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Biotech Open Source Science

Open Source Software Meets Do-It-Yourself Biology 113

Posted by Soulskill
from the releasing-your-genome-under-the-gpl dept.
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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Open Source Software Meets Do-It-Yourself Biology

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  • Uhhh... (Score:5, Funny)

    by Monkeedude1212 (1560403) on Tuesday January 26, 2010 @01:33PM (#30906858) Journal

    DIY Biology sounds pretty dangerous.

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

    • by onepoint (301486)

      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

      • by mollog (841386) on Tuesday January 26, 2010 @01:57PM (#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: (Score:3, Insightful)

        by Chris Mattern (191822)

        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.

        • by maxume (22995)

          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: (Score:3, Insightful)

        by interkin3tic (1469267)

        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 conce

      • by Anonymous Coward

        http://en.wikipedia.org/wiki/The_White_Plague [wikipedia.org]

        Scared me way more than any "grey goo" idea.

        • by H3g3m0n (642800)
          Grey goo would be much worse. A plague can be contained, vaccinated against, small holdout pockets, some people might have a resistance etc...

          Grey goo on the other hand could destroy the planet in 48 hours depending on the speed of the replicators, there wouldn't really be any defense against it since you would have to make enough counter defense goo to stop the grey goo (thats even assuming someone could design and deploy some kind of anti-goo in the time it would take for the grey goo to so its thing,
    • Re:Uhhh... (Score:5, Insightful)

      by fuzzyfuzzyfungus (1223518) on Tuesday January 26, 2010 @01:47PM (#30907050) Journal
      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.
      • by umghhh (965931)
        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.
      • by pydev (1683904)

        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.

      • Funny, I was thinking of the DIY Biologists working on a mutagen that would reverse the "age" of skin cells for the purpose of avoiding such accidents, and Nordstoms Semi Annual Sales. [nordstroms.com]
    • Re: (Score:3, Funny)

      by Hatta (162192)

      "Put tab A into slot B" is really all you need to know anyway.

    • Re: (Score:2, Insightful)

      by izomiac (815208)
      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.
      • by sonnejw0 (1114901)
        I do neurobiology for a living ... why would anyone do this for FUN?!
        • Re: (Score:3, Insightful)

          by PitaBred (632671)

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

        • 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.

          • by h4rm0ny (722443)

            Pet peeve = Anarchist != Mindless destructive types. If anything, I've found the reverse to be almost always the case.
    • by svtdragon (917476)
      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... (Score:4, Funny)

      by Hurricane78 (562437) <deleted.slashdot@org> on Tuesday January 26, 2010 @02:22PM (#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!

    • by mcgrew (92797) *

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

    • by Eudial (590661)

      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.

    • by geekoid (135745)

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

  • Depends (Score:3, Insightful)

    by robbyjo (315601) on Tuesday January 26, 2010 @01:45PM (#30907022) Homepage

    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 (Score:5, Interesting)

      by GameMaster (148118) on Tuesday January 26, 2010 @02:24PM (#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.

      • by Hatta (162192)

        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.

      • Dude you gotta cut back, on, the commas.

    • by Maglos (667167)
      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.
    • by tburkhol (121842)

      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 disco

    • Re: (Score:3, Informative)

      by interkin3tic (1469267)

      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 m

  • DIY?? (Score:5, Funny)

    by metamechanical (545566) on Tuesday January 26, 2010 @01:47PM (#30907066)

    Do it yourself biology??

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

  • Any progress? (Score:5, Insightful)

    by vlm (69642) on Tuesday January 26, 2010 @01:49PM (#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? (Score:5, Insightful)

      by laughingcoyote (762272) <barghesthowl@NospAm.excite.com> on Tuesday January 26, 2010 @02:03PM (#30907286) Journal

      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?

      • 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 gener

      • by norletsk (1567121)

        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

    • by dangitman (862676)

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

      Damn slashdot nerds, always nit-picking.

    • Re:Any progress? (Score:4, Interesting)

      by Explodicle (818405) on Tuesday January 26, 2010 @03:25PM (#30908560) Homepage

      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.

    • <snip>(and species!)</snip>

      Only on Slashdot.

  • 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.
    • by vlm (69642)

      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: (Score:1, Offtopic)

        by Locke2005 (849178)
        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!
      • Mod parent up!
  • 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
  • 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?

  • Dammit (Score:3, Funny)

    by JustNiz (692889) on Tuesday January 26, 2010 @01:55PM (#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.

  • sadly, i mostly encounter uncooperatives

    this leads to do-it-by-yourself biology

  • by the gnat (153162) on Tuesday January 26, 2010 @02:09PM (#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.)

    • 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.

  • by Grond (15515) on Tuesday January 26, 2010 @02:13PM (#30907406) Homepage

    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."

    • by nedlohs (1335013)

      "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.

      • by Rich0 (548339)

        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 ten

        • Re: (Score:3, Insightful)

          by Grond (15515)

          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

    • Re: (Score:3, Insightful)

      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 Swor [wikipedia.org]

      • by Grond (15515)

        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.

        • 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

          • by Grond (15515)

            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,

      • by geekoid (135745)

        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.

  • Kidding, right? (Score:4, Insightful)

    by Corson (746347) on Tuesday January 26, 2010 @02:27PM (#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.
    • by St.Creed (853824)

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

      Down the toilet, flush twice. :)

    • Re: (Score:3, Insightful)

      by Hatta (162192)

      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

    • "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.

    • by Zerth (26112)

      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.

    • by bwv549 (1730430)
      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).
    • 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 descri

    • by Corson (746347)
      Guys, if ethidium bromide and polymerized acrylamide were not hazardous then you wouldn't manipulate them wearing rubber gloves, a lab coat, and a protective mask. If bacteria didn't mutate spontaneously then selection wouldn't happen; remember how strains commonly used in the research lab were obtained in the first place. Don't forget that most B cells, primary or cell lines, carry the Ebstein-Barr virus, and that bacteria used for cloning were transformed with vectors carrying antibiotic-resistance genes.
      • by Hatta (162192)

        The fact that people overreact to a perceived threat is not evidence that the threat is real. In my state, all pressurized gasses in cans are considered hazardous waste when used at a research institution. That means we can't even have reddi-whip at a department party without talking to EHS. Does this mean that reddi-whip isn't safe to use at home? Of course not.

        You are over-blowing the risks. They are absolutely manageable. We have a lot more to worry about from people dumping paint-thinner down the d

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

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

    • by mcgrew (92797) *

      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.

  • "Sir, the new beetle you were working on? It crashed. Shall I reboot it?"

  • The wife and I have been doing DIY biology for years and we have 3 kids and 3 grandkids to show for it.
  • 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 prob
  • by bzdyelnik (1600135) on Tuesday January 26, 2010 @04:00PM (#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)
  • 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!
  • by geekoid (135745) <dadinportland @ y a hoo.com> on Tuesday January 26, 2010 @08:29PM (#30912124) Homepage Journal

    coming to a upper respiratory near you.

  • Um, cloning genes into plasmids and propagating them in E.coli so that you can manipulate (mutate) the sequence invariably requires some kind of antibiotic selection. Letting people muck around in their garages with plasmids conferring antibiotics resistance in bugs that have the potential to become resident in your intestines and persist indefinitely in the environment is a horrendously bad idea.

    It's why all labs that do this stuff routinely are required to adhere to physical containment guidelines.

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