Archive for April, 2009

Doing the infamous dna extraction

If you’re in the Boston area, drop by the Cambridge Science Festival between noon and 4:00pm this Saturday, April 25, to visit the DIYbio table! We’ll be in the tent at the opening Science Carnival – see the Cambridge Science Festival’s schedule for details.

Mac Cowell, Sandra Porter, and Meredith Patterson (who wrote her thoughts on the show) were in a fascinating discussion about DIYbio on the Food Chain weekly radio program with Michael Olson this morning. The audio will be available to download soon.

How can amateurs participate in iGEM? -

Several weeks ago the Director of iGEM (my old boss) asked me to drop by to chat. He basically told me iGEM wasn’t going to allow amateur teams for 2009, despite earlier statements to the contrary, for two reasons:

1. iGEM depends on the academic institution of each team to provide a safety framework for that team. Because there is no formal safety framework or guidelines or precedent for amateur teams working outside of traditional labs, iGEM is afraid of the potential safety liability and doesn’t want amateur teams to participate until there is some kind of framework (2010!).

2. Most of iGEM’s funding comes from grants to support undergraduate education. A host of amateurs who are not undergraduates would be supported by grants for undergraduate education, which could be a situation the grantors wouldn’t like. Randy didn’t want to take that risk.

Randy also said iGEM would clarify the situation by making a press release regarding these changes, or at least describe them in an organizational email to the iGEM-interest email list. That didn’t happen. So in the meantime, I’ve been verbally explaining the situation to groups of people I think may be starting iGEM teams.

There is some good news: if you want to participate in iGEM in an amateur capacity, you can still do so by collaborating with a local iGEM team. This could help a lot with the fundraising for both the local diybio group and the iGEM team. DIYbio-Boston and DIYbio-NYC are both exploring collaborations with local teams.

As a community we need to start addressing the safety concerns society and the larger scientific establishment has with garage and coworking space wetlab work. I’m sure there are a multitude of opinions on how and what to do, and even what not to do. But I believe we need to organize some kind of formal statement anticipating and addressing these safety concerns, preferably with the help of objective experts. If you are interested in helping figure out how to do this, email safety@diybio.org. I’m thinking we should establish a DIYbio safety working group to be responsible for taking a leadership role on this developing real solutions.

I spoke with Randy about organizing a 1-day DIYbio symposium at the same time and place as iGEM this year (which is at MIT on the weekend of October 31). He was receptive to this idea. I think it would be very valuable to bring as much of the community together as possible to meet and discuss these issues and to present a collective snapshot of their work and projects to the world. There would be cross-pollination with many of the iGEM participants, and lastly, I’d like to use the symposium as a deadline by which some group or groups of people could formally present thoughts and work on our safety strategy to the community and to the rest of the world.

diybio faq at openwetware.org

Bryan Bishop has herioically created a DIYbio FAQ (three cheers!).  In the interest of neutrality, I copied his latest version to OpenWetWare/wiki/DIYbio/FAQ today and I encourage everyone to edit that version mercilessly.  Otherwise Bryan will become the official keeper of the holy DIYbio FAQ flame and the canonical version will reside at heybryan.org – this may be a fine solution for now.

The FAQ contains information on Getting Started with DIYbio, local DIYbio groups, Synthetic Biology, iGEM, videos, Keiki gels, and MiniFAQs on DNA synthesis and microfluidics.  Obvious content to expand are the sections on social and legal issues, basic wetlab equipment, lab services available to amateur biologists, and current projects in the community.

Step 1. Planning our experiment

The pressure cooker shot out steam, like an enormous teapot. At over 200˚F, steam had just sterilized our liquid agar, the favorite food of growing cells.

We’re on our way to make glowing cells with the Carolina Sciences “Green Gene Colony Transformation Kit” (aka E. Coli K-12 + a GFP plasmid). This first step for DIYbio SF was a long time in the making!

Step 2: Josh measures and mixes LB agar

At the beginning of March, Praveen and Marnia began working with Noisebridge, a local hackerspace, to put together a Lab Safety and Ethics page. Tim ordered the Carolina kit and stored it at his apartment. Micah offered to donate a fridge, Meredith volunteered her pressure cooker , and Marnia brought a digital scale.

This past weekend, 5 DIYbiologists met at Noisebridge in the Mission district: Marnia, Josh, Tim, Micah, and myself, Tito.

Step 3: Marnia turns on the pressure cooker

We started the session by cleaning out a fridge donated by Micah and talking through the safety aspects of our tools and materials. We agreed that any broken glassware would need to be cleaned up immediately and Marnia showed us how the pressure cooker worked.

To the right, you can see the 4 steps that we took in order to make our plates. Marnia will be seeding the E. Coli K-12 on these plates and we will be adding our GFP DNA plasmid to these cells during our next session.

We will be completing this kit over 3 “Glow in the Dark” sessions:

Step 4: Pour and refrigerate agar plates

1. Making Agar Plates
2. Growing glowing GFP cells
3. Visualizing DNA with Electrophoresis

Kit: Carolina Green Gene Colony Transformation ($49)

Materials used:
Petri dishes
LB Agar

Equipment used:
Gloves
Scale
Pressure Cooker
Flask

DIYbio is a new and exciting topic — as a community we focus on making science safe and approachable by understanding our materials, following safe practices, and tackling tough issues like public perception. As well, remember these important areas outside of the science itself, especially when working in someone else’s space: schedule space with the owner, get everything approved, and say many “thanks” afterwards!

Thank you to Noisebridge for hosting us as we boot-up DIYbio SF!

Our project was accepted for the MAKE Magazine “Maker Faire“ — we’ll be showing off our cells from May 29-May 31st in San Jose, California!