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Biotech Science

Open Source for Biotechnology 262

Posted by michael from the bug-report dept.
LarsWestergren writes "The Economist claims that Open Source is such a success for software development, the model should be used more often in areas such as biotechnology and bioinformatics. The similarity between open source and the academic process with their 'you share, I share' principles is shown by the human genome project. The paper argues that this process should be used for instance to developing medicines unburdened by patents, useful especially for third world countries or diseases that affect relatively few people, where medical corporations have previously thought that the cost of research have not been worth it."
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Open Source for Biotechnology More

Open Source for Biotechnology

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  • Open source and GPL (Score:5, Funny)

    by JosKarith ( 757063 ) on Friday June 11, 2004 @10:53AM (#9398439)
    I'd say that the human genome is fairly open source.
    Tho I can see Darl McShyster trying to claim that since everyone's DNA is 99.99% similar to his it must have been copied and we all need to buy $399 Life Licences...
    • I'd say that the human genome is fairly open source.

      Not really. It is true that the software is widely distributed (and packaged in a handy interpreter!)

      But it's rather aggressively copy-on-write; changes generally show up in the child rather than the parent

      There's even a government program to try to stamp out self-modifying code! [nih.gov]

      So: widely distributed, yes. "Open source": not hardly.

  • I am all for this (Score:5, Interesting)

    by Lord_Dweomer ( 648696 ) on Friday June 11, 2004 @10:54AM (#9398448) Homepage
    If biotech becomes really easy for consumers to use/create, similar to the manner of open source software, I think something like this could put a lot of power into the hands of the people.

    Which is probably why something like this will never be allowed to happen now that people have seen how successful open source is.

    • Re:I am all for this (Score:5, Insightful)

      by Stargoat ( 658863 ) <stargoat@gmail.com> on Friday June 11, 2004 @11:03AM (#9398548) Journal
      Open source nothing. To really understand how a human works takes more than four years of university level study. You need to understand the chemistry of drugs, and the biology of what does what. There is a process that takes years of research before a person even understands how drugs really work.

      And then you need to create the drug itself. That takes another many years of experimentation. And then you need years of clinical trials. Then a manufacturer needs to then be found.

      And someone would propose that drugs be created using an open source process? What would be the incentive of creating drugs or getting the education to do so? This isn't Linux, it's a complicated process of creating a drug for a human. Get it wrong, and your monitor refresh rate is off? No, people die. This is clearly just a pipe dream.

      • Re:I am all for this (Score:4, Funny)

        by Lehk228 ( 705449 ) on Friday June 11, 2004 @11:05AM (#9398569) Journal
        if by pipe dream you mean thought up while totally blasted, you are probably correct
      • You seem to have missed the point I was trying to make. One of the best things about open source software is that the really experienced coders, some of the best in the field, are the ones making the software. Sure there's all the crap out there as well, but people tend to be able to spot which is good and bad.

        The benefit is that for people who know next to nothing about coding, or don't want to code, are able to use the software completely free of charge and be able to modify it to suit their needs.

        This

        • You're saying a few good drug manufacturers, some of the best in the world, could make the drugs. And then people that know nothing about medication, or don't want to be involved in the drug creation process, could then use the drugs free of charge or mix the drugs as they see fit?

          No offense man, but that is fucking insane.

          My wife manages clinical trials and the amount of oversight is crazy. The hospital had to call her at 1:05 AM so she could approve a change in dosing a patient because the nurse was liter

          • Perhaps I need to clarify further. When people use software, often times they use it through a front end which takes care of the complex parts. I am not saying that I want people to be tinkering around with every single little detail of the stuff (although if they feel qualified they should be able to at their own risk), but if there were some sort of front end that could handle the complex tasks, and let people customize biotech to their needs with no risk (similar to selecting something from a drop down
          • 25 years ago one of the better business minds said the same things about the brightest coders in software. Go check out the open letter from Bill to the hobbiest coders. Software costs a ton of money, one wouldn't have expected the brightest minds there to just give a way their research for free. Bill Joy is arguably one of the biggest innovators in the software business, and most of his ideas (SPARC, vi, BSD TCP/IP stack, c shell, aruguably JAVA) have been free since he first thought them up. There are

            • Re:So let me make sure I have this right... (Score:2, Insightful)

              by Anonymous Coward
              Yeah, you know absolutely nothing about the biotech world. Biotech drugs can be enormously expensive to produce. Bioreactors to manufacture antibodies cost millions of dollars. Open source has worked because computers are cheap and easy to come by, bioreactors and various other machines (spectrophotometers, ELISA readers, etc.) are ungodly expensive. Suffice to say no lay person can afford to produce biotech drugs, so stop trying to draw a parallel that doesn't exist.
            • There are a tremendous number of parallels betweeen the drug industry and the software industry from a financial perspective. Both require signficant R&D to develop new products that then require almost no cost to produce (what chemicals go into drugs and how much do those cost).

              Absolutely not. The R&D costs for software development are almost entirely* for salary. That's why developers with commodity hardware and software at home, willing to code for free, can make significant contributions. Salar

              • To what extent would public universities be willing to foot the bill? After all if the drugs go into the public domain and people get cheap treatments, that is a direct benefit to society. It would seem to be in line with universities' mission. Whether funding boards, etc, etc, can be convinced to spend the money is of course another question entirely, but a few high-profile successes would probably bring them around.

        • Re:I am all for this (Score:3, Interesting)

          by Lehk228 ( 705449 )
          Modify it!? you can't just modify drugs, people will DIE, worst case scenario for bad software is CC# or SSN etc gets into the hands of criminals, who fuck things up for you for a while untill you get it sorted out, sucks ass? yea, but not even close to worst case scenario for bad drugs, SLOW PAINFUL DEATH
        • You seem to have missed the point I was trying to make. One of the best things about open source software is that the really experienced coders, some of the best in the field, are the ones making the software.

          I don't think you understand the vast differences between biotech and software.

          First, software development is cheap because the price of entry for the tools required is very low. That's why some Finnish hacker can write his own OS in his spare time.

          Biotech on the other hand requires lots of ex

      • Re:I am all for this (Score:2, Informative)

        by Anonymous Coward
        "And someone would propose that drugs be created using an open source process?"

        Do you have any idea how insanely difficult it is to make a pill? And that's the simplest delivery mechanism. Dosage and delivery isn't science it's black magic.

        Trust someone who actually does know... There are still plenty of really hard things about the manufacture and delivery of drugs. There's still plenty of room for big capitalist corporations to make dump-trucks full of money.
      • The real future of open source is not geeks, but institutions and big organizations who find it a viable business model.

        The bulk of Linux developers already work for Redhat, Suse, IBM, HP, OSDL and so on.

        If drug developement is ever to become a sustainable model it will be done by paid searchers in phamaceutic labs, because they will feel it's economically sound

      • Re:I am all for this (Score:2, Insightful)

        by tigersaw ( 665217 )
        To really understand how a human works takes more than four years of university level study.

        Maybe I missed something, but most people off the street would have no clue about how to code a linux kernel, much less keep their computers from being spam servers. And last time I checked, most programmers aren't exactly GED cases. Yes, years of CS training, while not requisite, are certainly the norm among the best code writers.

        What would be the incentive of creating drugs or getting the education to do so
      • I tihnk that the grandparent poster made a bad point by comparing software development to medicine, because in essence, it is completely different. While there is a lot of room to make mistakes in software developement, and the ability to learn though trial and error, the same is not true for mecidine, there is little, if any, margin for error.

        However, open source software is created by not just hobbyists and organizations of them, but also by corporations. Take MySQL AB, for example, their software devel

    • Re:I am all for this (Score:4, Interesting)

      by Derkec ( 463377 ) on Friday June 11, 2004 @11:05AM (#9398578)
      No. We don't want a lot of power in the hands of the people biotech wise. The less people who can make a highly infective deadly virus in the privacy of their own home, the happier I am.

      What we do want to see is greater openness and cooperation between academia, doctors, and biotech companies.

      Cheaper drugs good. Death and destruction bad.
      • You'e just described one of the arguments for censorship on the internet in regards to things like posting bomb building instructions. Do you believe censorship on the internet is a good thing?

      • Re:I am all for this (Score:3, Insightful)

        by b0r0din ( 304712 )
        I agree, I'm not Bill Joy preaching the end of the world but there's something to be said about guarding some secrets. All it takes is someone posting their new virus on the internet and 'open' sourcing it for some terrorist somewhere to start developing a really nasty world killer. I think the way it is currently is pretty scary, we've got people basically building new viruses without first understanding how to create a vaccine or drug or other remedy. And there seem to be a lot of people who want to play

    • Re:I am all for this (Score:5, Informative)

      by sTalking_Goat ( 670565 ) on Friday June 11, 2004 @11:32AM (#9398875) Homepage
      If biotech becomes really easy for consumers to use/create, similar to the manner of open source software, I think something like this could put a lot of power into the hands of the people.

      I don't see this happeneding. I work in Biotech. The cost of instrumentation alone is astounding. Its not like you can go out and setup a sequencing lab in your basement. An older model used Thermocycler will cost at least 10K, and thats on the low end of the instrumentataion scale. Even if you scratch build equipment yourself (which I've done) its still going to cost you, and try convincing peer reveiw or god forbid, Mr. FDA that your findings on non-validated equipment is worth anything...

      I'm all for open source but I don't see it getting very far in high-end Biotech.

    • Well, like everything, this is a complex issue. A lot of data is already "open". You can go to NCBI [nih.gov] and download the entire genome of SARS or Bacillius anthracis (Anthrax) if you so wish.

      Also, if you are creating bioinformatics tools on Federal funding (NFS, NIH), a lot of times the stipulation is that the source code must be made available. This makes sense because your peers has to make sure that the way you did your calculations are actually correct. If people are to use your data or program i

    • Re:I am all for this (Score:4, Insightful)

      by American AC in Paris ( 230456 ) on Friday June 11, 2004 @11:41AM (#9398981) Homepage
      If biotech becomes really easy for consumers to use/create, similar to the manner of open source software, I think something like this could put a lot of power into the hands of the people.

      Does OpenGL make understanding discrete mathematics any easier?

      Biotech is hard. It isn't something you just pick up and do. Making it open source wouldn't make it any more accessible to non-biologists. Similarly, whether a program is open-source or not has virtually no bearing on how your 'average' user uses said program. John Q. Webmonkey isn't going to derive any value from the Apache source code unless he's already a competent programmer.

      Open source will help make work easier for biologists, but "the people" won't have a damn bit of use for it...unless, of course, they go through years of study and training first--at which point, they're biologists.

      Which is probably why something like this will never be allowed to happen now that people have seen how successful open source is.

      Oh, for pete's sake--don't be such a fucking cynic. It's not a sign of some deep wisdom, it's a sign of laziness. You're basically declaring that you're not about to lift a finger in trying to make things better, since you think it'd be a futile effort, anyhow. Here's a clue: humanity has dealt with power-hungry tyrants and money-grubbing shysters since the dawn of civilization, and yet somehow we've managed to progress beyond pointy sticks and thatch huts. You're nutty if you think that the little guys and the altruists have it harder now than they did before.

      There are people who make a difference on the world. These people generally do not kvetch about how it's not worth even trying, seeing as The Man will just put 'em down, anyhow.

      • Biotech is hard. It isn't something you just pick up and do. Making it open source wouldn't make it any more accessible to non-biologists. Similarly, whether a program is open-source or not has virtually no bearing on how your 'average' user uses said program.

        True. However, if we just skip the open-source bit:
        In science, software is a tool. In general, tools tend to get easier and easier to use.

        Galileo had to build his own telescope, today, you can just go buy one and start using it immediately and actua
        • Galileo had to build his own telescope, today, you can just go buy one and start using it immediately and actually find out stuff. No knowledge of optics required.

          ...yes, but 99.999% of all home telescope users aren't 'discovering' anything. A consumer-grade telescope allows you to observe and learn about known science--virtually anything you can observe through that has already been observed and meticulously documented.

          I'd wager most doctors and MRI operators have a fairly good understanding of how an

  • Open sourcing discoveries in bio-tech would lead to reduced research costs, reduced development times and ultimatly reduced prices of drugs.

    It will also by extendtion lead to more competition in the bio-tech industry, which can only be a good thing. And it will lead to more consumer scrutiny of what were popping into our bodies.

    This is a good idea all round. Except of course for the biotech monopolies who...
    [censor type="DMCA" excuse="Subversive,complaint"]

    [/censor] ..GNU for biotech
    • Nice sentiments, but no one really expects reduced research costs, more competition in the bio-tech industry, or consumer scrutiny simply by "open sourcing" biotech info.

      Rather, what the article points out is that there are niches - diseases which disproportionately affect the poor, that affect few people, or for which the patent for a drug has expired - which are ignored by drug companies. The costs of development and meeting regulation requirements would not be recovered in these situations. The articl
    • More competition is only good if the new "drugs" can actually compete in quality w/ the old ones. Worst case scenario is that this makes the "old" method of patent-drugs obsolete and now those companies stop researching new products. Maybe that will be fine, maybe it wont be profitable enough for these corps to only manufacture generic drugs unless they become more expensive and thus prices will go up. I'm all for the sharing of information and for taking life-or-death decisions AWAY FROM for-profit corp

  • Open-source medicine? (Score:4, Funny)

    by Apocalypse111 ( 597674 ) on Friday June 11, 2004 @10:56AM (#9398458) Journal
    So, when some of the strange, undocumented side effects of this open-source medication turns you blue, do you think the average Ethiopian will have net-access to go crawling through some message boards looking for a fix? Just kiddin' yo, but I couldn't resist.

    • Re:Open-source medicine? (Score:4, Interesting)

      by wes33 ( 698200 ) on Friday June 11, 2004 @11:01AM (#9398532)
      the post is funny but the point is actually very interesting. Drug companies face huge legal risks from side-effects of medication (think thalidomide). How would open source medicine pay for these risks (somebody has to pay, even if it the patients who pay with their health)? The obvious answer is via a public health care system (like Canada's say) but there would likely have to be limits on the compensation allowable. But the basic idea of zero patent medicine research is excellent!

  • Good idea but... (Score:2, Interesting)

    by alex_ware ( 783764 )
    the way drugs are developed in a patent based profit world by big companies will mean that big companies will be slow on the uptake as they want to control their market share 100%

    • Re:Good idea but... (Score:3, Interesting)

      by robslimo ( 587196 )
      I second this. They'll want to hang to what they consider proprietary knowledge. Folks will (have already) argue that in science (especially genomics) all related knowledge belong to all of us because it is part of us. That argument makes sense to me, but as long as a company acquires such information without sharing it, it is still "proprietary" in a certain sense.

      In bio-business there is a big dis-incentive to sharing information as they are out for the greater good of their stockholders first, humank
  • This is an argument that Steven Weber makes in The Success of Open Source [slashdot.org], which I reviewed recently. For more info, check out the list of reviews [washington.edu] I've put together. While it's possible that the Economist thought of the idea on its own, I'm disappointed they didn't at least mention his previous work.
  • ....i.e., right here [bioinformatics.org]. Looks sort of GForge-ish [gforge.org], although with frames and a custom theme and such-like...

  • also neuroinformatics (Score:5, Informative)

    by drfireman ( 101623 ) <dan.kimberg@com> on Friday June 11, 2004 @11:01AM (#9398528) Homepage
    The Human Brain project [nih.gov] funds neuroinformatics projects, many of which are released under free or open source licenses.
  • I've been saying this for ages - we need a bitoechnology GPL. In other words, you are free to use the technology and incorporate it into your own research/product developments etc., but if you distribute a product that uses this, your process must be made available under the same licencing conditions. So if I invent a process that's useful in producing a wonder drug, anyone can use it, but all other aspect of this wonder drug must be available for others to improve upon.
    • Guess what will happen. No one will use your process. They will do whatever is necessary to avoid anything which ties their hands in this way. Not because they are greedy, but because the part that you did, coming up with a good idea, is cheap and easy. Good ideas are a dime a dozen. The cost comes in when it becomes necessary to turn the idea into a useful product through years of additional research and clinical trials.

  • Who will pay? (Score:5, Insightful)

    by Anonymous Coward on Friday June 11, 2004 @11:02AM (#9398536)
    Open-source software? No problem. Unencumbered research? No problem, and I assume non-profit organizations or government sources are paying. However, as I like my drugs tested before taking them, who other than these non-profits will pay the cost to test the proto-drugs?

    No patent protection = no profits. No profit = no investment, and no desire to fund tests.

    • Re:Who will pay? (Score:3, Interesting)

      by maxwell demon ( 590494 )
      It would be a good idea if the source of test funding were not the company making the drug. Because that way the tests would be really independent and at least less likely to be influenced by the company which wants to sell the drug.

      Maybe the health insurance would be the right place for funding tests. First, they currently do anyway, just indirectly (through paying for the drugs). Second, they have both a desire to have good drugs on the market (because better drugs means better health means less cost), a
    • You Fool! Companies will grow that provide services and bundle the drugs! They will pay for research!

      But seriously, the profit motivation is there: They still have to make the drugs and sell them. I don't think it would lower the cost per se, but scientists or grad students could work on rare diseases in their spare time to find cures, which could then be manufactured.

      Openness is excellent. The more people who know about cancer treatments, the closer we will come to a cure.

    • And I will take that one step farther. Who will pay to develop the drug?

      Non profit/publicly funded entities have the same problem for profit companies do, limited funding. So let's take the case of tax-payer funded research. Do you spend millions to try to develop a safe, effective drug to cure a rare disease, or would that money be better spent on basic preventive health care or going after a more prevalent disease? For any type of research entity the question has to be asked about where you're going to g
  • Does that mean in ten years, we will bemoan the fact the Pfizer owns a prohibitive majority of the market share, and that argue that the free stuff put together in some Danish guy's basement is as good as the stuff they charge for?

  • Wikipedia is another example... (Score:3, Insightful)

    by dpbsmith ( 263124 ) on Friday June 11, 2004 @11:03AM (#9398556) Homepage
    Wikipedia [wikipedia.org] is another example of open-source-like methods being applied to a non-software area. Only time will tell exactly how successful it is, of course.
  • I remember reading a very recent Wired magazine article where advances in technology has made it possible to create in the open domain what we should call genetically improved crops, essentially genetic cross-breeding without creating a whole new genome from scratch for the crop at vastly faster rates than normal.

    The article mentioned how rice crops in India thanks to computerized genetic analysis for cross-breeding resulted in a rice crop that had 20-30% higher yields and vastly improved resistance to ins

  • It should be used for all patents (Score:5, Insightful)

    by argoff ( 142580 ) on Friday June 11, 2004 @11:04AM (#9398564)
    The simple truth is that patents really are a lie about free market economics. They treat it like it's a physical property, but it's not. If millions of people use my car it deprives me use of it in a serious way, but if millions of people use the same invention - then just the opposite happens. The inventor is not only able to keep and use his original invention however he wants, but also now has huge forces contributing to it's improvement.

    If the government gave someone a monopoly on making cars, because they didn't have an incentive to make cars when other people can make them too - most of us would see that as crap. Market share isn't an inherent property right. If the government gave someone a monopoly on growing oranges, on the premise that they wouldn't have an incentive to grow oranges if other people could too - most people would see that as crap too. But for some reason, that logic breaks down when it comes to invention.

    Finally, looking back on history to paraphrase "look at the great wealth and prosperity of the plantation system, the grand architecture, the vast and rich land, the free markets ... they paid for those slaves God blessed, surely that alone shows slavery is good, and the negros have been saved from their barbaric condition" ....

    I wish I could say that patents are causing less harm, but when they recently lokcked out 10's of millions of Africans dying of AIDS from getting generics because "they had no incentive", because patents are "a property right", becasue "the wealth of the pharmasutical industry in the US is proof that patents work" ... etc. - it really causes one to think.

    • Re:It should be used for all patents (Score:5, Insightful)

      by Derkec ( 463377 ) on Friday June 11, 2004 @11:25AM (#9398791)
      Patents are good.

      Let's assume we do away with them though. Now let's compare two business models. In one, I spend hundreds of millions developing new drugs. Once I pass the very expensive FDA process, I sell my drugs at market rates. In the other, I sit on my ass and wait for someone else to develop drugs. Then I spend a million bucks reproducing the other guy's results and sell the same drugs at market rates.

      Which one would you choose? I wouldn't waste my / my shareholders money on R&D, I'd wait. Everyone would. R&D would almost only happen in the public sector and in academia. We'd either see a drastic reduction in new drugs coming to market or the government would need to pay through the nose to do the research.

      True, you don't deprive me of the ability to make the drug I developed when you infringe no my patent. However, you get hundreds of millions of in research for free and by competing with me, make my return on that research far less than it otherwise would be.

      Throwing some quote in about slavery doesn't help your case any more. It's like if I saw eating candy is great and you equate that to saying slavery is great. Therefore eating candy is bad. You need to develop that argument some more so us dumb people can follow you.

      Further drug monopolies should only last 20 years. Some companies use tricks to extend that, and I despise that behavior. But in a properly functioning system, drug patents work just like car patents do. The airplane (and I believe the auto) were patented. That gave monopoly / royalty rights to the patent holders for 20 years. The system wasn't broken. The inventor profited nicely and with time competition could come in. Just as it comes in with generic drugs down the line.

      Now when there are life saving drugs in question with no alternative treatment, this takes on a bit of a morbid twist. Perhaps, the taxpayers of the industrialized countries would like to buy the patents on these drugs to make them widely available and still reward the company for doing the work to invent the drug. Keep in mind that if nobody spends the time, energy and cash to develop a drug, those people are going to die anyway.

      Now, in the case of catastophe like AIDS, it seems reasonable for American firms to provide low cost drugs to those who can't afford them - purely because that's a nice thing to do. There's been some progress along these lines, but it has been painfully slow. Equally painful has been conservative objections to the low cost item that could even prevent Aids - the condom.

      Unless you want to present a viable alternative where drugs will be developed and put through FDA trials by somebody else, patents still seem to be the way to go.
      • Let's assume we do away with them though. Now let's compare two business models. In one, I spend hundreds of millions developing new drugs. Once I pass the very expensive FDA process, I sell my drugs at market rates. In the other, I sit on my ass and wait for someone else to develop drugs. Then I spend a million bucks reproducing the other guy's results and sell the same drugs at market rates.

        Lets assume I spend 100's of millions developing a new car? get it? also, what you say doesn't reflect reality -
        • Lets assume I spend 100's of millions developing a new car? get it? also, what you say doesn't reflect reality - most big patent money is spent on marketing not R&D.

          You couldn't be more wrong [ncpa.org]:

          On average, it now takes $802 million, including the cost of capital, to come up with a new pharmaceutical product.

          The study found that the average development time for new medicines is 12 years.

          In the 1990s, drug firms spent an average of $121 million out-of-pocket in research prior to clinical trials --
          • From what I understand, the industry statistic is that companies spend almost twice as much on marketing as R&D. I'll half to look it up.

            Yeah I don't like patnets. I used to love them, but the more I learnt about them the more I've come to dispise them. They are not free market, they are not property, they are not an incentive, they lock out small inventors, they fragment research and industry innovation, they encourage frivolous lawsuits and bogus claims by their very nature.
            • ~$1.6 billion on advertising? On top of $800 million? Christ, it's hard enough to generate $800 million in sales, let alone $2.4 billion. Remember, once the patent runs out (which is not long after the drug is released, since the patent must be applied for the instant the compound is discovered, before the years and years of trials), anyone can develop the drug and undercut the company who created the drug in the first place.

              I'll half to look it up.

              Yes, please do. Hopefully you didn't find your stat
      • 'Unless you want to present a viable alternative where drugs will be developed and put through FDA trials by somebody else, patents still seem to be the way to go.'

        Here's the outline of one:

        Allow any drug manufacturer to repeat the FDA trials and thus be allowed to sell the drug or the original manufacturer can licence the drug and manufacturing process, thereby avoiding the (new) trials. The originating company would then be pricing the licences at a cost competitive with the cost of the trials plus R

    • Patents for medicine/drugs is ESSENTIAL, and you are naive and foolish if you think otherwise. Almost all drugs developed are developed by companies with one goal: make money. If you remove patents, the company that poured all the money into R&D gets no advantage over a company that can steal their results. If you remove patents, you remove incentive to develop drugs, and drug development will come to a screeching halt.

      You say that patents should be removed so that Africans dying of AIDS can get drugs

      • One more thing I want to say--I am certainly not opposed to medicine developed without patents. If a group wants to get together and develop beneficial drugs which they will share with everyone, that's great! Unfortunately, I don't see this sort of contribution being significant any time soon. Real research is too expensive, and the private sector will dominatie it for a long time to come.

      • Name one major cure that was made from patent R&D money? 90% of the ones I can think of were made by accident, or by independent researchers - then companies came in after the fact, grabbed the patents and spent the money on marketing.

        You are also making the mistake of assuming that there is no downside to patents interms of medical discovery. that's not true. Patents have a drastic effect on how researchers share and collaberate.
  • the drug company multi-nationals, I'd like to strongly dissuade everyone from pursuing this idea. If the "people" are free to concentrate on unpatentable, abandoned and unprofitable medicines in some sort of collaborative effort, this will severely hamper our efforts to develop ever faster erectile dysfunction medicines, baldness cures in a pill form, medicines for newly created social "disorders", drugs to strip the carbs out of everything (or proteins or whatever the new black is) and have people pay top dollar for them. Stop rocking the boat and someday we'll find a cure for something (as long as it's profitable).
  • Considering that, in the U.S. at least, most basic medical research is carried out at taxpayer expense it is about time that the fruits of that labour be availible to all taxpayers.
  • In an article [wired.com] some time ago, this was covered already. It's quite interesting ro read, the relation to biotech is on page 4 (Monsate et al).

  • good idea (Score:4, Interesting)

    by Da_Slayer ( 37022 ) on Friday June 11, 2004 @11:15AM (#9398678)
    Having these types of projects being "open source" is a very good idea. The exchanged and access of information will not only allow more people to work on a project but for medicines it would in theory make them safer. Instead of having to take a drug companies word about a product you would have direct access to all the research and testing of said product from the beginning to the end.

    This open source idea for medicine and science would run into the same problem that open source software runs into. Greed.

    People trying to get more money because they think they are entitled to it. Some examples would be Microsoft and SCO.

    CEO Darl McBride who is at the helm of The SCO Group is leading the charge so to speak against open source software with claims to owning rights. Honestly most people realize this is a bid for them to be either bought out or to gain money from legal battles. This strategy is employed because it has the potentional to make money. SCO having not really made any innovations and in a steady decline over the years in terms of revenue and stock value has choosen this path. Now personally I think it was McBride's idea based on his track record with IKON Office Solutions. But then again the shady nature of SCO and it's parent company (explained here: http://www.forbes.com/2003/06/18/cz_dl_0618linux.h tml )have to make you wonder.

    Microsoft on the other hand was sued due to a patent being violated by their Internet Explorer web browser. Reference here: http://news.com.com/Microsoft+appeals+Eolas+decisi on/2100-1032_3-5228882.html

    Not to get into a rant about IP and software Patents but both of these cases show how money can be obtained through legal matters instead of the time honored method of working for it. No matter which way either case goes the problem is with old laws and ideas messing up the free (as in beer) trade of ideas and information.

    Hopefully in the science field something like the above examples would not happen but there is always a chance. Big drug companies would not go quietly into the night if their development processes suddenly became public access and with more competition driving overall prices down. Big business loves to stay as BIG business.

    Personally the idea behind "open source" science and medicine is very sound and will help many people in the long term. I just hope the process of it becoming free is less painful than the software industry.

  • Won't Work (Score:4, Insightful)

    by kaellinn18 ( 707759 ) on Friday June 11, 2004 @11:25AM (#9398793) Homepage Journal

    I don't think this will work, and let me tell you why. First off, let me preface this by saying that my wife is a soon-to-be pharmacologist, so while I may not have any firsthand knowledge of this, she knows what she is talking about.

    1) The cost of research for pharmacology is infinitely (no not literally) more expensive than it is for computer science. In most research for CS you just have to pay for cost of equipment (basic computers typically costing a hell of a lot less than the specialized machines used in development of medicine) and the salary of the researcher. A lot of CS research can be done by one person. For pharmacology you have the cost of equipment (or even the USE of it, sometimes they have to rent time on more uncommon machines; this happens in CS as well, but not nearly as often since it's mainly for the processing power) as well as the cost of the researcher AND his/her assistants. It's almost impossible to do good research in medicine by one's self because of...

    2) It takes freaking forever. The number of steps required to find out if a proposed theory for a molecule even has a chance for working is phenomenal. My wife has spent the past few months trying to see if a certain molecule will bond with an AIDS neutralizer. Mind you, this is just the first step. Even if this step does work (which they don't know yet) they don't know if this molecule will a) bond with the aids virus b) will it bond long enough to neutralize? c) if it does bond, will the neutralizing agent be able to reach the virus? or will it be blocked by the bonding molecule? And the list goes on. No pharmacologist who does this for a living is going to volunteer even MORE time out of their lives for no pay. So we'll pay them right?

    3) Funding. Right now almost all pharmacology is financed by companies that already have patents or by third party investors. These people invest money into these projects because they expect a profit as return. Yes, I'm sure they also care for the well-being of others, but they do need to recover their costs if a drug succeeds. A vast majority of projects fail, which is why a lot of specialized medicines cost so much. These companies need to stay alive in order to do more research. And don't even talk to me about Federalizing the research. That would be pretty much the dumbest thing ever.

    I'm sure there are holes in my argument, but hopefully this will at least provide food for thought and further discussion. Basically, I just don't see it happening.

  • Costs aren't the same... (Score:5, Insightful)

    by One Louder ( 595430 ) on Friday June 11, 2004 @11:28AM (#9398831)
    This needs to be thought out, because the cost and regulatory structures for, say, drug development, aren't nearly the same:

    1) Developing new drug products requires substantial, very expensive facilities, while the hard costs of software development are very low.

    2) Drugs must go through a long and expensive testing and regulatory process before being released to the market. Open Source software simply wouldn't exist if it cost millions of dollars and took several years before you could release it.

    3) There are massive costs associated with product liability in drugs - no one would give away software if the same liability exposure existed.

    4) For every drug that makes it to market, there are dozens to hundreds that don't make it through the process but incur the costs of development anyway. The unsuccessful attempts are subsidized by the successful ones.

    While I think that the sharing of information in biotech is generally a good thing, I don't think the economics mesh with a software-like "open source" model.

  • While the author conceded that sharing data in biological studies is not new, he seemed to imply that there was something novel about collaborating on data rather than software tools and I think there are really many many examples of open colaboration in biology.

    What is much more interesting, in my opinon is open source lab hardware and, in fact, there is such a thing. There is a team at at UCSD who's whole lab is dedicated to using plain old PC-CDRoms to do analysis of samples. That is far more

  • I've been working in Healthcare IT for nearly 9 years. As an open source advocate, I am really excited by the progress and interest I've seen lately in FOSS solutions in the healthcare realm. There was a time that I thought the open source model would never work in vertical markets. Boy, am I glad I was wrong! Check out LinuxMedNews [linuxmednews.com] to get an idea of how much is happening in this area.

    Here are some links to projects that I find interesting and seem to have the most traction:

  • Follow through rate of Drugs (Score:3, Interesting)

    by artlu ( 265391 ) <artluNO@SPAMartlu.net> on Friday June 11, 2004 @11:34AM (#9398888) Homepage Journal
    Big Pharmas tend to develop hundreds of drugs per year. However, any drug that has a cost of production greater then 10% of its total cost is usually squashed due to the market. If those drugs were "given" in a "open source" manner, maybe some of those drugs would make it farther to help people. Who knows what drugs could have been developed and then squashed because it wouldnt make money?

    Anyway, im trying to get a new website off the ground right now. If you are into the stock market or day trading then please check it out at GroupShares.com [groupshares.com]

    Thanks,
    Aj
  • Just some examples of how bio very much is open already..

    In biotech software, there's lots of open source. BioJava [biojava.org], BLAST [lanl.gov].. etc.

    As for what they're talking about, e.g. databases.. Most data already IS open. The human genome [gdb.org], protein structures [rcsb.org] and sequences [nih.gov].

  • Open Source Viruses? (Score:3, Interesting)

    by abb3w ( 696381 ) on Friday June 11, 2004 @11:37AM (#9398921) Journal
    Um, I really don't think we want lots of people able to develop biological weapons in their basement. We already have enough problems with script kiddies making computer viruses, you'd think they'd learn.

    This may be one of those technologies which creates a problem, the resolution of which is that the civilization making it gets knocked back to where it can no longer make the technology. (Classic examples from Science Fiction include certain general-purpose teleporters, as discussed in Niven's classic "On the Theory and Practice of Teleportation", and to a lesser degree the time viewer in Asimov's "The Dead Past".) I suppose that's one solution to the Fermi Paradox....

  • The similarity between open source and the academic process with their 'you share, I share' principles is shown by the human genome project.

    Very true. "If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple. But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas." -- George Bernard Shaw (1856 - 1950)

    This is propably even more insightful when applied to biotechnology than to software at

  • Open source (and by open source I'm thinking mostly of the GPL. I know other variants exist.) and the academic world share a different overall goal. The idea is to *advance the field*, not the wallet of anyone who controls the process. I'm talking about those MBAs who slice and dice everything to add dollar signs everywhere. Those MBAs are the same people that are in charge of the biotech research, not the geeks that do the research. It's all about the finance department.

    I'm not really anti-capitalism
  • It appears that open source is making its way into the data side of things... See the The RCSB Protein Data Bank [rcsb.org], the human genome sequencing, etc.

    But the bottom line is the following:

    It costs (currently) about US$800 million to $1 billion to develop a drug. That is all of the initial trials, screening, 3 phase clinical trials, etc. This is typically a 10 year process-(there are some exceptions, but this is generally true).

    The _reason_ why any company would invest this sort of money is so that th

  • If you read the articles, the economist takes a balanced approach, it clearly lauds the open model in some places, but it does acknowledge that the model doesn't work in other places.

  • Last I heard, the human genome project was a great model of cooperation ... if by "cooperation" you mean "cutthroat race between competing academic and private-sector groups"...
  • This makes a lot of sense for GM organisms, particular crops -- open-source genetics. It means that farmers can reap the advantages (pun intended) of GM crops without the nasty side effect of becoming a slave to agrobusiness, which is one of the primary (and most legitimate) arguments against the widespread introduction of GMO in the third world.

    For the moment, lets assume that we're only dealing with basic GM (accellerated hybridization) and not transgenic crops -- although, click here [theatlantic.com] for a great articl

  • That is not how Research is done! (Score:3, Interesting)

    by hung_himself ( 774451 ) on Friday June 11, 2004 @12:24PM (#9399641)
    The Economist is usually very good in its bioscience articles. This article is completely abyssmal - the person who wrote it has absolutely no understanding of how scientific research works. and that is not flamebait but the sad truth

    First of all, we are a bio-informatics lab - all the software we produce is open source. This is not the exception but the rule.

    The motivation behind our research is not profit and again, in academia that is the rule not the exception.

    The article states that if aspirin were the cure for cancer - it would not be developed because there would be no profit. If that is true then it is a reflection, not of a flawed scientific research model but rather a flawed biotech/pharmaceutical model

    Researchers like myself would be looking into it - because it would be INTERESTING and scientifically important regardless of whether it would be profitable.

    Basic scientific research is done by publicly funded labs like ours. The results are freely communicated. Biotech companies use our results to make money (and rightly so) but in the end do very little basic research - because, as the article says, - it does not pay. However let us not get the two confused as our poor "science" writer did. The NIH funding model may not be perfect- for example there is probably too much emphasis on western diseases like cancer rather than third world problems like malaria - which sort of creeped into the article. And it is appalling that we have 10 versions of Viagra rather than cheaper generic chemotherapy alternatives but the blame for that does not lie with the lack of basic research but further down in the R and D food chain.
  • Then you could write all the code you wanted, but in order to run the compiler (or interpreter) even once you had to pay a million dollars. If your program generated compiler errors and you needed to run it again after fixing your code you would need to pay another million dollars for the compiler run.

    Still think that open source would exist in this world?

    What people posting to this thread seem to ignore is that fact that it is easy to come up with a good idea in biology and hiddeously expensive to turn

  • Been there under another name? (Score:3, Interesting)

    by smchris ( 464899 ) on Friday June 11, 2004 @12:58PM (#9400108)
    Sounds similar to the discredited [*cough -- Reagan *] idea of giving unencumbered federal research grants for universities to develop exploitable ideas for the common good?

  • Time to plug PLOS Biology (Score:3, Informative)

    by Xofer D ( 29055 ) on Friday June 11, 2004 @01:07PM (#9400193) Homepage Journal
    This is already happening. Behold PLOS Biology [plosbiology.org], the Biology journal of the Public Library of Science. This has been around for some years and was started up by Michael Eisen [lbl.gov] of the Eisen lab at Lawrence Berkeley. As Slashdot history will attest, I found the original introduction of the PLOS to be insipiring and in fact it led me to take up my current career in natural language processing (because someone has to search through all that science!). I had the pleasure of talking with Dr. Eisen at a presentation he made at VANBUG [vanbug.org] recently, and he was very enthusiastic about hearing that NLP people are interested in working on searching and managing open science information, so I again urge you to help out projects like the PLOS (not just Biology, although that's the only current journal).

  • Amateur Genetic Engineering (Score:3, Informative)

    by TheSync ( 5291 ) on Friday June 11, 2004 @02:14PM (#9401051) Journal
    I have links to many sources for amateurs to become involved in (peaceful) genetic engineering at DNAhack.com [dnahack.com].

    For example, there are Web sites where you can type in a list of DNA bases, and in a few days either get your custom DNA snippets (aka oligonucleotides), or even get the DNA delivered inside bacterial plasmids (aka custom genes). With custom genes, it is a simple kitched-top operation using heat shock to insert the custom genes into strains of research E. Coli.

  • 100k deaths vs. facial hair removal: an anecdote (Score:3, Informative)

    by geekotourist ( 80163 ) on Friday June 11, 2004 @07:24PM (#9403690) Journal
    I'd written about the need for open source genetics [slashdot.org] in a Slashdot article on Smart Breeding to Beat Biotechnology [slashdot.org]. Locked-hood genetics is like proprietary software in many ways, including:
    • The (food/software) itself is secondary to locking you into a company's support products and support cycle treadmill
    • The proprietary product is often based on (taken from / stolen from) older open source projects.
    • they have all or nothing security models
    • They break standards.
    • they're closed source, top-down implementations that lead to monocultures.
    But as others have pointed out, software development isn't as expensive as biotech / pharma development. On the other hand, the potential cost to human lives of closed vs. open source development for biotech is also huge. We should be talking about it at least as much as we talk about SCO.

    For example, look at trypanosomiasis- sleeping sickness. Infects 500k/year, kills 100k/year, drives you mad before you go into a coma and die. The older treatment (Melarsoprol [mcgill.ca]) contains arsenic (and anti-freeze) and kills over 5% of patients taking it. It also feels like injecting bleach into the body. Another newer treatment (Eflornithine) works better and has far less severe side effects [mcgill.ca]. It was used throughout the 90's as the best treatment. However, Eflornithine was only commercially manufactured as a potential cancer treatment-- once found to not work on cancer, there was no reason to continue making it, and Aventis ended production of eflornithine in 1999 [metanexus.net]. As the last of the old stock ran out, patients had to go back to the dangerous and painful arsenic treatment.

    Luckily for those 500,000 people per year, eflornithine was later found to have one important use: its a fine facial hair depilatory cream [vaniqa.com] . So as the production of this drug was re-started to prevent the horror of unwanted facial hair, 500k people get the side-benefit of a non-arsenic treatment for a deadly disease. But only because eflornithine was found to treat excess hair, not because it prevents painful death.

    This is just one anecdote- one illness. The analogy to software can still be made: when Microsoft discontinues support for a product, people suffer from the time and money to upgrade. When Aventis discontinues support for a product, people suffer as well. It could be argued that eflornithine wouldn't have existed without closed-source drug development: but that doesn't seem to be the case here. First, while drug production is closed-source, basic research is at heart open-source. Sencond, Al Sjoerdsma, the scientist who first discovered its properties was apparently more of a Tim Berners-Lee type [wayne.edu] than a Gates or Darl McBride type.

  • I gave a related talk last year (Score:3, Informative)

    by mattr ( 78516 ) <{mattr} {at} {telebody.com}> on Saturday June 12, 2004 @01:10AM (#9405185) Homepage Journal
    Sept. 16, 2003 I gave a talk at GLOCOM [glocom.org] called "Open Source, Open Knowledge: The New Alliance of Academia, Industry and Governments from East to West".

    That organization is an industrial / academic policy think tank and so I described open source, different uses of it, and suggested use of the GPL-like liscenses for research in bio/nanotechnology.

    I covered most of the objections stated in this thread but also noted an online talk by agricultural biotech people from around the world that was very interesting. Third world agriculture has been attacked by unethical corporations like Monsanto which use a suffocating mixture of intellectual property and biotechnology to make it impossible to develop without them, forever. These stakeholders suggested something like Open Source Life Sciences.

    However I also noted that while proteomics and discovery of pathways has until now been research given as a freebie to drug companies, at least in Japan it has been recognized that new legislation is necessary to enable development in these areas based on something like a patent.

    Nanotech (as the general public imagines it) however requires a far greater amount of basic research being farther away from becoming a product (of course it already is in lots of products, I am talking about machinery etc.) and so could benefit more from a GPL.

    The biggest drawback besides how to fund development and coordinate with commercial ventures is of course security a la Bill Joy ("some things we shouldn't make; we should monitor scientists"). And I have nothing against capitalism, I am simply interested in how to improve communication among scientists and use the Net to speed development. If money is what does it fine.

    But there seemed to me a number of interesting fields in which the open source / GPL paradigm could be useful and provide effective advantages especially for commercially disadvantaged participants.

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