Consider Bookhling

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!

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.

A while ago I came across a new program in MIT’s school of continuing education. Apparently the field of synthetic biology is popular, if not mature, enough to deserve a star-studded cast of lecturers doing lab circuit with the class participants for five full days. I was at once enthusiastic about going (the class would have takne place during summer vacation), but then I was faced with the unpleasant reality of the price tag associated with the course. The five day synthetic biology course for MIT’s school of continuing education would set me back $3250, which is a little more than what I can afford on my meager college student budget. Now, don’t get me wrong. Considering the quality of the lecturers and the range of synthetic biology materials covered in the course the $3250 price tag is not high. I would even go as far as to say that it’s rather cheap for what it offers (chance to attend a leture and possibly even a lab session with George Church? Any molecular biologist worth his/her salt would practically drool over the idea). However, the quality of the course offered wouldn’t make $3250 appear out of thin air, as much as I hate the reality of it.

So I let loose a bit of idea on the twitter and the diybio mailing list on exploring the possibility of putting together a $300 diybio course. Mackenzie Cowell was enthusiastic about the whole idea, as well as host of other people. There were a few dissenting voices as well, debating the need for a physical diybio class when the course materials are usually freely available through the net. Other people argued on the fact that diybio class put together by bunch of disparate groups will never be able to catch up to the qualit and scope of the course offered by MIT. Both are valid points and I think I will take some time to refute those claims while I have the chance.

First, physical courseware is always preferrable to virtual courseware given the choice. While diybio shares many parts of its ideological and historical roots with diy/hackerspace movements that center around computer interfaces and mechanical hacking, diybio is not computer hacking. Computer hacking may be part of what diybio is, but at the core diybio is more about citizen/open sciences initiative rather than diy engineering. The maturity of the techniques and tools of synthetic biology and other fields of biology in general is still not at the stage where we can simply treat it as a subset of personal engineering. It all means that diybio must at heart center around real practice of physical experimentaion in order to be successful (barring the diybio-bioinformatics). Computer simulations can only simulate what we already know. Virtual coursewares scattered across all corners of the net, however helpful and detailed they might be will not be sufficient for the vast majority of the people who have a reason to diybio. If diybio is to become what it promises to be, there is an urgent need for a unified and accessible syllabus that ties the materials on the net into one structured and comprehensible package. And we need human instructors capable of answering the student’s questions and demonstrating the physical methods involved in doing diybio instead of forcing people to search all over the net for a video whenever some part of instruction is unclear.

Second, the proposed $300 diybio class idea is never meant to compete with the MIT class in any capacity. It would be preposterous to even consider that. As one member of the diybio nyc pointed out to me, the fully-pledged courses at the institutions like the MIT are not designed with simple injection of knowledge in mind. It’s about shaping the student into a general academic capable of asking the right kind of questions. If simple lab-routine and knowledge already present in textbooks were the point of higher level education then there would be no need for researchers to pursue PhD. They can simply train to be a lab technician. Such vigorous cultivation of invetigative mind is absolutely beyond the scope of the $300 diybio class and there’s absolutely no way that anyone would equate the one to the other in any capacity. The purspose of diybio class (if it ever come to pass) would be to introduce the general public with no experience in any lab techniques and biological sciences to the physical methods of doing those sciences. Maybe some people will use that skill to do something worthwhile, slowly building up to a real pursuit of science in the future. Maybe some others will use that knowledge to make glowing bacteria and wow people at parties. It’s entirely upto them and it’s not within the scope of the diybio class to consider such things.

The purpose of $300 diybio class would be clear and concise. It would be to introduce people with no experience in sciences to the basic gateway tools and methods of doing biological sciences through combination of lectures and lab exercises. Period.

I think this is a very viable idea, considering that many high schools are beginning to adopt some form of biotechnology course into their curriculums. As long as the materials and scope of the class are kept modest low-cost introductory class incorporating lecture and lab exercise is a reasonable goal.

So how exactly would we be able to put together a diybio class? What kind of materials and execises will it cover? Well it turns out that it’s a nastier problem then I first expected. The problem is the identity crisis of diybio. While the whole notion of diybio was popularized along with the advent of synthetic biology and iGEM competition in mainstream media, diybio is not genetic engineering. It’s not even synthetic biology (and yes, genetic engineering and synthetic biology are different). Making a diy gelbox or any other biology lab equipment is diybio. Using bioinformatics to research genus of certain organisms is diybio. Collecting samples of everyday objects and analyzing what kind of things live in cities of the world is also diybio. I might even go as far as to say that programming visualization routine for DNA sequence for use in visual musics comes very close to being part of diybio.

As Mackenzie Cowell put it, the field covered by the term diybio is positively nebulous. It would be crazy to attempt to cover all of that stuff in a $300 class designed by a diybio group. We will have to make a list of things that people can diy in relatively meaningful capacity within context of modern biology. And we will need to figure out a way to put it all together within a greater framework designed to instill in the participant feeling of fulfillment and familiarity with biological sciences.

I’ve considered many options on the must-have list of things for a diybio class, and I feel that the class would have to center round understanding and practice of diy synthetic biology. I believe that the basic tools and knowledge that would allow non-specialist to do a bit of synthetic biology would allow him or her to pursue other areas of diybio from building a personal gelbox to begin learing basic tools of bioinformatics, provided that the diybio class devotes some of the time to understanding and usage of appropriate computerized tools. Of course, even if the diybio class was to center around understanding synthetic biology we would still need to make people understand that synthetic biology is a very small part of diybio movement as a whole.

If the diybio class is to take a form of rudimentary synthetic biology class it would be important to try to integrate lab component as a large part of the overall course. It would allow diybio class to avoid any overly technical discussion unless the participants actively ask such questions, since the class assumes no prior knowledge or experience in biological sciences (nothing beyond the basic high school level biology that is). Focusing on introducing the participants to hands-on experiences related to synthetic biology would work to the benefit of instructors and studens alike within the limited time and resources of the diybio-synthetic biology course.

Introducing synthetic biology to the layman would necessarily involve introducing the concept of biobricks. I believe that it would be nearly impossible to introduce inexperienced population to actual hands-on experience of synthetic biology without the compartmentalization offered by the concept of biobricks. That will prove to be a problem. At the moment it is very difficult for any private organization to obtain biobricks due to possible safety issues, and it is very unlikely for the diybio class or its administration to be able to simply ask for biobricks from the BioBricks foundation itself. In case the class cannot obtain biobricks themselves, I’m thinking of introducing some sort of graphical language that demonstrates the workings of biobricks as well as integrating the whole thing into some sort of graphical computerized environment, in fashion of BioCAD. I’ve seen more than a few of such programs being proposed or demonstrated at the Synthetic Biology conference 4.0, and I think I might be able to find a suitable platform given some time for research. Such simulated study and demonstration of biobricks would be combined with a simple lab exercise introducing GFP plasmid into E.Coli or any other available chassis. It would prove to be a sort of gateway exercise for inexperienced people, allowing them to understand the rudimentary process behind introducing foreign plasmid into a cell chassis. While this is certainly a gross oversimplification of the techniques involved in fields of genetic engineering and synthetic biology, I believe it would be beneficial in introducing people to deeper study of biology once the class is over. Besides, obtaining cell chassis/GFP plasmid kit is much easier then obtaining biobrick parts.

Whether biobrick parts can be obtained physically or not, the diybio synthetic biology class would center around the study of the parts and how they can be put together with aid of computerized models. Maybe it would be better for the class instructor to choose a proven construct made from biobrick parts to pick apart along with the class. Ideally it would be one of iGEM projects that have been experimentally demonstrated, or even a minimal project put together by the instructor or the diybio community itself. The general flow of the class would be as follows.

A-synthetic biology primer
B-obtaining and using biobricks
C-obtaining and using cellular chassis
D-putting it all together using computational tools/measurement standards
E-wet lab session as an extension of D

*each section will have its own bit of lecture session introducing concept and theory behind the physical exercise.

In all scenerio the goal is to have the student capable of building simple circuits using biobricks using graphic aid and pre-made computational tools. Depending on circumstances the students would participate in an actual wet lab session utilizing biobricks, either their own project or a single project being demonstrated for the whole class.

Incidentally this is also the general structure taken by the MIT synthetic biology course, according to the website.

“Fundamental tools of synthetic biology include:

ready access to off-the-shelf standardized biological parts and devices;

a reliable and defined cellular chassis in which engineers can assemble and power DNA programs;

and computational tools as well as measurement standards that enable the ready integration of simpler systems into many-component functional systems.”

The general class structure at MIT’s course will be:

“Day 1: Biological engineering and synthetic biology, computer science and synthetic biology

Day 2: Engineering principles for parts and devices, measurement standards, redesign of cellular chassis;

Day 3: Principles of protein and pathway engineering, computational redesign of proteins;

Day 4: Optimization of microbial chemical factories, redesign of metabolic pathways, standards of practice

Day 5: Summary and future directions”

The MIT synthetic biology course will prove to be a useful tool in figuring out how the diybio synthetic biology class should be structured, though it must be mentioned that diybio class will have to keep things as simple as possible, and stay away from ambitious topics outside the experience of the instructor.

So for now I need to research following stuff for diybio synthetic biology class.

1.inquire about obtaining biobrick parts, possibly from universities in the area after the iGEM competetion.
2.research biobricks graphical language and computer tools, targeted at novices.
3.figure out basic logistics, like the place, precise time and date, and the duration ideal for completion of the class.
4.find a way to obtain a simple GFP plasmid kit (with chassis), necessary equipments and etc.
5.find a biobricks based project that can be picked apart for the duration of the class. Or maybe even design one, in wetlab or on paper.

All this is of course a pipe dream without the diybio-nyc gaining more of a logistical foothold and legal status. Regardless a lot can happen between now and November or December of this year, which is the projected time for the class.

I will try to update as I go along with the research for putting a class together.