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Open Source for Biotechnology
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."
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...
'Don't worry' said the trees when they saw the axe coming, 'The handle is one of us.'
Which is probably why something like this will never be allowed to happen now that people have seen how successful open source is.
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Open sourcing discoveries in bio-tech would lead to reduced research costs, reduced development times and ultimatly reduced prices of drugs.
..GNU for biotech
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...
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May the Maths Be with you!
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.
There is no mod option "-1: Disagree" for a reason. "Overrated" is not an acceptable substitute. Post something instead.
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%
If you have nothing useful to say post as AC.
This is an argument that Steven Weber makes in The Success of Open Source, which I reviewed recently. For more info, check out the list of reviews 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. Looks sort of GForge-ish, although with frames and a custom theme and such-like...
The Army reading list
The Human Brain project 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.
43 - For those who require slightly more than the answer to life, the universe and everything.
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.
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 of open-source-like methods being applied to a non-software area. Only time will tell exactly how successful it is, of course.
"How to Do Nothing," kids activities, back in print!
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.
... they paid for those slaves God blessed, surely that alone shows slavery is good, and the negros have been saved from their barbaric condition" ....
... etc. - it really causes one to think.
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
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"
Communism and Open Source do sound similar (in their principles). The parent (was probably a troll) but only because they knew that everyone would see them saying "sounds like something bad to me" instead of "sounds like communism to me." Communism isn't necessarily bad. I was thinking in the shower (before I saw this article) that communism is a set-up where everyone benefits by the greater good of the community. This works by making sure everyone can benefit from the efforts of individuals. Sounds like Open Source doesn't it?
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).
Then all the technical superiority of the western world is based on communism? Because that technical superiority is to a large part based on research following this principle. I doubt that research would be as far as it is were this principle not followed.
Indeed, one of the main measures of scientific success is the number of publications (unfortunately not taking into account the quality of those), that is, you are considered a better scientist if you added more to the community. Indeed, that measure can be crucial to your career (if you don't publish your results, i.e. don't share, then you'll never get far in the scientific community).
Note that also the incentive of the patent system was to encourage people to share their knowledge. You cannot patent something without publishing it, and that means after your patent expires, it's free knowledge for anyone to use.
The Tao of math: The numbers you can count are not the real numbers.
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.
h tml )have to make you wonder.
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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.
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+decis
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.
Push harder towards Open Media/Content
Well, it has been argued many times and there is abundant evidence to support the notion that the success of the US wouldn't have been anything like it has if it weren't, in fact, a fairly socialist nation.
Teachers like to joke that the Democratic party is actually merely a front for the National Education Association and it's not that far from the truth. And when you look at this huge pillar of the American community that is the education system, you can easily see that it is a form of welfare state.
Look at the recent shake-up at Disney to knock Eisner down a peg. Who did that? That was done by the California Pulic Enployees Retirement System, CalPers. So, all the rhetoric about America fighting against socialism is just that, we've been socialists all along.
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.
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This isn't the sig you're looking for. Move along.
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 article proposes to use an "open source" model to address these niches.
While the article does point out that a freer flow of information would help these situations, I think what the authors really want is the large army of (largely) volunteer brainpower that open source software has.
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 literally 5 minutes late in adminstering the drug because the protocol said "administer at 1 AM."
The point is, biotech costs a ridiculous amount of money. And even "the best in the world" aren't going to give up their research for free.
-truth
I had a steady B+ in my AI class until I failed the Turing test...
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.
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 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:
There are many, many more. These are just some that came to mind. If you work in healthcare, do yourself a favor and check out this thriving community!
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?
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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....
//Information does not want to be free; it wants to breed.
It appears that open source is making its way into the data side of things... See the The RCSB Protein Data Bank , 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 they could have a monopoly on making it for 20 years. If everything were open sourced, and anyone could make anyone else's drug, why would companies put this much money into developing it? They would have no incentive to do so.
As someone else mentioned- this is not the sort of thing that you can just do in your basement. The company I work for makes a fancy robotic incubator to help you crystallize proteins. People want to do this so they can put them in an xray machine to get their structure, which can lead to possibly designing drugs that might interact with that protein. This machine costs about US$250,000. People need it because protein crystallography is hard- there's no way to predict under which conditions it will crystallize. You typically need to try 10,000-100,000 different conditions to get a reasonably sized crystal, that you can diffract and get the structure from. Some proteins _never_ crystallize.
This is way before you are even trying _anything_ in a biological screen, let alone animal trials, let alone phase 1, 2, and 3 (human) clinical trials.
If you do successfully crystallize the protein (and determine the structure, which is very straightforward once you have a good crystal), you can (and everyone does) submit it to the protein databank, and you can publish these conditions in a paper. So in this sense, lower level biotech is/becoming open source. But the higher level stuff requires a lot more thought and resources.
I'm not saying that there's no waste or greed in big pharma- Of course there is, like any other industry. Perhaps its higher than average, due to the large potential amount of money to be made.
My point is that the places that open source is successful- coding, which requires a $300 computer with an internet connection; wikipedia, which requires the same; there is a very low cost of entry to contribute. Even if companies and universities start open sourcing the lower level stuff more than it is now, Animal and human trials costs very large sums of money. Why would a company invest $10's of millions on one part of a trial if someone else could end up making (and selling) the drug?
I agree that cheap drugs would be great. But if its open source, and people start dying because of a side effect of the drug, who is liable? Not to mention who will fill out the FDA paperwork (there has to be $10's of millions invested just in complying with the paperwork. I've heard estimates that it is basically a medium sized room full of paper. And that's for 1 (one) drug.) -E
-ETF EOM
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.
I wouldn't say all along. America has been capitalist for most of its history, IMHO. But yes, there is definitely a small gradual trend towards socialism these days (ignoring the current buffoons in power). But I think this is a natural trend in all the rich countries. First y'all go thru a phase of hard-core intense capitalism and then when you've finally started reaching a certain level of wealth, the upper crust starts giving back to society, even if it is a trickle. But I think starting out socialist is a BAAAAAD idea for any new nation - i.e. India. It started out socialist and is NOW moving to the fre-market. Try breaking the entrenched attitude that the Government is there to do everything for you, and that you must accept what is given. The one thing that a capitalist economy will give its citizens is a good work ethic - i.e. work hard, and only deal with the govt. when things go wrong. But in socialist countries, people develop a dependent mindset, and this totally screws you over. "If you give a man a fish, he doesn't go hungry today. If you teach a man to fish, he never goes hungry..."
My Favourite Meme
Sounds similar to the discredited [*cough -- Reagan *] idea of giving unencumbered federal research grants for universities to develop exploitable ideas for the common good?
This is already happening. Behold PLOS Biology, the Biology journal of the Public Library of Science. This has been around for some years and was started up by Michael Eisen 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 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).
The Signal/Noise ratio can be improved in two ways. Remaining silent is the OTHER way.
I have links to many sources for amateurs to become involved in (peaceful) genetic engineering at 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.
- 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) 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. 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. 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 . 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 than a Gates or Darl McBride type.
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.