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Open Source Software Meets Do-It-Yourself Biology

Soulskill posted more than 4 years ago | from the releasing-your-genome-under-the-gpl dept.

Biotech 113

destinyland writes "This article profiles a growing movement — DIY biology — that's made possible in part by open source tools. Using programs like BioPerl and BioPython, DIY biologists write their own code (computer and genetic), designing their own biological systems and altering the genome. A protein-folding simulator, Folding@home, is now the most powerful distributed computing cluster in the world, and as the movement evolves, cooperatives are also springing up where hobbyists pool resources and create 'hacker spaces' to reduce costs and share knowledge. 'As the shift to open source software continues, computational biology will become even more accessible, and even more powerful,' this article argues — while intellectual property and other bureaucracies continue to hobble traditional forms of research."

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113 comments

Uhhh... (4, Funny)

Monkeedude1212 (1560403) | more than 4 years ago | (#30906858)

DIY Biology sounds pretty dangerous.

As long as the instructions it comes with are better than Ikea's...

Re:Uhhh... (0)

Anonymous Coward | more than 4 years ago | (#30906890)

Nah.. Easy as DIY Open Heart Surgery.

Re:Uhhh... (-1, Offtopic)

Anonymous Coward | more than 4 years ago | (#30906894)

All civilians must be locked in dark, padded rooms until they have been trained for their state selected profession. Amirite?

Re:Uhhh... (-1, Troll)

Anonymous Coward | more than 4 years ago | (#30906924)

You represent the pussification of western society.
Well done, and GTFO

Re:Uhhh... (1)

onepoint (301486) | more than 4 years ago | (#30906996)

this is something that I feel very uncomfortable with, it's the fear of something getting out of the lab, or the worst case example .... grey goo

Been going on for a long time now... (4, Insightful)

mollog (841386) | more than 4 years ago | (#30907204)

This concept of DIY biology is far, far older than science, itself. People have been manipulating livestock, crops, even our own genome, for a long time now. But the author of this article is right about new tools making the process that much more accessible and powerful.

The build-out of world trade over the last century has wrought some damaging changes to the world ecology. Invasive species, pernicious plant diseases, and the like are spreading world-wide. Government efforts in this realm have been sporadic and often do more harm than good. The ability of smaller, private organizations to conduct sophisticated science on a smaller budget will be a boon to the restoration of endangered species, for example.

But, I tagged this article with the whatcouldpossiblygowrong tag. Danger ahead.

Re:Uhhh... (2, Insightful)

Chris Mattern (191822) | more than 4 years ago | (#30907432)

I actually flagged this article "graygoo" myself, but in fact, it's not as likely as a lot of people think. The microbial ecology of the earth is a battlefield, with each micro-organism looking to expand its niche at the expense of others. Our would-be gray goo organism isn't going to take over the earth--it's going to get mugged for its lunch money and its carcass eaten by whatever can find nutrient value in it.

Re:Uhhh... (1)

maxume (22995) | more than 4 years ago | (#30907460)

Right. Any gray goo that comes about will have to find a way to deal with all the green goo before it becomes much of a problem.

Re:Uhhh... (2, Insightful)

interkin3tic (1469267) | more than 4 years ago | (#30908452)

Probably a bit pedantic, but grey goo [wikipedia.org] means nanobots out of control. You're thinking of biological threats, like artificial superflu or ebola reston [wikipedia.org] mutated to become pathogenic to humans or something similar, which I guess would be green goo?

Grey goo technically wouldn't be a product of DIY biology, that would be DIY nanotech.

Probably a bigger concern is invasive GMO taking over, but this I think is a bigger concern from say Monsanto, which has more money to put into making GMOs and seems a lot less concerned with ethics or long term consequences than individual researchers. If they were to find some genes that allowed plants to outcompete any wild plant, and it got out into the wild, it might be difficult/expensive to contain. Outside of several plant labs you can find Arabidopsis [wikipedia.org] that "got out", some could be harmless GMOs. I could easily see monsanto making a superplant arabidopsis and then being careless with the seeds.

I should state that I'm not a plant biologist, don't work at monsanto, and have no idea what if any legal or technical restrictions are in place to prevent that, they could be good ones. I'm just saying I'm more worried about dangerous biological threats coming out of corporate labs than someones garage.

Re:Uhhh... (4, Insightful)

fuzzyfuzzyfungus (1223518) | more than 4 years ago | (#30907050)

On the plus side, doing dangerous things that are more dangerous to others than to yourself is substantially harder than just doing dangerous things.

Until we get to the point where you can just buy a programmable matter synthesizer with a voice interface that will accept the command "50grams aerosolized anthrax, weapons grade" the only real danger of DIY Biology will be a few scientist wannabees ending up in the ER on a stiff antibiotic drip after spilling the wrong bacterial culture on themselves.

DIY Bio is novel, and sciencey, which makes it OOH Scary; but, if you just want to hurt some people, good old-fashioned all-american firearms are way easier, cheaper, and substantially more refined.

Re:Uhhh... (1)

umghhh (965931) | more than 4 years ago | (#30907302)

carpet knives do nicely too but you must also admit that the feeling of terror that is spread by media when envelopes with white powder are sent randomly around is also magnificent and much more efficient even if it has no real danger associated with it.

Re:Uhhh... (0)

Anonymous Coward | more than 4 years ago | (#30907930)

On the plus side, doing dangerous things that are more dangerous to others than to yourself is substantially harder than just doing dangerous things.

Yes, because what nuts would be suicidal enough to intentionally hurt themselves in the act of hurting others?

Re:Uhhh... (0)

Anonymous Coward | more than 4 years ago | (#30908604)

the rag heads

Re:Uhhh... (1)

pydev (1683904) | more than 4 years ago | (#30910394)

DIY Bio is novel, and sciencey, which makes it OOH Scary

If only that were the case; sadly, it isn't. DIY biology is extremely dangerous in a way that no other technology to date has been.

Re:Uhhh... (2, Insightful)

izomiac (815208) | more than 4 years ago | (#30907182)

Meh, most lab research in biology fail on the first few attempts. DIY biology is likely to have an even higher failure rate, especially with stuff that hasn't been done a thousand times before. Beyond that, if grey goo or a super bug was feasible the natural bacteria would've done it ages ago.

Re:Uhhh... (1)

sonnejw0 (1114901) | more than 4 years ago | (#30907420)

I do neurobiology for a living ... why would anyone do this for FUN?!

Re:Uhhh... (2, Insightful)

PitaBred (632671) | more than 4 years ago | (#30907498)

Why would anyone write computer programs for fun? Fun is completely in the eye of the beholder

Re:Uhhh... (1)

Remus Shepherd (32833) | more than 4 years ago | (#30907826)

What do they allow you to experiment on in neurobiology?

DIYbiology has no limits. Want to try and make immortal hamsters [turktel.net]? Design a superflu? Cross your pet terrier and a goldfish? Brew glowing yogurt? [thechemblog.com]

The 'fun' of DIYbio is in not being limited by money, corporate involvement, financial benefit, or -- in some cases -- ethics.

Which is why I also put the 'whatcouldpossiblygowrong' tag on this story. Anarchists with gene splicing facilities will make for a VERY interesting future.

Re:Uhhh... (1)

h4rm0ny (722443) | more than 4 years ago | (#30910034)


Pet peeve = Anarchist != Mindless destructive types. If anything, I've found the reverse to be almost always the case.

Re:Uhhh... (1)

svtdragon (917476) | more than 4 years ago | (#30907274)

Useful as it sounds, I think DIY bioweapons could be a *small* concern. Especially if they come with instructions better than Ikea's.

Re:Uhhh... (3, Funny)

Hurricane78 (562437) | more than 4 years ago | (#30907540)

Excuse me. In our days, we used to call that any of:
- Sex
- Pregnancy
- Having mold in the bathroom/basement/etc.
- Growing your own food.
- Brewing your own beer / making your own cheese/salami/etc.
- Letting the dog lick your face.
- Actually eating the sand-cake that you made in the sandbox where the dogs used to poop.
And we lived with it! (Not in that order, though. ;)

The youth today. A bunch of bubble boys in fear of the world.
Now get off my lawn!

Re:Uhhh... (1)

mcgrew (92797) | more than 4 years ago | (#30907866)

Naw, it's easy. The hard part is finding a lab partner. If it wasn't for DIY biology I wouldn't have kids.

Re:Uhhh... (0)

Anonymous Coward | more than 4 years ago | (#30907998)

Yay, no more school shootings. Now angry kids will just make novel time bomb viruses. Oh wait, that was Oryx and Crake.

Re:Uhhh... (1)

Eudial (590661) | more than 4 years ago | (#30911012)

DIY Biology sounds pretty dangerous.

As long as the instructions it comes with are better than Ikea's...

Not particularly so long as you're careful and use a condom.

Re:Uhhh... (1)

geekoid (135745) | more than 4 years ago | (#30912178)

If you can't understand IKEA instructions, then DIY biology IS then only kind your allowed to have.

This only makes sense. (-1, Troll)

Anonymous Coward | more than 4 years ago | (#30906914)

The OSS crowd is looking for a cure for AIDS because they all eat the shit out of the asses of other men and take cocks up their shit chute.

Fucking dirty bird faggots.

Distributed Cluster (0, Funny)

Anonymous Coward | more than 4 years ago | (#30906934)

...Folding@home, is now the most powerful distributed computing cluster in the world...

A Distributed Cluster? *Head Asplode*

Re:Distributed Cluster (0, Offtopic)

fuzzyfuzzyfungus (1223518) | more than 4 years ago | (#30907084)

The throughput and latency of a cluster that works over the public internet would make your basic 100Mb ethernet operation laugh, not to mention the cool kids in myranet and infiniband; but the difference is one of degree rather than kind. If your problem is loosely coupled enough, it works just fine.

Re:Distributed Cluster (0)

Anonymous Coward | more than 4 years ago | (#30907942)

I suspect that he was referring to the definition of the word "cluster" and how that isn't very compatible with "distributed".

Depends (2, Insightful)

robbyjo (315601) | more than 4 years ago | (#30907022)

Many of these biology experiments require very expensive machines, such as microarray machines, as mentioned by the article. I don't know if purchasing refurbished machines is a wise choice since we don't want data quality to be compromised. Also, don't forget about service plans when the machines break or producing inconsistent output. Not to mention various reagents, other chemicals, and supplies such as microarray chips that make the experiment yields high quality data. These easily reach hundreds of dollars a piece. Also, purchasing such chemicals will get you labeled as a terrorist.

Another issue is gathering the samples. If you're collecting yeast, that would be simple. Arabidopsis, other small plants, mice, or other small animals, you probably need quite some space. Humans? That won't be simple at all. You have to clear privacy issues, getting the research review board to sign papers, etc. Sample collection alone can cost you lots of money and time. You can always resort to publicly available data. But chances are that you won't be able to impress scientists much for going that route. Also, most of the important discoveries are already done on this data. Most likely, all you can do is to confirm existing results or to provide some tangential additional info.

Re:Depends (4, Interesting)

GameMaster (148118) | more than 4 years ago | (#30907562)

Sure some of the more exotic equipment will, probably, still be out of the hands of DIYers. However, one of the things that this movement is known for is designing home-made versions of some of the expensive lab-grade equipment (such as 30k+ rpm centerfuges from Dremels; digital optical microscopes from an optical scope and a webcam; home built electron microscopes; etc.) which, actually, work. Pair that with their willingness to publish their, individual, projects as step-by-step instructions and share all their info as a community and I think it's completely possible that their communal capabilities will ramp up, relatively, quickly. A similar effect can be seen in the, long existing, amateur astronomy community and the DIY CNC community.

Re:Depends (0)

Anonymous Coward | more than 4 years ago | (#30908176)

>DIY CNC community

Lets hope those guys don't team up with the DIY Bio guys making their equipment for them...

Re:Depends (1)

Hatta (162192) | more than 4 years ago | (#30908322)

I bet a PC with a custom cooling block and temperature monitoring software could be rigged into a thermal cycler for PCR. I'm sure there's a better way to do it, but it would be good for a laugh.

I'm wondering how they get their hands on the raw materials. A freezer full of restriction enzymes is expensive. Do they grow up RE expressing cultures and purify it all themselves? What about stuff like dNTPs, agarose? That's some expensive stuff too.

Re:Depends (1)

Maglos (667167) | more than 4 years ago | (#30908982)

Some guys will spend 100+k on a wood working shop; I'm sure there are enough people with money to put a few dollars down on cool biotech toys. A professor of mine bought a 30k drafting printer for printing large format photography.

Re:Depends (1)

tburkhol (121842) | more than 4 years ago | (#30909234)

Many of these biology experiments require very expensive machines, such as microarray machines, as mentioned by the article.

You'd be surprised what you can accomplish with half-assed equipment. For example, you don't have to buy Affymetrix latest 30,000 gene chip, you can spot, by hand, a dozen or more probes onto a glass slide and visualize them with a DSLR camera. The results may not be suitable for Nature (or even your most hated journal), but it's still discovery. It's discovery you can do in your garage that would have been impossible for a major research lab just 20 years ago.

That's the point really: a lot of this discovery is based on very straightforward techniques and tools, but they're so sensitive that you can get a pretty good result with care and poor equipment. Same as the guys who build rockets in their garage: they may not get to orbit; they may not clear the atmosphere, but they can do some exceptionally sophisticated physics without a NASA grant. If you're doing biology for your own joy, you can do some very sophisticated cell and molecular biology without an NIH grant.

Tissue? I passed a dead rat on my way in today - off limits for professional research, but there's nothing preventing an amateur from using it. Or from taking as much of his own tissue as he'd like. From his friends, too, if he can convince them it's cool.

Re:Depends (2, Informative)

interkin3tic (1469267) | more than 4 years ago | (#30910960)

Many of these biology experiments require very expensive machines, such as microarray machines, as mentioned by the article. I don't know if purchasing refurbished machines is a wise choice since we don't want data quality to be compromised.

A microarray is pretty expensive yes, but a lot of DIY biology could be done with just a computer and or a secondhand PCR machine. Used PCR machines apperantly can be had for under a grand [ebay.com]. Even less if you can service a broken one yourself, which many of these DIYers seem capable of. Probably won't have all the fancy options of a higher priced one either, but our academic lab has an expensive cycler with many options that we never use.

Data quality with many of these things is less tempermental than a microarray too. The secondhand PCR machine in this case might not be good for sequencing, but it would be a great tool if you were, say, making a plasmid to make glowing bacteria, using it to identify species of plants, making in-situ hybridization primers. There are a lot of things you can do with a basic cheap PCR machine.

As far as microarray data goes, an affymetrix premade microarray chip goes for about a thousand dollars. Obviously it's not feasible for most people to do many of these out of their own pocket, but not everyone does. Say you want to find out what genes are expressed more in dog breed A than dog breed B. If you were wanting to publish that data in a peer-reviewed journal, you'd probably need 6 chips, it seems like most people I know who do microarray do triplicates. If you were just wanting to find out for yourself, like to find canidates for which genes produced trait X that was in breed A, you could do just two, one for each, and hope it wasn't wildly innacurate. You could then focus your search based on that, taking it with a grain of salt until you confirmed it through other, less expensive means.

If you were going to be doing many microarrays, this website [stanford.edu] appears to be a guide for making your own microarrayer. The price tag for building it exactly as that lab says to would be about $24k [stanford.edu]. Again though, many DIYers are mechanically inclined and could cut corners for their own purposes.

Another issue is gathering the samples. If you're collecting yeast, that would be simple. Arabidopsis, other small plants, mice, or other small animals, you probably need quite some space.

I don't see that. Our lab studies chicken embryos. An egg incubator is pretty small. C elegans can be grown wherever you've got space. Arabidopsis can grow in the yard, you don't need acres. A research-grade mouse colony would be expensive yes (maintaining a genetically pure mouse colony in a sterile environment free of variation is harder just obtaining mice from the street). If you need other model organisms, there are farms. It can be a limiting factor, yes, but when is that not true? You can't exactly use elephants as a model organism in really any lab in the world.

Humans? That won't be simple at all. You have to clear privacy issues, getting the research review board to sign papers, etc.

Which research review board? If I'm comparing gene expression in human blood samples in my garage, without using public grant money, the "review board" is whatever poor saps I sucker into giving me their blood.

You can always resort to publicly available data. But chances are that you won't be able to impress scientists much for going that route. Also, most of the important discoveries are already done on this data.

I reject both of those claims. Real scientists recognize valid results independant of the professional nature of the researcher or his lab. Hell, most of us "professionals" are pretty much loony toons anyway, some nut doing experiments in his garage is just as believable as some nut getting paid to do it. Journal editors might not be, but many won't.

As far as "all that's worth knowing from public data sets is already known," that's wayyyy off. The specific area of your specific field you're thinking of... maybe, but I doubt it. Across all publicly available data? Just no.

For example, genomes are being published all the time. I'd submit that a genome just published a few months ago cannot possibly be tapped out. Find some homologous genes in far-diverged species, like sea urchin or platypus, and do the analysis from your own computer on your own time, using the free resources out there. There are plenty of interesting and useful discoveries left there on important genes.

Most likely, all you can do is to confirm existing results or to provide some tangential additional info.

Confirming existing results is a necessary and valuable task in science that, by and large, is not being done by biological labs thanks to the publish-or-perish system and the requirement by most journals that results be new and fresh.

"Tangential" additional info in biology is rarely useless and is also often neglected by professional labs for much the same reason as confirming results.

 

DIY?? (4, Funny)

metamechanical (545566) | more than 4 years ago | (#30907066)

Do it yourself biology??

I prefer "do it with someone else" biology...

Re:DIY?? (0)

Anonymous Coward | more than 4 years ago | (#30907216)

lol of course you do. You are an IT geek who is a bit starved for 'it'

Re:DIY?? (0)

Anonymous Coward | more than 4 years ago | (#30909474)

This is /. we all are DIY'ers here.

Any progress? (4, Insightful)

vlm (69642) | more than 4 years ago | (#30907092)

Any progress since the last time this was on slashdot? No? Thought so.

Downloading computational biology software, that you have no idea how to use, makes you a molecular biologist, the same way that downloading finite element analysis software that you don't know how to use, makes you a mechanical engineer, downloading a SPICE simulator that you don't know how to use, makes you an electrical engineer, or downloading Pr0n that you can't re-enact makes you a sex expert. At least the Pr0n is easier to apply than a FEM or SPICE package, it being a "pictorial diagram", the disadvantage being that it requires a member of the appropriate sex (and species!) to re-enact.

Re:Any progress? (4, Insightful)

laughingcoyote (762272) | more than 4 years ago | (#30907286)

Sure. And downloading an IDE you have no idea how to use doesn't make you a programmer, either. But it can certainly be a good first step in that direction. Knowing how to use those tools properly is part of what a (molecular biologist|mechanical engineer|electrical engineer) does, so if you're interested in doing that, you'll want to learn. The way to learn something complex is to see it, fumble around with it, make some mistakes, figure out what caused them, take a look at the documentation, mess up again, take another look, and so on. How will you ever start that process without first getting your hands on the tool?

Re:Any progress? (1)

caffeinemessiah (918089) | more than 4 years ago | (#30908044)

Knowing how to use those tools properly is part of what a (molecular biologist|mechanical engineer|electrical engineer) does, so if you're interested in doing that, you'll want to learn. The way to learn something complex is to see it, fumble around with it, make some mistakes, figure out what caused them, take a look at the documentation, mess up again, take another look, and so on. How will you ever start that process without first getting your hands on the tool?

In my experience, it's not that biologists can't figure out how to use the tools themselves, but rather that they sometimes don't understand the advanced algorithms that go into them. Many computational biology algorithms today are really advanced with a plethora of subtleties -- phylogeny trees are built using consensus and parsimony, sequence alignment aka BLAST is heuristics based on edit distance -- and the problem is more that they're blindly used as tools, where fumbling around incorrectly will generally produce some output, instead of understanding the assumptions and limitations of the underlying algorithms.

YMMV, as always.

Re:Any progress? (1)

norletsk (1567121) | more than 4 years ago | (#30910740)

I'm not an expert, but I do have several years of experience with molecular dynamics(GROMACS) and quantum chemistry(GAMESS) software. From my experience, the task of running a simulation using pre-packaged software is relatively simple. The difficult part is knowing enough biology, chemistry and physics to set up a meaningful simulation and being able to analyze and interpret the results. So yes, you could read the software documentation and learn something, but you are attacking the problem from the wrong end.

Re:Any progress? (1)

dangitman (862676) | more than 4 years ago | (#30907310)

requires a member of the appropriate sex (and species!)

Damn slashdot nerds, always nit-picking.

Re:Any progress? (3, Interesting)

Explodicle (818405) | more than 4 years ago | (#30908560)

I'm a mechanical engineer who uses finite element analysis every day. These days are numbered. Every year something new comes out that makes it even easier and more idiot-proof, heading towards the point where really anyone COULD do it. Red = "breaks here". "Would you like to use the Analysis Assistant?"

The distinction between the expert and the automated amateur is diminishing. Remember when you needed to know HTML to have a web page? It's only now getting started with DIY biology, but just wait... the progress since last time might not be obvious, but it's happening.

Is this really a new thing? (0, Redundant)

Locke2005 (849178) | more than 4 years ago | (#30907098)

People have been experimenting with DIY biology for years. My first experiment is named "Venus", she is 9 years old now and is a sweet, lovable (if hyperactive) cheerleader. Overall, I'd say this experiment was a resounding success, although I am still waiting for others to replicate my results.

Re:Is this really a new thing? (1)

vlm (69642) | more than 4 years ago | (#30907528)

My first experiment is named "Venus", she is 9 years old now and is a sweet, lovable (if hyperactive) cheerleader. Overall, I'd say this experiment was a resounding success, although I am still waiting for others to replicate my results.

Arrrrrr, I was going to snarkily suggest I'll try my best to replicate your result, if you send her mother over here, but then I realized I was assuming Venus is a H. Sapiens and not, perhaps, a Shetland Sheepdog ... nothing is more of a sweet lovable hyperactive cheerleader than a sheltie doggie. See, that is EXACTLY the kind of mistake an amateur molecular biologist like myself could make, scary, eh?

Re:Is this really a new thing? (0, Offtopic)

Locke2005 (849178) | more than 4 years ago | (#30908552)

Fortunately, in this case your initial assumption was correct -- Venus is indeed a Homo Sapiens. Nevertheless, some people still refer to her mother as a "bitch". Good luck with your experiments, and remember -- practice makes perfect!

Hurray great article! (2, Funny)

Vamman (1156411) | more than 4 years ago | (#30907108)

Awesome article. Our team has embraced the use of the R Stats package in our environmental assessment tool. We were sick of the COM object library to connect modern .NET tools to our tool so I decided to build a .NET wrapper for R. Still in early development but it works for us. We decided to release it under GPL for everyone to use. I think the title of article could read something like "Biologists take programming into their own hands" which is what I was forced to do during my MSc. and now once again in my position at U of S I find myself hanging out with the computer scientists a little bit too often.

It's bad enough here with electronics hardware. (2, Interesting)

Singularity42 (1658297) | more than 4 years ago | (#30907114)

A poll recently indicated 95%+ coders here. Something about computer science makes comments skew strangely. Look at an article on encryption, and you'll get quite a few accurate, thoughtful comments. Look at one on CPUs, or applied physics, and you got a lot of jokes and misunderstandings. Is there something peculiar about the field of computer science that makes a worldview tilted so much?

Re:It's bad enough here with electronics hardware. (0)

Anonymous Coward | more than 4 years ago | (#30907410)

Look at one on CPUs, or applied physics, and you got a lot of jokes and misunderstandings.

If you think that's bad, you should look at the comments on an article about law or sociology. :P

SpongE (-1, Offtopic)

Anonymous Coward | more than 4 years ago | (#30907148)

I'm discus5ing on my Pentium Pro market. Therefore session and join in least I won't

Dammit (2, Funny)

JustNiz (692889) | more than 4 years ago | (#30907176)

From the title I was looking forward to the news that I could DL the opensource software, get my PC hooked up to a robot arm and a webcam, and have it do my appendectomy.

i like cooperative do-it-yourself biology (2, Funny)

circletimessquare (444983) | more than 4 years ago | (#30907198)

sadly, i mostly encounter uncooperatives

this leads to do-it-by-yourself biology

Re:i like cooperative do-it-yourself biology (-1, Flamebait)

Anonymous Coward | more than 4 years ago | (#30907380)

just shut the fuck up. please. you're a loser and your spic film will never amount to anything. it's an embarrassment and so are you.

Stop it! (0, Interesting)

Anonymous Coward | more than 4 years ago | (#30907234)

"As the shift to open source software continues..."

Stop the shit, I'm going blind from it, stop it!

Oh... shiFt... Nevermind, continue, continue, good job...

Folding@Home is not a "DIY" project. . . (5, Insightful)

the gnat (153162) | more than 4 years ago | (#30907362)

Vijay Pande is a Stanford professor and funded primarily by the same agencies that fund most of the biomedical research in this country - most importantly, the NIH. (Disclaimer: they fund my work too.) He has full-time scientists (i.e. people who spent most of their 20s in school) and computer engineers writing code and assistance from hardware vendors (ATI/AMD and NVIDIA, at least). FAH is a great example of how to leverage distributed computing resources and volunteer effort, and it's an excellent technical solution to what is potentially a very expensive problem, but the intellectual effort is *not* distributed. I don't mean any of this as a criticism (I wish I had five petaflops at my disposal too), but this is not an example of "hobbyists" performing research free of bureaucracy. (In fact, the umbrella project for much of Pande's work now has a relatively large bureaucracy at Stanford, which surely wasn't suffering from a lack of bureaucracy to begin with.)

Re:Folding@Home is not a "DIY" project. . . (1)

GameMaster (148118) | more than 4 years ago | (#30907660)

Yes, the Folding@Home project, itself, is not a DIY project and the intellectual effort isn't distributed. However, the people contributing to the project by running the client software ARE amateurs. It can be suggested that the project has helped the DIY biology community from a PR standpoint because it has average people thinking about the nuts and bolts of biology and gives them a sense of involvement.

IP is not hobbling traditional research (4, Informative)

Grond (15515) | more than 4 years ago | (#30907406)

The article makes some vague statements that IP limits traditional biotech research. In fact, empirical studies do not back up such claims. John Walsh, Charlene Cho, Wesley Cohen, View from the Bench: Patents and Material Transfers [umd.edu] , 309 Science 2002-2003 (2005). Some highlights:

"Thus, of 381 academic scientists, even including the 10% who claimed to be doing drug development or related downstream work, none were stopped by the existence of third-party patents, and even modifications or delays were rare, each affecting around 1% of our sample."

"In addition, 22 of the 23 respondents to our question about costs reported that there was no fee for the patented technology, and the 23rd respondent said the fee was in the range of $1 to $100."

19% of the respondents reported that other scientists had not complied with material transfer requests (i.e. requests for data or samples), but analysis found that "The patent status of the requested material had no significant effect on noncompliance."

An additional, more focused case study of a highly-commercialized area of research with a lot of patent activity found that "only 3% of respondents reported stopping a project in the past 2 years because of a patent."

Re:IP is not hobbling traditional research (1)

nedlohs (1335013) | more than 4 years ago | (#30907570)

"only 3% of respondents reported stopping a project in the past 2 years because of a patent" so "IP limits traditional biotech research" is a true statement then.

Of course the limits might be made up for by the incentive such IP provides to doing research in the first place, but that doesn't mean they don't exist.

Re:IP is not hobbling traditional research (1)

Rich0 (548339) | more than 4 years ago | (#30908376)

Well, being stopped isn't the same as reporting that you were stopped. 3% isn't really a big figure.

In my experience biotech companies don't like messing with academia. There isn't any money to be made there anyway, and if some lab manages to increase the market for some patented technology it only means more money for the patent holder.

Now, if the "academic" lab wanted to start mass-producing vials of vaccines or something that would be a different matter.

Back when I was in the lab the biggest issues tended to be around expression systems and of course PCR (the patent on that is almost certainly gone by now). However, for the most part people just ignored these patents. Sure, the first time you bought a kit for some expression system you might have to pay more, but a lot of the components are easily reproduced once you have a kit, and the pricing wasn't all that bad compared to the convenience factor (you're studying a gene, not trying to perfect making bacteria competent for transformation). PCR had a big markup, but you could get stuff suitable for "primer extensions" cheap and the instructions would cover everything except telling your thermocycler to repeat the cycle 30 times.

Patents are really only an issue for commercialization of a technology. In fact, I'd be all for a general extension to patent law to explicitly allow violation of any patent for the purpose of non-commercial research where any devices made in violation of a patent are not sold or distributed.

Re:IP is not hobbling traditional research (2, Insightful)

Grond (15515) | more than 4 years ago | (#30908806)

In fact, I'd be all for a general extension to patent law to explicitly allow violation of any patent for the purpose of non-commercial research where any devices made in violation of a patent are not sold or distributed.

What's the need? If the research is non-commercial and no infringing products are sold or distributed, why would the patentee bother suing? It's non-commercial, so the defendant probably has little money and it would likely be a PR disaster. They didn't sell or distribute any infringing products, so damages are likely to be minimal. These are the main reasons why non-profit research is already basically in the clear.

So why not go ahead and codify the de facto research exemption into the law as you suggest? The reason is that it would be exploited like crazy (see the FDA safe harbor for an example). Companies would set up non-profit research arms to do their research, license-free, and then bring the results to market. It's very difficult (maybe impossible, given powerful corporate interests) to design a law that's narrow enough not to be exploited, broad enough to achieve its goal, yet also doesn't invite litigation or burdensome regulatory oversight.

Re:IP is not hobbling traditional research (0)

Anonymous Coward | more than 4 years ago | (#30909354)

I doubt that the harm happens at the level of actualised research, but rather research choices are effected by intellectual property. Thus, it slips by this study relatively unnoticed.

Re:IP is not hobbling traditional research (2, Informative)

Grond (15515) | more than 4 years ago | (#30910326)

I doubt that the harm happens at the level of actualised research, but rather research choices are effected by intellectual property. Thus, it slips by this study relatively unnoticed.

Actually the study authors looked at that, too. "[F]ew academic bench scientists currently pay much attention to others' patents. Only 5% (18 out of 379) regularly check for patents on knowledge inputs related to their research...Five percent had been made aware of intellectual property (IP) relevant to their research through a notification letter sent either to them or their institution." If they don't even know if something is patented or not, it can't affect whether they decide to research it.

Furthermore, "[E]ven for the few who were aware of others' patents, those third-party patents did not have a large impact on their research. Of the 32 respondents who were aware of relevant IP, four reported changing their research approach and five delayed completion of an experiment by more than 1 month. No one reported abandoning a line of research."

Re:IP is not hobbling traditional research (2, Insightful)

martin-boundary (547041) | more than 4 years ago | (#30911046)

Your linked paper is a report by a bunch of non-lawyers asking working scientists whether they think their work is adversely affected by IP law, and you consider that useful why?

We already know that most people break IP laws all the time, often without realizing it. Would you also quote a paper that claims the copyright threat is overblown, because the vast majority of music downloaders self-report that they aren't being sued?

The real problem is that the IP laws exist in the first place: they are a Sword of Damocles [wikipedia.org] upon researchers, whether they look up or not.

Re:IP is not hobbling traditional research (1)

Grond (15515) | more than 4 years ago | (#30911762)

Your linked paper is a report by a bunch of non-lawyers asking working scientists whether they think their work is adversely affected by IP law, and you consider that useful why?

Because the claim was made that IP (particularly patents) hobbles traditional biotech research. The paper shows directly that scientists are not changing their research behavior because of patents. If research continues unabated and unaltered despite patents, then the claim that patents hobble traditional research is incorrect. Would you care to explain why that is incorrect? If it's because the potential for lawsuits still exists, then I'll explain why that's wrong in a moment.

Would you also quote a paper that claims the copyright threat is overblown, because the vast majority of music downloaders self-report that they aren't being sued?

If the paper's claim was that the threat of copyright to the individual music downloader is overblown, then yes, I would. Most music downloaders will never be sued, especially now that the RIAA has basically stopped filing new suits (there were a few that were already prepared when they announced they were stopping and those got filed afterward but it's pretty much stopped now). According to the EFF [eff.org], there were 28,000 people threatened with legal action or sued and there are roughly 60 million file sharers in US [eff.org]. That's .05% or 1 in 2,000. You are more likely to die of injury in a year than to get threatened or sued by the RIAA. (odds of dying by injury in a year in the United States: 1 in 1,643, source [nsc.org])

But even so, music downloaders and biotech researchers cannot be compared so simply. For starters, copyright and patents are very different (e.g., no statutory damages for patent infringement). The nature of patent damages makes it such that it's not economically rational for patentees to sue non-commercial researchers in most cases. Thus, patentees are unlikely to start suing researchers, especially since the recent trend has been to weaken patents, not strengthen them (see, e.g., the eBay and KSR cases).

Furthermore, patent infringement by a biotech researcher is pretty obvious. If the researcher publishes that he or she used Chemical X in a study but the patentee never sold any Chemical X to the researcher, you can bet there was infringement. And researchers keep detailed logs of their experiments. So, again, if patentees aren't suing it's not because it wouldn't be easy to prove infringement.

There are also comparatively few biotech researchers. If one researcher gets sued it would have a much larger impact than the downloader suits. So again, if patentees wanted to shape researcher behavior through lawsuits they would've done it by now.

The real problem is that the IP laws exist in the first place: they are a Sword of Damocles upon researchers, whether they look up or not.

First, in all probability, no, they are not. We have decades of history to show that. Second, legally, no, they are not. Post-eBay it's unlikely that a patentee would be able to enjoin an academic or non-commercial researcher and the damages would be minimal in any case. The rational thing for researchers to do is to continue their research unabated, which is exactly what they're doing.

Remember, most of these researchers work for universities, which have money and patent lawyers. If there were any real risk from a patent suit, the university would tell the researchers to do something else.

Re:IP is not hobbling traditional research (1)

martin-boundary (547041) | more than 4 years ago | (#30912850)

If it's because the potential for lawsuits still exists, then I'll explain why that's wrong in a moment.

Yes. As far as I can tell, your counterargument does not address the ancillary costs involved. Even if a researcher does not concern himself with patents directly, someone does. The potential for IP infringement does push up insurance premiums, and causes contingency planning at some level in the university or company, which still costs money. These costs also have to be passed on, and in particular are likely to increase the licensing costs for the patents and machines that a researcher might wish to use, which in turn reduces the research money available for actual original research.

Remember, most of these researchers work for universities, which have money and patent lawyers. If there were any real risk from a patent suit, the university would tell the researchers to do something else.

Alternatively, the costs of doing research would simply go up, to transparently compensate for the risks.

Re:IP is not hobbling traditional research (1)

geekoid (135745) | more than 4 years ago | (#30912158)

It is intended that people can build on other patents. The system is specifically set up to do so.

I can take you patent, 'improve it', and patent the results.

Here is an example:
Lets say you invent a device that thaws meat faster. (basically a piece of steel you put the meat on.

I can take your device, add a piece that closes onto the top of the meat to thaw both sides at the same time. IT would be a valid patent, and I wouldn't be violating IP.

what's needed (0)

Anonymous Coward | more than 4 years ago | (#30907418)

I tell you what's sorely needed: an open-source biology that should be to Monsanto what Linux is to Microsoft.

AC

Re:what's needed (1)

BitHive (578094) | more than 4 years ago | (#30907764)

Yes, and maybe someday we can get an open source mathematics that will be to Wolfram Research what Sage is to Mathematica. Until then I guess I'll have to keep buying all my math online.

Kidding, right? (3, Insightful)

Corson (746347) | more than 4 years ago | (#30907610)

"many DIYers knowledge of these fields is so complete that the best among them design and conduct their own experiments at stunningly low costs. With adequate knowledge and ingenuity, DIYbiologists can build equipment and run experiments on a hobbyist's budget." That must be a (bad) joke. Forget the open-source/custom-made software and discount price hardware acquired on eBay, biology is first and foremost about wet lab. And not only it costs *a lot* but one needs licenses to purchase certain products. I have worked in biomedical research for almost ten years and I know that if you're in academia then you can purchase, say, enzymes and genetic vectors at their catalog price; but if you're industry then you get hit with 5-6 digit licensing fees. The only way to do at home what they claim to be doing is by using stuff from their academic research labs. Besides the risks involved (those cell line are actually cancer cells and engineered bacteria are mutant germs, not to mention the radioactively labeled nucleic acid probes that might end up in the toilet) the logistics are a nightmare. Storing liquid nitrogen in your basement? Discarding ethidium-bromide and acrylamide gels? Biological experiments are different from software development, they need follow up and supervision through the end, which may take 2-4 days. Drosophilla flys can't be frozen like bacteria. How do you discard biohazardous materials and mutagen/teratogen substances at home? There are many reasons why DIY biology is a very bad idea; it's a disaster waiting to happen.

Re:Kidding, right? (0)

Anonymous Coward | more than 4 years ago | (#30908640)

most of the negative responses here are similar to yours. They echo of a tradesman protecting his moneyed interests. How funny. FYI, I'm sure there are more difficult and expensive things to do in experimental biology than store liquid nitrogen or incinerate waste...

Re:Kidding, right? (1)

St.Creed (853824) | more than 4 years ago | (#30909096)

How do you discard biohazardous materials and mutagen/teratogen substances at home?

Down the toilet, flush twice. :)

Re:Kidding, right? (2, Insightful)

Hatta (162192) | more than 4 years ago | (#30909342)

The only way to do at home what they claim to be doing is by using stuff from their academic research labs.

Not really. You can get E. coli that express recombinant enzymes and purify it yourself. And patents don't cover stuff for personal use, so you're clear there.

Besides the risks involved (those cell line are actually cancer cells and engineered bacteria are mutant germs

None of which have a chance to survive outside of carefully controlled laboratory conditions.

not to mention the radioactively labeled nucleic acid probes that might end up in the toilet

I doubt anyone's using radioactive probes at home, probably more fluorescence, chemiluminescence, etc.

Storing liquid nitrogen in your basement?

Not really a problem if you pony up for the right container.

Discarding ethidium-bromide and acrylamide gels?

There are non-toxic stains for agarose gels. Polymerized acrylamide is not that toxic either.

Biological experiments are different from software development, they need follow up and supervision through the end, which may take 2-4 days. Drosophilla flys can't be frozen like bacteria.

For people dedicated to the hobby, there's no reason they can't deal with that.

How do you discard biohazardous materials and mutagen/teratogen substances at home?

This is a valid concern. The best way is to find ways to perform experiments that don't require hazardous materials. There is a lot of biology that does require hazardous materials, but there's also a lot that doesn't.

Re:Kidding, right? (0)

Anonymous Coward | more than 4 years ago | (#30909584)

Forget the open-source/custom-made software and discount price hardware acquired on eBay, biology is first and foremost about wet lab. And not only it costs *a lot* but one needs licenses to purchase certain products.

I don't think anyone's arguing that someone working out of his garage can do first class, publishable research. If you're just looking for results, you don't have to use triple-purified, ultra-certified AmpliTaq Platinum. You can extract and purify enzymes of modest activity from your own rainwater-derived bacterial colonies or grocery store chicken. Jesus, man, do you even know where those "certain products" that require licenses came from in the first place?

Discarding ethidium-bromide and acrylamide gels?

Do you know ethidium bromide is used to treat livestock parasites? Do you know contact lenses are made of polyacyrlamide? How do you dispose of the sodium hypochlorite in your home laundry?

Re:Kidding, right? (1)

marcosdumay (620877) | more than 4 years ago | (#30909618)

"Storing liquid nitrogen in your basement? "

Farmers have being storing liquid nitrogen on their (rural area) basement for a few decades now, with very few problems.

Re:Kidding, right? (1)

Zerth (26112) | more than 4 years ago | (#30909940)

How do you discard biohazardous materials and mutagen/teratogen substances at home?

A handful of rust, a heap of aluminum, mix in a concrete bowl, garnish with a magnesium ribbon, light and cover securely.

Do wear eye protection, though.

Re:Kidding, right? (1)

bwv549 (1730430) | more than 4 years ago | (#30910882)

DIYers discovering and/or promoting low risk/cost solutions to problems in experimental biology sounds like a big win for everyone (including those in academic/industrial settings).

Re:Kidding, right? (1)

interkin3tic (1469267) | more than 4 years ago | (#30912876)

Discarding ethidium-bromide and acrylamide gels?

If I were doing DNA gels at home, I'd be using sybrsafe [invitrogen.com]. As the name implies, it's a lot safer. Also less damaging to the DNA I'd be trying to isolate and can be reused many times. Slightly more expensive than dirt-cheap ethidium bromide though.

While unpolymerized acrylamide is a pretty dangerous neurotoxin, a polymerized polyacrylamide gel should actually be pretty safe. Granted, I wouldn't trust it, but plenty of academic labs do throw their in the garbage.

Biological experiments are different from software development, they need follow up and supervision through the end, which may take 2-4 days.

Some do, yes, but I'd say that doesn't describe most biological experiments. There are times when I need to work for half a day without interruption, but those are rare.

How do you discard biohazardous materials and mutagen/teratogen substances at home?

Depends on the hazardous/mutagenic material. There are quite detailed protocols and guidelines for disposal of almost all waste coming out of labs, with a little thinking you can find facilities to dispose of it, or find a way to neurtralize it yourself. And it's not like all research requires working with plutonium or exotic and dangerous materials. The most common teratogen I'd probably pour down the sink or drink (the most common teratogen being alchohol.)

You know what they really want (1)

SnarfQuest (469614) | more than 4 years ago | (#30907616)

Those geeky scientists really only want one thing: Cat Girls!

Girls with cat ears, and a tail. Just like in the manga!

Re:You know what they really want (1)

mcgrew (92797) | more than 4 years ago | (#30908610)

When my youngest daughter was a young teen, an artist for... I forget which game company it was, the one who did Jazz Jackrabbit, did a drawing of her like that. Turns out he was a fan of my Quake site.

"Dad, did you know you were famous?" I'm still grateful to the guy, made me a god in my daughter's eyes! Him and a few kids her age with their "Wow, that's your dad? Awesome!" when she'd mention me and my silly web site.

Been doing that (1, Funny)

edrobinson (976396) | more than 4 years ago | (#30907774)

The wife and I have been doing DIY biology for years and we have 3 kids and 3 grandkids to show for it.

Intellectual property laws are good (0)

Anonymous Coward | more than 4 years ago | (#30908250)

Intellectual property [law] hobbles research? Actually, intellectual property laws promote research, by giving inventors a means of supporting their work in a competitive marketplace that is independent of government funding. Without IP laws-and without respect for them-the government would wield even more power than now (already too much) and efficiency would suffer even more.

Not a surprise (1)

Scribbler'sEmporium (1310863) | more than 4 years ago | (#30908346)

Biology has not traditionally been computationally intensive, but that has changed in the last 20 years. Computer modelling of ecology, disease epidemiology, and cellular processes has been tremendously helpful. With the age of the genome merging into the age of the proteome the trend is only going to grow. Biology is or will shortly be as computationally intensive as physics. Witness the explosion of Bioinformatics departments in Universities in the last 10 years. The main trouble is that most of the problems in biology (finding patterns in nucleotide sequences for example) are not interesting problems for computer scientists. The computational techniques, for the most part have been worked out and are just a matter of number crunching. The trick now is to employ them on the mountain of data generated by the biologists. It doesn't surpise me that biologists are learning to do their own coding, or at least learning enough of the lingo to go talk to the local programmers.

Good, let's end the War on (some) Drugs.. (0)

Anonymous Coward | more than 4 years ago | (#30908482)

.. and create THC-producing dandelions or clover! Seriously.

R Bioconductor Cytoscape EGAN (3, Informative)

bzdyelnik (1600135) | more than 4 years ago | (#30908970)

Don't forget R/Bioconductor! Not only is R free/free, but there are thousands of available Bioconductor packages ready for out-of-the-box use. Also consider Cytoscape and or EGAN for graph visualization of established and experimental bio-knowledge. http://www.bioconductor.org/ [bioconductor.org] http://www.cytoscape.org/ [cytoscape.org] http://akt.ucsf.edu/EGAN/ [ucsf.edu] (full disclosure - I work on EGAN)

Andrew Ryan Already Tried This (1)

BJ_Covert_Action (1499847) | more than 4 years ago | (#30909208)

Don't you guys remember the underwater city of Rapture? It became easy and accessible to splice one's own gene sequence and all hell broke loose down there. What did you think those splicers were doing? Heroine? Mark my words, this will start with harmless science projects but soon the populous will be killing little girls for ADAM and shooting lighting at each other out of their hands. Hell's come the surface!

New meaning for "Making a Baby" (0)

Anonymous Coward | more than 4 years ago | (#30912474)

B: Honey, I've got my DIYbio kit and I'm headed to the basement! Don't bother me for a while I'm busy making a baby!
A: Don't you need me for that?
B: not anymore. not... any... more...

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