Consider Bookhling

I should definitely to a decent post some time soon, but it seems that I’m in middle of severe drought of ideas and writing abilities. Hopefully this is just a passing phase… Someone should definitely develop a drug against writer’s block I think.

A few things I’ve been working on so far between all the jobs I have to run to pay my rent. I’ve been studying the Exploring Complexity by Gregoire Nicolis and Ilya Prigogine since the beginning of the summer. Studying as in tearing through every bit of reference mentioned at ends of each chapters and working out all the equations, making up some of my own for practice. The progress has been slower than I would have liked but it’s still coming along nicely. I’m upto  the randomness and complexity chapter where they begin describing Markovian processes and different types of entropy. I’ve been trying to come up with some cool graphics describing some of the stuff in the book using Mathematica but couldn’t really find the time to get around to it, with all the other coding projects on my hand at the moment, but I’ll definitely have something to show for by the end of the summer.

I’ve also been reading up on some bioinformatics literature, beginning with the eponymous ‘For Dummies’ book on the subject which is surprisingly well written, or at least comprehensible (well, considering the title it would be hard to write a book on the subject that is incomprehensible). It’s part of my attempt at coming up with a decent diybio coursework aimed at 14 and above, centering around the kind of projects the laymen would normally find out of reach, like designing a biological circuit and putting it together in a wetlab. With so many computerized tools and advent of abstraction in biological sciences brought on by synthetic biology, I think it is possible to empower the citizenry with end-user scientist toolset. The average computer user don’t code in assembly or the machine language yet many of them are perfectly capable of coming up with useful high-level softwares and beautiful works of art (it still takes effort and mastery but what doesn’t?). In order for the biological sciences to become user-friendly I believe we need a tool to familiarize them with the higher level abstraction in molecular biology and computerized tools associated with it. In my experience the best way to break down an intellectual barrier is to make people do the impossible easily and cheaply. The first step of breaking down the biology barrier would be teaching people how to design genetic circuits using extremely high level abstraction symbols. Theoretically it should be possible to put together a very simple circuit on a napkin using symbols and diagrams using unified ‘visual language‘ of synthetic biology. Once the individual becomes scientifically fluent enough to visualize these molecular circuits within his or her head, and feel a real want for building something in real life, we can easily transfer the design into computerized tools for specification and optimization. After that it would be a simple process of transformation using mail-order kits (or using diy tools if you’re so inclined), which DIYBio NYC have already demonstrated to be easy and straightforward.

By then, maybe I’ll try to pitch my not-so-secret ambition of coming up with diy-minimal/synthetic cell ::evil laugh::

As you might have guessed I’ve also been spending a lot of time reading through E.O. Wilson’s Consilience: The Unity of Knowledge again. It’s amazing just how much of the book resonates with me, not necessarily in solutions but in problems he outlines as something fundamental that needs to be resolved if we are to further our understanding of the universe.

-From pg.93
“…the U.S. federal high-performance program has upped the goal to a trillion calculations per second by the end of the century. By the year 2020, petacrunchers, capable of reaching a thousand trillion calculations per second, may be possible, although new technologies and programming methods will be needed to reach that level. At this point the brute-force simulation of cell mechanics, tracking every active molecule and its web of interactions, should be attainable- even without the simplifying principles envisioned in complexity theory.“

The continuing battle (if there is one) between raw computing power against elegant universal systems like the kind proposed by some of the complexity scientists is interesting. For one thing, would we need raw computing power the world has never seen so far to replicate human-like intelligence? Or can it be done in smaller scale using some aspect of the logical system that gives rise to emergent trait we refer to as intelligence? Classification of life/intelligence as a type of physical system that very closely resembles phase transition due to complexity is an intriguing possibility that will need to be examined in detail… I’m especially interested in intelligence as not something that computes but as something that creates. Why am I sitting here writing down this stuff when the weather outside is so great? Why do people strive to create this stuff and ideas when it’s much easier to sit on their collective asses and eat chips? To some the activity of creating get to the point of destructive obsession. Am I alone in sensing that the society at large tend to be envious of those kind of people?

Curiosity is not a rational trait. It’s crazy and sometimes suicidal, and doesn’t serve any kind of immediate need for survival or propagation. It is the very picture of irrationality. So where does it come from? What aspect of the molecular system that we refer to as living beings gives rise to such weird behavior? And what’s with this crazy unreasonable effectiveness of mathematics in the natural sciences? Isn’t it weird how questioning the nature of mind, life, and human behavior so often leads us to the questions on the fundamental nature of the universe itself?

-From pg.93~94
In 1994 editors of Science, celebrating the inauguration of developmental biology by Wilhelm Roux a century earlier, asked one hundred contemporary researchers in the field to identify what they considered the crucial unanswered questions in the discipline. Their responses, in rank order of attributed importance, were:
1.The molecular mechanism of tissue and organ development.
2.The connection between development and genetic information.
3.The steps by which cell become committed to a particular fate.
4.The role of cell-to-cell signaling in tissue development.
5.The self-assembly of tissue patterns in the early embryo.
6.The manner in which nerve cells establish their specific connections to create the nerve cord and brains.
7.The means by which cells choose to divide and to die in the sculpting  of tissues and organs.
8.The steps by which the processes controlling transcription (the transmission of DNA information within the cell) affect the differentiation of tissues and organs.
Remarkably, the biologists considered research on all of these topics to be in a state of rapid advance, with partial successes in at least some of them close at hand.

Above questions were written around 1994 according to the Consilience. It’s been over a decade, so I wonder how many of above questions had been answered definitely and conclusively….

Also, it’s rather interesting that most if not all of above questions are in some way related to study of complexity sciences. It’s almost as if the whole field of complexity science is biology fused with mathematical abstractions.

“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. If only I wasn’t so shy to ask him for an autograph on my copy of the book. I feel like a kid who lost a winning lottery ticket.

Now that I think about it I should also do a post on the World Science Festival while the memory’s still fresh… So many things to write about, so little time to write them.

I just came across an article in the Wired stating that Amazon will almost certainly unveil a new ebook reader with larger screen size. While the article goes on to talk about possible tablet device from Apple as being a heavy competition on the ebook market compared to the text-centric ebook devices, my attention span more or less stopped with the mention of the new ebook device on the horizon. It’s not just a new ebook device that’s about to come out. It’s a larger screen ebook device specifically targeted at the academic textbook market. Apparently Amazon want a share of the 9.8 billion textbook market (and that’s just U.S.), and I say it’s about time. I can still feel the phantom pain imposed on my back by years of carrying around textbooks that are heavy enough to be used as a decent weapon. It would be great to be able to finally carry a book-bag that weighs a lot less than the standard combat gear.

I’ve been an avid ebook user ever since I learned about existence of those wonderful devices and the myriad of texts available on the web for free use, like the extensive collections in wikipedia, various blogs, and the project gutenberg. I had my first encounter with ebook devices a long time ago before Kindle made it cool to carry around ebook devices. In fact, as far as I know the ebook reader I use, the Sony Reader PRS-500 might be the first dedicated ebook reader in North America that uses e-ink display. This ebook reader  had been a trusted mobile library by my side for the past two or three years. Even before purchaing this dedicated ebook reader, however, I was using old discarded palm pilot devices (so old that they stil had this ‘volatile memory.’ It was a memory scheme used in palm devices before the advent of all-too-familiar flash memory. If the device ever ran out of power all the data stored on the device would be lost, thus the term ‘volatile memory’) to read ebooks on the go, most of them reformatted webages I made using a handy Palm utility program called ‘plucker’ with ability to turn any webpage/archive format into a palm-ready ebook. Later on I’ve also used my Nintendo DS as a dedicated ebook reader (instead of playing games like a good kid) burning multitude of memory cards with whole repository of text and HTML formatted ebooks I found through my sojourns on the net.

I love my paper books as much as anyone, of course. And even now, with my extensive ebook collection (most of them surprisingly DRM free) I always make a point of buying paper books now and then. Some people stock up on weapons and emergency supplies for the inevitable zombie apocalypse. I stock up on paper books for that one day when I won’t be able to recharge my digital book-reading devices anymore, and my vast library is lost within the magnetic patterns etched upon my external hard drives. However, there is an unavoidable allure to being able to carry around twenty to thirty books of my choosing in a slim and light package that weighs as much as my hard drive ipod. The fact that I’m a rather fast reader only adds to the attraction of ebooks and ebook readers. Before I came across ebooks how my luggage would be filled with books whenever I traveled far away from home, and I happen to travel often. It really made for quite a workout, carrying those bags all over the place. With ebooks, I just need to carry the little device and its charger for my casual reading needs, with a hardcover or two just for those tight spots when I’d need to study instead of read. Many people still debate the need for having a dedicated device for reading digitally formatted books, and they are right. having an ebook reader will not change your life if you don’t read in the first place. In that light dedicated ebook readers are certainly niche devices, intended for use by the relatively smaller portion of the population would would buy books through digital distribution channel and who would be willing to pay for a device that goes into the hundreds of dollars just to be able to read more. The two things I’ve just mentioned might sound insignificant hurdles to most people who consider themselves to be internet savvy, but when we think of the reading population as a whole whose members come from various walks of life and are at various stages of life, those are some significant barriers for entry to the ebook world. Yet Amazon’s Kindle demonstrated clearly what dedicated gadget community members knew all along. People actually read, and many of them are willing to pay to support their habit, as the multi-billion dollar publishing industry would attest (and this is just in U.S., and quite frankly, we aren’t the most reading-intensive country in the world).

Reading the article from the Wired, and listening to conversations related to ebooks on and off the net, the ebook question seem to be moving from ‘will people bother to read on machines’ to ‘will people bother to purchase dedicated reading machines.’ This is a good sign I think. The market’s beginning to acknowledge that people are willing to take time to read things and even (gasp) pay for them, which means larger selection of stuff to read and things to read that stuff on in the future. However, the answer to the question of whether we need to have an ebook reader instead of making people read on their cellphones is a thorny one. It’s a question of how far people are willing to go to support their reading lifestyle. How many people are willing to cough up close to $400 for a dedicated ebook reader that you will later have to pay more to load content onto it? When we simply look at the Kindle as the only ebook reader of choice, the answer is obvious: not so much. I’m a self-confessed ebook enthusiast who regularly dig through the net for that obscure script to translate Microsoft proprietary LIT format to Sony proprietary BBeB format. Yet even I am not willing (or rather, able) to pay more than a month’s living expense on student budget to buy an ebook device. So are dedicated ebook platforms doomed? Not quite. We must remember that there are still myriad of companies out there that manufactures cheaper ebook devices, some of them more hgih profile then others (Sony isn’t a low profile company). Add to them the quirky yet ambitious enterpreneurs of the East, who seem to be jumping into any and all kinds of electronics market with vigor and goods of varying qualities. I got my own Sony PRS-500 for about $50 dollars in a promotional offer. I get most of my reading materials purchased through limited DRM free channels or through public domain, and they usually don’t cost much, certainly not as much as their printed cousins. Unlike what people think, ebook reading devices themselves aren’t really that expensive. Dedicated ebook device is basically an electronic device with two features. E-ink display capable of displaying basic HTML-like formatting along with a few more conventional formats like PDF, and a cable to connect it to a computer so the end user can load content into it. Simply put, it’s a glorified USB thumbdrive with big E-ink screen along with some buttons. While Amazon’s Kindle is a notch or two above the rest with its fancy whispernet technology and over the air delivery system, those things are not absolutely necessary to an ebook device. I mean, these devices are capable of holding 20~30 ebooks each going a few thousand pages. You probably don’t have to constantly buy new content before you go home from wherever you are at the moment (besides, if you can chug through that much content before you get to a computer with internet and USB connection you deserve to buy yourself a $400 reading device). The real issue that will either make or break the future of ebooks is not with introducing newer devices with more features (though I would certainly like to see existing feature set get better), but with software- the DRMS and ebook formats. I can manage quite a different number of file formats and DRMed formats on my single PRS-500 device only because of the collective action of the volunteer ebook community, some of whom managed to code indispensable piece of cross-format software like calibre. Many people can’t. DRM leads to limited distribution, since investing in DRM of a specific platform or corporation means that you trust that platform or corporation to exist ten or twenty years from the date of your book purchase. That is preposterous to anyone with working mind. Average lifetime of a corporation in America is about ten or fifteen years, and that’s assuming they will continue to maintain and support whatever the DRM scheme they came up with up until the very last moment. You can browse through your old books ten and twenty years from now on, and your children and children’s children will be able to read or sell those books send hand, ensuring certain degree of propagation of the written content. With DRMed books, it’s highly unlikely for your own children to be able to access your book, and whether you yourself will be able to read your favorite passage years from now will be decided by a boardroom composed of people who don’t know you and quite possibly don’t care whether you want to read or not. Even when we don’t consider faraway scenario like this, the dangers posed by DRM on the general propagation ebook into larger market is obvious, owing to the simple fact that DRMed ebooks will impose limits upon its own market and distribution. The first thing most people encounter whenever they browse to an ebook store that isn’t Amazon is this: Name of the book:LIT, PDF, BBeB, MOBI and etc etc… When users somehow manages to find the book they want to purchase (despite the severely limited selection in most of those stores) they are faced with multitude of options as to the format of the book, most of them incompatible with each other. From what I know of people who are not familiar with ebook formats, this is the step when most of them will just give up and go buy a paper book in local bookstore for only slightly more, or maybe even less than the DRMed digital copy if the user knows how to shop around on eBay. Even larger scale distributor like the Amazon, with its almighty capacity to push their own content into their own platforms, is basically playing in an uneven field. the reality is that people will inevitably ask questions about the future of their books and all Amazon can do is to cross their fingers and wish that doesn’t happen anytime soon. Limiting their own source of income and praying for only good things to happen in the future is not a valid business strategy.

The valid business strategy in near future would be to get rid of the DRM scheme entirely. For everyone. Even giant like Amazon is hedging for uncertain bet with DRM restriction in their ebooks. Smaller distributors like Sony ebook store doesn’t stand a chance. Just sell ebooks like you sell books. Let the market grow and let more people get hooked on using ebooks on ebook reader devices. There are cellphones and laptops, sure. But the reality is that they don’t compare to dedicated ebook readers in terms of providing a valid reading experience. Cellphones are supposed to make calls and laptops are for computing, and no one will burn out their batteries on those devices and risk their bill-paying work just to read more books. Once the quantity and quality of DRM free ebooks reach a critical mass there will be cheaper ebook readers on the market. That’s the time for Amazon to introduce their new and improved Kindlets. Why go for generic, cheap ebook reader when you can get the same content on far better machine with awesome battery with life-saving features and innovative interface? Only way to achieve this end with DRM still in the picture would be to either open Amazon DRM specifications to other manufacturers which defeats the purpose of having a DRM in the first place, or having a unified standard DRM for all publishers/distributors that’s compatible across variety of devices. That would require deal making and engineering of ungodly devotion, and I doubt even Amazon will be able to pull it off on their own, especially considering that there are markets outside of U.S. as well, especially when it comes to reading materials both traditional books and ebooks. The market is moving on, and publishers should move along with it instead of trying to hold back the tide.

I finally got through the American Gods by Neil Gaiman. I’ve said it before and I’ll say it again. He’s a terrific writer. He’s not the best writer out there or anything (he won’t be winning any Nobel prizes anytime soon, but then does it really matter anymore?), but he’s certainly above the fray in bringing his ideas to life through words. His characters feel genuine and endearing, even the villains. None of the plot elements feel like a cop-out from a hairy situation of an author having to create unique situations for living, something I’ve seen a lot of writers succumb to.

Through the end of the book I was embroiled in some very mixed-up emotions. I wanted to see the story progress, but I didn’t want the story to end. I wanted to see the story between shadow and crow to its possible happy conclusions. I wanted to see shadow grow old and meet someone and I wanted to read what he would have been thinking at the moment. I wanted to see if he’d get to meet any other gods, and I wanted to know if it would be as humorous and wonderful as most of his other encounters with the gods of the world, past and future. As I read on to sate my curiosities, I couldn’t avoid finishing the book, and that’s the biggest gripe I have with the American Gods.

There are all sorts of heavy stuff that people trained in such arts can debate and write about all days and nights in American Gods. Some would like the feeling of America as a collection of old, used-up ideas and modern god like ideas struggling for control, afraid to be forgotten. Some would call it an old and washed out idea just like the gods of old, since it’s an archetypal picture of the American that journalists and novelists and anyone else who can write and has good enough eyes to see things around them had been writing for past half a century or so, maybe even longer. I don’t think it matters. Neil Gaiman didn’t write this novel so he can have grand disposition on the fate of the American ideas (if that were the case the future of America would lie in somewhere around Iceland, and that would be funny, not serious). He wrote this novel to write a good story with good people living in it and he did one heck of a job. I don’t think I’ll be forgetting about the three sisters, Mr. Wednesday, shadow, Laura, crow, and etc etc anytime soon. It would be great if I don’t forget about them for the rest of my life, but no one knows what will happen in the future, and hopefully I might be able to experience something even more intense.

I’d love to write about some elements in the story, but I don’t think I should. I made a blood oath never to write down spoilers when ‘reviewing’ a book in a public place. Let’s just say that I really enjoyed the book, and I never wanted it to end. I think I spent about four or five days reading this book. I would have finished earlier, but then I had sudden burst of workload on me this week so I had to pull a few late nights. I mostly read this book in the subways, and in the bed with the reading light on. I would frequently curse at myself for reading past three AM on a work day, just hoping that I would be fresh enough to not look like a zombie by the time I wake up a few hours later. I would actually anticipate the ride on the subways since it was pretty much the only time during the day that I could sit down and read for close to an hour or so. The crowd didn’t bother me but I might have bothered some nice old ladies for making weird faces while reading the book, from deadly seriousness to strange smile (the kind you get when you suppress an even bigger smile because it would be weird laughing out of the blue). But then I guess there were even weirder things on New York City subways at eleven in the night, so I probably didn’t stand out too much… Which reminds me, I’ve never seen people reading on subway who change their facial expressions before. Is it that everyone else is so well trained in managing their faces or are the books just really boring? I would say it’s the training issue, since I also become excited when I’m reading through particularly illuminating passages on a physics book, and most normal people probably don’t do that.

As I read through the American Gods, I was reminded of just how much I like reading, and sometimes even writing, creative stories. With my official status as a student I usually have to dig through a lot of journals and data, where they usually deal with diagrams and numbers without much creative license (I think I remember one of my teachers telling me that use of creative license in any scientific writing is a single ticket to ending your career. Or did I read it in a story somewhere? I can’t quite recall). Reading those dry, albeit enlightening, academic scripts seem to have taken its toll on me, and sometimes I feel like I’m a dry person myself. It’s like the case with Marge Simpson. I only think of crazy jokes or stories only after I leave the party and start my car. It drives me crazy.

That being the case, reading through the American Gods and some other fictional works before that was a cathartic experience for me. I wonder what kind of trait drives us to enjoy and seek out well-made stories involving fictional people and places? Was there some strange need for living organisms to be able to tell fantasies to each other in order to survive? The kind of fantasy where both the storyteller and the audience knows it’s fantasy but indulge in it anyway? That would be an interesting venue of research, something I sadly cannot seem to be able to find anywhere.

The American Gods also had me thinking about the archetype of stories. Whether we like it or not, elements of the ideas composing stories from various authors end up being similar to each other. Usually the difference is only made up through the skills of the writer/storyteller in masterful use of the language the story is transmitted to their audience. C.G. Jung built up a whole sub-discipline of psychology based on those archetypes found throughout human culture and even dreams, and it’s almost as if human beings are capable of only telling certain types of creative stories with varying degrees of proficiency. What would that imply in understanding human creativity? Maybe the trait of creativity isn’t as limitless as we tend to believe. Maybe creativity is just like most other mathematically derived abstract act, based off of some type of pattern that circles around itself. If that were the case, we would be able to make a machine capable of creating stories not by linking relevant words together but through linking relevant ideas together, into a preset pattern. An idea of conflict, an idea of resolution. The individual set of vocabulary and the storyline composing that single idea would be irrelevant as long as it can lead to the next part, and the transition won’t even have to be singular. It can be polyphonic like Bach’s composition, each event happening with  another in ceaseless pattern. However while I’m sure it would be interesting to create such a program/machine, I’m not sure how I would be able to handle the task of making a machine capable of creating a character. Will characters simply emerge out of the polyphonic storyline? Will their personalities simply emerge out of the series of events that the characters are subjected to, each of them simply beginning with a name?

The first thing I tend to do when I want a deeper understanding of a writer’s work is to look up information on the life of writer him/herself. The research can be illuminating in a lot of cases, which is funny when you think about it since most writers I know of make their living by creating stories that are considered very unique compared to the rest of the ‘writer population.’ Would that imply that the trait of creativity is inseparable from memories of the individual? And what should writers do when they are so prolific that they are faced with the possibility of patterns and familiar ideas appearing again and again within their works? Do they embrace the patterns and ideas and try to refine them? Or do they try to break free, staying away from such patterns and ideas appearing in their works altogether?

I feel a little guilty about posting on Coraline when there are dozens of science write-ups sitting in the draft corner of the webpage, but I think I might as well place emphasis on the recent event. Of course, it also helps that I’m a hopeless fan of works by Neil Gaiman.

I saw the Coraline at the Ziegfeld last night, a late night sojourn that ended with me coming back home around 2:30 in the morning. The film was marvelous, and I’d suggest anyone who was on the fence to go ahead and give it a try. It’s very much like the Nightmare Before Christmas, basically dolls captured scene-byscene composed into a whole film. The film Coraline is based on the novel Coraline written by Neil Gaiman, though there were few differences that anyone who read the book should be able to pick out. You would be relieved to know that unlike most other Hollywood book-to-film adaptations, I got the feeling that certain elements of the story were edited in order to best fit the medium rather than some insane rating criteria, and on the whole it works very well. Neil Gaiman always had that fantastic flare to his writing that weren’t quite fantasy yet fantastic enough to be unreal, very much like how Stephen King had a knack for turning the usual into unreality and explored the changes in human psyche within the metamorphosis of the world (personally I consider Neil Gaiman to be a much better writer than the Stephen King, if only in terms of the ingenuity of the imagination t work behind both writers’ works). Coraline definitely has all the trappings of a fairy tale. A little girl lost in the woods, the haunted house, mysterious old woman, evil stepmother, and the circus of jumping mice. The film as a whole feels as if it was a modern juxtaposition of all the elements of the conventional fairytale throughout history, a mish-mash of all the archetypes that we all knew and loved regardless of the individual cultural background (which would also mean that the film will not appeal to you if you don’t have the taste for the fantastic, but if that’s the case what are you doing in the Coraline theater in the first place? Go watch ‘he’s just not that into you’ or something, not that there’s anything wrong with the movie). And surprisingly enough, it works well. For the duration of an hour and a half (was it longer or shorter? I lost my sense of time during the film, I still can’t figure out just how much time I spent in the theater) I was lost in the fantastic yet familiar world of the Coraline, sympathizing with the cute-as-a-button main character and being awed at the visual tour-de-force of all the dolls being lighted up and blooming into living breathing beings.

Now, you should take Coraline for what it is. If you are looking for the kind of ’seriousness’ present in the indie film like the Pi you will not find it here. There won’t be any philosophical discourses and debates on the divinity or the holy moment in crafting film (as it was in the case of the Waking Life, another indie film which I suggest anyone with even a remote interest in movies to find and watch immediately, it might be a life-changing experience… It was for me, and despite all the heavy philosophical discourses in the film I’d say that it was also another form of fairytale distilled to the modern tastes). What you will find, however, is a very honest treatment of a little girl living and sometimes getting lost in a world where good and horrible things can happen when you open a wrong door (or should it be the correct door? Since if she couldn’t find it the story would never have taken place) in an old house. The film Coraline never tries to be what it isn’t. It’s just good at being what it is, and what it was intended to be. And shouldn’t that be mark of a good film?

The version of Coraline I saw was formatted to be watched using a 3D glass, the kind you frequently see in the IMAX theaters with all the whales swimming around and weasels poking their nose into you face. Anyone with decent theater going experience should know what the whole deal is about. On the whole Coraline works well with the given medium. If you are looking for some sort of thrilling experience with hands and eyes popping into your face you are rather unlikely to find it, but if you are looking for a beautiful 2D experience with some added flavor the current version will do. I must add that the 3D versions of the film Coraline will not be in the theaters for the duration of its run, and whatever the theater that carries Coraline will revert back to normal 3D glass-less film in a week or two I think. I especially loved the garden scene in the movie. The 3D flowers lighting up and blooming into full shapes were very beautiful to watch and brought a smile to my face… A little side note on the matter of 3D glasses. Despite the message at the beginning of the film telling you to return the 3D glasses after the film, I think the Ziegfeld theater in Manhattan (about the only place that runs Coraline right now, oddly enough considering the hundreds of theaters in the city) actually gives you the glasses as a souvenir, which I found out only after returning the glasses and walked out of the theater.

Another thing to watch out for after the film. If you are patient enough to sit through to the very end of the credits, the film will display a very special message. It’s a password. You can enter that password into the Coraline movie website to enter into a random drawing of special hand-stitched Coraline sneakers, and they even have adult-male sizes! (so it’s not just for kids) I don’t think I should tell you what the message is, but if you can’t find the password page on the Coraline website (I spent close to ten minutes clicking on everything), the nice rock given by the ladies Ms. Forcible and Ms. Spink will help immensely in finally figuring out where to enter that password (which I promptly entered at around 3 am). Will I be able to win the shoes? I have my fingers crossed. I’m definitely in need of some new pair of shoes (though it’s very unlikely that I’d actually wear the Coraline shoes even should I win it).

Fairytale always fascinated me. Fairytales are what we end up with when the gods and heroes pass away with their myths, the fantasy of everyday lives. Unlike what some people seem to think, fairytales are rarely if ever childish, unless the the creators of the fairytales actively try to sanitize it. The one word to describe the essence of fairytale would be ’shadow.’ Exploration of the hidden motif beneath everyday events, an act that is inevitable as long as the humanity is capable of conscious thought and emotional response.

Fairytales are ever present within the very fabric of human society, because the essences of fairytales are far beyond the simple archetypes of old witches in forests, locked doors and scary things roaming in the dark. Fairytale is the last resting place of any idea that once lived in the light, that’s been aged and killed with the passage of time and lapse of civilizations. That aspect of fairytale as a graveyard of once widely held beliefs that had been relegated to the flow of time is most obvious in cultures that had been more or less taken over by the so called ‘western ideas’ in relatively recent years after the demise of their indigenous culture. Japanese and Mexican fairytales and the like are the most coted examples, but we needn’t even go that far in search of exotic locations. We can simply look beneath the stories of cross-studded stories of kings and knights in Europe to find the most unexpected beliefs sustaining their meager life as fairytales in minds of the populace.

Once that grace and grandeur of the original myths had been stripped away with time, the old stories remain with us in its cold and naked forms since nothing holds them upon distant pedestals anymore. It descends to our level and stares into our eyes, whispering things into our ears that we have been so far away to hear in the past. When myths become fairytales they be come feral. When myths speak of the giant monsters in the dark it speaks of the pantheons of gods and individual tidbits and family affairs of the whole clan complete with intrigues and jealousies. When the same myth becomes a fairytale it only speaks of the huge thing standing in the dark, it has no name, and it has no family. At that moment we realize that while we were busy counting the number of fights the gods went through in their shining armors during their heydays, the thing in the dark had been staring at us all along, silent and waiting. The moment of that realization is the moment that we realize the true depth and value of fairytales, and that is the moment we begin to understand ourselves as not just animals born a few decades ago, but human beings with thousands of years of history behind us, with hearts too deep to fathom.

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

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

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

Just one thing though. Library of Alexandria. 

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

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

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

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

I picked up my Amazon Black Friday purchases from the post office today. Here are shots of the purchases I’m especially fond of.

“The varieties of scientific experience” by Carl Sagan. I didn’t plan on buying this, but at five something dollars per copy? Sign me up!

“Journey through genius” by William Dunham. Lovely book on mathematics, suitable for beginners and advanced readers alike. Sometimes I can’t help but wonder why so many children are released from the education system without ever becoming aware of the elegant beauties of mathematics (something I’m much more proficient at compared to writing). 

“Falling for science” with introduction by Sherry Turkle. It’s a book with ‘testimonials’ of sorts written by students and faculties at MIT regarding how they became interested in sciences. Very insightful, I highly recommend this book to anyone even remotely interested in field and pursuit of sciences.

Last, but not least. I’m especially fond of this particular acquisition. “The invention of Hugo Cabret” by Brian Selznick. I’ve been lusting after this book for months, but had to put off buying it for variety of reasons. I gave up buying a DVD collection of Ghost in the Shell season 1 so I could get this book (woes to the poor finances of a physics student!), but I say it was well worth it. Look forward to a full blown review of the book once I get through with it. Here’s the website of the book to tide you over until then. 

For a picture-story book, this one is quite thick.  Just how I like it!

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

TW: 

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

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

Are we seeing the beginning of the end for the workings of current generation pharmaceutical industry? Vaccinations and pills developed by relatively small scale biotech developers, perhaps even run by some of the poorer nations to counter against indigenous diseases? Perhaps in such a  universe, intellectual property rights can truly be something that protects the interests of the public instead of being a noose around their neck. 

I’ve been going through a number of Cory Doctorow’s works lately (thank goodness for DRM free ebook reader). He released a lot of his works under CC license to be available freely on the net, and I can’t recommend them highly enough. Visit his blog for a list.

I’ve finished reading Neal Stephenson’s Anathem some days ago. As is usual with all his works so far, I enjoyed it immensely. This is the kind of book that grips your attention and never let it go, the sort of reading experience that many people don’t get to enjoy very often past a certain age. Other than some technicality like how stable elements from one universe can remain stable even in another universe (and if it is because the physical laws are the same, what caused those elements to be different enough to be incompatible with life forms in another universe) that keeps on nagging at the back of my mind, I see no reason to criticize the book in any way. Of course, Neal Stephenson won’t be winning Nobel prize for writing the Anathem, but he never meant for it to be that kind of work, did he?

The premises of Anathem is obviously reflective of that of the current world we live in, notably the ubiquity and evanescence of information. The fact that most people lack learning of significant depth (which isn’t really all that much of a change from any other time in history) while becoming increasingly irreverent of the devotion to learning itself is a trait of the modern world frequently discussed in variety of media. Anathem also devotes quite a number of pages to discussion of the issue, and I hit upon a simple idea while thinking about a section on dangers of unintentional misinformation born through insubstantial learning.

In conventional process of teaching and learning, an individual opts to become a node of a degree of knowledge. The individual-node then connects with other individuals of varying degrees of learning and transmit his/her learning to those individuals in a process reminiscent of propagation of thermodynamic equilibrium. Currently the system of public knowledge-the web-is like an ever expanding vacuum. Lack of reliable sources of data and knowledge combined with abundance of random bits of knowledge that remain nonetheless incoherent and worthless in light of a greater system of thought is the symptom of such a vacuum. Maybe this symptom can be alleviated once the academic sector of the knowledge network begins to open its data to the world at large? Maybe the web itself can become a coherent learning environment through steady injection of respectable nodes of knowledge that expands along with the noise of the internet vacuum. I believe we already have the beginnings of the groundwork for such a project in the guise of openscience/science 2.0. If the openscience movement remains unhampered by the increasing haranguing of special interest groups and economic fundamentalists, we might be able to observe a true renaissance of human learning some time in the future that makes current advances in human network and information technologies pale in comparison.

There are two big events from today to tomorrow, one of them truly big in the sense of its possible impact on humanity and the sciences, and the other one big in the sense that it is a release celebration of a book by one of my favorite authors hosted by one of the more interesting groups around today. Both of them will be on the net through live webcast, so anyone interested should set the alarm bells on their clocks today.

The first and the most important is the upcoming live webcast of CERN lab LHC first beam. The Large Hadron Collider went though so much drama and uncertainty (pun intended) from inception to its recent power-up, this event will be quite emotional for the people who worked on the project as well as the large portions of the members of scientific community at large (and there are lot of them, I assure you). The first *beaming* of the tens of kilometers large apparatus is set to begin at 10th September 2008 9am CEST (GMT+2), which roughly translates into around 10th of September 3am EST in NYC. Considering that the technical and scientific magnitude devoted to this project likely dwarfs that spent for building the Great Wall, it would be tragic for anyone even remotely interested in the advances of sciences to miss this significant event. I know I will be up and about in the night, despite the fact that I have early workday tomorrow. It is worth the anguish of a day without sleep I say! So please remember to make a ruckus and wake up members of your family in support of the sciences when the beam goes off. (Fermilab in U.S. is hosting a pajama party in honor of the event, though the registration is closed I am sorry to say)

The second even is the release party for the book Anathem by Neal Stephenson, hosted by the Long Now foundation. While Neal Stephenson might not be the greatest writer alive, he is certainly one of the most interesting. I preordered my copy from Amazon in a heartbeat when I heard that he was set on publishing a new book after a long period of inactivity. The Long Now foundation itself sounds as interesting as the man himself, focused around the concept/building of millennial clock. Those people should be well worth checking out if you are interested in humane pursuits that stretches beyond mere decades or centuries. I personally find such devotion to long-term pursuits to be very attractive in this day and age where vast majority of information seem to be relegated to the role of a junk food.  Since the basic premise of the Anathem itself revolves around the millennial clock concept, the Long Now foundation is throwing a party of sorts in celebration of the release of them book, with some readings and performances that will be streamed through a live webcast at the Long Now website. The webcast is set to begin on 9th September at 7pm PST, so I guess it will be around 10pm EST in NYC (interestingly enough, the year is written as 02008 on the Long Now website. Maybe we should all begin adding zeros in front of our year marks from now on).

P.S. There is a teaser stream running at the LHC first-beam webcast site describing what they are doing at CERN. For some reason I can not stop thinking about the background music they used in the stream.