I’m alive again.

Stare at my awesome new PCR machine. And tell me the darn thing isn’t cute. And ignore the carpet from the 70’s it’s sitting on.

It’s been… More than a year since I’ve uploaded anything to this blog. During that time only thing I’ve written long form were occasional tumblr posts dealing with what’s been happening in my life or some dry master plan to rule the universe through the power of science, typical student stuff.

I’ve stopped blogging on this site ever since I started working at Genspace NYC as one of its co-founders and one of the three people who actually did things in the lab instead of talking about biosafety. In retrospect I should have expected to spend a huge chunk of my life helping to plan and run a fully functioning molecular biology lab on shoestring budget, but I never really realized what kind of commitment it would be before it hit me in the face full force. During the heydays of doing projects in the lab I was spending about 12 hours per day running experiments, no weekends, no vacations. And that was while working full-time in other jobs too, since nothing at Genspace paid anything… Well, that’s not strictly true. I did earn enough here and there to get by if I didn’t have to worry about rent and supporting other people, but alas, that’s not the case for me.

Now that I look back at it I feel like I was dreaming for the past three or so years. I dreamt that I was contributing to some pioneering vision, each hour spent while almost blanking out from lack of sleep building toward something greater. Something that might even change the world into a bit more agreeable place. Now, the dream is over. It’s been over for the past half a year, it’s only that I lived in rather characteristically stubborn denial during that time, probably causing some level of annoyance to some of the other Genspacers.

I’ve resigned all my positions at the Genspace NYC lab. I’m not a board member, not an officer, and not a member of the space, though I still have to get all the books and other things I’ve built up in there out. And I think I made the right choice.

Stepping back from Genspace brought me some new perspective, some of which I’m still trying to get used to. Maybe I’ll write about some of the lessons once my head is completely cleared up… I’m still suffering from a bit of a shell shock.  Here’s a short, non-comprehensive list before I forget them later though.

• DIYbio is not amateur biology
• Issues of biosafety, a byproduct of initial DIYbio hype being tied to the hype about synthetic biology, completely poisoned good people and good initiatives
• Despite the biosafety scare no constructive discussion on potential safety and other broader concerns about amateur genetic engineering ever took place. If it did I never heard about it in my three years of genetically engineering e.coli and plants in a warehouse in Brooklyn, some of them involving processes using toxic chemicals -disposed properly, of course
• Involvement of FBI in reaching out to the DIYbio-amateur genetic engineering community was a double edged sword, in that it helped form a weird perception of hierarchy in some of the people who were in more direct contact with the FBI
• One of the direct negative results of the biosafety scare and FBI involvement was creation of a group of amateurs whose sole responsibility, in a sense, is to tell other amateurs what to do. Coincidentally those people rarely have any projects under their belt, and are usually not very literate in lab safety practices due to utter lack of experience
• Considering that no one really listens to above group of people anyway (except maybe reporters, grant organizations and the FBI, none of whom practices garage biohacking, to my knowledge) it’s only served to keep people who had running projects underground due to potential nagging from strangers with no valuable input
• Despite my comments, I still give high marks to the FBI for deciding not to just tap everybody’s phone. It would have been a waste of their resources, and I view their assessment as very accurate
• TED conference is the hip rich people’s leadership seminar camp, with some amazing thinkers and respectable individuals thrown in (unlike leadership seminar camps). Still so much better and inclusive than Davos. Perhaps even more effective
• Maker Faires are what dreams are made of, and more places should have them
• It’s incredibly easy to put together a minimal molecular biology lab. I just finished putting mine together outside Genspace for about a thousand dollars, including essential reagents. I also helped one of my students put his own together
• Community lab model doesn’t work as is. Current model assumes new members to be incompetent, in a sense. At least not good enough to work in a ‘real lab.’ And current models drive managers of the community lab to have vested interest in keeping most of the members scientifically illiterate after a certain point, with a few outliers
• Education should be done by educators. Scientists should provide the materials the educators can work with – reproducibility and clear, comprehensive documentation
• There are more than a few high schools out there that covers genetic engineering with their students. There are a few that even covers synthetic biology
• Despite relatively minimal PR, they tend to have worse access to equipment and reagents than most DIYbio/amateur genetic engineering labs, but have better results

I’m definitely missing a whole boatload of important points. I’ll get back to them later when it’s not seven AM with zero sleep last night.

Outside of reflecting on what I’ve been doing for the past three years of my life, I also got a chance to get in touch with and work with lots of interesting people around the city. It turns out that the DIYbio-NYC list I founded couple of years ago was moderator locked after a group vote (that later grew into Genspace) due to potential security issues, and interested people around the city did not have a place to converse about local going-ons with each other. So I just remedied that problem as well.

Here’s a message that went out to people last night:

 

 

Good news, everyone 😉

I’ve just turned off all the moderation settings on the diybio-nyc mailing list, and renamed it biohack-nyc@googlegroups.com 

The list was dead for a while what with everyone needing permission to post on it (which was in place by group decision at the time, what with biosafety scares and all). It was also true that there just weren’t that many people out there who were working on stuff as well. 

Well I’ve been talking to quite a few number of new yorkers out there and things are happening all over the city now. And there has to be a place for people to brainstorm and meet up with each other with a little local flavor. Keeping the list moderated like in the past would have been disservice to the community at large. 

Hopefully this can serve as one of the many springboards available in NYC to help aspiring biohackers learn their trade. 

Spread the word, join up yourself, be excellent to each other and have fun! 

biohack-nyc@googlegroups.com

https://groups.google.com/d/forum/biohack-nyc 

 

 

And yes, I changed the name from DIYBio-NYC to biohack-nyc because

1) as a screw-you to people who are still scared of the term hacker

2)I keep hearing things about the term/group DIYbio that makes me feel like it’s something I can’t agree with.

Hopefully this will begin to attract some brilliant minds that I know are out there to coming out of their genetic engineering closet. And maybe some activity will spur me to write  a whole lot more as a well. God knows I really need to.

edit: before I pass out, I want to go on the record as having said that, despite personal differences, almost everything I know about biology now I learned from Ellen Jorgensen and Oliver Medvedik from Genspace NYC. And I still recommend students and hobbyists go check out the Genspace NYC lab over at 33 Flatbush ave, because, quite frankly, there’s nothing else like it.  

$300 synthetic biology class

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.

DIY synthetic biology

Just a short note about a cloning kit developed by Qiagen and Invitrogen. Will this be a first step in signalling the trend of the industry toward relatively freely available bio kits for DIY synthetic biology? I certainly hope so. Disposable lab kits packaged for small-scale labs and private hobbyists might prove to be a lucrative market in the near future once more universities get around to introducing synthetic biology curriculum to their students.

Of course, a number of such kits had been available for smaller scale purchase before, but I find this one significant in streamlining of the process, inclusion of ‘directions’, and appearance in mass-media outlet like the wired magazine… Some of the problems plaguing the field of synthetic biology at this point is the problem of general appeal and accessibility (other than the usual technical issues), and this might be beginning of an industrial trend in fixing it through the ‘hand of the market.’

Synthetic biology, being a biotechnology of information, will benefit greatly and show rapid growth from industrial level support. I can’t even begin to talk about the benefits of biological economy, and many in the field of economics and biology seem to agree on that issue.

There are some who are voicing concerns about streamlining of technology involved in the general biotechnological process pampering the scientific community, but I find such arguments rather shortsighted. The technologies available to us at the moment are not perfect. If we can’t get minor technical details out of the way of the real pursuit of science, the field of science as a whole will remain on the fringe of the human civilization. The pressing need here is to broaden the field and scope of the science itself so that the average layman might apply him or herself along with the traditional scientist population. Such a change will be able to trigger a whole spectrum of economic and social changes in creation of jobs and specialties, with more even distribution of knowledge which will further the advances of humanity as a whole.

No matter how much I’d like to deny it, advance of science is intimately linked with fostering of proper economical and sociocultural environment for such a change.

I will post more on the matter as I go along.