vital - the human genome project would certainly never have been possible without people like us working in the basement somewhere - the general absence of those hard and fast facts associated with real, tangible pieces of reality can be very trying sometimes. This is likely why you will see many of us get so excited about things like gardening and building fences in our backyards (even though such labor tends to damage are soft, uncallused hands).


marijke said...

on Duncans quote and your "This might be the essence of the bioinformatician's lament. ", may I encourage you then be refreshing your mind about the 1998 Nobel laureates in chemistry, Kohn and Pople (press release )? Pople got it thanks to "...his development of computational methods in quantum chemistry" and "Pople made his computational technics easily accessible to researchers by designing the GAUSSIAN computer program. The first version was published in 1970. The program has since been developed and is now used by thousands of chemists in universities and commercial companies the world over".

So a computational biologist or bioinformatician can receive a nobel prize. It's just that just-another-database/ontology won't do; I guess neither another perl script or the like, nor reusing existing technology. What would? well, apparently something that's not out there yet and that also lets you bump into a significant discovery that could not have been made without just that tech you've developed.

Neil said...

I lament with you! The question is: do you want to do research or enable the research of others? If the first, then look at computational biology as just a toolkit, to help you answer questions. If the second, then take every opportunity to remind your peers that tool builders are every bit as important as tool users and be passionate about what you do.

I'm afraid that academia does not reward, understand or appreciate tool builders. If that weighs on your mind, keep your job options open!

gotgenes said...

Great perspective. I understand where you're coming from. Two quotes I try live by assuage the ego in those jealous times:

"The mark of the immature man is that he wants to die nobly for a cause, while the mark of a mature man is that he wants to live humbly for one." —Wilhelm Stekel

"Whatever you do will be insignificant, but it is very important that you do it!" —Mahatma Gandhi

bgood said...

Thanks for the very inspirational and uplifting comments ;).

I will bear them in mind as I think about my next steps - either deeper into or out of academia. Something tells me I like building things too much to ever truly be a 'real' scientist...

Pedro Beltrão said...

Good tool builders are also on the leading edge. Even those that promote open source still have the competitive advantage of understanding the tools better than everyone else. Examples of great tool builders doing great research include Sean Eddy, Ewan Birney and David Baker.