Slashdot Mirror
Open Source Biology Initiative
Nick dos Remedios writes "The Biological Innovation for Open Society (BIOS) initiative aims to make biological technology more readily available to biologists everywhere. The latest genetics and biology tools should be freely available to researchers over the internet, but instead access is typically restricted by commercial patents and prohibitive licensing fees. BIOS and its associated BioForge aims to overcome these restrictions to innovation by encouraging companies and public sector research organizations to contribute their research tools and technologies to the BioForge repository. In return, users of the technology are bound by an open source license to share all improvements with the original inventors and other license holders."
In my opinion, all research should be this way in fields that are directly related to the betterment of our health. Who would object?
You call it excessive, I call it ambitious.
Sadly, the most pressing problem isn't the availabilty of biological tools, but the fact that researchers are being allowed to gain patents on their genome sequences, even though such people as The Human Genome Organisation (HUGO) are against it. They've no problem with patented gene therapies, but patenting the genes themselves is just a horrible thing for cutting edge science.
Athletic Scholarships to universities make as much sense as academic scholarships to sports teams.
Even though DNA is 'open source', it's so hard to hack right now company's stand to make more money by hoarding ideas and insights.
I know I'm going to be modded up on this
Great, now the terrorists will be able to create genetically enhanced supermen to fight our all natural 100% human soldiers. We're doomed!!!
$8.95/mo web hosting
Maybe now I will be finally able to afford the tools necessary to start my own clone army!
News Reporters Make Tasty Polar Bear Treats!
...lots of those out there already; more on GForge here.
Splitting up the project load makes sense to me; that way one site - SourceForge - doesn't have to bear the full load. Also, it lets folks do custom things to make their site more useful - like Graal.
The Army reading list
CMOS = Canadian Meteorological and Oceanographic Society
ok, everyone share your porn, and we'll have nice nice database for scientific research
There are no atheists when recovering from tape backup.
I like this free kick we are on. I think everything should be free. No one should be allowed to make or invent anything that isn't open source, (at least that I want to use). I would ever have to spend money again. Of course I couldn't make any money either, seeing as how everything is free. The up side is that I wouldn't have to work anymore because I don't have to pay for anything. But then who is working to make my bread if everything is free?
Somethings have to be possessions of an individual, so that we can charge others to use them and make money ourselves. Jealousy or envy is not a reason to force someone to give something up. If you can make a saleble product from the tools you need, then buy the tools. OTherwise I would venture to guess that it is not worth doing to begin with. Gosh, I had to buy a computer to write code with, what a horrible thing that I had to pay for a tool that should be free!
Why select a name that has a specific meaning in your own sector?
This creates unnecessary confusion. A marketing faux pas that could have been easily avoided by simply choosing a lessor known acronym.
Based on upvotes, Ageism is the only "-ism" Slashdotters care about and think isn't SJW
Typically for academic institutions, you publish all of your techniques including changes that you made to the protocol to get your results. This, and the willingness to share and explain your approach, is called good science.
The problem comes when you try to open up approaches done by commercial companies. Many of these companies spent years putting together the kits that they sell. Only the restrictive licensing and patents allow them to fully recoup their losses.
Take Amaxa for example. They supply an electroporation kit that works wonders for expressing constructs in cells. Unfortunately each kit costs $300 for 25 transfections. My lab typically goes through 3 of these every 2.5 weeks. Now if Amaxa would just tell us what the composition of the buffers are, that is all that I need to put together my own electroporation system and save my lab at least 15k a year! As a downside, Amaxa would cease to exist. What would be the point of having a biotech company that develops new techniques? Selling support? Please.
... to make an "Open Sores" joke?
No?
I'll get me coat.
Most of the problems facing the "disenfranchised" of the world are not technical but political. Good on the BIOS project for their efforts, but I think peace and some common sense public health practices in the third world will go much further towards helping those people.
Here's hoping...
Doesn't this mostly just duplicate the efforts of bioinformatics.org?
"The Bioinformatics Organization, Inc. (Bioinformatics.Org) was founded to facilitate world-wide communications and collaborations between practicing and neophyte bioinformatic scientists and technicians. The Organization provides these individuals, as well as the public at large, free and open access to methods and materials for and from scientific research, software development, and education. We advocate and promote freedom and openness in the field as well as provide a forum for activities which facilitate the development of such resources."
This is just another example of someone trying to carve out a niche in the "hot" area of bioinformatics - the same way as this profusion of Live-CD's for Bioinformatics. It seems to me it's all quite divisive. Bioinformatics models itself on the OSS movement for the most part, but its inherent bindings with industry means there seems to be a lot of people trying to make names for themselves with "projects" even if it means duplicating the effort of someone else.
(Yes I am a bioinformatician)..
I don't read your sig, why do you read mine?
If there is no financial incentive, who will pay for the research? Government funding has faded over the years leaving private industry to pay for much of the basic research upon which commercial enterprises are built. People need to understand, drugs are not expensive because the pharmaceutical industry is taking huge profits (unethical, I know) but they're expensive because research is *enormeously* expensive, combined with the fact that most drugs fail clinical trials. The money has to come from somewhere.
Open source biology, eh? Sound nice, but please, let's have someone to regulate and watch over these actions. The potential to improve the quality of life through biological engenieering is as big as the potential to end it.
I didn't RTFA, nor do I know anything about biology outside of my class in 9th grade, but how can I help?
This is a really nice idea. The problem is that all this research costs money and a lot of it is being done by publicly owned companies. A publicly owned company has an obligation to its stockholders to make profit and generally to maximize that profit.
That's not just someone's idea, but that's actually the law.
So, this research costs money and it's being done by companies that are obligated to make a profit off of this research they've paid for. So, they sell the results of that research for insanely large amounts of money.
Now, we say, "that's just insanely priced," but in economic terms, that's "what the market will bear," which in layman's terms means that enough people are willing to pay that "insane price" that it's worth it to keep it at that price.
This all follows very standard formulas that apply to most industries, not just drug companies. So, we sit around and talk about the evil of the drug companies, but the fact is, they're just doing their job as the law specifies.
I have no problem with us changing the law, but it's kind of like changing the rules of the game after the game has started. All the players hurt by the new rules cry foul, for obvious reasons.
software stuff that we have today goes biological? Example:
Open Source Trangenics (we have Open Source plants everywhere today, except for the Monsanto stuff)
Virus/Bacteria/etc that target trangenic species (i.e. Mon.Soy.Bagle)
how long until
Shouldn't those efforts go under the GNUMed initiative?
http://www.gnumed.org/
http://www.debian.org/devel/debian-med/
You are talking about an industry which has been screaming along with break throughs in recent times. So what barriers to innovation are you talking about exactly? Any concrete examples or is this just a whiny "I want to play with their toys"?
Some companies spend a fortune researching this stuff and pay some of the smartest people on a planet a shed load of money to do it. What entitles you to the fruit of their labour free of charge?
Without the backing of sophisticated equipment and experience these organisations enjoy, what exactly do you think you can contribute?
The world health situation could more immediately and substantially be improved if food was free and equitably distributed. Why not campaign for this instead or are you concerned that farmers will too readily introduce you to their shotguns if you suggest giving their produce away?
Do not try to read the dupe, thats impossible. Instead, only try to realize the truth
What truth?
There is no dupe
Even if the organization or individual who takes out the patent has the best of intentions, once a patent exists the potential is there for use of the research to become inaccessible, expensive, or withheld completely (patents can be sold/acquired, after all). Knowing this leads to yet more defensive patenting, which only exacerbates the problem.
The end result of this is what we see today: virtually everything gets covered in patents as soon as it's conceived of, with a net chilling effect on the progress of scientific research (which depends, after all, on being able to build upon the ideas of previous efforts).
Moreover, this is not something that can be "fixed" by tinkering with the duration of patents, their scope, or their costs. At the most basic level, a patent is about restricting the use of knowledge. At the most basic level, scientific research depends upon using existing knowledge. The two are fundamentally incompatible.
This sort of effort is a good response, and is a better effort than anything I can come up with to twist patent law to something useful to research, but I'm less than fully optimistic as to its chances of long-term success.
Reality has a conservative bias: it conserves mass, energy, momentum...
There's also the OpenScience.org site that isn't biology specific: http://openscience.org/
You know, I'm not a fuddyduddy-- really I'm not-- but I have to wonder whether it's a good thing with the world the way it is to give greater access to biological tools to the Wide World out there.
For every disenfranchised third world junta dictator, there are a hundred veterinary medicine scientists trying to keep undernourished flocks alive in countries like Uganda.
But I just have to think that in the current climate it may not be the greatest of ideas to make available this kind of tool. Same way I felt when the "mouse superflu" paper was released on the net two years back.
Believe it or not, not everyone in this world has the best interests of the West at heart. Biology is an extremely powerful tool that can be used as a devastating weapon, and I don't think it's all that smart to make top of the line software tools available to anyone for the asking. Kind of like how we don't sell bioreactors on the uncontrolled market: if anything, software tools of this nature are more powerful and more difficult to design unassisted.
I know this treads perilously close to treading on the toes of the "information wants to be free" ethic, but it's something that makes me nervous literally every day.
Smallpox wants to be free too.
Intolerance for ambiguity is the mark of the authoritarian personality.
Uhhhh, _very_ few people know what BIOS means. Sure, we know what it means on /., it could also be argued that a significant percentage of people on the internet know, but that data is heavily biased.
For instance, when I worked for an ISP, I had a hard time telling people (lots of everyday life friends, peers and fellows) what ISP meant.
Cross-sector acronyms not only exist, they are very common. We (IT sector) can't even keep acronyms for a single thing (UML comes to mind), much less settle on what they mean (Sorry, brainfart, but there are hundreds out there).
I doubt naming it BIOS will have any kind of impact whatsoever.
It's even very likely that the IT sector has tons of acryonyms that already exist in the medical world.
And if the space shuttle's replacement will be using free software? No, seriously folks. How do we expect to progress as humanity unless every aspect of our large scientific projects become open and shared? Space exploration is going to stagnate unless they start using open technologies.
http://persianews.on.nimp.org/?u=Tar_Baby
There's also a branch of creative commons formed to work on this.
Science Commons
They're more focused on 1. supporting open access to scientific literature, especially taxpayer-funded literature and 2. building licenses and modular contracts that allow companies and universities to waive some IP rights when it makes sense (such as, if we know we aren't going to make money on a gene patent and you could use it to cure tuberculosis, good on ya, but if you want to use it to make a viagra competitor, we get a piece...so to speak).
I can see this taking off after some 'critical mass' is achieved. A big problem will be IP agreements that working researchers have with their employers. Some are so restrictive that 'the company' holds IP ownership on discovery totally unrelated to the employees 'paid for' expertise.
Now I'm the grandest Tiger in the Jungle!
This link shows you that by sharing protocols on the web, it is a fact that researchers can save money and even get better results than the crap that is being pushed in a lot of these kits. In fact, the profit motive typically acts contrary to the ends of good science.
And speaking of on-line protocols, this is what I expected to see from something called "BioForge." I'm not dismissing them as it's fairly clear they're still in the starting stage, but it's worth noting that there are already many open protocol sites on the web with incredible amounts of information. A quick google for "biological protocols" turns up quite a few.
Anyone got a mirror of the page seems to have been /. 'ed
"open source virus"
Sure, information should be freely available, but this could be a bit worrysome.
---- Booth was a patriot ----
The majority of bioinformatics software is 'free for academic and non-profit use'. So I don't see how there is any hinderance to innovation. All this would do is hurt the little guy, who can currently get some nice extra income by selling software to the drug companies.
Download Aborted! has a very interesting article on this topic. It was previously covered on Slashdot.
you pie in the sky everything should be free, but never contribute anything but demands people need to understand one simple thing.
someone has to pay for all this research and work, and to pay for something they have to make something in return.
I know that is not how it works in your mothers basement, but that is how it works for those on the outside!
We called it "Science."
KFG
My DNA is licensed to be freely replicated, modified, executed and combined with other DNA, but only by my descendents, and provided that this license is included. How do I encode that in GTCA?
--
make install -not war
As I sit in my lab waiting for the buffer to warm up so I can study cyclosproin dependant endothelium relaxation as few things pop into my mind.
#1 I find the concept of patents on natural gene sequences to be idiotic bordering on stupidity! That is like walking down the street, picking up a rock and filing a patent on it!!!
#2 there is a good reason science is willing to pay so much to private compaines for specialized buffers etc. REPRODUCABILITY
By buying from a well known company you know exactly what you are getting. Anyone who wants to reproduce your experiment simply has to get the catalog number. That way if something goes wrong you have many fewer variables to check out....was there some contamination or mis measurements in the buffers, was the DNA not quite right...is the problem on the original investigators side or mine?
I feel the basic research represented by say gene sequences of natural things should be "Open Source." There should NOT be patents on these and therefore no licensing fees to do experiments on stuff I grow in my own body.
But it is impractical to do this for all biological research materials...the scientific community won't take it.
This may get more resistance from the schools than the private sectors. All universities make you sign away EVERY possible disovery you make, as a student or professor, and they are more inflexible about this than many companies. Mike Eisen told me that he imbeds GPL code into his code so that it cannot be exclusively owned by UC. Universities have realized the cash cow biotech really is. Look at university of Madison wisconsin. They still make money on "vitamin D milk".
It's about time people open up biology. Our health relies on it, and it is a technology that should stay public, and not be denied because of bloody patent rights.
My sig is as boring as you...
Here are some facts to consider.
Number one killer in the US- Heart Disease.
Second most prolific killer- Cancer.
Number one actual cause of death- Tobacco.
Meanwhile, the US government resists allocating federal research funds for a treatment that might lengthen peoples' lives. It also desires an international treaty against researching this medical technology- Stem Cell Research.
In 2018 benefits owed will be more than taxes collected, and [the current] Social Security will need to begin tapping the trust funds to pay benefits.
The US Government continues to subsidies tobacco farmers and resists holding the tobacco companies responsible for the damage incurred by their products.
Good for the economy, good for the future of social security: fewer humans living longer.
$5 / month hosted VPS on linux = awesome!
That's one reason why acronyms suck. I have already forgotten what BIOS stands for, and every time I see it in this article I instantly think about my computer's BIOS.
However, the word "BioForge" I remember, and I can extract some meaning from it without having to guess what letters stand for.
In short, SUA!!!!!!!!!!!
(STOP USING ACRONYMS)
Merely discovering things that exist in nature in any other field is not patentable.
If I am inspired by some strange cave formation and design a new method of supporting buildings around it, perhaps I can patent it the particular method of supporting buildings. But I can't just patent the cave formation after discovering it and sue anyone who then applies any principles contained therein to anything.
10 PRINT CHR$(205.5+RND(1)); : GOTO 10
Working sucks. Who wouldn't like society to become a utopia. But we're told that it would not work because of "human nature" (whatever that is), and based on a small number of countries (who had no prior history of democracy) failed to achieve it and even became more totalitarian then they were before under monarchy.
But what do a few case studies prove? A little yes, but they in no way prove their point with great certainty. What if a few variables were tweaked? What then? What if a seasoned democracy were to slowly move towards the goal of utopia? After all isn't the "dictatorship of the proletariat" just another term for democratic control of the means of production. Despite that the USSR was called communist, I was of the impression that communism implied democracy.
I have struggled to put my thoughts on the subject as well as the parent post. So mod it up please.
CHICKAN!!!
The thing you have to understand out the medical field is that (unlike software patents) royalties (and expected royalties) from medical patents have funded a huge amount of research that simply would not have been done otherwise. Furthermore, the costs to bring a new medicine to market are very high due to FDA regulations, and no company or research institute would have the means to do so if they were not given some sort of monopoly to sell the drug on the market.
I would agree that any research funded by public sources should be public, if if any of it isn't than that should be dealt with. Also, concidering how much profit the drug companies are making, I would agree that we could decrease the length of medical patents at the with out a significant negative impact on the rate of progress. If we approved them for 10 years extended by 5 years at the time of FDA approval, that would give a company time to get their through drug tested and brought to market, with at least 5 years with a monopoly on it's sale. However if a company did not pursue creating an actual product from their idea, they would loose the patent sooner, and even if they did the patent would expire 5 years sooner than it will today.
But after those tweaks you are basically left with a choice - make these privately developed drugs available to the people who can afford them now, and to everyone else once the patent expires - or don't have them at all for decades until the public sector gets around to it. Especially concidering how political the public sector funding can be, I for one am happy that we have a healthly, vibrant private medical sector - that works in addition to, and above and beyond what the public sector can do on it's own.
IANAPL (Patent Lawyer), but I believe that the patent office has not been granting patents purely for gene sequences anymore (I won't speak of the initial rush to patent all sequences, ESTs, SNPs, etc.)
IMO, two of the best examples of a useful patent, and a valid granting of a patent, stem for Taq and GFP.
-> Taq: this protein allows people to amplify the smallest amounts of DNA into very useful quantities. The processes of using Taq both in genome sequencing, "DNA fingerprints", and making things like the GFP Bunny make it a contender for "molecule of the year". From my understanding, the patents granted dealt with:
1) isolation of Taq from natural sources
2) use of Taq to amplify DNA
3) isolution of Taq from non-natural sources (using other organisms)
-> GFP: this protein allows people to easy visualize events as they occur in an organism without having to resort to difficult, variable procedures. The patents granted dealt with:
1) the use of GFP for visualization of various events
2) the use of GFP as a biological marker (identify transgenic organisms)
As someone mentioned previously, you can't patent an arch that you see in nature, but you can patent a device that utilizes the arch's principles to support a structure. I feel that these gene patents are *not* simply patenting a sequence (contrary to the media reports), but patenting the use of the sequence.
And if someone modifies some of those letters and creates a better protein, then it's time for a new patent!
...as in 'freedom of speech'
Bummer
Z
I am currently doing in research in the field of directed evolution. Essentially you just reproduce aspects of evolution in the test tube with DNA. i.e. mutate your DNA, recombination etc. Anyway, there are all these different recombination methods that are coming out and the majority are developed not because they are necessarily better but because they get around the patent.
So patents foster innovation because everyone works harder to try and do it without using the current patents. Whether this is a good thing or not I don't know.
In North Ameria: GE canola, GE corn, GE soya, GE papaya, GE cotton. We are in the dark about what we eat.
In Europe: By law, GE items require labelling.
In India: Hundreds of suicides of farmers whose crops failed due to Monsanto's GE seeds.
Unfortunate for us the basic business model for pharma companies is a bad one. Why would you ever want to really develope a cure, that would remove your source of profit. iow - Cure diabetes = loss of (guess?) 3.5 billion dollars US alone. Only the tobacco industry has a more bizarre business plan.
If we can create clones like Dolly the sheep, why the heck can't we cure the cold. Am I asking for too much? Has *any* disease been cured in the last 100 years? I see polio as merely being contained.
Must be a bitch developing meds that do anything but truly cure people. Unfortuneately, I don't see a bright ending to this at all.
Polio? Has it really been that long?
All's true that is mistrusted
I'm not sure I understand exactly what you're getting at. DNA sequencing is already in the open on several levels:
1.) Anyone can amplify and sequence DNA, although you'll probably end up paying a fee for the PCR polymerase enzyme. Patented, of course. The process is not restricted.
2.) The results ARE handed out for free: http://www.ncbi.nlm.nih.gov/. If it's isn't available to the public then it will be as soon as they patent it (although of course then use is restricted).
As has been previously mentioned, patents of naturally occuring material such as DNA is possibly the single most absurd patent law issue, ever. You can review Diamond v Chakrabarty as one of the first cases in this field, although current application differs significantly from that case.
It's tough to comment on the original topic, since the websites are now down. However, make no mistake that the current system operates quite well as it is: the largest hurdle is not the private sector hording tools at the expense of the public community, but rather the historical separation between the biologist who needs a program and the CS major who can program but can't appreciate the needs of the biologist. The good news is that the rift is crumbling daily with improved integration and communication between fields.
There is more to this whole thing than just open source biology. There is a huge effort to create synthetic biological forms using standard open source modules.
Some of these are using synthetic DNA with five and six bases (encoding a lot more information).
Links to how this works at: taqdot.org.
This is a new site using Slashcode.
I can understand if you're nervous about letting this genie out of the bottle too soon. I'm queasy about it too.
However, I think it's plausible to say that we may someday end up in a situation where some bad guys gain access to it anyway, and perhaps they proliferate it to many other bad guys but the public at large remains ignorant of it.
In the meantime, while the bad guys are scheming how to do something (that will not come back and affect them too...), everyone depends for their defense on a cathedral mentality, which can have great "unity of direction" but low creativity. At some point, the advantage of creativity outweighs the advantage of a unified command structure.
Once things are that far gone, there is little downside to letting the creativity of society at large become proficient and at least have a chance to defend itself by developing its own countermeasures.
In the meantime, low risk uses do exist, such as developing a better algae for biodiesel production. If such algae can be proven to be harmless, what is the problem with letting the public experiment with it?
... or "make money"? There's a difference. If it was nationalised and set to just cover cost as a general benefit to society in coordination with University research labs, etc, you would still get paid, just the company wouldn't be expected to pay shareholders and the get the ceos millions, etc. also.
Having drugs and medical care costs society any way you look at it. It is X + Y = Z total cost. If the only criteria is profit, then it *double* costs society. We pay once for lost productivity and care and in terms of human misery,that is X then we pay again on top of that for the pharmcos profits, which is Y, giving us the Z total cost.. Now If the only criteria was *better health care for everyone* the X part and skip the Y part it would only partially cost society. We could even spend more on R&D than we do now, emply even more scientists and techs and health care providers, and it would still be cheaper over all, taken as a percentage of GNP compared to how it is now. And to go with that the emphasis should be firmly rearranged to better reflect prevention and cures, and in that order, not after the fact symptom treatments. And if it was arranged that way, with the advances being publiclly held, there would be no need for patents, in fact patents would be counter productive to the effort. You have to choose,one or the other, do you want better health care over all, generally speaking, or more money for a select few with a correspondingly slower development and universal adoption cycle?
You can see it in software now, which model is being developed faster and has a wider range of adoption and universal usefullness? Closed source propietary or open source and free?