Could a bio lab be coming to a garage near you?

There was a time when only scientists used computers.  Now systems that are thousands of times more powerful are available to nearly everyone. Bio-technology could follow the same course. However, if you want to tackle genetic testing, synthetic biology, etc then you’re going to need some serious hardware. Electrophoresis, polymerase chain reactions, fluorescent spectrometry – these are all really basic techniques but they still require specialized machines that can cost thousands of dollars. Luckily, that may be about to change. We’ve seen several projects to make cheap and even open hardware versions of lab devices – helping biotech become more do-it-yourself. While at the Open Source Summit I had the chance to talk with some of the forces behind these projects, as well as with the DIY enthusiasts that hope to one day use them. We may be approaching the age of the personal biology lab but there are some major hurdles still in the way.

It’s been more than a year since we covered DIYbio.org, the online website where many would be bio-tech hobbyists share information. DIYbio is just the most prominent face on a much larger trend – the growing interest among amateurs and citizen scientists to perform modern biology experiments. Whether you want to isolate some genes, engineer new form’s of brewer’s yeast, or track diseases, there may be a place for you in the DIY biology movement.

If you have a lab. Unlike amateur astronomy or amateur programming, amateur bio-technology needs a lot of equipment and supplies. To that end, certain members of the community have worked tirelessly to provide cheap, simple, and hackable versions of lab necessities. Once they become widely available these devices could also have an impact outside amateur science. What works for DIY hobbyists will help high school education, and could be leveraged for third world medicine as well.

The Hardware

We’ve already covered one amateur biology hardware project: the Pearl Gel Box – an open hardware electrophoresis gel box from Pearl Biotech. The plans for that box have been online for months now. You can build your own or purchase it for about $500 (or less than half that as a kit). According to Tito Jakowski (one of the creators of the device) they’ve sold “dozens”.

Jakowski and Josh Perfetto are developing another open hardware lab tool: a polymerase chain reaction thermocycler. A PCR is basically a DNA amplifier – making many copies of segments of DNA for use in the lab. Open PCR is going to cost less than $400, maybe one tenth the price of modern PCRs. It’s built using off the shelf parts (including an Arduino board) and some laser cut pieces for the frame. Jaksowski and Perfetto made it easily hackable so that users can add in their own features or upgrade it as desired. There have been 14 pre-orders so far, and the first kits will be shipped “in a few months.”

Otyp, a group interested in bringing biotech into education, has designed their own open hardware PCR. They’ll be looking to lease this equipment (along with other supplies and education packages) to high schools for about $600 a class with 24 students per class. According to James Peyer (one of the founders of Otyp) these leases will be available starting with the upcoming 2010-2011 school year. Here’s a video that describes Otyp a little more.

PCR may also be able to fit in your pocket. Lava Amp is a handheld PCR device under development by Guido Nunez-Mujica, Joseph Jackson (Open Science Summit organizer) and collaborators brought together by a SciFoo conference. It is due to come out sometime in the first quarter of 2011, and has a target price of $400. While it may find use in DIY biology labs, Lava Amp is aimed towards bringing PCR to hard to reach areas around the world, where it may serve as a valuable lab tool in the efforts to fight disease. Jackson tells me that Nunez-Mujica was at TED Global this week, and that as they secure more interest and funding they will be able to move quickly towards their desired launch date. Here’s Nunez-Mujica presenting the device in a video from February:

So it looks like gel electrophoresis and PCR are going to be available to you on the (relatively) cheap. What’s next? Well, there are already some other neat open hardware projects out there. MudWatt from KeegoTech is a microbial fuel cell – a device that generates low levels of electricity from microbes interacting with soil. The Spiker Box, from Backyard Brains, lets you use a cockroach leg to explore neurophysiology. Here’s a video of that:

According to Mac Cowell from DIYbio.org, there’s a lot of interest in the DIY biology community to continue developing new open versions of lab equipment. These projects have varying amounts of support and we could see spectrofluorometers, microfliuidic systems, and centrifuges in the near term. But there’s another aspect to hardware that might be coming along in the same time period: automation. As was discussed during the DIY biology panel at the Open Science Summit, it’s only a matter of time before someone starts adapting non-bio open hardware into the bio-lab. For example, MakerBot’s 3D printer could be used to handle heated liquids. Essentially, open hardware from the ‘Make Culture’ could be used to bring robots into the DIY bio lab. That may help hobbyist biologists not only perform modern bio experiments, but to do so quickly and without tedium. Cowell himself if working on a webcam microscope that can pan across samples through a mobile phone interface.

I should perform a big reality check here, however, and point out how basic these lab instruments really are. We’ve had the majority of these technologies for decades. Putting them in the hands of DIY biologists isn’t going to turn them into MIT. Also, most of these projects are still in the beginning phase of their development. Selling a few dozen kits isn’t going to reshape an industry. Even if we enable a million amateur biologists with these kinds of lab tools (is that even possible?) there would be a wide range of modern biology that would be outside of their capabilities.

Problems with Wetware and DNA

That’s because hardware is just one part of the modern biology equation. As Mac Cowell and James Peyer both pointed out to me, hardware might be the easiest of the hurdles to clear on the path to bringing biotech to the masses. We know how to build machines, how to strip them down or optimize them to make them cheaper. But labs also need wetware – those reagents and biochemical components that are required to perform experiments. Polymerases, ligases, etc are hard to produce in an amateur environment and have to be bought from companies. This costs a pretty good amount of money, and the wetware is typically consumed during a project. Otyp’s classroom education package costs about $300 even if you have your own hardware – this price covers just the necessary wetware, biological samples and educational materials. And the Otyp lab experiment is extremely basic. As they put it, the lab is the modern biology equivalent of printing “Hello, World!”. The DIY community is going to need to find a way to cover wetware costs or find new means of supplying them if it wants to enjoy long term vitality and growth.

Hardware and wetware, however, might be easy to acquire compared to actual biological samples. Sure, many DIY biology projects probably don’t need anything strange and exciting. You can test your own cells from spit, you can take bacterial samples from the environment, and Cowell told me about a really cool bio-experiment that just requires some squid and a refrigerator (you get glowing tentacles!). But if you really want to do advanced biotech, as some amateur biologists are interested in, you’ll need DNA samples from hard to obtain micro-organisms. The BioBrick standard (and the MIT Registry of Standard Biological Parts) has gone a long way towards making DNA hacking-friendly, but MIT does NOT send those materials out to just anyone. While you may be able to build the hardware and buy the wetware, getting your hands on the most interesting biotechnology materials is going to be difficult if not outright impossible. That’s not going to change in the foreseeable future because it depends more on politics than on science. Many people worry (rightfully so) about biosecurity. What guarantees do we have that a DIY bio-hacker is going to follow all the necessary protocols for handling possibly dangerous substances?

Are Community Labs the Solution?

Well, the guys at DIYbio and many others have been working tirelessly to make sure the DIY community follows stringent guidelines of safety. The Open Science Summit had a big panel discussion about biosecurity. My take away from that panel was this: DIY hobbyists are actually much more interested and dedicated to safety than anyone gives them credit for, but there is still more that regulatory agencies want from them, and the two groups are working together to solve this. No matter what intentions the community has, however, the idea of people performing biotech research on their own (even at a low level and just for fun) doesn’t sit well with many in power. It often doesn’t sit well with me. DIY biologists are generally a responsible bunch, but DIY biology does have the potential to be dangerous.

What can we do about that? Well, we could ask amateur biologists to get together and form their own labs, complete with insurance and documented adherence to safety regulations, just like any professional group. That’s an idea that’s already springing up all around the world. ‘Community labs’, like Biocurious in the San Francisco Bay Area, are working towards providing a space where amateur biologists can get together and pool resources in order to perform safe and interesting science. These community biolabs are probably going to follow the hackerspace model with monthly member fees, group education, and a mixture of private and community wide projects. Here’s a video about Biocurious that was played at the Open Science Summit:

Biocurious is an interesting example of the community lab concept because it has been very successful in some of its efforts but is still working on establishing itself. Tito Jakowski (Open PCR, Pearl Gel Box), Jeff Perfutto (Open PCR) and Joseph Jackson (Lava Amp, Open Science Summit) are all associated with the lab. While BioCurious started in a garage, it is now between homes. The founder, Eri Gentry, is looking to get the group into a real commercial space complete with liability insurance. Gentry and the rest of her crew are a great example of how the DIY community lab is a legit enterprise capable of performing good science. They’re also all very fun people, as you can see in the video above.

If you’re interested in joining the DIY biology global community, finding and joining a local community lab is probably the best way to get involved. They generally provide space, equipment, education, and social interactions that the amateur biologist desperately needs.

These labs, however, need money to form. Biocurious is trying to raise $30,000 to help them secure their new space and equip it. Even if you’re not ready to go join a lab, you can support the DIY community by donating to their cause. In fact, the majority of projects I’ve mentioned above are looking for financial help. Some have links to where you can directly fund them via the web, others you’d have to contact:

Biocurious
OpenPCR
Otyp
LavaAmp (contact via email)

These groups continue to work towards bringing the modern biology lab to the masses, but it’s the public interest in biotechnology that really fuels the DIY biology community. As people learn more about the power and promise of new biotech the interest in tinkering with bio projects increases. However, it’s unclear what meaningful change amateur biologists will bring to the world. With simple hardware, basic wetware, and very restricted DNA samples there are limits to what you can do. That’s unlikely to change even if DIY biology becomes very popular and widely practiced. What then, can amateur biologists hope to accomplish?

We have to remember that for decades high school biology education was stuck in the 1960s. Most of us simply have never had the opportunity to isolate DNA, replicate it, play with it in a lab. DIY biology can be education. We also need to remember that people all over the world could benefit from cheaper and wider access to labs to help with epidemiology and healthcare. DIY biology can be humanitarian. Finally, we can’t forget that growing a base of researchers, even just amateurs who tinker, are capable of making some (albeit usually small) meaningful contributions to a field. DIY biology could crowd-source science. For whatever that will be worth. Once we make the hardware, wetware, and DNA widely available, the amateur biology lab could form a valuable supplement to the modern industrial approach to biotechnology.

And one day, when biotechnology really takes off, DIY biology could become a true research partner for industry. When we can engineer cells the way we engineer computers, individuals working at home or in community labs could make their own important advancements. Just like amateur computer programmers do now. If we build the biotechnology, and make the modern biotechnology lab accessible, citizen science will arise. Parts of the lab are already here, more is on its way. Get involved now and things could arrive much faster.

[image credits: Raneko, Keck Graduate Institute]
[video credits: Otyp, Lava Amp, Backyard Brains, Biocurious]
[source: Tito Jakowski, Eri Gentry, Joseph Jackson, Mac Cowell, James Peyer]

Cambridge University won this year's iGEM competition for their pigment producing bacteria.

iGEM harnesses two of the most potentially powerful resources on our planet: synthetic biology and youth. The International Genetically Engineered Machine competition took place during the Halloween weekend this year, as always hosted by MIT. College aged (and sometimes younger) students from around the world came together to display the genetically manipulated microorganisms they had produced during the year. Using MIT’s Registry for Standard Biological Parts, competitors were able to transform bacteria into biological machines that could accomplish amazing tasks. Mac Cowell from DIYBio was in attendance at the jamboree during iGEM and recorded some of his conversations with various teams. Check out those videos after the break.

This year’s iGEM winner was Cambridge University who produced the E. Chromi bacteria. These organisms act as biosensors that produce visible pigments in the presence of designated substances. Imagine a world where the bacteria that already cover most surfaces would become red in the presence of a biohazard. You could instantly see if you were in danger. E. Chromi could one day be adapted to such a purpose. To that end, the Cambridge team developed two important ingredients for E. Chromi, a sensitivity tuner and a color generator. The tuner allows bacteria to be triggered into pigment production only when a detected substance passes a certain threshold. The color generator then creates a pigment. The Cambridge team was able to produce 7 different colors, all of which could be easily spotted without the need for fluorescence.

The seven pigments produced by E. Chromi.

In the following video, Daisy Ginsberg and James King (not actually part of the Cambridge team) give a brief and humorous glimpse into how E. Chromi could be used.

The BCCS Bristol team focused on a more mundane, but very useful task: protein delivery. Bacteria create outer membrane vesicles (OMVs), external packages that can deliver materials to other cells. Such materials could be proteins, DNA, RNA, or other important cellular products. One day, OMVs could provide the means to directly (and perhaps selectively) deliver necessary proteins to cells in your body. This could open up entirely new avenues of medication. Bristol also made improvements in simulation and BioBrick fusion as part of their research.

City College San Francisco was the first junior college team to compete at iGEM and really performed well. Their project aimed to create a solar powered fuel cell by culturing two different types of bacteria. One strand of bacteria would oxidize iron, the other reduce it, and from these chemical reactions would generate an electric current. When fully realized, this method could provide a means of efficiently generating electricity from sunlight using a medium that could be grown by consumers. Imagine having a friend give you a small pill of bacteria that you cultured into a solar panel that covers your entire roof. As part of getting these cultures to work together well, the photoreactive strand has been fitted with a glucose leaking hole so that it can share food with the non photoreactive strand. This glucose hole figures largely in the discussion in the following video:

The University of Virginia took on poor water quality by developing e. coli that could safely absorb arsenic in drinking supplies. About 137 million people worldwide are affected by some level of poisoning from water borne arsenic. By removing the gene (a technique called ‘knocking out’) which allows the bacteria to expel arsenic, Virginia assured that the heavy metal would stay in the cell. They also included a sequestering agent in the bacteria so that it could absorb arsenic and still survive. The safe removal of toxins from the environment by bacteria is called bioremediation and could one day be used all over the world.

As I explored some of the great teams from iGEM 2009, I noticed that safety and security is an increasing focus at the competition. Each team was given a safety survey and toxicity/biohazard awareness figured prominently in the discussions for different groups. While there’s yet to be a single (reported) hazard created by an iGEM team, MIT is obviously being very cautious and proactive about such potential problems. Hopefully this vigilance will quell some of the critiques of detractors of synthetic biology.

Another interesting development at iGEM was the involvement of Daisy Ginsberg and James King, who for the lack of a better term are sort of art and design explorers. They took an active interest in the Cambridge team’s E. Chromi and tried to map out some of the implications of a world where bacteria produce colors that have important and inherent meanings. You can see their musings at the E. Chromi website, and Mac Cowell has an extended video of their explanation of their work:

As always when discussing iGEM, I feel compelled to point out that the majority of the projects at the competition are no where near being brought to market. Many teams aren’t even able to culture large quantities of the synthetic organisms they design. Yes, Cambridge was able to demonstrate how the E. Chromi could produce pigments, but there are many engineering hurdles (production, safety, maintenance, tasking) between that demonstration and a fieldable product. Still, these four teams (and the many others you can explore on the iGEM website) have designed some amazing biological machines and I can’t wait to see which continue on to help improve our world. Even if none of these organisms make it to market, this year’s iGEM didn’t just give us cool new bacteria, it also speculated on some of the concerns and possibilities of its own work. That’s the sort of forward thinking and holistic approach to engineering that makes iGEM so spectacular.

Thanks to Mac Cowell for his videos, and make sure to check out his Vimeo channel.

[photo credit: iGEM, Cambridge University]
[video credit: Mac Cowell]

In the traditional model of scientific progress, researchers share information through two channels: published research and discussions at conferences. Six to twelve months could pass before one scientist learns about the discoveries made by another. OpenWetWare is a precursor to Science 2.0, a new paradigm wherein research learns some of the lessons of open source computer programming. By sharing information quickly online, scientists could reduce the duplication of work, create a quicker dialogue between teams, and develop dynamic and productive collaborations. In other words, the democratic dissemination of information would increase the efficiency of the scientific community, accelerating the rate at which the world benefits from their discoveries.

OpenWetWare evolved from a wiki called the Endipedia that was developed by two groups at MIT. As such, most of the steering committee for the site is based in the Boston area. DIYbio founder and friend of Singularity Hub, Mac Cowell, is one of the members of the committee (though I don’t know how active he is). Still, if the leadership of OWW is heavy with Cambridge citizens, its base of users is much more global. There are dozens of groups, and more than 100 labs that contribute to the site, including scientists from Imperial College (UK), University of Sao Paulo (Brazil), and Peking University (China). The diversity of its members reflects the diversity of the synthetic biology competition iGEM.

Which is fitting because a good deal of the OWW content is geared towards iGEM competitors. Synthetic biology requires a host of lab skills that often have to be developed quickly. There are a myriad number of lab protocols required even for the most basic of genetic engineering tasks. OWW provides descriptions of these protocols, as well as allowing users to describe their experience with them.

User editing in OWW isn’t as open as with Wikipedia. While ‘anyone’ can edit Wikipedia, you have to be a registered user to edit OWW. This restriction is a necessity. For although 7000 scientists is an awesome amount of intellectual power, it is no match for the teeming millions of vandals that troll the internet. So, while you or I could benefit from reading OWW, we can’t put in our two cents without first letting them know who we are. This has meant, according to OWW, that there have been no known instances of vandalism on the wiki. None. Zero. That’s amazing.

If you’re a biologist or synthetic biologist, or other professional, you may be asking yourself if you should get involved in OpenWetWare. The answer is yes, and OWW has an entire page dedicated to convincing you of that. In short, the website believes that shared information is better information. It is more robust, able to survive the loss of a labmate or a small typo much better than secret information. Wikis benefit those who share as much as they benefit those who receive.

Scientists often lose track of that “sharing is caring” vibe because the reward system in the scientific community is publication-centric. You don’t see Nobel Prizes handed out to scientists who haven’t published in a major journal. Large grants – all funding, really – comes from proving the validity of your work by having it appear in esteemed publications. That’s the on-the-ground truth of the situation. In order for OWW to become a viable means by which scientists feel inclined to share their most up to date and precious data, a new rewards system will have to be introduced. That system could be as simple as members of the scientific community recognizing and acknowledging the work shared on OWW. Every time a scientist joins OWW, or allows their lab to share information on it, or edits a page, they legitimize it as a respectable hub for the exchange of scientific thought. If enough biologists do so, ‘publishing’ on OWW will carry the prestige necessary to launch the community into Science 2.0.

Of course, there are ways that non-scientists can use and contribute to OWW as well. First, DIY biologists can read up on the protocols, materials, etc they need to perform their projects. Newcomers to synthetic biology are valued too. OWW needs the feedback of people who are autoclaving for the first time, or who have never isolated DNA before so that the wiki becomes a useful tool for those entering into the field. The more powerful a web resource OWW can create, the quicker prospective students will be able to become fully fledged biologists. About half a dozen college level courses already use OWW to share their curricula and help their students.

If we want to benefit from exponential returns on technology, we need a method of sharing ideas that is fast, reliable, and dynamic. I think a rigorous science wiki is that method. OpenWetWare is a great biological resource -looking at their site stats you see their wonderful increase in cumulative data over time. It’s inspiring and I would like to see parallel websites develop in other fields. Robotics and computer science already have several. Currently, different research teams use OWW differently, and that diversity of utility is part of what makes the wiki so appealing. In the future, I can only see benefits arising as more scientists divest themselves of the current scientific rewards system and favor the evolving wiki-model of collective knowledge. There will be less ownership of ideas and experimental results, but that loss will be balanced by a growth in the number and quality of those ideas and results. Less individual prestige but more shared understanding and benefit. Isn’t that why we started using science in the first place?

Synthetic biology has been called the science of the 21st century. Rewriting the genetic information of micro organisms can allow scientists to create new genetic machines that can perform extraordinary tasks. You remember MIT’s Registry of Standard Biological Parts we discussed? iGEM teams are given access to that database in order to come up with useful, interesting, or just plain cool genetic machines for the competition. MIT is allowing these undergraduates access to some of the most advanced synthetic biology tools of today in the hopes of developing students into the best genetic engineers of tomorrow. That’s exciting stuff.

For those completely new to the iGEM competition, undergraduate teams are formed in universities all over the world. They receive standard biological parts in the beginning of the summer and present their results during the jamboree in the fall. Not every institution can sponsor an iGEM team. They require funding, access to advanced equipment, and most importantly: synthetic biology expertise. Each team has faculty advisors that help students understand biotechnology, and guide them in its use to accomplish the task they desire.

While an iGEM team’s requirements are severe, the number of institutions sponsoring them has increased dramatically. The first iGEM competition in 2004 had just 5 teams attending. Last year saw 84 teams. This year there will be more than 110. The interest and capabilities of synthetic biology undergraduate programs all over the world are increasing at a wonderful rate.

iGEM 2008 had 84 teams. This year will have 110+. Like the bacteria they engineer, iGEM teams are growing at a phenomenal rate.

It really is wonderful news to see so many groups interested in iGEM. These undergraduates aren’t just creating neat science projects that will help them get genetic engineering jobs in the future, they are making differences now. Last year’s grand prize winner, Slovenia, engineered a vaccine to Heliobacter pylori, a bacteria that infects up to half the world’s population, causing gastritis and ulcers. H. pylori is often drug resistant, meaning that Slovenia’s vaccine is a new and needed solution to infection.

While it is the premier undergraduate competition of its kind, iGEM could be more. Our old pal Mac Cowell from DIYbio was trying to get a do-it-yourself team into iGEM 2009 but was (kindly) told that iGEM wasn’t ready for DIY biology groups yet, mainly due to issues surrounding safety and funding. We still might see a DIYgem team in 2010.

For now, I’m just anxious to see what amazing biological machines will be debuted on Halloween this year. Stay tuned to Singularity Hub for coverage of the competition and discussion of the results as they are announced. Trust me, folks, cool things are coming out of synthetic biology, and iGEM never fails to impress.