Sunday, May 31, 2009

Consider distraction

I spent the morning reading an article named 'in defense of distraction' (http://is.gd/KAem), also on my blackberry (meaning that I'm typing this on my blackberry as well, thank god for copy&paste). Interesting stuff, it's probably one of the most widely debated topics in recent memory. I think I might as well jot down a few notes before the meta reference surreality wears off.
 
My take on the story is this:
The world is definitely suffering from some sort of ADD but it's not the kind of doom and gloom story some people like to portray it as. Rather, the flood of information in recent ages might simply be emphasizing a problem that had been inherent in human society for a long time... The light only serves to reveal what's been there all along, not create new stuff out of the dark, so to speak.
 
People get so caught up in technology when talking about change, that they often lose the sight of the real problem. The information technology and subsequent increase in information distribution and uptake doesn't really matter. What really matters is how it might reduce productivity of the masses exposed to the new century saturated with information by providing endless sources of distraction when they might be doing something productive, maybe even important.
 
But you see, most of the modern distractions are distractions of choices. People choose to get on twitter. They choose to read emails and they choose to answer their blackberries/iphones. None of the modern distractions are forced on people (except in some cases where people make living off of it) and it is possible to live like a medieval monk if you choose to do so.
 
When you get right down to it, this is the issue of willpower and motivation in society. Face it, for most of us life is a kind of drudgery, and we struggle to get free from the limitations of the world around us through distractions. If you're living like a slave chained to a galley you can't be blamed for getting distracted by every shiny thing that comes along. Unhappy people are distracted easily.
 
Contd
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Wednesday, May 27, 2009

Architecture

It's been a while since I've written something of interest on the blogs, and that trend will probably continue for a while. Despite the brief respite of the summer I have a whole bunch of things planned for the summer, mostly things to study before the summer's end. In between works, write-ups to do, and the references to sort through there doesn't seem to be much free time for anything else.
 
One of the things I'm studying during the summer is architecture. Nothing too formal, mostly on the theoretical side of things. I'm interested in studying architecture of the fantastic, utilizing the manipulation and configuration of space. When put in such context design of buildings become aesthetic, philosophical exercise, and there are some quite interesting utility to that. Like an entire fiction built around the concept and practice of architecture. The characters become more of ornaments on a gothic building, each of the facades coming together in hundreds to form a general pattern that leaves the shaped marbled and hardstones to shaping and manipulating the very nature of light itself within the building. From the cold, rough beginnings of material endeavor emerges the aetheric architecture of shaped and colored lights, dedicated to the very pinnacle of platonic ideas.
 
The architecture as narrative is especially interesting to me since I think I've been practicing it without knowing what it is for a while now. A lot of the creative writings I've done over the years rely heavily on formation of the spaces around the characters, using the world itself as main motivator for the characters within the stories. The world itself increasingly took on resemblance of a huge, sprawling architecture exercise of the fantastic bent, a lot of it inspired by the dreamlike worldscapes of Mamoru Oshii as exemplified by his earlier work like the angel's egg (when I think about it Mamoru Oshii also has a very vivid architectural imagination, with reoccuring imageries of museums as gigantic wunderkammers at the cross-section of the material and the ideal). Many of my longer works, both texts and images, always end up having images of fantastic cathedrals and the curtains of light, gigantic whale-like structures both organic and artificial slowly swimming across the skies, life-like yet impossible sculptures, unreal cities and winding alleys, ancient libraries and museums of the world. I've always loved those things and with better understanding of the philosophy of architecture maybe I can write/draw something even better, perhaps even in time for this year's nanowrimo.
 
A good source of the kind of architecture theories and practices of more esoteric kind is the bldgblog.blogspot.com I'm even thinking of picking up a book of the blog's author.
 
Combined with rapid computerization, advanced manufacturing, nanotechnology and synthetic biology, we might not recognize architecture in a few years. And I like that. The world is changing for the better.
 
It's pretty crazy to be writing stuff like this on my blackberry at 4 in the morning, but I seem to have hard time falling asleep these days. Maybe I should try to have another dream of the architecture.
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Friday, May 22, 2009

The day's end

Now I'm sprawled over the sofa contemplating whether to go to sleep or read a bit more at the day's end. I move around a lot so being in a new place doesn't make me feel one way or the other... I think whatever I'm feeling is probably something like either a fear or the anticipation of the future.
 
It's the summer, and now I have a bit of spare time to get things done outside of my usual internship/sidejobs/the stuff that pays the rent. I've been thinking of what to do with this summer, and I think I'm going to turn this one into a watershed moment of sorts in my life. I'll be working on several self-improvement projects that will in turn help me to get to better places in the future.
 
The first and foremost of the things I want to work on is the basic knowledge of biology and lab techniques. Maybe I can take a simple associate's degree or technician level class at local college outside of my real studies. I'll also be studying an entry level complexity science textbook with goal of finishing and completely absorbing its content by the summer's end... Completely absorbing meaning digging into the mathematical techniques as well as outside references written in the book's bibliography. In fact, I've been making some strides to that end already, with my new complexity science text book that arrived here about a week or so ago. It's been quite intriguing with the topics ranging from biological signals to chemical oscillators forming greater systems, a treasure trove of informations that can be adapted to synthetic biology/biobricks project in a heartbeat, provided with some level of ingenuity.
 
I'm also thinking of studying a bit more about the Renaissance Italy, with eventual goal of culminating the study with a lengthy essay on the coming future as the second renaissance of humanity and just what kind of forms it would take with the kind of financial base and technological/industrial expertise available to us. It's been shaping up to be an interesting experience so far, devoting significant amount of time to the growing artscience trend and the rise of hackerspaces, biological and otherwise, while comparing them to the master workshops of the Renaissance.
 
Of course, there's also the project I've been working on with another diybio member using the processing language. It's a project to build a DNA organ or sorts (organ meaning the musical instrument), generating graphic and aural patterns based on the DNA sequence entered into the device.
 
This summer is beginning to feel like a good chance to turn my life around for the better. If successful, the things I can gain from the experience will go a long way toward making my dreams come true. Sent via BlackBerry by AT&T

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Saturday, May 16, 2009

purification

 
The problem with running a heavily networked life that spans multiple email addresses and filters delivered near instantaneously to handhelds and other devices:loosing password messes everything up. I had to frantically try to find my lost password at 3 am last night/this morning.
 
About three days ago our little diybio group participated in a little purification experiment that lasted multiple hours of sleepless concentration.
 
The experiment is based on the results of the previous session of diybio that involved transforming K-12 E.Coli by introducing GFP plasmid into the cells. The previous session was a huge success (had to be, with multiple biology people of advanced degrees leading the session under very controlled environment) and we finally obtained that mysterious gateway product, the glowing living cells.
 
The purification experiment refers to the process of purifying the noble proteins produced as a result of introducing foreign plasmids into a native cell. In this case we were trying to extract a purified essence of the GFP proteins produced as a result of introducing GFP plasmid into the living cell. 
 
The earlier steps of the session was an elaborate reproduction of the strawberry/etc DNA extraction experiment we did before, though this time we were using advanced tools and precision measurements under carefully controlled environment. It involved lysing the cells and then treating the end product (pellet) with variety of bonding chemicals to isolate the proteins from other inner organelles of the cell, centrifuging the resulting protein complexes for filtering them out of the cell innards and etc.
 
The resulting extract is a beautifully purified essence of GFP proteins in liquid format that glows green under ultraviolet light. From what I know this is the same process that scientists use to extract purified protein complex for x-ray crystallography (as demonstrated quite beautifully by the documentary Naturally Obsessed: making of a scientist). Proteins are based on codon sequences, which means that they are ordered structures though not necessarily in the same way as it is with RNA and DNA. One of the universal traits shared by ordered molecular structures is that they are susceptible to crystallization under the right circumstances. This process is also used for extracting protein products from engineered cells for pharmaceutical purposes.
 
It's rather amazing how simple the procedure is. Of course it would require some amount of study to fully understand the theory behind the extraction method, but the protocol itself doesn't require much in terms of prerequisite knowledge. DIYbio is born from the belief that majority of the techniques composing the biological sciences are simple enough for the laymen to execute on their own, and this session demonstrates the validity of that idea perfectly. It may not be obvious to some, but the fact is bunch of people who have no background in biological sciences (with help of a professional) succeeded in performing manipulation of living molecular systems to produce designer molecules and extracting them for further research. Who would have thought it?
 
The general atmosphere and execution of the diybio lab sessions are beginning to remind me of the workshops of the renaissance. People gathering into one place for vibrant pursuit of multiple areas of research, indeed the modern concept of hackerspace itself is an extension of the old renaissance contraptions reinforced with modern economy and technology. Am I going too far in thinking that the world itself is slowly edging towards an age of a new renaissance of humanities and technologies, freed from the monolithic research and industrial complexes that defined the late twentieth century? 

I would love to write more about this particular topic but I'm afraid my mind is rather dull this afternoon. Maybe I will return after a bit of outing to get my blood circulating again. 

Tuesday, May 5, 2009

Testing

Testing my wireless connection. The net seem to be acting up today.
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Sunday, May 3, 2009

Mobiles

I'm sitting in a bar at the GC waiting for the darned train to arrive. I've went through most of my books and don't feel like straining over study texts I have compiled on my ebook reader. So here's a bit of rant on mobiles written on a mobile: my blackberry.
There are five major mobiles that are set to change the market in one form or the other. Here, by mobile I'm referring to what most people call 'smartphones.' You see, mobiles are like very weak, small computers with ridiculously good battery life. Meaning that unless you are trying to calculate coefficients of turbulent plasma at break-even temperature the hardware doesn't matter as much. Maybe for playing graphic intensive games and bragging to other kids, but outside of that what really matters is the software, the operating system. Operating systems are composed largely of two things, at least when we are talking about mobile systems.
1)Interface: interface as in interfacing between the human user and the circuitry guts of the mobile device that crunches numbers. Anything between the machine and the user is part of the interface. The screen, the keyboard, if any, the software installation routine, backup methods, email/message push techniques and how they are represented on the desktop, whether there will be a 'desktop' or not, the size of the machine to the color scheme and extensibility of the interface itself by the user which covers everything from applications to skinning. It's mind boggling. And with the limited size of the device combined with lack of universal specification it would be possible to write an encyclopedia on the issue.
2)Kernel: I'm no specialist when it comes to computing (scientists only use computers well. Knowing about computers is a whole different issue), so I'm just going to call it kernel like it is with linux. I'm talking about the very core of the operating system that is in the end a collection of filesystems that put stuff together so that the machine can process information in a form that is coherent to human beings. The nucleus of the cell that is the mobile device. This is the part that more or less remains the same across most devices, mobile or desktop, though mobiles to go through quite a bit of optimization aimed at reducing unnecessary processes to lengthen battery life.
 
Conventional 'mobiles' that aren't smartphones really don't fulfill the above two criteria of having an operating system. What they have are one-way java sandboxes with no real filing system to speak of, a one-way interpreter with no real way to compose content on those machines. The difference between regular cellphones and smartphones is the difference between a 99c calculator and a laptop.
 
So there are five mobiles that are set to change the ecosystem of mobile market for better or for worse. And the name of the mobiles are not names of the machines or their manufacturers, but names of the operating systems, some of which can be adapted to practically any machine with decent cpu and human interface.
 
Android, iPhone OS, WinMobile, BlackBerry, and Symbian. Each of those operating systems are results of the fantastically interesting evolution of human computing paradigms dating back to the days of mainframes and UNIX, the beginnings of the digitization of human society. Android, iPhone OS, and Symbian operating systems are direct descendents of the old UNIX systems that are still used to run the vast majority of real supercomputers across the world. Doesn't matter where you're from. The supercomputers North Koreans use in rocketry and nuclear weapons engineering runs a flavor of UNIX, albeit heavily modified, but still descended from the same origin as the UNIX based mainframes I use in my school. By descendent I'm not just talking about historical relations. I mean real codes, real architecture that still lives and breathes in all those operating systems from the mainframe that calculates some despot's hidden bank account balances to UNICEF's tracking data for sixty million insect nets and vaccination data for seven million children spread across half the world. And, of course, the laptops and mobiles as well, Android, iPhone OS and Symbian. Winmobile is a product of an attempt at producing commercial GUI based operating system that is itself inspired from UNIX based operating systems, though the main windows operating system is still playing catch-up to the dinosaurs of the past. BlackBerry OS is a hybrid of the java sandbox approach used in conventional cellphones with more conventional operating systems approach, built on top of a huge java virtual machine that translates human-readable computer code to machine code. The core of the BB operating system, the Java, is itself a product of the computer age, a distant cousin of the aftereffects of the operating systems revolution that more or less trace its lineage to UNIX, with the intepreted language structure tracing back to the grand-ancestors of all programming languages and de-facto artificial intelligence/mathematics modelling language called Lisp.
 
Each of these mobile operating systems have diverse technical/cultural/economical background to them that I can't go into detail here, with the limitation on the time and space (that train's going to have to come sooner or later, right?), but it's all quite fascinating and worth looking into if you're interested in that sort of thing.
 
The fact of the matter is that the five operating systems serve different types of customers at the moment, though not necessarily single type of customer.
 
Winmobile's primary customers are business users, not because winmobile operating system is great, but because it's the most widely distributed operating system that interfaces with the most widely distributed desktop operating system on the planet. Of course Winmobile is better built compared to its desktop cousin, with variety of push messaging technology and cryptography patterns built into it. It's only that the platform as a whole is significantly outdated compared to the competition and the interface portion of the operating system is almost painful to use.
 
iPhone OS's primary customers are twofold. First would be what I would call 'average joes.' Basically people who want smartphone without worrying about it too much. The remarkable interface design and resilience of the UNIX based platform (meaning it won't crash too much) makes it easy for first time mobile device user to approach it. The second class of users are professionals in scientific field who don't want to deal with nitty gritty details of the operating system yet want a powerful scientific programs and libraries they can access on the go. The UNIX based core means that it is relatively easy to develop applications for the mobile platform with minimal overhead, especially considering that most scientific applications are already running on UNIX operating systems.
 
Android OS, as the youngest one of the mobile os sibilings is still trying to find its niche. Though as an open platform that can be run on practically any kind of hardware with capacity for anyone to write java based programs for the operating system is quickly shaping up to be the coder's platform of choice, offering an intriguing mix of variety in applications ranging from torrent, augmented reality, shopping helpers to video streamer/editors and stock traders. There are moves to bring some portions of the Android os platform to third world computer/networking solutions, and from what I hear they are shaping up nicely.
 
Symbian is another UNIX/Linux based distribution for mobiles, though you need to use C/C++ language with rather incomprehensible set of libraries if you want to program for the operating system. Also, the symbian platform is closed source and until recently you needed to purchase a license to even program for the platform. The target audience for symbian tend to focus on the media-savvy and coders who want variety in their programs, something of a cross between Android and iPhone OS's target audiences.
 
BlackBerry operating system is a huge virtual machine optimized for BlackBerry hardware, based off Java. BlackBerries are commonly referred to as information junkie's main device. While lacking in freedom and variety of the applications, BB still offers significant stability and ability to organize through massive amount of information: webpages, texts, contact info, emails that number into hundreds. It's surprising how much information get passed around in form of text in this day and age.
 
Well, that's it for my short-ish overview of the mobile operating systems available at the moment. My wine's almost done and it's time for me to leave... I must say, I forgot to mention the web OS being developed by palm, but it isn't out on the market yet, so I guess it doesn't count. Maybe later.
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 I didn't really have time for leisure writing lately. What can I do? It's the finals/deadlines season, and I've been busy out of my mind just like every other students in this part of the country. Of course, it didn't really help that I don't have much to write about, just the typical musings on arts sciences and things I do as part of my research, things that doesn't really belong on this personal blog. I did lock down my livejournal blog to friend-only however. As the diybio-nyc slowly gains some degree of prominence there's a lot of people browsing around content I have on the web, and there are somethings on here that I'd like to keep private if possible. All my other blogs and web-based contents like tumblr/twitter are all still public though, and I have no wish to keep them locked into privacy. I mean, what would be the point of social media if it's locked down from being social, right?

The keyboard on thinkpad saved my life a few times this semester, in those all-night coding/calculating/writing/simulation sessions with deadlines staring at me beyond the sunrise. I've used many laptops and this one certain beats the pants off the rest, especially most of those generic offerings from Dell/HP (though their business class lines have decent keyboards as well). I've also found Apple's keyboards to be quite responsive as well. Although I don't personally own an Apple computer there's a few at the lab I use for imaging/running simulations. The Mac pros at the lab are the standard workstation quality desktops offered by Apple, with 18GB of RAM and 8 core processors, they are like small supercomputers and quite fit for pretty much anything I can throw at it (and people complain about how underpowered Apple computers are --;).

The weather's like summer now. It's been slightly colder for past day or two but mostly it had been warm enough to walk around outside without any jacket on. The flowers and trees are blooming nicely, and there are some flower blossom events scheduled at local conservatories and Botanical Gardens. Quite beautiful, and all this abundance of life is making my heart feel at ease. At least I think it's a nice change from the scalding cold of the winter. The warm-yet-not-quite-hot weather is a perfect opportunity to open up all the windows and let the fresh air in. Since my apartment is right next to a park, whenever I open up the windows the whole apartment begins to feel like middle of a forest. When the wind sweeps through the forest I can hear the leaves crashing like the ocean, a perfect occasion for some nice cup of green tea, though I've taken a liking to some western white tea servings as well. There's something innately attractive to a simple cup of tea accompanied by a small dish of sweets like mochi or cheese cakes. How should I explain it? Such experiences make me feel awake and focused for some reason.

The coming of the summer is obvious in the air. It'll only be a few weeks before the summer comes full-force. The change in flora&fauna is more obvious when I go outside in the morning for jogging, something I've more or less stopped during the cold of the winter (in the coldest days it was actually possible to freeze to death out there). I usually jog around the park beginning 4~5 am, and the whole session usually takes an hour to hour and a half. I walk through bridges on a lake, a wide grass field (New York Philharmonic orchestra plays here during summer), and a bit of mountain/forest. The change in weather is felt not through the change in temperature (it's still quite cold early in the morning) but through the smell of living things, the plants and trees emitting their distinct aroma of green into the morning air, and the feeling of dissipating morning dues soaking into my skin. By the time I see birds flocking in the air the sun comes up, throwing its rays that feels warmer than ever. The sunlight at this point of the day is something I would recommend anyone to go out and enjoy. While it doesn't have the quiet beauty of the twilight, the purity and warmth of the light is such that it almost feels like reflecting through your very heart, as if the thin rays of the light shines through the matters of the world in some higher dimension in their travels.

The warm weather reminds me of a lot of things, among them are the memories of good games I've played. It sounds weird, but for some reason warmer weathers always remind me of the days when I was into playing emulator classics and the first diablo game was the newest kid on the block... That was quite a while ago, when most people still had dial-up. I remember cutting class one day in middle school to go out to the city and buy a copy of diablo. I came back home with high anticipation, and practically spent the whole night engrossed in the game. I also remember the game Xenogears for PSX as related to summer. Quite possibly the game with most engrossing story ever, I still remember the memorable dialogues and characters by heart. There was something about that game that reminded me of Bach in some of the imageries, I think that was also the time I was big into classical composition, and wrote a play that later helped me get into a sort of gifted-children program for high school students.

The summers generally leave great memories for me. Lot of horrible things happened, of course. My life wasn't easy by any stretch of imagination, fighting down debtors who'd knock on my doors at eleven in the night. The feeling of the summers, however, come from the many amazing people I've met throughout the summers of my life (I travel in the summers. I bought my own air ticket and traveled on my own ever since I was in sixth grade), as well as the fact that summers are the time that I've devoted myself wholly to some sort of pursuit. One time I drew all the time for two whole months. I would literally wake up six in the morning, go out to the central park/the Met/libraries and draw until my hands hurt. In the evening I would come back home and draw until late into the night. In other summers I would write to the extent that all I could think of was the imageries and characters of the piece. I would sketch out the individual scenes and then write on the sketch, trying to feel the very smell of air in that imaginary places as I wrote about the light and shadows composing the place of words. And of course, gaming. I must have devoted close to 200 hours on the game, maybe more. I would complete it and then play it again and again. I've discovered all secret items/characters/events in that game through multiple playthrough. I even managed to use certain system glitch in the PSX console to uncover contents that were left unreleased yet printed into the programming codes of the game. I had quite a blast doing those things with my pals, camping out in the living room for days at a time.

I've come to understand something of myself over the years. Pleasant memories in my mind always match the periods of intense concentration and devotion to pursuit of something, whether it be sketching, writing, painting, violin (I've played until my hands bled, and I was happy about it), or digging through scientific literatures. Now that summer's come again maybe it's time to find something else to obsess over, perhaps go for another round of travel to other corners of the world. There are quite a few options open for me right now. I can always take an internship at a lab somewhere, maybe even in Europe. I'm already putting together a resume for the scienceblogs HQ in the city. I can devote my summer to the diybio, finding labspace and even work on that artificial cell project I've always wanted to do. I can travel around HK/Korea/Japan like I usually do, sleeping at my relative's places, though I've been around those places so much it's starting to get a little boring. Or I can work on something that might someday become my dissertation, prep my future so to speak. Whatever I do, I want to do something that will really take my mind away from the private circumstances surrounding me. Throughout my life I've learned that obsessive pursuit is about the only thing that puts my heart at ease. I wonder if this is normal for others as well.