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DIY Bio FAQ

photo of Michel Bauwens

Michel Bauwens
23rd March 2010


These excerpts from an interview with Mac Cowell, cofounder of DIYbio, give a good overview of the DIY Bio movement’s vision. Below details about a concrete initiative in that field, Gingko BioWorks (via Erin Kutz).

1. Mac Cowell interview

What exactly is DIYBio?

DIYbio is a group of people who are interested in doing amateur biotechnology. Amateur, meaning doing something that you love for the sake of doing it. In a broad sense, we’re developing an infrastructure that enables people not in traditional institutions to take advantage of the tools that those institutions typically provide.

Why did you start DIYbio instead of pursuing a PhD or collaborating with an established lab?

I really fell in love with the general idea that biology can be engineered. But I was disappointed with the huge barrier of entry for average people, or for anyone who wants to get involved but is not already in a PhD program. The open-source computer-programming movement became ubiquitous, and computers became a platform that enabled a huge amateur or hobbyist culture of people to push the field further. Many people got organized and started working on projects collaboratively. So why can’t we do that with biology? Why does all biology happen in academic or industrial labs? What’s the barrier to entry for doing something interesting in biology? It’s a four- to seven-year PhD program. There must be another opportunity.

What do amateurs bring to the table that trained scientists don’t?

That’s a great question. The number one thing is a “cross-pollination” of expertise. We are trying to develop the tools that enable people, who might be experts in other areas, to do biology as a hobby in their spare time, bringing some of that expertise to the lab. That way, there is a lot of potential for innovation. For instance, one of the projects that we are working on right now is an “augmented reality benchtop.” There has been a lot of work in the last 10 or 20 years on things like multitouch, big-screen tabletops. What if we made a benchtop for a lab that could recognize the stuff on top of it, walk you through a protocol visually, or connect you to a microscope on the surface of that lab bench and show you what it sees? So that you’re not just scribbling in a lab notebook, you’re actually recording at an equal or better granularity what you’re doing. Another example of where advancements in other fields could apply to biology is pipetting. During experiments, you pipette over and over again, hundreds or thousands of times a day. Every once in a while you might zone out and think, “Oh, my God. Did I just pipette that two times in a row? Five times? I don’t even remember.” Why don’t we just install a little wireless data logger into a pipette that keeps track of how much and every time you press a button? Some of the people we’re collaborating with are installing little wireless data loggers into pipettes that keep track of how many times you press the pipette button. And it only costs $40. Why aren’t all pipettes like that?

Is a crowd-sourced approach especially well suited to synthetic biology?

Synthetic biology aims to make biology easier to engineer by adopting basic engineering principles: modular parts, standardization, abstraction, standard units. And as these practices become more developed, the opportunity for people to do biology on their own increases. As the system of weights and measures is realized, the less you have to be a vertical expert, or a specialist. Furthermore, a crowd-sourced network of hobbyists might help measure and characterize the needed toolbox of thousands of biological parts in the first place. Hobbyists don’t have the same set of goals as PhDs. Measuring things is not very sexy, meaning you probably couldn’t write a paper about it. Many synthetic biologists are having trouble getting papers about different measurement standards published because it doesn’t clearly advance the scientific agenda. Maybe it could be construed as scientific progress, but really, it’s about engineering progress. There’s a lag between what needs to happen to make synthetic biology more of a reality in certain ways. There’s a lot of science that had to happen to make synthetic biology possible. But there’s also a lot of grunt work?—?measuring, trying different combinations, characterizing?—?that I think a lot of traditional scientists aren’t necessarily going to do. Scientists who are trying to write their thesis or publish a paper in Nature might not have as much compulsion to perform that initial grunt work.

Does amateur science affect the peer-review process?

Right now that function is being provided mostly by the mainstream publishing industry, which is now a couple hundred years old. These publications have become academic currency. If you want to get tenure, you need the pedigree of having been published in prestigious journals. Until we can find alternative ways of crediting good work, we’re going to be stuck with the existing publishing system. The current way to have a scientific conversation is to take six months to two years to publish a paper, and the paper is the end product of research that’s taken six months, maybe many years. All of that data is stored in lab notebooks. And maybe only the best analysis of that data gets published as an auxiliary file on a publisher’s website, even though useful experimental data was generated much earlier. As we develop tools that make it easier for scientists to capture the process of actually doing research, I think that will enable a faster scientific conversation than the current six-month to two-year process. Software platforms that make it easier for scientists to capture, on the fly, what they are doing at a granular level?—?that’s what the scientific dialogue is all about.

How do you respond to critics who claim that you’re potentially putting dangerous biological materials in the wrong hands? Or, to use the computer-programming analogy, are you aiding the development of viruses in a very literal sense?

All the hazardous sequences are available publicly from GenBank, etc.: Ebola, H5N1, the 1918 plague; they’re all there. DIYbio won’t change that. We’re looking to mostly focus on doing wet lab work in a very public, transparent group setting. So that if anyone?—?a neighbor, a governmental agent, a journalist?—?wants to know what is going on, it’s evident what we are working on. Forming that community is the first defense so that the 99.9999 percent of the group who are positive will stop the .0001 percent of the group that’s negative. Today, at the ground floor, I think it’s best if we blaze a path forward in a very public and open way. A small minority may have unleashed computer viruses over the years, but it’s the computer hacking community at large who created many of the solutions that safeguard us from them.”

2. The Gingko BioWorks initiative:

“The founders of Boston-based Ginkgo BioWorks think that assembling synthetic biological systems shouldn’t just be for experienced researchers. So they put together a kit that consists of the “scissors and glue for putting together pieces of DNA,” says co-founder Reshma Shetty.

Unlike the electronics industry, which sets standards to ensure compatibility and interoperability, the methods for putting together pieces of DNA are typically much more fragmented and ad hoc. Biologists build biological systems and organisms for functions such as producing everything from fuel to drugs to consumer products. The Ginkgo kit builds on a publicly available standard for connecting pieces of DNA, developed in 2003 by another Ginkgo co-founder, MIT senior research scientist Tom Knight. Called the BioBrick standard, it facilitates the assembly of multi-gene systems, and allows parts to be more easily shared within the synthetic biology community.

Ginkgo’s BioBrick Assembly Kit includes the reagents for constructing BioBrick parts, which are nucleic acid sequences that encode a specific biological function and adhere to the BioBrick assembly standard. The kit, which includes the instructions for putting those parts together, sells for $235 through the New England BioLabs, an Ipswich, MA-based supplier of reagents for the life sciences industry.

Shetty didn’t release any specific sales figures for the kit, but said its users include students, researchers, and industrial companies. The kit was also intended to be used in the International Genetically Engineered Machine competition (iGEM), in Cambridge, MA. The undergraduate contest, co-launched by Knight, challenges students teams to use the biological parts to build systems and operate them in living cells.

The assembly kit is the first product from Ginkgo, which was started in 2008 by Shetty, Knight, and three other MIT PhDs, but the company is also working on rolling out a consulting-style service for more elaborate DNA construction. They plan to work with companies on determining how they can design biological systems to fit their business functions, modeling what that system would look like, and testing it. “We’re focused on the tools and services for engineering biological systems,” says Shetty. “We think of ourselves as a biological design firm.”

Ginkgo (named after the tree) isn’t pursuing any venture capital funding, because it hasn’t needed it.”

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