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Open-Source Biology
nicholast writes with this "article describing the growing use of open-source collaboration methods in biology. The subtitle and main question is: Can a band of biologists who share data freely out-innovate the corporate researchers who hoard it?"
I'm all for the free flow of information, expecially in science. But if there isn't an opertunity to make bundles of money, where is the funding going to come from? Government grants only go so far, after all.
Personally, I think that corperate funded science is a must...though I'm glad to see that some scientists are freely sharing information. The best way to do science is to combine both (which will never happen) and show corperations that they can get rich even when they share their data.
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http://nemilar.net - Not your grandmother's soup kitchen
For instance, we're doing an open source phylogenetic project called The Tree of Life, which promotes both the open access to phylogenetic information, and open source software through the code itself. Many biologists are using open source software to further their research - case in point in O'Reilly's recent Bioinformatics conference.
"What we have here, is a failure to communicate." - Cool Hand Luke
"The subtitle and main question is: Can a band of biologists who share data freely out-innovate the corporate researchers who hoard it?"
Answer: No, certainly not. That will never work. Why do you ask such silly questions?
Sincerely,
NiftyNews
Automated Response Unit for Data-Hoarding Corporate Researchers, Inc.
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especially when studying the
(drumroll please)
female anatomy.
Seriously folks, I don't want to read about sharing and caring groups of biology folks working together for a the betterment of mankind. I mean, it's nice and all but against companies with bottomless pockets they are hopelessly out gunned.
What I really want is for greedy out the ass corporations to start cloning dinosaurs and creating new kinds of pets like squirrels with four asses.
That and some kind of new food that's blue. Ever notice there isn't any naturally occurring blue food? Don't say Blueberries cause the darned things are really just purple.
Appended to the end of comments you post. 120 chars.
As a scientist involved in a largescale database (www.pbdb.org) that is trying to build a large collaborative project I can say a couple of things about my experience.
1. Working in groups can be very difficult... i.e., when people don't share the same priorities, or see the same sources of bias as important.
2. It can be very helpful... often times getting other people's perspective is very informative. Generally in science we get feedback at the end (publication review), but here it happens at all stages, including data collection. This is really good.
3. People tend to start off thinking that they need to protect and hide data, but once they start to share data they tend to become big fans of sharing data.
4. Data transparency is essential to good science, these type of projects make that more and more possible. It does not take people long to realize how useful it is to have open and easily excessible data.
5. It is very important to open code used in analyses. I am in the process of working on a couple of papers where we have written some code to perform some fairly complex calculations. While I would like to say I am a great programmer, reality has a way of intruding. Collaboration has vastly improved the code, and I fully intend to post the code when I am finished with it. (for fear of being slashdoted I will not post the URL here).
Can a band of biologists who share data freely out-innovate the corporate researchers who hoard it?"
Competition is sometimes relevant, but not in general. The scientist seeks to further the knowledge base, to reinforce his hypotheses, and their sub-hypotheses, etc. The corporation wants to make money.
Now, the scientist, in his quest to further knowledge, has no responsibility to avoid the intellectual property of others. If something is copyrighted, he cites it. If something is patented, he uses it anyway for research, with no necessity to pay to use the patent (unless, of course, there is no other way to get the invention).
The corporation, in its quest to make more money, need not even establish that something will work before it can establish IP. Knowledge is not directly relevant - they only need to set up tolls on the highway to commerce in the form of patents and copyright.
Sometimes, conflict exists. Celera is patenting genes, but only if they find them before NIH (which makes their database public). But in general the goals are different, patents can come from the work of scientists without interfering in the future work of the scientist (it is important to avoid conflicts of interest, usually by the scientist having no control or material interest in patent licensing - this is often not the case), and corporations establish their tolls without even paying attention to knowledge.
"question is: Can a band of biologists who share data freely out-innovate the corporate researchers who hoard it?"
Unless this isn't 'biology' the human genome project has already succeeded in beating out a private commercial project with the human genome map.
Adults are obsolete children. - Dr. Seuss
Indeed. I'm an undergrad doing ecology research with computers. The Bio* (bioperl, biolisp, &c) projects have nothing to do with a lot of other branches of biology and bioinformatics. Perhaps they should all just rename their projects to genetic* (geneticperl, &c).
At least some of bioinformatics stuff (eg bioperl) includes some phylogeny stuff. Or, so I was told by someone on #bioinformatics on OPN.
Working toward a usable PDA environment in the spirit of Newton OS: Dynapad
Two points:
1) The idea of sharing information within and beyond the scientific community is hardly a new one. On the contrary, if anything secrecy has increased in recent decades, partly because of industrial applications but mostly becuase science is much bigger and more cutthroat than when it was a wealthy gentleman's pursuit.
The sort of collaboration described here is new and is driven by the Internet and by the large data sets in current biology. But to say that scientists got the idea to share information from Linus Torvalds is idiotic. That's not even where computer scientists got the idea.
2) Claiming that patents encourage "hoarding" of information is the sort of thing you expect to see in +1 Slashdot comments. The whole point of patents is to _encourage_ the sharing of information instead of relying on secrecy. Inventors trade disclosure for a temporary monopoly.
Again, there's a germ of truth here that companies after a patentable discovery need to be closed-mouthed about their progress, but that's probably given the author too much credit.
What I'm listening to now on Pandora...
I agree. "Open Source" in biology is more the rule than the exception.l I have been astounded by the FREE resources out there available for anyone to use! Databases like Genbank and Swiss-Prot are invaluable to modern molecular work. Pedro's Biomolecular Tools is just a sample of the plethora of free resources available today.
Incidentally, I can't recommend Ensembl highly enough. Not only have I been able to significantly further my research with their tools, but they have open-sourced the entire code behind their site! And the documentation is even in Wiki! I really think what they have done is incredible and should be one of the first projects anyone mentions when expounding the virtues of open-source software as well as sharing information in the field of Biology.
-Ryan
"fist in the air in the land of hypocrisy"
I agree with you that the point of patents is to promote disclosure in return for a limited monopoly. The problem is that because of the running time of the monopoly (about 10-15 yrs for a drug, because the first 5-10 years deals with the approval process), the patents will be left until the last moment.
The other issue is the non end-use related patents. Large companies can swap licenses on this but smaller companies and the third-world need to carefully avoid the intermediate steps that have been patented.
Again you are right that the Open Source movement is a bit of a Johnnie-Come-Lately as regards disclosure, but the use of copyleft is something that has come from the computer field and has given vast leverage to developers. You are right about the purpose of patents, but essentially they have become a way of sowing a legal minefield in a competitor's path.