Consider Bookhling

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.

This is a bit of rant post on something I thought of after watching bunch of old hacker-themed movies from the Hollywood. It continues to amaze me how I can participate in all sorts of crazy things even with the summer studies and jobs I need to keep up with. I guess that’s the benefit of living in place like NYC.

I’ve been watching some old hacker movies lately.  And I just can’t believe what kind of cool things those movie hackers were able to pull off with their now decades-old computers and laptops. Computers with interfaces and hardware that exudes that retro feel even across the projector screen. I know a lot of people with brand-spanking-new computers with state of the art hardwares and what they usually do, or can do with those machines aren’t as cool as the stuff on the movies being pulled off with vastly inferior hardware and network access. Of course, like everything in life it would be insane to compare the real with the imagined, and Hollywood movies have a bad tendency to exaggerate and blow things out of proportion (I’m just waiting for that next dumb movie with synthetic biology as a culprit, though it might not happen since Hollywood’s been barking about indecency of genetic engineering technology for decades now). Even with that in mind, I can’t help but feel that the modern computerized society is just way too different from the ones imagined by artists and technologists of the old.

Ever heard of younger Steve Jobs talking in one of his interviews? He might have been a rather nasty person but he certainly believed that ubiquitous personal computing will change the world for the better. Not one of those gradual, natural changes either. He actually believed that it’s going to accelerate the humanity itself, very much like how Kurzweil is preaching about the end of modernity with the upcoming singularity. Well, personal computing is nothing new these days. It’s actually quite stale until about a few months ago when people finally found out glut-ridden software with no apparent advantage in functionality were bad things, both in terms of user experience and economics. Ever since then they’ve been coming out with some interesting experiments like the atom chipset for netbooks (as well as netbooks themselves), and Nvidia Ion system for all sorts of stuff I can’t even begin to describe. And even with the deluge of personal computing in the world we have yet to see the kind of dramatic and intense changes we were promised so long ago. Yeah sure, the world’s slowly getting better, or changing at least. It’s all there when you take some time off and run the real numbers. It’s getting a little bit better as time goes on, and things are definitely changing like some slow-moving river. But this isn’t the future we were promised so long ago. This isn’t the future people actually wanted to create.

We have engines of information running in every household and many cellphones right now.  Engines of information meaning all sorts of machinery that can be used to create and process information content. Not just client-side consumption device where the user folks money over to some company to get little pieces of pixels or whatever, but real engines of information that’s capable of creating as well as consuming using all of the hardware capabilities. It’s like this is the Victorian Era, and everyone had steam engine built into everything they can think of. And nothing happened. No steam cars, no steam blimps, no nothing. The world’s rolling at the same pace as before and most people still think in the same narrow minded niches of their own. What’s going on here? Never had such a huge number of ‘engines’ responsible for creating an era in history been available to so many people at once. And that’s not all. Truly ubiquitous computing made available by advances in information technology is almost here, and it is very likely that it will soon spread to the poorer parts of the world and remoter parts of the globe traditionally cut off from conventional infrastructures.

But yet again, no change. No dice. Again, what’s happening here, and what’s wrong with this picture? Why aren’t we changing the world using computers at vastly accelerated rate like how we changed the world with rapid industrialization (not necessarily for the better, of course)? That’s right. Even compared to the industrialization of the old times with its relatively limited availability and utility of the steam engines we are falling behind on the pace of the change of the world. No matter what angle you take there is something wrong in our world. Something isn’t quite working right.

So I began to think during the hacker movie screening and by the time the movie finished I was faced with one possible answer to the question of how we’ll change the world using engines of information. How to take back the future from spambots, ’social gurus’, and unlimited porn.

The answer is science. The only way to utilize the engines of information to change the world in its tangible form is science. We need to find a way to bring sciences to the masses. We need to make them do it, participate in it, and maybe even learn it, as outlandish as the notion might sound to some people out there. We need to remodel the whole thing from the ground-up, change what people automatically think of when they hear the term ’science’. We also need the tools for the engines of information. We need some software based tools so that people can do science everywhere there is a computer, and do it better everywhere there is a computer and an internet connection. And we need to make it so that all of those applications/services can run on a netbook spec’d computer. That’s right. Unless you’re doing serious 3D modeling or serious number-crunching you should be able to do scientific stuff on a netbook. Operating systems and applications that need 2GB of ram to display a cool visual effect of scrolling text based documents are the blight of the world. One day we will look back at those practices and gasp in horror at how far they held the world back from the future.

As for actual scientific applications, that’s where I have problems. I know there are already a plethora of services and applications out there catering to openness and science integrated with the web. Openwetware and other synthetic biology related computer applications and services come to mind. Synthetic biology is a discipline fundamentally tied to usage of computer, accessibility to outside repositories and communities, and large amateur community for beta testing their biological programming languages. It makes sense that it’s one of the foremost fields of sciences that are open to the public and offers number of very compelling design packages for working with real biological systems. But we can do more. We can set up international computing support for amateur rocketry and satellite management, using low-cost platforms like the CubeSat. I saw a launching of a privately funded rocket into the Earth’s orbit through a webcam embedded into the rocket itself. I actually saw the space from the point of view of the rocket sitting in my bedroom with my laptop as it left the coils of the Earth and floated into the space with its payload. And this is nothing new. All of this is perfectly trivial, and is of such technical ease that it can be done by a private company instead of national governments. And most of the basic the peripheral management for such operations can be done on a netbook given sufficient degree of software engineering and reliable network connection. There are other scientific applications that I can rattle on and on without pause, and there are plenty of people out there much better versed in sciences who can probably come up with even cooler ideas… So why isn’t this happening? Why aren’t we doing this? Why are we forcing people to live in an imaginary jail cell where the next big thing consists of scantily clad men/women showing off their multi-million dollar homes with no aesthetic value or ingenuity whatsoever? Am I the only one who thinks the outlook of the world increasingly resembles some massive crime against humanity? It’s a crime to lock up a child in a basement and force him/her to watch crap on T.V., but when we do that to all of humanity suddenly it’s to be expected?

We have possibilities and opportunities just lying around for the next ambitious hacker-otaku to come along and take. But they will simply remain as possibilities unless people get to work with it. We need softwares and people who write softwares. We need academics willing to delve into the mysterious labyrinths of the sciences and regurgitate it in user-friendly format for the masses to consume, with enough nutrient in it that interested people can actually do something with it.

This should be a wake-up call to the tinkerers and hackers everywhere. Stop fighting over which programming language is better than others. Stop with the lethargic sarcasm and smell the coffee. Learn real science and hack it to pieces like any other system out there.

Get to work.

Change the world.

An ex-senior curator finally succeeded in replicating all known features of the 2000 years old Antikythera mechanism, the first known mechanical computer in human history. Technically this is in similar spirit as a 19th century clock. There is some strange notion among some people regarding how people got smarter over time. Sometimes I feel like throwing the Antikythera mechanism in their faces. Or, I could just tell them to go read a good history book instead. Yes, I could always do that. 

All in all, amazing mechanism. Perhaps there were even more amazing things lost to time in other ancient civilizations as well.

As I’ve continuously whined about past few months in various places around the net, I need to buy a new laptop. Yes. I haven’t bought the darn thing yet. I’ve been doing all my computing on school desktop (by remote connection) and the Asus EEEpc 701 ‘netbook’, which comes equipped with Xandros linux (buggy as a sin would be an understatement), 7in screen, 516mb RAM, and 4GB SSD (which I complement with another 4GB SD card). The little laptop have been surprisingly useful, and I don’t know what I would have done without it by my side. Only if the default OS was a bit more stable… The system is more shaky than a vial of nitroglycerin on a centrifuge.

I’ve actually ordered my laptop on the net already, Lenovo Thinkpad T400. It’s scheduled to ship sometime in the week of Nov 12th, so I will be receiving it near the end of the November, which would be roughly a month from now. Yes. While Lenovo builds some decent quality laptops, they certainly suck big time at customer service and shipping arrangements.

The problem is, Apple released their aluminum MacBook line a week or two ago. And from what I’m seeing, the performance on that machine is amazing. The integrated graphics on that machine trumps the dedicated graphics card on quite a few laptops of similar class, and actually does slightly better than the T400 with dedicated video memory I have on order. I’ve  stopped by at the Apple Store on Broadway to take a look (at 11 PM, those guys are open 24hrs), and the weight/design impression is fantastic. Even better, if I decide to pick up the new MacBook, I don’t have to sit around sucking on my thumb for a month. Oh, and then there’s OS X. Aesthetics wise, I hate OS X and its outdated brushed aluminum look, but the system is built on top of UNIX, so it affords some unique advantages for someone in the field of sciences. The wealth of biology-oriented scientific softwares in OS X and native mathematica integration is staggering, and user even has an option to utilize OS X variety of apt-get software repository for installing some of the more obscure and specialized softwares and frameworks. Extensive software development environment like the Xcode is included free of extra charge, and you are allowed to reinstall the OS as many times as you want. (learn from this, MS!!!) The rumors of impending update to the OS X that would allow users to utilize the GPU component as a secondary (primary?) processor for calculation-intense tasks doesn’t sound too bad either… If done properly, it might even be possible for regular MacBook to have near workstation quality number crunching capabilities.

There are several disadvantages in getting the MacBook/OS X, though. The first issue is software compatibility. OS X library might have grown by leaps and bounds in past few years, but it still pales in comparison to what is available on windows platform. Things get progressively worse when you try to use web services/programs in foreign language, i.e. entirely different software culture and financial ecosystem. Take, for example, QR-Code. QR codes are almost universally available in Japan and used in some other Eastern Asian countries to lesser extent. Windows have hundreds of different scripts and programs for generating and reading QR codes. Quick search of google nets us three or so read-only programs for OS X and it is not certain whether they are actively maintained or not. How about interactive fiction utilizing the infocom Z-machine? (My secret passion…) Gargoyle program on windows runs nearly all possible formats used in IF, while OS X needs about two, maybe three of such programs installed on same machine for maximum compatibility. Some people would say that I can run windows on a Mac machine using bootcamp or a virtualization software, but frankly I find the notion of running multiple OS on a single computer to be unrealistic on usability perspectives. Theoretically it might sound like a great option, but the prospect of turning off a computer and ending all my working sessions just to use another program or two is certainly not attractive to me.
The price ratio is also something of an issue. In my configuration of the T400, I get 1440×900 resolution 14in screen, built-in 7in1 card reader, three USB ports, express card slot, 6 hours of wifi-using battery life, 2.2 ghz processor, bluetooth, and WiMax/WWAN upgrade capacity. All of it for 1180 dollars. If I choose to go with the MacBook, I get two USB ports, bluetooth, 1280x 800 resolution on 13in screen, 2.0ghz processor, and 3~4 hours of wifi-using battery life. All of it for whopping 1400 dollars including taxes. That’s roughly a 200 dollar difference, with the machine obviously lacking in feature set costing more. Mac aficionados out there will tell me that the OS X itself (with its unlimited reinstallation capabilities), variety of built in software tools, the iLife suit (which looks quite amazing), and UNIX based performance boost/stability offsets the 200 dollar premium, and they might be right (build quality is stacked in favor of the Thinkpad, since Thinkpads have industry-approved build quality record under their belt already). But then I know a good number of free, open source programs available for the windows platform that can do all of those things… Perhaps not better than the Mac software, but certainly adequate. Aesthetics-wise, as I’ve stated above above, I am not very fond of the OS X design and its ‘Aqua’ theme, and I personally find how they shove the ‘dock’ interface down their user’s throats to be insulting and grotesque. Windows has such issues as well, but at least I am familiar with some very hard-core theme-patching under the windows platform. It doesn’t hurt that I know precisely how I want my computer/OS to look design-wise (and yes, I don’t think T400’s black box look is ugly, contrary to popular opinion).

I guess for the time being, my ideal machine would be T400 capable of running OS X out-of-the-box. I am aware of certain projects like OSx86 that tries to tune OS X so that they can run on non-native hardwares, but they are just too darn clunky to be used on a mission-critical work laptop. Maybe I should install Ubuntu within the windows partition of the T400?

Whatever the case, logic dictates that I should wait for a month for my cheaper and faster T400 to arrive. It’s only that I get constant urge to cancel my order and just go pick up a MacBook like some primal impulse beyond the reach of civilized consciousness… (insert witty H.P. Lovecraft reference here)

Like most people, I was tuned into the WWDC keynote address on Monday. Most of the stuff on the keynote were more or less expected, including the iPhone/Dev kit and the OS X 10.6. However, the way they were presented were intriguing to say the least… To this scientist-in-training at least.

First the iPhone. Inclusion of medical applications within the presentation was the real eye-catcher of the show for me (other than the $199 price point for the iPhone, but that was expected). Why go through the trouble of including such specialist application in a presentation aimed at developers and consumer-enthusiasts? Of course, it would be nice to be able to present applications from variety of fields to showcase the capacity of the iPhone and ‘grow the image,’ but something tells me that medical imaging application and med-school study guide are probably not the most interesting of the applications submitted to the Apple in time for WWDC. Based on circumstantial evidence, I think Apple planned to have presentation for medical application included from the beginning, and I think they wanted more than one to showcase the professional academic muscle of the iPhone. The very fact that they took the trouble to include a testimony from Genetech regarding their enterprise functions of the iPhone seem to support this assumption.

Second, the OS X 10.6, also known as the Snow Leopard. The primary idea of the OS seem to be out-of-the-box utilization of multi-core processors that are mainstream these days. Most of us run dual processors right now and it wouldn’t be farfetched to think that we (and by we, I mean the normal computer users. There are already quite a number of quad core users in more specialized communities I hear) might as well be running quad processor systems a year or two from now. It’s a reasonable move, considering that no OS of any flavor seem to be taking noticeable advantage of the 64 bit architecture that had been around forever. Apparently Apple is calling their own system for utilization of expected slew of multi-core processors Grand Central (after the beautiful Grand Central in my hometown, no doubt), which will no doubt form the headstone for the new OS X 10.6 iteration when it is released a year or so from now. Is it pushing it to far to say that this might as well be a move on Apple’s part to appeal to the professional scientist community that actually has real and pressing need for more computing power? The distributed computing projects like the BOINC and the folding@home for example (both of which I am an active participant. I urge you to join up if you think you ave some cpu cycles to spare). My Intel Core 2 Duo 2.3 Ghz processor isn’t enough to complete complex work cycles in any reasonable frame of time. What if we can run more simulations and calculation on our own laptops/desktops for faster results? It’s no secret that Mathematica and Apple seem to be on something of a favorable ground. Apple’s ethos on this particular attempt will be simple. Keep the computer out of the scientists’ way. Just plug in the numbers, get the results, no worries about 64 bit support or any complex refitting of scientific programs (unlike what most people seem to think, studying physics or any other branch of science doesn’t make you good at computer science. Those are entirely different fields! Physicists are merely proficient at limited skills needed for physics computing). Who wouldn’t want that?

Third, the OpenCL (which stands for Open Computing Language). This part might as well be a dead giveaway of the Apple’s company wide strategy to woo the scientific community. OpenCL is a method Apple is developing that would allow developers to use the GPU of computers to do CPU tasks. A few years ago the news of PS3 GPU being redirected for mathematical calculation made some news. I believe there were other ones where conventional graphics chipsets were utilized for complex physics calculations that gave results that far surpassed what was possible when using only the conventional cpu. It’s been such a long time that I am somewhat surprised that only now they are thinking of integrating it into mainstream computer market. Mind you, this method of diverting gpu to do cpu work was done at first to provide more muscle for physics simulations using conventional computer systems and components rather than specialized supercomputer systems. I do not foresee normal Apple toting screenwriters and web surfers needing all that computing power anytime soon. If this is coming, it’s coming for us, the scientists, who need to crunch numbers most people haven’t even heard of.

If we put the three together with the assumption that Apple might be shooting for the scientific computing community, we have possibly mobile computing platform with serious power (macbook pro), able to run variety of scientific programs (Mathematica+Matlab, BLAST etc), with built in ability to sync and wirelessly connect to/controlled by a dedicated mobile phone with some serious computing power of its own (iPhone+community apps). So the actual computing can be done at home, while the user receives output and sends input from his iPhone. Would this work? I think there are plenty of people doing the similar thing already. But there will be possibly significant differences between device that had been essentially hacked together and series of devices that were designed to work in conjunction from the beginning. I see this as very exciting development on part of Apple and computing industry in general.

Having a science-oriented Apple isn’t the only thing I’m excited about. Let me put it this way. iPhone made people who didn’t use text messages on conventional phones to text each other constantly. iPhone also made people who never used the browsing capabilities of their conventional phones to browse around the web. This is the problem and effect of accessibility that I mentioned in some of the other posts on this blog. When people don’t do something, it might not be because they want it that way. It might be because there is an accessibility barrier between the individual and the activity. We complain about how people are no longer interested in sciences and other higher academic pursuits. Maybe we’ve been unwittingly placing accessibility barriers on the paths to higher education? If such ideas about accessibility barrier between the public and the sciences have a grain of truth in it, maybe this new direction of Apple can do for sciences what it did for telephony. Especially with the community based distributed computing projects and DIY mentality across variety of scientific, but especially biological disciplines on the rise, (the term synthetic biology itself isn’t even new anymore, despite the immaturity of the field itself) maybe I can hope for some sort of change in today’s somewhat disappointing state of affairs.

The ‘hacker’ culture had been around for so long, and involved in so much of the substantial progress of the last half of the decade, to have their own ethos and philosophy into codified laws, somewhat like the ten commandments. Except that these rules are, as pertaining to the hacker subculture itself, a matter of choice for the most part. If you are finding yourself agreeing to the code, than you are probably a hacker, regardless of whether you know about computers or not. Even if you regularly write in assembly language for living, if you cannot agree to the codes outlined by the hacker culture, you are probably not a hacker. In a way calling it a ‘code’ and comparing it to the ten commandments would be something of a misnomer. Think of it as something of an identification tag, to be used between people of similar disposition.

There are five fundamental common attitudes shared by most hackers, and they are as follows.

1. The world is full of fascinating problems waiting to be solved.
2. No problem should ever have to be solved twice.
3. Boredom and drudgery are evil.
4. Freedom is good.
5. Attitude is no substitute for competence.

It is rather interesting that all of the five attitudes go against common beliefs and pratice held by most public school education system. At least for the inner city schools I know of. Around those schools teachers and administrators can say they are trying to teach children how to respect the authority without even blushing in shame. That’s right folks, not respect to your fellow men/ladies, and not respect to yourself. The primary goal seem to be built around having the kids in middle and high school stages of education to respect the person who has the right to call the police or security on them. Of course, I am being rather crass here, but this is the sentiment shared by most if not all urban city youths, the same feeling I shared when I was their age. And who am I supposed to blame for current less-than-fantastic state the public education system is in? Kids or experienced, supposed ‘professionals’ who get paid to study the children and lead them to the best possible future?

As I grow older I’m finding that this ‘hacker’ mindset is not new at all. I believe it had been around since the very beginning of civilizations, and that this is a part of natural instinct of being a human being. It is becoming increasingly certain that you don’t need to know about computers to hack things. What you need instead is the insight and wisdom to seem through the system of the world. It’s like applied cybernetics. As long as things affect each other in certain way they form a system. A system of human society is a system like any other, albeit fundamentally more complex since such systems are usually evolved rather than designed. As long as something can be considered a system, it can be, and perhaps should be, hacked. A mudlark in highly hierarchical society later becoming a shipping magnate, or a leader of a nation, is as much a hacker as the computer science major hacking with python and C++ in pursuit of digital artificial life. A writer, a cook, a musician, the applicable list goes on and on. The field of synthetic biology, though fledgling at the moment, seem to be shaping up as the next contender to the hackerdom’s primary pursuit, in the search of the ability to hack the life as we know it. Who knows what we’ll be hacking some distant time into the future? Perhaps the very nature of space and time itself. Maybe even designer universes.

And from this standpoint of the universal hackery, I must ask, would it be possible to hack the human world? Would it be possible to hack the public mind and the generational zeitgeist to nudge the rest of humanity into some vision of future? Is it possible to hack the origin of all the situations and motivations, the human itself?

I must admit, there was a time when I would play computer/video games late into the night. I was a wee-lad back then, so impressionable and curious about the whole plethora of things of this universe. And the allure of the virtual worlds to such mind was just too sweet to resist. I gave a lot of thought to my then-current condition during the phase of my life. Why would I be captivated by certain types of virtual reality? Is there something shared in common between the hundreds of different worlds constructed using a number of different mediums-writing, visual, and aural-that composes the fundamental idea of what an enjoyable world should be? Would the impression of such an ‘idea’ of the mysteriously attractive world be common to all human beings? Or only human beings of certain memories and experiences? I would spend many days just thinking about the nature of all possible virtual worlds imaginable by human mind and their possible implications while my hands played the mechanical play of controlling my representation within the display.

Deus Ex was a computer game created by the now-defunct ION storm that came out during the aforementioned impressionable period of my life. This game isn’t aesthetically pleasing by any stretch of imagination. It’s gritty, ugly, in a very superficial and unintended kind of way. It is based in imaginary near-future where nanotechnology and artificial intelligence are just coming into full gear among the financial and political turmoils of a new human age. Conspiracy theories based on some real-world conspiracy fads play an important role in the setting and the plot, and there are lot of techno-jargon thrown around in one of the numerous conversations within the game world which might add to its depth. Any way you look at it, Deus Ex is not a work of art, and it was never meant to be. Deus Ex as a game was designed to be immersive. Immersive as in realistic within the confines of the plot and available technological means to execute that plot. Whatever the Deus Ex was meant to be, it did its job and it did its job fantastically. Deus Ex took itself just serious enough to be immersive.

I played and finished Deus Ex numerous times since the day it came out. The game had the semblance of a virtual world, just enough to be a better game, not enough to be a real virtual world, which was actually a good thing. I’d figure out a number of different ways to achieve the objective of the specific stages and the game as a whole, each of those paths gradually beginning to encompass different processes that the designer of the game probably never intended in the first place-a first form of truly emergent game play on digital medium. I can still remember a number of quotes and conversations from the game by heart, not through any diligent study, but simply through repeated exposure stemming from the interest in the world itself. And to be perfectly honest, while I was aware of nanotechnology and its growing prominence before playing the game (I was a little precocious for my age), I began to truly comprehend what such technology could mean to the world and the people in the far future by seeing it applied within the virtual world built and maintained by fictional premises. It would not be far from to truth to say that my interest in ‘industries’ of biology and other fields of science (with my current ‘official’ pursuit being plasma physics, which is an entirely different field altogether) began with my introduction to this game… I place much emphasis on the term ‘industry’ because it was through the application of the idea of technology within a virtual (no matter how absurd it might be compared to the real) world that I began to grasp the requirements of science and its true impacts in the modern human civilization of rapid prototyping and mass production. Yes, I’ve come to learn that science effects the human world as a whole, just as the hand of economy reaches into the deepest pockets of the remotest corners of the globe, and such permutation of ideas and information might have a reasonable pattern of causality behind it, forming a system of sorts. All this at the first year of high school, all this because I’ve seen it applied in a limited virtual world whose goal was to entertain, perhaps mindlessly.

People talk of the web 2.0, the web based virtual reality (like the second life) all the time, perhaps without grasping what it truly means. To me, the change on the web and its technical and semantic updates are merely superficial effects of the real change that is taking place right now. The real change we are about to face at this moment, is the change to the nature of the human network. I find that I’m using the term human network more often these days. The human network had been present since the very first moment of human civilization (perhaps even before, going back to the start of the human species) and has the same mathematical and sociological properties of networks that more or less remains the same on some compartmentalized level. The changes we are seeing in the emergence of the web 2.0 ideas and virtual realities merely reflect the technological advances applied to the same ever present human network that had been in place for as long as anyone can remember. At the core of the web 2.0 is the idea of user interactivity. What happens when there is a freedom of interactivity between millions and billions of people? The medium providing the room for interactions itself begins to take on closer resemblance to the concept we call ‘the world.’ Forget reality. What is a ‘world?’ What satisfies the definition of a ‘world?’ The core of a ‘world’ as it stands happen to be a place where people can interact with the very components of the world itself and with each other. In that sense, if our reality somehow forbid certain type of interaction between us and the ‘world’, it would cease to be real.  The world as seen from information perspective, is a massive space/concept/thing for interactivity, and interaction between the ‘things’ within the world builds and evolves the form of the world itself.

The web 2.0 in that sense, is the beginning of a virtual world that builds upon human interactivity rather than superficial (though still quite important) reliance on resembling the physical characteristics of the real. And the real change being brought on by the advent of the web 2.0 thought to the general population is the enlargement of the perspectives of the real world brought on by interactions with other human nodes within the virtual world. I am not suggesting that people are somehow becoming more conscious. Just as I have demonstrated with my old experience with the computer game Deus Ex where seeing certain kind of ideas applied to a virtual world left an impression of impact of such ideas on a rapidly prototyping, global world, the population of this world is becoming increasingly aware of the true global consequences of their and others actions and thought. It is the awareness that in this highly networked world, science, industry, economics and politics all walk hand-in-hand as ‘ideas’ and its currencies, a single change in one sector of one corner of the world giving birth to certain other events on the opposite corner of the globe in entirely different field of ideas. It is the beginning of the understanding of the malleability of the human world and its thought.

I’ve started with remembering my experience with an old computer game, and came to the talks of virtual reality, the human network and the changes of the world. I hope I didn’t confuse you too much. This is what I call ‘taking a walk’, where I begin with one thought and its conclusions and apply them to different yet related thoughts to arrive at interesting ideas. In case you are wondering about the game itself, it seem that they are giving it away for free now. Go grab it and spend some time with it. It’s still fun after all these years.

There is a semi-community project to simulate human brain using spare computing cycle in the works.

The members of the projects seem to be looking at eventual commercialization of what they achieve using this project. I assume that it might turn off some of the more devoted advocates of GNU philosophy among us, but I still think this is project is interesting enough to devote some of my unused cpu cycles to the cause… Since, well, what’s the point of letting the spare computer time go to waste? Right?

Science is fundamentally specialist and will never be able to achieve the kind of 2.0-everyone pitch in- status afforded by larger community web services today. However, the systems such as BOINC (the system used for the simulation project as well as a number of other worthy, non-commercial projects) gives us a glimpse of what ‘open-science’ in the future might be like, in that it allows concentration of necessary energy and resources to make the research come to fruition, not through any large scale departmental bureaucracy but through a sort of grassroots recycle programs of the commonly wasted byproducts of our civilization. Indeed, I’d refer to it as making full use of the machinery of the human civilization itself.
I’d like to urge anyone even passively interested to visit the BOINC website and participate in a project of your choosing. They have a number of projects in progress and the list is likely to grow in the future. Who knows, our little contribution might make the future a bit more interesting place to live.

I’ve been looking around the synthetic biology scene for a while now. Although my academic specialty doesn’t revolve around the field of biology, I try to keep at least an amateur’s perspective upon the advances and techniques of the field. Considering that my passion lies in the study and realization of artificial life I find it important to keep broad view of things irregardless of specialty or the immediate requirements of my own job.

I’ve often noted that the field of synthetic biology had suffered quite a bit of misunderstanding since its inception (which wasn’t that long ago actually), so I thought I might as well do a little write up of what synthetic biology really is.

Synthetic biology is an approach to engineering biology instead of being an academic field of specific goals. Simply put, synthetic biology as a whole is an approach, which may be utilized toward a specific application dictated by the case/individual/group etc.

In order to become a tool in engineering biology its link with conventional genetic engineering is inevitable. The breakdown of the similarities and differences between synthetic biology and genetic engineering is as follows.

Conventional genetic engineering is composed of three primary stages.

1)Recombinant DNA

2)PCR (stands for polymerase chain reaction)

3)Automated sequencing

The step one and two are about writing the DNA of specific purpose, and the step three is about reading the recomposed/component DNA. While these three steps are integrated to the core of the field of synthetic biology, it includes three more stages which differentiates it from pure genetic engineering.

4)Automated construction of DNA

5)Standards

6)Abstraction

The fourth stage, automated construction of DNA refers to the divide between the designers and builders of the DNA. Within the structure of the synthetic biology the designing of a DNA sequence and actually working in forming such DNA sequence (which is an expensive and time-consuming process) is separate from each other, making student-amateur oriented biological machine design possible within currently existing technical/industrial infrastructure. However, simply having a separate industry deal with mechanical parts of the synthetic biology would be meaningless without stage five and six, formation of standards, and abstraction of genetic interface. The last two stages run along the lines of the advance of computer programming scene, where formation of standard (html) and abstraction (most users don’t type in zeroes and ones anymore. We click buttons) brought on an explosion of global userbase and subsequent integration of the computerization into the very fabric of modern human civilization. Synthetic biology as a field encompasses all the six stages I’ve written about so far, each of them an integral part that reinforces another. In a way, synthetic biology is intimately linked with the garage-biology or biohacking movement in that it allows individuals to focus on designing their own novel biological contraptions using freely available and globally present database of biological/genetic abstractions and standards, while leaving the complexities and drudgeries of bioengineering to the mechanism of economy/industry.

I personally consider the field of synthetic biology to be a movement. Nothing as pretentious as some political gather-up, but a real movement like a wave spreading across the surface of the human society, a tell-tale sign of something gigantic beneath the surface. People used to build computers in their garage. Look where we are now. I can’t begin to imagine to full impact of well-executed synthetic biology as movement/industry/economy in the course of the future. Many little children these days are aware of tools like python and java, and some of them even utilize them with surprising efficiency and familiarity. Imagine the same children in the future, not with imaginary numbers but with the stuff of life. A little risky, but it’s certainly the type of world I want to live in.

What I also find to be interesting is the method of thinking behind synthetic biology. I don’t know how to put it succinctly yet, but as I have noted in the previous write up ‘transhumanism and the human network’, there is an underlying method of thinking that is showing up in universal scales, regardless of locale and cultural background. Am I correct in assuming this peculiarly wide-spread method of thinking as a type of zeitgeist? If so, where and how did it originate? And what role does the human network and its emergent properties take in the shape of the world we live in?

Maybe, once the biological hacking is done, the little children will hack the human civilization itself.

For those of you interested in slightly more detailed insight into synthetic biology, I give you two links.

www.openwetware.org

The openwetware website, definitely worth a look.

http://openwetware.org/images/3/3d/SB_Primer_100707.pdf

A simple primer to synthetic biology, covers the basics so it applies to other fields of biology as well.

I’ve been reading up on the concept and practice of the upcoming Will Wright game called the Spore. It is basically a game of artificial life management, where certain designer creature made by the player can be controlled by the player to adapt and semi-evolve into more advanced forms, eventually forming cabals and civilizations until they are star-faring and space colonising force in the galaxy. There are numerous number of galaxies in the game (each composed of many, many solar systems) each inhabited (possibly) by other user created creatures all in process of evolving.

Is this an interesting practice in the field of artificial life? I doubt it on the player side, since everything is basically controlled on semi-micro level management for the most of the game. However, for the computer managed downloaded user-created creature population, how such creatures play out will be very interesting to see, and there might be many people who would spend their time observing what other creatures do and react to instead of nurturing their own (now that I think about it, I hope Will Wright paid much attention to the effects of weather and geography to the determination of the creature behavior/culture). I know I would spend much of my time doing that. A sort of infinitely malleable aquarium.

I am quite disillusioned with the approach taken by the computer-based artificial life community. While there are quite a few noble pursuits out there, most of them doesn’t seem to have a clear idea of what an artificial life is, or should be. The general trend of the day is calling a thing an artificial life study for lack of a better term, rather than the intention of the thing, whether it be a search engine algorithm or a type of number generator. That is the reason why I try to stay away from the computerized practices of artificial life, instead opting for physical modelling based on replicable complex systems-based experiments happening in physical medium. Just so that there is no misunderstanding, I do believe that a type of artificial life can be achieved by the practice of computer programming. It is only that what most people seem to be doing at the moment is closer to a debate on how many angels can sit on the head of a pin, and I believe such lack of ingenuous ideas stem from lack of physical and experimental basis for the study of the actual phenomena of life. It is very depressing when the crossing of the line between the art and the science through the means of artificial life is mostly expressed through computer generated patterns of ‘organic’ looking things when there are practically infinite range of possibilities using variety of medium available to us at this moment. Life, I believe, doesn’t have to be convinced.

Will Wright’s design of the Spore is somewhat reminiscent of the disillusionment I’ve described above. The program of the Spore, at least the foundational idea of it, is very simple. Actual complexity that enriches the ‘game experience’ to the point that it is of interest to someone actively pursuing artificial life stems from the complexity of the human interaction with that simple basis. It is structured in such a way that the infinite variety of options open to those simple building blocks inevitably give rise to a type of complexity that can not be predicted in any algorithmic pattern. Thus, he is attempting to create a complex system not by act of coding a complex system, but by involving pre-existing complex system of complex environments (human beings) to simple deterministic systems. When certain feedback forms between the two wildly different systems, the outcome is nigh unpredictable, giving rise to depth and variety that cannot be replicated by any hard-coded complex system at this juncture.

Perhaps this idea of metasystem transition can be applied to variety of other platforms/mediums in the search for artificial life. I think I can already draw a rough outline of how such structure and resulting interaction is fundamental to formation of various complex systems, including the system of complex plasma.