Random thoughts- bioart

I’ve found that one of the greatest barriers to writing something down regularly these days is a concern that I’d piss someone off.

What a way to grow up.

 

While wrapping up last of the sequencing reactions accumulated these past few days I found myself wondering about bioart again- there was a time when I was completely nuts over the concept of artscience, and pushed as hard as I could to get some bioart representation within the Genspace hierarchy. We didn’t even have PCR machines back then, it was before Ellen got the equipment from Vector donated after it downsized and closed down the lab she was managing, and way before we found MEx through bunch of random people. It was a life time ago.

Anyway, my earlier perception of ‘artscience’ at the time, as vague as it was, brought to mind something curious, something like Leonardo Da Vinci but for the modern age. Scientific discovery and application dictated by aesthetic sense to create something beautiful and perhaps even meaningful. Being freshly out from school it was a view uninformed by realities of both scientific research and how many artists operate.

From a general point artscience as it stands right now seem to refer to anything and everything created and curated using tools normally reserved for usually inaccessible scientific research for purposes of artistic expression- and nothing else. It’s art as usual except the tubes of paints and canvas got switched out to some other things associated with science (or should I say popular perception of science? No real scientist I know plays around with that much colored liquid, or uses racks of test tubes). 

It brings up an interesting question on what artscience actually is. When you really dig into the history of arts from across the globe, the techniques of art was never really far away from experimentation and keeping track of data- the practice of simply walking into a store to buy tubes of paint without knowing how it’s made and where it came from is a ridiculously modern one. Same goes for architecture. The amount of experimentation and fundamental knowledge that has to be learned to be even remotely adapt at the craft is extensive- otherwise you have a lot of dead people on your hands. Experimentation, data gathering, perfection over life time and generations- are all rather common practices in the arts.

In that light, what IS artscience? It’s highly probable Da Vinci was on the cutting edge of chemistry at the time just from making his paint and gunpowder for fireworks. Same goes for almost all the older masters. If it’s simply using scientific means and tools for purposes of art how is that so radically different from what people had been doing for most of history, when you consider that ‘traditional’ tools of art themselves were products of experimentation?

Here’s another kicker- the relatively recent interest in bioart, itself a practical artscience of sorts, is based on broader accessibility of the tools and better abstraction of ideas that allows any sufficiently funded and motivated artist to use the tools usually associated with pure research. Easier accessibility to better and more professional tools of the scientific trade by the layman will be a continuing trend for the foreseeable future… So what does artscience do that’s really different when the science part of it is as normal as walking into an arts supply store and buying tubes of paint?

Is it even real? If it is, where is it going?

 

And all this is without even getting into the difference between science and technology.

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.  

Barcode the World

I’ve always been curious about DNA barcoding. Interest in wides-scale DNA barcoding exercise had been around for a long time, in part due to potential for amateur scientists to contribute to cause of the sciences using relatively minimal and easily obtained equipments and reagents. There had been some high-profile events and articles involving DNA barcoding techniques applied to everyday life in recent memory, like the infamous ‘sushi-gate‘ incident. Yet how many people really know what is it and how many people have a clear understanding of how to do it? I certainly was clueless for a long time.

It’s a little weird now that I think about it. Despite doing tons of PCR reactions day-in and day-out at the Genspace lab for one reason or another, I never tried  to dig into what exactly DNA barcoding entails in its visceral, barcoded details. Well, recently some of our Genspace members including yours truly went out on a sort of field trip to the Harlem DNA lab (situated within a junior high school in Harlem) for a day-long DNA barcoding workshop in preparation for the upcoming NYC Urban Barcode Project.

And the process couldn’t be easier. In a nutshell it just involved amplifying specific segments of DNA from a sample organism and sending it in to Genewiz for sequencing. The specific DNA segment to be amplified differs slightly from the kind of organism (is it a fish? Plant? Or insects?) but in case of most vertebrate mammals you use a portion of its mitochondrial genome called cytochrome c oxidase subunit I (COI) as the bacoding region. Mitochondrial genome (something I’ve been working with a lot for the past few months, ironically enough) is ideal for this sort of genetic species identification since they hit the exact sweet spot between homogeneity and differentiation within similar branches of the phyla, due to their rate of mutation and how mtDNAs are only passed through the maternal line. If you’re interested in performing your own DNA barcoding experiment outside regular lab settings or any official competition you can do so with the pdf files of requisite primer sequences already online and just order it straight from places like IDT. While specific protocols for running the PCR and prepping samples differ from place to place (I’m still looking for that perfect optimized protocol) what you are doing is a basic PCR amplification of the specific part of the mitochondrial genome, so when push comes to shove I’m sure simple chelex based DNA extraction (crush and pop in the sample with chelex beads for 10 minutes at ~99 C, centrifuge at 13000rpm for about a minute and extract the supernatant) combined with primers and PCR mastermixes or GE PCR beads (which already contain pre-made taq polymerase and buffer mixtures for optimal performance) will work just as well, provided that the sample is fresh enough. I think I’m going to run some experiments with the materials we already have at the Genspace lab and post the results later on. Once we put together a library of verified barcoding primer parts we should be able to do some very interesting projects and classes with the NYC biology community at large.

During the barcoding workshop we had a chance to pick out our own samples and run through the barcoding process with the instructors. I picked regular house ants, some random plant Ellen brought from her garden, and a YFP producing zebrafish that’s been dead for some time (it’s a long story). I went through the DNA extraction, purification, and PCR process outlined briefly above, using appropriate primers (for students participating in the competition the Dolan DNA learning center & Harlem DNA lab will provide the kits for free!). Here’s a picture of the gel we ended up with, dyed with syber-green (thanks Oliver!).

Now I seem to have misplaced the list of what each lane does, but the point is, all the barcoding amplifications worked except for the transgenic zebrafish. And it’s not just me, transgenic fish samples prepared by everyone else failed as well, something I can only attribute to the condition of the sample at the time of the barcoding experiment. You see when living things die cells lose structural integrity and rupture all over the place, mixing existing DNA molecules within the cells with all kinds of junk and nucleases that will damage the sequence. Considering the fish was stinking up to the high heavens by the time we got it to the lab that certainly sounds like a very likely scenario to me.

All the other samples works beautifully, and we prepared about 10ul aliquots of each PCR product and sent it in to Genewiz to get sequenced (the same Genewiz I got my mitochondrial DNA sequence from). They’ll be getting back to use within few days with the sequence data we can feed into public databases of DNA barcodes to determine what kind of organisms they are.

People always talk about how the field of biotechnology is advancing by leaps and bounds, and how the infrastructural developments like massive DNA sequencing centers for cheap sequencing will change how most view life and themselves. For a person not previously versed in biology like myself this was a great opportunity to come face to face with capacity for people outside of traditional academia to contribute to the sciences, using largely off-the-shelf technologies and public databases. The entire process of obtaining the sample, amplifying a specific genome within the sample, and getting it sequenced probably cost me about $5 in terms of materials. Think about that. $5 dollars to gain some level of insight into a genetic makeup of an unknown organism, open to everyone. Although this is nowhere near the kind of stuff we can do with true deep sequencing the day is coming, and it will certainly make for a very interesting world.

If you’re interested in learning more about the NYC Urban Barcode Project or DNA barcoding process in general, feel free to contact me at sung at genspace dot org. Genspace is one of the sponsors of the NYC Urban Barcode Project and we are looking forward to input and participation from students and teachers around the city!

New career path

I can’t believe I didn’t write here for so long. Welp, can’t help what’s done already, I’ll try to document all the cool stuff that’s happening right now at&around myself, iGEM and Genspace a bit more. I’m officially a team member of the NYC-iGEM team and there are plenty of real biology being done at Genspace now that we’re public and all. I just have so much to write about.

But first, let me give you a news, this is the one that got me writing on this blog again after months of vacation:

Virgin Galactic is hiring astronauts! Not just any astronaut, but a private astronaut presumably for their SpaceShipOne based launch program at Mojave spaceport.

You need all the qualifications usually associated with being hired as a pilot for any Aerospace corp, with preference given to those with real experience in spaceflight. I guess all those out of work astronauts from the space shuttle program can still get their flight on :)

I kept asking myself why I didn’t go to a flight school instead of bothering with all this physics baloney. I think my friend who does aeronautical engineering thinks the same way too. I was more or less blaming my own shortsightedness before I hit upon a memory from decade ago.

I wanted to go to space, become an astronaut. That meant I had to enroll in the airforce, go through the officer’s training, and get really, really lucky. Now luck part I never really had a problem with. Don’t worry about things you can’t control, as they say. But enrolling and spending my life in the military just to get to space? Man that just put me way off. It’s probably the same story with my engineer friend. And I’m not even sure what women go through when they want to become an astronaut. I’m thinking it’s something a lot more different from what males have to go through, whether we want to admit it or not.

I’m not really crazy about the idea of libertarian capitalism, but I can’t help but to welcome this development of private space industries. I think years of treating space as if it was a special military domain really killed lots of initiatives that could have happened, and just shelved decades worth of scientific progress under the guise of national security (for all nations with capacity for spaceflight, really).

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 ;)

Is it game night yet?

It’s Thursday night. Just one more day to plow through until you reach Friday night with all its movies and drinks. Well, we can’t tell you how to speed up time but we can tell you how to feel like it’s going faster. Play computer games. 

Now, we are talking about Genspace, and we do have a bit of reputation to maintain. So as much as I would like to recommend everyone to get cracking on the battle.net with Starcraft 2 we’ll have to make do with something different; a computer game with science in it.

It’s called Phylo, and you can find it here. Phylo is an entirely browser based (flash based, to be specific. Sorry to disappoint all my iPad toting readers) and doesn’t require any serious computing muscle on the player’s end. I’ve been playing it for the last hour or so, and it’s an odd piece of work. On the surface the game follows some basic rules of pattern matching casual games you might be familiar with like Bejeweled. Yet the experience of playing the game feels far more complex than that, and I don’t necessarily mean that in a bad way. Also, there’s a real benefit to playing this game on your spare time, other than gaining the l33t skills to pwn the n00bs with.

You see, Phylo is ‘a human computing framework for comparative genomics.’ Basically it gives you real multiple sequence alignment problems represented by 4 color blocks scattered on a grid. And of course, budding bio-enthusiasts like us know what’s up when a science programs give us 4 of anything- they represent nucleotide sequences. As you match same colored blocks with each other, you contribute some of your brain power to finding aligned sequences between different genes. If you misalign the blocks you lose a point, and if you create gaps between the blocks (which represent mutation) you lose lots of points. You can gain points by aligning same color blocks on vertical row and you need to gain certain amount of points to pass a level or get another gene to align with your existing sequence. This is a very abstract process of optimization that is usually done with complex computer algorithms and lots of processing power, which would be prohibitively expensive when brute-forced. The authors of the program hope to use the human-computer interaction on a large scale to come up with optimized heuristic pattern.

 

This is how Phylo looks
The logic is sound. After all, usefulness of human ability to find patterns in complex biological simulations have already been proven worthwhile with the fold.it protein folding puzzle game and the Nature paper that came out of it. Guess who’s a co-author of a nature paper.  ;)
 

This is how it might look on a scientists’ computer
I’ve played around with the DNA code responsible for idiopathic generalized epilepsy and already 160 other people attempted to solve the puzzle… And 146 people failed. And there lies the problem of biology-turned games. You see, unlike regular puzzle games like Bejeweled or Tetris, not everything will fit together with perfect logical coherency. Granted, there are a few techniques you can use to treat this like any other game (for example, don’t waste your time moving around single blocks in the beginning stages. Crush them together into single group for maximum points in shortest amount of time), but the fact is not everything will fit together and it can be rather jarring for a beginner to figure out what he/she’s doing right, since there isn’t any satisfying feedback to a ‘correct’ sequence formation. It can’t be helped though. This is science, and no one knows the correct answer to detect and give you feedback with. Maybe that’s the whole reason why you should play this game. After all, would you play a match in starcraft with predetermined outcome?
I for one, am looking forward to the future where all games contribute to the discovery of science in some shape or form.

Genspace Grand Opening

December 10th was the big day. NYC will never be the same. Let me elaborate: after two years of blood, sweat, and labor (only a few tears), we finally announced the birth of Genspace to the world on December 10th. The preparation leading to the big day way typical of the ragtag crew of Genspace: chaotic, intense, lasting way past most people’s bedtime, but mysteriously it worked out in the end.

Everyone showed up: art students, scientists, writers, and long lost faces from two years ago. Turns out two tables filled to the brim with food, wine and beer weren’t quite enough to accommodate the bio-curious (not to confuse our counterpart in SF crowd in the city. It’s almost funny how we worried that no one would turn up.

The entire laboratory was strewn with Christmas lights. A light box illuminated an algae bioreactor in testing at the space. Screens were set up showing videos of microscopic organisms, and on our desktop in the study a live feed of the strawberry tissue  streamed from $12 USB microscope in the lab. Even our neighbor Chris pulled out all the stops, demonstrating his  ‘animal sense’ contraption for people to try out.

We still have ways to go, however. We need to reach out to the population of the city and show them that science is within reach. We need to work ever harder to break the walls surrounding learning and practice of science, and we need to create ever more ingenious, useful, and beautiful things.

The Genspace grand opening isn’t about the past two years, it’s about the future from here on out. Let’s bring back the romance between the sciences and the public.  I am proud to be a founding member of the first community biotech laboratory in NYC.

Who knows, maybe we really will end up changing the world for the better.

Alan Kay on OOP

Some update before I move on to the main post:

I’m an official team member of the 2010 NYU iGEM team! I’ve learned a ton of biology from Russ, and worked on some cool stuff like visualizing and simulating the Immunoyeast system using Processing language. I’m also working on having a touch-screen installation for the Jamboree, so don’t forget to check it out if you plan on being there.

Genspace is up and running, and it is totally awesome. We collaborated with the BioBus at the World Maker Faire and won the Maker Editor’s Award, which is apparently a kind-of-big deal. I did about 40 DNA extraction, purification, PCR and restriction digest myself, teaching people about basic lab processes and a bit of theory behind genotyping. There were lots of screaming children and spitting involved, but it was totally worth it. The target of the exercise was TASR38 coding SNP, and I should have a detailed post of the whole process up in a few weeks.

There are tons of more stuff I should be writing about, and maybe I’ll find enough time to do that when the iGEM is over (although I’m already thinking about how awesome 2011 iGEM can be).

Back to the main post: I’ve been reading stuff written by Alan Kay again. I think it’s safe to say that he’s one of my all-time heroes by now. There’s a cool book about him and his work called Points of View available for free on the net. It’s not directly relevant to biology or physics, but if you’re interested in education, information abstraction and history it will be a fascinating read.

It’s not that I’m actively seeking out stuff about him. I just seem to run into them whenever I do research for my own projects, whether it be methods for abstracting complex sciences for public consumption or coming up with useful programming tools for beginner’s bioinformatics curriculum.

I was reading up a bit more on structure of Ruby and its use in bioinformatics. I eventually ran into the legendary Ruby hacker _why and his Shoes and Hackety Hack toolkits, which mysteriously led me to another one of Alan Kay’s letters, written in 1998 after OOPSLA. The piece itself isn’t directly relevant to biology. He just talks about how most people don’t really understand OOP in computer sciences and how it’s not really about objects but dynamic messages passed between objects. Here’s an excerpt from the letter I found interesting.

“The key in making great and growable systems is much more to design how its modules communicate rather than what their internal properties and behaviors should be.”

Alan Kay had biology background before he went into computer science and he explicitly stated that his most well-known achievement, OOP model and Smalltalk systems are inspired by biological processes… Which is one of the reasons why I tried to use Squeak Smalltalk system for earlier iteration of my synthetic biology curriculum for high school children (something I’m still working on and need a ton of help with). Considering that earlier versions of synthetic biology in form of BioBrick system is based on core engineering principles I can’t help but to think about possibility of re-applying Alan Kay’s OOP model back to biological systems.

BioBricks based synthetic biology strongly resembles ‘object’-oriented OOP paradigm, where people build parts with unique internal characteristics and then link them together into a whole system. Entire system is focused on functionality of the individual parts with almost no care taken to characterize and document how different parts interact with each other. It should be interesting to imagine a different type of synthetic biology where the biologist considers how different segments of DNA (or perhaps the system should be built on top of larger scale composite parts) modules communicate and work with each other, and how to coerce them into forming larger systems. Systems built on top of message passing rather than minute details of the molecular system.

Sigh, the more I learn about things the more I have to study.

 

EDIT:(Oct/31)

Now you might be wondering why anyone would ever want to worry about implementing true OOP like paradigm or message based system building in biological systems. The answer is simple. All these programming paradigms were created to handle complexity. When we consider that existing paradigm of synthetic biology borrows heavily from that created for engineering and programming computers (one of the prominent figures of synthetic biology, for example, is Tom Knight, of the original MIT lisp hacker fame), ability to handle complexity within engineered framework becomes a fundamentally important issue.

One of the main difference between silicon based computation and that within in-vivo environment is scalability. Conventional programming languages are not very dynamic, and are terrible at scaling up compared to biological systems. If we are to bring any sort of computational/engineering approach to biology we need to address the issue of scalability that works in orders of magnitude difference from initial state. Biological systems do not go through processor bottleneck to transition from one state to another, and they have billions of processes operating in parallel. Engineering and programming approached as we know them will not be very useful for long without efforts to address these issues.

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.

8bit tools of science

According to the founder of Playpower.org, more people in India have TVs at home than tap water. And there are $12 computers everywhere that uses the TVs as monitors, like so many of the personal computers of old.

Now consider that these hardwares based off older 8bit chip designs and the softwares that run on them are more or less in public domain. We are looking at a significant portion of the entire human population just poised on the verge to hackerdom. It’s not just typing education and language training. We could build entirely new framework for education in 3rd world urban area using existing tools of education and science. Imagine being able to design an 8bit program for those machines (some of them can actually do internet) that pulls data from research institutions of all kinds (BLAST, Wolfram Alpha, and etc etc) and scale it down to a form those machines and people using those machines can understand. We already have beta versions of synthetic biology CAD program that undergraduates regularly use for their school assignments and private projects, so it’s not that far away in the future.

Will a child capable of programming computers and pull data on SNP variations to do his/her own genotyping using soon-to-be widely available opensource PCR machines still languish in poverty and despair? I don’t know. I’d sure like to find out though.