Textdrome

Jaron Lanier and the fall of Opensource

2010-07-14T10:58:00.001-07:00

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

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

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

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 When a whole culture based on ideals of innovation and sharing begins to look outdated and conservative next to hulking multi-billion/trillion dollar corporate entities, they are in trouble.

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

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

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

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

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

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The problem of modern web-centric age...

2010-07-08T00:35:00.001-07:00

...is that there are just too many places we leave our trace on, some of them worthwhile, some of them meaningless... And I keep on forgetting passwords to every single one of them.

I just finished the process of moving my posterous accounts around, and it seems there was some sort of mistake in linking different blog together (gulp). My blogspot blog will be updated as usual, since whatever I write on posterous will be autoposted to the blog. So my faithful readers on google's blogging platform, there's no cause for worry. The whole note thing about not writing there anymore was actually for the posterous blog that was feeding to the blogspot blog that I've deactivated. I'd get in there and erase it to save everyone (and my oblivious self) from confusion if it weren't for the fact that I forgot the password to the blogspot page. Hopefully I can remedy this situation in the future when I figure out my own password from the deepest recesses of my primal memory.

Now that the boring stuff is out of the way, some update on the community biotech lab we're building in Brooklyn. I think I still can't share the intimate detail of the experience with you all yet (look forward to the Genspace webpage for whacky adventures of amateur biologists later on!), but it's been amazing. The excitement and passion of all the members who've pitched in their time/effort/money is just inspiring... It took us a year and a half of work, but we finally have a BSL1 compatible labspace where one can pursue dreams without the barriers of bureaucracy and politics, and moving boxes and boxes of lab materials/equipments in middle of heatwave today was totally worth it. Me and other members of the group will be putting together our experiences into some single resource so that anyone around the world can use it as references to start their own community science laboratory, so be on a lookout for that. It'll be chock full of juicy information about how to get supplies, how to find physical spaces, how to figure out a monetary stuff and etc etc, along with other will-be classics like 'Synthetic Biology Crashcourse for Kids!' courtesy of ex-iGEMer and honorary DIYbio dude Zhou! There'll be some huge announcement of the next phase of our public activites within few weeks as well. I wasn't kidding when I said 2010 will be the year of DIYbiology earlier this year.

No part of blog posting on the net in modern era is complete without some talk of computers and hacks. I have two words for you. Next HOPE (Hackers On Planet Earth)! It starts next week on the 16th (which is incidentally the opening date of the movie Inception) and I'll be there in one form or another... Being a perpetually broke student I am I can't really afford the $85~$100 entree fee so I'll either be working as a volunteer or find some mysterious workaround that will net me access privileges. Make sure to check out their page if you're even remotely interested in hackers. HOPE events are one of the grand-daddies of hacker-centric events.

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Note

2010-07-04T23:15:00.001-07:00

I kind of screwed up the blog import function over here, so I'll be using http://seabook.posterous.com as my primary posterous account in the future...

Posted via email from Between Motion and Act

How to use computers

2010-07-04T23:13:00.001-07:00

The reason Alan Kay got into computers in the first place. It's not about hardware, software, or even user interface. It's about augmenting human intellect.

I still agree with Alan Kay on most of the things he said. Computer revolution never happened. We still have absolutely no idea what computers are capable of. And we're still nowhere near the kind of world originally imagined by pioneers of computers where a high school kid with no significant social or economic advantage would be able to gain intimate understanding of the system of the world in terms of sciences and history through the tools of computerization.

I'm beginning to think that the real computer revolution might not have much to do with computers at all. Maybe it about laying out systems of ideas first. Systems of ideas for interaction between certain devices and a human being. Systems of ideas for interfacing a human being with existing knowledge base. Why can't object oriented programming framework be applied to formation of educational curriculum? Why do we still consider object oriented programming, something that was formed and finalized during the days of hulking mainframes as cutting edge programming technique, in that it finally addresses one significant facet about the act of programming, and thus computing; programming is not about feeding linear list of instructions to a computer, it's an act of reorganizing ideas into most efficient form of instruction.

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Reason for computers

2010-07-04T23:05:00.001-07:00

The reason Alan Kay got into the computers in the first place. It's not about hardware, software, or even user interface. It's about augmenting human intellect.

Posted via email from Between Motion and Act

Untitled

2010-06-25T13:34:00.001-07:00

Playpower: An introduction from Playpower Foundation on Vimeo.

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

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

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

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Moving about

2010-06-10T03:29:00.001-07:00

It's really difficult to concentrate on writing something these days (as I've been saying for the last year). Maybe it's because of my hasty decision to move to a blogger from previous livejournal account?

Right now I maintain about four main web presence. Twitter gets used most often, followed by tumblr, blogspot, and lastly wordpress. Twitter is really what I'd call an idea stream. I use it as a combination of microblog, mobile scratchpad and IM of sorts, and it's been pretty great at all of those things so far... Even at its current clumsy state it's a pretty good learning and research tool for a student like me (where else can you find a propulsion specialist at 3 am and ask random questions to him/her?). Tumblr is a web scrapbook. I just pour in most of the links, pictures, and videos I find interesting into it, though most of the time content on tumblr tend to be from other tumblr blogs... So while it's more colorful than a traditional blog or microblog, it doesn't hold nearly as much original content... I'm not sure why, but there's something about tumblr that stops me from uploading text heavy original content onto their services (or maybe it's just because I'm already using a number of different web services already). The blogspot one I use for relatively larger written pieces, though I never think about quality of the stuff I write there. It's meant to be a free form journal where I talk about anything from latest political scandal to promising developments in sciences and favorite books. And then the wordpress blog is the one that's supposed to be the face of my web presence... It's the kind of place where I watch my language when I write.

Well the arrangement isn't working so well now that I can hardly find the time to sit in front of a computer and do private stuff. These days, if I'm sitting in front of a computer I'm working on something, sometimes for money. It's difficult to come up with my usual text blog posts that range anywhere between 1000 to 5000 words.

When I can write presonal stuff is when I'm walking or riding around the city to get to someplace else. While the MTA keeps deplorable timetable it gives me ample time to go through my books and write stuff down. The problem is it's difficult if not impossible to open up a laptop in a crowded F line train during the rush hour. The best I can manage is a handset, and regular blogs without straightforward mobile uploading scheme (that encompasses all froms of media, text, audio, video and etc) doesn't quite work as well as I'd like.

So, I'm reaching out to another web service again, to use posterous for all my 'flights of fancy' type posts on the run. Maybe I can do something new with this service and modern smartphones, like working on real videos that demonstrate interesting ideas rather than just simply writing about it. I always seek out professors and grad students for advice on the work I'm doing or just to talk science. Maybe I can upload some of the talks onto the web. I don't know. I think there's a lot of interesting possibility (most of which will be made unrealistic by AT&T's rather pathetic dataplan pricing scheme in which they eliminate the unlimited data and replace it with something that can't handle sending high quality videos on air).

Let's see where this idea of cloud scrapbook can take me for now. (oh, and I should look for some way to backup my posterous posts offline)

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Update

2010-05-31T15:29:00.001-07:00

Summer's here again, and it's harder than ever to write a decent post while sitting in front of a computer. It's ironic that I'm beginning to use pen and paper far more than laptops and smart phones to do my leisure writing. Lot of things on my mind lately, like whether all this science stuff I'm trying my hand at will eventually work out somehow. With the basic issues like being able to find and hold down a job (I don't really want) so that I can pay my way through school and all that weighing down on my mind all the time, being able to pursue science as a vocation feels like a pipe dream all too often. Yeah, sure. Everyone works, more or less. And a lot of them actually work to pay their own rent, tuition and buy their own food like I'm doing right now (oh right, I'm talking about undergrads). All too often it's really a problem of future, and repercussions of mistakes I might make. Neal Stephenson wrote something about that in one of his books... Some kids go to jail for 10 years for striking up a joint, and some other kids get to protest in front of the city hall after making it to college. Some people just live in a very fault-intolerant world. That's about where I am. Not quite as bad as some kids I teach, but still enough to worry about becoming homeless after some idiot run me over with a car. And after you're homeless... Well it'll be a whole lot harder to beg professors to let me into a lab without being treated like some junkie or a maniac.

Something like that probably won't happen, but I can't help but feel that chill in the back of my neck time to time. And about the only thing that makes all the fears and uncertainties worth it... Well I'm still not sure what I'm supposed to call it. Most people seem to call the practice of it science. It's some kind of pursuit toward something. And it makes life worth it.

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Wikileaks video

2010-04-05T15:42:00.001-07:00

Just a quick post before I run off to work (it's so hard to find time to blog properly these days, maybe I should try one of those audioblog autodictation addon...)

Found out about this while I was browsing through the tweetstream

It's a video on a site called 'wikileaks' that specialize in sensitive information and documents. It's been around for a while but this must be its biggest case yet (or second biggest if we count the case of a certain pharmaceutical firm in Switzerland).

I don't think release of this video will really change anything. I just hope this can be a wake-up call to a lot of people out there believing in nonsense like 'clean war' but even that's doubtful.

Before I go, here's something for the death of journalism. I don't think it's the internet.

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First DIYBio rant of the year

2010-03-11T16:42:00.000-08:00

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

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

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

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

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

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

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

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

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

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

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

At the Met

2010-01-23T13:27:00.001-08:00

It's been a long time since I've walked through these halls. I'm only now realizing just how many memories I've left here, as I pick up all the little pieces and gaze through them. And I am a little happy about the little nagging question at the back of my head that just won't go away. Just what cnfiguration of molecules in this universe gave birth to these shapes and colors we call art? What is the equation that leads from the Big Bang to the Bernini, linking the two together into a greater, coherent whole?

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Recent reads&update

2009-12-01T20:57:00.001-08:00

It's been a while since I wrote anything for reasons other than school work. While it's definitely fun to write for the lifelong dreams of understanding the complex systems we collectively refer to as life, I can definitely feel the effect of writing rather dry academic stuff all day and night. It's a slow and subtle process that will one day burn me out. Kind of funny considering just how beautiful the systems in nature can be, I guess it's one of the facets of the human psyche that I just don't understand very well... One day I should really think about this...
It's a weird process that I can only describe as drying out, just like lush forests slowly drying out into a desert.

Sometimes everything I do, including the studies of sciences and the essential acts of reading, listening, and sleeping are all just my life's automatic attempt at trying to hold back the inevitable tide of desertification of the mind... The imagery saturated with sand inevitably bringing into my mind the vision of sand castle being built on the beach against incoming tides.

Two sometimes opposing elements help me against such natural tides into inflexibility and forgetfulness. Singular obsession in action and variety in life. The more I live singular, almost obsessive dedication to something in life is essential in maintaining one's human quality, through ceaseless pursuit of truth, understanding and change of the status quo. However any decent human being tend to be supported by pool of experience that are at once more varied and detailed compared to the generation's norm. Obsession I fulfill with science, and variety I try to fulfill through act of reading.

And writing... Well this is my equivalent of eating junk food. Something I just 'do for fun' to vent out the inevitable stresses of life.

Two of the most recent books n my memory are 'The Bottom Billion' by Paul Collier and 'Tokyo Vice' by Jake Adelstein. Both are books I'd recommend any adult to give a chance, though Tokyo Vice can get a little graphic at times in its depiction of sex and violence, and is quite frankly not much of a literary masterpiece (the book was written under a duress that should be understandable to anyone aware of the back story... I'm not going to spoil anything for you).

The Bottom Billion was one of the most, if not the most compelling and rational analysis of the very peculiar 'bottom billion' world we live in right now, with some very insightful suggestions as to how we might be able to change it for the better.

Bottom billion in the sense of the book refers to more than a simple collection of 'poor people'. It refers to a collection of nations and its people that are caught in economic and political traps of decline, much like wells and traps of physical systems certain elements of the system just cannot escape from. The world in economic sense is expanding. It keeps on getting bigger and richer (in a sense). Even the poorest nations in the world are subject to some level of growth. However, there are certain groups of nations in this world that seem to be stuck in unnaturally low, almost zero growth rate, and they all happen to be situated in the African continent.
The best part of this book for an economics layman like me is the clarification and classification of the problem that had been haunting this world order for past few decades. It's incredibly simple to simply talk about 'poor people' and'poor nations.' While most of us might have best of intentions in discussing world issues using such loosely defined terms, the end result of such discussions just end up being something so obvious and meaningless, a philanthropic equivalent of discussing how many angels can sit on top of a pin.
The freak accident of the modern world is that people can immediately identify just what geographical region of the world is the poorest on the Earth, and by extension, what kind of people. It might be impossible to eliminate human misery from the world, but allowing certain geographical region to fester with the lowest, most miserable conditions of the human world is something that's

1)Inhumane
2)Irrational
3)Wasteful

I don't believe for a second that current barrier between the so called 'developed' and 'developing' world that allows members of the developed nations to live their entire live without thinking about the consequences of their nation's international dictates will last. Either it will implode with catastrophic consequences, or be intentionally maintained with heavy price in terms of commodity, human lives, and human future.

In the book 'The Bottom Billion', Paul Collier is successful in providing the reader with two things in regards to the issue of the bottom billion. Clarification and analysis of the problem through rational thinking, and suggestion of possible solutions based on actionable items.

Compelling, is the word to describe the book, and if you are a young college student who might be thinking of changing the world, this is a book to read whether to agree with the author's specific analysis or not.

I will write up another post on Tokyo Vice later on. It's getting a little tough to type up entire blogposts on my mobile handset.

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Importance of hackability

2009-10-02T23:51:00.000-07:00

This is something I wrote down on my blackberry during one of those sleepless nights.

As I huddle in the darkness of my room with my Blackberry in my hand, listening to the mp3 rip of the Deus Ex soundtrack, and reading Cory Doctorow's the Makers serialized on the web, I am inevitably reminded of a question that had been plaguing me for a long time.

I read about the greatness of the old computer systems all the time, being something of a retrocomputing enthusiast. I read about all the wonderful stuff people did with their first Apple computers and Spectrum ZX, making and running crazy things on 128kb of memory. I also read about the demoscene where people squeeze old retro hardware to it last reserves of computing power to create fascinating works of pop art.

And then I look at my handset. I remember my old nokia running symbian, which is a modified version of linux fitted to run on mobile platform. I scrounge through the apps on my blackberry. Any modern handset I can remember using, and I can remember other people using is vastly superior to most of the retro hardware that are remembered so fondly. Even my older model Blackberry can kick the pants off the old Apple computer in terms of hardware spec, and it has much more sensors to boot, allowing it to communicate with the world through its eyes (camera) and location awareness (GPS). I'm not even going to talk about the always-on data connection because it's a given on any working handset.

Yet despite the reserves of computing power and amazing array of sensors available on this little buggers, they just don't seem to be able to inspire that same level of awe and creativity the first generation of personal computers did for its users. Just what happened? What is the difference between modern handsets and first generation PCs other than how superior many of the modern handsets are in terms of spec?

The answer I think, may have to do with the hackability of the handsets compared to the first generation PCs. First generation PCs were intended as computers. They had moderately sized screens (though the resolution was mostly worse than even the poorest smartphone out in the market today) and a full complement of input device you can use for extended period of time (just a full sized keyboard really, though it does make a difference). Yet these are still superficial hardware differences that can be made up for quite easily. Most high end Nokia phones support connecting to tv screens and what not, and most bluetooth equipped smartphones can interface with a bluetooth keyboard. Can, but not allowed to.

The biggest difference, perhaps the only difference, between the old first generation PCs and current handsets seem to be the software. The PCs were intended as computers meaning you were provided with the tools to develop new content for that platform, usually in form of BASIC implementation for the given system. It was possible to code in assembly and such if you were good enough. The best memories of the old systems and their wonders are almost always linked with the entry level development for the system.

You can't find that on handsets. Even Google Android doesn't yet provide a suitable platform on top of the mobile that can be used to manipulate the machine fully. There is a zero chance that a user of a blackberry handset would be able to run a code on the handset itself, and even linked to a full scale PC the road is usually long and confusing.

Granted, modern smartphone hardwares are complicated which necessitates (really?) the need for complex development environment. Yet, what if the mobile OS itself just gave the users just a slight bit more control to their own hardware? What if we can bring the modern BASIC equivalent like python onto the mobile OS, capable of interfacing with, and controlling the hardware?

Would it lead to another wave of developers and tinkerers world wide to create things that were completely unexpected?

Alan Kay applied to synthetic biology... And other late night notes.

2009-10-01T00:17:00.000-07:00

I always find it very hard to blog. Even when I have the time to write something, not necessarily sitting in front of a laptop, mind you (I'm rather known for writing stuff that needs some word processor access and sending it in straight from my handset). It's only that I always feel that whatever I'm writing or trying to write at the moment just doesn't feel exciting or important enough. Which is why I keep multiple blogs around the net, each serving as a rant template for the other. Something would begin as a rant template on place A only to be edited into another form for place B, to place C, so on and so forth before the same yet radically altered post ends up as a follow up at the place of origin.

I know I should be writing about some other things as well, like how the diybio nyc might be amazingly close to getting a real lab space, or how I'm prepping to stop by for this year's iGEM jamboree. Oh or the pictures from this year's major diybio nyc event, where we set up a stall on the green market and extracted dnas from the natural produces with common household material (with the city people of course). Each of those things would probably make for some lengthy and interesting reading, and the list goes on (my life's actually kind of exciting right now). Yet whenever I find the time to write something down, nada. Nothing. My mind just shuts down and nothing I can commit to paper or the keyboard seems good enough.

Tonight though, aided by my weird bout with insomnia, I'll just write something down I've been meaning to say for a long time. I'm not even spellcheck this thing (god save my soul).

I've been looking into the history of computing and computer languages recently. I've always had some level of interest in computers, not just the spiffy brand-new muscle machines but in what most people would refer to as 'retrocomputing' (I once ended up practicing some AIDA because of that. Ugh), which is a story for another time. It's not that I think old ways of computing were better than others. It's just that it's much easier to trace the evolution of the concept of computing when you see beyond the immediate commercial products.

Synthetic biology is effectively a pursuit of engineering biological organisms. Biological organisms are based upon very singular information storage and processing system that has quite a bit of parallels to computerized systems. I've been wondering whether it would be possible to predict the future development of synthetic biology by looking at how computer programming languages evolved (because they deal with information processing systems applied to physical counting medium). Maybe it might even be able to predict some of the pitfalls that are inherent in developing any kind of complex programmable information processing system that will apply to the synthetic biology in the future. Maybe it would be possible to bring a conceptual framework to the synthetic biology that would have taken decades if left to mature naturally within mere years.

While I was rummaging through the texts in both real life and the web (with many of the promising links on the web leading to dead-ends and 404s) I ran into a programming paradigm and environment I was only superficially familiar with before. Smalltalk and Squeak, respectively, both the brainchild of the computing pioneer Alan Kay.

Here's an excerpt from Alan Kay's biography I found on the net (I can't find the website right now. I swear I'll edit it in later, when my brain's actually working!)

“Alan Kay postulated that the ideal computer would function like a living organism; each “cell” would behave in accord with others to accomplish an end goal but would also be able to function autonomously. Cells could also regroup themselves in order to attack another problem or handle another function.”

This is the basic philosophy behind smalltalk/squeak and object oriented computer programming paradigm. It is no coincidence that Alan Kay’s vision of the ideal computer language and computing environment would take to a biological allegory, since he came from molecular biology background.

While I’m reading through the history of different computing paradigms for the purpose of figuring out how it might be applied to understanding and usage of synthetic biology, there’s something else I found awesome and perhaps a little heartwarming. Alan Kay throughout his life as a computing pioneer held onto the belief that the ideal computing platform isn’t a platform capable of crunching the numbers the fastest, but a platform that can be integrated into the educational function of the user through ease of manipulation and control. Ideal computing platform should be hackable because it makes logical sense to do so.

Can we say the same of synthetic biology? Perhaps not. The direct comparison of a complex biological system to computerized circuits and cathode ray tube projections can only take us so far. Yet I can’t shake the nagging feeling that synthetic biology might be looking at some very unique opportunities for change precisely because it is different from regular electronic systems, with documents of the early days of computer and programming already here for our perusal.

A good, elegant system that allows programmable extension must be at the same time easy, or at least logical to learn. And there are systems that both run and learn better compared to other systems. This might become something of an issue of how synthetic biology parts/devices/systems are put together in the future as the capacity of the synthetic biologists to handle complex systems increase.

I think it might be able to pursue this idea further. As it stands this is nothing more than an interesting parallel in concept without substantial scientific reasoning.

Which is why I should get myself to learn smalltalk/squeak sometime in the future. Maybe I should knock on the hackerspaces in the city, see if anyone's willing to mentor me.

Now, it's about time for me to get some sleep.

Testing

2009-09-15T04:31:00.001-07:00

Testing mobile posting for the blogger&posterous. Nothing to see here, folks.

Posted via email from Textdrome

Babelfish Twitter

2009-09-10T20:34:00.000-07:00

As all my friends know, I'm something of a twitter addict. I regularly spend certain amount of time per day on it checking other people's tweets and I tweet almost everywhere I am, thanks to Blackberry dataplan and a number of wonderful twitter clients available for that platform like ubertwitter and twitterberry (I have both. Don't ask why). Contrary to some of the popular opinion on twitter being unnecessary time-waster I find it an interesting tool to keep in touch with academic communities and enlightening people around the world. If anyone cared to look, they'll find surprising amount of meaningful conversation on variety of topics like artificial intelligence and synthetic life taking place on twitter time to time. They are the kind of conversations normal mortal like you and I won't be privy to if it weren't for twitter or its very close cousin friendfeed... Who knows, maybe some of the people on twitter or any other number of social network platform out there got the chance to hear the conversation between future Einstein and Tagore... I should definitely do a post on the development and practices of science in the internet age sometime soon.

As a bilingual one of the more interesting thing about twitter is how so many people outside traditional U.S. internet service sphere of influence seem to have no trouble picking up twitter and turning it into part of their daily routine. So far I believe I saw about seven different languages on twitter with their own little communities, including Korean, Japanese, Chinese, Portuguese, Hungarian, Russian, a bit of Arab, and a number of languages I don't quite recognize. This is quite surprising that traditionally it's very difficult for a web service from one particular nation to break into other cultures/nations due to variety of obvious and not-so-obvious reasons.

So here I am, thinking how would we be able to use this growing database of all sorts of different languages and cultures? How would twitter community and the twitter administrators be able to encourage such diverse usage demographic so that we have more people speaking multitudes of languages on a single network? My American friends might be unable to understand this but the fact is, despite the presence of the internet as an international unifying medium people from different cultures and languages tend to be locked into their own proprietary communications service protocols within it. For example, vast majority of internet users outside of America don't really use facebook. And vast majority of people outside America don't use Google as their default search engine. Likewise people in each respective internet ecosystem tend to use their own service that none of us have ever heard of. Twitter, for some odd reason, seem to be able to transcend that traditional barrier for some odd and as of yet unknown reason...

Would first step in such a venture be building a type of sorting engine into twitter capable of differentiating between different language input? And gradually grow that system into something capable of translating one 140 character snippet into another language of equal substance? The 140 character limitation might impose some interesting mechanism on the whole computer based automatic translations service.

... There seem to be something incredibly awesome at the end of this tunnel, but at the moment I seem to be rather incapable of figuring it out...

Imagine Science Film Festival

2009-08-31T22:14:00.000-07:00

Just a quick note before I doze off for tomorrow's work.

NYC, befitting its status as one of the more interesting places to live in around the world, is the host to this amazing event called the Imagine Science Film Festival. Now I'm nuts for all things science, but I especially love this festival in comparison to other science-y things to see and do around the city (with possible exception of DIYBio-NYC).

I personally believe that arts and sciences go hand in hand and that current division between the sciences and the 'humanities' is something of a temporary cultural aberration that we'll all look back and laugh at. And the kind of works I saw at last year's Imagine Science Film Festival events showed me a glimpse of what a future with sciences and humanities intermingled together might look like. It's not so much as the specifics of the individual films but the overarching theme pervading through the atmosphere of the whole festival itself that caught my attention. Perhaps it's the passion of the event organizers rubbing off on others watching the films. Perhaps it was just me realizing something I already had inside me through the mirror of projector screens.

If you're in the NYC area, make sure to check out the webpage for the imagine science films and mark the dates on the calenders (there's a screening benefit program this September 9th). Last year most of the screenings were free and I get a feeling that it will continue to be that way this year as well. If you're not in the NYC area, feel free to donate in return for some cool t-shirts ;) You'll be supporting a worthy cause.

And here's the festival trailer for your viewing pleasure.

ISFF 2009 Trailer from Imagine Science Films on Vimeo.

Pi Cubed, the iPhone app

2009-08-17T16:17:00.001-07:00

Just a little post on an awesome app I found on the twitter.

The application is called Pi cubed, and it's basically a calculator on iPhone that utilizes the touch interface. The description I'm giving here sounds depressingly simple, but you need to see this application in person in order to understand how cool it is, and how relatively mundane act of calculation can be made fun and interactive simply through some interface change.

Here is a video of the application in action via http://theapppodcast.com site.

As you can see, this isn't the kind of calculator designed to help you out with your pocket change. The support for formatting the equations of increasingly complex form to pdf or text output through email means that the application is aimed at students and possibly professional who might have some great ideas for equations on the go (though in that case the absence of LaTeX formatting is a little jarring). This application is obviously aiming to be a type of mobile Mathematica.

I'm a huge supporter of scientific apps on mobile platforms. I think the market for scientific applications on the increasingly sophisticated mobile handsets is a huge opportunity and is one of the things that might actually help in changing the world for the better by bringing the lab out of the universities and corporations. So the whole Mathematica-mobile aspect of this application, and inevitable coming of even more sophisticated mathematics/sciences packages for mobile platforms is exciting to me.

I just have one problem with this though. Why iPhone? iPhone isn't open. If you want to develop for an iPhone you need to clunk down for a computer capable of running OS X natively, and you use Apple proprietary toolset that no one else in the industry uses. The draconian app approval process and anti-competitive behavior at Apple had been making the headlines in tech communities lately. I guess this is just a market issue, but I find myself keep hoping for a decent Android based replacement for iPhones that developers can distribute their work for.

Synthetic Biology on KQED QUEST

2009-08-16T00:43:00.000-07:00

Here are two videos on synthetic biology. The first one is a short introduction to synthetic biology produced by the wonderful people at KQED QUEST program, which goes into some level of detail on what synthetic biology is and what we are doing with it at the moment. Certainly worth some of your time if you're interested in this new exciting field of science.

QUEST on KQED Public Media.

The second video is the extended interview with Drew Endy available off their website... While the field of synthetic biology in the form we now know and love probably began with the efforts of Tom Knight at MIT, Drew Endy is certainly one of the most active and clear thinking proponents of the scientific field of synthetic biology.

QUEST on KQED Public Media.

If you hadn't guessed yet, I'm really big on synthetic biology. I think it's one of the most exciting things happening in the sciences today, not just for biologists but for mathematicians and physicists in that synthetic biology might one day provide a comprehensive toolset for studying the most complex physical system known to humanity so far... That of complex life-like systems.

I also believe that abstraction driven synthetic biology cannot manifest without a reasonably sized community of beta-testers willing and able to use the new parts and devices within original systems of their own creation. Computer languages like python and ruby needed efforts of hundreds of developers working in conjunction with each other for a multiple years to get where they are today. Complete operating system like Linux took longer with even larger base of developers and we still have usability issues. Synthetic biology must deal with systems that are even more complex than most computerized systems, so it's not unreasonable to think that we'll be needing an even wider deployment of the technology to the public and active community involvement in order to make it work as engineering capable system.

So I am a little dismayed, along with legions of other people who were initially excited by the promises of synthetic biology in conjunction with diybio community, to find that access to BioBrick parts and iGEM competition is severely limited against any amateur biology group operating outside conventional academic circles.

You see, unlike computer programming, constructing synthetic biology systems require BioBrick parts from the registry of standard biological parts. Right now it is next to impossible for diy-biologist interested in synthetic biology to get his or her hands on the BioBrick components through proper channels. The DIYBio-NYC group alone had quite a few number of people lose interest because of uncertain future aspects of being allowed access to the BioBrick parts and talking to people from around the world on that issue I'm beginning to think that there are a lot more of such cases. So far the major reasoning behind the restricted access seem to be the safety issue, but considering that the regular chassis used to put together BioBrick parts is based on academic strains of E.Coli that are even more harmless than your average skin cell I can't see much wisdom in restricting access to the parts on basis of safety.

The bottom line is, the state of synthetic biology and BioBricks foundation at the moment is forcing a lot of people, some of them quite talented, who are enthused about contributing to a new emerging field of science to back down in either confusion or disappointment. Considering that the very structure of synthetic biology itself demands some level of public deployment to stress-test and demonstrate the effectiveness and stability of its individual parts and devices (with creation of those individual parts and devices left to the highly trained professionals at up scale laboratories) this is highly unusual state of affair that is not motivated by science behind synthetic biology. I might even go as far as to say it has the distinct aftertaste of political calculations of public relations kind.

The field of synthetic biology will never achieve its true potential unless the BioBricks foundation and iGEM administrators come up with some way for people outside traditional academy settings to participate in real design and construction of synthetic biology systems.

Whole Foods CEO on UHC

2009-08-14T21:07:00.000-07:00

UHC, of course, refers to the universal health care, which seem to be the hot topic these days. There are lots of arguments flying around on both sides of the health care reform and universal healthcare in America, some of them more reasonable than the other.

Well, I just though I'd share an interesting article I read on Whole Foods CEO John Mackey's editorial on the Wall Street Journal. Apparently, the CEO argues that the constitution does not make guarantees on the life and health of the individual citizens, so it's not the business of the government to get involved in health care. He alternatively suggests that people buy and eat from Whole Foods market for preventive health care.

Now mind you, this is a blog post by a college student (with our infamous liberal leanings) with a bitter memory of childhood torn by his father's kidney transplant surgery. So yes, I'm all for universal health care. It wasn't' easy watching my mother trying to pay $4700 per month hospitalization fee during my father's dialysis period, and it wasn't easy selling practically everything we owned to pay for his surgery.

There's something really odd when I hear people talking against universal health care. What's exactly bad about it? Most other developed countries in the world have it like Sweden, Japan, and Germany, and they seem to like it. I experienced it first-hand when I lived in South Korea, and I liked it too. With the billions (if not more) the U.S. government's already spending on health care insurance companies, it should be possible to run some form of universal health care in this country as well... And yes, you're reading this correctly. The U.S. government already spends quite a sizable amount of money on health insurance companies. In fact, U.S. government spends the most amount of money on health care out of all the developed nations in the world, and has the least number of people covered with least life expectancy out of all the OECD nations. Something a lot of those people at the 'town hall meetings' seem to conveniently ignore.

But that's not all. If it's a simple matter of getting the data out most people out there should be proponents of universal health care system by now. If they were actually interested in providing good health care, whether private or government mandated, they should be combing through the proposed health care reform bill pointing out excesses (I'm sure there are some) in the list and pointing out improvements. But it's not happening. The most extensive combing-through of the health care bill done by its opponents so far concentrated on the clause on hospice care counseling, labeling it as 'death panel.' Well from what I'm seeing the same hospice care counseling is included as a part of standard employee coverage package from many private insurance companies (in this episode of the Colbert Report, the UHC proponent Jonathan Cohn points out that employees of the Colbert Report show are all covered by contracts with the so-called 'death panel' clause).

The opponents of the health care reform seem to be against the 'idea' of any kind of change made by the Obama administration regardless the real benefits or disadvantages resulting from the change... However, do they truly believe that low confidence in certain regime and certain political characters is enough reason to reject a bill that might end up saving thousands if not millions of lives in this country? Are human lives so fickle and worthless that they can be thrown out for the sake of political rhetoric?

Then there are people like John Mackey. The kind of people who believe that government has no business ensuring the well-being of its citizens. Such arguments usually go hand-in-hand with the kind of low-brow, thinly veiled suggestion that people who cannot afford conventional health care, notably the ones in lower income bracket, are probably not worth helping. While such notion might work with running a corporation, it would be a mistake to think such attitude scales to the level of national governance. Maybe Mr. John Mackey leaves mess around his house. Maybe Mr. John Mackey like to target practice in his personal property. Such behaviors are perfectly legal in his own personal microcosm. However, if Mr. John Mackey applies that same behavior to public properties by leaving garbage around the City Hall offices and performing target practice in the crowded Times Square... The results would be disturbing.

If there's one thing I've learned during the history courses through my high school years, it's that nations come and go. Contrary to some popular belief there is no natural law that states the United States of America will exist regardless of how its members treat each other. This nation only exists because there is a united will and cycle of trust and responsibility. If a national government that collects taxes and enforces its codes of law cannot take care of the very basic well-being of its citizens, why should they be loyal to the country? Never mind the capacity. If the government does not even have the will to safeguard its citizenry why should they be loyal to that government? Why should they go out to wars and die to protect that country? It's a very simple matter of loyalty. If the government itself insists on not providing for its citizens certain level of amenities required for the very basic act of survival (we're not talking about luxury condos or spa vacation here, folks. Just staying alive), the said government cannot possibly expect the same citizenry to follow its rules of law, perhaps except through application of force. Sensible people usually call that oppression. Sensible people don't kill people and rob stores because they are scared of getting hurt in the process. They don't do it because it's morally objectionable, and because they have faith in continuation of the society in which they are members.

I am profoundly disturbed by some people coming out of the woodwork for the universal health care debate, by their blatant lack of respect for human dignity and lack of concern for the well being of their fellow human beings... And in the case of Mr.John Mackey, the horrible financial sense in suggesting that buying overpriced groceries is a replacement for genuine health care system.

How to change the world Rev.

2009-08-13T15:54:00.000-07:00

This is a minor revision of the how to change the world post I made a while ago.
I still think most of the stuff I've written here are quite relevant. The importance of science and access to science for the general public in the coming age will decide the path of the future. And reliance on computing intensive coding for things that should not be computing intensive in the first place would be IT equivalent to driving a Hummer to a grocery store 3 blocks away.

The information superhighway is more or less in place. It's upto us to decide what that infrastructure will be used for.

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

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

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

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

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

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

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

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

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

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

Get to work.

Change the world.

NASA proposal to move the planet.

2009-08-11T19:46:00.000-07:00

Scientists at NASA are discussing an interesting theoretical exercise in cooling off the Earth, by moving it further away from the Sun. According to their calculation it is possible to move the Earth to another orbit through controlled impact with a few meteors, which will end up prolonging the useful lifespan of the planet by about six billion years, effectively doubling it's life.

Sure, the bit with meteoric impact has me wondering if anything will be alive in that cooler planet, but still, this means that it is possible to work out the numbers for artificially engineering an existing planet's condition. It's all theoretically possible, and not at all far fetched.

Me, I'm interested in seeing this idea applied to other large masses floating around the solar system. Maybe sometime in the distant future we'll capture an asteroid the size of a planet, like the one as large as the Earth that recently impacted against Jupiter. Maybe we'll slam other large masses at the asteroid through careful application of rockets and mass drivers, putting it into a synchronous orbit around the Earth. We'll mine the asteroid for its rich minerals and other natural resources, gradually turning it into a habitable planet with its own wonders and mysteries.

Fast forward another thousand years, and such planetary system building exercise had become so trivial that you can take a course in universities (assuming they're still around in some form) for planetary systems engineering. Maybe people will even begin to see it's utility beyond resource and land grabbing. People will begin to construct large stars held together by the bonds of gravitation, slowly turning the universe into a large architecture, with myriads of different cultures and ideologies dwelling within its arches and bases.

What will happen to nationalities and histories in such a world?

Meteor Shower tonight!

2009-08-11T15:36:00.001-07:00

According to the information gleamed from the twitter, tonight is the night of the biggest meteor shower of this year.

The meteor shower will be visible starting around early evening lights of 9~PM, peaking at 1 AM. I'm certainly looking forward to staying up late and checking out the shower of the stars. It's only feels like yesterday that I checked out the solar Eclipse and first private rocket/satellite launch through web feed, it's good to finally get a chance to check out the spatial event with my own eyes.

I just hope all the light pollution from Manhattan doesn't get in the way too much...

Lectures and Presentations

2009-08-09T18:22:00.000-07:00

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

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

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

On to the main post...

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

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

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

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

Synthetic Biology interlude

2009-08-06T12:20:00.000-07:00

This blog is currently underconstruction, since I wanted to port all the posts on my previous blog on livejournal over here before I wrote anything new (a tiresome process since Blogger only allows 50 entries per day, and I have about 280~300 posts that are waiting to be imported).

Well I'm afraid I'm going to have to break the rule here because I found something that's really just too awesome to wait.

There's a six hour lecture/presentation by George Church and Craig Venter on the Edge website right now. It's about the most rigorous introduction to the field of synthetic biology on the net in continuous video format at the moment, given by two of the most brilliant minds in the field. If you have even a modicum of interest in synthetic biology, you should run and watch the video right now... I'm trying to find a way to download the vids so I can watch them on my iPod.

This is a refreshing change of pace from all the synthetic biology stuff on the net targeted at broader audience, most of which tend to focus on conceptual sides of synthetic biology instead of the technical background that makes it so alluring.

Abundance of educational data on the net these days is staggering, compared to the days of my prepubescent web surfing days when everything revolved around telephone modem connection and American Online services actually mattered. If only I had access to this caliber of information during those days.

Morning

2009-07-30T04:33:00.000-07:00

It's a sunny morning on Thursday, and like before I haven't caught a wink of sleep. Will I be able to look sick enough to get out of work early today as well? I don't know. At least I finally manages to be productive in this particular insomniac binge.

I'm in a very complex love-hate relationship with my laptop. I like it for being retro in a strangely stylish way. I like it's awesome keyboard that's actually a step above pratically all the competition out there. I like how the thing had been running on battery power since one in the morning and now it's... 7:30 in the morning. Pretty darn durable for a laptop with dedicated graphics card.
But then there are some serious issues with this machine. Like the irrational behavior of some of the lenovo patched drivers in sleep-wake cycle. Or how my wallpaper disappears whenever I use the battery stretch mode. Most of all, I hate how flaky the ATI driver for the dedicated graphics card on this machine is. It gave me two BSoD last night due to amdkmp driver crash (that Lenovo's been 'working on' since last year at least) and another one as a sort of graphics driver related cascading failure showing the dreaded NMI/memory parity error. The same exact BSoD message I received before my last dell's motherboard fried to a crisp due to faulty die casting of the GPU. I never get any errors when I'm using the intel integrated graphics mode which probably uses 4500HD chipset, but why should I settle for the crappy integrated chip when I paid good money for dedicated graphics solution? If I wanted a laptop that will just run off of intel IGP I would have bought much cheaper, and light laptop... Though to be fair cheap/light laptop with 1440x900 resolution is a rarity these days for some reason. The manufacturers including Apple are still sticking with crummy 1280x800 resolution for ~13in screen solutions. Way behind the times those people.

Ok, I'll be honest. This laptop's still pretty good running on intel IGP. Things I do for work don't usually need dedicated GPU unit with separate ram. They need processing power, and this 2.5GHz core 2 duo machine packs enough wallop to blast most consumer class desktops out of the water. I'm just pissed that I can't play any games on this machine without risking the whole OS going down in blue flames... To be fair I haven't been playing much of anything these days, and I certainly haven't been playing anything that would actually need the punch offered by a dedicated graphics card, but still, I'd like to keep my options open. In fact, only three reasons stopped me from purchasing a new Aluminum MacBook instead of a thinkpad. Screen resolution, lack of SD card drive, and dedicated graphics solution. Well since the macbooks coming out right now have much better GPU with SD card drives to boot, not to mention phenomenal battery life estimated at around 6~7 work hours, the only thing Thinkpads have going for them is the screen resolution, something that can be managed if you're an external monitor kind of person.

With the unstable graphics card giving me grief, I keep on thinking about bringing another gadget into my life. Maybe a new netbook (the ones on the market today lasts for upto 10.5 hours per charge). The 701's getting really old and it's a real pain to type up a full report on that keyboard. I can manage, but it makes my fingers feel like I've been playing on the piano for hours. While a new netbook would certainly be nice (especially since even the worst netbook out there can run starcraft on it, thus satiating some of my entertainment needs), I'm not sure this is a good time to buy a new system though. The Nvidia ION is just around the corner and there is the disturbing rumor of the Apple tablet coming out as early as September or possibly this winter season.

Oh yes, the Apple tablet. People had been dreaming of it for a few decades now, ever since the Newton died. If Apple pulls it off there's a very good chance that I'll end up with one of those things, especially considering the wealth of science applications on iTunes Store at the moment. Some of the applications like the Papers are a godsend to anyone in academic profession. And I know for certain that Drew Endy et al are planning an iPhone-OS based mobile version of the biobuilder platform, which is a beginner friendly yet heavy duty synthetic biology CAD program that integrates into regular computer based distributions... Yeah, even speaking without gadget lust there's a good chance I'll get a touch or a tablet in the near future, since my professin almost seem to require having it for some reason these days. Kind of understandable when you think about it. The last time academic profession saw some mobile platform that was reliable and consistent enough for field/lab deployment was close to ten years ago, when the term PDA was new and Palm ruled the Earth.

On the other note (what are rant posts without multiple number of topics to dazzle the readers' minds?), only 95 days until Nanowrimo. I'm definitely participating this year, with my trusty laptop and all. I even have most of the rough draft and settings lined out in clean text based wiki format. I didn't expect myself to be able to come up with such awesome ideas, but I think I might have hit the real jackpot. I haven't read anything even remotely close to it for years. Very hundred-years-of-solitude-y. With some undeniable influence from all the Japanese light novels I've been force fed over the years.

I'm really looking forward to it.

Well, time to get to work!

Writer's Block: Technology’s Impact on My Family

2009-07-30T00:30:00.000-07:00

Rainy day

2009-07-29T13:49:00.000-07:00

Thanks to the wooziness induced by the late night last night, I was able to get off from work way early today. If this can keep up with my schedule I might as well sleep late every day. It's good to be outside and free when the sun is shining, except that it's not quite the case right now.

After days of half-formed rainstorms that only lasted an hour or two, damning the whole of the city into the pre-rainstorm humidity and heat that would make Tokyo proud, it's finally pouring down. I don't know whether to feel happy or sad about this. Certainly I've been waiting for a decent rainstorm for a while now, with thunder and lightning. But why does it have to be the day I could have taken my laptop out to the park to get some personal workspace? The world works in really strange ways.

With the rain, and with my brain still a little soggy from lack of sleep and rest, I just came back home right away instead of hanging around the city to do whatever. I could have spent some much needed (and decidedly cooler) time in bookstores in the area, but I didn't feel up to it. Maybe it's the weather.

So now I'm sitting in the sofa in my room, looking out the window being riddled with raindrops, wondering what to do with this unexpected freetime. I've already read most of the books in my personal library a few times. There might be movies in hard drives that I could be watching but I don't like being so passive when I'm feeling tired and under the weather. Yes, I'd rather act opposite of my mood and condition. Otherwise there's no end to the depths I might fall to.

Maybe I can try playing some games? I've already burned through my collection of Deus Ex mods couple of times before, so that's rather out of the question. I don't feel like exploring synthetic biology right now, since while I'm looking for something involved, I don't want to wreck my brain over other stuff, just not right now. Maybe I can look into some mmorpg options? Like one of those free to play games that are all the rage these days.

Online games are one of those interesting things in life that has just so much potential to be awesome, but never is. It's like looking at a seed that continuously ends up dying instead of blooming into the amazing flower we were all promised. Take a look at the .hack// franchise on the playstation consoles for example (actually now that I think about it they only came out for PS2, with final one being promised for PSP). Now THAT's how the mmorpg games should be. Except that .hack// games aren't mmorpgs. It's what they call a simulated mmorpg with simulations of real people populating a virtual server that exists within the game. The game even has a virtual operating system with virtual web browser and virtual email client, with unreal people sending you email during your virtual off-time. The premises sound weird, but it works well in practice, and the franchise continued for close to a decade with one awesome anime series acting as prequel to the game (the game spanning 4 DVDs, with sequel of 3DVD lengths) with not-so awesome other things populating the marketplace (actually, one of the light novels based off the franchise is quite good. AI BUSTER 1 and 2, I personally prefer the second one). Maybe the whole faux-mmorpg setup only works precisely because none of the stuff is real. They are all made-up, make belief people living in make-belief world (oh wait, did I just describe the heart of 'real' mmorpgs as well?).

As Bernard Shaw himself have said before, hell is other people's company. This game can probably better explain the Japanese fixation with androids than any number of academic thesis out there.

Well, I think I'll stop writing for a moment and seek out some interesting mmorpg to waste time on.

Late night or early morning?

2009-07-29T01:05:00.000-07:00

This isn't good. It's four in the morning and I still can't get to sleep. I'm currently running some good lounge music in the background with the evil alchemy of the internet radiostation, courtesy of the smoothjazz. Thinking about things like diybio, synthetic biology, artscience and upcoming nanowrimo competition, which I plan on participating this year. Only 96 days left to go. I'm thinking of telling bunch of my friends to register just to see if they can actually do it. Yes, even the ones that can't write artsy-creative stuff to save their lives.

The filter for the ac might have gone bad. My throat feels sore, but if I open the window the room will get hot again, meaning more sleepless agony for me. Listening to the music and looking outside the window at all the blinking buildings in the main city down the broadway, the whole scene reminds me of setup for many classic Japanese scifi-futurescapes, of the kind that can be seen in the games like the snatcher (if you haven't played it yet, don't call yourself a gamer) and its sequel policenauts, both my favorites.

Picked this picture of an apartment in Seattle from a blog of one of my favorite otakus on the web. How long will I have to live to be able to have a view like that outside my own apartment window? Hopefully this science gig will work out better than it is now... I've never been much of a home person. I prefer cool apartment in high places surrounded by pretty lights of the city over any house any day of the week. There's some quality about those architectures that's really appealing to me... The prices of the apartments in the city are dropping across the board. Maybe I should shop around for the time when I finally get my degree and become a more or less productive member of the society.

It's always interesting that the impression I get from such semi-futuristic landscapes tend to be nostalgia of some sort.

I'm nostalgic about the future.

Another workspace pics. And other things.

2009-07-28T22:20:00.000-07:00

As usual my blog is running a late night double feature, like how the old theaters used to do it. Or will it be a triple feature?

Here's a link to another collection of workspaces, this time workspaces for science fiction writers. All of them are quite well known. Some of them are even known to me. Although I'd have loved to be able to see actual workspace of William Gibson/Neal Stephenson/Warren Ellis with their computers as well. For reasons explained elsewhere I really dig that kind of stuff. I think Neal Stephenson is the person who taught me to take the Apple platform seriously way before it was cool to be Apple (writing this takes me back. In the past there was a time the Mac OSes were horrible systems with windows based computing platforms being the operating systems of the future. People would always get into a fuss about how the public school system was failing the children by letting them use Apple based products while the rest of the world ran on windows. They were so naive back then).
Like I guessed, writers certainly live in a whole lot of clutter. Most of them are surprisingly clean though, even when counting the fact that most of them probably cleaned up a little before the scheduled photoshoot... It's the same with research labs actually. Kid, I'm speak this from experience, so listen up. While everyone out there will tell you that a well-organized workspace/rooms etc are essential for productivity you should see the workspaces/rooms of the most brilliant people in arts and sciences. Trust me, none of them are capable of maintaining a clean room on their own. There's always some kind of mess, some kind of clutter. Ever looked at desktop of Albert Einstein? The thing is like a maze. And, I too have some clutter issues when I'm running large private projects that span months at a time. It's only that I try to clean everything up and keep them clean when I don't have anything long-term running out of my own place (I once covered a whole wall with post-its for notes and plans/numbers for my thesis (of sorts). My then-room was in a truly crazy state back then). However, despite the clutter the workspaces of people who actually work on things tend to have some weird method to their madness. For example, it's rare to see actual 'filth' among the clutter. Sure, there are notes, pieces of papers, books and gadgets everywhere. If the person is in laboratory oriented profession perhaps even some reagents. But never filth. No half-eaten food rotting away, no weird yellow/brown stuff of mysterious origin. All the clutter is information, all of them information vital to whatever he/she is doing. Food isn't information and it's not vital to finding out some new law that governs high energy plasma. Or writing science fiction. Or designing proteins to save human lives. So yeah, if you walk into a work/room of a person and smell rotten food all over the place, the chances are he/she isn't working. Just being lazy and wasting time. But if you walk into a work/room and find crazy amount of papers and scribbled pieces of stuff everywhere, don't touch anything. Those people get stuff done.

Here's a July system guide from Ars Technica aimed at building gaming machines. Even the 'value' gaming machine on here (~$900) is effectively futureproof. You'll be running contemporary games four years from now on with that kind of machinery. you can add some more oomph with careful attribution of either 4 or 8 core processors into the machine, with 16GB RAM or more. But then that would be overkill. Not only would such machine be future proof, it will be on equal standing with some of the heavier single semi-supercomputers in some labs, the kind used for rendering in-house protein calculation. Of course, machine like that will guzzle electricity so anyone who can run that kind of machine for four years is probably very rich or don't pay his/her own utility bills.

Despite the fact that most of my computing needs these days run around mobile solutions systems like that are very tempting to build. Just imagine the things I would be able to do with a graphics card with 1GB DDR3 dedicated memory with all sorts of crazy shader appliances. Not just games, mind you. With upcoming frameworks like CUDA it would be possible to offload computing intensive processed to GPU instead of running them straight out of CPU, in fact turning them into mini suprecomputers, at least compared to the puny units of our current generation. Even laptops might be able to run some serious number crunching once the system's perfected.

Late night. What to do?

2009-07-27T23:06:00.000-07:00

Every so often I'm faced with a conundrum.

It's late night, and either I have something I need to finish before the sun rises, or I'm midst of some strange problem that just won't let me sleep, both mentally and physically. I would normally get some work done in situations like that, but for some reason I can't. There's something in my mind that just stops me from functioning normally, as if some pebble got caught between the cogwheel of my mind. I can feel the urge to do something building inside myself but I can't channel it to something more useful, the energy just disappearing like anything else that follows the course of slow, painful thermodynamic dissipation in this universe. (that makes me think. It would be so interesting to be able to come up with a model that describes human creativity as a function of the thermodynamical mechanism in the universe.)

When I'm faced with such difficult situations I usually try to do something that doesn't require much coherence yet still need some kind of input from myself. And over the years I've found writing (and sometimes drawing) to be the perfect solution for those late night blues... I also play a bit of violin (just picked up a new one a few weeks ago, in fact), but that's a difficult hobby to have in the city where the walls between the apartments are usually thin enough to be punched through (though it isn't nearly as bad as the situation in Japan).

I've picked up a few useless skill over the past few months as well. Did I ever write here about how I never learned to touchtype and how my friends were always giving me weird eye (living around geeks and geekettes have that side effect)? Well I've learned to touchtype about a few weeks ago, roughly around the same time I got my new violin. It only took me about a day or two to memorize the layout of the keys, only to be expected I guess. Considering how I lived with a computer for half my life. The rate at which I got used to writing on the keyboard without using the hunt&peck approach surprised myself a bit however. Right now I'm writing this without looking at the screen. That''s right. I'm writing this while I'm looking out the window of my room, without looking at the screen or the keyboard. Who would have thought it? Learning to type completely blind in course of a week or two.
I still need to get used to the keyboard though. I still make some odd typos and my wpm isn't all that high. Average at best. It's something I really need to work on considering the volume of writing I do on everyday basis, both for pleasure and for work.

When I'm writing things like this, all alone in my room sitting on my couch, I always play some kind of music. In fact, I can barely remember the last time I went on without playing some kind of music around me. The ipod is plugged into my ear practically every single moment I'm outside, and whenever I'm home I play a music on the speakers on my laptop or when it's late at night I use wireless headphones that plug in to the speaker port of my computer (I only use bluetooth for syncing my cellphone with my computer for some reason). Of the terabytes of data I'm sitting on vast majority of the space is taken by music from all over the world, across all sorts of genre. I have Bach, Mozart, and Beethoven, all representing their own era. I have some rock, some of them the harder variety. I also have crazy collection of jpop compilations and singles, and I have many of them in form of original cd sitting in some storage space in the city, since it was way too impractical to bring them with me in my frequent moving binge. I regularly buy musics from promising bands and composers, like the OST/inspired album for Neotokyo. It makes me look like some sort of freak in this day and age where people my age doesn't quite seem to buy anything if it's available in digital format.

Music must be one of the most fundamental invention of the humanity. Perhaps the invention of the music is the event we can clearly mark as the moment of divide between human the homosapiens and human the semi-ape. It's logical, yet impulsive. It's formless, yet the sytem that makes music come true can be observed all across the world, across the universe in weirded places, like the shape of galaxies, pulses of the stars, or patterns of moss in a forest. Music is very mathematical in that regard, and it is probably no surprise that expertise in one usually accompanies the other... There are some people who say arts are too different from the sciences for them to coexist together, but I tend to think it's only a method to cover for their own incompetence. All the greatest artists in the human history had been scientists in one form or the other, and this pathetic division that forces a child to choose between a path or arts or paths of sciences is a freakish accident of social nature that had nothing to do with the arts or the sciences themselves. I say this a lot these days, but really. One day, the future generation will look back at the state of arts and sciences today and laugh or be horrified at how crazy and irrational it all is...

Well I think I'm through venting for now. Gotta get back to work for the day ahead.

It's almost annoying-- And pretty pictures

2009-07-26T17:18:00.000-07:00

I keep on writing double topic posts on this blog for some reason. I think it has something to do with how it's ridiculously difficult to concentrate on something these days, with the weather, the financial situation, and very weird family matters I shouldn't even be worrying about at this age.
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How hard it is to blog properly these days. I mean, sure it's easier than ever to type things up either using my notebook or the blackberry and publish it all right to the net, but it's just way too difficult to write a blog post with properly thought out reasoning and half-decent grammar. The problem is coherence. It's getting more difficult to write things that are coherent. Without coherence within reasoning behind the writing I might as well let my python script do the talking by linking together random words from a dictionary (now that I think about it, that might be fun. Should try it on another blog).

Due to the difficulty of writing lengthy yet coherent pieces of writing I've missed a lot of opportunities for some good posts. New developments in technology like growing of a whole rat from its iPS cell culture from another adult rat (with some issue, but that's only to be expected), or protein-induced pluripotency within cells (the actual paper I have yet to read), or even the hypothesis that emergence of life might be hardwired into the complex system that is the universe (which is something I've suspected for a long time, but this is probably the first time it's been capitalized in a popular science publication). Don't even get me started with the plethora of amazing TED talks out there that I'm just dying to share with you all.

This is one of the most annoying thing in maintaining a personal blog. Am I a content creator or am I just copy-pasting cool news of other people's accomplishments into a digital medium for further copy-pasting, like how it is with most tumblr accounts (with some notable exceptions)? I always to try to write my own stuff but then the product of such creative exercise rarely if ever looks as exciting as the discovery of quorum sensing, new take on complexity sciences, or new developments in synthetic biology...

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On the other note, here are some interesting pictures of other people's computer workspaces. I think I should post my multiscreen setup here sometime in the future as well.

There are more at this webpage. Looking at other people's workstation setup is always fascinating for me. I guess it's a kind of technofetishism/infornography that's so common these days. I know a number of people who maintain elaborate workstation environments and give them lavish names like 'the cathedral' and such (I'd much prefer the term temple or a library, but each to her own I guess). And while I don't operate anything as fancy as that except in my lab, which doesn't count since the hardwares in that place don't really belong to me (8-core with 16GB RAM, 3 screens, wowowiwa!), I understand what they are going for. With the society being built increasingly around the engines of information we call 'com-pu-ter' it's become an essential feature of any semi-viable household. All of my friends think that while it's possible to live without TV, it would be impossible to live without the access to the internet and some sort of computing device. Even the non-techie ones who can't tell the difference between Java and C++. It's a shielded environment where one can fulfill both the functions necessary to life (earning a living) and functions necessary to keep the mind alive. Through education, fun, contact with other people, and just plain-ol time wasting. So the swordsmen take meticulous care of their swords, providing lavish casing and decoration of highest materials for their tools of trade and mental compass. So many of us do the same for computers.
I would love to be able to set up a beautiful workstation like that in my own house, but it is a little difficult at the moment. I move around frequently, both in terms of going around the city for jobs and moving to another place of living for whatever the reason. So my main computer had been a laptop for a long time. And since I can't seem to completely give up the computer gaming side of myself (well, console gaming as well, with PS2 and NDS-lite, but haven't really played them for... Months) all of them were light-yet-workstation class machines with dedicated graphics solution.

Even with mobile computing, however, I still maintain something very close to what those people do with their physical workstation. In the real world I like to keep my desk area meticulously clean. Just some spare USB cables for my netbook/ereader/blackberry connection, my external HD solution totalling at close to 2TB storage space, a lab notebook (paper), and my laptop. That's it. The rest is white and wood. No carpet, no dust. It's really wonderful. You'd be surprised to know how much clean workspace contributes to productivity.
As for 'pimping out' it's usually all in the computer. Instead of buying new exotic figurines or lighting fixtures for workspace like some other people I stick with software side of things. I run custom theme that looks cool, clean, and eats through less memory than the default vista theme. I have personal organize software running on my sidebar as a separate application instead of running windows supplied sidebar, which is, while nice in functionality uses too much memory and is a possible security risk. I am also very careful about choosing my desktop background image. Being pretty isn't good enough to be chosen as my desktop background. It needs to have certain aesthetic quality that works with rest of the software platform. I'm currently running a 3D simulation of human brain neurons as my desktop background and it fits in with all the rest of the computer and my work applications perfectly. It's like the whole thing's made with each other in mind. And the desktop's just the beginning. I also pay significant amount of attention to my web browser, which is probably between the first and the fourth most used application on any computer I use. Choosing a web browser is a really complex, sometimes draining process. Not only should I be aware of the kind of aesthetic look inherent to a browser, I also need to consider their technical capacity and memory consumption. Since mobile computing is a big part of my life I really need to watch the memory and processor power consumption on all my applications. I can't have my machine run out of juice just when I'm about to deliver that paper I've been struggling with three months, you see. Web browsers serve all sort of purposes for me. It's a banking terminal. It's a programming tool. It's an entertainment machine and a terminal to a different world.

At the moment I run three web browsers on my computer. Opera 10b with Opera Unite service activated (more on that later), Firefox 3.5 with greasemonkey and all the necessities, and Google Chrome. I just can't seem to figure out which browser I like the best, but the default browser on my computer remains Firefox for its wider compatibility. Opera 10b is something of a mixed bag. I think I can write a few things that really needs to be improved with the browser but overall the build is very tight, with all sorts of different functionalities and widget availability that makes this browser feel like a separate operating system independent of windows vista it runs on. I'm also in love with the Opera Unite service that turns any instance of Opera browser into a personal webserver with configurable programs/services you can download directly off the net. I can see where this service is going and I like it. Google Chrome is something of an oddball. I liked the browser so much that I briefly used it as my default browser. It's the fastest one of the bunch and you can certainly feel the speed difference compared to all other web browsers. It's secure with the whole sandbox mechanism, perhaps even more so than other web browsers on the market. Google is working on all sorts of crazy projects to increase the functionality of the browser, and it already had significant amount of improvements built into it. Yet the interface remains minimalistic with most of the 'gears' hidden beneath the clean shell some people think is 'too clean'. I like it. It does everything I would ever want from a web browser, and it's open source with full might of Google standing behind it, meaning it's going to places with new and innovative technologies. The problem is with the memory and processing requirements of the browser. It slows my brand new laptop to a crawl when left on for a whole day or two, which is something I usually do with my computers. Opera and Firefox so far doesn't seem to suffer from that problem.

Writing about all these things makes me feel like a geek, or an otaku of sorts. Definitely vast majority of people out there usually don't bother with theming their operating system or figuring out the perfect color sheen of the desktop wall paper or worry about ACID3 test results on their browsers. I guess I am a semi-otaku of sorts. Otaku meaning person obsessed with information, may it be about newest anime or computer technology, biotechnology or robotics. Infornography seem to be the description of how otakus treat information... More on that later.

Wake-up call. Change the world.

2009-07-25T11:13:00.000-07:00

Just a rough draft of something I've been thinking about a lot lately... It's good to be able to do some draft publishing before releasing things as full version. Normally I would do this kind of thing on my handset, but why type away on the miniscule keyboard when I can write in comfort of my own laptop, courtesy of the free wifi access points throughout the city? (which is truly marvelous. Not that many major cities in the world offer muni-supported wifi access points. Like Japan for example. Those people are obsessed with getting paid for letting people browse on their wifi spots)

As usual, I'm busy with all sorts of studying and jobs to keep myself alive. If I've realized one thing abut myself over the course of the years, it's that I count curiosity and pursuit of ever greater 'stuff' of the world to be an integral part of the human existence. I probably can't live without being able to learn more things and step closer and closer to the edge of the world. Sure, food and shelter are about the only things a human being needs to survive directly, but if that were the case the ideal lifestyle would be being locked up in municipal insane asylum, wouldn't it? Freedom of mind and body is just as integral to a living existence as much as immediate nourishments and protection from elements of the world. It sounds obvious when laid out like this but there are surprisingly many people who think otherwise. People with power who effect lives of other people. Goes to show how sane this world is, doesn't it?

I've been looking into more of the synthetic biology stuff, making use of the relatively ample free time made available to me during the summer. I think I'm beginning to come up with a tangible idea and time line for the impending DIY-bio artificial/synthetic cell project. I still don't know if the other members of the NYC group will approve, all I can do is to work on the stuff until it's just as realistic as getting off the couch and going out for an ice cream. As long as I keep the target relatively simple, like having functional DNA snippets within an artificial vesicle, it might work with standard BioBrick parts... Just maybe.

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

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

We have engines of information running in every household and many people's cellphones right now. What is an 'engine of information?' It refers to all sorts of machinery that can be used to create and process information content. Not just client-side consumption device where the user folks money over to come company to get little pieces of pixels or whatever, but real engines of information that's capable of creating as well as consuming. It's like this is the Victorian Era, and everyone had steam engine built into everything they can think of. Yet still nada. Nothing. Zip. The world's rolling at the same pace as before and most people still think in the same narrow minded little niches of their own. What's going on here? Never had such a huge number of 'engines' beyond the expansion of the humanity in history been available to so many people at once. And that's not all. Truly ubiquitous computing made available by advances in information technology is almost here, and it is very likely that it will soon spread to the poorer parts of the world in similar fashion as is with the large cities of the G8 nations.

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

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

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

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

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

This should be a wake-up call to the tinkerers and hackers everywhere. Stop fighting over which programming language is better than what. Stop trying to break into facebook accounts of whoever the snotty-nosed brat is. Get off your fat sarcastic asses and smell the coffee.

Get to work.

Change the world.

Posted via email from bookhling's posterous

VirtualBox and other things

2009-07-14T18:30:00.000-07:00

These days I see less and less utility of full sized laptops as a media tool, since it is technically possible to do most of the basic multimedia and creative works on a well-equipped mobile. I've been watching quite a lot of youtube videos using my blackberry which is surprisingly usable despite its limited memory and processing power. This is with a mobile that's already outdated and in process of being phased out, so the experience is only better on higher end handsets coming out these days... It's a little weird to have access to all the online research papers, video journals and dubbed animes (subtitles will turn me blind on this screen), not to mention IRC and instant messaging clients on the palm of my hand. The ubiquity of information is addictive when you're sufficiently exposed to it and that is a lesson the mobile/connectivity corporations should do well to remember. (That makes me think, the mobile market trend today might have turned out a lot differently if some innovative company could be in charge of both communications infrastructure and handset design, or even, handset design without having to worry about the politics of communications infrastructure. I played around a bit with virtualbox this afternoon. Usually I run vnc within windows to access alternative platforms but thought it would be interesting to be able to run a minimalistic linux/UNIX os within windows installation. I used #! linux, and the whole process took about 5 minutes. It's remarkable how simple it is compared to only a year or so ago. The virtualbox still has a bit of issue in resolving graphics driver that displays resolution higher than 800x600 so I had to do some manual tweaking that involved hosing down one system installation and reverting back to a previous session and reinstalling guest permissions/editing xorg.conf, but compared to some other installations it was all a minor hurdle. ...
More stuff on the state of minimal cell research.
Sent via BlackBerry by AT&T

Posted via email from bookhling's posterous

2009-07-13T19:41:00.000-07:00

It's funny, and somewhat unfortunate that I keep choosing two different topics to cover in a single day's post. Perhaps this type of indecision is the reason behind the stagnant state of my wordpress blog, which tend to demand a bit more quality and coherent thought compared to my livejournal?

I've been watching some Hunter S. Thompson biography materials on the net for the last few days, including a biography tv show on Hulu. An interesting person who gave birth to the style of writing we now refer to as gonzo... Basically a subjective, free form exercise in journalism unrestrained by traditional format. While some might cringe of subjective journalism but then what journalism is truly objective? When you get right down to it the difference is in the language used, and gonzo style journalism never makes any pretense towards their own objectivity. The technique of allowing the reader to gain a first person account of the experience in question was revolutionary in its time and it permeates throughout all sorts of different medium today, starting from the faux-reporting seen in Warren Ellis' Transmetropolitan series, where the whole of the comic was more or less written through the eyes of Spider Jerusalem who was probably modeled after Hunter S. Thompson.

Compared to all the psychos and sickos out there Thompson certainly maintained certain method to his madness until the very end. It would have been really interesting to see what kind of things such character can do given the technological tools of the future/transhumanism. Maybe he might have ended up blowing his head off all the same due to psychological burdens?

I've been having some rekindled interest in Lovecraftian writing recently, mostly due to my little toy project of making a python based program that churns out random, endless stories drawn from expressions in its database. I call it the Monkeyshaker 1000, from an acquaintance's suggestion that 1000 monkeys typing randomly into a typewriter might really end up producing a Shakespear. I've been thinking of all sorts of different things for the program to draw upon and create, and the answer's one of the two.

1)Scientific literature that draws on official (meaning verified, unlike the heap of steaming #$%! we call wikipedia) databases on the net to produce comprehensive reports on rather meaningless, machine dictated topics.
2)Creator of cheap knockoff novella, the kind of stories people commonly refer to as the dime store novel. Such generic novels for entertainment (paperbashing?) usually follow such vapid structure and vocabulary that I don't see much difficulty in making a program to churn out (albeit rather peculiar) pieces of short writing.

I think I'm going with number two. It is decidedly much easier than the first approach, and I already have a cool database to draw upon. The license-free works of Lovecraft. I just wonder what kind of peculiar roman the computer program will be able to come up with using a database full of antediluvian references. Maybe I can title the resulting piece as a result of gonzo journalism in an Lovecraftian universe written by some haywired android.

On the lighter note, there's a science competition going on over at the spacegeneration aimed at anyone under age of 33. You are supposed to come up with a novel method for stopping possible asteroid strike of the Earth using currently available technology or the kind of technology that can be reasonably developed in the future. Novel meaning ingenious. Not another crappy knock off of 'building a superweapon' or 'nuke it' or 'shoot a linear canon nuke' crap that every other one billion and one people proposed already with detailed drawings and technical requirements. Something really new and scientifically feasible. The contest is obviously aimed at students just starting off their interests in space engineering and astronomical sciences, so they might be willing to overlook some of the more incredible ideas, but they are still looking for something worth presenting at the science congress they are having in Korea later this year.

Maybe I should stop by Korea in autumn, see how the whole event goes. Sounds interesting.

Wireless and junk DNAs

2009-07-12T23:02:00.000-07:00

It's very weird how putting things of my day to day life together in title makes it sound like some other whacked out story reminiscent of Haruki and his line of chic-absurdist fictions.

I'm glad to say that after some hassle I got the wireless at my new apartment working at last. The contract for the rent actually comes with free broadband internet access, which I guess isn't too unusual in this day and age. But the thing is, the cable modem in use by the apartment I'm in is a piece of relic that came from when dial-up was still the king and people flocked to American Online services. The initial attempt at connecting the cable modem with a wireless router ended in the cable modem sending out a corrupted packet so arcane that it instantly screwed up the wireless card on my new-ish thinkpad (the roommate's Macbook and my Linux laptop were fine. Ugh, vista why do you suck so much?) to the point that I had to spend the next week figuring out how to get it to work. In the end I fixed it by deleting the device from the system panel and reinstalling it, which was something of a gamble, since according to the google it only fixed anything half the time with no-one knowing the actual reason behind the malfunction.
After my laptop got back into networking-ready shape I stuck with ethernet cable connection for a while at home since I didn't want to risk frying my wifi card again on the poisonous packets sent out by the antediluvian cable modem. I strongly suspected some sort of Lovecraftian mystery filled with murder and hideous secrets behind the nature of the unassuming block of grey plastic and was content for a while living like someone from mid 90's.

Alas, the life chained down by ethernet cable in my own home grew too vapid for me. For someone who needs good access to computer almost 24/7 to pay the bills couch/bed/front porch computing is of huge importance for me. If I'm going to be stuck in front of the screen at least let me choose the location (as a sidenote I frequently work in the park even when I'm outside, the whole sunlight/fresh air around me when I'm working does wonders for productivity). So I decided to do some real research on how to get the modem to work nicely with my wireless router.

Well, it turns out the problem was the age of the router itself. It's made from so long ago when wireless access to net was a precious opportunity for the rich and the cutting edge, it's not properly shielded from electromagnetic field of other appliances within one to three feet of its location. From there on the solution was simple. Use the ridiculously long ethernet cable I've been using for my laptop and place the modem and the router at opposite ends of the room. Funnily enough it worked and I'm writng this from my couch. I don't know whether to be happy or be infuriated by the hurdle I had to go through to get something as simple as encrypted wireless network running.

On the other note, I've been following the Dresden Codak webcomic since the days of its first inception. Even made an id on the forums, though I've only posted there a few times at best. Here's the newest comic at the site. There's something about the combination of the fantastic and the scientific in those webcomics that I find very charming. Yet unlike some other webcomics dresden codak still retains a sharp outlook on the reality that makes me wonder if the author is really drawing the future.

I really like the main character. There's something about her that's very appealing to me on some basic level I can't quite explain. Maybe it's because she's an eccentric mad scientist. And as I have stated numerous times before, everyone at their hearts secretly long to become a mad scientist. I want to be able to stable some portions of my DNA on the fly as well, provided that I have much better understanding of it mechanism and quirks than is available to the academia at the moment. I also want to ponder the questions of the universe and work at solving it or at least understanding it instead of playing second fiddle to the real researchers on the cutting edge of the humanity's learning (and someday I might be able to achieve that, if I play my cards right).

I'm just trying to join the ranks of the diy-mad scientists with my slow-but-steady research on viability of minimal cell system using cheap affordable tools. I really do think it's possible. The more I learn about it, the better the chances look, provided that I don't do anything too elaborate. I'm a little skeptical about the research tool potentials of the diybio minimal cell but then we'd actually need to have something on hand to decide that kind of thing, won't we?

Crunchbang linux and Giant robots

2009-07-11T15:08:00.000-07:00

I'm always on the search for the ideal operating system that would make my life much easier and actually get more work done instead of wasting my time. I guess this is my way of looking for the shiny new thing, just like how some people shop around for accessories and clothes, except that in my case it's all a bit more practical since I get to work in most of the oses out there (but then those people wear clothes to their work too...).

The world's operating system is roughly divided into two at the moment. Linux/UNIX derivatives and Microsoft Windows. In terms of general engineering and architecture MS Windows isn't really top of the line. I'd say Windows as a whole is more like an inexpensive housing and UNIX derivatives Gothic cathedrals (it's actually quite an accurate description of the codebase of both operating systems), except that the housing project costs and arm and a leg and the cathedrals are more or less given away for free, provided that you have the technical proficiency to configure and maintain the juggernaut. Of course, the analogy is a little off in modern days. MS really made strides on their operating system (partly because everyone loves to hate MS) and current vista/win 7 lineup is leagues better than what xp and 98 was, at least in terms of general architecture of the os. And some of the linux/UNIX based oses are really cleaning up their acts and becoming impressively user-friendly, though there are still aberrations like some of the more hardcore BSD oses that seem to view usability=os hazard... Am I alone in thinking that kind of behavior is reminiscent of the old-old times when they complained about schools because having too many people learn will devalue education? (Yep, they really said that.)

Well, of the oses out there Ubuntu distribution more or less tops the chart in terms of user friendliness, along with OS X, which is really just a shiny shell on top of a BSD. Ubuntu is in turn based on Debian which isn't as user friendly but has remarkable stability and wonderful application depository meaning that whatever your needs are you'll probably be able to find and download it for free using synaptic or apt-get. The wonderful thing about such system is that you don't have to google for applications you need. You can just use synaptic and search-download on the spot, with the application being integrated cleanly into the os with rare need for post-installation configuration.

The problem with Ubuntu however, is their opensource-spirit inspired stance against anything proprietary, which is a big thing in this day and age. Take flash for example. It's everywhere and there are nebulous uses for it, ranging from online lectures to lab reports (ah the sad life of a sci student, first things to come to mind when thinking of flash isn't movies or youtube). On conventional Ubuntu distribution anything proprietary usually needs an extra step or two from the user to install them, unlike most modern oses of commercial flavor that tend to come with such necessities. Might not sound like a big deal but this is a deal breaker for a lot of non-hacker pc users out there. I mean, if you're going to advocate opensource to people at least provide them with a decent alternative. Don't just expect people not to use something just to safeguard some philosophical ideology. I'm sympathetic with opensource but some of the approaches being taken by its hardline proponents has a taste of cloistered conceit in them, which I think will hurt the movement in long run. There is a second problem in that Ubuntu is big. Of course, Ubuntu is probably one fifth the size of Vista even at its biggest, but when compared to other linux/UNIX distributions out there they just feel a little sluggish for some reason.

Well, I think I just found the ideal free operating system that has no qualms about providing its users with first rate experience regardless of whether the services are opensource or not. It provides basically all the essentials I can think of in an os, both proprietary and opensource, and it's much lighter compared to similar Ubuntu install. In fact, my fully tricked out installation of that os only clocks in at 1.2 GB of hard drive space (that's os+all the third party apps I installed off the net&depository) with 200MB of RAM usage when browsing with firefox at 5+ tabs open. The installation was a snap too. It recognized all my hardware including the wifi and SD-card reader, and all the laptop-system built in shortcut keys are working out of the box.

They call this the #! linux, which is read as crunchbang linux. It's a modified version of the Ubuntu os I mentioned earlier., except much lighter and more responsive. Unlike most other lightweight distros out there #! has really great hardware support and even better application compatibility. With #! you have the whole of Ubuntu depository on your finger tips, it would practically be impossible not to be able to find an application you need.

If I ever go all out with linux on my primary machine, I think I'll choose #! without a moment's hesitation.

Oh by the way, in case you haven't been keeping up with the news, Japan's Tokyo built a full scale replica of the original Gundam in the Odaiba area.

It's full scale, meaning it's ridiculously huge. For some reason the original UC gundams are rather big with following series progressively introducing smaller, sleeker models.

The amount of detail on this replica is amazing. They actually worked out all the decals and directions for the fictional Earth Federation engineers for repairs/upgrades/tuneups etc. It's obvious they put in a lot of thought into the whole thing. They should really, I think this is for the 30th year celebration of the birth of Gundam.

Again, amazing detail. And the building in the background somehow fits in well with the mecha.

Here's a picture of it at twilight. Just too cool for words. As a side note the apartments in the background aren't really that expensive. In many cases such apartment towns are for middle class housing and common sight in many parts of North East Asia. Some of the newer apartment towns have little streams and parks between the buildings. It's surprising how some people consider the dilapidated and overpriced housing condition in and around NYC is the same in other parts of the world.

And Gundam at night, with the eyes lit up. From what I hear it doesn't move, but the very fact that they were able to build something like that in a major city itself is a big news. Why won't NYC do something fun like that once in a while?

By the way, all the picture are from the Flickr and the wonderful people who decided to upload their pictures.

Life extension

2009-07-09T07:14:00.000-07:00

There are a lot of life extension enthusiasts out there these days. It's been progressively getting more and more media attention with advances in biotechnology and pharmacological sciences... The relatively recent mainstreaming of transhumanism really helped too. It's gotten to the point that there are full scale research institutions out there supported by prestigious universities and grants devoted to the research of the solution to the intriguing problem of death. Maybe it's driven by the life-like system's innate desire to live on. Maybe it's just a show of curiosity, an emotion that had never been too rational to begin with.

Regardless of the validity of the concept of transhumanism in modern world, process of possibly halting senescence is an attractive prospect for the many. Only thing certain in life is death and people are looking toward scieces to possibly ward off that certainly, maybe forever. And there had been a lot of interesting developments in the area as well. Most of the research is being driven by new technologies of gene and protein discovery/extraction, and the latest discovery that came from a fungus of the Easter Islands might serve to demonstrate how some of the most intriguing researches in biological sciences might be made by simply studying the mechanisms inherent in one of the many variants of the living systems already on this planet as a product of years of evolution.

The linked article is more about the effect of the chemical compound rapamycin on older mammals and its rather intriguing effect of prolonging lifespan of mammals from 9~13% even when administered late in life... I am not entirely too sure of the mechanism that allows the mammals to prolong their lifespan through injection/intake of the compound, since aging and effects of aging tend to be results of different innate and outer factors surrounding the organism. If it is possible to use a chemical compound to somewhat prolong natural lifespan of an animal even late in its life would it be possible that there is a definite central mechanism that runs the process of whole-body aging behind the show? Would it mean that it would be possible to prolong lifespans using such artificial compound therapy to prolong lifespan of human beings without resorting to a life time of controlled diet and full scale genetic modification?

Rapamycin is apparently a compound that is already approved by the FDC and in use by the medical community for purposes of immunosuppressant therapy. Would that imply that the aging system built into mammals are somehow linked with the basic immune systems as well? Intake of rapamycin would lower the immune response of the subject, so there definitely is a chance that the subject will in fact die from infections despite increased base lifespan. It's something of a catch 22, and an interesting reminder of the folly of common conception in treating senescence as some kind of flaw or even a disease. If anyone is serious about artificially halting the processes of senescence we must consider the possibility that death might be a natural result of the kind of physical system we have for our body, just as our body requires us to eat and drink in order to sustain it for any significant lengths of time.

google chrome os update

2009-07-08T13:35:00.000-07:00

The Google Chrome OS update

(here's another article with simple overview of what the Google Chrome OS will be about, so far. http://www.fastcompany.com/blog/kit-eaton/technomix/google-drops-bomb-its-own-operating-system)

There's no real new news on the state of the Google Chrome os (from here on referred to as the chrome os). But glossing over the last night's post on the chrome os told me that I didn't really write anything that contains useful information as well, so here's an update (don't blame me, I really needed to go to sleep).

The chrome os will apparently be running on top of (albeit heavily modified) linux kernel. I can only begin to envy the guys who are working on this stuff as part of their paying job... For now from whatever the scant information I can gather on the architecture of the future os points to the Chrome browser acting as a sort of front-end for the minimalistic operating system, though Google's description of that arrangement was more like running an operating system inside a browser, not the other way around.

We should do well to remember that the Chrome browser is a different beast from most other browsers on the market out there with such elaborate processes like... Well, process separation for all the individual tabs within a session, with very likely support for multi-core processor rendering in the near future (an interesting tidbit: apparently someone in FireFox community suggested building separate processes mechanism into the FF browser way before the Chrome ever came out. He/she was more or less ignored of course. And as they say, the rest is history). I guess they are thinking of making every event within the os happen within the browser with each tab of the browser working as separate applications within the os? I can certainly visualize the idea in my head, but I don't know how to make it run well in practice... But then I'm not an operating systems engineer at Google.

The emphasis of the chrome os will be on four things. Simplicity, agility, security, and cloud. The first three seem to be the golden standard for operating systems these days. And they should be. People had been domesticated for overly large clunky operating systems that gets two times slower every year for a while now. And it's not even because of new functions. It's because of the legacy codes. The official Google blog post on the chrome os puts it best as 'not wanting to wait for the operating system to come up so they can use the browser.' Well in my case it's not just the browser, but I certainly sympathize. I have work to do, things to read and write. And I need to sit in front of my computer staring at a logon-splash-loading screen cycle every single day, and then wait for the operating system to calm itself down after the os finishes loading. After all that ritual is over I can finally begin to get some work done, though sometimes I need to wait for the antivirus/firewall program to stop acting up as well if I want a quiet, stutter free computing experience. Sure, the whole thing I just described takes about half to a full minute, and then another minute for operating system stabilization on most modern laptops. At most it takes about two minutes on a bad day, and less than a minute on a good day. Yet, most people don't have 'modern laptops.' Any operating system that performs 'ok' on moder hardware will probably slow any older hardware to a crawl. Since most people these days use their computer at least once every day they get used to such slowdown to the point that they don't even notice something's wrong with it. Only after running into a newer hardware or a different version of operating system do they realize how painfully slow their own systems are (which might have been one of the many factors that contributed to Apple's rise to stardom in the os arena).

Google is stating that they will get rid of the useless middleman, or at least squash him into size of an invisible midget, with the new chrome os. They are promising instant-on functionality with smaller memory footprint and processor usage. They are promising a fully pledged operating system fit for a netbook. Granted, there are a lot of smaller linux flavors out there that measures in the megabytes with full GUI and applications suite, but Google is also promising the Google level of engineering, architectural innovation, and technical support. From what I read, they are shooting for an os that takes 'only a few seconds' from booting to getting work done, which would be unprecedented even among smaller linux distributions out there. The whole of the operating system will run in web browser with no need for things like desktops and docks. All the applications for the os will run within the browser windows (with, as stated before, each of the browser window being separate sessions) and those applications can range from wordprocessor, movie player, and mmorpgs, to a whole sale emulation of another operating system running off the cloud without requiring too much processing power from the client side computer. For someone who lives with the net all day such an os is a dream come true, especially when one of the primary ethos of the os is being secure and lightweight.

Yet the cloud technology (writing about it makes me feel like I'm talking about the luminous ether) which is being considered as the enabler of the philosophy behind the google os might prove to be one of its biggest weaknesses... Or rather, I'm fine with it being a weakness of the os, but there are some people out there who fear that the cloud computing would actually do harm to the computing culture in general. Like Richard Stallman, and Cory Doctorow (to certain extent), both huge proponents of the liberal software movement most people refer to as opensource. I do think they hace a point there. Exclusively cloud based computing culture is not longer a technological movement, it's a consumer movement. As computer technology becomes more and more pervasive in human society (think MIT's oxygen project) they can't help but to become consumer oriented, ruled by the laws of economy rather than creativity... Unlike some other radical proponents of the freemarket (who views the principles as some sort of universal panacea) I view the possibility of consumer oriented computing culture as something with significant potential for harm, especially when it gives the tools for separating the consumers from their own machines to larger scale corporations capable of building and maintaining large scale server complexes required to support cloud computing on any significant level. Of course, the cloud computing scenario isn't all doom and gloom and portents of doom. It's fully possible that the server technology of the post cloud future would advance to such a point that any interested individual can run a 'cloud computing service' out of his or her garage, a private property where he can dictate his own terms.

One thing chrome os can do to, or rather, must do to remedy such possible weakness of cloud based operating system would be including a development/scripting environment with the os. Since the chrome os is based in large part on the chrome web browser I'm guessing the browser+address bar interface can provide some type of shell access to the user. The command line-shell application can run in the browser windows itself when called through the address bar. I don't know about compiled languages but it should be relatively simple for the os to provide a scripting language support like python/ruby and lua... Android OS's recent inclusion of scripting environment that supports lua and python certainly is a good sign of things to come, even though both operating systems are said to be different from each other... The important thing for the chrome os would be to have great support and tools for letting users develop their own applications within the chrome os, instead of making them rely on other systems/pay-to-purchase tools/high end hardware dedicated to software development.

The chrome os isn't set for release until the second half of 2010 on netbook platforms, although the official platformless release will come much before that. I'm guessing it's a move to optimize the os before it gets released to the wider audience. Surely we'll get to catch more glimpses of the os in development or perhaps in action soon.

I'm sick and tired of oses that fail me all the time. I just can't wait for the chrome os to be released and bring something unique to the dull and constricted os marketplace.

Google Chrome OS

2009-07-07T22:47:00.000-07:00

It's almost two in the morning now in the city. I was just about to wrap up my writing session with Mathematica/LaTeX when strange news of a new operating system came flooding in through the internet. The RSS reader registered a mention of Google Chrome OS from ArsTechnica while I received links to an article on NYTimes on the possibility of Google OS, and then the flood gates opened on friendfeed and twitter. Apparently the Google OS is something people had been secretly fantasizing about all these years, since it's currently trending at the top of twitter trend list recently occupied by MJ's death. Yes, MJ fans. A news of a computer operating system that's not set to be released for another whole year just beat out MJ's death news on twitter. Read it and weep (no disrespect to MJ, but it's about time though).

There aren't any detailed news coming out of the Google regarding the OS at the moment. I'm risking disturbing my sleeping routine on a workday (yet again) to find more news about it, being an OS junkie I am (not good with computers, I just like Operating Systems for some odd reason). Yet no new news beyond the single blog post on the official Google blog and some smatterings of articles on the web, most of which point back to the official Google blog post.

I don't know what to say. I'm probably one of the few zillion people who've been waiting for Google to get to work on some kind of major operating system for a while now. I'm something of a hobbyist of the Android platform already, and my primary web browser was set to Google Chrome right until Firefox released 3.5 and one of my favorite otaku web celebrity went some lengths to support it. I'm seriously considering switching back to Chrome now, since all my bookmarks are on delicious now I don't have to worry about switching browsers anymore. It's all available from the web through the horrible alchemy of cloud computing.

I am somewhat skeptical on the whole Google OS issue though. While I love the idea, and I certainly will install it on a new pc (will need to hunt down some old boxes I don't use anymore... Sadly I can't really experiment on my work laptop), pushing out a whole new operating system is kind of a big deal. And this OS is supposed to be based on Chrome, the web browser. Last OS to attempt something with such bravado was Windows OS (the whole of the operating system runs on i.explorer shell) and they really got burned for it. Although I must say it would have turned out a bit differently if the web browser Microsoft used as their operating system shell wasn't such a clunky mess... So would it mean that Google Chrome OS would stand a chance of becoming a classic operating system like the hollowed OS X and WinXP (I know, I know, but lasting for a decade as the defacto operating system of choice for the world needs something more than marketing savvy)? The Chrome web browser is certainly leagues better than what Internet Explorer was/is afterall.

There's one more thing I'm worried about in particular though. The Chrome web browser is something of a resource hog, though not nearly in same level as I.E. Chrome, perhaps due to some of its advanced features, can't run on older operating systems wherein modern Opera browser for example have no problem running on Win98. Also I do remember some people complaining about the responsiveness of the browser under anemic/archaic hardware settings. I still remember the day I found out that 5-tab strong Chrome session will slow my then-3 months old Thinkpad if I left it open and running overnight due to some issue in memory/processor management. The most recent update to the Chrome fixed most if not all of such conspicuous issues but I still have my doubts. This is especially alarming since the first iterations of the Google Chrome OS will be coming out for netbooks, which tend to have even weaker hardware than laptops, which falls behind desktops.

There's also the danger of how viable future market for netbooks might turn out to be. It's always possible that people decide they want cheap larger laptops afterall (which is probably the reason why some of the bigger companies still don't have a decent netbook line-up of their own. I'm looking at you, Sony. The jokes you put out on the marketplace shouldn't even be considered netbooks, though you do make some good laptops).

And of course, as with the Google Chrome/Chromium web browsers the whole operating system will be open source, I'm guessing in similar style as linux or BSDs. Which in itself should be enough to make people drool over themselves... Now that I think about it, my current netbook Asus 701 4G (the first commercial netbook that ever came out in the U.S.!) is about due for an upgrade. Maybe I should hold out for an year and get my hands on the first production units of the Google Chrome OS netbooks!

I eagerly await for our future Google overlords.

Biolinks

2009-07-07T20:03:00.000-07:00

Just some bio related links for people who might be interested.

The molecular biology webpage usually have really cool resources for biology scientists and enthusiasts alike. So it's a given that they would have something pertaining to perhaps the most widely used web browser among biology/biotech people out there.

This year's list of must have biotech extensions for firefox researchers have some useful research tools, though for some reason they neglected to mention some of the other cool extensions like the biofox and other in-browser biosequencing tools. There are operating systems out there that are geared toward scientific research, and it's about time we have something like that for the scientific community as well. Before someone gets the idea to build a fully-pledged research web browser firefox is the one that best fits the profile due to its extension system.

They also have a website listing 10 best podcasts related to biology. I highly recommend the U.C Berkeley molecular biology course. They cover most of the basics in a very beginner friendly and comprehensive manner without skimping out on the details like some of the other beginner friendly academic podcasts out there.

I think the idea of academic research oriented web browser is something worth thinking about. Since the opensource webkit rendering engine's already out there most of the major works would involve figuring out the best services and layouts for academic research built into the browser (with extension support?) and optimizing the codes for lower memory usage... Huh, put in this way the project suddenly sounds a bit overwhelming.

An excerpt-small hours of the morning

2009-07-05T22:25:00.000-07:00

It's way past three in the morning and I still can't go to sleep for some reason. Maybe I'm suffering from an onset of insomnia? I do certainly feel rather tired, so why won't my brain stop spinning thoughts and go to sleep? I'm getting worried. I have early day tomorrow.

Anyway, might as well make the best of the waking time I have. Read an interesting article pointed through Doctorow's twitter post. It was an article about science fiction and abundance of practicable facts. I want to share an interesting quote I found in that article.

""
Or, more succinctly, in order to get the marketplace off its ass to solve the impossible, you have to just pull off the highly improbable and make sure everybody knows about it. Show it can be done, show how you did it, and watch the "marketplace" attack because you've made the "premise" "plausible."
""

Hopefully my blackberry-to-email-to-blog scheme is working out here, I'd hate to have the whole page messed up like some other times before.

I love that quote. Maybe it would have been better if I could find something cleaner and concise, but hey this is a post being written on a handset while waiting to fall asleep.

The best way to make people what you want to do, is to do the improbable. The best way to teach a subject to a person might also be to show them the possibility of the impossible. Between students who've witnessed first hand the possibility of an improbable exercise-composing working genetic circuit on blackboard through abstraction symbols-and students who think those things are still within the realms of science fiction or upscale laboratories, it is obvious who would be more enthusiastic about learning. Of course, when you get into it there's the whole issue of the student possessing certain degree of curiosity in the first place, but I won't get into it here and now.

I love the idea of always-on network access and unlimited internet on mobile devices. I can definitely understand how many Japanese people almost exclusively use their handsets for their online presence and blogging/photo sharing needs. Makes sense. If all you need to do is write up informal blogposts and post pictures of your favorite moments in life & keep digital connection with friends why bother getting even a laptop? All that is possible with your handset and it has added benefit of allowing you to compose your works while on the move. It means you can use that wasted times for something a little more productive. The modern society at large, despite its rapid pace, is surprisingly wasteful in terms of time management. Many people waste hours per day just to get where they need to be, and classes waste hours per day waiting for kids to sit down. Mobile technology offers people a chance at using those wasted moments to do something creative, whether it be writing a keitei novel, taking and posting interesting pictures and videos, or just plain reading... The apparent lack of interest in mobile technologies by large corporation in United States (at least before the iPhone came out) is difficult to understand, and just goes to show how complascent those people can get.

Now that I think about it, are current generation bluetooth-ready cellphones have the capability to connect to a printer? Now that would be awesome. The cellphone os can provide the basic framework for setting up a page and the user would simply type in their mobile, printing their product directly from the printer, whether it be a short story, important email, or pictures taken on the way you want in paper format for whatever the reason. It would certainly be possible to do lighter homeworks on mobiles.

If there is a problem with the mobile oriented internet society, it would be difficulty of content creation inherent to the platform. You can certainly write and compose/draw using the tools the corporations give you, but most often you can't go beyond that. Japanese keitei culture, while impressive, is also one of the most oppressive I can think of in terms of software/hardware freedom (what makes it even more impressive is that the contents generated by the harshly locked-in culture is even more impressive than supposedly 'freer' U.S. market. What does that imply?). It's more or less out of the question to be able to run scripts or program things on your mobile. Most often applications available for purchase for your mobile is locked in by carrier with no opportunity for transfer, and all the rights to the application is owned by the carrier. It would be preposterous to demand sourcecode to anything. It's almost as if the customers of the carrier companies are spending machines that print money for the corporations within tightly controlled ecosystem (don't be too hard on those Japanese carriers though. U.S. Carriers are more or less the same, and some others are even worse, it runs like communism with cellphone carriers sitting at the center). Cory Doctorow once tweeted that such locked-down nature of mobiles make it unlikely to be a suitable communication/computing platform in third world nations. It's a good point.

And that is precisely why we need to work toward open specification open cellphone systems. Google's Android is a good first step, integrating relative platform freedom with user ability to write and run scripts like python/lua on their own machines. Yet I believe it would be unrealistic to count on developing nations getting their hands on those multi-hundreds of dollars gadgets that need to be recharged every day. In realistic terms, deploying current android based handsets in developing nations would be forcing many families to choose between a half-year's schooling for their kids and a fancy handset. At least OLPC was an education platform. A mobile is something that might go beyond that. Any realistic deployment of mobile must be based on commercial viability of the nation's people to afford that piece of technology, even should the telecommunications infrastructure for the mobile is subsidized by their local governments.

It means that we need a new strategy for future-proof mobile deployment in developing worlds. Something simple. Something that DOESN'T HAVE TOUCH SCREEN. It might not even need touch screen, just something monochrome that can be visible during the night. Something that does not need PC sync. Something that last for days on a single charge like any decent business phone. Something cheap with flexible enough OS that user with enough technical knowledge can program/script it from within. Something cheap and reliable and DRM free so people all over the world can knock off their own versions like they did with AK-47 from old Soviet Union, except that these handsets save lives and businesses instead of ruining them.

That would be the mobile to bring the rest (read:majority) of the world into the wired future. It might even be the basic framework to build our own future on. iPhones and Google Ions, remarkable devices they are, just don't cut it when we begin talking about the future.
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Mnemosyne and personal commuters

2009-07-03T14:50:00.000-07:00

I'll get the personal commuter bit over with first.
The modern American society is built around the culture of suburbanites. While I've spent practically all my life in urban centers with high rises in America and elsewhere, there's no doubting that the very culture and technology that runs what we now refer to as American, as opposed to Japanese or European, runs around the concept and execution of suburban living centers. Indeed, in this country life-long urbanites like myself living in nyc would be more of an aberration. And one of the major factors that makes such suburban based social system even possible in the first place is the personal mobility offered by presence of cars. Lots and lots of cars. Most of my friends in city areas don't own a car and frequently don't feel the necessity to own a car, since using public transportation system + some assortment of short-term rental car service almost always work out cheaper and easier than the endless battle with cars, insurance, and parking space. Yet it would be suicidal for any suburbanites who compose the vast majority of the population of the United States to not to own a car unless he or she expects to walk on highways with groceries and school children in tow.

Apparently this is T3's new model of personal commuter vehicles, designed to ship people to their jobs within smaller urban and suburban settings. I'm dearly hoping for something like this to hit the marketplace soon, It's three wheeled design is certainly underpowered in any rugged terrain, rugged in this sense meaning any terrain with above average elevation, covered or not. Yet there are convincing evidences that suggest that such vehicle support design is actually much more fuel efficient and mobile compared to the traditional four wheeled drives. No matter how you look at it this is a kind of vehicle designed for simple grocery pickups and short range commutes, a perfect fit for anyone who needs a simple mobility system that's more powerful than a segway but smaller footprint than a fully pledged car. The design leaves much to be desired (personally) but I can imagine something like this practically flying out of the dealerships in droves around price-conscious middle class income area. I can also imagine many of the developing world markets flocking after a vehicle like this, especially if the nations get around to supporting international emission standards through some sort of tax break to manufacturers of fuel-efficient vehicles like this.

This makes me think, it's surprising how we still take mobility for granted. Even in this age of internet shopping malls and semi-omnipresent network, the world comes to a standstill without a real mobility solution in place, something that can get people and things from one place to the other fast and cheaply. And it's all the more surprising how we still don't seem to have made any major breakthrough in the area of physical transportation since the heyday of Ford. Almost makes me feel that the world had been standing still in certain aspects of technology necessary for the future.

This is a new 'luxury' usb based memory storage device named Mnemosyne, after the Greek goddess of memory. It's ridiculously expensive for what it offers. 16GB of storage within a 3D jigsaw puzzle container made out of aluminum (what's with element Al and people these days? Everyone's building something with it. Did mineral prices suddenly drop or something?) costs about 7k euros or pounds, I can't recall which but in either case the drive is crazy expensive. As any computing enthusiast should know, running industrial strength multi-terabyte hard drive array won't cost half as much, though it probably won't look as good.

Personally, I don't think there's anything wrong with charging a premium for design. Someone actually need to work to make a good design. You see, there's this prevailing myth in modern age where people for some reason equate good design with good decoration. They are different. There are some zen buddhist temples out there that's been standing for hundreds of years. They are very simplistic with almost no variation of colors with thick beams and practically no decoration in any traditional sense. It's a huge building that exists as a pure manifestation of geometry in corporeal world, a place of meditation where the Platonic ideas meet with the changing nature creating a timeless void of contemplation. In my mind such temples represent the very pinnacle of what 'good design' means. Not just in their simplicity but in that the architect used that simplicity as a tool to create a piece of space where the human will manifests along with physical reality. There are some late-Gothic cathedrals out there that also embodies the very same principles through the irrational exuberance of decorations, the opposite of the zen temple architecture but nevertheless achieving the same goal of good design, creating a timeless yet dynamic space where the human spirit manifests.

And ridiculous prize aside I think I like what the designer of this 'memory device' was going for. Solving through tangles of timelessness into the very core that contains the memories the owner deems most essential to his or her being. I just wish someone who'd buy that would actually have the mental capacity to meditate on their experience, but for some reason I remain skeptical on that regard.

Nethernet and Mr.Brain

2009-07-02T11:34:00.000-07:00

The title to today's post sounds a lot like a title to some quirky Japanese NT novel (really, maybe I should write one). I love the NT/light novel scene in Japan. While vast majority of the works being printed out are of rather dubious quality (to put it mildly), the scene is a sort of youth oriented counterculture to the traditional literature scene which is also as stale as it can get despite the significant volume of works being put out to marketplace. It gives many of the genre writers certain degree of freedom in choice of characters and scenario, which often ends up producing easy-to-read works of Borges-ish fantasy coupled with an eye for modern trends definitely influenced by Murakami Haruki's style. It means fantasy novels that are called such because they are removed from conventional reality, not because they follow 'conventions of fantasy' like it is in the American publishing industry. The first time I looked through the American fantasy novel market after arriving from Korea/Japan cultural sphere was certainly a memorable moment in a very bad way. Hundreds, if not thousands of novels set in roughly the similar worldscape, so similar that they could easily interchange characters and settings between each other and it still wouldn't feel out of place. I felt as if I was standing in middle of a desert, a desert of dry, parched books filled with apathetic heroes all cloned from the same gene pool. And this was back in the late 90's, when Japanese mangas and animes were still a very underground thing, with major T.V. stations airing any kind of anime being some kind of wet dream. It is during those days that I gave up on fantasy entirely and instead turned to fantasy-like literature novels of European and South American variety, namely Neil Gaiman, Michael Ende and Jorge Luis Borges. I can't believe anyone would choose to read those dry fantasy novels when they can choose from any of the three authors I linked to above, and get lost in the true epitomes of human imagination, fantasy as it was meant to be. But I digress.

Nethernet in the title of the post is in fact a name of a weird mmorpg-like game that you play through an add-on toolbar on top of your firefox browser. It's a weird game where the majority of the action takes place in form of exploration of webpages, with different character classes capable of laying traps or countertraps through various websites, or leaving portals and lamp-posts forming missions and stories by piecing together the random components of the web into a structured whole. Some of the missions created by the Pathmaker class include 'the most amazing temples in the world', 'the list of unusual inventions', 'Jabberwocky' and 'brief history of the tubes.' In many ways the game reminds me of everything2, a predecessor service to our current wiki-dominated landscape, though they were much more whimsier than some of the wikipedians who seem to think they know everything (hint: they don't). All in all, a very interesting experience, and I can see it's utility as a very useful learning tool for kids and adults alike. I also love the steampunk inspired design of the characters and terms within the game. For someone like me who doesn't really have time to devote to a full-length game anymore the nethernet certainly provides an interesting alternative.

I've always been partial to j-dramas due to their quirkiness. I think it's some sort of side-effect of having real actors imitate manga or anime situations and premises, but despite some corny moments here and there the experience tend to have some weird, addictive joy to it here and there. My interest in j drama was recently rekindled by my cousin's visit a while ago. She's a serious j drama nut, and she brought me a gift of dvd box set of a series called Nodame Cantabile. It's just as quirky as the rest and serious fun. I love classical music and comedy, the show has both. You would have to be one pretentious piece of work to not to enjoy it.

Well I've run across another j drama on the web that I plan on following through. It's about a neurologist working in Tokyo metropolitan science department's criminal sciences laboratory, a setting obviously influenced by the likes of CSI, with the important difference being that this show doesn't really take itself too seriously (just like vast majority of j drama out there). I've only seen the first episode so far so I don't really know what to make of it right now, but if this show's only half as good as Nodame I'm good. It's really refreshing to see drama series that doesn't take itself too seriously. So many people these days seem to suffer from the disease of pretentious philosophizing without any depth, you might as well get some laugh out of it.

Demoscene and mathematics

2009-06-30T21:24:00.000-07:00

"Noted mathematician, Marston Morse once said “Mathematics are the result of mysterious powers which no one understands, and which the unconscious recognition of beauty must play an important part. Out of an infinity of designs a mathematician chooses one pattern for beauty’s sake and pulls it down to earth.”"...

Thus begins an interesting post over at the spillspace.com , a blog on life and art that might be worth browsing through if you're interested in that sort of thing. The quote captures perfectly the very essence of mathematics that attracts people and sometimes captivates them to such a degree that they give their lives to uncover more of the infinite secrets of mathematics. I've always had a very complex relationship with mathematics, a weird mixture of constant hate and obsession that held a significant part in forming the human being I today recognize as my self. Mathematics might as well be the closest thing to a link that connects the separated realms of arts and sciences, the mind and the body...

I don't know what to call mathematics, I can only describe bits and pieces of it in fractured and stuttering words since my heart and my mind lacks the experience and wisdom to fully describe it's promises and truths.

The task of describing mathematics become even more labyrinthine when we consider the single most curious trait of the mathematics so far. People in the business of academic studies frequently refer to it as the unreasonable effectiveness of mathematics in the natural sciences. This mysterious trait of mathematics as a whole is the single most important factor behind the perceived difference of humanity from other common life forms. Indeed, it won't be too much of a stretch to say that this is about the only difference between human beings and other animals of similar genus, making this in effect the heart of the spirit of humanity next to the mysterious mechanism behind the constant urge of living things to create... And both the primary questions of my life, one of the things that constantly haunts my mind and my heart through every waking moment.

So a guy I know introduced me to the computing cub-culture demoscene before. I was aware of their activities even before that but the quality of their works way surpassed my expectations. Demoscene in modern era is basically a form of computer art derived from first generation personal computers of old like Commodore and Apple ][, and in many ways continues the tradition through strict adherence to economic memory management and other programming techniques which sets it somewhat apart from other programming oriented computer arts based on processing language and such. (and no, who those who have no idea what processing is, it's not a computer graphics package. It's Java based programming language used for algorithm based arts, and there is no 'drawing' involved in it)

From what I'm seeing the demoscene is a little dead, probably due to the difficulty of asm based program optimization (though I must say, even those people don't code strictly in asm anymore. They run optimization programs on a program completed using more conventional programming language like C). And then there's also fact that there are more powerful and easier computer art programming languages out there such as processing (and others I can't remember at the moment).

I'm beginning to consider the possibilities of applying the algorithms for simulating complex multidimensional mathematical shapes within computer to demoscene toolsets.... Seeing how so many of the computer based algorithm arts projects in demoscene and elsewhere lacks stylistic creativity, application of advanced techniques of computer aided mathematics and sciences simulation will be able to bring a breadth of fresh air this fascinating field of hackerdom and art.

Imagine science film festival fundraiser

2009-06-27T07:09:00.000-07:00

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Mahou Sensei Negima

2009-06-23T08:07:00.000-07:00

It was a rather cloudy morning when she came to visit that day. I was still a little zoned out from prior night's outing with bunch of friends which only ended around 3am. The doorbell rang and I found her standing outside the door with bags and manga books in tow. I guess it's that time of the year again. My cousin came to visit me in New York.

Time to time my cousin comes to visit me, or vice versa. She, her brother and I practically grew up together when we were young, and we feel like siblings all in but the name. We always have so much fun when we are together, and our last meeting culminating in cross-national journey spanning remote forests of Korea to the Metropolitan center of Osaka and temple of Kyoto. We had so much sushi back then. And of course, sake. Lots and lots of sake. Oh god I miss all those food.

Her brother is in New Zealand right now, finishing up his studies though. And she should be busy prepping for college in Asian cramschool hell (where school day for average student not particularly diligent starts at 5 am and ends at 12 am) so I was a little lost to see her here. I guess she's thinking about attending NYU or something if her testing doesn't work out?

I was still a little woozy at the time she showed up so I went back to bed after letting her in, at which point she began jumping up and down the bed and such, the usual for her... Apparently she's only staying in the states for two days (well, at least in NYC, she still needs to stop by San Francisco) since she can't take a break from her studies for too long. It's a shame really, I was secretly looking forward to seeing the guys before the summer's over. And with the pace at the internship I can't really take a break until the summer's over. I guess life is catching up with everyone having fun.

She brought some of her NT novels and mangas along (yes, even for a few day trip). And she introduced me to a series titled 'Mahou Sensei Negima.' I wasn't really interested in the manga at first, especially since the manga was written by the guy who made that harem manga with guy and lots of girls in love with that guy for some inexplicable reason (can't remember the title). But then I read through a few chapters (I was forced I tell you) and I was captivated by a single location/plot device within the manga.

They call it the library island. The physical design of the library island is lifted off a real world location of the island of Venice.

It's an island within the school Negima works as a teacher. The island itself is a huge library that goe back hundreds of years and it seems no one is really aware of the full layout and content of the library. It's apparently of such complexity that there is a separate department and clubs within the school that are devoted to exploring the library and all it's secrets. Who cares about the creepy setting filled with crazy pedophiles and incredibly dense (yet certainly likable this time, unlike that other previous work I can't remenber the name of) elementary school student who has magical powers with such an awesome library as one of the primary settings?

I don't know why but there's something about the idea of a magical library that really makes me feel giddy. What mysteries and hidden truths of the world await? It's a real shame that our civilization at this time does not seem to have enough understanding of the universe to be able to build such a library... Perhaps the coming of the self-aware web would be the first step in putting together the disparate informations of the human world together into a cohesive form, a singular library where the collective spirit of the humanity lies.

Anyway, it's about time to take my cousin out to something delicious. I'm thinking Max Brenner's with either sushi or bbq.

Excerpt from a book

2009-06-22T18:19:00.000-07:00

"The intellectual power, honesty, lucidity, courage, and disinterested love of the truth of the most gifted thinkers of the eighteenth century remain to this day without parallel. Their age is one of the best and most hopeful episodes in the life of mankind." - Isaiah Berlin

There is a book titled 'Consilience: the unity of knowledge' by E.O.Wilson. Buy it, and read it. It's worth more than a hundred iPhones, unless the said iPhones have copies of the Consilience on it.

The book had such profound impact on me when I was growing up, I really think I should do a review/post on the book and some of its themes one of these days. It came out years ago yet the prescient insight of E.O. Wilson rings true to this very day in many fields of human endeavor. I had the chance to listen to his talk live in the closing event during the wonderful World Science Festival in NYC, and I should say he still seem to retain that certain edge even after all these years. I guess that's what we Koreans call No-Ik-Jang for you.

pretty pictures.

2009-06-21T08:38:00.000-07:00

I make a pretty good use of a lot of web 2.0-ish services out there. Although I haven't had much chance to use it lately due to my schedule, I'm (or at least used to be) a pretty heavy user of tumblr as well, linked to my friendfeed and google reader syndication.

Today's been one of those remarkably free/lazy day for me, waiting for a pending application of sorts that I need to confirm before my life can continue its ever ambitious spiral toward freedom. So I spent some time browsing through the aggregated content from my contacts in tumblr and thought I might as well share some interesting pictures I came across, no doubt influenced by the habit of my acquaintance (I suspect that he uses picture posting when there isn't much to write about).

Here's one I found first. As those of you who know me are already well aware of, I'm something of a gadget geek. I love things I can tinker with, whether they be molecular systems or robots, or even something entirely trivial like desktop computers. I also happen to like classical sculptures (though I guess you can't really call a Rodin classical sculpture), so the well known pose of the vehicle-robot was something that instantly caught my attention. For some reason I thought of German cars after I saw that robot, but then the logo is that of Honda, the eponymous Japanese car maker.

It's one of my secret lifelong ambition to be able to create a thinking system that is not based on human anatomy. I've been doing quite a bit of research on the subject (which is itself inspired by the dreams and methodology of Juergen Schmidhuber, the genius scientist in pursuit of an artificial scientist) and I'm beginning to suspect that there's something fishy about how every single thinking system in the observed universe are built on top of complex biological systems. Am I going to far in assuming that there might be a fundamental correlation between the two traits on a very physical basis?

Here's a beautiful picture of Tokyo skyline. Well, not really a skyline, more of a single building with interesting composition of colors. I used to travel to the Asian region almost every summer for the past ten years or so. I have relatives living all over the place so it became something of a fun thing to do when I couldn't think of anything more fun. Now that I look back on it I lived a pretty luxurious life. Not everyone travels across two continents and four countries almost every summer 'just for fun.' I've even been invited to Cannes and Florence (for those of you who don't know, France and Italy). If it's not luxurious on a student budget, I don't know what is.

Now that the summer's come again, I'm starting to get that yearning. Whenever I see pictures like this I get caught up in such nostalgia. When you travel like me, you begin to notice the differences of minutiae, like subtle change in smell of the air for example. I love Japanese air. Oh, and the colors. The colors forming the cities and towns, even natural flora and fauna are all different in each countries. It's like there's a different aesthetic theme that composes different societies across the world, with different emphasis on different colors.

Although I'd love to pack up and leave right now, I can't. At the rate my internship is going I'm under the impression that it would be much better for my future to stick around until the very end. Since I plan on making my living doing odd bits of research I can't afford to go off on a tangent at this point in life. Although, I am seriously looking into stopping by Seattle before the summer's over, with the pax happening there. I might even arrange to visit local chapter of diybio while I'm there. I also need to stop by Boston later, but that's all the way in October, so I'm not going to worry about it for now.

An idea

2009-06-20T21:14:00.000-07:00

I should definitely do a post about the impending second Renaissance on the global scale. I can always use the significant emphasis being placed on visualization and simulation of complex systems that stands at the boundaries of arts and sciences as a supporting reference. In most cases, I find that scientific art tend to be the most profound one of them all. And I also find that most of the masterpieces of modern and classical era to be scientific in their approach and practice. The currently perceived 'divide' between arts and sciences might even stem from the behavior of the artists refusing to do anything other than what they've been doing for hundreds of years. You might not want to learn vector calculus for the sake of your art, but that doesn't make it right.
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Architect and Architecture

2009-06-19T23:53:00.000-07:00

Those of you in the know are probably aware of my fixation with computer games. I haven't been able to play like before though, with real world jobs and school works getting more intense by the day. Yet I still like it enough to manage to play some whenever I can afford to do so, and I'm certainly guilty of some recent sleepless nights spent on playing the Nameless Mod for the pc game Deus Ex (I'm still so impressed by the one gigabyte modification that I plan to do a full-ish review on my blog at certain point in the future, barring any major catastrophe).

Although I should say, my relationship with games doesn't seem to resemble experiences a lot of my contemporaries seem to share with the medium. It's not really that I enjoy the normal leveling or the adrenalin rush that comes as part of the experience. I certainly enjoy the experience when occasion arises, but thrill of playing computer games isn't enough to keep me up at night. If it was just about dodging bullets and jumping over ravines I would have all but completely given up the hobby entirely (or rather, I would never have gotten acquainted with the medium in the first place). As such, I can't understand the degree of fixation some people seem to have toward what we now refer to as 'arcade' games, the kind of classics that came with the very beginning of the art of making video games itself synonymous with long-dead titans like Atari and Spectra ZX. Maybe Alfred Hitchcock was right in obsessing over the obsessive nature of human beings as the primary vehicle in lot of his works. Maybe Pascal was wrong in concluding pleasure as the primary vehicle of human endeavor. Maybe it's all about satisfying that life's constant unspoken problem that comes as part of being a conscious being.

I play games for their immersion. I love some of the stories in the games. They needn't even be complex. I'm not looking for Nobel-worthy wordsmithing in games. Even simplest plots, when used honestly and effectively in conjunction with variety of other elements like characterization, visual effects and beautiful sound, bring the world alive... I play games because good games have the tendency to bring its own world alive through most marvelous means available to the medium, which tend to be some complex juxtaposition of light, sound, and audience participation. I guess you can say that I like games for the same reason I like to read stories. There's something about such experiences that stirs the heart and makes me feel like a human being, not just another animal that happens to walk on the face of this planet. As such, the kind of games I like are not usually the most popular of the games, though interestingly all masterfully crafted games young and old tend to share the quality I just described regardless of their genre and play mechanism. Immersion through any medium isn't just about exploring and looking at pretty things however. Good engines of immersion offer something more than that, a certain feeling of almost spiritual stability and yearning.

As I play around with games, I've come to discover something about the experience that I found interesting enough to warrant some quick note for future reference (and fleshing out?). I've come to consider computer gaming as an exercise in recreational architecture. Sometimes it's more like a stage design rather than full-on architecture, but from what I'm seeing the gap between theoretical/recreational architecture design and in-game world design is narrowing, and I believe they will merge to something new in the near future as the computer technology that forms the backbone of the artistic design of computer games become more powerful and flexible through the evolution of developer oriented SDKs and growing divide between a game creator and computer programmer. Indeed, we are looking at a growing number of computer/video game directors who are only proficient in ethos of computer programming, as compared to the hacker geniuses that gave birth to the likes of Id software and first generation of truly mass-market consumer friendly gaming experiences.

Aside from treating the virtual medium as tool of architecture, architectures present in game worlds themselves always fascinated me. They were the pinnacle of the manifestation of the impossible, their impact magnified many-fold by the nature of the computer game as a virtual reality. Escher could always draw twisted dimensions on a flat sheet of paper and people would wander through it using their eyes and imagination. If Echer was alive today he would be crafting such worlds using the computerized medium, and the audience would sit in front of a screen and literally walk through the ever recursive halls of the creator's imagination, as long as they aren't caught by some clipping bug that so frequently haunts complex geometries of the virtual world. A popular example would be the Combine Citadel in the eponymous game, Half Life 2 from valve software. The very ominous presence of the building that you see in the beginning of the game sets the mood of the entire game universe throughout, it's design and enormous scale impacting the user as a continuous source of psychological burden and morbid fascination. Other examples would be most larger scale 3D mmorpgs out there. Games like lineage 2 frequently placed heavy emphasis on elaborate and grand architecture within their landscapes, perhaps to compensate for the relatively lackluster content on other ends of the medium like the story and characterization (both of them issues that haunt most if not all mmorpgs today). I used to play mmorpg called Ragnarok Online a few years ago. I've played it so much that I've practically been to every single map on the game server, and there was this particular location I would always 'hang out' in the game world when I'm not off to some labyrinthine corridor killing undead monsters (which still is the best way to level fast in that game btw, the priests trump over most other classes in face-to-face combat over there). It was a library located in a floating magical city called Juno. The city of Juno would always be enveloped in perpetual autumn due to its altitude. At the edge of the city was a huge library of multiple levels at the center of which was a huge book one must read if he/she was to transcend, which is a method used in that game to let characters of maximum level ascend to more advanced classes. Me and some people I know within the game would frequently go out on a monthly field trip of sorts to the most architecturally significant yet dangerous areas within the game universe, series of trips that became ever more life-threatening due to the fact that monsters in mmorpgs like to invade and inhabit the most elaborate architectures imaginable.

I'm probably not the only one who have fond memories of such experiences. Kids in Korea and Japan frequently meet up in some game world on holidays and visit interesting locales, as one would sometimes visit six flags or Disney Land on holidays. The effect on the children seem to be more or less similar, except for the severe lack of exercise reliance on such outing would have on the children. There is a lesson here, and it's not that game designers should take architecture classes. I'm more of the opinion that architects need to learn from some of the game/level designers out there in developing real world or even theoretical architecture. Architecture being the crossroad of applied sciences and art, its practitioners are frequently constrained by the imaginary need to forcibly insert some socially relevant message into their works. Such behavior is dangerous in practice of any discipline, as it is simply another version of the teenager too busy to follow the trends of the 'popular kids' to get anything real done. Architecture needs to be artistic in the sense that it imparts aesthetic pleasure on the people and the creator. There is a slowly emerging genre of writing that is referred to as 'architecture fiction.' It's born of the awareness that an architecture is in the end nonlinear narrative of the people living inside of it or at least interacting with it at some level. It's something good game designers had been aware of for ages. As long as there is a good level of interactivity and exploration between the user and the game world it inevitably tells a story, sometimes even the ones it's original creator never intended to tell. And by subjugating architecture to the limits of the 'reality,' the architects of the world are risking telling the same story over and over, disguising their lack of creative talent to the fallacies of the world like so many other failed artists of mediums. By taking the architecture out of the hands of the real world needs and placing them in the virtual medium, where the architecture's only job is to tell a compelling tale in a suspended world with flexible laws of physics, architects will be able to tell the most compelling stories ever written in the history of humanity, something that doesn't even need words to compel the audience's hearts.

I am ranting on as usual, and I'm not sure how coherent all the things written above are... I guess leisure free-write has its share of faults.

All I'm saying is, architecture is the story medium of the modern age, and will continue to evolve towards that path aided by advancement of virtual and real technologies that makes architecture manifest. And in such a world, what better way to tell a beautiful tale then building an architecture of the worlds of imagination?

Night

2009-06-15T23:14:00.000-07:00

It's 2 am. I just got back from the diybio nyc meeting, tired and hungry as usual. While having a high rate of metabolism helps me stay in shape even when I'm wolfing down whole plates of sushi and pizza, it also means I get hungry rather quickly. Beats being worn out every few hours though, I guess.

I felt that I should be writing a post on the experience at the wsf, but then my tired neurons don't seem to agree with me on that, so I think I'll just jot down some stuff that randomly pops into my mind.

The diybio meeting itself was a planning session among close associates, discussing stuff on future direction of the group and its immediate priorities. Some healthy discussion on the viability of bioart ensued among some of our members and I was a little lost for a while, debating whether I should step in and force the immediate issue down everybody's throat or let people talk out their opinions first, since this might as well be the beginning of series of discussions.

What the group need at this point is simple. We need a space. The disposables and the lab equipments we can manage more or less. The space in nyc is rather hard to find without some financial backing. We might apply for grants, but we'd need a project to apply for a grant, and we would need a space if we're to have a decent project. Things are moving at a slower pace than I would have liked, but this is still better than what we had before, especially that the diybio nyc is officially incorporated now.

As the things stand right now, we need backing, and some sort of legal representation. I plan on contacting nyc resistor for some help on bylaws and questions regarding their early days. I'm also thinking of contacting some of the other art spaces in the city, see the prices and the utilities I can expect from such places. Another member is looking into getting a biotech incubator space to help us out for the time being.... Dan also suggested that we do a bit of volunteer work for middle schools through a program called citizen schools. It sounds promising but none of us have any experience with kids so that might be an issue... One of the reason for tonight's meeting was that we need immediate and specific goals and plans for the group. The long term goals we can all picture and more or less agree upon. However we just can't seem to be able to figure out how we would get there. Hmm... Sent via BlackBerry by AT&T

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World science festival

2009-06-15T21:15:00.000-07:00

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Visiting livejournal

2009-06-08T22:51:00.000-07:00

1.Check out my new profile pic. Did I mention how I think Warren Ellis' Transmetropolitan/Doktor Sleepless series are awesome?
2.I haven't visited my own journal page on livejournal for so long I forgot how awesome the night sky skin was.

Despite my rather semi-persistent presence at the livejournal blog, this is probably the first time in months since I've actually visited the livejournal website and used the built-in blogging service. As you might have guessed from the tags that plagued my recent blogs all of my recent posts were composed on my blackberry and sent off via the posterous email service.

Part of the blame goes to the fact that I've been a little busy, with settling into the new apartment (with roommates no less), the mess I have to resolve for my parents I won't go into here and etc etc, the usual requisites of living a normal, healthy life. Being able to post a thought or two while int he subway or waiting for my coffee is an invaluable perk that I need to make full use of. Yet that's not all. Most of my research/work/study at present time makes heavy use of my computer and I've been lugging around my trusty thinkpad everywhere, so if I was inclined to do some blogging at all costs I should have been able to manage it.

When I'm writing something on the livejournal blog I'm usually doing it to vent off some steam and have fun while doing it. It's only that most people vent off steam by talking trash about their friends/families and I do it by talking about fiction/art/architecture/futurism and whatever that happens to require some cerebral function instead of the basest level of nausea-inducing rant that seem to permeate the personal blogosphere these days. It means the primary purpose of writing on the livejournal blog is to write, keeping my brain and fingers busy for any given length of time. It also means that I don't need to cite sources or link to other stuff on the net, post pictures of videos unless they are straight from my own blackberry (and yes, I can post them, I just choose not to. Maybe I should remedy that, given the cool events and things I've been seeing lately).

On the other hand, my main blog over at wordpress had hardly been updated in nearly a month, and I'm still wrecking my head on how to convert the two lab sessions I had with the DIYbio NYC into blog posts, along with a plethora of half-finished drafts on and off the net that goes on to talk about all sorts of topics. The posts on that blog usually takes a bit more effort compared to the stuff I put on the livejournal blog, meaning I try to research the topic, gather some graphics and links, may some videos, all in all the stuff that most people expect in any proper blog posts that's over 500 words. I get about four to five hundred hits per month on that blog and it's been going steadily down for a while now due to lack of new content. Whenever I sit down to write down a proper blog post (using notepad++ and jdarkroom, both essential writing tools for anyone thinking of writing something at length without distraction-the choices were inspired by my good friend dracova) I run into a nasty writer's block. If I should somehow manage to drag myself to the tortuous process of writing blindly through the writer's block by using plans and outlines the product reads like a painfully dry, and worse yet terribly written lab report, something I'm not too eager to post on a casual blog with some technical/scientific bent.

Writing on the livejournal blog is usually easy. I more or less think something and let my fingers run, like playing a rhapsody on a musical keyboard. The end products are usually readable, and sometimes they even maintain a coherent theme throughout the rant. It's almost as if the generally low quality of the writing is covered by the fluid connection of the low-quality parts themselves.

With the 'real blog post' becoming increasingly harder to do and most of blog posts becoming something of an exercise out of boredom/collecting my mind before writing something really important, the need for me to be present before an actual computer terminal for writing blog posts falls drastically. Why bother myself with a large, clunky interfaces on a computer already burdened with running multiple simulation programs that pays my bills when I can simply type up simple text based blog posts on my handset without much difficulty, like playing a portable video game except that this is actually good for me on some level with something to show for it? Just tap tap tap, write down whatever that comes to my mind at the moment, and I have an instant blog post that can double as some sort of field report on interesting things that are happening right at that moment around me, like my experience at the NYU ITP summer show that demonstrated quite a bit of interesting art-technology constructs.

And apparently I'm not alone in this lifestyle choice. According to the mobile-oriented news sites majority of the personal blogs being run in Japan are now written on mobile handsets (distribution rate of computers in Japan is surprisingly low, especially considering the level of consumer technology. Mobile handsets with advanced features however, permeate through almost every facet of their society with unlimited data services for cells being the norm in Japan and Korea for a long time now), with mobile-based video and picture edition softwares and location aware services being rolled out now. Some people would question the wisdom of typing up a blog post on handsets and their T9 input systems, but then those people probably aren't proficient in handling handsets anyway so their argument is moot. If the user simply wants to post a blog with simple video/picture captures around them with some words explaining what they are/formatting contexts, even the lowliest modern cellphone has plenty enough capabilities. And with most modern cellphones capable of playing internet videos, for casual users of computers (people who don't need top of the line workstations with dedicated GPUs and 8 gigabytes of RAM, which turns out to be most of them) mobiles are more than enough. The mobile-based computing in U.S. had been slow to take off only because of the aging infrastructure rather than capabilities of the machines themselves, combined with near-monopoly some corporations have over the telecommunications market (corporations stifling an entire generation so they can squeeze more money off of the population with outdated infrastructure is the reality, it's difficult to support pure libertarian ideals when corporations are this corrupt and incompetent, to the extent that they are beginning to make government regulators look good).

United States is still a very computer-based society, so I doubt we'll move on to the Japanese like mobile-centric society ever. there's also the fact that it is hard to create real content on handsets, at least not yet (though it will change very soon. Current generation smartphones already ship with video/photoediting capabilities/programming toolkits). Technology-wise, I think we are in a very odd stage where U.S. actually has a choice on where to go from here. Whether to take lead of the neglected parts of the market through reforms and innovation, or to squeeze out more dollars off of already struggling population for services that are barely 'good enough.' Yes, it is a choice, and yes, we didn't have it before.

Palm Pre

2009-06-07T14:31:00.000-07:00

Before I begin, I spent some time recently checking out the new mod for the original Deus Ex named 'the nameless mod'-google it-. Full seven years in the making with complete voice-overs and over 30 hours of playtime, I've seen commercial games released this year that's not as good as this. If you are interested in the Deus Ex franchise at all (and no, for the last time you're not supposed to play it like unreal! The game's not FPS) you should really check it out. The whole file clocks in at about one gigabyte, so I suggest you use the torrent available on the official site. This mod's so amazing I think I might even do a full review once I find the time to finish the darned thing... Which will be something of a challenge if it weren't for the fact that I've been dragging my thinkpad everywhere with me... Some of the cool things in the game so far include awesome voice acting (by the mod community members no less, some of them sound better than so-called professionals in some other commercial games), built in IRC client within the computers in game levels, the cool computer hacking minigame of sorts at the elevator out of DXI, and whole host of other things I can't write here since this isn't a gaming post :) Granted, I haven't had this much fun in playing a computer game in long time.

So, Palm Pre. As is usual with me I'm down with any interesting new gadget that comes along. I and the other millions who are following the industry trends really expected Palm to die out sometime in the year 2004, and they probably will if this new Pre device doesn't work out. I've been something of an off-and-on palm user for a while now. While I've never used their Treo line of smartphones I certainly went through some of their PDAs, using them as small digital note-takers and e-readers using the plucker utility. The old palm certainly had (have?) a loyal userbase. Some of the applications on the classic palm OS are of such utility and imagination that I still can't find the equivalent app on any other platform. The old Palm Tungsten that I used to carry around doubled as a programming environment of sorts as well, capable of interpreting the scheme/lisp and brain#uck language through add-on applications developed by users. I'd say the wealth of amount and variety of applications available for Palm predates that of Apple by a large margin, the only (but significant) innovation on part of Apple being introduction of app store and over the air delivery of chosen applications.

While I do admire what Palm had done, I was significantly disappointed with the Palm corporate's steady decline into obscurity mostly due to lack of innovation, and I moved on after the whole Foleo fiasco. Well, the history is going the way of spiral this time, and people are holding their breath to see if the once-mighty Palm can get its act together this time with introduction of a new handset and new (and improved, though not compatible) operating system.

I've had the pleasure of seeing one of the handsets up close by the virtue of mooching of one of my friends. And I must say, the design and general build quality of the device is gorgeous. It's very zen-like, looking like one of those small-ish, round stones you can see in Buddhist ponds in Japan and elsewhere. It's both cute and classy at the same time, and the device as a whole feels solid in my hands, which was surprising given my bad experiences with sliders before. I actually prefer this design over the standard iPhone design that seem to revolve around slab of glass/aluminum mantra (while I love their operating system I'm not too hot with their design, especially the back that feels a little cheap for some reason). The keyboard isn't as comfortable to type on as my blackberry (I'm writing this one on my blackberry) given the small-ish form factor, but then it's something you can get used to. I've read reports of people getting decent wordcount on those keyboards only after hours of use, decent in this case meaning about ~30 wpm, which is better than what some people get with full sized keyboards on desktops (I'm talking about people who aren't technically oriented of course). And no. Please don't compare wpm on handheld device keyboard to how much you can do in front of your 3+ years old desktops, unless the said desktops fit snugly in your pocket and is capable of ubiquitous internet connection.

Of course, in this day age the physical shell of a device don't count for much on it's own. We're all about operating systems here. Without a good operating system the smartphones on the market would be glorified texting devices without much real world utility. A good smartphone operating system would be composed of two things.

1:Good interface so users can get things done without straining their eyes/fingers or flipping through ten pull up menus to get anything done.
2:The guts of the operating system itself, how well it's organized and how easy it is to program new apps for the operating system. They both go hand-in-hand with each other, as it turns out.

I'll give Palm pre a huge thumbs up for the category one. I loved their operating system interface. Sure, there were a few kinks to be ironed out later like the not-so-universal universal search and the delay when starting applications but they are both things that can be improved with future patch. The touch based gestures felt natural to me, and on the whole the experience felt pleasurable to both my hands and my eyes.

I'm not sure what to say about the second category though. The Palm Pre just came out so there aren't a whole lot of applications for use. I don't think there's even a dedicated twitter client for the Pre yet, though people will be quick to remedy that :)
The extensibility of the operating system (webOS) at the moment remains to be seen. From what I hear the webOS is designed to be heavily dependent on the web-based programming languages and interfaces, using CSS to construct the basic interface for the apps and etc. Will such an approach be enough for people to develop emulators and lisp compilers for the device? Average users might not be interested in such applications, but those types of obscure applications usually do better to push the capability of the hardware and software better than any twitter client or pull my finger apps. Granted I'll be keeping a close eye on how this thing works out.

The web browsing experience on this device is on par with that of iPhone. And throughout my brief time with the device I was under constant impression that I could see more in the same page compared to iPhones browser, despite the smaller screen. Triumph of interface design? I didn't have enough time to uncover the specific reason for that. With the whole multitasking capabilities of the operating system itself I can see this becoming a very useful research aid for our pubmed browsing medschool friends.

One thing I'm noticing with the newer generation of mobile operating systems is how they seem to ship with built in web browsers that might or might not follow the web standards. This will definitely work to kill the market for third party web browser manufacturers like the Opera, unless they can get their act together and find some sort of solution.

The mobile operating system market is about to heat up even more (hopefully) with the introduction of the webOS into the marketplace. And unlike how it turned out with the desktop operating systems market, I don't think any single flavor of operating system will gain a decisive and nigh-permanent control of the market like MS does with their 90~% hold on the desktop OS world...

Am I the only one beginning to see some need for interoperability within the mobile operating systems market?
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Consider distraction

2009-05-31T11:18:00.000-07:00

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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Architecture

2009-05-27T23:00:00.000-07:00

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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The day's end

2009-05-22T18:21:00.000-07:00

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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purification

2009-05-16T13:51:00.000-07:00

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.

Testing

2009-05-05T13:47:00.000-07:00

Testing my wireless connection. The net seem to be acting up today.
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Mobiles

2009-05-03T11:18:00.000-07:00

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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2009-05-03T06:48:00.000-07:00

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.

Spring cleaning/musing

2009-04-26T12:14:00.000-07:00

I did some much needed Spring cleaning of my apartment. Washed every fabric I can see, dusted every single piece of furniture, and wiped everything down till they were shining in the sunlight. The weather outside is hot (90F), but there are advantages of living on 6th floor apartment right next to a vast grass field/lake. The wind through the windows are cool and they carry the pleasant fragrance of flowers and trees. Now this is what I call Spring cleaning.

The whole thing took about 4 hours. Dusting all the bookshelves alone took some effort, and I had to sort through all sorts of notes and sketches strewn across my desk to figure out which ones to keep and which ones to throw away. It might not sound like much, but the problem is in that my desk is a converted workbench I picked up for cheap in some yard sale by the wave hill park. The thing is vast. I can actually go onto it and sleep with all my limbs spread out. I'd say it's about half the size of my bed, which is also inexplicably large for a bed in a bachelor's apartment. Whatever. I'm not complaining.

There's something about maintaining well-organized, clean living environment that's very fulfilling for me. I think it has to do with how dojos and zen temples place so much emphasis on cleaning and wiping down everything all the time. I used to think it was annoying (and yes, I spent some time in both of those places. Maybe I should write about that sometime), but now that I'm older, I think I can see some point in all that. There's a serene and calming quality to organization of the environment around yourself, and the fact that inevitable wave of entropy will eventually make everything messy again just adds to the quality of the experience.

The fact that my entire apartment begins to smell like middle of a pine forest whenever I open my windows just adds to the experience I think. I probably won't be as committed to cleaning stuff up if my apartment was facing a railroad tracks for example.

The only sobering fact of the whole necessity of cleaning the world is that I feel like I'm missing out on so much simply to maintain some semblance of order in my life. The four hours of cleaning is fours hours of time I couldn't spend on working with the synthetic biology software suite (something I'm using to study biological systems in synthetic context these days, fascinating piece of software, though I'm just beginning to learn the ropes myself).

That is why the humanity needs robotic butlers/maids I think.

I'm impressed with myself for connecting robotic butler/maids with the zen practice of self-reflection. I think I'll go out reward myself with some burgers.

Net

2009-04-24T10:29:00.000-07:00

Look at this website http://startpanic.com

If you give that website a permission it will scrounge through the database of your web browser in use and list every single webpage you've ever visited using that browser (unless you were using some session masking ability available on some browsers like the chrome and safari). Of course, it's a mere showcase of the security vulnerability of web browsers on the market, and all the private data is perfectly safe and for your eyes only, so I suggest you to try it just for the scare factor.

It's rather surprising that the utility/algorithm for the webpage is capable of retrieving even deleted histories of the web browser in question. I think the sites does that by reading through permissions files and cookies, but then I'm not too proficient with the internet technology in general. That is, I know what tools to use to get my stuff done, but not enough to know how those tools work in practice, just like the vast majority of web users out there.

Considering the continuous push from governments around the world toward 'controlling' the net and its information content for one reason or other, this is rather disturbing. I'm even more amazed that most browsers that are considered better compared to internet-standards-ignoring heap of mess they call IE are still vulnerable to such simplistic snooping. The whole issue of internet security and privacy is edging closer toward some kind of critical mass, and I don't know what will happen once the movement hits the threshold. I don't want to sound too alarmist or anything, but this seem to be something worth worrying about.

Only way to stay safe from such snooping would be to run a separate server that encrypts ever one of your signals, but that would be an overkill not to mention detrimental to general web performance, something that can't be tolerated in this day and age. The most consumer-friendly way to offset the danger of privacy would be twofold. First would be continuous pressure on the governments from the population itself, and the second way would be for software developers to come up with better, more secure web browsers.

I'm pretty big on the whole search for the ideal web browser. I think I might have used practically every single major web browsers on the market by now. How many layman these days can say they've used Sleipnir/Lunascape/Opera/Chrome/Firefox/Chromium/Lynx/Telnet/IE on regular basis just to find the web browser that is perfect for almost every usage scenario? I certainly tried them all and quite extensively too. And every single one of them fall short in one way or the other, some of them even more so then others.

At the moment I'm leaning towards a mix between Opera and Chrome. I used to be a major firefox user, but all those extensions really bog the browser down, to the point that it takes some ungodly amount of time to just start the browser, at least compared to the competition. I thought I would miss the extensions for firefox, but the fact of the matter is extensions built right into the browser are becoming increasingly niche in this age of web 2.0 applications. For example in Chrome I can block ads and pull websites off the browser and onto the desktop, transforming them into an instant program I can access by double clicking a single button that opens up in its own application window. Like Gmail/Gchat and even third party sites like the del.icious bookmarking service (which had been quite a life saver in my cross-platform journeys). So the focus of web browser for me is in speed and safety. At the moment Chrome is the browser that fits the two profiles perfectly. The whole java sandbox idea is much more isgnificant than it would first appear. The sandbox system is capable of stopping almost every single unintended break-in to the system from the web front. It's also quite possibly the fastest browser on the market, and has full backing of the google corp. Lot of people have mixed feelings about google corporation, but I like them. At least they are better than microsoft.

If there's one trouble with Chrome it would be the amount of RAM and processing power the browser requires. I think the whole architecture of separate tab processing cycles and sandbox mechanisms make it necessary to consume such resources. For a compulsive multitasker and laptop user like me resource consumption of web browsers is something to keep a keen eye on, and Chrome is a monster in that regard. Which is the reason why I keep Opera at hand for some excessive multi-tabbing. Opera is really well optimized for older operating systems. It's probably the only modern web browser capable of running in win 98/95 environment.

Waiting

2009-04-21T22:21:00.000-07:00

It's four in the morning. I came back home at around two thirty from the diybio nyc meetup. I've been trying to get some simulation codes working in mathematica that I need to use for tomorrow's presentation. This may not have been the best idea, since I'm now tired enough to actually feel pain in my head.

Well, the code's already rolling and I need to stay awake until it comes to a conclusion, one way or another. I might as well write something while waiting. It feels a little strange to be writing on this little device when I have a thinkpad with fantastic, full sized keyboard right in front of me. I just don't want to waste any part of the main laptop's processor cycle in anything other than work though.

I'm not a computer savvy person. I just happens to do a lot of things that require thinking, and in modern society it means using a lot of computerized tools. What will come of this? What will come of the world where doing science means interacting with and using computers to some specialized degree (at least in the eyes of the layman)? Whatever the outcome may be, the future will be an interesting thing to see.

The nyt interview/GFP experiment went swimmingly. I had a lot of questions I had on structure and function of plasmids answered. I think I'm about prepared to do an actual wetwork using the biobrick parts. (Dracova, if you're reading this, maybe we should talk about more bio stuff?) I'm thinking of beginning by putting together a little cellular automata that's capable of turning its own light on and off. Maybe I can do it with algae and make a little glowing garden that is also a form of cellular automata computer. Not very productive, but it will be beautiful, something straight out of Miyazaki Hayao's best works... Maybe I have better qualification as a bioartist rather than biotechnician.

I think I've decided. I'm going to actively pursue the idea of using biobrick parts to construct a living cellular automata that changes its signal through GFP induced light. After it is done I might be able to reapply the same methodology to algae, which has a far more complex architecture compared to the naturally competent strain of E.Coli K12 we usually use.

The mathematica is about to churn out its results. I guess it means I can get some sleep at last.
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Dreams

2009-04-16T15:45:00.000-07:00

What are dreams? I think I've been having quite a few vivid ones lately, the unusually vivid and memorable kind. Those kind of dreams mark a visage upon the dreamer that extends even into the waking world.

Maybe it's just the weariness getting to me. Maybe it's something else, an alteration in my brain chemistry. Maybe it's the stress I've been getting from people around me. The dreams are getting more and more vivid yet I can't seem to be able to recall them all too clearly. I might not be able to remember the exact stories of the dreams but individual scenes and moments of the dreams are burned into my memory like they actually happened to me. What is the difference between a memory of unmistakably realistic dream and memory of things that really happened to me? Only the physical consequences remain to help me make the distinction.

It's really interesting when you think about it. What part of the emergent system that is the human intellect drives such a phenomanon? What composes the fabric of the dreams and merge it within the framework of human memory? Will it be possible to engineer dreams in such a way to combine it directly with the everyday memory?

And just what drives people to keep on finding fascination within their dreams?

It would be interesting to be able to apply the framework of synthetic biology to the study and manipulation of the nervous system. A controlled study of dreams on cellular levels might even be beneficial to learning the characteristics of complex emergent systems...

Speaking of vivid memories and dreams, I need to ask if they are in any way related to imagination as well. From my experience people who have interesting dreams don't necessarily have vivid imagination, but then how many people with capacity for imagination do you see these days? A lot of trash-heap sentimentalities (meaning:without compassion) or vulgurities disguised as realism/realpolitik, but no imagination. Nothing that breaks out of the usual mould of cause and effect that direct the development of minds.

Yes. It's my sincierest wish that I might someday be able to have a genuine capacity for imagination, that is beyond the simple result of environment and time. At least I try, and I know that most people can't seem to be able to recognize how pedestrian and downtrodden many of their most imaginative ventures are, so I might be making a step toward having a genuine imagination... Just think about it. What kind of future would we build without a true capacity for imagination? Without the ability to imagine, the future will simply end up being a stale derivative of what we have at the moment. And that is one thing people interested in future tries to avoid, isn't it?

Or am I just a sarcastic clown now? The time will tell.

I'm thinking all the dreams might have to do with my longing for long journey to faraway places. The timing certain feels on the spot. It's funny. The will to find another future intermingled with memories of the past, all of them one and the same. I must be a lot more interesting guy than I give myself credit for.

At the moment I'm seriously considering taking the plunge and get some unique perspectives on biosciences and physics from other places around the world. The academy is still as fragmented by location as any other human endeavor, and from what I hear there are a lot of different advances and discussions going on in other parts of the world.

I might be able to come to a real decision in a month or two.

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The longest journey

2009-04-13T14:33:00.000-07:00

I've been a little busy lately. Oh who am I kidding I've been busy for a long time. The events of the days happen so fast in such rapid succession next to each other that I'm beginning to find it all very tiring. I'm under a serious need to stop myself and think about what it's all for, that kind of stuff. I keep on thinking about going on a long journey, or at least moving my base of operations to somewhere else, maybe in Europe, to study with new people as well as taking in the sights.

I'm currently eying the institutions in Germany or somewhere in that region, maybe even enroll in the SymbioticA course for the time being. I'm sure the credit will be transferable to the colleges in U.S. I think I might even be moving to Boston soon, so it might be something worth thinking about. I'm coming to realize that I'm usually the happiest when I'm on the move for some reason.

I haven't been keeping in touch with my family, that is my mother and father for a long time now. I do keep in touch with my extended family in other parts of the world though. It's rather odd now that I think about it. All I know about my birthparents at the moment is that they are still living within the North America, so I guess that doesn't mean much. I have no wish to see them anytime soon either. All they are are like specters of bad memories and abuses.

I've been thinking about fantasy... Or rather, imaginative worlds a lot lately. In literature scene the d&d and other licensed products (the lord of the rings even) destroyed so much of the people's individuality that you cannot use the word fantasy without evoking scenes of wankers with swords playing around in pseudo-medieval getup. It's really a sad state of things. When I say fantasy writing, I'm really talking about the kind of writing that doesn't happen within the confines of the 'real world', or whatever it is humorless dicks call their shallow interpretation of the world these days. Worlds and ideas that are really 'fantastic' and imaginative, fitting of the namesake.

When I write, and I do a lot of that these days, I write much better and faster when it's directly from my head, with no regards for facts and figures and equations. No political considerations and no concern about where and when I should use certain types of vocabulary. When I write within soe sort of confine the result tend to come out horrible and I end up spending just as long trying to salvage the whole thing as I spent writing it in the first place. But when I write something off the top of my head, a sort of extended freewrite exercise, I can just go on and on writing about my own thoughts and various imagined situations and characters, and the whole experience brings me such a feeling of fulfillment. I don't know why that is. Maybe it has something to do with all the wanderlust I've been feeling lately.

I'm thinking, maybe I should really write something. Of course, I write pages after pages of stuff every single day, I'm talking about something more imaginative and dedicated. Something fantastic and coherent. I've been writing little bits and pieces of such musings all over the place now. Like the bits set in the universe of the library of Babel. Or the hundred years of solitude. things set in art schools and laboratories, little bits of poetries and whatnot. Maybe I should try to pour all of those things into a single coherent story, a single universe with such fantastic components. Maybe I can even steal a character or two from my favorite writings, like the script for the adventure game longest journey. I'm even thinking of making a different version of April Ryan as the main character in the world. She'll probably be an art student just like in the original story. Maybe she can major in the field of bioarts, where they use tissue and genetic engineering to create works of art. There would be such wonderful worlds waiting for her.

Snowing in the rose reading room

2009-04-08T05:25:00.000-07:00

Got into the reading room for the morning, will need to head back to school after lunch. I can see some flurry outside the window, in the backdrop of skyscrapers and murals of twilight clouds.

It's beautiful and the world looks good. There are people in the reading room silently going about with their business, all reading or writing something with a sort of intense concentration that can't be seen with most people outside of here.

My laptop is on the desk crunching away at numbers and figures, and I have an old book of Ovid open in front of me to pass away the time of calculation. I love the smell of old books and slight scent of coffee in the air. I guess some of them just got off the daily dose of morning bagel and coffee.

In this brief moments of the days I feel very much alive and and recharged. It's a calm feeling that your life is going in the right direction, and the reminder that you are, and will be devoted to your dreams. It's a very gentle promise of the world that there are people who see far enough to worry about something more than their immediate comfort and survival. It's the sound of the future being laid out, probably for the better.

I might move to Boston sometime soon. I'm trying to get to MIT and there's a chance that I might actually be able to make it. I'll really miss this city once I'm gone.

While I'm still here though, I really need to get the diybio nyc rolling. It's really hard to find good people who are interested in diybio itself, rather than showing off with half-baked notions of 'biohacking' and whatnot. I need people who have demonstrated a capacity to stick with something and see it through to the end. Not something that takes months but something that takes years of continued effort and devotion. At this stage of the group letting in unproven people with questionable devotion and motivation would be devastating to the morale of the group. Not to mention, the group is in a very financially uncertain state. I would need people capable of supporting the group financially as well as technically. The members would have to be givers as well as takers. There have been some progress but I still need to find some way to get more of such qualified people working with the group. Once the group itself stabilizes a bit more, with decent funding and reliable, dedicated members, we would be able to accomodate people who are not as dedicated.

Well, it's time for me to go off and do some real work again.

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Productivity

2009-04-06T15:03:00.000-07:00

Spent the early hours of the morning going through papers in the lab. Since about 6 in the morning to be precise. I needed some place to work on my stuff and it turns out that I didn't have much choice during such wee hours of the morning.

Now the day is almost over and I'm writing this as I wait for a friend of mine to join for dinner. Such is the lifestyle of the modern datamancer.

Also got some light lunch at the cafe zaiya's. The place is really beginning to go down hill I think. I can still remember the days the cafe had a whole lot more on the menu for a lot less. I guess the economy is hitting away at one of my favorite hangout spots as well(at least in the midtown region I guess).

Spent much of the day cooped up in the rose reading room at the central library, concentrating on drafting papers for my lab work and some side stuff for the diybio group. There must be something strange in the air at that place. It feels as if I do my best works in that place. I just find it much easier to concentrate in that place for some reason. There is a kind of intensity in the air, and you can't find anyone dicking around in that place. No one chatting with a friend, no one watching some video on the net or browsing some meaningless website. The air of pure academic learning and pursuit of something that normally remains beyond the reach of average men.

As I was writing down equations after equations, and drafting course ideas for the synthetic biology class I saw rays of afternoon sunlight streaming through the old windows. The effect was nothing short of solemn. I wish I was able to capture the feel of the

Other than the usual, I wrote some rough draft for diybo $300 course. The idea is to be able to offer a decent 2-day diybio course with full wetlab component for $300 per head. It's a sort of side idea I came up with after reading about the $3000 five day MIT course. Mac Owell sounds quite enthusiastic about that idea, and I really think it might be able to take off. I think the group will be able to offer something by the October of this year, but of course I would need to talk the whole thing through with the group members first and thus the need to think about all possibilities and come up with a workable draft. I will be putting the whole thing up on my blog soon, after I put some finishing touches on the agenda and such.

Being able to come up with some sort of diybio courseware had always been a secret passion of mine. How amazing would it be to be able to do a full scale wetlab exercise in diybio style? Any suitably motivated person would be able to do a biology related research on his or her own. Well, it's already possible actually. Anyone can learn minimal amount of python coding and run BLAST interface through the internet by connecting to GenBank. It's diy bioinformatics and there are some people making noticeable contribution to the field by working with a laptop and minimal scripts.

I see two main problems at being able to run a diybio class though. The first is the relative ignorance of the target audience. Any diybio class would be targeted at novices with no background in academic research. I'm fine with that. I am however, worried about the kind of people who have preconceived notions of what diybio is/should be. There are so many people out there who can't tell the difference between reading stuff on computer screen and actually researching something in academic capacity. It's easy to teach something to people who don't know. It might even be fun. But attempting to teach something to someone who already thinks he/she knows everything there is to know about the subject is painful both for teacher and the student. It's very disheartening to see people who cannot tell the difference between studying and glossing over textbooks.
The second problem is the usual. The need for materials and resources for diybio. It's very difficult, perhaps impossible to grab hold of basic biobrick materials, at least any organization that is not sanctioned by the local government as an educational institution. There will be a lot of red tapes to jump through if I were to pursue an actual wetlab project.

On lighter note, I finally got the java based irc client working on my blackberry. Apparently the program can run on 'regular' cellphones as well since it's completely based on java architecture. Maybe I should give it a try on some of my older cellphones as well. I'm having a bit of fun speaking to the peeps at phys lab and funcom server people trying to solve the arg puzzles. Sent via BlackBerry by AT&T

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Life, typing, and Monday

2009-04-04T16:03:00.000-07:00

For starters, I almost electrocuted myself in the shower today. Apparently it's about time I get myself a new electric razor. Another expense in my book that I really don't want to afford myself. I have books to buy for crying out loud. I think I have close to, or maybe more than a hundred books and other related stuff on my amazon wish list. Will I ever get through them all? I'm trying but it's not likely to happen anytime soon.

It's been a long time since I've written something for the web on my laptop keyboard. Of course, I try to write everything for the wordpress blog while I'm in front of an actual computer, but then I only write around once a week for that place. I think most of the past entries for my livejournal blog had been written on either my cellphone using the T9 input or on my blackberry using the posterous service. It's a real nice pastime really. Doing bits of writing while on the go, like waiting for the subway to arrive or in middle of waiting my computer to finish some huge work related stuff. Some people play games when they have spare time, I write meaningless ponderings on my mobile.

I was a little worried that I'd have forgotten how comfortable the thinkpad keyboards are due to so much blackberry writing. I'm rather happy to find that my fingers travel just as fast and accurate as before. Blackberry keyboards are definitely a step above that of T9 input in regular cellphones and even that of most touchscreen input systems, but they just can't replicate the feeling of using a real, full sized keyboard in terms of tactile feedback, speed and accuracy. It's much less strain on my fingers an wrists as well, meaning that I can write for longer periods of time without needing a rest.

While I find that I do my best creative works while I'm using pencil and paper, there is certain joy in using a good keyboard to jot my thoughts down in very instantaneous manner. Sure, the pencil and paper format affords me much more freedom in terms of the things I can do with them. I can draw, write in every language I can think of, including made up ones, I can rite and solve equations, and I can fold the paper and turn it into a neat origami bird containing all sorts of musings and ideas (it would be cool to be able to have a jar full of paper birds, each of them containing ingenious musings and stories). It's only that keyboards afford certain degree of spontaneity within the act of writing that's almost on the equal footing with being able to play an instrument. I type away at the keyboard inscribed with symbols of the alphabet and they in turn form patterns recorded down onto the screen as digitized information, to be recalled later into memory, evoking all sorts of thoughts and images into the reader's mind. Why would the act be any different from playing an actual instrument, other then the dilation of time involved in the act of recording the experience to be enjoyed later on? When I think about it, all forms of art I can think of seem to rely on a few fundamental and shared characteristics. Bringing together of random components into a coherent pattern by the artists' imagination, and recording of the process of the pattern so that the impression of the pattern can be recalled in minds of outside audiences. It's all about forming coherence within the chaos of the world.

How is it that living systems are capable of forming such coherence within the universe they live in? What kind of laws govern the impulses behind the creation of such coherences? What is the mechanism behind the creation and why? Is it psychology? Is it physics? Freak accident common to biochemical organizations?

I have another Monday off, so I will be spending the day at the central library in the city studying, getting stuff done that should have been done a while ago. I will need to think of bunch of diybio stuff as usual, not to mention read through the text book 'biotechnology for beginners.' I still have something more concrete to do though. I will need to do some finishing touch on the mathematica model for the plasma simulation, write some blog posts, get through my mails, and most of all, finish the processing project I started almost a month ago.

I've been trying to write an engine in the processing language that would take DNA sequence input, reinterpret them as codon sequences and generate music and graphics/animation based on the sequence. It would be a cool little piece of software that I plan to submit for a little underground webzine. Maybe later on I can do a little web based service that would identify the user's single point mutations, cross reference it to the base human DNA sequences, and generate customized music/animation for the user to download. Imagine being able to see and hear the mathematical permutations of your own DNA sequences, each of them unique to the single individual. My rudimentary understanding of the processing language had been getting in the way (not to mention I don't know the first thing about music theory, nearly flunked my jazz class during high school days), but I think I'm about there. It also helps that the processing language itself is really easy to use, at least compared to most of the alternatives out there. Since the processing language itself is a slightly modified Java, I'm hoping I would be able to put the whole thing on the net with minimal modification.

There's something I'm worried about using my laptop in the library though. While the clickiness of the thinkpad keyboard is good for receiving tactile feedback through the fingers (in turn allowing me to get an intuitive feel for whether some key registered correctly or not), it does make that mechanical 'click' sound you hear with older keyboards, which is a big no no in a silent library reading room. I would have to pay more attention to how I type so that I don't make too much noise in there. I've already sort of gotten into trouble with keyboard noise already, I don't need another one.

April fools

2009-04-02T00:25:00.000-07:00

It was the April fool's day, and on this day I take particular pleasure in collecting especially crazy or delicious pieces of rumor, and help in spreading them through the channels of the social media like the twitter. Through some very strange course of events the April fools had become a sort of international past time, on the similar level as Christmas (itself derived from a pagan tradition, the birthday of Mithras, but that's a story for another time), celebrated in their sardonic and twisted methods on the global scale. People used to do some funny things for April 1st in Japan and Korea, and to lesser extent China. I guess we all look for excuses to have fun with each other. And with the outrageous growth of the power and reach of mass media with the advent of information technology, I think the tradition of the April fools day will grow into something very significant as the time goes on, something that might even make schools close down someday like it is with the Jewish holidays in NYC (seriously, what WASP thought they would have their public school system close down for the religion of ethnic minorities?).

I had some crazy workload for the day though. So I wasn't in any condition to do my typical info hunting and related propagation. There were a few tidbits I found delightful though. Like that CERN LHC collider piece. Anyone interested in keeping taps on physics news probably heard of it by now. Their April 1st joke was that LHC was in fact temporarily been closed down due to damage caused by appearance of black hole within the testing chambers. I think there were some number of poor souls who actually believed that one, before they realized that it was a piece for the April 1st. The amount of hype the largest science project in human history generated was really beyond expectation, in many parts thanks to the nut cases who probably doesn't know the difference between differential and integral calculus (you learn those, or at least passively browse through those topics in most high school curriculums btw).

Other than that, there also the news I got from the official blizzard home pages for the games Diablo 3 and Starcraft 2. For all their vaporware-ness, they do consistently keep updating their sites on the 4.01 day with crazy info and units, and they did not disappoint this year as well (SC2's last year 4.01 unit was minotaur in rocket suit).

Diablo 3 homepage showcased a new character class archivist, with spectacular powers like power to throw books and shush the monsters to death. Oh, and apparently the archivist have a lot of customized conversation options as well, ranging from 'in my days it was black and white' to 'where's my pants' and 'where am I?' I'm thinking the eponymous oldman Cain (stayawhile and listen guy) is the archetype for the class design. Those of you who know me that I go a little crazy over books. The central library in the city and various independent bookstores are actually my favorite places in the city, and I have a habit of buying some crazy amount of books at once, usually going over a hundred dollars per purchase. And I still suffer from the chronic lack of reading material even in the busiest of days... So I think the archivist might actually be a cool idea, if the guys at Blizzard (Blizzard or Blizzard North?) can take the time to flesh out the class a little, maybe turn it into a little hidden class or something...

For all the misinformation surrounding the D3, I'm really looking forward to that one, especially now that the diablo world seem to be expanding a lot more, like the metropolis of mages and the return to the town of Tristram and the exploration of the catacombs beneath the Cathedral. I still remember the times I spent with my friends turning that place inside out in the original diablo. Compared to the rather eerie and hopeless atmosphere of the original diablo the diablo 2 was something of a cakewalk, a relative disappointment. It was almost physically impossible to die in the beginning stages of the game unless you were really terrible at clicking your mouse, and that cut into a lot of fun...

The starcraft 2 homepage also showcases a new awesome unit for the terrans, which will actually be integrated into the mapbuilder program that will be provided along with the game (just like it is with the minotaur units). The new unit (or should I call it upgrade?) is called the Terra-Tron. It's a ginormous robot built by combining the buildings of a standard terran base, with laser canons, machine guns, and who knows what else. The unit is an obvious throwback to the eponymous voltron and other Japanese robot anime (sc series give a lot of nod to the anime fandom. As is with many other U.S. made computer games I guess. Did you know that in the special thanks section of the credit for the game Sacrifice the dev team mentions 'Escaflowne'?). I don't know about the sc 2 game itself, but the community created content for the sc2 game will be amazing. There's no doubt about it. Maybe that's the main purpose of the sc2 dev team after all. I expect to see robot to robot fighting in futuristic city maps, with tanks and other standard armored stuff you might expect to see in Masamune Shiro's works.

Blackberry, girl genius

2009-04-01T17:22:00.000-07:00

Today had been one seriously exhausting day. I dropped into my bed almost as soon as I got home and slept like a log. I haven't felt this tired for a long time now. It's a real shame too, since today was the day of the secret science club, on the topic of Mars exploration. I just can't understand why I'm feeling this tired though, I don't think I've done anything that I usually don't.

I woke up around 10:30 pm. Since I got to home and to bed around 5 I'd say I slept close to six hours. I didn't eat anything yet so I might as well get out of bed now and grab something to eat. Sleeping early and staying awake throughout the night, this cannot be a healthy lifestyle.

I was rather hesitant in getting out of the bed though. There still was a little hope in my heart that I might be able to go back to sleep and stay more or less unconscious throughout the night. So I turned on my blackberry and browsed through the net for something to read/play on the net. It turns out that there is a version of simcity for blackberry devices, probably based off the released code (as a donation for OLPC) of the original simcity game. I was rather excited until I found out the game would cost about 14 dollars. Seriously, 14 dollars for a mobile game whose original code was written in the year I was born? Ridiculous!

I continued my search and that's pretty much the state of blackberry software ecosystem right now. Over charging for old and outdated softwares, simply because there just aren't too many softwares on the market itself. The software market for blackberry is ages beyond that of iphone or even that of android, and RIM should really pay attention to it if they are even moderately interested in putting bb into the public pocket. This trend is somewhat strange though, considering that the sdk for blackberry os is available on the net for free, and from what I see developing for bb devices would be a lot more easier than developing for symbian os, since bb os is entirely based off java with a bit of difference in byte code compilation (not to mention who have to fork a fortune over if you want to develop for symbian, something Nokia is trying to amend). I guess the bb people just don't game much? It's somewhat understandable, since I read and write email when I'm bored with bb as well, instead of running some sort of game.

What I don't understand is the lack of two of the most fundamental gaming programs that's almost universally available on practically every single mobile devices with keyboards. Interactive fiction interpreter program like the frotz and old school rogue-like games, like moria and nethack. I would think that the keyboard based interface of the blackberry devices would be perfect for playing those two types of games, not to mention the small sizes and relatively low complexity of the games themselves that would lend well to modification and porting. Apparently someone has time to program a poker/texas hold'em game with full graphical interfaces from scratch but don't have the time to port over existing code. It's really a nonsense.

Sick of looking at overpriced and crappy games for the device (although I must give credit for the cool yellow pages/google apps/notepad with full spell checking/free spreadsheet for bb), I hunted down an ongoing web comic series titled 'girl genius.'
Girl genius is a web comic set in fantasy/steampunk alternate world where there are people called 'sparks' who are capable of utilizing all sort of crazy techniques to build lumbering steam robots, death rays, clockwork devices of nefarious purpose, and floating castle/airships. In the beginning the art style put me off somewhat, but I've already grown to see them as unique rather than off-putting. The years of reading Japanese manga really seem to have done a number to my sense of aesthetics, with their impeccably polished and proportioned characters (even the homeless are clean and well proportioned!). I should really watch out for that.

Girl genius has one of the most intricately developed characters/world and storylines I've ever seen, and I'm amazed that they are releasing the graphic novel onto the net for us to view for free. Even if they stick with pay-to-view or paper only publishing model they would be able to make a tidy living with the girl genius universe (it's that good), so this isn't some publicity stunt.
The world of magical steampunk where people scream 'for science' as a catch phrase in popular stage plays, with mad scientists roaming around every corner? Jesus christ it must be like heaven (except for the whole death and misery part of the world torn by conflict between impossibly powerful princes and secret societies).
What if I could combine all of those lovely worlds into one cohesive form? The library of babel, the steampunk universe akin to the girl genius world, and others... It would be quite exciting. Sent via BlackBerry by AT&T

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The day, of interview and studies

2009-03-30T15:52:00.000-07:00

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ï»¿Spent most of the day outside today. It was a good chance for me to browse through the textbook 'biotechnology for beginner'. I did most of reading in the quiet of the central library, though I did spend the early morning relaxing with some coffee in the Bryant park (before going off to a lecture for a while). Actually relaxing is not an accurate description of what I was doing. I was sending off emails and calling people left and right trying to arrange interviews for the diybio nyc peeps. I've never done anything like that before so things were getting a little chaotic, with last minute announcements and schedule changes. Mistakes and misunderstandings were plenty, and I was beginning to think that I was making some horrible decisions on the spot.

Well I was able to get one of the members onto an interview with the reporter (who I mistakenly thought was a man, and working for a school newspaper. She was neither), and arranged another one for myself in the evening. The whole process involved a whole plethora of trials and tribulations that happened due to my characteristic over thinking preparation and careless execution. After the whole planning and calling I stuff I met up with a friend and had some much needed lunch at the cafe Zaiya, which was overcrowded as usual.

The interview is done for the day and I'm in a bookstore trying to cool off my nerves with some Feynman adventures. My portion of the interview was interesting. The reporter lady was quite friendly, and was patient with my answers that sometimes turned into something of a rambling (I knew I should have taken that public speaking elective in High School). During the course of the interview I had to frequently ask her to repeat her questions though. For some reason my ears were picking up a whole torrent of background noises... Maybe I should get them checked out.

We spoke about the reason for my interest in diybio, along with the difficulties involved in getting a group working together. The topics moved onto interest in science itself, and I gave some lazy answers on that one. I feel very passionate on the issue of the nature and utility of the sciences in general but I couldn't find a way to put it in short eloquent statements... Not to mention that I felt disclosing such intense emotions would have been rather embarrassing.

All in all, my first experience in arranging interviews for a group (or arranging anything for a group for that matter). I keep on feeling that I should have been better informed and prepared, but I guess beating myself over it won't change anything. Time to give the Feynman book a little pause and arrange yet another interview for the valued member of our group. Just hope this one turns out to be better than mine.

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New textbook

2009-03-27T18:28:00.000-07:00

Today I spent some part of the afterwork night in the nearby jazz bar. It's slightly expensive (but considering how it is in the rest of the city it's not all that outrageous), but a cozy enough place that's directly below a bookstore (how cool is that?). While we were talking about life universe and everything to the tune of piano my friend handed me a book. It's 'Biotechnology for Beginners' by Reinhard Renneberg. Apparently she got her hands on it as part of the leftover things from her roommate's stuff, and since she doesn't have any use for it (she's a grad student in proteomics, certainly nbot someone who needs a beginner's primer) she's giving it away to me. The little ol' me the synthetic biology enthusiast and biohacker/madscientist hopeful. This is one of the coolest gifts I've received in a while. I'm looking forward to dig into the book and geek out to my heart's content. Maybe I will put up a mini review of the textbook on my blog, either this one or the one on the wordpress.

The scheme of having a two blog is working out nicely. At first I was rather hesitant about having two blogs that more or less share the contents, but as I meet and work with more and more people it's turning out to be a very prudent decision. I would have to draw the line between work and privacy and some point and the division of the blogs provide a nice semipermeable membrane of privacy. These days I keep on thinking about writing a short fantasy series of sorts, possibly something steam-punkish or perhaps something related to the library of Babel, or maybe even both. Maybe I can try one of those keitei novel stuff, since I'm doing most of the personal writing published to the web on my blackberry anyway. I'll see how it turns out.
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Insomniac at the library of babel

2009-03-25T21:17:00.000-07:00

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ï»¿It's about three in the morning and I really need to go to sleep so I can get to class/work a few hours from now on. Yet I keep on getting new ideas I have to jot down before falling asleep for the fear of losing them. It really does feel like my whole life in the memory is a house of cards that will collapse at the slightest touch.

I keep on thinking about that short story written by Jorges Luis Borges (one of the greatest writers who ever lived), the Library of Babel. Aside from the obvious metaphysical food for thought present in the story, I've been having a lot of fun building a little physical simulation of the library in my notebook. Or should I say mathematical simulation?

I love mathematics. I love how it brings the structure of the universe and ideas so thrillingly close to the everyday mind, and I love certain taste of aesthetic purity present in good mathematical forms like it is with sublime music. Most of all, I love how it is so rich to the extent that I can confidently say that humanity as a species still do not have a very goods understanding of what mathematics is and its place in the physical universe. I also love libraries. In fact I love books and libraries so much that I'm a regular visitor of the Morgan library museum and I spend much of free time going bookstore hopping with my friends. I even have a special section in my flickr account devoted to things related to books and libraries. As such, the library of babel with its exuberant mathematical structure (almost like verbal music) and its subject matter of an entire universe of books just appeals to the deepest core of my soul.

The library of babel, according to my rough calculation, is orders of magnitudes larger than the estimated size of our current universe. Borges set a certain superficial size of books each containing random combination of 23 alphabets (their language isn't English). The library is the place containing books formed of all possible combinations of the 23 alphabets within the given length individual books, each of the books arranged randomly on a uniform shelves that is calculated to span a few billionbillionbillion years at the speed of light, meaning people die within those libraries without ever getting out. In fact, the method of disposal of the dead within the library is to throw the dead over the railings (there are multiple levels within the library), and the body will rot and decompose into nothingness without ever hitting the floor (I would hate to be on the floor of the rough location of the total decomposition. The place should be covered thick with dusts that were once human). There are religious sects and scientific communities within the library, some of them making pilgrimages of the more coherent sites (and sometimes turn to banditry), and discussing the nature and structure of the library without being able to see the whole. Apparently there are librarians of the library as well, though they always despair on the futility of their exercise, for it would be impossible for any single human mind to be able to learn the secret organization of the library (if there are any) due to its vast size and complexity. We are talking about a library within which the distance from one bookshelf to some other bookshelf would take billions and more light years.

The setting is of such mind boggling complexity and imagination, as well as that peculiar brand of dusty yet elegant aesthetics present in Borges' other works, I'm actually writing a small fanfic/diary based on the library of babel universe. It hasn't been too long since I started but I plan on keep writing, based both on my own experiences and my imagination.

Sometimes it pains me that while I have the power to imagine such worlds, I do not have the power to make them come true. At least not within my life time.

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Synbio ideas

2009-03-24T16:28:00.000-07:00

I got through another meeting with the diybio nyc peeps. Mostly it was a management related talk with what came to be the founding members of the group, in terms of getting legal status and finding space for the group. The biggest problem for the group at the moment seem to be lack of a reliable space (with running water and power). Another big problem is finding a suitable project idea for us to go ahead with. Actually, if you ask me the lack of an agreed-on project idea is a bigger problem then the lack of physical space, since lack of project means lack of traction and focus for the group. I would really hate to see the group evaporating due to lack of activity at this stage of the game.

I'm wrecking my brain daily over finding an interesting enough project to proceed with, but so far I'm drawing a blank. The fact that I'm practically ignorant on the deeper nuances of the biological sciences doesn't really help matters either.

One member of the group had been very generous in providing the group with much equipment and other resources, and the other member is doing much to get the problem of incorporating the diybio nyc group as a nonprofit. I'm trying to look into the space issue by working with other groups outside of diybio, but I'm not too sure how it will work out to be... Not a lot of people want to work on unproven projects with unproven people. There is a biotech group within the city that might be able to provide us with labspace and resources but they are about incubating professional businesses which doesn't sit well with the diybio ethos.

I'm a little embarrassed to admit that sometimes I feel like a third wheel in the group, but I guess everyone feels that way at one time or another when trying to get a meaningful movement going. I will have to remedy it by trying harder... I really want to do something significant for the group but I don't know which direction I should start with, and I'm getting a feeling that this is a common sentiment shared by many of the ghost members of the group (and yes, there are quite a few ghost members, it's to be expected I guess).

At the moment all I can do is to provide more logistical data for the group, like rent, spaces, and possible collaboration with existing hackerspaces to get those things. I guess I can give a bit more info about the s.b. 4.0, there are still whole notebooks of data on that conference. I actually gave then the booklet with abstracts of presentations and posters, I hope it will be of more use to them then it was for me, with their experience with actual wetlab stuff...

I am trying to come up with a project idea, though it is more likely that we'll be going with an idea that more experienced members of the group will come up with. Just juggling through ideas of completed projects isn't good enough. I need to think about the realistic design and research process that will lead to that finished product, which isn't easy for someone who still has trouble digging through some of the simpler and widely known gene pathways. I guess this is time for me to go dig up more igem stuff, and try to make sense of it all in terms of technical execution and practical resource requirements. That is, we won't be coming up with a model of minimal cell in basement lab anytime soon (as much as I would love to see that happen).

I'm beginning to think about something on the lines of building in light sensitivity into the bacterial chassis (at least I might be able to help out with physics side of things in project like that) but what exactly? What kind of project would I be able to conceive of that incorporates light sensitivity of cells while remaining imaginative and practical within the technical limitation our group face?

E.Coli chassis that follows light? Or avoids light even. Now such idea would be a problem considering that I do not have a very clear idea of the mobility mechanism behind E.Coli (CAN they move? Or will it be a cycle of dying out when within the light rich or deficient environment?).

Considerations like that makes me feel like suggesting simply doing some simple exercise of making bacteria glow, document the whole process and materials used so that I and other less experienced members of the group can have clearer understanding of the techniques and limitations involved in the process- notably, introduction of foreign plasmids into a native chassis. The plus side of such an approach is that it lays nice groundwork for future experiments for those who aren't experienced with molecular biology. The negative side would be that such experiment would dig into the resources and time the group doesn't really have. Possibility of boring more experienced members of the group is also something I need to watch out for. Diybio nyc will not be able to sustain itself without the help of the people experienced in experimental biology.

I just don't know what to do. Even if I were to suggest the glowing bacteria as a sort of introductory warm-up exercise, we still need to come up with a great project idea.

I'm writing this in the subway on my way home. It's beginning to sound like the diybio nyc is in some mortal peril now that I read some of the stuff I've written. It isn't. Considering all the odds things are going swimmingly and possibly even faster than I expected. The whole atmosphere of excitement at being able to think about manipulating biology of living systems for academic pursuit is something that makes me feel alive. And I enjoy wrecking my brain over this stuff. It's only that I'm under constant pressure to do more and get more things done, to make the group really work, because I believe that we have something with a potential for some truly wonderful stuff here. And it would be a real shame to let it die out not with a bang but a whimper.
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The world baseball classic

2009-03-23T20:17:00.000-07:00

I'm certainly not the one to rattle over sports. About the only sports I like (and have experience in, meaning winning a few trophies) are skiing and kumdo (sword-fencing of the Asian kind). Yet I sould not help but to gather some of my friends and watch the world baseball classic tonight. The game continued until one am in the morning. I'm actually writing this after the game waiting for all the beer and food to be processed through my stomach, and I'm quite worried about the fact that I have a full day of class/work/diybio related stuff I have to go through tomorrow. But I'm still happy that I went ahead anbd watched the game.

This particular world baseball classic game was between Korea and Japan, both of which have quite a history between each other. It was only to be expected that any competition between them to be an intense one, and I'd say the game fulfilled the expectation perfectly. Long story short, Japan won by two points, both of them netted about ten or so minutes before the end of the game due to the freakish skill of Ichiro who is like one of the biggest players in the Japanese baseball history. It's only to be expected, when you consider the fact that Japan had a hundred year head start in baseball tradition compared to Korea. The reason why this game is worth remembering is because of the rollercoaster ride of the game's progress. For a nation that had a hundred year headstart in baseball tradition Japan did not have an easy time beating Korea and that's not because Japan sucks at baseball (those guys are actually pretty damn good). The thrill and intensity of the players and the audiende of the stadium were infectious, turning even someone like me (pretty much ignorant in the matters of baseball) excited and anxious to see the outcome. The USA team was rather lackluster from what I hear. If only other sports games were as exciting as this!
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Stupid gadgets

2009-03-22T18:06:00.000-07:00

Spent most of the day in cafe and lab trying to get through the bundles of paper I have lying around, ranging from music theory to synthetic biology. I guess I'm teetering towards fulfilling my dream of becoming a renaissance man/mad scientist.

I tried to keep away from the web for better portion of the day, except for occasional tweeting. I wasn't alone the whole time though. I was with a chemist friend of mine who's also working on an artificial life related personal projects. So it was rather easy for me to stay away from the normal distractions. It's difficult to fool around when you're around someone in such a deep concentration, and I'm sure I had similar effect on my friend as well (besides we were constantly throwing ideas back and forth so there really wasn't much room for real distraction).

So I'm reading and typing away on my trusty thinkpad, when my friend pulls out a brand new macbook from backpack. Considering how much time and agony I've pulled myself through when choosing my new laptop (being a hopeless gadget geek that I am) I couldn't help but to admire the laptop. I've seen and touched it many times in the Apple store on broadway, but there's something about looking at it under the light of a new strange place. I've got to give it to Apple, for better or worse they really know how to design their products, so that anyone who sees them are overcome with sudden urge to get one for their own. It's not that I subscribe to minimalist design philosophy. It's only that someone put a lot of time and effort to designing that machine, and it shows. It's a mark of craftsmanship rarely seen in today's world of mass manufactured goods that surpasses simple division of style.

I don't know. I really think I will be getting a macbook once I am through with my current machine, though I'm half hoping that the legendary durability and reliability of thinkpads would kick in and the purchase would be put off for a long time.

I didn't spend the whole day admiring my friend's computer of course. I did get a lot of work done, both for school and personal projects. What riles me though, is how I can't seem to be able to come up with a decent project idea utilizing synthetic biology yet stays within the realm of possibility with the kind of limited equipments and resources at the group's disposal. I guess the first project would have to be a practice in introduction of foreign genes into a bacterial chassis for production of noble proteins. The problem is, what kind of genes to what kind of chassis? E.Coli chassis is easier to manipulate due to the characteristics of the prokaryotes host. Yet it's a nightmare to obtain due to lot of legal and financial hurdles. The yeast chassis would be easier to obtain but it would be complex to handle in the kind of garage biolab our hackerspace can provide. The genes themselves provide a nasty problem as well. Should we introduce prebuilt genes for established protein production network or should it be a synthesized gene designed and built from scratch? Or built from one of the many gene repo blueprints on the web? Doing something that's epigenetic in nature (morphology mutations etc) are completely out of the question at the moment.

I need to be able to come up with ingenius idea for creating something new, crazy, and possibly even useful using chassis and collection of plasmids, either prebuilt or synthesized... Perhaps something related to light sensitivity?

This is with me not even getting into how to figure out funding for such experiments. Sigh. The path to madscience is long and harsh.
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blackberry

2009-03-22T12:15:00.000-07:00

I've been doing most of my personal writing on the blackberry device I obtained recently. It's a novelty thing. Writing on the keyboard is of course much more faster and efficient, not to mention accurate. I've looked through some of my posts and tweets from the first time I've used the blackberry and as expected they were riddled with typos and unsightly mistakes I would normally be able to avoid if I had been using a proper full sized keyboard. However, for someone who moves around all day being able to type in comments and posts on the move with a fully featured keypad (instead of the t9 predictive input system) is a real godsend. Most of the things I've posted using the blackberry were either written while I was outside waiting for something or inside cuddled up in a bed waiting to fall asleep. Both the types of situation that carrying around a full sized laptop would have been rather inconvenient. I've also been able to read and sometimes do a quick fix on various ppt graphics and documents I would be needing in my lab projects, and I'm looking for ways to integrate some sort of mobile mathematical simulation suite to the blackberry device so I can do some serious work on the device without having to sit in front of the desk. Of course, considering the limited hardware of the device being able to replace my trusty laptop is a mere pipe dream at the moment, but who knows. Being able to do decent work on anything less than a full workstation was a pipe dream a few years ago. I can still remember the days when mobile laptops weighed around 7 or 8 pounds. That was the first Apple powerbook I had I think. Modern laptops of relatively larger and heavier frames weigh around 4 or 5 pounds. There are heavier laptops around but you are not supposed to lug those things around in the first place.

Will mobiles be able to replace most of the laptop functions we know and use today? I believe so. The nokia n85 I had before could connect to a TV screen and use it as a monitor, while interfacing with a bluetooth keyboard, so we are really close to making such technology reality. There are a lot of naysayers to the mobile technology as well, but those people tend to be either 1)doesn't really use computers enough to make a distinction between a laptop and a desktop, they might as well work with pentium from 2000, 2)doesn't move around in the first place, so it's either sitting at home with a cellphone or sitting at home with a desktop, the choice would be obvious to them. Ubiquitous computing where the device is divided into mobile interface and centralized processor/server cluster is coming whether you like it or not.

Unlike my old nokia however, the blackberry only runs on the EDGE 2.5 generation network. In this age where 4.0 generation networks are already being implemented in limited locations (guess where they are. Hint: they are somewhere in the Asia) this is a crime. The 2.5 generation networks are only slightly faster than the dialups of the old, and we all have a pretty good idea of the atrocious speed on those things. the funny things is this is the network the At&t was rumored to plan to keep as a major network channel until the 2010 (instead of rolling out 3G), under the very typical American idea that the neglected and outdated stuff are still good enough for the unwashed masses of the American public to consume... Those same guys are saying that the financial meltdown is the fault of the people who took the mortgages by the way, instead of the banks who approved them after month long review processes during which they really didn't review anything.

Things on mind

2009-03-21T04:46:00.000-07:00

I came back home around midnight after a little bit of bar hopping and late night snack with a couple of my friends.

As I lay in the bed trying to fall asleep (I always found it very peculiar that I have to try to fall asleep even when tired) with the ipod playing the audiobook of Jonathan Strange and Mr. Norrell playing in my ears (I recommend anyone who haven't read that book to pick up a copy asap), here are some ideas I want to write down.

First, the movie 'naturally obsessed', I should try to obtain a copy, or perhaps even schedule a local screening. I was at the R.U. screening before and the film is certainly unforgettable. It's not that the film is a visual tour de force or anything, I just found it to be oddly compelling and honest in a very enjoyable way. I must have spent half the night extolling the virtues of the film to my friends over the draft beer. It would be much better to be able to show them the film instead of sitting and talking about it like a maniac. This is the kind of science film that's worth sitting through. I just hope this year's imagine science film festival has films like this. I don't think I can wait until October for the festival to begin... I guess I have to be content with the Tribeca film festival and the world science festival for now...
And yes, in case you've miraculously missed it somehow, I'm something of a film nut, or at least an enthusiast. Combined with my love for all things science the imagine science is a god send.

I'm wrecking my brains over possible project ideas for the diybio nyc group. I just can't seem to be able to come up with a novel idea that can be executed with limited budgets and materials. I blame my limited understanding of the molecular biology. I think it would be better for me to re-browse the previous igem archives and the S.B. 4.0 abstract book/lecture note I have, instead of waiting for good ideas to emerge out of thin air.
I'm trying to figure out if creating a designer/artificial ribosome is within the possibilities of existing biobrick parts. I hope so. It would be so cool to be able to create a home-brewed universal constructor of sorts using biological parts. Since ribosome is a mere protein construct that reads mRNA feeds, it shouldn't be impossible to create them through manipulation of the original cell.
Of course, a whole artificial minimal cell is something I'm interested in getting into at some point but I'm not sure amateurs can tread that far at this stage. I guess I should get some more info on the PURE system from Tokyo as well.

At some point I should do a little post on the origin of stories. It's related to the origin of creativity so it's a topic definitely related to lot of things I'm doing at the moment. The origin of stories in its purest form should be mythology, and among them creation myths. It might prove to be an interesting analysis.
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Simulacra & Simulation

2009-03-18T15:00:00.000-07:00

Jean Baudrillard's book 'simulacra and simulation' is one of the many books I tried to read on and off for a long time, my attempt always thwarted by some freakish chain of coincidences. It's an interesting book that defies classical genre specification (I think). The closest I can classify what's in the book would be a disposition of philosophy coupled with some degree of psychology. Some others would say that the book is a treatise on the nature of the modern society that titters on the boundary between the real and the simulation of the real. I haven't read through the book yet of course, but the general gist of the text seem to flow towards analysis of the modern civilization built on the production and availability of massive amounts of information.

The whole thing is very relevent with the kind of world we live in right now (though the book itself was written some time ago). This book provided a lot of background for much of the popular culture phenomenon we know and love today, like the matrix and the ghost in the shell. I can't look it up right now (virtue of tapping out a blog post with a blackberry while in a bar) but I'm sure there are a lot more references out there. The coming era will be the day of fantasy and reality intermingled, as humanity continues to build on their perception and knowledge of the world and technologies inch us ever closer to seeing our imaginations and collective manifest in reality. If the tools to shape the reality remain in hands of a chosen few such future will be the new dark age. If the tools can be used by anyone with sufficient force of will the future will becomeb the new Renaissance. Sent via BlackBerry by AT&T

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Naturally Obsessed

2009-03-17T14:57:00.000-07:00

I was at the imagine science festival sponsored screening of the science documentary 'Naturally Obsessed: the making of scientist.' I did a little post on it yesterday right at the caspary auditorium while waiting for the film to start, which was caught short by the starting of the film (so much for semi-gonzo journalism, eh?).

I can't post the link to the website here since I'm on the move right now (ah the wonders of smartphone culture) but you can simply type the title of the film (naturally obsessed:the making of scientist) into the google and you should be able to find it. The makers of the film also has a youtube channel with the film trailer. I highly recommend anyone with even a passing interest on life of people in research laboratories or any science in general to stop by.

I would also recommend that anyone interested in above things to go out and buy a dvd but I don't think it's out yet. If it was out I would go out and get it in a heart beat. The film is made by independent filmmaker, so you'll be supporting a good cause in both sciences and arts while getting away with one exciting film (something I can't say for most of the films out these days. What happened to works like the waking life by Richard Linklater?).

The film centers around the lab life of researchers in a certain protein crystallography laboratory at the Columbia University. The basic premise of the film might sound boring to some. That's what I thought first before I saw the film's trailer. Now, x-ray crystallography is an exciting field in its own right, I just felt as if it would be very difficult to make a compelling film out of such a premise. Boy, was I wrong. I had so much fun watching the film I completely lost myself for the duration of the film. The film concentrates on the human side of the individual characters within the lab, and there aren't that much science talks in there. It really doesn't detract from the experience of the film though. There are enough drama, humor, and intensity in those characters to make up for the lack of scientific content and then some (I'm not being too fair with my assessment here, since the absence of heaviee scientific component within the film was a conscious choice of the filmmakers themselves).

You see, contrary to what some people seem to think (for some inexplicable reason), life in science laboratory is rarely calm and uneventful (you would have to be some sort of idiot to be able to lead uneventful life in an actual research lab). Science is a venture that takes years and years of life for a single result that might or might not agree with the intent of the researcher. You can not continue that kind of lifestyle without some sort of great force of will, driven by intense human desire whether it be greed, ideal, or hunger for more knowledge. As I have written before on the post on workshops of the Renaissance era, modern science laboratories are the focal points of the most intense personalities of the era. It's the place you truly become human. And the film is successful in portraying that intensity within the people involved in such grand projects, however brief it may be.

I am in love with this particular style of films that tries to portray the pursuit of science as a noble yet unmistakably human endeavor. Looking at the film's website and the groups that lent aid to production of the film I think this may be a beginning of series of films sharing such premises (at least I hope so. It would be a real shame to stop making such wonderful things).

Maybe my admiration for the film comes from the fact that I'm a filmb junkie who works in a somewhat similar science based setting. Regardless, one thing I can say with certainty. The film 'Naturally Obsessed:the making of scientist' was one hell of a fun, and I'd love to be able to experience it again. Sent via BlackBerry by AT&T

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While waiting for the screening...

2009-03-16T13:53:00.000-07:00

I'm under sudden urge to write something, so here it is. Something.

I'm sitting in the caspary auditorium in the Rockefeller university (which is the coolest place on the Earth by the way) waiting for that science film documentary to start. This is part of the screening affiliated with the new york city imagine science festival. I have a bit of personal history with this particular festival that I will have to elaborate on later, let's just say that I'm a huge fan of good science films (not necessarily science fiction films) for now.

The university is an amazing place. The Rockefeller U is university in name only, it's a research organization of immense size and presitige that happens to accept grad level students as researchers on their path to advanced degree. The kind of research being doine here is possibly mind blowing... Oh the screening's about to start.
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Workshop

2009-03-16T11:55:00.000-07:00

I stopped at the Met a few days ago, admiring the Renaissance bronzes and the interiors of the workshops of the era they reassembled within the galleries.

Along with my professed love of the libraries both real and imagined that borders on the mystical, I also hold a softspot for Renaissance era workshops somewhere in my heart. There's something mystifying about those spaces that places them on the same level of the library of the universe penned by the eponymous Louis Jorges. Something that just boggles my imagination when I think about them. The master's workshop of the era were not simple art studios. They handled everything from metallurgy and architecture to alchemy and mathematics, and the polymath of Leonardo Da Vinci's style was a common sight during those times, though interests did not necessarily translate into true calibre. Basically they were the science laboratories of the time before science was born, akin to a magician's library in many ways.

Just think about it. The blue gleam of twilight flows through the closed windowsill. Bits of orange light from the furnace of molten bronze laid on top of the thick wooden worktables. And you can catch glimpses of sketchs of real and geometric experiments buried somewhere among illegible scrawls of mathematical formulae. The maestro work with his tools pouring molten metal into a crack on the wax shape that will soon turn into a statuette of life like quality. We are witnessing transformation of a chunk of rock into a life like shape that still retains all the emotions and memories of the artist's intent.

To me those workshops are the places where sciences and arts intermingled with each other under the will of the human creator to form wonderful things, crafted from a lifetime of pursuit and mastery. And that is why I stubbornly refuse to compare those workshops to most modern artists' galleries and workspaces. I may be a bit one sided on this issue but many of the products of modern art makes me question the degree of mastery and understanding the artist has on his or her chosen medium. Do they pay attention to their colors? The surface tension of the pigments? The light and surfaces at an interplay of the quantum nature? The construction and porosity of their wood? The thermodynamic characteristics of their molten metals? People who lived centuries ago paid attention to those things so why can't the modern men/women do it? It feels as if vast majority of the artists out there pay attention to the fad and fashion of the times instead of true perfection of their arts.

Of course, I am not an artist, and most of the knowledge and impression I have on arts are superficial at best. Yet I cannot shake the feeling that what I just put to words above is more relevent to the art scene then I would like.

I love those old workshops, but most of all I love what those workshops represent. Ceaseless pursuit of perfection not limited by superficial boundaries of genre and scene. Modern forms that most closely resembles the workshops of old are probably science laboratories and hackerspaces (not art galleries, I'm sorry to say). There is something incredibly satisfying about being able to pursue something to a degree of perfection, spending sleepless nights and skipping meals left and right. It's intellectually stimulating and it makes me feel alive, something I can't quite say with most of the lifestyles out there.

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Night comes

2009-03-15T15:47:00.000-07:00

The night is here. I'm strangely exhausted today, strange because I didn't get any real work done. I took it easy and even played a game for an hour or so, the most I've used in such trivial pursuits for a long time... A few months I think.

Maybe it's the relaxation. Maybe I needed something like that, apart from the pursuit of arts and sciences I usually try to devote my life to (at the risk of sounding pretentious). For some reason I feel very rested and relaxed right now, in both body and mind. It feels as if little pieces of myself that's been torn away to little pieces are slowly finding their way back to me, making me whole again.

For some reason I am reminded of the long road trip I took back when I was little, in California. Everything was quiet and there wasn't any obstruction to any direction. It was a largest empty field I've ever seen, the thin strip of highway coming from one horizon going off into another. The land was arid, but it wasn't hot. It was quite cold actually, as if I was high in the sky among the atmosphere. There was unmistakable scent of green in the air, like spring wind. The world was enveloped in the dark blue hues of the sky with a thin streak of red light just emerging from the violet horizon... The world felt impossibly pure, and in the middle I felt as if the sky was falling into my heart.

I don't know how I would be able to describe what I am feeling right now, so I listed down bunch of stuff from the time in my life I felt something similar. It would be simple to define the whole exxperience as something like 'relaxed catharsis' or something such, but would it have been enough to portray my impression in full? Shouldn't I write down the very form of the world that gave birth to my impression of the world to ensure maximum fidelity with the reader? With myself? How would I be able to explain such feeling of calm revelation intermingled with such intense sensation of nostalgia?

I'm tapping this away as I lay in my bed, waiting for the sleep to overtake me. Maybe, if I'm lucky, I might even be able to dream of the memory I just described above.

Such amazing feeling of calmness and wonder. It would have been sad to live a life without such an experience, something so pure that my meager linguistics just can't seem to be able to describe it.
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Blackberry so far

2009-03-15T09:48:00.000-07:00

Okay, so I've been testing out (read:playing with) the new blackberry I picked up this morning. This is a cheap-o blackberry model that comes with full keyboard, GPS, and 2mp camera with video recording capability but no wifi. And it's on the lacking side when it comes to the number of bands it can transmit in, though the comm options are still much better than most mid range cellphones out there.

All in all, it's pretty good for something I picked up on a whim until I can get my hands on a decent android based phone. I was somewhat surprised to find video recording capability and LED flash on the phone though. It's not the kind of feature that's available on machines of similar class. For example, iPhone has neither.

I love the keyboard on this thing. It's much better than tapping messages on the standard T9 keypad, and surprisingly enough I get quite an impressive wpm on this device... It's no where near what I can do with a full sized keyboard of course, but still impressive considering that it's only been a few hours since I got my hands on the blackberry. No one will be writing a novel on this thing but it's still plenty enough for an occasional blog post (like what I'm doing right now).

The GPS is something of a disappointment though. It's nice to have the functionality on a mere 50 dollar device but the accuracy and lock on time leaves something to be desired. It almost makes me think that the chip may be running some sort of triangulation scheme instead of a full GPS module. I need to mention that I've only used the GPS inside the building with google maps application I downloaded off the cellular web though. Considering how carrier-locked devices are I may get a better performance with the bundled At&t navigator application. I do remember that the blackjack II smartphone from At&t had its GPS locked in so that it wouldn't even turn on if you didn't use the paid app supplied by the phone company (there are ways to get around it of course).

The photo quality is good enough. It's no where near the quality of the nokia N series phones I had a brief fling with but it will still serve its purpose in a tight spot. The picture quality is still better than what you would get with an iPhone under similar light condition, if only marginally. I will take a few pictures and post it up on the flickr when opportunity arises.
I am delighted to see video capture capability on this phone. For some reason a lot of carriers and device manufacturers leave video capability out of otherwise fine smartphones (like iPhone and the G1), so I wasn't sure if there would be video capability on this device. You won't be filming any hollywood movies with this, but it still does its job well enough.

How many words did I write so far? It's been about five minutes since I started writing on this phone. Marvelous.

The bundled web browser is nice enough. You can watch youtube videos on it, and the video loads swimmingly despite this device only being capable of data transfer over the infamous EDGE network (more on that later). Other pages load nicely as well, and the browser supports javascript and full CSS rendering (so far). I have a secondary opera mini browser loaded on the device though (among other myriad of applications).

Careful calibration of the web browser turns this device from a messaging centric smartphone into a fully featured synthetic biology reference, among other things. I have numerous web-widgets that links directly to the PLoS journal, openwetware web services, the GenBank database with full DNA table search capability and etc. Combined with the ability to view flash videos off the web, the innovative will be able to find a lot of crazy uses for this device.

The main reason people get their hands on blackberry is so they can maintain ubiquitous email presence. I have four email accounts registered to this device for work/school/mailing list/personal, with full filters. The email experience on this device is definitely solid. People say that blackberry is the best system on the market for messaging and emails, and I must say that I am inclined to agree. Other smartphones doesn't even come close to this, and this isn't even the best blackberry device (I'd say the place is reserved for the blackberry bold model, something that costs four times as much as this device even with 2 year service agreement). Now only if I could get rid of that annoying 'sent via blackberry from at&t' marking at the end of all my emails...

This device is all about communication and it shows. There's a program called blackberry communicator on the device that acts as an instant messaging protocol for any and all blackberry devices without any extra charge. I can see how corporates and research groups can go nuts for such a feature set.

The first third party application I installed on this phone is the twitterberry. As some of you might know already I'm something of a twitter junkie. I know that there are a lot of useless noise on that thing ('what I ate for lunch today' and etc) but once you can get through that part and link up withb worthwhile people the whole thing becomes indispensable. Not to mention that it acts as a field report on my day to day thoughts. The second application would be a full suite of google mobile apps including Gmail client, google maps, and rss reader among other things. I also got mobireader for blackberry, turning this device into a semi-decent ebook reader.

Not all is well in the blackberry land however. There is one glaring and quite frankly insane omission from the standard application set that comes preinstalled on the device. This particular model of blackberry does not come with any kind of instant messaging program. There are a few for most of the major protocols like ICQ and Gtalk available on the net. Many of them programmed by the device manufacturer (RIM) themselves so that they sit flush with the operating system, but users of this type of message centric device should not have to jump through hoops like that in the first place. Also, all of those free applications are single protocol only. Having multiple instant messaging programs open on your desktop was ridiculous five years ago and it is ridiculous now. Maybe the time I spent with nokia's symbian operating system spoiled me, but I can't believe the lack of free multiprotocol instant messenger clients on the blackberry os. There are a few programs available but they are all commercial apps you have to pay for. It's crazy I tell you.
I added 1 gigabyte memory card to this phone, and it didn't have any trouble recognizing it. I'll be needing it for the crazy number of photos I'll be taking with this phone.

Hardware-wise I have no complaints. This phone is surprisingly small now that I have it in my hands, it's almost a miracle that I can type away with my fingers like this. The size is more or less a fine balance between mobility and usability. The construction feels very solid and hardy without being heavy, and I would definitely refer to the overall feeling as being classy without being boring. For a smartphone with a full keyboard I found this phone to be surprisingly pocketable, but then I have skinny legs so your mileage may vary on that. At least this phone is significantly smaller than the G1. This phone is also slightly smaller than the Samsung blackjack II(an interesting bit of trivia, the blackjack II is the smartphone of choice for the female lead of the scifi tv show Fringe), something I couldn't really notice until I got the two devices side by side (thanks Ann!). The trackball interface needed some getting used to, but it worked out nicely in the end. I don't particularly see the advantage of trackball over other navigation methods though. Maybe it's the aesthetics?

The biggest gripe I have with this device is of course that it doesn't run android os. An ideal handset at for me would be blackberry hardware with Asian band compatibility, better camera, running the android os. Well, one can dream on, right?

Well that about wraps it up for preliminary review of the device. I'll write some real world usage impressions later on...

I'm beginning to notice some pattern to my gadget purchasing habit. I settled for thinkpad T400 for my laptop and now a blackberry? Both are criticized for rather conservative design yet praised for superior build quality. I wonder whether this is a good thing or not... Hmm.
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Testing

2009-03-15T06:32:00.000-07:00

Testing blog posting using blackberry.
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frustration

2009-03-15T05:30:00.000-07:00

I just wrote a two thousand-ish word post on the livejournal website only to have my browser revert back to a previous page because for some combination of keys I pressed. The whole day's post down the drain just like that. Apparently the 'restore from saved draft' option doesn't work properly on the opera browser. I don't fee like writing something I've written all over again, so I guess I'll have to write a brand new post.

Just in case you were interested, the post was about how amazon was selling the android G1 for fifty something dollars, which is a ridiculously cheap price for a fully featured smartphone. If you're in the market you probably should get it.

I've been using opera as the personal browser of choice for a while now. Of course, firefox still remains my browser of choice for all the work related stuff due to the bevy of science related extensions I can no longer live without (zotero and evernote, etc etc, programs that makes automatic bibliography of the resources I pool into the browser off and online, with full notation engine for any kind of file format including pdf, and I'm not even going to begin with the full journal article search engine I can build into the FF itself using extensions). Yet the sad reality is that while firefox is the swiss army knife of web browsers it's fast becoming rather unwieldy with its large memory/processor footprint and slow startup time. I've also used google chrome for a while (for all their faults, I like google and the weird products they keep on pumping out) but for some reason chrome gets ridiculously slow when you leave the browser window open for a long time, something that's unacceptable on a modern laptop with dedicated graphics card and top of the line processor. I think it might have something to do with the processor intensive architecture of their browser itself. Hopefully they'll iron out the faults soon, since the chrome browser really is blazingly fast compared to the competition.

For some strange reason, Opera browser is capable of maintaining the smallest memory/processor cycle with multiple tabs compared to the competition, considering how many functions are built into the browser itself (torrent engine, irc, etc etc). I did a little tweaking with proxy engine (also built into the browser itself) so opera is now ad-free as well. The interface to make that happen is a little bit clunky compared to the simple button interface of the adblock plus extension on the firefox, but it works.