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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."
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.
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.
"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.
A lot of development in bioinformatics is already open source. Check out http://www.bioperl.org http://www.biojava.org
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...
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!
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.
My days of not taking you seriously are certainly coming to a middle...
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.
The talk was his acceptance speech for the 2004 Benjamin Franklin Award at the BioIT-World conference.
The award was presented by bioinformatics.org. In his speech Lincoln talked about essentially open sourcing the R&D process and leaving the manufacturing and distribution to big Pharma. Thus, in theory, allowing academic R&D to push new drugs towards current public health concerns versus the money making drugs big Pharma produces now.
Not likely to happen but interesting to think about.
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.