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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.
--
http://nemilar.net - Not your grandmother's soup kitchen
Think about it. One group shares information, one group doesn't. So, the group that doesn't share takes information from the group that does, and *boom*, automatically one group knows more. It's a nice idea though.
Condemnant quod non intellegunt.
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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"No dear, I'm not having an affair with my secretary! It's... open source biology!"
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.
The subtitle and main question is: Can a band of biologists who share data freely out-innovate the corporate researchers who hoard it?"
Who says you won't be able to have your very own clone of yourself someday? Now if we could just get some of the other fields to go this route, we could make our own antibiotics at home, have a horde of clone slaves, and power our houses with cold fusion reactors.....
I Am My Own Worst Enemy
I work in the power industry. While we do not necessarily share our source code outright (well, no one has asked), we share data like crazy. We don't hoard it because it wouldn't make sense. Our matrices and equations and system solving methods HAVE to be shared with our clients so they can ensure that we're actually giving them something that does what they think it does. Does this mean that other people are going around doing what we do? Not really, because we do it better.
If you are really good at something, other people aren't going to bother trying to do what you do because it's not worth the trouble. Just like the way I paid for someone to move my piano today. I could have gotten a bunch of friends together to do it and rented a dolly and truck, but that took way too much effort.
Convenience, much like advancements in science are going to benefit everyone. Someday, everyone who doesn't add value to society in some way is going to operate on the fringe (well, they already do to some extent), and all information will be shared for the greater good of all. If we collaborate with other industry leaders to come up with new features for our software or to help our clients do things better, it will always benefit us in the long run. The same will be true for the biologists and eventually corporations will get a clue as well.
Liora
Not if the corporate researchers have access to the open work too. You would need a group of researchers who share information only amongst themselves, but then it wouldn't be "open research".
One reason why this won't work, is that researchers depend on their discoveries in order to write papers and grants, which gives them more money to make more discoveries. If a small lab of a few people were to share all their information, then right before completion a huge corporation comes in and takes all credit, then that little lab is screwed.
Another problem is that researchers can go months, even years on wrong information, and theories. If these were published, yes theres a possibility they could be discounted, but they could be perpetuated, with lots of wrong data all over the place.
Finally, there is alot of information being shared within the biomedical industry. Many experiments are based on those found in published papers, there are guest speakers bi-weekly telling people about their successful research and we can take that information and test it, or we can tell them we have found that method doesn't work.
I believe that adding an extra layer of communication would further cloud things.
This
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
But it did make me think of one thing. All of the following are true:
Research is hard
Experiments aren't cheap
Many excellent biologists will hoard their work out of enlightened self interest. There will of course be individuals who see farther than that.
Some of those embracing the open source idea in this area (and anywhere an approach like that is used) will be riding coat tails and merely opportunistic. There will of course be a greater number of these men and women who are genuine in their desire to collaborate regardless of their abilities.
The real opportunity for something exceptional to come of this is when someone who IS better than his peers at what he does shares what he has with those other biologists.
Then you have a chance for one or more of those people to see that information from a different perspective and that's when the benefits are going to be obvious. It's a more optimistic take but I think in this case it's also more realistic as well.
Appended to the end of comments you post. 120 chars.
Whooops. I forgot to mention what Free/Open Source Software I use. The open source software I use for ecology research is: a lot of custom software in Squeak Smalltalk (including a dataset visualizer), CLISP Common Lisp, perl, and gnuplot. On top of Linux sometimes even.
Working toward a usable PDA environment in the spirit of Newton OS: Dynapad
The only thing that worries me is the six day schedule to ship...
"Prepare for the worst - hope for the best."
Is it just me, or does getting to the front page of Slashdot involve adding certain statements to articles.
"And that's what I think about Australian jumping elephants... oh and:
Linux, Open Source, and Microsoft Sucks"
"Open Source" science was practiced long before "Open Source" programming. In fact, it was the rule, rather than the exception until just recently. Bonding science to the corporate marketplace, while extremely profitable, also leads to a great deal of "Re-inventing the wheel". Hopefully this is the beginning of a trend back toward a detached scientific community.
With my dying breath, I curse Zoidberg!
The open source model is something I readily dream about in finance research. The greatest proportion of papers published in journals come from universities with big reputations, not because of there being smarter people at Havard, for example, although to a certain extent that's true, but because of the amount of money they are free to spend on data, and the amount they already have, whereas smaller, lesser known universities, with never-the-less, a capacity for valuable output must scrape the bottom of the barrel just to get enough data for a decent conference paper.
I think there is a sort of un-uttered agreement that the journal review process exists, and that data is kept tightly protected because the establishment ensures proper quality of published output. In days gone by, perhaps that was a feasable approach, but with the advent of open source, and the thousands of developers forums throughout the web, I believe that finally there is a tangible example that argues for a complete overhaul in approach.
Despite the massive size and wide distribution of the community, there is still some, nay much, order to open source. There is some sort of consensus on the best distro, or the best app. for this or that. Reliable, secure and stable abound in open source; the bolts of excellent software are clear despite the storm. Open source has tipped arguments for the Cathederal, or a stuffy establishment that upholds integrity, on its head. The Bazaar works. People can be rewarded for the value of their output, and not their ability to horde.
In terms of a long term world view, I believe open information is the future in all areas of human endevour. How does a company create value by selling the same data, the same idea, a billion times. Let them be fairly recompensed for their effort in gathering the data, or putting the idea into a servicable form, and leave it at that.
Open source has demonstrated that the Bazaar is able to sort the elite from the mundane, and what's more, the volume and value of the output would not have been possible within a single closed establishment.
Oh, I wish, I wish, I wish that data and information was open. I wish that governments would legislate against data and idea hording; I believe such intervention passes the test of expediency. All hording does is hold back the ability of so many people to produce so much valuable output. This is the future for all important areas of human endevour if we ever want to make more of our precious progress before the earth is consumed by the sun.
I have much more to rant about, but you've probably stopped reading by now anyhow.
I have no sig
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...
1. GRANT OF LICENCE. $PERSON1, along with the cooperation of $DIETY (hereafter known as the GRANTOR) grants you, $PERSON2 (hereafter known as the GRANTEE) a non-exclusive, non-transferable licence to the GRANTOR's genetic material. GRANTEE accepts that she cannot tranfer the EULA to anyone without GRANTOR's concent.
2. RESTRICTIONS. The GRANTOR 0wnz j00. GRANTOR can change the licence at any time and can withhold all genetic material at any time without the GRANTEE's concent. The GRANTOR has all right. The GRANTEE has none. Amen.
3. LIMIT OF LIABILITY. THE GRANTOR TAKES NO GODDAMN REPONSIBLITY FOR ANYTHING. THE GRANTOR IS ALWAYS RIGHT WITH EVERYTHING AND ANYTHING. SHOULD YOU DISAGREE GO FUCK YOURSELF. IF THERE IS ANYTHING YOU WILL GET IS THE BURDEN OF RAISING ANY DERIVIATIVE OF THE GRANTOR'S AND GRANTEE'S GENETIC MATERIAL. OFFER VOID FOR EVIL DOERS AND ANYONE GRANTOR THINKS IS UNACCEPTABLE.
Do you agree to the licence terms? [I have no choice] [Screw you, I actually read the EULA!]
Karma whorin' since 1999
out innovate.
The purpose of a corporation is to create wealth for the shareholders. Wealth is created in markets. Corporations produce marketing first and foremost. People commonly confuse marketing with innovation. Just because a label says "New and Improved" or "Upgrade" doesn't represent a genuine innovation in the academic sense. To the consumer it is often enough to produce a sale and so it's a valuable corporate tool. But confusing this image of innovation with genuine innovation as the term is used in universities is foolish in the extreme.
Moreover, the patent strategies of major corporations, particularly since the formation of the pro-monopoly Court of Appeals of the Federal Circuit in 1982, has been to stifle innovation by staking a claim around a certain financially rewarding intellectual avenues by flooding those patent areas with patents to be used as offensive weapons. This is not innovation by any means although it involves applying for many patents which can be used to provide a false argument that such corporations are innovators when they are, in fact guided by financial and legal experts rather than technicians.
Almost all innovation takes place in schools and not by professors, but by their students. It has been this way all along and people who don't understand this can be forgiven because the history of education is a boring subject for many of today's youth. However, it is not mysterious by any means and the subtitle of the paper suggests the authors are uninformed at best.
It seems backwards to say that biology is copying the methodology of open-source. If anything, I thought that the open-source/free software movement was created to bring the openness of scientific research communities (in academia, at least) to computer programming.
Cheers,
IT
Power corrupts. PowerPoint corrupts absolutely.
Many excellent biologists will hoard their work out of enlightened self interest. There will of course be individuals who see farther than that.
;-)
One of the nice points of the current scientific system is that there's no (academic) reward for hiding your results or failing to disclose some special secret technique you invented. No results = no publication. No publication = no reputation. No reputation = no grant funding and no tenure, or at least inglorious obscurity if you're already tenured
Of course, once money is involved, there's a tendency to want to keep everything under wraps until it's patentable. And to be sure, often labs will withhold their data from competitors until it's been submitted to a journal. But that's only fair, and even competitors will usually cooperate on some level in "academic" science. I remember a friend saying how her lab and another lab agreed to publish their very similar papers in the same issue of a journal, so neither one was "scooped". As a result, they reinforced each others' credibility instead of fighting over it.
Freedom: "I won't!"
So the people who win Nobel Prizes are a primary source of most innovation? Is that right? It's not the millions of students filtering through the universities doing unpaid research under the guidance of people who may or may not have been rewarded Nobel Prizes that develop innovations, but rather the recipeints themselves posses a shamen like aura that produces a constant stream of this substance called "genius" that is then converted to innovation in these places called corporations.
Huh. Man, you must be one of these fucking geniuses.
There is also OVID, which is an online database of journals available at most universities. Not completely opensource, but for all practical purposes (at least from the perspective of the scientist), it is "open source" "policy of scientific journals to not publish that has been "published" previously"
Science literally changes hourly. There are things I thought were true on Monday, that I know are patently untrue today (seriously, specific things). There's no point in writing them down until you reach a reasonable degree of certainty. Publication is the last step before it leaves your hands entirely, it finalizes what you have say.
Presentation at conferences, retreats and workshops; poster sessions, informal review (passing your manuscript around to all of your buddies before publication), and the all important coffee room are what comprise the "open source" community of science for works in progress. Sharing prior to publication is like sharing prior to ever trying to compile your code. You'd look like an idiot.
There is a reason for everything. Sometimes that reason just sucks.
Get open source bioinformatics tools from:
bioinformatics.org
bioperl.org
biojava.org
and even www.cvbig.org for a talk on bioinformatics with PHP/Ming
First entomology, then virology, and finally bioinformatics systems. Bugs follow me wherever I go.
This title of the article seems to suggest that this is a contest to see who "wins", the open source guys or the secretive corporate guys. I just don't think that really matters.
The parallels to open source programming run rather deep. There are many advantages to open source software (or open data science). However, there will always be room for people to work on propriatary projects. Micro$oft currently co-exists with open source developers. There is room for both. Sure, they don't always get along, but that's another story.
The way I see it, every scientist builds upon the research of others. That's just how science works. The open sharing of data only serves to speed up that process. Ultimately, every scientific discovery will be "borrowed" by some other scientist down the line. So what if a company takes some of that data and uses it's additional monetary resources to turn the data into a pill that can cure a disease. The point is, science and mankind, benefit in the long run.
There is another side to this as well. Corporate research tends to be very focused on solving a specific problem or answering a specific question. While this type of scince is very valuable and necessary, there is another type of science. The kind where researches study a phenomenon just find out what's going on and how things work. Often this type of "basic research" uncovers answers to problems that previously seemed unrelated. It appears that open data sharing would help to promote this kind of "basic research".
Hmmm,
Well it might be Open Source, but it certainly doesn't seem to be accessable... Did a web search and was unable to find any website or other access to any information.
Lando
/* TODO: Spawn child process, interest child in technology, have child write a new sig */
While we're rallying for Open Sourced Biology (OSB) or Free Biology (FB) [which is good], why not rally for OPEN SOURCED TRANSPARENT CORPORATE OPERATIONS. This way, the Martha Stewarts and Gary Wennig's can't defraud their investors.
Also -- this one's nothing new -- how about transparancy in ICANN?
Ok, back to biology. Open Sourced Biology is nothing new: its as old as science itself. Back in the good old days, we didn't call it that becase it was just assumed. It was assumed that when something was discovered it would be shared with the world. Watson & Crick & Franklin made their findings available to the public for free upon the presumption that that information would be used to generate more information which would be freely dispersed, ad infinitum. Of course, now the scientific community is moving towards a proprietary model -- the dark side of the force, so to speak. But don't be fooled. The overwhelming majority of science is still transparent and "open sourced".
E-mail any professor at a university about the method they use for a particular protocol, or a finding they've found, and they'll more likely than not respond helpfully if they have time. Try e-mailing Celera on their protocols and see what you get.
You can see the parallels between the science world and the software world. Both started out completely open. Both migrated towards the proprietary closed model (in the case of software, almost completely). Now, both are having lash-back movements of evangelicism for transparency, open source, free software/biology, etc.
social sciences can never use experience to verify their statemen
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.