The Kojo Nnamdi Show invited a few folks from the DIYbio community to have a discussion about the amateur biology movement.  Appearing on the show was:

• David Rejeski: Director, Synthetic Biology Project, Woodrow Wilson International Center for Scholars
• Daniel Grushkin: Vice president and a founder of Genspace; Freelance Science Writer
• Jason Bobe: Co-founder of DIYbio.org; Executive Director of PersonalGenomes.org

More details about the program, or listen to the archived stream.

For those in the NYC area who are ready to roll-up your sleeves and learn new biotech skills, I received the following note from Ellen Jorgensen, President & Scientific Program Director at Genspace:

Genspace is repeating its popular Biotech Crash Course starting Sunday March 20th. It will run from 2PM to 6PM on three consecutive Sundays and cover all the basic techniques used to cut and manipulate DNA. This is a hands-on course where you will isolate DNA, cut it using restriction enzymes, amplify it using PCR, and clone it into bacteria.  The cost for the course is $300.  We have 12 slots available, with two at a special discounted student rate. Please let us know ASAP if you are interested, since we anticipate this session will fill up fast.

In case you missed the December 2010 launch party in Brooklyn, Nature Medicine takes a tour inside the new Genspace community lab and talks to co-founder Daniel Grushkin (video link):

One of the most intriguing features of their space is a big glass box where all the lab equipment lives (much of it donated from a bankrupt biotech company).  The lab is constructed from several sliding glass doors drawn from the vast supply of found and recovered objects that occupy several floors of the Met Exchange building.  When I visited in December, I asked the Genspace folks the obvious question: Why did you build your lab in a glass box?  I learned that they had help from the (wonderful) Met Exchange owner Al Attara, who asked them for some basic requirements and they said “well, for starters, we know we want our lab to be open and transparent…”  They came back to the space a few days later, and, voila!  Lab in a (glass) box!  Made from sliding glass doors!

Read more about Genspace at their blog or follow them on twitter @genspacenyc.  See also the nice profile piece of Al and his Met Exchange in the nytimes.

Charlie Schick is an ex-scientist and a determined practical microbiologist. He writes about science, media, and other lofty subjects at http://molecularist.com.

Recently, I’ve been prowling the aisles of liquor stores and supermarkets reading labels of fermented foods, looking for new cultures to use. Am I violating any copyright?

Image from Wikipedia

Back in June, the DIYbio folks in the Boston area had a fun meet-up on yoghurt making, led by Vaughn Tan. One thing that was brought up but we really did not discuss was the copyright of culture strains found in yogurts. Mac asked if there were legal ramifications to using strains taken from commercial yogurt.

I remember a time when it was hard to find commercial products with live cultures, for example beer or yogurt. Beers were pasteurized (ugh) or, later, filtered to remove live cultures. And in the 90s, I remember Stonyfield’s as being the only “widely” available live yogurt.

But now it seems almost all yogurts have live cultures (though not necessarily with a rich set of bugs – some seem to have 1 or 2 instead of the usual 5). And I was impressed with my local liquor store carrying a wide range of beers with live yeast, such as lambics (fermented with a complex collection of wild yeasts and bacteria) and a breton beer, that caught my eye because it was made with two yeasts.

When I need to, I start my yogurt cultures with a starter taken from a commercial yogurt, such as Stonyfield’s. And I’m considering pitching (inoculating) my next beer batch with the two yeasts of that breton beer.

Is this “fair use”? If I give the culture to someone else, is that piracy? And what if I start selling my product?

And how can anyone prove it is their strain? These bugs are easily available, and most are naturally occurring. Will commercial strains need to be fingerprinted somehow for copyright protection?

You can see where this is going: Who will be the RIAA-equivalent in this story, to crack down on infringement? Who will be the EFF- or Creative Commons-equivalent to promote openness? Will we have a Napster-like bug-sharing service, freely sharing strains among all sorts of practical microbiologists?

In the lab, there are usually rules in place to restrict the free sharing of strains or samples. But these are usually for recombinant organisms, where it is clear what was created. What about for naturally occurring organisms?

Open sharing of information is a cornerstone of DIYbio. Will the same freedom extend to the sharing of microorganisms, especially if those microorganisms come from a lab or commercial product?

I don’t have the answers. Do you?

Charlie Schick is an ex-scientist and determined practical microbiologist. He writes about science, media, and other lofty subjects at http://molecularist.com

Long ago, people discovered that not all food-spoiling processes were harmful. Indeed, people have harnessed fermentation, a spoiling process, to preserve foods – beer, wine, cheese, sauerkraut, cider, kimchee, yoghurt, and, of course, surströmming (you won’t believe what it is).

To me, humans have always been practical microbiologists: we probably settled down to farm barley for beer, one of the oldest pieces of writing is a recipe for beer, and it’s not surprising that early biochemists studied enzymes in the fermentation process.

The ancient (1800 BC) sumerian Hymn to Ninkasi encodes a rudimentary beer recipe

For us DIYbiologists, making foods like beer or yoghurt offers a great way to learn sterile techniques, handling of microorganisms, and many of the principle of microorganism culturing – growth media, inoculation, and strain growth conditions.

I brew beer and make yoghurt. Making yoghurt is stupidly simple. Starters are available from any live-culture yoghurt found in the supermarket. And I use mason jars (usually from spaghetti sauce) for the fermentation.

Brewing beer from malt extract doesn’t require an inordinate amount of time or equipment. Brew shops have various strains of yeast you can use as a starter. And if you’re adventurous, you can capture natural bacteria and yeast to form a starter.

Do you ferment anything? Beer, wine, or cider? Do you use microorganisms for food production?

Silkworms have been engineered to produce a more durable silk by augmenting them with properties from spiders.  The applications of the transgenic silk include textiles, sutures and wound healing, and even new bulletproof materials.

(HT Christina)

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See also a recent paper on the miraculous spidersilk produced by “Darwin’s bark spider”, Agnarsson et al. 2010. Bioprospecting finds the toughest biological material: extraordinary silk from a giant riverine orb spider. PLoS One 5 e11234 doi:10.1371/journal.pone.0011234

Dr. Todd Kuiken is a research associate for the Synthetic Biology Project at the Woodrow Wilson International Center for Scholars. He is collaborating with DIYbio.org on a project to ensure safety within the rapidly expanding community of amateur biologists.

If the “MAN” was just one man, dealing with new and exciting movements such as DIYbio would be rather easy. Unfortunately the “MAN” consists of numerous federal agencies ranging from the FBI to the EPA, all with different jurisdictions and oversight concerns. Add to that state and local agencies, neighborhood associations and your curious neighbor looking over the fence and the complexity of engaging with all of these groups becomes clear. The DIYbio community needs to take these agencies concerns seriously, as I think we are doing, and turn them into excitement over this new field of biology and the larger movement of citizen science as a whole.

As I began talking about DIYbio with various agencies a theme began to emerge amongst those who were tasked with “oversight”, for lack of a better word, of DIYbio. There was a general excitement about the community and the conversation frequently turned to “remember when science was fun”. While these various agencies have legitimate concerns surrounding the DIYbio movement, the conversations thus far have been positive and seem to be more about helping the movement move forward safely while encouraging more people to get “excited” about science again. By no means do I think this will be an easy task, but an exciting one as we begin to engage the larger public and move deeper into the caverns of regulations, local ordinances and address people’s fears and concerns about moving into the realm of citizen science. I believe strongly that if we follow three simple principles we can calm these fears and produce an environment where the DIYbio community can flourish and the larger citizen science movement can grow.

1. Turn concern into excitement
2. Make science fun again
3. If we engage them they will get it

I recently finished reading “The Radioactive Boy Scout” by Ken Silverstein, which describes the true story of a young man named David who over the course of his childhood became fascinated with DIYchemistry and by the time he graduated high school had designed and built a small nuclear reactor in his backyard (with a little help from a book published in 1960 called “The Golden Book of Chemistry”, long out of print and probably for good reason, but in short, has some pretty amazing experiments designed for the DIYer, including how to make chloroform!). In the end the EPA arrived, tore down his makeshift lab and turned his family’s suburban Detroit backyard into a Superfund site. This true story is an excellent example of how curiosity and people’s desire to explore science can both lead to pretty amazing accomplishments, from a technical standpoint, but can also carry with it serious safety concerns and potential over reaction by the federal government. I plan on writing future posts describing the significance of this story and how it relates to the DIYbio movement and the lessons we can take from it in order to better engage with the “MAN”.

Daniel Grushkin is a science journalist who has written for numerous national publications. He’s a cofounder of GenSpace, New York’s first community lab.

It’s been 25 years since Steven Levy came out with his seminal book Hackers, and we still can’t agree on a definition for them. Hackers are deft programmers and designers, they’re whiz kids who break into computer systems, they’re guys who wear leather overcoats à la The Matrix.

But let’s face it: in popular culture the term “hacking” is cool because it suggests a reversal of power. People who we thought were powerless turn out to be powerful, and those who we thought all-powerful end up weak (or at least silly). It’s cool when a 7-year-old blind boy figures out how to trick phone systems into giving him unlimited free calls by whistling at the right pitch. It’s cool when misfits take down a shady company by exposing their secrets (see Wikileaks or Lisbeth Salander).

It fulfills a fantasy we all have—that through moxie and smarts the little guy can upend the system. (I suspect that if you don’t consider yourself the little guy, then you don’t find it that cool.) But without the little guy on top, it doesn’t come off. Case in point, when China launches a cyber attack on the Pentagon, or when a government agency hacks into the little guy’s computer, it’s not that cool. Actually it’s scary.

I’m not sure who coined the term biohacker, but it sounds super- f#@ing cool. To others it sounds super-f#@ing scary. Unpack the term, and I’ll show you why.

You and I are the little guys in the biohacker scenario, but who’s the big guy? Where’s the reversal? At first you might think, ‘Oh, it’s the corporations and universities that spend billions to do what we’re doing on the cheap.’ I don’t think so. Though we may one day democratize science, if anything, we operate in parallel to these institutions.

I think the phrase biohacking suggests an even bigger “big guy,” at least it does to the popular press and culture-at-large. Hacking, at least in this context, assumes that the system has a purpose. When a hacker hacks a system he subverts its original purpose for his own. The little boy takes a system designed to trade telecommunication for money and makes it free. The misfit takes a system originally meant to secure information and turns it into a system that reveals information.

Similarly, for many when you use the term biohack, embedded in the notion is that biology has a purpose, that the designer (presumably God) created it to fulfill that purpose, just like the phone company or the security system. To hack it is to somehow subvert the design, and through it, supplant the designer (again, presumably God). Now granted, if you took an insider’s view of the term “hack” this would all seem preposterous. But look at this graphic from The Economist illustrating the creation of the first synthetic bacteria. That’s man playing the role of God in Michelangelo’s Sistine Chapel.

Credit: Economist, May 20th 2010

And you wonder why some of the public sees us as dangerous (parables like the Tower of Babel follow thereafter). At the same time, for others it’s also the reason why “biohacking” seems so cool (in this case, fantasies of creating a more logical world follow thereafter). Because, in a way, it’s the ultimate reversal of power: Hello God, here comes mankind.

Replace the theological with a Darwinian lens and the term again degrades into nonsense. Why? Because “purpose” is a term that doesn’t apply to evolution. A firefly shines bright not because it was designed to, but because it found utility in a string of mutations. Life is a MacGyver, “purpose” only comes after the biological change is made. So if you put the gene to shine bright in another organism (which we do), you are not subverting what some might call “divine will.” You are, however, throwing your own purpose into that life. Whether that organism finds utility in it is up to the organism (and the conditions you set).

Back to the term biohacker: I’m not saying you shouldn’t use it. Go ahead. But when you do, be aware of the associations you’re drumming up. Personally, it’s not worth it because the associations just don’t fit my worldview.