Synthetic Biology on KQED QUEST- and some comments on the diybio aspect

(((I was trying to embed the videos from the KQED site directly in the post, but apparently copy pasting embed code in HTML panel isn’t good enough for wordpress. I’ve linked to them instead. They are quite good. You should really check them out.)))

Here are two videos on synthetic biology. The first one is a short introduction to synthetic biology produced by the wonderful people at KQED QUEST program, which goes into some level of detail on what synthetic biology is and what we are doing with it at the moment. Certainly worth some of your time if you’re interested in this new exciting field of science.

The first video is the original KQED QUEST video on synthetic biology.

The second video is the extended interview with Drew Endy available off their website… While the field of synthetic biology in the form we now know and love probably began with the efforts of Tom Knight at MIT, Drew Endy is certainly one of the most active and clear thinking proponents of the scientific field of synthetic biology.

Here is the link to the second video, the extended interview with Drew Endy.

If you hadn’t guessed yet, I’m really big on synthetic biology. I think it’s one of the most exciting things happening in the sciences today, not just for biologists but for mathematicians and physicists in that synthetic biology might one day provide a comprehensive toolset for studying the most complex physical system known to humanity so far… That of complex life-like systems.

I also believe that abstraction driven synthetic biology cannot manifest without a reasonably sized community of beta-testers willing and able to use the new parts and devices within original systems of their own creation. Computer languages like python and ruby needed efforts of hundreds of developers working in conjunction with each other for a multiple years to get where they are today. Complete operating system like Linux took longer with even larger base of developers and we still have usability issues. Synthetic biology must deal with systems that are even more complex than most computerized systems, so it’s not unreasonable to think that we’ll be needing an even wider deployment of the technology to the public and active community involvement in order to make it work as engineering capable system.

So I am a little dismayed, along with legions of other people who were initially excited by the promises of synthetic biology in conjunction with diybio community, to find that access to BioBrick parts and iGEM competition is severely limited against any amateur biology group operating outside conventional academic circles.

You see, unlike computer programming, constructing synthetic biology systems require BioBrick parts from the registry of standard biological parts. Right now it is next to impossible for diy-biologist interested in synthetic biology to get his or her hands on the BioBrick components through proper channels. The DIYBio-NYC group alone had quite a few number of people lose interest because of uncertain future aspects of being allowed access to the BioBrick parts and talking to people from around the world on that issue I’m beginning to think that there are a lot more of such cases. So far the major reasoning behind the restricted access seem to be the safety issue, but considering that the regular chassis used to put together BioBrick parts is based on academic strains of E.Coli that are even more harmless than your average skin cell I can’t see much wisdom in restricting access to the parts on basis of safety.

The bottom line is, the state of synthetic biology and BioBricks foundation at the moment is forcing a lot of people, some of them quite talented, who are enthused about contributing to a new emerging field of science to back down in either confusion or disappointment. Considering that the very structure of synthetic biology itself demands some level of public deployment to stress-test and demonstrate the effectiveness and stability of its individual parts and devices (with creation of those individual parts and devices left to the highly trained professionals at up scale laboratories) this is highly unusual state of affair that is not motivated by science behind synthetic biology. I might even go as far as to say it has the distinct aftertaste of political calculations of public relations kind.

The field of synthetic biology will never achieve its true potential unless the BioBricks foundation and iGEM administrators come up with some way for people outside traditional academy settings to participate in real design and construction of synthetic biology systems.

Here’s a little bonus, the QUEST show producer’s notes on ‘Decoding Synthetic Biology.’

The first encounter

This past Monday was the first meet-up date for the diy-bio nyc… I was thinking of writing a little post on the meet-up from the day one, but the papers kept rolling in and I had to put it off for a day or two. I won’t be naming any names in this post for fear of possibly breaching someone else’s privacy (my name’s Sung won Lim, by the way).

The plan for the meet-up was a little shaky at first. We were planning to use the American Museum of Natural History as the location of the first DIY-biology meetup in the history of the New York City (as far as I know). It would have been really epic if we could make it happen (I’m still really sorry that it didn’t happen). Alas, due to the policy change at the museum we were faced with last minute location change. I had to keep checking the mailing list on my phone’s web browser to get some updated info on the place and time for the meet-up, and for a moment there I thought the whole thing would be scrapped. Fortunately most of the people on the diybio-nyc mailing list came through and we met at a cafe on the 75th street which wasn’t very far away from the AMNH.

Out of the eight people on the diybio-nyc mailing list four people showed up, which really isn’t so bad when you think about it. I arrived at the cafe about 10 minutes from six, and found two members already seated and busy chatting away on some biotech topic. Bit of introduction ensued and we were soon joined by another, making it four.

The composition of the group showed some biotech bias as expected. One of the members is pursuing a degree in biochemistry with lab experience, and the other already went through the courseworks for advanced degrees and is currently working in a related field. I on the other hand, is a physics major whose biology education stopped at around high school, and the last person was a writer teaching at a local high school (with same degree of biology education as me). This was something of a relief for me since I was worried on the prospect of bunch of people with no lab bench experience sitting together trying to figure out what to do. And since we have a real writer amongst us, I won’t have to be the official blogger of the group 🙂

Since this was a first meeting we didn’t really discuss anything too technical. The meeting generally revolved around personal introduction, reasons for our interest in diy/synthetic biology and managerial issues. For people meeting each other for the first time in their lived with scarcely any introduction on or offline, the atmosphere was very friendly and amicable. It’s the kind of group that you can bring your friends to, and the diverse background of each individual members definitely helps to foster that certain mood.

We managed to set up some priorities. We listed a few issues that might get in the way of forming a fullscale diy-bio operation, and it inevitably boiled down to a few very specific things.

Workspace: Lab needs space. We might be able to manage with meeting up in a member’s home (which is what we’re thinking of doing for a while) but once we get to doing things with E.Coli that’s not really an option due to smells, possible contamination, distractions, and etc etc. We need a dedicated hackerspace like what the NYCresistor has with running water and fridge. Which leads us to the second issue…

Money: The real estate in and around NYC can get ridiculously expensive. Since we’ll be gathering at the lab in afterhours stocked with lab materials and equipments, we need to give a bit of consideration for environment as well. I’m not even going to begin with the actual cost of materials/utilities/fees that will be needed, all of which will only increase as the time goes on and we decide to do bigger things, like going on the iGEM. Since we already have two members somewhat connected to existing biotech establishments we have it a little better than some other groups in terms of obtaining lab materials. One solution at the moment is to collect bits of monthly fee from the members of the group ($10 per month as of this writing), but that won’t be able to make up for half of what we really need (the mailing list has 8 members). So right now, we need some sort of heavy weight backing that ranges from preferential tax breaks to lab equipment/materials support. Which leads to…

Mission Statement/Goal: It might sound silly (I’m still not entirely convinced it doesn’t), but we need it. With a proper mission statement and clear goal, we are thinking of possibly turning the diy-bio nyc into a full-pledged nonprofit organization for educational outreach and techno-evangelism (yeah, we need to work on how to write it better. Thank god we have a writer). Doing so will allow us some flexibility in obtaining labspace and materials since any organization/individual who contribute to the diy-bio nyc efforts can make it a tax write-off. Not to mention having a clearly defined goal helps people to focus their efforts instead of running around all over the place. I was also thinking of possibly working with one or more of the universities in the area (there’s a lot of them), but according to those in the know that can get dangerous. Lot of colleges treat IP like cashcows (which isn’t too far from the truth) which might get in the way of the opensource spirit of the diy group. We’ll need to do some planning on that front.

I think above three points apply equally well to any other possible diy-bio group, regardless of location. I am beginning to think that we need a reliable tutorial on how to set up a decent lab-worthy group that explains the whole thing in terms of laws and economics involved. I am also planning on using high school level biotechnology class syllabus to set up a mini courseware for introductory diy-bio stuff, so we don’t spend too much time explaining stuff during the real project sessions. If I can make it work, maybe diy-bio nyc can work in conjunction with local high schools which would sidestep the IP problem we might encounter in partnership with universities. I’ll see how it turns out.

All in all, it was a very meaningful meeting. I’m literally getting an adrenalin rush from all the excitement. I’ll report more as the group moves along.

If you have any questions regarding the membership or the meeting location of the group (we are actively recruiting!) feel free to email me or leave a comment.

Mad science contest!

Who in their right mind does not want to become a mad scientist? Underneath the prim and proper veneer of sanity and polite gestures, I know that there is a darker longing gravitating us toward the callings of mad science.

Yet the fact of life is, there are usually few opportunities, if any, to pursue and perfect the dream of mad science in this world, whether it be societal taboo or physical restraints. In the light of the scared world we live in, I am very happy to announce the contest for mad scientists, aimed primarily at the emerging field of synthetic biology.

There are two categories of the contest, and each category offers a delicious prize for the taking. The category one is the more realistic mad scientists in all of us. You are supposed to work with the real BioBrick parts and form an artificial synthetic organism/something to sate the mad genius inside you and possibly even help the world in the process. The prize for the category one winner is an all-expense paid trip to Hong Kong for the upcoming Synthetic Biology 4.0 conference and a chance to present your work before the whos who of the synthetic biology scene today.

The category two is the one for the imaginative madhouses in all of us. While scientific reasoning behind your creation must be present to certain plausible extent, the second category does not force you to figure out real PCR amplification rates or the roles of each specific BioBrick parts, something you should be proficient with should you decide to compete in the first category of the contest. Instead, category two seem to be leaning toward discovering truly imaginative applications of the tenets of synthetic biology and possible social/industrial implications of such a noble craft.

This is not a contest cooked up by bunch of enthusiastic crackpots either. Some of the judges are full-time professional devotees/founders of the very field of synthetic biology itself, like Drew Andy.

So spread the news, and get all of your families and friends involved. This is a contest for the mad scientists of the world, and we really need diverse and crazy ideas that deserve the mantle.