Berkeley Engineering Blogs

Instead of the normal grind and tedious pipetting that normally fills our days, the comp team and the wet team got together on Monday for a little bowling action. The outing was an unambiguous success!

Around noon we all met at the mining circle to discuss how we were going to fit 18 people into 3 cars… Somehow we all managed to end up at the Ranch 99 plaza at about the same time. There was a period of intense indecision about where we would eat, but finally Bing made an executive decision: Korean Food!

The poor waitress looked a little horrified when 18 hungry iGemmers walked through the doors. Someone mumbled “Table for 18 please,” and the waitress hurried away to play tetris with several tables in the corner. A short time later, we were all seated in relatively close proximity, laughing and discussing non-biological subjects.

I thought the food was outstanding. But then again, I’m not really picky and you would be hard pressed to find food I don’t like.

Bing led the caravan to Albany Bowl and we all stood in line to be outfitted in our super stylish bowling shoes. I had a particularly fly pair of neon kicks. The management dusted off the old disco vinyls and turned on the laser lights and smoke machines.

Patrick and I were desperately pursuing a turkey (three strikes in a row). After a single strike we would cry “33% turkey!! 33% turkey!!” Even though we got dangerously close to a whole turkey, with a whopping “66% turkey,” several times, neither of us were able to catch the elusive gobbler.

Reluctantly, we exchanged our chic footwear at the counter and began the journey back to campus to continue the grueling pipetting regiments.

Finally all of us would like to thank iGEM for sponsoring this social event. It was a blast and a welcome break from the lab =]

Well who wouldn’t?!?

You may think that if you don’t have access to a University Laboratory and fancy, enigmatic equipment (not to mention expen$ive), then practicing synthetic biology is out of reach.

Well, I found a website dedicated to
“makeing biology a worthwhile pursuit for citizen scientists, amateur biologists, and DIY biological engineers who value openness and safety.” DIYbio.org is a really interesting site with blog entries and information on local events and conferences. While clicking around the site I found an interesting entry concerning amateur participation in the iGEM 2009 competition. It seems that amateur participation won’t be allowed this year due to safety and bureaucratic concerns…

So, I’d like to pose this question to the other iGEMers: What would you imagine a safety framework for amateur of DIYbio might look like? How would it be enforced?

It’s 3:15 pm Eastern time, and our presentation is scheduled to start in 45 minutes.  We have spent the day watching other presentations and getting a feel for what other teams have been doing.  Presenting late in the day is a little nerve-wracking.  

I have also been interviewing people about their opinions on synthetic biology, its attachment to iGEM, and friction between the open source philosophies and the realities of the technicalities of doing the research and the needs of the researchers for characterized systems, parts, and devices.

Here is a pictoral depiction of our day so far:

Beautiful Stada Center!!

Searching, searching for presentations.

Last minute practice, this time with hard hats.

Thursday night found us sitting around in the Oakland Airport, playing sudoku and utilizing precious free wifi before setting off for a night flight to Boston.  We have spent the week finalizing our presentation and our poster, so everyone is a bit exhausted at the beginning of the journey.

Action shot of Bing in the airport.  Bam!

Dramatic cell phone shot.

No action or drama here.  Just sudoku.  The adventure begins!

Our presentations (those of the Wet Lab and the Computational Team) are both on Saturday, and we have all of Friday to practice the presentations over and over, to make sure that they are informative, but captivating, and most of all that we keep them within the 20 minute time limit…  There will be a question and answer session after the presentation, and this is a new concept to many of us, so Terry and Chris will be coaching us on how to reach into the resources of the work we have been doing to answer questions effectively and interestingly. 

We came into the predawn world of drizzly Boston at 5:30 am, surprisingly not too grumpy and even a bit cheery. We were, however, in great need of some shut-eye to get rid of that red-eye to face the rest of the day full of practice presentations.    

You can feel how extreme the predawn Boston was with the blurriness of this picture.

Jamboree, here we come!  

On an e-mail discussion list for synthetic biology, the question was posed, in regards to what iGEM teams produce specifically: “how is this organism going to be contained, if it’s use is suggested for release in the real world?”  The author then makes an excellent distinction between the actors involved in using synthetic biology: there are the “good guys,” the “greedy guys,” and the “bad guys.” The vast majority of recent discussion surrounding things going dangerously wrong within synthetic biology focuses on these bad guys and forgets about the others.  Even if we could distinguish what makes a bad guy bad, we would miss the point entirely, as they make up a miniscule percentage of those dealing with genetically engineered organisms. It is easy to think about keeping the tools of synthetic biology away from those who would want to intentionally do anyone harm (although, once again, how does one go about defining who such “malicious forces” are?), and certainly a basic level of regulation is necessary for restricting access in general. 

The real question, and the more difficult one to answer, is what sorts of regulations can be set up within the extremely diverse synthetic biology community (which includes academics, industry affiliates, garage “bio-hackers”–discussed at length here–and others) to restrict the possibilities of accidental contamination? 

How is containment dealt with with the UC Berkeley iGEM wet lab team’s project? Even though the argument could be made that this project is directed at ameliorating the process of doing synthetic biology instead of actually existing in the “real world,” what steps can be taken within the iGEM community towards preparedness? Would you agree with Drew Endy that the problem of containment is properly dealt with within current requirements of the iGEM competition?

Here, more than a month after “lysophonix” was deemed unrealistic for completion in time for the iGEM competition, we find the team has gathered together the research completed and has decided to change the focus of the project. A biologically encoded lysis device is still in operation in the team’s new project, coined “Clonebots,” but it now focuses more precisely on the in vivo assembly of parts (which is now regularly referred to as the “manufacture of parts” within the lab) and the easy accessibility of those parts (or product).  

The sound promoters were found to be faulty, which thus led the team to reformat their project for the competition. This is interesting in light of Drew Endy’s past comments that the only way synthetic biology will work and be understood is through the investigation and analysis, on the part of the scientists themselves, of experiments that failed or did not go to plan and the presentation of that analysis to others conducting synthetic biology research. iGEM would seem a perfect place for such presentation of the analysis of complexities involved in attempts and re-attempts to get biological systems to produce what we want them to produce, but it would seem that the environment and situation of the competition could restrict positive inquiry in “failures” as it simultaneously tries to support positive inquiry through “successes.” At the heart of the synthetic biology being done by countless teams across the globe for iGEM is the desire to be recognized at the Jamboree in November–and focusing a project’s presentation on why it did not work according to plan could realistically be an obstacle of access to such recognition. 

But how frequently do scientific experiments go completely to plan?  Synthetic biology focuses its efforts, at least given some of its self-description, on the production of “novel systems,” and biology is an unquestionably largely unknown frontier (though, arguably, less unknown in relation to E. coli or yeast). Unexpected outcomes would appear to be the norm with such a set of parameters. And wouldn’t understanding how to troubleshoot a biological system be the basic requirement for a mapping of electrical engineering onto biology or for engineering biological systems? 

Click here to see this interactive slide show.