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DIY Biologists To Open Source Research
destinyland writes "Falling costs and garage tinkering are creating a grass roots movement of amateur biologists whose research is more transparent than that of academia. They are building lab equipment using common household items and even synthesizing new organisms, and their transparency also allows the social pressure which creates more ethical research. DIY Bio.org fosters lab co-ops for large equipment and provokes important discussions. (Would it be ethical to release a homegrown symbiote that cures scurvy in hundreds of thousands of people?) This movement could someday lead to bottom-up remedies for disease, fuel-generating microbes, or even a social-networked disease-tracking epidemiology. 'In much the same way that homebrew computer science built the world we live in today, garage biology can affect the future we make for ourselves,' argues h+ magazine, which featured the article in their summer issue."
The concept isn't to doing ground-breaking research per-se, but to bring everyday biology to the masses. Rarely are people doing research in universities or with biotech firms interested in teaching and making available techniques cheaply to the masses and making it something that everyone can access. Also a severe leaning toward open source isn't common with 'big bio' research either.
Tibbon
tibbon.com
h+: There has been a lot of discussion about the dangers of people doing this sort of research at home. Do you think this is over-exaggerated?
MP: I really do. The chances of someone accidentally creating a dangerous organism and the chances of it surviving in the environment outside a laboratory are vanishingly low.
Rudy Rucker has a great quote on that, "I have a mental image of germ-size MIT nerds putting on gangsta clothes and venturing into alleys to try some rough stuff. And then they meet up with the homies who've been keeping it real for a billion years or so." The bare facts of it are that there's nothing random about synthetic biology research. When we design a transgenic organism, we're deliberately adding one specific piece of new functionality, maybe a small pathway that leads to a new piece of functionality -- and the organism has to expend energy on producing the new proteins that those new genes code for. Because of this, the synthetic organism is necessarily less competitive than its wild-type relatives who are much better suited for the niche they already occupy in the environment.
So any accidental release is fated to die out within a few generations, because itâ(TM)s just not competitive enough.
That's right. When rabbits were introduced in Australia, they died off right away because they were less competitive than their wild-type relatives who were much better suited to the niche they already occupied.
Maybe they're folks who got Biology undergrads and ended up in medical or, GASP! software development because that's where the opportunities were.
There are only so many academic posts available. Also, many folks don't want to work in the "publish or perish" environment, the academic BS environment, or the simple fact that they just didn't want to be professional scientists.
To put it in perspective; how many amateur software developers do you know? You can ask the same thing about them. And we all know why one would rather be an amateur developer than a professional one!
Really, if they are THAT good at research, then why not at a university?
Because you shouldn't have to.
I wouldn't worry about "DIY biologists" cooking up some terrible superbug that wipes us all out. I would, however, worry about these biologists' personal safety. If they want to crunch data at home, no problem, but if they're trying to set up actual home labs, then there is a pretty good chance that at some point they will find their doors being broken down by armed men who are notorious for their lack of willingness to listen to reasonable explanations as to why there's all this glassware lying around.
The correlation between ignorance of statistics and using "correlation is not causation" as an argument is close to 1.
You don't like what 6.5 billion people are doing to the world now? Wait and see how badly we'd treat it if we were all starving to death.
However, we're moving away from such "crude" techniques towards more sophisticated analytical tools, since in many ways biochemistry is now technology-limited. Single-molecule work, such as that pioneered by Carlos Bustamante provide insights that would never be possible with classical methods, and on the other end of the spectrum, we're now working on characterizing the entire network of small metabolite molecules simultaneously and quantitatively. This kind of work just isn't easily carried out by amateur enthusiasts.
That said, there is certainly quite a bit of research that DIY biologists would be capable of performing, especially considering that they could have access to the same kind of resources that professionals do. For example, after amplifying a gene, no researcher will sequence it themselves: it's shipped of to a specialized lab that will do it, for a fee. That sequencing step requires equipment and expertise that's at a higher level than even the pros don't have.
But regardless of theoretical ability, the professionals retain the advantage that it is their job to work on these projects. The time they can dedicate to their work will be far greater than someone who does it as a hobby.
Back to the subject of "openness", the professional scientific world isn't nearly as closed-off as the article would have you believe. It is true that there is a persistent fear of being "scooped", but the standards are changing for staking your claim on a particular piece of research.
It used to be that a full manuscript in a scientific journal was the only thing sufficient to get credit for something. Now, people are gradually embracing online resources are a valid way to communicate, and by extension, to prove that they were the source of any particular bit of publicized material. Even non-finalized material is now more common to make public: Nature has a pre-publication online source for publishing findings, and there are journals devoted entirely to negative results, which was previously unheard-of.
The walls are coming down, it's just a question of finalizing the transition, and winning over the old guard.
Disclosure: I am a professional research scientist, one of the younger ones. I have a substantial hardware/software project in the works, which will likely be simultaneously published via classic journal, online website, and software via SourceForge.
How does one ensure the integrity of a bio filter system at a random University?
Here's a hint: You don't. There aren't heavy regulations on this stuff until it gets to the point of mass productionf or public consumption. There are standard practices for safety and such, but these aren't government regulated and can very to a degree among institutions and among researchers.
There are no regulations regarding home chemistry aside from the control of some classes of chemicals and some types of equipment. There are a hell of a lot of regulations regarding releasing medical products for mass consumption. Just putting a "cure" for anything out on the market without going through federal processes is a good way to incur heavy fines have your equipment siezed, probably even some jail time.
That's where the check is, and that's where it needs to stay. Nothing needs to be done with DIY bio-engineered product X until it is ready for mass consumption. At that point, one could likely sell their idea to a major corp, or perhaps get donations to support it, and get it pushed through the propper FDA vetting and safety processes.
Security is mostly a superstition... Avoiding danger is no safer in the long run than outright exposure. - Helen Keller
I think you may be drawing too direct a comparison. It used to be that cloning a gene responsibly for a known phenotype was enough for a significant publication. (That was before my time). Now to get prestige in academia you need to map out the surrounding regulatory networks or at least do a lot more work to characterize WHY gene X is creating phenotype Y. I assume the level of complexity required to publish has expanded similarly in biochemistry
I see the benefits of this DIY work as twofold. First, a huge fraction of genes (in my field, plant biology) are still annotated only as unknown function. Figuring out those functions may not be the path to a career of academic fame and fortune, but I'd really appreciate any group of people who start making a dent in them. But I doubt they'll do a lot of this, they sound a lot more like synthetic biologists. So secondly, in the field of synthetic biology right now a lot of the work being done is very conservative. For example reconstituting a photosystem from an algae in another microbe. If that works it'll be really cool, and tell us a lot about the genetic regulation involved in the process, but it's not as risky as a lot of things these garage biologists are doing. Not risky in a threat-to-human-life-as-we-know-it way obviously, but risky in a this-probably-won't-work way. You try telling a grad student "here's your thesis project, there's a 90% chance it won't work and after four years in the lab you'll have nothing to show for it, you won't publish, you won't graduate, but good luck with that."
People in garages can afford to fail, and that means they'll potential develop a few useful things that would have been easy to do in a professional lab, but appeared so improbable no one would want to gamble on them.
Historically, universities ignore "research" done by any person w/o a Ph.D. To the extent that this is a useful bias, your question is well posed and these guys will never emerge from the shadow of University research. To the extent that the usefulness of such a bias is becoming antiquated, this is how reform begins and how those that cling to dying models become irrelevant.
This is more like worrying about toy poodles going feral... in an area that's already got a coyote problem.
And yet, when you're sick, you take medicine. When you're hungry, you get food. When you're thirsty, you have clean water. That's all preventing a decrease in the population. So, claim we should keep the population down. Prove it. Walk the walk, or you're being hypocritical.
Didn't really think this one through too well, did you?
universities ignore "research" done by any person w/o a Ph.D
Academic researchers tend to ignore "research" which is not published in peer-reviewed journals. I've never had a journal ask to see my degrees.
The correlation between ignorance of statistics and using "correlation is not causation" as an argument is close to 1.
So just from reading the summary I want to say that I have grown somewhat tired of the attitude towards academia on here. It is not a place of suppressed ideas, incompetent people, publish or perish, and faked results to get more funding. While publish or perish can be very true at the most elite universities, it ain't true everywhere. There are plenty of profs doing good research at upper tier liberal arts schools, teaching only a bit more than they would at UC San whereever. Hell, you can even go to a decent sized research school and not feel like you are in hell. As an UNDERGRAD I worked 60-80 hours a week on classes, grad school applications/related stuff (like the GREs) and working in a lab. It sucked, but I worked longer hours than the majority of professors. I think anyone that earned a decent Ph.D. to get tenure shouldn't complain when they are working less than their students.
Lack of transparency? The biomedical research industry is far worse on this issue. "Getting scooped" (idea stealing) is only a problem when you are working on a project. Once it is done and sent off for publication or discussed at a conference (or brown bag seminar in your own department) everything is way more open than it would ever be in the corporate world.
Can't get access to an article? Try scholar.google.com. Many journals allow researchers to post PDFs on their personal webpages, and such documents come up in this search. I went to a liberal arts college with a shit library, and google scholar was how I got work done (That and a zippy interlibrary loan service). No one actually pays $30 to read some article, and if you think that is how the system works then you have been completely duped.
There is more to science than physics!
www.iomalfunction.blogspot.com
I've done this very successfully using liver instead of spit. You get much more dna that way, since you're using chunks of cellular matter instead of just a few stray epithelial cells.
A few words of advice- Use everclear instead of rum. Get it as cold as possible; I used a salt/ice bath. The colder the better. Instead of pouring the alcohol into the glass, decant it using a glass stirring rod or something similar ( http://www.csudh.edu/oliver/demos/gravsulf/pour-r2.jpg ). Do this as slowly as possible. Pre-chill your stir rod to keep the alcohol cold. If you use cellular matter like liver or meat, grind it with a mortar and pestle. A spoon and a bowl will work in a pinch.
It is a very neat experiment to do with kids around, since you can see the results and there's nothing too toxic involved.
-b
No offense, but I've stopped responding to AC's.
When it comes to research, I hate that phrase: do-it-yourself. Who else is going to think your thoughts for you?
Frankly, just like with astronomy, if you can do the research, you're part of the club. Period. I don't think there needs to be any distinction between DIY hobbyist science, academic research and industrial science. There's good research and there's not-so-good research. If you can purify a protein in your garage that no one else has been able to, then the NIH should be happy to post your procedure and contact information somewhere.
Interesting question: If you catch a GPL virus that is only being distributed as binary, are you guilty for copyright violation when it redistributes itself?
Ahhhh SNAP! It's time for the Kazza and bit-torrent MP3 virus!!!
Step 1. Take existing bot.net code and add utorrent with registry settings to start in hidden mode.
Step 2. Have it set to automatically download mp3's via rss or something.
Step 3. Distribute to the pleebs.
Step 4. Pleebs become seed servers.
Step 5. Watch RIAA sue all the pleebs.
Step 6. Watch everyone in the world get really pissed off.
Step 7. New defense, My system had that damn virus.
Step 8. No Profit for dem guys!
Step 9. Move to underground lair and work on those sharks with freaking lasers baby! BRILLIANT
When garage developers out-University the Universities, one must ask if Universities are following their obligations towards learning and understanding. If they are not, honouring those obligations, maybe we should dispose of them and replace them with groups that can.
If I choose to write an Open Source application using my $300 Dell laptop instead of attending a university with the latest and greatest hardware, has the university failed?
Honestly, I don't understand this notion that universities should be the repository of all knowledge and research in the age of the internet. I could have a bigger collection of books in two days (probably less, but factor in the seeders too) than the local university has.
Just because the university has the expensive tools, the cheap ones still work at home.
Not sure about your local university, but the John Rylands Library of the University of Manchester started with 40,000 titles and is now over the 4 million mark. And, to be quite frank with you, I regard that as being the bottom-of-the-barrel minimum for a University - especially in Britain, given that it's a day's trip to Hay-on-Wye (one of the few places you'll find more books than Amazon.com).
Secondly, sure you can write an Open Source application using your $300 Dell laptop. And within a matter of days, the local University should (if it is doing its job) have obtained a copy, and if it's an application with significant potential, said University should have dissected the logic, assigned students to work on it, and be contributing patches.
Sir Isaac Newton is supposed to have said that if he could see further, it's because he was standing on the shoulders of giants. University researchers are standing on the shoulders of the best the planet has to offer, whether those "best" are at University or not. If they are not leveraging what you and other people produce, they are not doing their jobs.
This is less about being the repository of all knowledge and research and more about the fact that (in theory) they know where to look, what to look for, how to look, and what to do once they find something. If they're not looking, and aren't doing anything significant with what they find, then there's something wrong. They don't have to do everything, but they should always be doing something.
It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
Now, I'm not far enough along to have refereed any papers yet, but my impression from talking to those who have is that anonymity restrictions mean that the referees don't know who wrote the papers and certainly don't know whether or not they have even a high school diploma. So, how you get a bunch of PhDs to review something seriously is to write a good, thorough description in clear, concise, proofread prose of well done research, and not throw in any unsubtantiated or irrelevant crank-agenda drivel.
SIGSEGV caught, terminating
wait... not that kind of sig.
There are standard practices for safety and such, but these aren't government regulated
OSHA et al?
SIGSEGV caught, terminating
wait... not that kind of sig.
More important, why does the article not have the whatcouldpossiblygowrong tag?