Consider Bookhling

This is something I wrote up a few days ago, probably around four or so in the morning. So take whatever it says with caution.

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. I also have the pictures from this year’s major diybio nyc event, where we set up a stall on the NYC green market and extracted dnas from the natural produces with common household material (with the passers-by 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’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 what we have now (protected memory FTW). 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 somewhat unified information storage and processing system that has quite a bit of parallels to mechanical 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’d be possible to predict some of the pitfalls that are inherent in developing complex programmable information processing system that will apply to the synthetic biology in the future. Maybe we can bring a conceptual framework to the synthetic biology that would have taken decades if left to mature naturally to 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, 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 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 won’t be a platform capable of crunching numbers the fastest. It will be 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 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 to learn, since one thing must inevitably lead to the other. And there are classes of 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.

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.

(((I was trying to embed the videos from the KQED site directly in the post, but apparently copy pasting embed code in HTML panel isn’t good enough for wordpress. I’ve linked to them instead. They are quite good. You should really check them out.)))

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

The first video is the original KQED QUEST video on synthetic biology.

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

Here is the link to the second video, the extended interview with Drew Endy.

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

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

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

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

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

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

Here’s a little bonus, the QUEST show producer’s notes on ‘Decoding Synthetic Biology.’

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

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

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

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

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

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

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

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

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

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

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

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

On to the main post…

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Get to work.

Change the world.

I just read an interesting paper on the three common misconceptions people normally have about the field of bioinformatics. I’ve been eyeing bioinformatics as a possible venue for bringing more people into DIY sciences, so I took some notes for future reference. It turns out that I’ve been suffering from same hype and illusion about the field of bioinformatics just like the vast majority of the non-specialists out there.

Simply put major misunderstandings about bioinformatics might be narrowed down to three myths permeating the science culture, according to the author.

Myth#1: anybody can do this
-bioinformatics is inexpensive
-bioinformatics software is free

Myth#2: you’ll always need an experiment
-bioinformatics is a rapid-publication field
-all bioinformatics does is generate testable predictions

Myth#3: this is news technology but technology nevertheless
-bioinformatics is a new field
-bioinformatics is an application discipline

*FYI the statements under the Myth headings are the ones the author refutes in his writing.

Myth#1 is that everybody can do bioinformatics, using only the cheap or opensource tools available off the net. The author does admit that this is indeed the case to certain extent. However once you get into any serious large scale research about or involving bioinformatics the initial assumptions will prove to be a burden on the organizational level. As the author will elaborate in later parts, bioinformatics is a field of scientific research on its own not subservient to the conventional wetlab biology. Indeed, while reading the article I was under the impression that the main statement for the whole article revolved around how people do not realize that bioinformatics is a field of scientific research with its own goals and complications. Very unlike the laymen assumption that bioinformatics is in fact just biology done with computers, or application of computerized tools to wetlab based biological research just like how the researchers would use word processors or LaTeX to type up their reports. Personally I found it a little disheartening that bioinformatics research is just as complicated as any other field of scientific research for DIY implementation, possibly more depending on what the amateur scientist is trying to do. But then I can only blame my naivety. The author also makes a point that bioinformatics can be very expensive to begin due to some number of proprietary software services that must be purchased (never went into much detail on that. I guess it’s different according to the theme of the research?) and the resources needed to write and maintain codes for the project. It makes sense when you think about it. While it would be possible to come up with some bioinformatics application in-house, after certain level it would be vastly cheaper to simply buy some number of components and just use in-house resources to link them and tune them into giving results needed for the project (which shouldn’t be easy to begin with).

Of course, I still think that we can, and maybe should, use some approaches of bioinformatics to provide interesting DIY science framework to the public, like the Annotathon metagenome annotation project that had been open to the public for a while now. I’m just glad that I got a chance to listen to some of the intricacies of the field from someone already working with the tools of the trade.

While I now understand some stuff about what the field of bioinformatics is about, I’m still unsure as to what kind of project idea I can come up for DIYBio curriculum using the technology… It’s a problem I’ve been running into a lot lately in doing stuff involving DIYBio. I know there are tools and tutorials out there, but I just can’t seem to be able to put them together into a coherent whole. DIYBio needs some sort of project that would turn knowledge into skill… More on that later.

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.

Just a quick note on early Sunday morning. 

I’ve been reading up a bit on the topic of quorum sensing, which turned out to be a very interesting phenomenon. I’m not qualified to get into the specifics but it’s basically a cell to cell communications method used by bacteria. The mechanism is based on signal molecules and receptors that activate or deactivate certain sets of genes depending on signal strength. The strength of the signal would be determined by the density of the signal molecules within a given area. It means that bacteria (of all kinds I think) have built-in coordination mechanism for group gene expression.  This is news to me. I always thought bacterial behavior was more or less solitary with some mathematical mechanism behind emergence of bacterial colonies, rather than any specific signal mechanism that works to coordinate their behavior as a group. I guess the deeply ingrained eukaryotes/prokaryotes and multicellular vs. unicellular organisms chart from the middle-high school days left its mark on me. The Bassler lab at Princeton University’s department of molecular biology seem to be the leader in the field of quorum sensor studies, something I should definitely check out later. Here’s a TED talk by the lab’s very own Bonnie Bassler on bacterial communication.

This reminds me of a few iGEM project outlines I read on using BioBrick parts to form some sort of macroscopic structure using bacterial components. They all more or less failed as far as I know, but maybe something like that will be possible if we can build a BioBrick based mechanism for controlling quorum sensing mechanism of the E.Coli chassis… Or maybe there’s one in the registry already? I should remember to check it out. Maybe diybio-nyc can build a cellular automata system based on quorum sensing as a demonstration project later on. The prospect of studying complexity mechanics behind the quorum sensing and coordinated bacterial behavior is intriguing to me as well.

I’m also thinking of proposing a simple artificial cell project to the group. From what I’ve been reading the first steps towards building an artificial cell isn’t that complicated as long as we keep the goals modest. For now the goal would be to have DNA replicate and produce proteins within an artificial vesicle.

I spent all of 18th in the openeverything conference at the UNICEF headquarters. This was the first barcamp style meeting I’ve ever been to in my life, so I thought I might as well jot down some notes.

For those of you who don’t know about what barcamp is, it’s like an emergent conference. You get bunch of people together in a building, and everyone who wants to talk about something just post their topic card (or whatever the equivalent you are using) on the main board. When the time comes you either present something or have a discussion on that topic with people who were interested enough to show up at your session. It sounds a little chaotic, and it really is sometimes, but on the whole the system works very nicely. Even the people who aren’t as talkative as others get to talk in such settings, and there is no barrier dividing the audience with the speaker so you can actually get work done with people who share the same interests as you without sitting there waiting for some guy/gal to finish talking. If you wanted to talk or listen to something but there’s no one talking about it you can always walk up to the schedule board and write up your topic, and voila, you have people showing up trying to figure out what to do with your chosen topic (I actually tried it and it worked, surprisingly enough).

As far as traditional barcamps go this wasn’t really the most ideal of the camps, since of the 220 or 250 people who said they were going to show up only about half (maybe even less) arrived. Even so, the diversity of interests and objectives were electrifying to me to say the least. Being hosted by the UNICEF most of the topics revolved around programming or infrastructure projects that can benefit the causes of UN, like the rapid SMS which is a computer based SMS system that interface with cell-phones to create different kind of low-cost wide area logistic coverage. The system is completely open-source and scalable, and it’s been used in the field for various UN related activities like education and keeping logistic tracts of 65 million insect nets that were set to be distributed across some parts of Africa. Other interesting topics included a brief discussion on the nature of AI (though none of the people in that particular session seemed to have a very good idea of artificial intelligence), cheap open-source aerospace programs, and computerized education systems/web 2.0 services that might be used to keep track of education and qualification of individual members in form of a flow chart. Using such a system a kid might be able to copy and follow the skill/education set of, say, an astronaut if he/she’s interested in pursuing such a future. I do realize that while education goes above and beyond simple skill set qualifications the idea itself is sound, and I would love to see it implemented in a real web system someday.

I was hoping for some people to do a tract on diybio/open-source biology and open science in general, but for some reason no one really set up a topic that relates to those interests. So in true spirit of a barcamp I decided to set up a topic myself, which was a little overwhelming at first, this being the first barcamp-style con I’ve ever been to. It didn’t help that I’m usually not the one to speak in public venues. It was something of an adventure, and I decided to take the plunge. I was helped by some of the onlookers who pointed out the processes of barcamp that makes it work as a sort of emergent conference with emphasis on ‘burst activity’ and getting stuff done.

Well to be frank, the talk I gave was a mess. It wasn’t prepared and I was really wiped with other talks by the time I got to my session. Having people who knew even less than me in regards to biology didn’t really help either, since I was constantly double checking my facts so that I wouldn’t give any twisted impression of diybio to people who are new to the idea. I more or less wandered around the topic of diybio and synthetic biology, and though I did stress that synthetic biology is not diybio, I’m not too sure if other people got that message clearly enough. It’s my fear that a lot of people who showed up at my session went away with inflated and unfounded hope on the current state of diybio and synthetic biology… I did learn a lot from the experience though. Maybe as I get more experienced with this stuff someday I can give a compelling talk on diybio that would lead people into participating in this very exciting intellectual movement.

I did receive a lot of interesting input from various people regarding the state of licensing and what it really means to creative open-source content (it was ‘openeverything’ conference after all. Lot of license-related people). I always thought I knew a thing or two regarding the basic ideas of CC license and GNU/open-source license terms (which btw, Richard Stallman insists is separate from each other). It turns out that I didn’t know squat. Penetrating the thin veil of ignorance: that’s what I call an education!

I should have a post on diybio-nyc’s recent GFP E.Coli session sometime this week. Stay tuned!