New Year

Just a quick note before I go off.

Happy New Year, everybody! 

Here's little something to brighten the new year.

It's a segment from the News Hour featuring DIY bio

Rest

 Got back late night yesterday, and slept until ten in the morning today. I spent the rest of the day sitting at my couch with my laptop on my lap (a distinct advantage portable computers have over desktops, the matter of comfort), reading through variety of physics and mathematics related websites and ebooks I've been meaning to go through for a while now. It's nice to be able to rest like this. 

I also got out my lab note and did some leisurely note-taking on some of the maths and people I've read about on the net, like Aleksandra M. Walczak, postdoc studying Stochastic Biology at Princeton. Maybe someday I'll be able to study in the frontiers of sciences like her (the whole issue of stochastic biology itself, which is actually statistical mechanics applied to biology, is intriguing enough on its own, btw). 

This evening (or late afternoon, really, it's only around three pm right now) I plan to finish some of the books I got for Christmas (yes, I read ridiculously fast when I'm not distracted), and the Invention of Hugo Cabret. I'm completely captivated by that book. The only reason I;m not finishing it in a single day is so I can savor the book in slow, controlled pace. The experience of reading the Invention of Hugo Cabret is like watching an old classic movie that you can't keep you eyes off of. I'll place this book on the same level with the Ghost in the Shell series and Videodrome in best use of the medium/captivating the audience. A good hot coco definitely adds to the experience. 

The weather is almost hot today. 60 something degrees. It's like a cold summer day, with the rain/cloud and all. I kind of like it. I'm a snow person but it can't hurt to have mild weathers like this once in a while. Besides, there's something in the air that brings back some beautiful memories in my mind, like how a gentle wind stirs up a pile of leaves into vibrant foliage of colors. I can't quite figure out the individual memories, but they are beautiful nonetheless.

Maybe I'll cook up something decent tonight, and get a bottle of wine. The day just seem to call for that sort of thing. 

vacation

I'm taking something of a break from work today, until the new year. I've even dropped out of my conventional twitter circle and stopped checking my google reader. And another tab in background is running play videos of persona 4 (quite hilarious, by the way), something I might as well continue to watch into the afternoon... I might go out in the evening to the MoMA  Friday, but otherwise I feel like acting a little lazy for the few days I have.

I wonder what I should do with my time? I hate TV... I might run some nonstop Videodrome on the DVD player. Maybe I should dig through the mathforums topics on music and mathematics?


Ugh, I get a decent vacation once in a while, and I feel like there's nothing to do. maybe I should play something? I need to finish that P3 and the FFXII is still in the closet somewhere. 

Amazon certificate

 Just got an email from Amazon telling me that I have $3 credit toward amazon market place mp3 or movies becuase I was gracious enough to do my holiday shopping with them. 

Hmm. I already got boxes of DVD for Christmas... Now I just need an unlocked G1 phone :)

I wonder what I should get from amazon? Classic anime? TV shows? I haven't watched Dexter in a long time. Maybe I should download an episode or two, since they seem to be going at around 99 cents each. I just wish they'd send me a $3 book instead though. Or even, $3 credit toward a new kindle. A discount on kindle would be awesome. 

Indie game recommendation

 I just played two indie games I picked up from the www.tigsource.com webpage (it's a veritable goldmine of indie game info and demos. Make sure to check it out).

Two interesting games worth pointing out. 

Lovecraft's commonplace book-inspired typing game. It's basically a typing game where you need to type up words in appropriate locations as the list comes floating down from deep within your psyche (you are supposed to transcribe them using your typewriter, and you'll be paid by each coherent ideas you can piece together). A little rough around the edges, but it might really be something if the author can take more time to flesh out the feature set.

Knytt stories. At surface it's a simple enough platformer, that doesn't eat up processor cycles or memory so it can be played while my computer's busy compiling through large piles of data depo. Quite possibly the best indie game I've ever played, right next to Aquarion (which you should also try if you haven't already). 

Both Knytt Stories and the Clatter of Keys are only available for Windows platform. Aquarion recently had a Mac release from Aspyr games. Makes me a bit glad that I didn't pick up that MacBook when I had the chance. 

wikipedia

 Just a quick note. 

Wikipedia seem to be going through some sort of financial crunch lately. I guess volunteer based community service like the wikipedia isn't structured to weather the recent international financial log (though there are some other economic theories that suggest otherwise).

It's scary to think of the world without wikipedia, but recent turn of events had been forcing me to think that such future is fully possible... Maybe it's a time to pitch in a bit and donate? 

Maybe this is a kind of problem that the government can get involved in, like NSF funding without political clause. 

Attraction of transhumanism

 Here's an interesting blog post I came across titled "Why I want to be transhuman."

Nevermind the content of the post itself (it's an interesting read, but it's not the point of my post). I want to point out the Marvin Minsky's quote lifeted from his book the Emotion Machine. Here's the quote posted in the blog article I linked above.



"I was once giving some lectures on longevity and immortality. I noticed that people didn't like the idea much, so I actually took a poll of a couple of audiences. I asked how many of you would like to live for 200 years. Almost no one raised their hand. They said because you'd be so crippled and arthritic and amnesiac that it would be no fun. So I changed the question. How would you like to live 200 or 500 years in the same physical condition that you were at half your age. Guess what, almost nobody raised their hand. But when I tried the same question with a technical audience, scientific people, they all raised their hand. So I did ask both groups. The ordinary people, if you'll pardon the stereotype, generally said that they thought human lifetime was just fine. They'd done most of the things they wanted to do. Maybe they wanted to visit the Buddhist statues in Afghanistan, but they could live without that. And surely another 100 years would be terribly boring."


The lesson is simple. Regardless of the validity or moral conviction regarding transhumanism and life extension, people who lead mostly 'normal' conventional lives thinks longer lifespan is not really necessary. People who've chosen intellectual pursuit as the primary way of life, however, tend to support artificial longevity more readily. I am not saying that those of academic pursuits somehow value life more than the 'vulgar' normal people who just happen to live out their lives. Douglas Hoffstadter, one of the most learned man of our time (and someone I greatly admire) once criticized the transhumanism movement and many of its leaders to be way too obsessed with death (something I agree with, despite my support for transhumanism movement in general. I mean, Kurzweil avoid trips to reduce his chance of death. That's just sick, considering the scope of things he's supposedly trying to accomplish). 

I just want to point out certain mindset that I find disturbing. People who feel no pressing need of longer lifespan may be the silent majority of the society we live in. This brings in my mind pictures of luddites who protest against advancements of medical technologies because they feel 'simpler' life is better, while third-world people die in droves because of lack of our ability to manufacture more effective medicines more cheaply. Or how about the college kids I knew a few years ago? Who regarded higher learning and pursuit of grand life-time goals with frank cynicism and suggested a 'simpler' life with a day job working at the groceries or community farms, living out their lives with those they love? I always wanted to point out that their parents were paying for their college tuition while they purchased expensive coffee from a single mother working three jobs to support her child.  

I think the culture of overtechnology is dangerous. Thinking of technical advances as some sort of panacea that will solve all of humanity's problems is a twisted and shortsighted thinking that later generations might have to pay a hefty price for. Just as dangerous, however, is the culture of pseudo-philosophy and half-baked soul searching that takes on the superficial trappings of transcendent wisdom while lacking substances of foresight, action, and compassion towards all of humanity...  

Holidays and information overload

 The holidays are here. And despite the crazy schedule that has a number of deadlines starting right from January third, I am swept up in variety of end-of-the-year parties and such, including a two day ski trip to the upsate area. Might even end up visiting Boston sometime in the January of the new year. 

Lately I'm beginning to feel the pressure of some information overload. There are just so many interesting new things to learn and experiment with, and not enough time to even gloss over all of them. I want to try bunch of new games (with the added power of my new laptop it should be possible to play some newer games), read dozens of books, try my hand at learning some new mathematical analysis techniques, apply the said mathematical technicques to composing, brush up on my drawing skills with my wacom tablet, brush up on my violin playing skills, write a novel, experiment with the processing language and etc etc...

And there are quite a number of things I'm actually doing as a part of my job as well, like learning /using the mathematica language, learning/using python, learning more math, learning more plasma physics, digging through molecular biology texts, digging through mathematics texts, digging through plasma physics texts, learning complex systems analysis and digging through related texts, learning wet-lab techniques for possible future iGEM involvement, attending interactive technologies and arts exhibitions and lectures, maintaining two blogs (one personal and one more 'official'), maintaining a tumble log, trying to keep up with art museum programs, part time counseling with underprivileged kids, tutoring, 2 NASA related contests, reading through a number of novels all at once, and a number of other things. 

I think my new year resolution would have to be to streamline my life a bit more, cut down on things I don't need and try not to overload myself. Hmm.

Some links of note

 A quick write-up before I go off to work/last minute shopping

I've been really into tumblr lately. Tumblr+twitter had been my medium of choice for past month or two. 

I want you to check out two links I put up at my tumblr on the subject of augmented reality. 

http://bookhling.tumblr.com/post/66220823/books-infused-with-augmented-reality-illustrations

http://bookhling.tumblr.com/post/66220638/augmented-reality-graffiti-heres-a-cool-idea  (this one's especially cool)

Amazing article

If you are even remotely interested in education you should read this article. 
In case you didn't know, the author is the one who participated in the iGEM competition entry about banana-smell E.Coli culture. 

I found the part he wrote about his success being 'because he dropped out of high school' rather than 'despite dropping out of high school' to be especially compelling statement... Apparently most people seem to have disturbing tendency to equate schooling and education regardless of the educational content of the schools themselves. I can't speak for other parts of the country, but in nyc many kids really do waste their life away in third rate schools and third rate colleges with scarcely any education being given in the process... I mean, I've had numerous experiences of sitting in a cafeteria for six hours staring at a wall since half the teachers didn't come to school because of the weather, and from what I'm seeing many kids today go through the same experience today. And for the children who really do opt out of the inefficient school system the city  practically spits them in the face by providing them with 'job education.' Sure, it would be nice to provide some job training to a thirty/forty years old homeless man. But to bunch of teenagers with their whole lives ahead of them? How can you tell if they aren't interested in more intellectual pursuits? And yes. The bureaucrats will probably cringe at the mention of 'intellectual pursuit' despite their higher-than-thou stance on matters of education. They'll probably say 'intellectual pursuit' have no place in real life. In their world learning to fix other people's toilet for a lifetime is considered more realistic compared to learning to develop a vaccine, or teaching children.

Here is the vicious cycle.

The people who run the education system are so severely undereducated that they force little children to live upto subpar standards and punish anyone who deviates toward a better life using methods they do not have the ability and the will to comprehend. The undereducated children then graduate and come back to run the system, the same way as they were taught.

In this society fondling little children is considered the height of perversity while relegating them to what is for all intends and purposes a life of bonded servitude under their 'betters' is considered normal. I consider them to be the same in terms of potential psychological damage to the child.


The world as a whole seem to be too caught up in demons of its own to be able to understand just what knowledge and education is. Mathematics and Sciences are pretty darn easy. Perhaps even easier than the arts, because you don't need as much 'gift' to be successful in the matters of maths and sciences. 

Quadratic equation was once the height of mathematical pursuit, solved only by people devoted to the mathematical arts. Now middle school children and moderately well educated gradeschoolers can solve that as part of the standard curriculum. 

Quadratic equation itself didn't somehow magically become easier. Human beings didn't suddenly evolve better brain in last few centuries (and if any teachers are doubting this please quit your job now. You are a threat to little children). The mathematical method for solving and teaching quadratic equation however, became easier, more streamlined and to the point compared to its archaic predecessors. The same goes for the basic Newtonian physics. 

It's only logical to assume that whatever we consider to be height of learning today will inevitably end up in high school curriculum in a century or two. 

The education system as a whole is deliberately pushing people away from pursuit of anything that cannot be understood in a ten minute  glance because they think future middle school/ high school curriculum topics are too difficult for the masses to understand. In the end, it all works out as a self-fulfilling prophecy, and the so called educators and public servants gets to sleep at night while generation after generations of children are assigned to a fate they did not choose and does not comprehend. 
   

cellphone novels

 Cellphone novels are quite a hit with Japanese female demographic, as outlined in this article. This might sound strange to westerners who until recently considered a bare-minimum camera phone as a luxury item and live in places where bluetooth still isn't the standard on many laptops and cellphone models being offered. As the common stereotype suggests, North Eastern Asia in general is in state of some unusual acceleration of integration of technology into the basic fabrics of the society, starting with the higher than double the concentration of robot population density in Japan compared to anywhere else in the world and my Grandpa in Korea who knows how to install custom firmware for the GPS in his car, which isn't all that unusual in that country.... Sigh. The level of technological proficiency in America is difficult to understand since most of the high-tech being used in Eastern markets came right out of American universities, like MIT media lab and NYU ITP program (I attended their show yesterday and took bunch of pictures. Quite a blast. I might post something someday. The pictures are on my flickr account). 

Anyway, back to the cellphone novels, it's an interesting concept. Now I know somepeople are already scoffing at the notion of having a fully pledged novella that's actually written on a cellphone for a cellphone... That would be shortsighted for a number of reasons. It's like comparing a full length essay and a poetry based on their length and word count. Cellphone novels are written to be brief, to be read briefly on the go... Most people don't hang onto their cellphones when they're in their homes. They read it when they are using subways and commuting from work, a bit of breaktime between classes and etc. Within the constraints of the medium people found a unique way to convey coherent story and characters the readership can sympathize with (which is probably one of the reasons why cellphone/microprose novels aren't catching on with the European/American crowd. We need a whole new set of word use and prose styling to write a decent microprose novella, and not that many people are working on that)... We are looking at a medium that's adapting to its physical manifestation like a living being, originating from something familiar (full size fiction), yet turning into something else that only retains superficial similarity to its origin while developing an entirely different DNA of its own.

What I am really excited about cellphone/microprose fiction isn't in being able to write stuff down and read on a cellphone. We've had that in some form since 90's, late 80's if you consider some of the experimental works limited to college labs.
Rather, I am excited about the streamlining of the story writing medium this change represents. Even those people who needs to go to work everyday and don't have the time to sit down and write a full-prose novel might be able to tell a decent, compelling story using certain techniques and vocabulary. What kind of story will people be able to write if they can spend less time writing and more time imagining it? 


  

sky crawlers screening

Just got back from nyc Sky Crawler's screening. I'm a little burned out, so let me just jot down a couple of points for further recollection tomorrow.

1)The screening opened with a recorded message from the venerable Mamoru Oshii himself. He said that the movie was about people who stopped/refused to grow up, and drew a parallel between the immortal pilots and the mindset of the current generation. Despite being spoken in Japanese, his words felt well thought out and serene. He obviously gave a lot of thought into this.

2)The basset hound, the major Kusanagi look-alike, gothic architecture in part of the film, strange machinery possibly playing music, lot of thoughtful dialog, and reference to the Albert Camu's the stranger. This film has Mamoru Oshii written all over it, and that's a good thing. 

3)Everybody smokes a cigarette. Seriously, I think I saw someone lighting up practically every five minutes (the film was two hours long). It's definitely intentional, but to what end? I think I know what Mamoru Oshii wanted to say, but won't write it here since there's a spoiler.

4)Lot of daring here folks. Remember that the main characters are immortal teenagers that must be killed through violence. These teenagers don't shy away from adult situations, and Mamoru Oshii might have done some intentional dare to the censorship system. I like the realism, but some people might have issues with it. Of course, nothing perverted here. Nothing we wouldn't expect teens in kill-or-be-killed situations to do.

5)The movie was two hours long, and in typical Mamoru Oshii style there's a lot of philosophizing dialog, blank stares, and silent scenes. Amazingly though, I couldn't take my eyes off the screen. And the characters, despite not saying very much, felt very alive and understandable through their facial expressions and motion. This movie isn't boring. If someone does find this boring, they will probably find anything that has thoughtful dialog to be boring.

6)This is a movie adaptation of a novel and it shows. Time to time I needed to glean a lot of information from a simple scene or two, the kind of things the novel might have spent a chapter describing. I think the overall transitions were done masterfully, but it is noticeable.

7)The musical scores are done by Kenji Kawai (who also did the Ghost in the Shell soundtrack), and it's beautiful. I know I'm hunting down an ost for this one.

Will I get a DVD once this comes out? Yes. Definitely. Do I expect this movie to make full theater circuit in America? Unfortunately, that's very unlikely considering the subject matter. As stupid as the censorship is, it's not going away anytime soon, and this film has a few things that might make your normal High School Musical lovers feel uneasy (not that there's anything wrong with High School Musical).

I think I had a couple of other points I wanted to make, but my brain is all mushy right now. Gotta go to sleep for tomorrow's lab session.

Japan: Robot Nation

A new documentary from Current TV. Unlike some other (let's be honest. MOST other) Japan/robot documentaries, this one focuses on the social conditions leading to the Japan's apparent love of robotics. It sheds something of a harsh, yet realistic view on the state of Japanese society and their labor market, something I am somewhat familiar on indirect level through experiences of those close to me. Only at about twenty or so minutes long, this is a worthy watch, I think.

Top ten bioscience advances of 2008

Here's the link.

cheap microfluidics

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

Original article from the Wired.

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

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

I did think of doing a io9 madscience entry on synthetic biology-utilizing mTAS chip that can be used to manufacture minuscule amount of specified chemicals that can be used for periodic medications or for recovering out-house patients, but I scrapped it in favor of epigenetic production using extracellular matrices. Oh well.

science commons

Here's the link to the science commons video

Just a quick post before going to sleep (it's 2:45 in the morning and I have class at 10:00 ugh).

This is one of the coolest things I've seen on the net today. 120 second introduction to what science commons is.

I can think of lot of things that can explain why the idea of 'opensourced' science or science commons must be one of the coolest and most revolutionary ideas of the generation, but my brain is turning into a jello right now, so detailed post will have to wait.

Just one thing though. Library of Alexandria.

Just think about it. Why was library of Alexandria so important? Was it because it housed a lot of books? No, it isn't. If anyone believes that the significance of the library of Alexandria was about stacks of books he/she lacks the understanding of the origin of modern civilization. Books or any individual units of information pop into existence all the time. Libraries are meaningful because they centralize and organize those individual information clusters. Centralize and organize, meaning giving accessibility to.

Greatest threat to any knowledge is not in its misuse or incomprehension. It is in obscurity (as Cory Doctorow pointed out as he released his works under CC license). Libraries made human civilization by providing accessibility to knowledge that would have been forgotten otherwise by centralizing them in one geographic location and organizing them according to a system. From that location new ideas were born since people no longer had to spend their lifetime re-learning what someone else figured out half a century ago.

Science in general, lacks accessibility. Which is very weird when you think about it. Science is about accurate description of this universe, this universe every single member of the Homo sapiens sapiens share. Yet science lacks accessibility, both to the nonspecialists and specialists alike. It's like having limited access to one of your eyes or limbs or organs.

Accessibility is catalysing and empowering. When economic systems become accessible we get flourishing finances and trades system, with all the subsequent benefits of arts and culture. When human opinions become accessible we get one of the biggest human community ever, with subsequent benefits of policies and philanthropy. The first time academies and libraries became accessible we began a march toward a new civilization. What will we be able to accomplish once the sciences are truly open and known to every willing member of the humanity?

artscience rant

(((Just a little something I wrote up in a notepad a moment ago))) 


A machine to create as we know it can only a machine that follows certain mathematical patterns giving output that can be interpreted by both the machine and observers as being coherent. Would it imply that there is something missing in such interpretation of the acts of creation or that act of creation and all subsequent endeavors are in effect replicating mathematical algorithms/formulae? Moreover, what exactly is the drive behind the origin of the will to create? In case of artificial machines we can say that we coded its mind/body to act in certain expected way, but the same cannot be applied to the creators of the creating machines, since (as far as we know) we haven't been programmed by some entity in such specific manner as to will to create objects and ideas (and even that would create the question of who created the entities, so the whole line of questioning is more or less a dead-end). The obvious answer to the explanation of the behavior of creativity as things stand right now, would have to be drawn from the thermodynamic characteristics of the life-like intelligent systems themselves. Arts, and any type of object/idea creation by life-like intelligent systems must be a direct result of the thermodynamic system that forms the basis of the life-like intelligent systems themselves. In short, art is science.

megami tensei online IMAGINE

 I've known about this game since its release in Japan.... It was a commercial failure from what I hear.

Apparently they licensed it and released it in the states. I got an email telling me that I'm invited to the closed beta (I think about a million other people got the same email). Since I'm somewhat crazy about all things megaten I decided to take the jump and participate. 

The game has rather modest system requirements. I run it in a window while I'm doing web browsing/writing/chatting etc and there's not even a hiccup, so that's a plus in this age of over specced computer games (and they wonder why people are moving to consoles?). Very stylish,with occult+cyberpunk influence like the good old SMT universe. though it's in beta stages so the character selections are limited at the moment. They seem to have an interesting story going on, leading Shin Megami Tensei 1's storyline to SMT2. I'll try to figure out what's going on as I play on.

I don't know how long I'll be able to play this with my schedule being what it is. I guess I'll enjoy it while it lasts. If there's anyone who wanted to take the plunge to the megaten-verse yet couldn't because of the console barrier, here's your chance. You can find the keys to the beta floating all around the net. If you can't find one for some reason, leave a message and I'll try to send an invite.

 

 Poor children brain activity=Stroke victims

All I can say is, I KNEW IT ALL ALONG!

I work with disadvantaged children in inner NYC (a part-time gig), and the amount of stress these kids go through from the moment of their birth would probably make most normal adults cringe. They see their parents get humiliated, and they see themselves get humiliated, usually by their own school faculty who usually live in upstate NY. There’s nothing for these kids to do in their school due to lack of funding and quite frankly, lack of effort on the part of the teachers. Even slight rainfall is enough to stop half the teachers from coming to school, after which the kids are forced to sit in a classroom or cafeteria all day doing nothing since the law requires the kids to stay off the streets (and the authority seem to place an abnormal amount of emphasis on kid staying off the streets, rather than giving them an actual education).

New York City is a city by the sea, yet many of the kids I’ve seen in inner city haven’t seen an ocean in their lifetime. Their parents are too busy pulling 12 hour shifts and the kids are intimidated to visit any place in the city that’s even remotely affluent. “I don’t feel like I belong there” they say. Whenever I bring them to a museum/library/bookstore etc they tell me that other people (security guards) are looking at them funny. Whatever the case might be, we are resigning an entire generations of children to very twisted social stereotypes and future that’s not quite worth living for. An entire generation who either has to choose to be dumb or brave the whole weight of their own society. Am I the only one seeing a problem in this?

Futurepast

Plenty of room

 This is a cross post from my other blog.

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

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

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

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

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

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

Orwellian diary

 They have a daily blog displaying entries from George Orwell's diary. I found this one through the ever increasing might of my google reader service (I don't know how I managed to live in the dark age without a decent RSS reader, which is weird because most people in Japan/Korea don't use RSS service for some reason. They use portal sites). 

I haven't really read it in detail yet, but Orwell seemed to have had some strange obsession with the number of eggs per day... Many of his entries consist of "One egg" or "Two eggs", nothing else. It's so concise as to be surreal... I'm reminded of E.E. Cummings for some strange reason. 

Why the number of eggs? What did he do with the eggs? Did he eat them? Was he using them in some strange ritual that gave him the inspirations for his works? Was he just a little bit bonkers? Hmm.

Immortality

There are so many things about quantum mechanics that makes it so fun to play around with it in my head when i'm bored. 

Schrodinger's cat is famous for being alive and dead at the same time, right? (Though he really proposed it as a way to point out the absurdity of the Copenhagen interpretation of the quantum mechanics) 

Well, following that same logic it is fully possible to turn someone near-immortal in the eyes of the humanity. Lock him or her in a box that allows for complete separation from the observable universe. It needn't even be a box of physical walls. It can be a box of, say, distances. So far that the man/woman is effectively outside the range of observable sphere around the known space. 

(using time and space as an effective 'wall' is a notion frequently used by military strategists of old and new alike, btw. It's a principle of maneuverability)

It sounds funny, but technically we won't be able to tell if the subject of such a process is alive or dead, so that's immortality in a sense. 

excerpt from Cory Doctorow

 In answer to a question posed by an interviewer at the end of a comic "Futuristic Tales of The Here and Now"


TW:

Many people in your story suffer from a disease you term as "Zombiism." Is this comparable to, say, the horrendously extreme amount of AIDS cases in Africa, a continent also rife with warfare?


CD:

Yeah, and all the other diseases-like malaria, which kills one person every second-that our pharma companies can't even be bothered with because boner-pills are so much more profitable. 
We grant global monopolies to these companies over the reproduction of chemical compounds. They argue that they need these patents because otherwise, no one would do the core research they do and we'd all be dead of disease without them.
But what do they spend their regulatory windfall on? Figuring out how to reformulate heartburn pills that are going public domain so that they can be re-patented, cheating the system and the world out of twenty more years of low-cost access to their magic potions; marketing budgets that beggar the imagination; lobbyists arguing for stricter rules. 
Meanwhile, people are actually dying, in great numbers, of diseases treatable by drugs that Roche and Pfizer and the rest of the dope-mafia won't sell them at an accessible price, and won't let them make themselves.


This reminds me, there were quite a number of people representing pharmaceutical interests at the Hong Kong Synthetic Biology 4.0 conference... The possibility of building or reconfiguring microbial organisms to produce noble chemicals is certainly an attractive prospect, and is fast becoming an industrially viable production method of rare chemicals. A case in point, recent iGEM 2008 competition's winning entry was a synthetically designed vaccine against Halicobacter pylori which causes gastritis, built using immunobricks biological components designed in-house by undergraduates (albeit with support of graduate level faculty and facilities). The BioBricks foundation (upon which most of the synthetic biology practices today are based upon) runs on the principles of opensource like many of the server side technologies and programming languages in use today, and the possible social and economic ramifications of the growing field of synthetic biology is promising even at this early stage of development.

Are we seeing the beginning of the end for the workings of current generation pharmaceutical industry? Vaccinations and pills developed by relatively small scale biotech developers, perhaps even run by some of the poorer nations to counter against indigenous diseases? 

testing posterous

Testing email posting. Ignore this.

Posted by email from bookhling's posterous

Bunch of cool things.

 First, USB Tachikoma! 







Sometimes I get a feeling that Japan gets away with the coolest gadgets (which isn't really the case I assure you, as was the case with 1G iPhone and XO laptop). Apparently the above USB-Tachikoma can connect to the Japanese Windows OS (no love for linux???) and do some minigames, hang around the desktop, and inform the user of any new emails using their cute Tachikoma voice. I've tried looking for one, but the GS4U website seem to be out of stock. The photo and the article come from way back, so I guess it can't be helped.

Speaking of gadgets, the amazon is going strong with their XO laptop give one get one program since this monday. I have some pocket money (a bonus for a job well done), so I was thinking about buying a cool new gadget/book to satisfy my cravings (curses, this hollow consumerist society!)... I have around ten or so books I'm laying my eyes on that I'll be picking up dirt-cheap from the Strand bookstore, a lovely benefit of living in middle of NYC.  As for gadgets, I'm trying to decide between an iPhone and a XO laptop... Both of them can be used for my work, so I'm not entirely wasting my money away. :)

iPhone is more refined of the two devices, with beautiful human interface design, OS X, and a plethora of applications available for free or for real cheap that can be directly attributed to my work at the lab (though I must note that most science apps on the iPhone seem to lean toward the biology side of things. When will physicists get some love from the Apple community?). It's light, it's portable, the benefits of the machine goes on and on. XO laptop on the other hand, is a little clunky. I love the little machine (I've had chance to use both the iPhone and the XO laptop first hand), from its kid-friendly design to some amazing engineering employed in construction of the machine itself. It's only that at this stage the laptop is still a bit rough around the edges from the bits of bug in the OS to some tweak necessary to turn it into a fully functioning work-capable machine... Also, considering the nature of the laptop, it's not much more powerful compared to the iPhone's computational capacity, as odd as it might sound. 

On the surface, iPhone is really a winner. Being a phone it's connectivity is ever present, and it's more mobile compared to a full laptop, no matter how small it might be. Since I'm already a AT&T customer the monthly bills are not much of an issue... Yet when I sit down and think about it there's this pesky issue of philosophy. The popularity of iPhone is not built on its novelty multitouch/design factor. It;s the extensive software library available for the phone... As you can see I'm more of a google Android type of person you see :P Seriously, the matter of openness on hardware platform is something I'm rather concerned with, so the claustrophobic software landscape espoused by Apple isn't something I feel comfortable supporting by buying their product... Compared to the iPhone, XO laptop is the platonic ideal of software freedom materialized. And it's ever-hackable.

If I was only a few years younger I would have snapped up the XO-laptop in a heartbeat.... Now that I have a full time research job now I just don't think I can spend the amount of time required for me to do all the DIY stuff required to fix the XO laptop to fit my usability profile though. Sigh, choices choices. Maybe I should just be grateful that I eve have time to type up something like this on a weekday? 

bloody pillow

The red stuff isn't blood. It's a pillow.

This is so cool. I want one.

Chrome rant

 First, take a look at this. Bunch of 'monsters' written in the processing language. This little language from MIT is even more versatile than I first thought. I'm thinking of writing a small visualization bot of sorts later on, which might take some time since my primary medium of choice Mathematica just got bumped upto version 7. I'm harassing the school depot so I can get the latest copy without having to pay the ridiculous pricetag that comes with this (albeit vital) program environment. 

These days I find myself using three web browsers at once, four if I include a little text-only script stuff (much like modified emacs) that I use exclusively to communicate with my school computer (which does all the heavy lifting these days).

I use IE for all those pesky Korean/Japanese community sites that requires all those active x for full functionality (yes folks. For all the glitter the Asia is a backwards place when it comes to CC licences and GNU philosophy) so I can keep in touch with people there. I'm currently in process of bugging them to ditch the crappy web services and migrate to twitter/tumblr/swurl/friendfeed. Fro somereason there's already a sizable Japanese community on the twitter I think. Though most of them just ends up making a post or two and revert back to their original active x crap services (because all their other friends are still on the other service. Ugh).

I use firefox for all the research stuff. I have noscript which block out practically every single content on the website except for pure txt unless I manually configure the site to show its content, which is a lifesaver when I have fifty tabs open and some website decides to pull in 'bling is the thing' flash content on my computer. The ADP is just as essential. I usually spend most of my time in firefox without encountering a single ad, so less distraction, and less processing power/RAM wasted for something I'm not going to buy anyway. The zotero and 'science toolbar' courtesy of the thriving firefox plugin/extensions community makes making notes and bibliographies a sinch. I can practically fly through dozens of archives and scientific data depots on the web in course of minutes using my fully customized setup.

And then there's the google chrome. The chrome is still in the beta stage (like most other google services really), and lacks some significant functionality like ADP and zotero integration, but I still come back to the browser time and time again. There's something innately elegant about the basic design and layout of the chrome browser that make it a joy ot use it to surf the web. And the speed isn't half bad either (I guess all that webkit engine hypes have a good reason). I like how the bookmark bar appears and disappears at the touch of a shortcut, and I like how I can browse the web without using the mouse with some modification.  I love the maximum amount of screen estate allotted to the content of the website itself instead of browser interface, a big faux pas firefox 3.0 made with its big shiny buttons. I love how i don't have to lose entire sessions of tabs when a single tab fails to respond. I can just shift-esc, pull up the in-browser taskmanager, and cancel or troubleshoot the problem tab. I love how the ctrl-f brings up the search bar at the top of the browser window instead of the bottom, and I like how it doesn't take an entire line of my screen estate. it's ergonomically sound, and just plain makes sense.

Google chrome is the browser I use when I 'just want to go to Disney Land', so to speak. And since the chrome is open source I can live with my conscience, unlike with IE (though I wouldn't use it if it was open source). Google chrome in its basic design is the web browser firefox 3 should have been.



 

blood of bahamut

Something I came across at random on the net. Apparently this is a concept art for an upcoming DS rpg called Blood of Bahamut. I'm not too interested in the game itself (I hardly get to play anything with the onslaught of materials I have to cover these days), but the concept of a world that exists on back of a roaming giant, which gets into conflict with other gigantic creatures sound really interesting.

all-nighty

Part of being an adult is pulling an all-nighter, and then getting paid for it. You see, kids pull all-nighters all the time on ridiculous schedule, but they (usually) don't get paid.

I just took a relaxing stretch in the living room, with all the lights off and only the monitor of my trusty laptop blinking at intermittent intervals in the study while crunching numbers with Mathematica and running some minimal cellular automata written in python.

Of course, I had the obligatory glass of alcohol in my hand. A cheap, mild merlot. What is a night without a decent drink?

As I lay myself on the sofa in the dark, my eyes adjusted to the darkness, with remarkable haste, I should add, since I've been staring at a full-brightness LED screen for past five hours straight.

For a moment I thought I was standing on the edge of a skyscraper in Tokyo. A trick of the tired vision.
You see, my living room, for all its tidy appearence (I like to keep things organized), is filled to the brims with electronic gadgets ranging from draft-N wireless router to media center laptop I have cabled to external HD and a HDTV. I didn't notice it before with the light on, but the whole room is apparently dotted with constantly blinking LED diodes embedded into the electronics.

Distantly blinking lights of green, red, and blue, all around the dark rectangular and squarish masses.

It seems that I've been unwittingly creating a skyline within my own living room.




P.S. I found another web-augmentation to play around with. The good thing about this particular service? I don't have to do anything to it. I'm just syndicating all the existing input-services to a central location, so that bits and pieces of myself can permeate the web further. Have you ever searched for Bookhling on the Google?

http://bookhling.swurl.com/ -DEAD. Leads to some advertising website.

EDIT:

Like all things on the net, the service died away soon after. Such a shame too. It was pretty cool.

Now most of my web activities are aggregated in friendfeed site, which is about the same thing as the swurl service.

http://friendfeed.com/bookhling

augmentations

I've had a chance to encounter a service on the web called 'tumblr.' So far I like it.

Tumblr is a service that's somewhere in between the constant microbursts of the twitter and full-scale blogging of the wordpress. Only more modern, not in sense of any aesthetic faux pas, but in sense of integration with the user, like being able to post animation/picture directly from one's cell phone, rssing different services on the web and etc... More media centric friendfeed would also be a reasonably accurate description of the Tumblr service.

While I am somewhat tired of such deluge of 'web 2.0' applications that are practically everywhere these days, I do feel that the whole experience is a posititive one. Some people might argue that broadcasting one's own thoughts and lives are somehow 'arrogant' or something such because no one would care about their lives in the first place anyway... Well people who argue that point must not have enough friends. :P

Seriously though, I do not see services like twitter and Tumblr as a channel to reach out to people. Rather, such web applications are augmentations of modern human mind, something physical technology is hard pressed to catch up to. Augmentations of memories and visions one would encounter in the daily life, recording bit and pieces of 'experiences' that are separate from carefully mediated thoughts that permeate the decent portion of the web these days...

A rough continuum created to fill the vacuum left by the lack of physical technology of memories and experiences.

And when you tinker around with one of those services, you are tinkering with an augmentation service for your mind itself, albeit in crudely executed form that requires multiple intermediaries.

It is interesting how then the user's lives get increasingly intermingled with the web, as the experience of the living stands next to the fantastic shapes and movements scrounged from the remotest corners of the infosphere.

Inform 7 or HTML?

I've been thinking about creating a largely text based simulation of basic techniques and projects of synthetic biology, based on successful iGEM entries and BioBrick components. A sort of interactive fiction with real synthetic biology goodness, suitable for introducing the laymen into the world of synthetic biology and some of the more simplistic projects/lab protocols... Since interactive fictions are based on textual description (for the most part) and the reference materials one would encounter these days when attempting get started on synthetic biology are text based as well, I think it is fully possible for someone to learn the basics of synthetic biology in programmed virtual environment as long as that individual is dedicated enough and the material rich enough.

Since the whole idea was inspired by interactive novels, like the infocom Z machine interpretor, I though it would be prudent to base this project on Inform 7, utilizing their Z machine architecture that's free to use, and runs on practically any known platform in existence. The fact that the whole set of authoring tools and extensions come with the free-to-download Inform 7 doesn't hurt anything either.

However, I'm beginning to question such approach. As some of you might know, I'm working in a laboratory right now, pursuing advanced degrees. I can only do this as a hobby project with bit of free time I can accrue while working on my real job/project etc. Would it be a smart idea to actually learn a whole new language and its principles with my schedule? After all, I'm having quite a time re-learning python and mathematica as it is. And if I'm going to learn a whole new language, wouldn't it be better to learn something I can use outside the limited context of IF writing? Like HTML. It's old, but it's the back bone of the web, and other more advanced formats on the web (like XML) are still based off of the HTML codes and its structures. Not that I'm thinking of going into web design or anything, (though web design certainly has merits as a fulfilling side job for both the artist and the geek in myself, let's be realistic here) it's only that I like to have my options open. 

I wonder what i should do.


P.S. btw, I've begin to learn to use Tumblr, which I think is a cool service for random rants, short movies, and image dumping with theme. Shorter than blogging and longer than twittering.

Madscience!

Just as a side note, I've become increasingly aware of the fact that I sincerely desire to become something of a mad scientist.

Now that my ceaseless ranting with the choice of a new laptop had come to an end, I have to rant on the laptop I've chosen... A little pathetic, but this is what I do for relaxation after five or so straight hours of tweaking OS for work and crunching numbers on mathematica at the same time... Whatever the though provoking posts I have usually go on the bookhling.wordpress.com... Livejournal is strictly for venting steam and ranting for typing's sake. I love how laptops have 'Full performance mode' that can be further tweaked to give performance far more improved from the basic paper specs. I've been subjecting this laptop to so much workload that it's already beginning to stutter a bit when in any mode less than the modified 'full performance', which is no mean fit I tell you. I'm running simulations fit for a fully featured workstation.

So far the laptop experience had been satisfying. Certainly leaps and bounds better than the EEEpc 701 I've been using exclusively for past month or two. I love the keyboard. When they rave about the keyboard on Thinkpads, they aren't kidding around. This is a keyboard you can write your dissertations on... Though this 14 incher keyboard is slightly large for me, but that may be simply because I've been using the EEEpc's keyboards for too long. 

The Vista continues to annoy the hell out of me. I do admit that there is a certain degree of innocent joy in being able to tinker with your new computer for the first time, but the problem is I need to use this computer for work, and I need to work in more than one OS. Not to mention that this particular tinkering with Vista isn't to make things better, it's to make thing work...

Of course, I must add that the Vista SP1 is solid as a rock, and I've been throwing a whole lot of work load at it lately, so I think you can trust me on that issue... Vista is good at what it does (for the most part), it's only that the majority of the computing world doesn't seem to be its target audience.



Ugh, I really should stop writing about computers, but I can't help it. I think I haven't read a decent book in weeks, it's bringing this odd cramping sensation to my brain.... I really need to find something good to read.

The T400 is here.

Well, only a day after the shipment notice, I have the T400 in my hands. I'm actually writing this on my new laptop right now.

The construction and design of the chassis definitely shows the signs of being targeted at 'Business' class of users, which I'm beginning to take to mean as people who need to earn their living using computers. Yes. this computer is very reliable, and various human interfaces buttons and their layouts show careful thought and experience on allowing for greater efficiency on the part of the user. I'm new at this particular layout and am still stumbling along, but someone who are used to this particular shortcut/keyboard layout will probably be able to get a lot of work done in a fraction of the time most people would take on 'normal' layout, i.e. those commonly seen on most Dell/Toshiba laptops.

The screen is very bright, very crisp. The webcam is of acceptable quality, nothing to be writing home about. The keyboard is spill-resistant, and the tactile feedback is marvelous. I find this to be even better than the full-size keyboard I use at the lab, and definitely light years ahead of the Asus mini keyboard I've been forced to use exclusively during my leisure. Despite my worries, the size of the laptop is not as large as I thought it would be. And the weight is surprisingly light for its size. I don't really feel any real-life difference between the T400 and the MacBook I tested in the Apple store. I fell comfortable swinging this computer with one hand.

The performance is as expected, it should be considering the extensive amount of research I had to do before ordering this thing. >.> The processing speed is certainly better than my old XPS 1210, and the graphics performance is better by leaps and bounds, though I do need to perform a bit more tests later on (work comes first, right?). I am somewhat saddened by the fact that this laptop is only slightly better performing than the MacBook, (2.0 vs 2.3 ghz, ~2100 3Dmark 06 vs ~2500) but then this laptop cost me 300 dollars less for more performance, so I'm not complaining...

If there's one thing I can't stand about my brand new laptop, it's the windows Vista. Now, I'm not the one to be subject to fanboyism for a particular brand of OS simply for aesthetic preferences or menu interfaces. I regularly use all sorts of operating systems due to the nature of scientific computing, with varying degrees of proficiency... And speaking from the experience, windows series operating systems must be the most irrational and difficult operating system to handle for any sort of hard-core computing on the market. I've spent nearly four whole hours into tweaking the system so it can run the programs required for the labwork, and I'm still not finished. I still need to hunt down a few obscure wrappers and modified shells, and some of them are of different version from what I actually need, so I'm looking at some version incompatibility headaches in the future. If I was on OS X, or Linux, I'd be able to simply apt-get the required programs and let the built-in systems handle the rest... I admit that those platforms entail their own brand of headache-inducing issues, but I think it'll be far less than what I would have to encounter while using Vista. (Being able to use exe installer for python is nice, but needing to fix every single pathway by hand isn't. It's much better than I remember but it's still an issue that shouldn't even exist in the first place.)

The worst crime of all, this Vista gobbles up system resources like there is no tomorrow! Thinkpads have advertised battery life of six hours, so I was expecting at least five hours of wifi using work performance. Well, so far I haven't seen the battery life timer rise beyond the four hour mark, with the six cell extended battery. Considering that the MacBook gets 4.5 hours in OS X using similarly specced hardware and lower capacity batteries, this is simply ridiculous. I'm currently trying to find all sorts of tweaks and peripheral programs I can add on to Vista for near-advertised battery life, which is in itself a ridiculous endeavor the user should not be subjected to in the first place. I want an operating system that doesn't make its own user spend hours 'fixing it' so it can do what it's supposed to do in the first place. This is SP1 version, so it is supposedly significantly improved over the original release of Vista.

For Vista's credit, however, the interface is much cleaner than the XP version I've been using for years. The general program-side design and performance definitely felt improved, though not quite mature. Despite all the negative press (generated primarily by Apple and people with no knowledge of computers), Vista will prove to be a decent, if not good operating system on Desktops where you don't quite have to worry about limited battery life and component devices... The failure of Vista isn't quite the failure of software engineering. It's the failure of software execs who failed to predict the trend of the personal computers market.

The increased screen estate is certainly welcome. I can have a lot of stuff on screen and running all at once on this brand new system with 1440x900 resolution... Less than the 30 in screen at the lab, but more than useable on a laptop.


All in all, I love this laptop. The Vista woes might be remedied by installing a partition of Linux on it. I'll write something up on that process later.

Near the end of the drama

Well, I just got an email notifying me that the T400 shipped from HK(!) and is bound to come to my apartment sometime soon, probably by Saturday this week or sometime next week. I guess all those days of using my EEEpc for nearly everything is coming to a close...


Now I need to get a decent Linux distribution for secondary (work) use on that laptop. I can hardly wait... Though not being able to make the OS X jump this time is leaving an odd aftertaste in my mouth, especially since now I have to all sorts of secondary installs/tweaking on the vista distribution to make it compatible for work (ugh, and the fact that Windows has no apt-get repo equivalent simply pisses me off. That's one thing the next version of windows needs. Not some fancy eye candy gimmicks.)

I saw one of my colleagues using one of the new MacBook models in the lab today. I'd say the only fault in the computer, designwise, is the glaring Apple logo on the top of the computer that lights up. As much as I like Paradise/Newton reference I don't feel comfortable becoming a carrier of such an obvious corporate logo.

Oh well, maybe this is for the best.

Musing

People love fantasies. They fantasize about things all the time. Act of shaping the most compelling traits of that fantasy in real world is called art. And the process that allows the conversion of idea to shape is called technology. Look at this.



Beauty may be in the eyes of the beholder, but I think this will definitely appear beautiful in the eyes of the majority. Now, this is merely a model. But sciences and technology might as well make this come true sooner that most people expect it.

What I find truly interesting, however, isn't the shared trait between arts and sciences. That much had been obvious since the days of Leonardo Da Vinci, and the hints of the inseparable relationship between the two had been acknowledged even before then... Or rather, would it be correct to say that modern separation between arts and sciences is a freak accident of history that was given birth a few centuries ago at most? I guess we are all collectively reeling in from the aftershock of the events that happened centuries ago (and people ask why we should bother to learn history).

What I really find interesting, to an almost obsessive degree, is where the beginnings of arts and sciences came from. That is, what would drive bunch of complex systems of collections of molecular compounds to form ideas, worldview, beliefs, and etc... Whether you are a religious fundamentalist or a Dawkins-ian atheist, the fact is that most if not all of humanity have some capacity at aesthetic sensitivity that borders on mystical. Like any prudent scientist (to-be), I believe in things happening in front of my eyes rather than some abstract ideas floating in the clouds. It is a fact that people keep on creating and reacting to stuff, tries to keep themselves alive (though survival seem to take on varying degrees of priority in individuals), and are a system of molecules. So it should be reasonable to suspect that there is a method in nature to create systems of creativity out of components we already know about, using systematic pathways/algorithms that can be replicated.

What is creativity? It is a constant drive to do stuff. Is that enough? Not really. Simply being active isn't good enough... Creativity is a drive to do stuff in coherent manner. Thermodynamic work with coherence, which I might even call 'memory' though it might be too hasty at this point. Would this mean that a metabolic engine with capacity for coherent action (memory?) on the system-wide level contains innate ability to create? Like bacterium? Localized complex chain reaction with proper coherence eventually leads to self-replication? So would this mean that the human capacity for arts is in some deep level related to the capacity to procreate in minimally life-like systems?... That what would be the concept of beauty? And why would human beings pursue aesthetics/ideas outside of that necessary for survival?

It's fun to do a bit of musing like this. Yet it always get frustrating when the time to apply all this into real hard-science comes, because quite frankly, I don't see any physical way of testing all this.

All I can do at the moment, is to sit here and wait for my muse.

QR codes

I saw my cousin playing around with QR codes while I was in Korea, and found it to be cool beyond pretty much anything I've seen icon-wise. (oh, except for that multi-card/PMP/cellphone/scanner/USB/drive/creditcard/internet tablet thingie I caught her carrying around. When will U.S. get off of the morass of technological stagnation???).

Look, I just changed my default userpic to a QR code based one. How cool is that?

Living in U.S. makes me feel as if I'm living in some backwater farming town sometimes. Not that backwater farms are bad, just that it's significantly out of proportion with the level of economic/political might this nation wields at the moment. And yes, even with the failed NeoCon doctrine and falling economy this nation is a superpower, just in case people forgot about that fact.

People may be failing to participate in the major political process of this nation (i.e. voting) not because they're lazy and/or ignorant, but because the political machine of this nation and its goals are so out of touch with the modern world....

That sounds really plausible. Maybe I should do a long post on that one sometime.

recently

Just a little post to confirm my continued presence on the net.

I've been a little busy trying to pick up the pieces after my little excursion to the HK SB 4.0 and South Korea (never got around to Osaka. The school schedule didn't really let me afford that luxury. I actually had stop by school on the same day I got off the plane at JFK). The whole gradschool process is a bit harsher than I expected... Reading three books a week, doing a full report on them (for my sake, really), and pouring through the references and indexes at the end of them... Not to mention that my field of study is extensively interdisciplinary, so I have a lot of fields to cover all at once, makes me regret all the slacking off in my innocent days... On top of that I've got to brush up on some rudimentary computer skills like how to handle Linux/Unix, coding in python, and Mathematica (which I've been dabbling in a while now, though I'm nowhere near proficient as I need to be).

Oh, and I plan on doing the whole Synthetic Biology thing a full time, though my major will remain physics. I'm actually thinking of putting together NYC based iGEM team, someday ;)

Despite the crazy schedule I actually get to rest a bit on the weekends, so I guess I'm having it better than most immigrants out there with all the economy going to hell (a bit of analysis reveals an interesting trend in the current economic downturn, something I'll go back to in a later post).


As I've continuously whined about past few months, 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 had 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 1440x900 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 (with its better graphics performance) like some primal impulse beyond the reach of civilized consciousness.... (insert witty H.P. Lovecraft reference here)       

Catching up with life.

Another update after four weeks of silence. I can't help it. The life's been keeping me busy lately... I guess it beats having nothing to do. I won't be updating much for the next few weeks since I have to attend the Synthetic Biology conference 4.0 in Hong Kong, stop by Korea, possibly Osaka, and see my much missed family members. Not that I'm complaining. I love traveling.

Despite my lack of update on the web, I've been writing a lot. I think I filled up about three notebooks with writing in past few weeks. Most of them are lab journals, and most of the writings are of technical nature, of course. There are some more contemplative/creative its thrown around in there somewhere though. It's only that I can't find the time to update all my physical writing into the digital form, and typing on the computer is not always available despite the 7in compact laptop I've been using (extensively) for the past few... Months. Maybe I'll post something of more substance once I finally get some time to waste.

I've been using the friendfeed and twitter service extensively for the past few months, and I must say that I quite like it. Both services are practically tailor made for community oriented professional networking, between scientists and other such people who need to communicate wide variety of ideas and informations on a moment to moment basis without spending a whole afternoon blogging about it. It's true that most of the stuff on those services are rather without substance (what they're eating for breakfast etc), but as long as you know how to subscribe to the right kind of room/people, the amount of valuable information/insight that opens up to you is enormous... It's interesting to note that the vast majority of the scientific community presence on friendfeed/twitter tend to be those of biological background. I guess that's the impact of bioinformatics and increasing prevalence towards treating living organisms as chemical information processors (of sort). What happened to all the physicists and chemists though? They should all wake up and smell the cupcake, I think.  

Four weeks since last update?

I can not believe that it had been four weeks since my last update to this blog. Maybe Livejournal should include a functionality in their service where a warning email goes off once you do not post for significant length of time....

Now, I have been busy these four weeks or so. Crazy busy. First the moving to my beautiful new apartment, which I did all by myself, then taking care of my fathers remarriage, his citizenship test tutoring, multiple school stuff deadlines (in preparation for gradschool!), and the io9 synthetic biology contest I must have mentioned a few times in this blog and beyond. 

All of that with my main laptop still broken, so I am still working/playing on this finicky little 7in. laptop called Asus EEE. The default linux distro on this machine is not quite so hot either, and the keyboard goes into a panic whenever I try to do something like Im.... See the lack of punctuation mark over there? The B key does not seem to like getting pushed either. And the hilarious part is that the machine itself is working fine. There is simply something wrong within the OS itself... Something I probably tinkered with.... The replacement board for my laptop will arrive soon, but I plan on purchasing another laptop anyway since the old one is, well, old. I am on the fence between new macbook update supposedly in preparation for September 15ish announcement, and a thinkpad.

Now that things are beginning to gain some semblance of peace at last, I think I might be able to update on this blog quite frequently now... Hopefully.



Now that I think about it, I spent the whole summer working! Now the summers gone and schools are starting... Ugh.

Bit of an update

I have not written to this blog in a while... Or any blog, for that matter.

My schedule had been rather hectic with all the school stuff and the aforementioned io9 contest preparation, as well as some arranging for the October Hong Kong trip.

Right now I am waiting for the update in the Lenovo thinkpad line so I can get a decent new laptop for once in my life (my xps 1210 had aged badly, with the faulty GPU). Apparently current t61 generation will be updated to t400 in early August (5th they say, but I am not too sure about it), so I might as well wait it out and get the newest option, especially since the performance gap between Santa Rosa and Montevina platform in laptops seem to be rather significant.

Ugh. I hate it when I have to wait for things. Humanity simply must discover a way for time travel sometime in the future.

Abstraction=Engines of art

Note: This is something I have also posted on my other blog. Might be an interesting read.

The update at this blog had been intermittent for a while due to my personal circumstances, with moving to a new apartment, and the need to write up bunch of papers happening all at once. Now that I am a bit more settled I should be able to write here regularly. At least I hope that is the case… I do not think I can handle as much workload for a while.

I have always been interested in writing things. Writing is something that comes natural to me, in that while I am certainly not good at it, I can always pick up a pen or sit in front of a keyboard and scribble/type away as I drift away to a state of reverie. It is the same as with reading a good book. There is no need to force myself to concentrate. The process is quick and natural like playing an old instrument while intoxicated by its melody, a sort of self-reinforcing phenomena.

As such, it was only natural that I would try to fulfill my predilection toward the ever vague idea of beauty. I have always been puzzled by the nature of beauty since young age. I can tell for sure when something is beautiful to me or not, yet it is quite impossible to pinpoint the specific quality of the thing/person/situation that makes it appear/smell/feel beautiful in my senses. There is no consistency in the things that are capable of displaying the traits of beauty, as a garbage can and a work by Michelangelo might display the similar sense of sublime, that strange trait that we can only refer to with the vague term called beauty. And this *beauty* appears quite immaterial. I do not believe there is a single thing in this universe capable of appearing beautiful to all observers for all lengths of time. The trait of beauty can be highly subjective, and is bound to fade away after a period of time (when in view of a single observer) regardless of the hardiness of the physical material that radiates the feeling of beauty in its observers.

Would such traits suggest that the beauty literally is in the eyes of the beholder? There is no evidence to think that inorganic objects in this world is capable of reacting to certain objects in a way that an organic, conscious object would react to a thing of beauty. So it would be possible to assume that the ability to perceive beauty and react toward it in this world is limited to complex life-like systems (this is an assumption based only on what we know about complex systems and the physical relationships within the universe at the moment, of course). Yet the problem does not quite end at that point. Prokaryotes are complex life-like systems, yet can we possibly assume that such microbiotic systems are capable of feeling the thing we conscious human beings refer to as beauty? I have never talked to a prokaryote culture before, so I would not know. Let us re-examine the trait of beauty and beautiful things in this world for a moment. From what I can tell, beauty requires significant amount of neuronal resources in terms of sensory organs and processing units, aka the CNS. Would that mean that the ability to perceive beauty must be limited by the capacity of the senses? That external catalysis of sorts is always required in order to perceive/imagine beauty? It might be tempting to say yes to such an assumption, but I think we must remember that there are plenty of things in this world that are considered beautiful despite having no physical counterpart. Beautiful ideas. Beautiful future. Such are more or less information based constructs that might be represented by certain physical objects and situations in this world but not tied to the specific characteristics of the material. If beauty is intimately tied to its nature as a construct of information, then it is possible that the ability to perceive and react to beauty is intimately tied to the information processing capability, like the brain, which is in itself a vast complex adaptive system.

I think we might be onto something here. If the things I have outlined above have even a modicum of truth in it, the illusive nature of beauty might in fact be tied to the informational structure of the brain and its interaction with the external world, within which learning and memory themselves might act as catalyst between the world and the brain in perceiving and reacting to beauty…

Here is a million dollar question. If the immateriality of the concept of beauty and its acting in concert with innate mechanisms of brain and memories are true, would it be possible to write a finite-length work capable of giving persistent impression of beauty by conjuring up any and all images and ideas that can be felt/perceived by the readers mind? Would it be possible to write a piece that can simulate almost infinite gradient of human ideas and feelings within the readers mind by the virtue of ever changing yet persistent nature of human memory and innate information processing capacity of the human brain itself, using only limited number of imageries and terms that can be utilized in a single work of writing? The idea behind such a writing would be similar to the idea behind the evolution of natural language, of how limited number of alphabets are capable of composing rich vocabulary and astronomical variety of written, spoken works and ideas born from those works. Instead of alphabets, however, the work would have to discover and utilize certain archetypes of ideas, patterns and imageries as to make it possible for the reader to create something entirely new every time he/she reads it, the only characteristic shared between the infinite variety of reconstructions being the persistent presence of the indescribable beauty.

The ideas of artscience and artificial life takes on an entirely different perspective when viewed in such light. Artificial life would no longer be static art, but rather an *engine of beauty* in a persistent yet ever changing universe. Just as Kurzweil proposed the universe of meaningful information, artificial life might as well be the first step in a whole universe of sublime beauty.

Engines of Art

The update at this blog had been intermittent for a while due to my personal circumstances, with moving to a new apartment, and the need to write up bunch of papers happening all at once. Now that I am a bit more settled I should be able to write here regularly. At least I hope that is the case… I do not think I can handle as much workload for a while.

I have always been interested in writing things. Writing is something that comes natural to me, in that while I am certainly not good at it, I can always pick up a pen or sit in front of a keyboard and scribble/type away as I drift away to a state of reverie. It is the same as with reading a good book. There is no need to force myself to concentrate. The process is quick and natural like playing an old instrument while intoxicated by its melody, a sort of self-reinforcing phenomena.

As such, it was only natural that I would try to fulfill my predilection toward the ever vague idea of beauty. I have always been puzzled by the nature of beauty since young age. I can tell for sure when something is beautiful to me or not, yet it is quite impossible to pinpoint the specific quality of the thing/person/situation that makes it appear/smell/feel beautiful in my senses. There is no consistency in the things that are capable of displaying the traits of beauty, as a garbage can and a work by Michelangelo might display the similar sense of sublime, that strange trait that we can only refer to with the vague term called beauty. And this *beauty* appears quite immaterial. I do not believe there is a single thing in this universe capable of appearing beautiful to all observers for all lengths of time. The trait of beauty can be highly subjective, and is bound to fade away after a period of time (when in view of a single observer) regardless of the hardiness of the physical material that radiates the feeling of beauty in its observers.

Would such traits suggest that the beauty literally is in the eyes of the beholder? There is no evidence to think that inorganic objects in this world is capable of reacting to certain objects in a way that an organic, conscious object would react to a thing of beauty. So it would be possible to assume that the ability to perceive beauty and react toward it in this world is limited to complex life-like systems (this is an assumption based only on what we know about complex systems and the physical relationships within the universe at the moment, of course). Yet the problem does not quite end at that point. Prokaryotes are complex life-like systems, yet can we possibly assume that such microbiotic systems are capable of feeling the thing we conscious human beings refer to as beauty? I have never talked to a prokaryote culture before, so I would not know. Let us re-examine the trait of beauty and beautiful things in this world for a moment. From what I can tell, beauty requires significant amount of neuronal resources in terms of sensory organs and processing units, aka the CNS. Would that mean that the ability to perceive beauty must be limited by the capacity of the senses? That external catalysis of sorts is always required in order to perceive/imagine beauty? It might be tempting to say yes to such an assumption, but I think we must remember that there are plenty of things in this world that are considered beautiful despite having no physical counterpart. Beautiful ideas. Beautiful future. Such are more or less information based constructs that might be represented by certain physical objects and situations in this world but not tied to the specific characteristics of the material. If beauty is intimately tied to its nature as a construct of information, then it is possible that the ability to perceive and react to beauty is intimately tied to the information processing capability, like the brain, which is in itself a vast complex adaptive system.

I think we might be onto something here. If the things I have outlined above have even a modicum of truth in it, the illusive nature of beauty might in fact be tied to the informational structure of the brain and its interaction with the external world, within which learning and memory themselves might act as catalyst between the world and the brain in perceiving and reacting to beauty…

Here is a million dollar question. If the immateriality of the concept of beauty and its acting in concert with innate mechanisms of brain and memories are true, would it be possible to write a finite-length work capable of giving persistent impression of beauty by conjuring up any and all images and ideas that can be felt/perceived by the readers mind? Would it be possible to write a piece that can simulate almost infinite gradient of human ideas and feelings within the readers mind by the virtue of ever changing yet persistent nature of human memory and innate information processing capacity of the human brain itself, using only limited number of imageries and terms that can be utilized in a single work of writing? The idea behind such a writing would be similar to the idea behind the evolution of natural language, of how limited number of alphabets are capable of composing rich vocabulary and astronomical variety of written, spoken works and ideas born from those works. Instead of alphabets, however, the work would have to discover and utilize certain archetypes of ideas, patterns and imageries as to make it possible for the reader to create something entirely new every time he/she reads it, the only characteristic shared between the infinite variety of reconstructions being the persistent presence of the indescribable beauty.

The ideas of artscience and artificial life takes on an entirely different perspective when viewed in such light. Artificial life would no longer be static art, but rather an *engine of beauty* in a persistent yet ever changing universe. Just as Kurzweil proposed the universe of meaningful information, artificial life might as well be the first step in a whole universe of sublime beauty.

Finally.

Most of the stuff related to moving to the new apartment had been settled, and now I get to write by a new window of a new place. Finally I'll be able to have some regular presence on the web again.

Sometimes it feels as if human beings are tagging along on a ride of evolution of ideas... Whatever the ideas are. Plato never quite figured out himself it seems. Is it possible for a human being to be so captivated by certain archetypal form of idea/idea processing as to act as an extension of the incorporeal idea upon this universe?

I believe such people are usually called lunatics.

Curiosity

Something just came to my mind.

The Harry Potter series gave birth to a whole generation of readers. Now that the series is over, what are they reading now? What kind of books in what genre?

The moving is going smoothly, albeit a little hectic. The integrated heating/ac system in these new buildings are quite charming.

I haven,'t had much time to hone my syn bio studies, with all the school works converging on me during this transition period and all. Considering that I plan to be in Hong Kong this October for SB 4.0, this is a rather pathetic state of affairs. I hope I can make some substantial progress by the end of this week.

The days

I've been just a little too tired to make a decent post lately. I've been pushing myself at the lab, working out some models.

There are a few things I've been thinking about writing, and probably will do so by the end of the week.... Eric Drexler's predicament and future of nanoassember concept, or the nature of information and its relation with the practice of art? Hmm.