Monday, March 30, 2009

The day, of interview and studies

Sent via BlackBerry by AT&T

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.

Posted via email from bookhling's posterous

Friday, March 27, 2009

New textbook

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.
Sent via BlackBerry by AT&T

Posted via email from bookhling's posterous

Wednesday, March 25, 2009

Insomniac at the library of babel

Sent via BlackBerry by AT&T

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.

Posted via email from bookhling's posterous

Tuesday, March 24, 2009

Synbio ideas

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.
Sent via BlackBerry by AT&T

Posted via email from bookhling's posterous

Monday, March 23, 2009

The world baseball classic

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!
Sent via BlackBerry by AT&T

Posted via email from bookhling's posterous

Sunday, March 22, 2009

Stupid gadgets

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.
Sent via BlackBerry by AT&T

Posted via email from bookhling's posterous

blackberry

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.


 

Saturday, March 21, 2009

Things on mind

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.
Sent via BlackBerry by AT&T

Posted via email from bookhling's posterous

Wednesday, March 18, 2009

Simulacra & Simulation

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

Posted via email from bookhling's posterous

Tuesday, March 17, 2009

Naturally Obsessed

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

Posted via email from bookhling's posterous

Monday, March 16, 2009

While waiting for the screening...

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.
Sent via BlackBerry by AT&T

Posted via email from bookhling's posterous

Workshop

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.
 
 
Sent via BlackBerry by AT&T

Posted via email from bookhling's posterous

Sunday, March 15, 2009

Night comes

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.
Sent via BlackBerry by AT&T

Posted via email from bookhling's posterous

Blackberry so far

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.
Sent via BlackBerry by AT&T

Posted via email from bookhling's posterous

Testing

Testing blog posting using blackberry.
Sent via BlackBerry by AT&T

Posted via email from bookhling's posterous

frustration

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.  

Thursday, March 12, 2009

android

I've been testing out android os for a week or two now. I got through the basic hello-world examples and ran them on the emulator without much fuss. I didn't get to try the iPhone development environment before, but I don't think the android development environment is half bad. It's much better than anything else I've seen so far. As for the hello world program, I tried "Close the world, open the neXt" from the serial experiment lain series instead of the standard example. Just a few line changes and it was all done very smoothly. I feel like a geek saying this, but seeing that phrase actually displayed across the emulator screen for quite possibly the most Navi-like device ever made me feel quite giddy. I have secret ambition to be able to code a decent augmented reality software for the android os someday. Something people can use for fun, different from all that business-like GPS and location tracking softwares that already seem to be on the android os (in beta forms? I don't think they are actually on the marketplace). Augmented reality rpg games where you use the camera of the android-phone to watch see your world. Web-connected graffiti application, where you can draw on real things you see on camera using location awareness. It will be shared through the network connection so that you can also see what other people drew on the city hall or whatever. Hidden item game, exploration game where you explore city-in-city using the virtual world of augmented reality, transmitted to you through you android phone. 

They all sound so cool, and so in line with what had been predicted in the anime like serial experiment lain and other cyberpunk-ish media. I wonder how the kids who will grow up with such technology would think of reality. Will it become something more magical for them? Or will the magics become trivial?

Of course, as the things stand right now I'm just a newbie who just finished his first notepad-like application on the android, following step-by-step instructions. I guess I have to learn to be patient, putting together something like an augmented reality program for handsets can't be easy, especially when we think about the rather minimal hardware it will run on.

While the software side of the android os development continues to wow me (it's really a first real software development environment for me), the advance on the hardware side had been disappointing so far. As I might have mentioned in an earlier post, I'm in the market for a new smartphone (eversince my N85 died on me and I got that refund) and I was dearly hoping that it would be an android phone. So far the only android phone on the market is G1, and it lacks some features I deem critical on a handset. Like the ability to capture video. I still can't believe they decided to leave that function out. It's too nonsensical to the extent that I am beginning to believe the whole 'Apple pressuring Google/HTC to cripple the G1 hardware' story that's be making the rounds on the net lately. The G1 itself isn't such a terrible phone. I would say that it's rather average. Being average wouldn't be so bad if it didn't cost US$399 unlocked (I'm talking about the developer's version. There seem to be other ways of getting somewhat cheaper G1s though). 

I would wait for a new android phone to come up on the horizon, but so far the only model that's been sighted is a touch-screen only model. Seriously, what are they thinking? I've used Samsung Blackjack II and had a brief fling with a Blackberry. And the general usability level of input system on handsets goes like this. 

1)Keyboard (like on Blackberries)
2)T9 input system (the predictive input system for regular phones)
3)Touchscreen keyboard (like the one on the iPhone)

People can rave about touchscreens all they want. The fact of life is that in terms of pure input, nothing really beats a real keyboard system embedded into the handset (at the moment) and touchscreen remains an interesting novelty interface. I'm not saying they are unusable or anything. Far from it. I'm just stating how they perform compared to the competition. So I'm in a dilemma here. Do I wait for a keyboard android phone that may or may not happen? Should I just grab the new touchscreen android phone when it comes out? Or should I just grab a decent handset of non-android variety to tide me over until the ideal android phone comes along (how long that will take, I have no idea)? I'm leaning toward the third option, with the BlackBerry Bold and Nokia E71 prices that keeps on dropping.

However, if I were to go for the third option it would still mean that I have to choose between locked-in but roaming capable BlackBerry Bold or E71 that's unlocked yet lacks the kind of international roaming frequency I need (the 2100 UMTS etc for Korea/Japan). The price difference between them is about 50~100 dollars, and then there's the matter of software library. I know I can download whole map database into E71 and use it as a GPS even when offline, but I'm not so sure about BB. 

And when I consider the whole pricing issues of the phones and how long I would actually use them, and compare it to my study of the android platform, something just tells me to make the jump to the new touchscreen android phone and get used to it...

Wednesday, March 11, 2009

Internet consciousness

So here's an interesting short article on the possibility of internet gaining some type of consciousness due to its network based emergence-friendly structure. The author is the famous Ben Goertzel, one of the foremost minds of the futurist/AI school. If you've got time you should check out his blog for other articles as well. I've found a number of them to be quite compelling. I've always been interested in artificial intelligence, though my concentration is with artificial life. In time I've come to view the two as the same type of system manifesting in different mediums, and I've come to think that intelligence is a trait that naturally comes along with the collection of characteristic called life. Intelligence is life and life is intelligence. In that sense I consider even minuscule bacteria to be intelligent, though not in a way we usually think about intelligence. The very fact that certain collection of molecular machines can work in conjunction to behave in such a way that allows it to feed, evade harm and propagate, even in evolution-aided unconscious manner means that certain system should be considered intelligent. Of course, this is merely my personal view that is not backed by evidence based professional study. This is more of a personal impression with reasonable causes, something that's on it's way of becoming a hypothesis but not quite there yet as the things stand. Considering that I consider our current definition of intelligence to be lacking in many ways, I will be at ire of many neurobiologists should I exclaim such opinions carelessly. And for some reason there are a lot of neurobiologists around me so I try to keep my mouth shut most of the time regarding that issue.

Ben Goertzel's answer to whether the net can become an intelligent construct is somewhat vague, but then he probably can't help it himself. The question itself is a bit on the vague side when you think about it, including the whole uncertainty of the definition of intelligence that I just wrote about above. He briefly mentions the pervading ethos of the neurobiologists of the recent years, that many of them believe that intelligence/consciousness is a property that will inevitably emerge from any complex system that has the right sort of internal dynamics. I do definitely agree with him on that point, since when you think about it it's about the only scientifically feasible explanation of the emergence of intelligence/consciousness without attributing some specific part of the brain to the trait of intelligence (like how Rene Descartes attributed ganglia as the sit of the soul). I also suspect that life arises in a very similar manner, and whether that pattern of internal dynamics can be an abstraction that can be applied to different types of physical systems is a major part of my current research as a fledgling science student (the one that's helping paying my rent). Hopefully I'll be able to come up with something in my lifetime, since I view the possibility of such a universal theoretical platform to be a big game changer in the upcoming human century, something that might as well change the world we live in along with applications of nanotechnology and modular biology.

Will internet itself become intelligent at some point? I'm sure it will. Dr. Ben Goertzel points out that the internet is way too fragmented to display a coherent vision of an artificial intelligence and instead suggests that there might be a way to construct a sort of unifying backbone using the network infrastructure of the internet itself as a sort of raw data feed/complexity provider for that central structure. It makes sense, in a way that no one really thinks about it before someone else says it first. Most complex emergent systems, when laid out using some elements of graph theory (the graph theory, we are not talking about bar graphs and such nonsense here, for those who haven't been keeping tabs on mathematics) displays inexplicable tendency to form central clusters around certain limited number of nodes instead of distributing indefinitely. And the change usually isn't gradual or predictable. It happens rapidly under certain critical threshold as Stuart Kauffman put it very succinctly on his book "At home in the universe." Internet is very obviously following in that pattern. The last graphic map of the internet I've seen displayed certain number of nodes (websites/services) with overwhelming number of links with a lot of nodes with limited number of links. Similar pattern is also observed in the growth of neural pathways and formation of galactic clusters, and who knows what other phenomenon in this universe escaped our notice, considering that complexity science is still a new field. Now I don't have a very clear idea of what form that central structure would have to take to make the internet truly intelligent to observable degree... I assume it would be something on par with designing CNS for the distributed system that is the internet, possibly with a hint of recursive structure via Douglas Hofstadter, but this is all just some ideas bouncing around and I have no idea what physical/informational form such a construct would take. I'd assume it is something far past the simple matter of linking a lot of links within network nodes or providing raw processing power (that would be like saying any game of go can be won with large enough number of stones, which is just dumb. This isn't a chess, kiddo)... I should definitely give some more thought to this, the ideas on the nature of the 'central structure' might as well be the catalyst I've been looking for.

The problem that continues to bother me whenever I think of artificial intelligence is the vague definition of intelligence we seem to share. Just how can we tell what is intelligent or not? Most definition at the moment seem to be about figuring out how human-like other organisms/systems are without regards to the actual 'intelligence' of that organism/system. I may not be a professional but I smell a very homocentric perception whenever I read something that pertains to the nature of intelligence. If intelligence is about being able to communicate with other beings then antisocial foreigners are not intelligent. If intelligence is about being able to react to the environment so that you can find sources of food and multiply, then bacteria are intelligent. Maybe even viruses. Both of them do not have any sort of nervous system like we do with 'higher organisms' so it makes the problem of intelligence a bit more complex. 

Internet may become intelligent someday. This is the year that the internet will have the equal or higher number of hyperlinks as there are synapses in our brains. The real question is, how will we be able to tell if it is intelligent? Are we looking for intelligent traits or are we looking for human traits?  How would we be able to tell the difference when the time comes? Maybe the first machine intelligence that blossoms on the world wide web will be trampled on by us as a mere bug in the system. After all, we do it to each other all the time.