Tuesday, December 1, 2009

Recent reads&update

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

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

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

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

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

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

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

1)Inhumane
2)Irrational
3)Wasteful

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

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

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

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

Posted via email from Textdrome

Friday, October 2, 2009

Importance of hackability

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


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

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

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

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

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

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

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

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

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

Thursday, October 1, 2009

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

Tuesday, September 15, 2009

Testing

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

Posted via email from Textdrome

Thursday, September 10, 2009

Babelfish Twitter

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

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

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

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

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

Monday, August 31, 2009

Imagine Science Film Festival

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

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

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

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

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

ISFF 2009 Trailer from Imagine Science Films on Vimeo.

Monday, August 17, 2009

Pi Cubed, the iPhone app

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

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

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



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

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

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