Openeverything-NYC April 18th

I spent all of 18th in the openeverything conference at the UNICEF headquarters. This was the first barcamp style meeting I’ve ever been to in my life, so I thought I might as well jot down some notes.

For those of you who don’t know about what barcamp is, it’s like an emergent conference. You get bunch of people together in a building, and everyone who wants to talk about something just post their topic card (or whatever the equivalent you are using) on the main board. When the time comes you either present something or have a discussion on that topic with people who were interested enough to show up at your session. It sounds a little chaotic, and it really is sometimes, but on the whole the system works very nicely. Even the people who aren’t as talkative as others get to talk in such settings, and there is no barrier dividing the audience with the speaker so you can actually get work done with people who share the same interests as you without sitting there waiting for some guy/gal to finish talking. If you wanted to talk or listen to something but there’s no one talking about it you can always walk up to the schedule board and write up your topic, and voila, you have people showing up trying to figure out what to do with your chosen topic (I actually tried it and it worked, surprisingly enough).

As far as traditional barcamps go this wasn’t really the most ideal of the camps, since of the 220 or 250 people who said they were going to show up only about half (maybe even less) arrived. Even so, the diversity of interests and objectives were electrifying to me to say the least. Being hosted by the UNICEF most of the topics revolved around programming or infrastructure projects that can benefit the causes of UN, like the rapid SMS which is a computer based SMS system that interface with cell-phones to create different kind of low-cost wide area logistic coverage. The system is completely open-source and scalable, and it’s been used in the field for various UN related activities like education and keeping logistic tracts of 65 million insect nets that were set to be distributed across some parts of Africa. Other interesting topics included a brief discussion on the nature of AI (though none of the people in that particular session seemed to have a very good idea of artificial intelligence), cheap open-source aerospace programs, and computerized education systems/web 2.0 services that might be used to keep track of education and qualification of individual members in form of a flow chart. Using such a system a kid might be able to copy and follow the skill/education set of, say, an astronaut if he/she’s interested in pursuing such a future. I do realize that while education goes above and beyond simple skill set qualifications the idea itself is sound, and I would love to see it implemented in a real web system someday.

I was hoping for some people to do a tract on diybio/open-source biology and open science in general, but for some reason no one really set up a topic that relates to those interests. So in true spirit of a barcamp I decided to set up a topic myself, which was a little overwhelming at first, this being the first barcamp-style con I’ve ever been to. It didn’t help that I’m usually not the one to speak in public venues. It was something of an adventure, and I decided to take the plunge. I was helped by some of the onlookers who pointed out the processes of barcamp that makes it work as a sort of emergent conference with emphasis on ‘burst activity’ and getting stuff done.

Well to be frank, the talk I gave was a mess. It wasn’t prepared and I was really wiped with other talks by the time I got to my session. Having people who knew even less than me in regards to biology didn’t really help either, since I was constantly double checking my facts so that I wouldn’t give any twisted impression of diybio to people who are new to the idea. I more or less wandered around the topic of diybio and synthetic biology, and though I did stress that synthetic biology is not diybio, I’m not too sure if other people got that message clearly enough. It’s my fear that a lot of people who showed up at my session went away with inflated and unfounded hope on the current state of diybio and synthetic biology… I did learn a lot from the experience though. Maybe as I get more experienced with this stuff someday I can give a compelling talk on diybio that would lead people into participating in this very exciting intellectual movement.

I did receive a lot of interesting input from various people regarding the state of licensing and what it really means to creative open-source content (it was ‘openeverything’ conference after all. Lot of license-related people). I always thought I knew a thing or two regarding the basic ideas of CC license and GNU/open-source license terms (which btw, Richard Stallman insists is separate from each other). It turns out that I didn’t know squat. Penetrating the thin veil of ignorance: that’s what I call an education!

I should have a post on diybio-nyc‘s recent GFP E.Coli session sometime this week. Stay tuned!


DIYbio NYC meeting: Apr. 15th

Okay, here we are, the fourth meeting of the diybio nyc group. As you can see the meeting was on the April 15th, almost a week ago, so I’m a little late in writing this post. The week had been a little crazy (I’ve been saying this a lot lately), so I really didn’t have the time to get around to it… It didn’t help that I had a bunch of class works that were already overdue and I had to spend the whole of Saturday and Sunday with bunch of UN/Google/open-source people related to the openeverything conference/bar-camp, which I will have to write about soon.

The April 15th meeting was a discussion meeting wit no lab session involved. It was held in a restaurant downtown called Veselka, an Eastern European restaurant serving some good pierogi (never had one before). While the food was good, the atmosphere wasn’t the most ideal to have a complex discussion though. It’s more of a family place, with lot of people coming and going, everyone talking at rather loud volume and etc. It was a refreshing change of pace from sometimes pretentious NYC food world… But I’m not really about to write a review on the restaurant am I?

The situation worsened due to the fact that a reporter from the New York Times Magazine was planning to show up. Some people in the group had experience with journalists (one of them is a published journalist actually), so we were afraid that something we say might be used out of context. There’s a lot of scaremongering out there in regards to the possible dangers of diybio, and it’s something we really have to avoid at all costs. And then the new members showed up. Total of three. All of them came from very unusual and interesting backgrounds but the venue and the circumstances weren’t very ideal for personal introduction between the old and the new members, especially owing to the fact that the ambient noise was to such an extent that we could not hear people from across the table. I would have loved to talk to them a bit more but didn’t really get much of a chance in between trying to hear what other people were talking about and trying to get actual work done in regards to the mission statement, identity and direction of the diybio nyc as a whole. One of them came from biotech background and I’ve been keeping in touch with him for a while now, through IM and twitter. The other person came from art background, working with a type of bio-art club/collective called the Grafting Parlour, which is kind of like the SymbioticA, pursuing the techniques of biotechnology for artistic pursuits. The last person to show up was from computer sciences background with interest in film making, who seemed a little surprised that she’s the only one with computer sciences background in the whole diybio nyc group (quite frankly that surprises me as well, considering that the whole concept of biohacking came along with the advent of computer sciences and biology’s increased dependence on variety of computerized techniques). I’m afraid that some of us (including myself) might have seemed a little distant to the new members of the group. I will have to try to remedy that somehow later on. DIYbio is about the spirit of openness in science and it would contradict the implicit founding spirit of the group to make new members feel out of place. I’m especially looking forward to talking more about the activities and purposes of the bio-art movement. I believe the whole concept of bio-art itself is replete with incredible possibilities that only art can dare to explore, though the group would have to find a compromise between ethical and scientific constraints and the spirit of exploratory arts… Even finding that fine line between arts and sciences sounds intriguing to me, to be honest.

The basic agenda of the meeting was on drafting the mission statement, establishing the main short term and long term objectives of the group, and finding a way to realize those goal within realistic budget and time constraints. Whenever we talk about doing some sort of project one problem gets in our way. Any biological project of even moderate complexity requires a dedicated lab space that’s not located within residential address. We might be able to pull it off within private residential setting like those people trying to build a bio-lab within their closet, but it won’t do for any long term experiments or groups, since there are just too many legal hoops and hurdles we’d need to workaround. And the last thing diybio as a whole needs in this age of terror-related scare-mongering is questionable legality and dubious safety measures. A member of our group experienced in operation of biotech laboratories is strongly pushing for strong safety protocols comparable to those applied to commercial labs, and I agree with her point. It might sound a little bothersome right now but it will go a long way toward the group being a fully pledged biological lab space.

The problem in obtaining a real lab-worthy space in the city is that it’s just too expensive. We would need a way to raise some funds, by ourselves or with cooperation with other educational institutions in the area like one of our members suggested. We can do a lot of those things if we decide to keep things hush hush and work under the table, but again the risks are just too great. In the nightmare scenario what we do wrong might effect the diybio movement as a whole, pushing the public opinion toward opposition. It’s the group’s implicit agreement that we can’t take that kind of risk at this very crucial time. Compared to finding the space, obtaining real lab equipment is a child’s play, and we’ve already made a lot of progress in that area thanks to one of our member’s generous input.

We need to find a path that would work toward to solving the space issue, and at the moment that happens to be working toward obtaining a legal status for the diybio nyc. It’s our collective belief that having an actual legal identity will help us toward raising funds, cooperating with existing lab spaces, and establishing supply relations with bio-companies we would need to contact in order to get perishable experiment resources. The ideal legal status for a group like diybio nyc would be a registered non-profit, whose tax-exempt status would afford the group with some negotiable leverage when it comes to financial negotiation and support. Drafting mission statement and by-laws for the group would be first step in establishing legal and ideological identity of the group.

All this sounds like a lot of financial and legal talks for a group supposedly dedicated to bringing science to the open. Experiments cost money and requires space, so it can’t really be helped for the moment. At least we do have an actual wet-lab session coming up this Tuesday. It’ll be an experiment to introduce GFP plasmid vector into K12 E.Coli chassis (the E.Coli chassis in this case is completely harmless to human beings. You can actually drink it and it’ll pose no threat to you. It’s a special, non-toxic strain of the E.Coli we all know and fear, that’s been used in laboratories for about a century, as well as variety of high school biology classes). It’ll be a first experiment that would actually allow us to observe and experience the process of introducing plasmid into a bacterial chassis with visible results, so saying that I’m excited about the prospect would be an understatement.

There’s been a lot of trials and tribulations for the group, and I’m sure that there will be more to come. But we are going somewhere with this, and it’s really good to see so many people interested in learning more about the techniques and science of biology outside the traditional medium.

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 Sky Crawlers screening

Just got back from nyc Sky Crawler’s screening. I’m a little burned out, so let me just jot down a couple of points for further recollection tomorrow.

1)The screening opened with a recorded message from the venerable Mamoru Oshii himself. He said that the movie was about people who stopped/refused to grow up, and drew a parallel between the immortal pilots and the mindset of the current generation. Despite being spoken in Japanese, his words felt well thought out and serene. He obviously gave a lot of thought into this.

2)The basset hound, the major Kusanagi look-alike, gothic architecture in part of the film, strange machinery possibly playing music, lot of thoughtful dialog, and reference to the Albert Camu’s the stranger. This film has Mamoru Oshii written all over it, and that’s a good thing.

3)Everybody smokes a cigarette. Seriously, I think I saw someone lighting up practically every five minutes (the film was two hours long). It’s definitely intentional, but to what end? I think I know what Mamoru Oshii wanted to say, but won’t write it here since there’s a spoiler.

4)Lot of daring here folks. Remember that the main characters are immortal teenagers that must be killed through violence. These teenagers don’t shy away from adult situations, and Mamoru Oshii might have done some intentional dare to the censorship system. I like the realism, but some people might have issues with it. Of course, nothing perverted here. Nothing we wouldn’t expect teens in kill-or-be-killed situations to do.

5)The movie was two hours long, and in typical Mamoru Oshii style there’s a lot of philosophizing dialog, blank stares, and silent scenes. Amazingly though, I couldn’t take my eyes off the screen. And the characters, despite not saying very much, felt very alive and understandable through their facial expressions and motion. This movie isn’t boring. If someone does find this boring, they will probably find anything that has thoughtful dialog to be boring.

6)This is a movie adaptation of a novel and it shows. Time to time I needed to glean a lot of information from a simple scene or two, the kind of things the novel might have spent a chapter describing. I think the overall transitions were done masterfully, but it is noticeable.

7)The musical score is done by Kenji Kawai (who also did the Ghost in the Shell soundtrack), and it’s beautiful. I know I’m hunting down an ost for this one.

Will I get a DVD once this comes out? Yes. Definitely. Do I expect this movie to make full theater circuit in America? Unfortunately, that’s very unlikely considering the subject matter. As stupid as the censorship is, it’s not going away anytime soon, and this film has a few things that might make your normal High School Musical lovers feel uneasy (not that there’s anything wrong with liking High School Musical).

I think I had a couple of other points I wanted to make, but my brain is all mushy right now. Gotta go to sleep for tomorrow’s lab session.