Slashdot Mirror

← Back to Stories (view on slashdot.org)

Open Source And Genetics

Posted by Hemos on from the young-einstein-should-be-part-of-this dept.

UnanimousCoward writes "SFGate has an article about some researchers pushing for the open sourcing of genetic research software. Of course, the pros and cons are debated." It's the age-old debate; what follows the heart of the scientific method more? Peer review, or getting the information out as fast as possible?

9 of 81 comments (clear)

  1. for dummies... by vinnythenose · · Score: 2, Insightful

    If it gets open sourced can we expect to find a book on our bookshelves titled "Genetic Engineering for Dummies..." and "Learn Genetic Engineering in 21 days"?

    --
    --- I used to moderate, then I read the -1 articles and decided having to filter through them was not worth it.
  2. Redundancy... by metlin · · Score: 3, Insightful

    Despite all the arguments favouring IP rights et al, I'd say that most of the research has to be open-sourced, so to speak.

    There is no point in re-inventing the wheel. It becomes ridiculous when 10 different companies engage in enormous investments independently on 10 different projects, when they could have all done 10 different projects to begin with.

    IP has it's own say, no doubt, but over doing it leads to commercialization of science, and defeats it's very purpose. Engaged in silly patent and copyright wars, we have no doubt postponed many a useful invention by at least a few decades, IMHO.

    1. Re:Redundancy... by Anonymous Coward · · Score: 2, Insightful

      I think IP rights HELP the dissemination of knowledge.

      As you mentioned, property rights (basically the right to exclude others from making using or selling your property) in knowledge does seem at first to be a problem. Everyone should be allowed to benefit, and widespread knowledge leads to more discoveries using that knowledge.

      But unfortunately, today lots of "knowledge" comes at a high investment cost. To get many of the products we want, we have to let the maker get a little money out of the deal. So we grant them propety rights and tell them they can profit exclusively from this idea for a finite period of time, both to recoup investment they made (which beefitted us all but which the maker alone paid for) and to profit (to create incentive for the maker to make more useful things in the future).

      In fact, granting IP rights allows inventors, etc. to publish their ideas when they often would be forced to keep them secret for fear of others appropriating their ideas. The vast majority of trade secrets are ideas that do not meet the threshold for patent protection. So the only way the maker can protect it is to keep it secret.

    2. Re:Redundancy... by Anonymous Coward · · Score: 1, Insightful

      no. most ideas are patent protected AND kept a trade secret. look at all the patents out there -- how many actually give the necessary info to duplicate the invention ? not many. and this is a BAD THING.

  3. open source of university researchers' code! by phranking · · Score: 3, Insightful

    Be more clear in the writeup: the subject of the article is a petition to open-source any code that results from federal grant money from reseachers in a university setting. It is *not* about open sourcing all bioinformatic software, everywhere. In other words, code developed in a private setting, independant of university grant money - who cares? (at least in this case). Alternatively, grad students who strike it rich on code they wrote while on the government dole? Open source *their* work, since it was already paid for by the taxpayers. I don't see anything wrong with this particular distinction.

  4. Re:Redundant? by Heem · · Score: 3, Insightful

    nono. Not essentially. its the same article. word for word.
    However, I'm glad it got posted again, for I missed the first posting of it, and I work for a biotech company. I don't know how the programmers in my company feel about this, but I tend to agree with Brenner in that it should be kept open-source. Of course, the size of my paycheck may depend on it costing an arm and a leg.

    --
    Don't Tread on Me
  5. Re:Scientific Method by Bikku · · Score: 2, Insightful
    Hear, hear.

    Speed is of no interest wrt scientific objectives (although it may be of some value in engineering - the application of scientific knowledge for practical benefit). The biggest problem in trying to figure out how the world works, and get some reliable "knowledge", is that nature is extremely subtle and we humans are very good at fooling ourselves into believing our latest theories are actually true descriptions of nature. Hence the rigorous insistence on peer review as just one more mechanism to try to ensure researchers are not inadvertently deluding themselves.

    I can't understand why anyone would think "It's the age-old debate". Seems crystal clear to me that the value of science as a method of generating knowledge lies in not making errors (and does not lie in making errors quickly).

    Re-read The Feynman Lectures for a refresher on this?

  6. Advantages of open source scientific software. by rice_burners_suck · · Score: 3, Insightful

    *O*H***W*E*L*L*

    Software for research in genetics, biology, fluid dynamics, astronomy and any other subject that requires such colossal amounts of computations should, in my opinion, be open sourced. This way, several things can take place:

    • While some folks are using the software, others can optimize it for increased speed. One of the things that bothers me when I read about some great new supercomputer is wondering how many of those bajillion cycles per second goes to waste because of nonoptimal computation loops. A small change here will make a large difference in the amount of time it take to achieve results.
    • The software can by analysed and broken up into distributed programs which can be run on millions of computers worldwide, a la SETI@home.
    • Distributed programs can be analysed and combined into one monolithic program that runs on a supercomputer.
    • Scientists (or programmers) can add features to these programs, making them perform multiple similar purposes. Or, scientists can pick out a specific computation that they need done on huge amounts of data, and save countless hours, days, or even months that would have been spent computing unnecessary data.

    Well, you get the picture. All of this becomes incredibly expensive with closed source software. Of course, nobody said it has to be free software. Obtaining the source code could very well require an NDA, if that's what will float the developer's boat.

    *O*H***W*E*L*L*

  7. But science is open-source by DaoudaW · · Score: 3, Insightful

    Unlike scientists who keep research secret until it is published in a peer-review journal, some software developers -- who get little credit when their code leads to a genetic breakthrough -- want to share their work as soon as it leaves their keyboards.

    It's an old debate in the world of computing -- and a new culture clash in bioinformatics...

    It seems like there is some confusion here. Sure there is some time-lag between the research and its publication, but peer-reviewed journals are in fact similar to bugzilla.

    The problem being addressed by the petition isn't what is published in peer-reviewed journals, its what isn't being published. Making scientific techniques proprietary not only slows the advance of science, but takes technology which could benefit the public and allows a few people to benefit disproportionate to their contribution.