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Saturday, February 02, 2013

A Great Rant

I tend to enjoy what some refer to as "rants". I think this spirited dialogue posted on the "In the Pipeline" blog yesterday was most enjoyable.
I’m leaving bioinformatics to go work at a software company with more technically ept people and for a lot more money. This seems like an opportune time to set forth my accumulated wisdom and thoughts on bioinformatics.
My attitude towards the subject after all my work in it can probably be best summarized thus: “Fuck you, bioinformatics. Eat shit and die.”
 One commenter had this to say:

When someone finds fault with the way a field conducts itself, I would implore them to constructively influence that field. You might be surprised how many are actually sympathetic to your concerns. 
I'm not dismissing this author's concerns: to do that would really require knowing the molecular biology field (which is more than sequencing, it turns out). I do neuroscience right now, and programming can be a problem for some. But a constructive suggestion to change can have much more impact than a long rant.

This "long rant" was chock full of interesting ideas. The human genome project was not a science project, for example. Good science require an understanding of the limitations of ones tools. That is good stuff. This was a rant, devoid of mitigated speech. Notice how quickly the lack of mitigated speech became the topic of discussion for the commenter. He did not dismiss the author's concerns, nor did he have anything constructive to say about those concerns. What was at issue for the commenter was the rant.

Here at the CCS we feel that the rant was fun. It was real, written with obvious passion, and spot on. We too spent a short period of time at a bioinformatics company called Protein Pathways. Garbage in, garbage out. Our competitor, Rosetta, beat us to a buy-out from Merck. Neither Rosetta nor Protein Pathways are in business today. The cargo never came.

If you were an investor, you could easily discard such rants, my entire blog included. To some, we are not offering constructive criticisms. But read with a critical eye, vitriol in italics, big picture idea underlined.
All the molecular biologists, devoid of skills beyond those of a laboratory technician, cried out for the mathematicians and programmers to magically extract science from their mountain of shitty results.
The big picture idea here is straight out of the Cargo Cult Science speech from Feynman:

Now it behooves me, of course, to tell you what they're missing. But it would be just about as difficult to explain to the South Sea Islanders how they have to arrange things so that they get some wealth in their system.

"extract science from their mountain of shitty results"

"get some wealth in their system"

This is what it is all about. This blog and the numerous rants all focus on this area. Sure we are angry. We want to explain, using our education and experience at your Cargo Cults, what you are missing. We want to point out why there is no wealth in your system, nor your investors bank accounts. But it is as difficult as explaining to the South Sea Islanders how to arrange things.

Good job Fred Ross. You are an official ex-tribesman of the Cargo Cults of Biotechnology.


Anonymous said...

Michael Gruber. "Map the Genome, Hack the Genome". Wired, Oct.1997, pp. 152-156, 194-198.

a link to 18-year old prescient article about a genome conference in Santa Fe by Seattle writer Michael Gruber.

Anonymous said...

ps Gruber's article was about the event: "After the Genome 2: Towards a Predictive Functional Genomics" Conference/November 9-13, 1996, Santa Fe, NM".
( through the hype Gruber saw the field as ignorant greedy conquistadorial exploration )