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New Startup Hopes to Push Open Source Pharmaceuticals
waderoush writes "Nothing like the open source computing movement has ever caught fire in biology or pharmaceuticals, where intellectual property is king. But drawing inspiration from the people who make Linux software, and the social networking success of Facebook, Merck's cancer research leader has nailed down $5 million to launch a nonprofit biology platform called Sage, which aims to make it easier for researchers around the world to pool their data to make better drugs. 'We see this becoming like the Google of biological science. It will be such an informative platform, you won't be able to make decisions without it,' says Merck's Eric Schadt, a co-founder of Sage. He adds: 'We want this to be like the Internet. Nobody owns it.'"
You mean like when research was in the domain of the university, and when science was done by building on the prior work of others? The big dollar companies siphoned away the talent from universities and went patent crazy. They're the ones that started this in the first place.
The same can be said for internet technologies - people forget that fundamental web technologies such as web browsers and LDAP came out of university research, not out of the big companies or the major standards bodies.
Next thing they'll be telling us is we could GROW our own medications in gardens. Medicine and pharmaceuticals are *hard* and require a lot of big government seed money, research, lobbyists, more money, more lobbyists, advertising, etc. The idea that you could grow, say a drug to suppress inter-ocular pressure in glaucoma patients, or a nausea-suppressive for chemotherapy patients is patently absurd! I mean, what next? Analgesics from tree bark?!
Hippie, commie, open-sourcers will never learn.
Learning HOW to think is more important than learning WHAT to think.
If you believe in Sesame Street for kids, you should be interested in online education for adults. The reason why you can't do every subject known to man on television is that there is only limited air time and people would be uninterested in stuff they already know. But you can make an online education school which has videos of lectures for every level of education. Throw in some tests and written course(book) work, and you can guide people through education if they have the drive. You put in a lot of redundancy so there are many ways of looking at the same subject matter if it doesn't click with the student asap. And then you have a pay service where you can ask a teacher question through IM or email.
I don't know how to start this though. I considered being a jerk and just linking everyone's educational videos on a site that is just a giant index to start... But I don't want people complaining that it is their Intellectual property. The task is too big for me to tackle alone because even though you only have to make a years worth of videos one time for a subject, it still takes a lot of time to do this. To make an online education school with videos would take a lot of work, but I think it'd be worth it for society. Anyone have ideas on how to start something like this?
God spoke to me.
A major expense in the development of pharmaceuticals is the testing and approval phase. Only wealthy entities like corporations or governments can afford it. I don't see how the open source concept can get around that problem.
If one gathers data from many sources, in order to justify to the US FDA some claim about a drug: how can one certify that those data are accurate?
I was under the impression that despite its horrific flaws, the current regime requires the drug researchers to seriously vouch for the (subset of) the data they present to the FDA.
Intellectual property may be king, but the lawyers are queens (pardon the expression), and their games are hideously expensive. You can't get into the legit end of the drugs business without a strategy for covering legal liability. You should budget at least as much for this as for clinical trials or production facilities. $5M is peanuts in this game.
Those who can make you believe absurdities can make you commit atrocities. - Voltaire
drugs coming from a bunch of guys in their garages
As long as experts contribute, there shouldn't be a problem. Maybe a registration with credentials would be good.
Software is special, in that all the hardware required is now commodity, and all the knowledge can be accessed fairly easily. At least, you won't see $300 biochem labs from Dell.
Open access journals such as those from BMC and PLoS, databases such as those at NCBI and EBI, software repositories such as Bioconductor and the Open Bioinformatics Foundation projects (Bioperl, Biopython, etc.) If Sage can take it to the next level, good for them, but I'm not sure I see how one group is going to accomplish this. I suspect it will have to happen more, um, organically, the way open access publication and biology-targeted OSS have.
The correlation between ignorance of statistics and using "correlation is not causation" as an argument is close to 1.
When I saw the title I thought "How the HELL can you have 'open source pharmaceuticals' in a legal regime where new drug compounds are illegal by default?"
Then I read TFA.
This has NOTHING to do with making "open source pharmaceuticals". This is about sharing data among drug companies and doctors to try to get a better handle on things like:
- understanding the gene-regulation changes that occur in major diseases
- designing better drugs using this data
- customizing drug therapies by selecting drugs that are a good match for a patient's genetics and disease, picking those that will be safe and effective for him in particular while avoiding those that would cause dangerous side-effects due to his particular genetics.
It looks like it will run afoul of HIPPA unless it's very carefully designed.
BAD article title. No donut.
Bantam Dominique roosters crow a four-note song. Once you've heard it as "Happy BIRTHday" you can't NOT hear it that way
Informatics for Biology... Bioinformatics. Is RUN by open source software. BLAST http://en.wikipedia.org/wiki/BLAST ,one of the most important Bioinformatic tools ever written, is public domain. It's paper is one of the most cited of the past 30 years http://archive.sciencewatch.com/sept-oct2003/sw_sept-oct2003_page1.htm .
Bioinformatic clusters almost universally run Linux. Almost all popular tools are written by academics and supplied under open source licenses. To the degree that I'd say closed source software finds it hard to break in to this area, not the other way round.
This is not only true of Bioinformatics, but also large scale Protein simulations. Namd p://www.ks.uiuc.edu/Research/namd/ is also available under and open source (though more restrictive than GPL or BSD license). And is one of the most popular Molecular Dynamics codes available.
What's interesting about this (I think) is that they're trying to open up research data that usually gets discarded or hidden. They're not necessarily talking about clinical trials of drugs in the FDA approval process. There's lots to be learned from the effects of drugs on various cell or tissue types at various stages of disease or age or any other variable of interest.
If a research group is studying the effects of compound A on some disease (atherosclerosis, for example), they might use a microarray study the effects of the changes in gene expression on endothelium. Maybe that compound turns out to be useless in this context, but they have data that might be meaningful on some other pathway like cell adhesion which is often implicated in cancer. That data would have been tossed because it was uninteresting to original question but could be meaningful to someone looking at something else.
But now you have two bits of information. Compound A doesn't effect atherosclerosis but it effects cell adhesion. And that tells us something about the wiring of the cell type in question. In their view, the interaction of genes forms a network and hitting one part of the network has an effect on cell adhesion but not atherosclerosis. So those pathways must not be directly linked. But compound A hits something in the cell adhesion subnetwork.
With a lot of little stories like this, you could build yourself a detailed idea of how different aspects of cellular machinery interact. And what targets are good to hit and what aren't.
drugs coming from a bunch of guys in their garages
As long as experts contribute, there shouldn't be a problem. Maybe a registration with credentials would be good.
Minor problem. Who gets to determine that some researcher isn't an expert, as opposed to that biochem college dropout who knows what he's doing, as opposed to the well meaning schmo whose job is construction, but he knows some folk remedies, as opposed to a methamphetamine dealer whose knowledge of how to brew some rocks is exceeded only by his stupidity in smoking around ether?
Disclaimer: The opinions and actions of the US Gov't are in no way representative of those held by this author or its ci
According to your ideas, then, Linux would have never got off the ground and yet here we are.
I wish they would invest more time in making available drugs that have already had their patent expired. I am not talking about stuff that expired yesterday, I am talking about stuff that been out for years but the market is too small for a large company to invest in it.
I forgot the name of the drug, but it was a cheap drug that served a small market, but it very vital. It was being produced cheaply for years from one factory that served the whole market. Somebody bought it and then jacked up the price by 100 fold. Why? Because no one was going to bother with drug that had such a small market share, but it was critical the people who depend on the drug.
Someone tell me what the drug is? I believe there was an article in the NY Times a few years ago about it.
Very Simple,
If antibiotics are over-the-counter, then they will be over-used, and/or misused in ways that lead to more antibiotic resistant strains of bacteria (e.g. penicillin-resistant gonorrhea, or MRSA). Shelf life is another concern. Several common prescription medicines not only become ineffective as they age, but eventually become toxic. OTC interactions with prescription drugs are a common problem that would spread as more medicines are made OTC. Too many people take dosage and usage directions for prescription and OTC drugs too lightly as it is. Making more drugs OTC will only make this problem worse.
DMCA - Chilling free speech since 1998.
Noob mistake and karma burn. I forgot to post as plain text. My apologies.
This turned into a book. Sorry. This post lacks citations and specifics for reasons that should become clear.
A full-fledged fully-stocked bioengineering lab isn't really necessary. A high school chemistry lab would be overkill for most of it. Most plant extractions can be done with nothing more than an acid (hydrochloric preferred), a base (sodium hydroxide preferred), distilled water, a separatory funnel and a set of mason jars. Some extractions might further require a bunsen burner, while others might require an alternate solvent such as ethyl alchohol. A blender and a freezer is helpful.
Anyone that has passed a lab course should be able to extract aspirin (and a bunch of other chemicals) from willow bark in their kitchen. Purifying it down to a single active ingredient is much more complex, but that step is often unnecessary. Provided the plant has no materials with higher toxicity than the sought-after chemical, a simple extraction can be done relatively easily. It takes at least a week (without good equipment), usually more like 4 weeks, so this isn't a 'pick that from the garden and extract' process.
Actually purifying these extracts is generally either a crystallization or gravity separation process (or both), both of which can be greatly enhanced by the appropriate solvent or by the use of a centrifuge. There are some plants that contain other, unwanted toxic materials with similar physical and chemical properties. This is where the difficulty level starts to ramp up. If you know what you are doing, you can cause either the desireable or the undesireable substance in solution to react and precipitate out, then continue the refinement as normal. All that is required here is access to the appropriate reagents and an understanding of which chemicals to use (in addition to lab process familiarity).
A person could become competent at all of these processes given a few hours' training and a guidebook with specific instructions. It would be no more difficult than passing a Red Cross first aid test. They would not be chemists, but they would be able to make useful medicinal plant extracts. Of course, this would never happen. The same skills allow access to a number of interesting compounds which are illegal, where the source plant is not (due to proliferation).
-1 raving lunatic; +6 subGenius... Things even out...
Sage is not a research project, it will not conduct trials. it is a data-mining project. They idea is simply to create a standard API so that all the current research will be more effective. The $5M is just to get the thing off the ground. As soon as it has a single success, the funding will flow like water.
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