Alan Kay applied to synthetic biology, and other stuff.

This is something I wrote up a few days ago, probably around four or so in the morning. So take whatever it says with caution.

I know I should be writing about some other things as well, like how the diybio nyc might be amazingly close to getting a real lab space, or how I’m prepping to stop by for this year’s iGEM jamboree. I also have the pictures from this year’s major diybio nyc event, where we set up a stall on the NYC green market and extracted dnas from the natural produces with common household material (with the passers-by of course). Each of those things would probably make for some lengthy and interesting reading, and the list goes on (my life’s actually kind of exciting right now). Yet whenever I find the time to write something down, nada. Nothing. My mind just shuts down and nothing I can commit to paper or the keyboard seems good enough.

Tonight though, aided by my weird bout with insomnia, I’ll just write something down I’ve been meaning to say for a long time.

I’ve been looking into the history of computing and computer languages recently. I’ve always had some level of interest in computers. Not just the spiffy brand-new muscle machines but in what most people would refer to as ‘retrocomputing’ (I once ended up practicing some AIDA because of that. Ugh), which is a story for another time. It’s not that I think old ways of computing were better than what we have now (protected memory FTW). It’s just that it’s much easier to trace the evolution of the concept of computing when you see beyond the immediate commercial products.

Synthetic biology is effectively a pursuit of engineering biological organisms. Biological organisms are based upon somewhat unified information storage and processing system that has quite a bit of parallels to mechanical computerized systems. I’ve been wondering whether it would be possible to predict the future development of synthetic biology by looking at how computer programming languages evolved (because they deal with information processing systems applied to physical counting medium). Maybe it’d be possible to predict some of the pitfalls that are inherent in developing complex programmable information processing system that will apply to the synthetic biology in the future. Maybe we can bring a conceptual framework to the synthetic biology that would have taken decades if left to mature naturally to within mere years.

While I was rummaging through the texts in both real life and the web (with many of the promising links on the web leading to dead-ends and 404s) I ran into a programming paradigm and environment I was only superficially familiar with before. Smalltalk and Squeak, both the brainchild of the computing pioneer Alan Kay.

Here’s an excerpt from Alan Kay’s biography I found on the net (I can’t find the website right now. I swear I’ll edit it in later, when my brain’s actually working!)

“Alan Kay postulated that the ideal computer would function like a living organism; each “cell” would behave in accord with others to accomplish an end goal but would also be able to function autonomously. Cells could also regroup themselves in order to attack another problem or handle another function.”

This is the basic philosophy behind smalltalk/squeak and object oriented computer programming paradigm. It is no coincidence that Alan Kay’s vision of the ideal computer language and computing environment would take to a biological allegory, since he came from molecular biology background.

While I’m reading through the history of different computing paradigms for the purpose of figuring out how it might be applied to synthetic biology, there’s something else I found awesome and perhaps a little heartwarming. Alan Kay throughout his life as a computing pioneer held onto the belief that the ideal computing platform won’t be a platform capable of crunching numbers the fastest. It will be a platform that can be integrated into the educational function of the user through ease of manipulation and control. Ideal computing platform should be hackable because it makes logical sense to do so.

Can we say the same of synthetic biology? Perhaps not. The direct comparison of a complex biological system to computerized circuits can only take us so far. Yet I can’t shake the nagging feeling that synthetic biology might be looking at some very unique opportunities for change precisely because it is different from regular electronic systems, with documents of the early days of computer and programming already here for our perusal.

A good, elegant system that allows programmable extension must be at the same time easy to learn, since one thing must inevitably lead to the other. And there are classes of systems that both run and learn better compared to other systems. This might become something of an issue of how synthetic biology parts/devices/systems are put together in the future as the capacity of the synthetic biologists to handle complex systems increase.

I think it might be able to pursue this idea further. As it stands this is nothing more than an interesting parallel in concept without substantial scientific reasoning.

Which is why I should get myself to learn smalltalk/squeak sometime in the future. Maybe I should knock on the hackerspaces in the city, see if anyone’s willing to mentor me.

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.’

Life during summer and consilience notes

I should definitely to a decent post some time soon, but it seems that I’m in middle of severe drought of ideas and writing abilities. Hopefully this is just a passing phase… Someone should definitely develop a drug against writer’s block I think.

A few things I’ve been working on so far between all the jobs I have to run to pay my rent. I’ve been studying the Exploring Complexity by Gregoire Nicolis and Ilya Prigogine since the beginning of the summer. Studying as in tearing through every bit of reference mentioned at ends of each chapters and working out all the equations, making up some of my own for practice. The progress has been slower than I would have liked but it’s still coming along nicely. I’m upto  the randomness and complexity chapter where they begin describing Markovian processes and different types of entropy. I’ve been trying to come up with some cool graphics describing some of the stuff in the book using Mathematica but couldn’t really find the time to get around to it, with all the other coding projects on my hand at the moment, but I’ll definitely have something to show for by the end of the summer.

I’ve also been reading up on some bioinformatics literature, beginning with the eponymous ‘For Dummies’ book on the subject which is surprisingly well written, or at least comprehensible (well, considering the title it would be hard to write a book on the subject that is incomprehensible). It’s part of my attempt at coming up with a decent diybio coursework aimed at 14 and above, centering around the kind of projects the laymen would normally find out of reach, like designing a biological circuit and putting it together in a wetlab. With so many computerized tools and advent of abstraction in biological sciences brought on by synthetic biology, I think it is possible to empower the citizenry with end-user scientist toolset. The average computer user don’t code in assembly or the machine language yet many of them are perfectly capable of coming up with useful high-level softwares and beautiful works of art (it still takes effort and mastery but what doesn’t?). In order for the biological sciences to become user-friendly I believe we need a tool to familiarize them with the higher level abstraction in molecular biology and computerized tools associated with it. In my experience the best way to break down an intellectual barrier is to make people do the impossible easily and cheaply. The first step of breaking down the biology barrier would be teaching people how to design genetic circuits using extremely high level abstraction symbols. Theoretically it should be possible to put together a very simple circuit on a napkin using symbols and diagrams using unified ‘visual language‘ of synthetic biology. Once the individual becomes scientifically fluent enough to visualize these molecular circuits within his or her head, and feel a real want for building something in real life, we can easily transfer the design into computerized tools for specification and optimization. After that it would be a simple process of transformation using mail-order kits (or using diy tools if you’re so inclined), which DIYBio NYC have already demonstrated to be easy and straightforward.

By then, maybe I’ll try to pitch my not-so-secret ambition of coming up with diy-minimal/synthetic cell ::evil laugh::

As you might have guessed I’ve also been spending a lot of time reading through E.O. Wilson’s Consilience: The Unity of Knowledge again. It’s amazing just how much of the book resonates with me, not necessarily in solutions but in problems he outlines as something fundamental that needs to be resolved if we are to further our understanding of the universe.

-From pg.93
…the U.S. federal high-performance program has upped the goal to a trillion calculations per second by the end of the century. By the year 2020, petacrunchers, capable of reaching a thousand trillion calculations per second, may be possible, although new technologies and programming methods will be needed to reach that level. At this point the brute-force simulation of cell mechanics, tracking every active molecule and its web of interactions, should be attainable- even without the simplifying principles envisioned in complexity theory.

The continuing battle (if there is one) between raw computing power against elegant universal systems like the kind proposed by some of the complexity scientists is interesting. For one thing, would we need raw computing power the world has never seen so far to replicate human-like intelligence? Or can it be done in smaller scale using some aspect of the logical system that gives rise to emergent trait we refer to as intelligence? Classification of life/intelligence as a type of physical system that very closely resembles phase transition due to complexity is an intriguing possibility that will need to be examined in detail… I’m especially interested in intelligence as not something that computes but as something that creates. Why am I sitting here writing down this stuff when the weather outside is so great? Why do people strive to create this stuff and ideas when it’s much easier to sit on their collective asses and eat chips? To some the activity of creating get to the point of destructive obsession. Am I alone in sensing that the society at large tend to be envious of those kind of people?

Curiosity is not a rational trait. It’s crazy and sometimes suicidal, and doesn’t serve any kind of immediate need for survival or propagation. It is the very picture of irrationality. So where does it come from? What aspect of the molecular system that we refer to as living beings gives rise to such weird behavior? And what’s with this crazy unreasonable effectiveness of mathematics in the natural sciences? Isn’t it weird how questioning the nature of mind, life, and human behavior so often leads us to the questions on the fundamental nature of the universe itself?

-From pg.93~94
In 1994 editors of Science, celebrating the inauguration of developmental biology by Wilhelm Roux a century earlier, asked one hundred contemporary researchers in the field to identify what they considered the crucial unanswered questions in the discipline. Their responses, in rank order of attributed importance, were:
1.The molecular mechanism of tissue and organ development.
2.The connection between development and genetic information.
3.The steps by which cell become committed to a particular fate.
4.The role of cell-to-cell signaling in tissue development.
5.The self-assembly of tissue patterns in the early embryo.
6.The manner in which nerve cells establish their specific connections to create the nerve cord and brains.
7.The means by which cells choose to divide and to die in the sculpting  of tissues and organs.
8.The steps by which the processes controlling transcription (the transmission of DNA information within the cell) affect the differentiation of tissues and organs.
Remarkably, the biologists considered research on all of these topics to be in a state of rapid advance, with partial successes in at least some of them close at hand.

Above questions were written around 1994 according to the Consilience. It’s been over a decade, so I wonder how many of above questions had been answered definitely and conclusively….

Also, it’s rather interesting that most if not all of above questions are in some way related to study of complexity sciences. It’s almost as if the whole field of complexity science is biology fused with mathematical abstractions.

$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.

Synbio interview

Spent most of the day outside today. It was a good chance for me to browse through the textbook ‘biotechnology for beginner’. I did most of reading in the quiet of the central library, though I did spend the early morning relaxing with some coffee in the Bryant park (before going off to a lecture for a while). Actually relaxing is not an accurate description of what I was doing. I was sending off emails and calling people left and right trying to arrange interviews for the diybio nyc peeps. I’ve never done anything like that before so things were getting a little chaotic, with last minute announcements and schedule changes. Mistakes and misunderstandings were plenty, and I was beginning to think that I was making some horrible decisions on the spot.

Well I was able to get one of the members onto an interview with the reporter (who I mistakenly thought was a man, and working for a school newspaper. She was neither), and arranged another one for myself in the evening. The whole process involved a whole plethora of trials and tribulations that happened due to my characteristic over thinking preparation and careless execution. After the whole planning and calling stuff I met up with a friend and had some much needed lunch at the cafe Zaiya, which was overcrowded as usual.

The interview is done for the day and I’m in a bookstore trying to cool off my nerves with some adventures of the Feynman kind. My portion of the interview was interesting. The reporter lady was quite friendly, and was patient with my answers that sometimes turned into something of a rambling (I knew I should have taken that public speaking elective in high school). During the course of the interview I had to frequently ask her to repeat her questions though. For some reason my ears were picking up a whole torrent of background noises… Either I was nervous or I really need to get my ears checked out.

We spoke about the reason for my interest in diybio, along with the difficulties involved in getting a group working together. The topics moved onto interest in science itself, and I gave some lazy answers on that one. I feel very passionate on the issue of the nature and utility of the sciences in general but I couldn’t find a way to put it in short eloquent statements… Not to mention that I felt disclosing such intense emotions would have been rather embarrassing…

All in all, this had been my first experience in arranging interviews for a group (or arranging anything for a group for that matter). I keep on feeling that I should have been better prepared, but I guess beating myself over it won’t change anything. Time to give the Feynman book a little pause and arrange yet another interview for the valued member of our group. Just hope this one turns out to be better than mine.

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 Debate:Drew Endy and Jim Thomas

Here’s the link to the talk between Drew Endy and Jim Thomas on various aspects of synthetic biology, sponsored by the Long Now foundation.

The talk is about two hours long, and is available for download on the website. From brief look the talk is more about basic exposition of synthetic biology and possible social and ethical implications, rather than technical execution. I’ll do a bit more detailed post on this once I get around to finish watching it.

cheap microfluidics

Just a quick note before I go off to fire up a new report. (Cross posted from my tumblr feed)

Original article from the Wired.

Ok, here’s my take on it.
There seem to be a way to build a cheap microfluidic array using household materials costing around three cents. The materials involved are standard double sided tapes and paper (which acts as the pump for the liquid), etched using off-the-shelf laser cutter, a process usually relegated to multimillion dollar semiconductor fabricator.

Provided that mTAS chip systems utilizing chemical fluids follow a law similar to the one that seem to govern standard silicon chips, we might be living in an age signaling the beginning of largest medical sciences revolution in human history. Cheap and effective medical testing and possibly production solutions that can be distributed all over the globe for practically anyone to build on. If such technology can be combined with the openscience movements like the science commons, well the humanitarian and commercial potentials will be endless.

I did think of doing a io9 madscience entry (on science-fictional applications of synthetic biology) on synthetic biology-utilizing mTAS chip that can be used to manufacture minuscule amount of specified chemicals that can be used for periodic medications or for recovering out-house patients, but I scrapped it in favor of epigenetic production using extracellular matrices. This will be a promising development well-worth following up on.

Plenty of room

Just a quick note before I drift off to study for my exams.

I re-read the famous ‘there’s plenty of room at the bottom‘ speech made by Richard Feynman recently. Aside from being inspired by his genius and foresight (as usual) I think I hit on an interesting idea.

At the end of the speech Feynman half-jokingly proposes a contest for high school students with the goal of writing smaller than anyone else. I think we have enough industrial infrastructure and technical expertise to make that contest come true, albeit with possibly different goal than simply ‘writing small’ and perhaps geared towards undergraduate students.

Those of you who have been following this blog or any other one of my web presence knows that I am deeply interested in synthetic biology, to the extent that I ventured into the recent Synthetic Biology conference 4.0 in Hong Kong armed with my meager knowledge of genetics and molecular biology. In fact, I’ve been so interested in the discipline that I’ve been driving my professors crazy with questions, delving deep into molecular biology texts and courses outside my proclaimed field of expertise (which is plasma physics), even touching up with a bit of crude wet work.

The reason why I became aware of the field of synthetic biology and began taking its possibilities and my involvement with it seriously, was the International Genetically Engineered Machine competition or iGEM. It is an international competition for high school-to-undergraduate students to build the best synthetic organism (or genetically engineered machine) using opensource biological parts termed BioBricks, which can be pieced together like puzzle to form a working genetic system complete with chassis (usually E.Coli or Yeast). The quality of the competition entries have been phenomenal so far. The winning entry in this year’s iGEM competition actually prototyped a whole new vaccine against gastritis. It took undergraduates six months to come up with that stuff (with help of graduate level faculty). Just imagine what people will be able to do once we streamline the whole process and work out some kinks inherent in dealing with biological systems!

Now, let’s imagine something similar with nanotechnology. I believe that it is possible to put together some minimal nanotech components/chassis in the fashion of the BioBricks, opensource them, and apply it toward high school-undergraduate level competition. Of course, the things we can come up with using today’s technology won’t be as vibrant as the projects pursued by those of iGEM teams, but I still believe that we have enough room for ingenuity and improvisation in constructing minimal nanotechnological systems and parts. With suitable industrial support the international nanoengineered machine competition (iNEM?) might lend the field of nanotechnology accessibility and interest the field rightly deserves.