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Open-Source Biology 122

Posted by timothy
from the sharing-knowledge dept.
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?"
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Open-Source Biology

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  • Sources of funding (Score:3, Insightful)

    by jonman_d (465049) <nemilar@optoDEBIANnline.net minus distro> on Wednesday July 10, 2002 @01:42PM (#3858831) Homepage Journal
    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.
    • Most biology is colloborative to a pretty high degree. Places pay for pertinent research and they pay for a well selected team if money exists, then those on the team have their own alliances to rely on etc... so normally there are several names to a project. I used to work in a USDA lab doing little piggy behaviour research at a NW Indiana University we worked with Drs from Pennsylvania on that project. Opening it further would be of significant value to the world but taking competition ouot would be detrimental to their paychecks I think... Karl
    • Open-source biology will never appear to the outsider to be outpacing 'closed-source' ones, because the closed-source ones will quickly absorb any information presented to them and create a derivative product. After which they will market the hell out of it.
  • 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.
    • I had the same notion. But then reconsidered a bit after reading a post further down. The "closed" scientific group will never benefit from an open review of their modifications. This could send them down the wrong tracks for long periods. IN the OSS movement it is the equivalent of the group debug session. Simply stated there is value to the giver in sharing knowledge openly.
      • That is true, to an extent. Corporations do have a peer review system, but it is nowhere near as elaborate as what you have in the "open" community. They have networks of collaborators that have signed nondisclosure agreements that review proposals and research, and this does give them a degree if peer review. It pales in comparison, however, with presenting your project at an international conference in a focus group of dozens of the top minds in your field. One weekend at one of these can alter the whole course of your research, show whole new avenues to pursue, and open you to things that had never before even crossed your mind.
  • by jfrumkin (97854) on Wednesday July 10, 2002 @01:44PM (#3858854) Homepage
    For instance, we're doing an open source phylogenetic project called The Tree of Life [tolweb.org], 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.
    • 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.
  • Answer (Score:4, Funny)

    by NiftyNews (537829) on Wednesday July 10, 2002 @01:46PM (#3858871) Homepage
    "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.

    • Corporations are patenting human genes as they find them, without even knowing what they do. Hence, any gene-related answers found by "open source" methods of research are pretty much screwed if theres a related patent. Just take a look at this [theregister.co.uk] for an example of how that method of profiteering already works, albeit for M$ vs OpenGL.

      You know, I'm pretty sure I heard an American (!!!) president say something to the tune of "The human genome belongs to the human race!"... Hmmm, nevermind.

      Ali

    • 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.
  • "No dear, I'm not having an affair with my secretary! It's... open source biology!"
  • by unformed (225214) on Wednesday July 10, 2002 @01:49PM (#3858909)
    especially when studying the

    (drumroll please)

    female anatomy.
    • Most medical schools do use cadavers for studies of human anatomy. An open cadaver would allow the proto-doctors to study placement and composition of human tissues and organs in as close to a real, live patient as one can get without endangering a life.

      If you meant that you wanted your high school introductory biology class to cut open live women so the you could look at a fallopian tube, you are all kinds of sick.

      If you wanted to stare in non-comprehension at a naked female in class, you would have been better off with a figure studies class. Those are art classes, FYI.
  • by JudgeFurious (455868) on Wednesday July 10, 2002 @01:50PM (#3858913)
    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.
    • While I'd love to see more blue foods, I'd be content with a personal blue slushee machine. Ah, to be back at my alma mater [hmc.edu], with the blue slushee machine in the dining hall...

      Some of my favorite recipies:

      • blue slushee + sprite or similar = sparkling blue slushee
      • blue slushee + cranberry juice = red and blue parfait-style beverage
      • blue slushee + orange soda = "swamp water"
      • 9:1 chocolate milk:blue slushee = raspberry-chocolate milkshake (sorta)

      -Greg "C'mon, try it! It's really good!" Mulert

    • what about really cold raw chicken?
      • But it's nature is not to be blue. It's "normally" for the sake of argument a different color and so unless a certain number of circumstances were met then it would be disallowed by the judges.

        If it was rendered cold and thus turned blue naturally then you are still in the game however if it had to become so cold that it was rendered un-eatable in order to get the color than it would be hard to consider it food. Artifically making it cold enough to turn blue would put it the same catagory as a multitude of man-made blue foods that are all better tasting and more palatable than cold raw chicken.

        It could be chicken-sickle on a stick I guess.
    • Don't say Blueberries cause the darned things are really just purple.
      These blueberries look pretty blue. Blue berries [ismennt.is]
  • Back when it was possible to read all the journals relating to a particular field cover to cover, it made sense for scientific dscoveries to be published in journals. Now, however, there is just too much data out there and what is needed is a curated (by online volunteers) heirarchichal database. From the article, it sounds like Gilman is doing just that. I wouldn't be surprised if scientific journals become obsolete in the next 20 years.
    • Been there, done that.

      PubMed [nih.gov]

      • My impression was that PubMed was a database of journal articles rather than a database of the data itself.

        Along those lines, I suspect that an equally important factor preventing "open source biology" will be the policy of scientific journals to not publish that has been "published" previously. That is, if you contribute your data to an open source database, you may not then be able to publish it.

        • PubMed is just part of the database. I should have labeled it more properly, it's really NCBI (National Center for Biotechnology Information). IT consists of BLAST , GENBANK, PubMed , OMIM , Entrez, taxonomy information, and structural databases. You can also link out to more specialized databases from NCBI. Some of these are incredible; you can find out (for example) all that is known about tissue distribution of protein X. Or all gene products found in, say, the kidney. Or the cortex of the kidney. Or the distal tubule.

          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.

  • Can a band of biologists who share data freely out-innovate the corporate researchers who hoard it?

    Ron Jeremy doesnt hoarde his biologly and hes as successful as they come... Ohhh Scientists... well Ron was a school teacher before he became a star, maybe he was a biologly teacher.
  • 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.....
  • ...in the long run.

    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.

  • 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.
    • 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.

      How is this different from any other science. I mean, in physics, there's lots of papers out there that will eventually be shown to be wrong. That's how science is supposed to work.

      It's a shame that biology has become so profitable. Hoarding data and discoveries is not how science advances. The history of chemsitry and physics are ample illustrations of that fact.

      • 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.

        How is this different from any other science. I mean, in physics, there's lots of papers out there that will eventually be shown to be wrong. That's how science is supposed to work.
        Agreed. However it's not so much that people don't want to publish things that will be disproven as it is that they don't want to publish negative data. This is a real problem as the above poster points out. If you have 3 or 4 labs pursuing the same project, you could end up with them all pursuing the same dead end leads wasting years of work and hundreds of thousands of public research dollars. If on the other hand, the first group to get those negative results had published them (and part of the problem is that there isn't really anywhere to publish negative results) then that group would have had another publication on their collective roster and the other groups could have avoided wasting time on money on this line of investigation.
        It's a shame that biology has become so profitable. Hoarding data and discoveries is not how science advances. The history of chemsitry and physics are ample illustrations of that fact.
        FWIW there is still plenty of sharing going on in biology. The genome projects (human, mouse, yeast and others) are good examples of that. Sure, there's the private, Celera stuff out there but the public projects at NIH-NCBI [nih.gov] and EBI-Ensembl [ensembl.org] are excellent examples of those.

        E
        • 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 [expasy.ch] are invaluable to modern molecular work. Pedro's Biomolecular Tools [iastate.edu] is just a sample of the plethora of free resources available today.

          Incidentally, I can't recommend Ensembl [ensembl.org] 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 [wiki.org]! 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
  • by mkoz (323688) on Wednesday July 10, 2002 @01:57PM (#3858977)
    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).
  • Although to control the knowledge is an extreme source of power, we must remember there is a plethera of unfound, hidden talents and ideas out there. Corporate research is bound by the limits of their budgets, organization, internal abilities, etc... Where open research has many advantages, such as being able to slip into research projects with universities, possibly coming across some great innovations that would have otherwise remained hidden. I would equate it to mining and processing. When your mining, you may get lucky and strike it rich. When your processing, your rather constant and steady. It does have interesting aspects though!
  • by blakestah (91866) <blakestah@gmail.com> on Wednesday July 10, 2002 @02:02PM (#3859017) Homepage
    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.
  • by IQ (14453) on Wednesday July 10, 2002 @02:05PM (#3859035)
    "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.

    • Unless this isn't 'biology' the human genome project has already succeeded in beating out a private commercial project with the human genome map.

      This is not true for a number of reasons:
      • The completed human sequence was available from a company called Celera, months before the public 'open-source' version was. You had to pay for it.
      • The public and private version were published back-to-back (at the same time in the same journals). Celera had to put a lot of effort to get it published, because the 'public' guys wanted to keep them out (clear case of academic ego & envy - nothing to do with the good of humanity).
      • The quality (and therefore usability) of the public version is still below that of the private version. The high quality public version is expected to be announced in May 2003.
      • Without the private version to stress the academic guys, they would probably still be debating about which method to use for sequencing (trust me, I know most of them). The threat from a private club, made them do it (by copying the methods, Celera used.)
      I'm not saying that private companies should own data and methods. All I'm saying is that sometimes some good old competition, can help to accomplish research goals.

      The company in this case, should get the credit they deserve for the innovative methods and their application to this enormous problem to get the first completed, high quality human genome version in such a short period of time.
      • The company in this case, should get the credit they deserve for the innovative methods and their application to this enormous problem to get the first completed, high quality human genome version in such a short period of time.

        And they definitely should get the credit for doing all their own sequencing and not using any of the GenBank data...except, well, they didn't.

        The "genome race" was never a race, because you can't have a race where one side can never win (Celera could use the Human Genome Project's data as well as their own) but also could not lose (since the real goal was to guarantee a freely available version of the genome).

      • "The completed human sequence was available from a company called Celera"

        And was based on the publically available version.

        "the quality (and therefore usability) of the public version is still below that of the private version."

        Ditto.

        "Without the private version to stress the academic guys, "

        This is the "academics can never do anything" argument, and its a fallacy. The public effort has still produced more sequence than the private.

        "All I'm saying is that sometimes some good old competition, can help to accomplish research goals."

        Celera did force the pace and this was no bad thing. But competition is not unique to the private sector, its present in academia as well.

        "The company in this case, should get the credit they deserve for the innovative methods"

        Indeed. Celera's main innovation was their generation of the best techniques for contig assembly, and their techniques still outstrip those publically available. Of course most of the work for this was done in the public sector, so the public/private argument is somewhat fallacious. But producing data which is not freely accessible is of limited value. Nature is complex enough without adding lawyers into the mix.

        Phil

  • I'm announcing a new project, ADAM 2.0. Think of it as GNOME, but taller. I'll need a team of designers, developers, and unit testers. Recombinant DNA experience a plus. Naturally, I'll be team leader - don't all team leaders (open source and otherwise) think they're God anyway?

    The only thing that worries me is the six day schedule to ship...

    • I'm announcing a new project, ADAM 2.0.

      I'm sorry, but as the father to one Adam Lewis Remy, I'm afraid you are infringing on my trademark.

      You have 30 days to alter the name to something that will not be confusing to any person in the human race, or I will sic my battalion of trained attack weas^H^H^H^Hlawyers on you.

  • Keywords (Score:2, Interesting)

    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.

  • by sheepab (461960)
    Does that mean my brain is GPL'ed?
  • 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.
    • It takes a lot of funding to make data more open. For instance, the Murray Center at Radcliffe [radcliffe.edu] does an incredible job of making social science data, collected by primary researchers who had the funding, available to other researchers. But it takes lots of moolah to archive the data, make it available to students and researchers, preserve the original docuements, maintain permissions, etc.

      In economics, the scientific standard of replicability of results has made people more willing to share their data for that purpose. (Happened much later in econ than in natural and physical sciences) But it is a long way from open source.

      So how do we pay for it?

      • Who pays for open source software? For the most part, noone: the effort is supported largely by those who WANT to make it work. Support of course is provided for a fee; some things will always require payment. I believe the same thing would be possible in most areas of science, if only it weren't illegal to make copyrighted data available at will.

        Replicability of results is one issue. But this is really a technical issue; the real questions of interest are: how do your findings fair out of sample, and how does to exact same data look under different analytical methodologies?

        Yes, you are correct, some journals and other institutions do endevour to make data publicly available, but only some (Review of Financial Studies is the only journal I can recall at the moment).

        How do we pay for it? I don't think people would have a problem with providing funding for efforts to make data open source, but US$25,000 per year for one database is just way too much for some universities.
  • by Otter (3800) on Wednesday July 10, 2002 @02:18PM (#3859131) Journal
    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.

    • I disagree with your first point. Although some areas of commercial science may be increasingly cutthroat, in the academic- and philanthropic-funded world of research, sharing has increased tremendously because science _is_ too "big", or rather too tremendously detailed and complicated. There's no way that any one group could collect all the data needed, even in very specific areas; only by partitioning the work can the researchers hope to make significant discoveries.
    • Otter,

      regarding your first point, of course it's true that science had an ethic of sharing before software. In the first draft, there were several paragraphs explaining the role in distributing information that scientists such as Nicolas Peiresc played in the 17th century and noting that RMS was originally inspired by scientific ethics. See the middle of this for his clearest explanation http://www.gnu.org/philosophy/shouldbefree.html.

      I cut that out because it seemed obvious, the Einstein quote gives some context, and it's really important and challenging not to bore peoeple writing about science in a political magazine. Maybe that was an editing mistake. But I certainly don't disagree with you or think that Linus influenced Einstein.

      WRT your second point, as you surely know patents have a mixed impact on sharing. They do allow more information to get into the public domain, but they also allow for hoarding and blocking other research (see the Costa Rican rice example). I certainly don't think that they are entirely nefarious. My contention is simply that the overall trend is clearly going in the wrong direction (the lack of sharing amond geneticists is the clearest evidence) and that overuse of patents, particularly upstream patents, makes the problem worse.

    • Shall we say that certain parts of the industry, particularly those relation to pharmaceuticals have been a little too fond of hot money. Some academics like to have one foot at the University whilst the other is at a professional lab, tending to reduce the quality of 'open' work.

      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.

  • In order for the use of this product, you must agree to the following terms.

    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!]

  • Check out the Linux for Biotechnology cdrom at www.randomfactory.com [randomfactory.com]
  • 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
  • Most of the non-commercial science (including biology) has been done according to this 'open-source' model since eons ego. It has always been the cycle: read publicly available papers on a given topic - do something new - publish results in a publicly available, peer reviewed journal.
  • Get open source bioinformatics tools from:
    bioinformatics.org [bioinformatics.org]
    bioperl.org [bioperl.org]
    biojava.org [biojava.org]
    and even www.cvbig.org [cvbig.org] for a talk on bioinformatics with PHP/Ming
  • 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
  • Many scientists are the corporate powers who hoarde the innovations. Often when one comes up with a good idea they publish, claim a conflict of interest and get out of the Universities.
  • 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.
  • Open-sourcing scientific data can be great for science, although it needs protocals and conventions to be workable.

    For example, it is common in my field (oceanography) that funding agencies require that data be shared openly, but only after the original investigator has had a certain amount of time to work with the data and to publish findings.

    It makes sense to give the data originator "first dibs" on the data because

    • The data originator is probably the person most able/interested to leverage the data into a scientific result (commonly, a peer-reviewed publication).
    • Denying the originator a first chance at publication thwarts the funding/promotion processes, and thus can cause problems in getting personnel to do the science.
    • Better science often results if the data originator has some time to think deeply about the data, without rushing to publish before others do so.

    However, it's often the case that there is information in the data that the originator had not thought of, or that becomes clear only by integrating the data with the results of other investigations. That's why open sharing is crucial. Indeed, we would know very little about the state of the ocean, and of the climate system, without open sharing according to established "publish, then share" principles.

    PS: throughout the above, please take "data" to mean either the results of measurement or the results of calculation.

    Dan Kelley, Dalhousie University, Halifax, NS, Canada.

Little known fact about Middle Earth: The Hobbits had a very sophisticated computer network! It was a Tolkien Ring...

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