Today’s diybio nyc meetup

I got through another meeting with the diybio nyc peeps. Mostly it was management related talk with what came to be the founding members of the group, in terms of getting legal status and finding space for the group. The biggest problem for the group at the moment seem to be lack of lab-worthy space. Another big problem is finding a suitable project idea for us to go ahead with. Actually, if you ask me the lack of pervading project idea is a bigger problem then the lack of physical space, since lack of project means lack of traction and focus for the group. I would really hate to see the group evaporating due to lack of activity at this stage.

I’m wrecking my brain daily over finding an interesting enough project to proceed with, but so far I’m drawing a blank. The fact that I’m practically ignorant on the deeper nuances of the biological sciences doesn’t really help matters either.

One member of the group had been very generous in providing the group with much equipment and other resources, and the other member is doing much to get to the issue of incorporating the diybio nyc group as a nonprofit. I’m trying to look into the space issue by working with other groups outside of diybio, but I’m not too sure how it will work out… Not a lot of people want to work on unproven projects with unproven people. There is a biotech group within the city that might be able to provide us with labspace and resources but they are about incubating professional businesses which doesn’t sit well with the diybio ethos.

I’m a little embarrassed to admit that sometimes I feel like a third wheel in the group, but I guess everyone feels that way at one time or another when trying to get a meaningful movement going. I will have to remedy it by working harder… I really want to do something significant for the group but I don’t know what I should start with, and I’m getting a feeling that this is a common sentiment shared by many of the ghost members of the group (and yes, there are quite a few ghost members, it’s to be expected I guess).

At the moment all I can do is try to provide more logistical data for the group, like rent, spaces, and possible collaboration with existing hackerspaces to get those things. I guess I can give a bit more info about the S.B. 4.0, there are still whole notebooks of data on that conference. I actually gave then the booklet with abstracts of presentations and posters, I hope it will be of more use to them then it was for me, with their experience with actual wetlab and all…

I am trying to come up with a project idea, though it is more likely that we’ll be going with an idea that more experienced members of the group will come up with. Just juggling through ideas of completed projects isn’t good enough. I need to think about the realistic design and research process that will lead to that finished product, which isn’t easy for someone who still has trouble digging through some of the simpler stuff of molecular biology and pathways. I guess this is time for me to go dig up more igem stuff, and try to make sense of it all in terms of technical execution and practical resource requirements. That is, we won’t be coming up with a model of minimal cell in basement lab anytime soon (as much as I would love to see that happen).

I’m beginning to think about something on the lines of building in light sensitivity into the bacterial chassis (at least I might be able to help out with physics side of things in project like that) but what exactly? What kind of project would I be able to conceive of that incorporates light sensitivity of cells while remaining imaginative and practical within the technical limitations our group face?

E.Coli chassis that follows light? Or avoids light even. Now such idea would be a problem considering that I do not have a very clear idea of the mobility mechanism behind E.Coli (CAN they move? Or will it be a cycle of dying out when within the light rich or deficient environment?).

Considerations like that makes me feel like simply suggesting doing some exercise to make bacteria glow, document the whole process and materials used so that I and other less experienced members of the group can have clearer understanding of the techniques and limitations involved in the process- notably, introduction of foreign plasmids into a native chassis. The plus side of such an approach is that it lays nice groundwork for future experiments for those who aren’t experienced with molecular biology. The negative side would be that such experiment would dig into the resources and time the group doesn’t really have. Possibility of boring more experienced members of the group is also something I need to watch out for. Diybio nyc will not be able to sustain itself without the help of the people experienced in experimental biology.

I just don’t know what to do. Even if I were to suggest the glowing bacteria as a sort of introductory warm-up exercise, we still need to come up with a great project idea at some point.

I’m writing this in the subway on my way home. It’s beginning to sound like the diybio nyc is in some mortal peril now that I read some of the stuff I’ve written. It isn’t. Considering all the odds things are going swimmingly and possibly even better than I first expected. The whole atmosphere of excitement at being able to think about manipulating biology of living systems for academic pursuit is something that makes me feel alive. And I enjoy wrecking my brain over this stuff. It’s only that I’m under constant pressure to do more and get more things done, to make the group really work. It’s because I believe that we have something with potential for some truly wonderful stuff here. And it would be a real shame to let it die out not with a bang but a whimper.

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.

Synthetic biology

I’ve been looking around the synthetic biology scene for a while now. Although my academic specialty doesn’t revolve around the field of biology, I try to keep at least an amateur’s perspective upon the advances and techniques of the field. Considering that my passion lies in the study and realization of artificial life I find it important to keep broad view of things irregardless of specialty or the immediate requirements of my own job.

I’ve often noted that the field of synthetic biology had suffered quite a bit of misunderstanding since its inception (which wasn’t that long ago actually), so I thought I might as well do a little write up of what synthetic biology really is.

Synthetic biology is an approach to engineering biology instead of being an academic field of specific goals. Simply put, synthetic biology as a whole is an approach, which may be utilized toward a specific application dictated by the case/individual/group etc.

In order to become a tool in engineering biology its link with conventional genetic engineering is inevitable. The breakdown of the similarities and differences between synthetic biology and genetic engineering is as follows.

Conventional genetic engineering is composed of three primary stages.

1)Recombinant DNA

2)PCR (stands for polymerase chain reaction)

3)Automated sequencing

The step one and two are about writing the DNA of specific purpose, and the step three is about reading the recomposed/component DNA. While these three steps are integrated to the core of the field of synthetic biology, it includes three more stages which differentiates it from pure genetic engineering.

4)Automated construction of DNA

5)Standards

6)Abstraction

The fourth stage, automated construction of DNA refers to the divide between the designers and builders of the DNA. Within the structure of the synthetic biology the designing of a DNA sequence and actually working in forming such DNA sequence (which is an expensive and time-consuming process) is separate from each other, making student-amateur oriented biological machine design possible within currently existing technical/industrial infrastructure. However, simply having a separate industry deal with mechanical parts of the synthetic biology would be meaningless without stage five and six, formation of standards, and abstraction of genetic interface. The last two stages run along the lines of the advance of computer programming scene, where formation of standard (html) and abstraction (most users don’t type in zeroes and ones anymore. We click buttons) brought on an explosion of global userbase and subsequent integration of the computerization into the very fabric of modern human civilization. Synthetic biology as a field encompasses all the six stages I’ve written about so far, each of them an integral part that reinforces another. In a way, synthetic biology is intimately linked with the garage-biology or biohacking movement in that it allows individuals to focus on designing their own novel biological contraptions using freely available and globally present database of biological/genetic abstractions and standards, while leaving the complexities and drudgeries of bioengineering to the mechanism of economy/industry.

I personally consider the field of synthetic biology to be a movement. Nothing as pretentious as some political gather-up, but a real movement like a wave spreading across the surface of the human society, a tell-tale sign of something gigantic beneath the surface. People used to build computers in their garage. Look where we are now. I can’t begin to imagine to full impact of well-executed synthetic biology as movement/industry/economy in the course of the future. Many little children these days are aware of tools like python and java, and some of them even utilize them with surprising efficiency and familiarity. Imagine the same children in the future, not with imaginary numbers but with the stuff of life. A little risky, but it’s certainly the type of world I want to live in.

What I also find to be interesting is the method of thinking behind synthetic biology. I don’t know how to put it succinctly yet, but as I have noted in the previous write up ‘transhumanism and the human network’, there is an underlying method of thinking that is showing up in universal scales, regardless of locale and cultural background. Am I correct in assuming this peculiarly wide-spread method of thinking as a type of zeitgeist? If so, where and how did it originate? And what role does the human network and its emergent properties take in the shape of the world we live in?

Maybe, once the biological hacking is done, the little children will hack the human civilization itself.

For those of you interested in slightly more detailed insight into synthetic biology, I give you two links.

www.openwetware.org

The openwetware website, definitely worth a look.

http://openwetware.org/images/3/3d/SB_Primer_100707.pdf

A simple primer to synthetic biology, covers the basics so it applies to other fields of biology as well.