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.  

Wings of Genspace

With the Genspace business and other stuff I’m working on picking up steam, it’s getting increasingly difficult to come up with decent enough blog posts these days. I’m still not sure whether this is a good thing or not. I love being busy pursuing my dreams, but writing is about the only thing that’s keeping me sharp, so that worries me a little. Maybe I’m slowly slipping into some state of waking coma…. Either way, I’m doing some really interesting things, so I might as well have a record of some of them here.

Genspace is in full swing, and Ellen’s busy running her biotech crashcourse, with other group-wide projects planned out already. Who would have thought we’d actually have a functioning biotech lab in NYC two years ago? Kudos to the people who stood by us all this time. Just having a lab is not enough though, we’ll be introducing some pretty awesome projects soon, just stay tuned!

I have so many things I want to write about now that I’m finally sitting in front of a computer and logged into my blogging account… But good things need time to mature, like hot pot. So I think I’ll just write about that one thing I’m supposed to talk about in this post 🙂

So we (me and Oliver) are planning to launch a high altitude microbial sampler into the stratosphere and do metagenomic analysis of whatever the samples we can gather from there. Right now I’m thinking of about 25~30km altitude, which should be around temperature range of -50 ~ -20 degrees C, which is really cold but not quite as cold as the furthest reaches of antarctica. Just to give you a scale of how high we’re going, latest version of Boeing 747 has top service ceiling of about 13km altitude. Our device will be flying at or above the double that altitude. Here’s an interesting picture of the Earth taken around 20 km.

Now simply launching a weather balloon into the stratosphere with some minor circuits, GPS and a digital camera would be simple. In fact, if it’s all I wanted I can just walk out there and launch my own balloon-sat right now. Yet, what’s the point in doing what everybody else is already doing, am I right? Now that we have a working biology lab we need to do something to bring my love of space together with my love of biology. Which means microbiome sequencing using samples taken from the above.

You see, there’s practically no real research data on the microbiome of the high altitudes. Considering the resilience of life (if you throw bunch of fruits out into the space from ISS, they’ll survive -kind of) and interlinked atmospheric conditions of the planet as a whole, we personally find it impossible to think that the realm of high altitude is totally devoid of life. There are papers out there tracing back to the era of the cold war suggesting that the maximum height of the planetary biosphere might in fact reach far beyond conventional height, with some evidences suggesting spore presence at mesosphere (~80km).

In order to have at least modestly reliable results from our experiment however, we need to design a device that can remain sterile to and from the stratosphere that will function despite heavy shaking, blistering cold, and falling. So far we’ve been making good headway into design and building of the device (Oliver is practically a McGuyver, with PhD in molecular biology) but it’s been a whole lot tougher than simply throwing together balloons, parachute and a camera that most of these projects tend to do. I’ve accumulated some interesting resources and research results during the course of the project, and will be uploading it to the net soon so that other people can follow in our footsteps and do their own high altitude sampling as well. Maybe it would be possible to grow this into an international program of sorts, considering the nature of the kind of organisms that might be found in the stratospheric range (if we find anything at all).

Recently we launched a simple tethered balloon sat to take pictures of Brooklyn from above. The contraption really had nothing to do with the sampler we’ll be launching, but it still gave us a good feel for what the real launch in the future might feel like.

The balloons were attached to a simple digital camera, a 1.99 semi disposable that took really horrible pictures. I’ll try to find a good one or two and post it later.

We launched the balloon on top of the Genspace building. The weather condition was really great, not too much wind at all. The sunlight was beautiful as well.

I’m one of those kids who used to stay up late at night thinking about the space, the high sky where the deep blue voids split over a thin red line of the sun rising, or setting somewhere over the distant part of the planet. Really, to this day the images still have the power to stir my heart, and make me feel like a human being. This is a meager start but who knows, maybe somebody’s already working on a synthetic biology satellite design that might one day take to the skies 😉

Jaron Lanier and the Fall of Opensource

Jaron Lanier, one of the pioneers of opensource movement and virtual reality, thinks the opensource movement had been a total failure. He does point out the opensource movement and the web culture are two different things and agrees the latter had been a phenomenal success in demonstrating the capacity of the unknown, average individuals out there to create beautiful, useful, and interesting things.

I don’t agree with everything he said, but I think he has some important points we should pay attention to.

1.Opensource movement is boring. Seriously, sitting down and writing Wikipedia entries (of often questionable accuracy), worrying about how to format texts? Sure, it’s something you and I might do in our spare time, but we are geeks. Opensource is about serving all of humanity, but as it stands opensource just serves the narrow interests of a very small portion of the population: Geeks and nerds. As long as grandma and primary schools kids next door can’t use opensource products/projects/frameworks simply because it’s fun, the whole culture is just another outlet for elitism and fascism most hackers are supposed to hate so much. Ever said something on the lines of ‘I hate being the tech support for the whole family’? That means the people who wrote those programs and services suck, not the users.

2.Major opensource products are built upon nostalgia of the ‘better times’, the golden age of the hackerdom during the 60’s~80’s. Linux, gcc the vast majority of the main opensource projects are built upon, vim vs. emacs war, and etc etc. Linux distros had been making some good strides in this department but we still need to face facts. To anyone who didn’t string together shell scripts when he/she was in high school, major opensource projects and the tools they are based upon look downright archaic. It isn’t because they have bad user interface design (they do). It’s because they really are old and deprecated. I am continuously amazed by how many people tell fresh young minds entering hackerdom to go learn C. Kindergartners don’t start learning English language by starting with Latin. Why is the whole darn culture based on a fast-but-bad programming language designed before many of us were born? Let’s be honest here, most people who recommend C to beginners started with BASIC. When a whole culture based on ideals of innovation and sharing begins to look outdated and conservative next to hulking multi-billion/trillion-dollar corporate entities, they are in trouble.

3.This is a repeat of above statement, but it bears some reiteration. There isn’t enough innovation in the opensource community. Again, large corporate entities that takes three days to ship an empty box innovates a whole lot more than most of the opensource communities out there. Sure, there had been some interesting developments that’s making the world a better place, like Ruby and Python. The same Ruby and Python people praise for finally getting around to implementing great ideas of programming languages like Smalltalk and Lisp. Smalltalk and Lisp was invented back when the idea of a cheap personal computer was the stuff of science fiction. Linux is playing catch up in terms of features and architecture with commercial operating systems and in critical applications UNIX is king (guess how old it is).  Meanwhile Microsoft is making strides with .NET framework and Google/Apple is on the cusp of next era of personal computing. Based on real world progress, opensource community as a whole lack clear vision of what the future should be.

4.There is an inherent elitism within a lot of the opensource communities. Personally I have no issue with elitism on personal level. It’s when such attitude permeates within entire communities that they begin to do real harm. Common sense dictates that any software targeted at Jane Doe should be easy enough for J.D. to use. Not so in a lot of opensource communities. If Jane Doe has hard time using an obscure text editor with more commands than the usual operating system it’s her fault for being so lazy and/or dumb. If a kid who can barely type can’t learn C and work with pointers the kid must be stupid. If it’s too difficult for artists to use computer systems to create beautiful things without pre-packaged software it’s because artsy types aren’t supposed to be good at computers. These problems are being addressed by a new wave of hackers and hacker-minded people but they are still tragically present in many of the present communities, even when they don’t specifically come out and say those things.

There are other interesting traits about opensource and opensource oriented communities Jaron Lanier pointed out as well, like how most of them are structured to shout down any voice of dissent based on fear of isolation, and how there is a culture of complacency among its leading members, but those things apply to almost any large group of people, so I felt no need to single out and discuss them.

I’m an optimist. I think there are movements within the opensource community that are trying to address this problem. I think the prevalence of web platforms, popularity of light weight scripting languages, and web/user interface designs are all in some form a reaction to the perceived stagnation of opensource community. People are increasingly becoming aware of what a stupid idea it is to teach C in middle schools, and how even stupider it is to begin computer education in a middle school instead of much, much earlier. I might go out on a limb and say that some people are beginning to realize that programming as an activity is not difficult at all, and that it is the teachers who don’t know what they are doing, not the students.

Yet I am still worried about the culture of opensource. Opensource as in framework of idea, not of computing. How can we apply the ideas of opensource and innovation to the fields outside computing, like CNC based personal manufacturing, scientific research and DIYbio when it’s running into such problems on what should be the culture’s home ground? Are those open-manufacturers/scientists/biohobbyists/etc about to run into unforeseen trouble inherent in existing idea of opensource itself? Are we already in trouble?

edit: maybe I should say that the woe of current opensource community (as a whole. There are many brilliant people and groups out there, can’t stress that enough) is that they don’t hack as much as smaller groups?

Edit: Aug 28
Some people wrote me some valid (“you don’t seem to understand opensource in the post”), and some vitriolic (“what’s wrong with being a nerd?!” but with lots of swearing in it), rebuttals to this post. I refrained from replying to those responses individually and getting into arguments since I think this post is terrible myself (like how I used opensource and web2.0 interchangeably throughout some of the parts). I must stress that I’m a student of all things Free software and what I say or write here should never be taken as something it isn’t.

I personally like to consider myself as someone with geek tendencies. I love emacs, and I love the idea of emacs. I think GCC is a huge thing that changed the course of humanity as much as development of steam engine changed the face of humanity forever. And yet I think all of those tools are old, based on older ideas and inaccessible to anyone who doesn’t subscribe to the lifestyles of people like you and me, the people who wouldn’t mind staring at a screen for hours on end.

I’ve had a chance to talk to some ex-programmers turned artists at the ITP exhibition last year. There was a particularly interesting exhibit with a type of evolving display system. He did all of the graphic generation within the exhibition by hand, by putting together a library of hand-drawn images. It was rather obvious he could simply do some coding in the Processing language and get it done faster and more efficiently, so I asked him why he bothered with the manual labor… And he told me that he simply doesn’t like to program. I’m not sure how I can portray the eye-opening effect it had on me at the time. The artist was fine with studying algorithms and working them out on paper, using it to generate obviously computational results. He was a very logical guy with mathematical proficiency to spare, certainly more than what I can say about myself. It’s only that he just couldn’t stand the whirring of the computer fans, the monitors, the endless clacking of keyboards and always worrying about battery life of one device or another. And I get a feeling that he is not alone in this. Maybe there are some people who are allergic to certain type of things used universally in building computers. Maybe there are some kids who just can’t handle the physical environment that comes with using a computer as we know it due to some psychological trauma. Such cases aren’t unheard-of in education circles and there can be hundreds of thousands of reasons why someone would shy away from programming activities while possessing logical acuity and vision that would normally lead to the act of programming.
I subscribe to the Alan Kay notion of describing computer-use: every interaction with a computer is an act of programming, but programming activity isn’t exclusive to usage of computer devices. And that’s why I agree with his frequent statement that the computer revolution never really happened. Computer revolution was supposed to be the revolution of the mind-ware. It was supposed to be this awesome tool of abstraction that would elevate (for lack of a better term) all of humanity to a state of freedom through better understanding of subjects that were distant and foreign to them… It was supposed to make science easier, a goal that is near and dear to people like me interested in DIYbiology. Easier not as in being lazy but being accessible, like how calculus was once considered the pinnacle of human knowledge but is now being taught even in some of the worst educational curriculums in the world as something every human being should know regardless of their intellectual rigor.
The original post was how I tried to address the inconsistency between the ideals that I believe should be applied to opensource community and the reality of the tools deployed. It’s called open-source, purists call it Free-software. Despite some differences between the two they really are about openness and freedom, but as long as its users and contributors subscribe to a certain type of lifestyle. Is there any way to change that? Can Free software be so free as to be no longer confined to the silicon and copper frameworks and languages of C and (gasp) Fortran?

I know this is all sounds like a pie-in-the-sky talk right now but I feel it’s a goal worth pursuing for those in the opensource community.

First DIYBio rant of the year

I can’t believe I’m uploading the first post of the year in March. Still, better late than never to show people that I’m still alive and kicking. While I haven’t been able to think about personal writing due to deluge of job and school related stuff I’ll try to keep things more organized in the coming months. If half of what I hope comes true this coming year will be the most awesome so far, for myself and for other activities and organizations I believe in.

This post is, like it says in the title, a rant post of what DIYBio ought to be and how I plan to do my part this year. It’s also written on my blackberry which I later copy-pasted into the wordpress… I just hope half a year of writing boring technical stuff didn’t burn out creative writing part of my brain. I’ll be using it a lot from now on.

Year 2009 was series of exciting experiences, with ISFF, DIYBio and iGEM jamboree. I’m trying to pan it out into this year without losing momentum, through activities like synthetic biology crash course for beginners, various internships and private research projects. Hopefully I’ll have more time to write about them in the coming months.

I’ve been thinking a lot on diybio, about what it’s supposed to be & what it needs, and I think I’ve arrived at some sort of conclusion.

DIYBio must inevitably find the way to bridge the gap between the enthusiastic members of the public and tools and devices that makes synthetic biology feasible. While there are many members out there who seem to work toward specific gadgets and other physical tools of biological experiment, I think we still need something more.

DIY or not, biology is a science. If we want to bring hard science to the public with aid of ever cheapening yet sophisticated lab equipments we need to look beyond the hardware.

I’ve written quite a few times about Alan Kay (on this blog and elsewhere), the pioneer of modern computer programming/interface paradigm and his relationship with synthetic biology… There are mountains of information on him and his works that are relevant to the discussion of models in biology and how they might be used to organize information, with emphasis on education as a sort of interface between data and human mind… All of which are beyond the scope of this particular post.

The important point is this. I believe true potential for diybio is to bridge the gap between the complexity of bleeding edge science with the innate human ability to learn and tinker. And the main tool in making it happen is idea, not low cost lab tools (the costs of the lab tools are coming down anyway. Why DIY every single appliance when you can buy a used one that works just as good, oftentimes even better?). While low cost lab implementations are important, the true future lies with the ability to abstract and package/rebuild complexity into something much more manageable.

Some people seem to have difficulty understanding what I’m trying to say from the few times I’ve tried to talk about… I’m talking about reviving and revising the notion of knowledge engineering, something that was supposed to be the corner stone of true computer revolution that never really took off (google and wikipedia are some remnants of the original idea).

Synthetic biology is a good example of what knowledge engineering coupled with physical science might be able to achieve. None of the specific pieces forming what we perceive as synthetic biology are new. They’ve been around for quite a while in one form or another following course of gradual improvement rather than truly new scientific advance.
Synthetic biology at heart is about how dedicated professionals can organize scattered pieces of knowledge into something that can potentially allow ambitious undergraduate students to undertake projects that would have been beyond their ability a decade ago. Never mind the actual success rate of their projects for now. They very fact that those students are able to plan for the future with much broader sphere of possibility is significant enough.
And why stop with undergraduates? Wouldn’t it be possible to have motivated high school students design something that at least works on paper? Wouldn’t it be possible to build a conceptual framework so that those kids can at least discuss possibilities of future projects on back of a napkin without resorting to sci fi?

If diybio is to do what it originally set out to do, we need to look beyond gadgets and tools. We need to think about ideas and how they come together… We need to make biology easier, not just cheaper. This is the mantra that will drive my DIYBio related activities this year.

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.’

Lecture and presentation

Long time no see on the blogosphere. I’ve been busy during the summer with all the usual stuff, mostly learning and working. I’m glad to say that I’ve almost finished the Exploring Complexity: An Introduction book during the summer, and I was even able to get some of the mathematics out of the way. I think I was able to model a pretty neat animation on some of the methods demonstrated in the book, and I’ll try to post it soon.

I’ve also been saving up for going skydiving before the summer’s over… I’ve always dreamed of the skies (my first choice in college education was majoring in aeronautics, never quite made it though), so it’s only natural that I do something that involves full-contact with the air up there. Living on the student budget means that I have to work some extra jobs for that though. Some a bit more crazier than the others.

And of course, there’s always the DIYBio NYC. I’ve been trying to come up with some decent ideas, but everything I can think of at the moment mostly revolves around the kind of project that would require some sort of dedicated labspace. All I can do at the moment is to prepare for that inevitable day when we’ll obtain access to a labspace through independent studies. Some of the things I’ve talked about the members during a recent meeting regarding the state of the group and the processes that are involved in constructing artificial vesicles were very enlightening, and I intend to do a full-length post about that some time in the near future.

On to the main post…

During today’s twitter and identi.ca browsing I happened upon some interesting resources for scientists and potential scientists.

The first one is a collection of links and documents on how to prepare a scientific presentation. I haven’t had the time to read through it yet, but I know some of the posts on the list, and if the rest are like the ones I know, they are definitely worth a read, especially for an aspiring scientist like me. It’s amazing just how many things are involved in preparing a half-way decent presentation, and how most people are just plain terrible at it. I’ve sat through my share of lectures/symposiums/conferences and there’s nothing more painful than a horrible presentation with irrational powerpoint.

The second resource I want to share with you is osgrid. It’s a virtual environment tool like the second life except that it’s opensource. It’s relatively simple to download the environment and run it off your own servers, though it also means that you ‘need’ to run it on your own server for the whole thing to work. I’m really interested in finding out how this environment can be used for scientific research. Perhaps virtual laboratories running off university computer clusters? Open educations tool like a virtual university? A method for scientists to interact with their own 3D datasets in clean and intuitive manner? There are plenty of possibilities out there.

… I can also think of a few ways to utilize some of the stuff for the DIYBio community.

Bioinformatics Misconceptions

I just read an interesting paper on the three common misconceptions people normally have about the field of bioinformatics. I’ve been eyeing bioinformatics as a possible venue for bringing more people into DIY sciences, so I took some notes for future reference. It turns out that I’ve been suffering from same hype and illusion about the field of bioinformatics just like the vast majority of the non-specialists out there.

Simply put major misunderstandings about bioinformatics might be narrowed down to three myths permeating the science culture, according to the author.

Myth#1: anybody can do this
-bioinformatics is inexpensive
-bioinformatics software is free

Myth#2: you’ll always need an experiment
-bioinformatics is a rapid-publication field
-all bioinformatics does is generate testable predictions

Myth#3: this is news technology but technology nevertheless
-bioinformatics is a new field
-bioinformatics is an application discipline

*FYI the statements under the Myth headings are the ones the author refutes in his writing.

Myth#1 is that everybody can do bioinformatics, using only the cheap or opensource tools available off the net. The author does admit that this is indeed the case to certain extent. However once you get into any serious large scale research about or involving bioinformatics the initial assumptions will prove to be a burden on the organizational level. As the author will elaborate in later parts, bioinformatics is a field of scientific research on its own not subservient to the conventional wetlab biology. Indeed, while reading the article I was under the impression that the main statement for the whole article revolved around how people do not realize that bioinformatics is a field of scientific research with its own goals and complications. Very unlike the laymen assumption that bioinformatics is in fact just biology done with computers, or application of computerized tools to wetlab based biological research just like how the researchers would use word processors or LaTeX to type up their reports. Personally I found it a little disheartening that bioinformatics research is just as complicated as any other field of scientific research for DIY implementation, possibly more depending on what the amateur scientist is trying to do. But then I can only blame my naivety. The author also makes a point that bioinformatics can be very expensive to begin due to some number of proprietary software services that must be purchased (never went into much detail on that. I guess it’s different according to the theme of the research?) and the resources needed to write and maintain codes for the project. It makes sense when you think about it. While it would be possible to come up with some bioinformatics application in-house, after certain level it would be vastly cheaper to simply buy some number of components and just use in-house resources to link them and tune them into giving results needed for the project (which shouldn’t be easy to begin with).

Of course, I still think that we can, and maybe should, use some approaches of bioinformatics to provide interesting DIY science framework to the public, like the Annotathon metagenome annotation project that had been open to the public for a while now. I’m just glad that I got a chance to listen to some of the intricacies of the field from someone already working with the tools of the trade.

While I now understand some stuff about what the field of bioinformatics is about, I’m still unsure as to what kind of project idea I can come up for DIYBio curriculum using the technology… It’s a problem I’ve been running into a lot lately in doing stuff involving DIYBio. I know there are tools and tutorials out there, but I just can’t seem to be able to put them together into a coherent whole. DIYBio needs some sort of project that would turn knowledge into skill… More on that later.

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.

Quorum sensing

Just a quick note on early Sunday morning. 

 

I’ve been reading up a bit on the topic of quorum sensing, which turned out to be a very interesting phenomenon. I’m not qualified to get into the specifics but it’s basically a cell to cell communications method used by bacteria. The mechanism is based on signal molecules and receptors that activate or deactivate certain sets of genes depending on signal strength. The strength of the signal would be determined by the density of the signal molecules within a given area. It means that bacteria (of all kinds I think) have built-in coordination mechanism for group gene expression.  This is news to me. I always thought bacterial behavior was more or less solitary with some mathematical mechanism behind emergence of bacterial colonies, rather than any specific signal mechanism that works to coordinate their behavior as a group. I guess the deeply ingrained eukaryotes/prokaryotes and multicellular vs. unicellular organisms chart from the middle-high school days left its mark on me. The Bassler lab at Princeton University’s department of molecular biology seem to be the leader in the field of quorum sensor studies, something I should definitely check out later. Here’s a TED talk by the lab’s very own Bonnie Bassler on bacterial communication.

This reminds me of a few iGEM project outlines I read on using BioBrick parts to form some sort of macroscopic structure using bacterial components. They all more or less failed as far as I know, but maybe something like that will be possible if we can build a BioBrick based mechanism for controlling quorum sensing mechanism of the E.Coli chassis… Or maybe there’s one in the registry already? I should remember to check it out. Maybe diybio-nyc can build a cellular automata system based on quorum sensing as a demonstration project later on. The prospect of studying complexity mechanics behind the quorum sensing and coordinated bacterial behavior is intriguing to me as well.

I’m also thinking of proposing a simple artificial cell project to the group. From what I’ve been reading the first steps towards building an artificial cell isn’t that complicated as long as we keep the goals modest. For now the goal would be to have DNA replicate and produce proteins within an artificial vesicle.