New career path

I can’t believe I didn’t write here for so long. Welp, can’t help what’s done already, I’ll try to document all the cool stuff that’s happening right now at&around myself, iGEM and Genspace a bit more. I’m officially a team member of the NYC-iGEM team and there are plenty of real biology being done at Genspace now that we’re public and all. I just have so much to write about.

But first, let me give you a news, this is the one that got me writing on this blog again after months of vacation:

Virgin Galactic is hiring astronauts! Not just any astronaut, but a private astronaut presumably for their SpaceShipOne based launch program at Mojave spaceport.

You need all the qualifications usually associated with being hired as a pilot for any Aerospace corp, with preference given to those with real experience in spaceflight. I guess all those out of work astronauts from the space shuttle program can still get their flight on 🙂

I kept asking myself why I didn’t go to a flight school instead of bothering with all this physics baloney. I think my friend who does aeronautical engineering thinks the same way too. I was more or less blaming my own shortsightedness before I hit upon a memory from decade ago.

I wanted to go to space, become an astronaut. That meant I had to enroll in the airforce, go through the officer’s training, and get really, really lucky. Now luck part I never really had a problem with. Don’t worry about things you can’t control, as they say. But enrolling and spending my life in the military just to get to space? Man that just put me way off. It’s probably the same story with my engineer friend. And I’m not even sure what women go through when they want to become an astronaut. I’m thinking it’s something a lot more different from what males have to go through, whether we want to admit it or not.

I’m not really crazy about the idea of libertarian capitalism, but I can’t help but to welcome this development of private space industries. I think years of treating space as if it was a special military domain really killed lots of initiatives that could have happened, and just shelved decades worth of scientific progress under the guise of national security (for all nations with capacity for spaceflight, really).

Alan Kay applied to synthetic biology, and other stuff.

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.

The Whole Foods CEO on Universal Health Care

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.

From Consilience:the Unity of Knowledge

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

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

The book had such profound impact on me when I was growing up, I really think I should do a review/post on the book and some of its themes one of these days. It came out years ago yet the prescient insight of E.O. Wilson rings true to this very day in many fields of human endeavor. I had the chance to listen to his talk live in the closing event during the wonderful World Science Festival in NYC, and I should say he still seem to retain that certain edge even after all these years. I guess that’s what we Koreans call No-Ik-Jang for you. If only I wasn’t so shy to ask him for an autograph on my copy of the book. I feel like a kid who lost a winning lottery ticket.

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

The antikythera mechanism

 

An ex-senior curator finally succeeded in replicating all known features of the 2000 years old Antikythera mechanism, the first known mechanical computer in human history. Technically this is in similar spirit as a 19th century clock. There is some strange notion among some people regarding how people got smarter over time. Sometimes I feel like throwing the Antikythera mechanism in their faces. Or, I could just tell them to go read a good history book instead. Yes, I could always do that. 

All in all, amazing mechanism. Perhaps there were even more amazing things lost to time in other ancient civilizations as well.

Science commons

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

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

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

Just one thing though. Library of Alexandria. 

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

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

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

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

LHC first beam moment!

(Update: The LHC beam came full circle at last!)

The LHC first beam came and went. The LHC experiment itself is active right now, with about 3/8th of the ring active and 60,000 particles observed in one shot. Of course, it is set to increase to the full capacity eventually.

I am very proud to say that I have participated in the biggest scientific experiment ever undertaken by humanity no matter how indirect the method. Those of you out there who have not participated yet style yourselves supporters of science should hang your head in shame… Just kidding. Though you should really feel disappointed.

The main goals of the LHC experiment is put succinctly by Michael Sean Wright at his blog (which I happened to catch by chance).

Why did Matter triumph over Anti-Matter?
Why do particles have mass?
What is the nature Dark Matter?
What was the state of mass in the moments right after the Big Bang?

These are some of the questions entire cabals of scientists lose sleep over in their ceaseless pondering and amazement at the face of the universe in front of us. I am exhilarated to say the least. What will this experiment (the LHC experiment is, of course, a long term experiment. It is not about singular results obtainable over an experiment or two) teach us about the universe? What system of the world? I would have to be dead on the inside if such questions did not get my heart running!

McCain and Obama will be gone and done away with sooner or later. LHC experiments will remain with us so long as the human civilization thrives, perhaps changing the fundamental nature of how humanity sees the universe around themselves.

Here are some resources in case you are still interested in a bit of LHC first-beam catch up.

http://blogs.uslhc.us/?p=346

U.S. LHC blog.

http://cosmicvariance.com/2008/09/09/live-blogging-the-lhc-startup/

LHC live blogging.

http://webcast.cern.ch/index.html

LHC webcast service (severely congested at the time of the first beam event. I had to switch to BBC livecast)

Support LHC, and the Long Now event

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

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

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

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

Great things at the Met

I have been crazy busy lately, preparing papers for my discipline of choice (physics), brushing up on my synthetic biology, and catching up on some art related reading materials, centered around Jasper Johns. Will they all condense into some masterful singular post? Maybe… Maybe not. Regardless, I’ve been rather enjoying my new-ish vigorous lifestyle. All the intellectual stimulation really makes me feel alive!

Today I’m just going to make a note on some events at my favorite place in the NYC, the Met. As I am perpetually broke just like so many other students of science, all the events are free with museum admission. And as everyone who spent their teenage years in the city knows, the admission fee to the museum is negotiable. I’d suggest at least paying around five dollars though. Just to be polite.

Among the many things going on at the museum this week, I am particularly looking forward to the guided tour on Tuesday. Titled “A treasure hunt for book lovers”, they would guide me through the various galleries of the museum ranging from Mesopotamian to European while tracing the history and nature of books through the collections at the museum. As you might have guessed from the blog title and my alias, I am something of a bookworm, a bibliophile-in-training, so to speak. I’ve read them all, from Latin codex to Asiatic scrolls and ebooks… Though I lack the expertise to read the old tablets of ancient Middle Eastern origins, something I would mend soon enough. I am not particularly good with languages, but I’m still very fond of them. Beautiful phrases and imaginative stories hold certain profound depths and aesthetics that might as well be linked with the fundamental nature of mind and even the universe itself, I think. The time is at eleven in the morning, at the gallery talk stanchion in the Great Hall. This is at Tuesday folks!

On Friday, there will be a gallery talk about Gustave Courbet and his works at the Tisch galleries on the second floor of the museum. That’s where they are holding the special Gustave Courbet exhibits. While his works might not appeal as much to trained eyes of the modern popular culture, they still retain certain flair unique to the artist. The adventurous, and yet tragecomedic life of the artist himself lends certain spice to what might be a dull showing to some modern audience. The time will be seven in the evening.

The next gallery talk I am interested in is titled “A Closer look: Agnolo Bronzino’s Portrait of a Young Man.” The artist is from the 16th century, so this is not a modern exhibition. I was always fascinated by the refreshing and ingenious workmanship present in many of the Renaissance paintings, so this is a good chance to finally learn something of the era and one of its more prominent artists. The time is at seven in the evening, at the gallery talk stanchion in the Great hall.

The last, but not least, this event is series of professional lecture on Gustave Courbet’s work in the Grace Rainey Rogers Auditorium on the first floor, starting at two in the afternoon. The topics range from the significance of the female dress in Courbet’s art, to the artist’s relation to the modern art. These fully featured lectures are also free with admission, so anyone interested should partake.

A lot of leisure activities this week. The real question is whether I would be able to make the time to get to those events… Since skipping my own lectures are out of the question, I’m in something of a tight spot. The fact that I am in position to need to study a discipline of science outside my own doesn’t really help things either. Of course, I do them because I enjoy them, so there’s no regret. I’m just hoping that I can get some free time this week…

Arts and sciences being separate from birth is an illusion dreamed up by the modern era. When will the world learn?

Solemn dictations

This is a cross post of something I wrote before. I liked this post too much to leave it in middle of nowhere, so I’m moving it here.

This is something I ran across in my visit to the Met today. It’s a funeral marker of the ancient Greece, around 500 B.C. or so. According to the description given by the little placard at the bottom, there was an inscription on the stele at the original site. The translated version of the inscription reads like this.

“My daughter’s beloved child is the one I hold here, the one that I held on my lap while we looked at the light of the sun when we were alive and that I still hold now that we are both dead.”

The time was almost three thousand years ago, but the human sentiment runs the same. I might even argue that the dying grandmothers of the old were much more articulate than the living young ones we have right now. Nonetheless, I feel saddened and glad at the same time when I remember this scene, bathed in a solemn and melancholy light, phrases and situations telling its story through subtle hints which later echo in the heart of a young man from three thousand years in the future. Will we leave something behind as such? Will we leave behind something so that people living in three thousand years in the future would shed a tear or feel their heart wrench at the tales of people long gone and forgotten? Will the human identity remain resonant throughout the times?

Another something I picked up. It’s from roughly the same era as the above funeral marker. This one depicts a little girl saddened to let her pet pigeons go. This clumsy photo of mine doesn’t do justice to the subtle nuances and expressions that were retained in this piece despite its age. People talk of evolution and change all the time, but what we consider to be fundamentally human trait doesn’t seem to have changed much, if we can communicate across space and time like this through frozen motions and facial expressions.

I am beginning to suspect that the fundamental nature of what we consider to be humanity is more closely linked with the body at deeper levels. Perhaps the overall nervous structure and its extent affects the development of consciousness itself to some degree. Perhaps there is a minimal template of what we can consider to be a ‘mind’ just like the minimal framework of gene for the base artificial life, and the traits we consider to be human consciousness arises from there just like how the base gene later expresses itself in multiple ways, as a complex synthetic life form. If so, human psychology, and much of the subtle traits of being a human being, is locked with the type of body to certain extent, and therefore can be engineered like genes and engines.