"If you could only meet him, only speak to him, you
would see his sincerity," Agnate said.


"A man can be sincere and still be wrong, Commander."

I walk the groves of Damherung.
Below a dappled sun go I
And sing of Volrath's coming doom
Beneath a brilliant sky.

O forest, hold thy wand’ring son
Though fears assail the door.
O foliage, cloak thy ravaged one
In vestments cut for war.

For what are leaves but countless blades
To fight a countless foe on high,
And what are twigs but spears arrayed
To slay the monstrous sky?

O forest, hold thy wand’ring son
Though fears assail the door.
O foliage, cloak thy ravaged one
In vestments cut for war.

Though death has guile and killing power,
Though bloodlust rules the steaming tides,
It's life that wrestles hour by hour
And finally abides.

O forest, hold thy wand'ring son
Though fears assail the door.
O foliage, cloak thy ravaged one
In vestments cut for war.

~Skyshroud Hymn

I think, therefore, I'm old.

Apparently I'm halfway through college. This is kind of (really) scary. College has been a reasonably good experience so far, of course, but I have this terrible feeling that I haven't really done anything. I was fairly happy with how things were going halfway through high school, though, and the following two years, though extremely fun, were kind of a bummer on the getting things done side, so who knows how the last two years of college will go.

Anyway, a little about the finale of my semi-undergraduate life, since for the most part this has received little to no attention during the actual meat of the last two years. For background, I really dislike the idea of a secluded university, cut off from everything around it. This doesn't mean I like college situated in bustling cities, or anything like that - if I were in a college town, where everything revolved around the school, then I'd be fine with that. But wherever I am, I want to feel like I actually live there, like I'm part of whatever larger community exists. This drives me to some fairly silly things, like walking 2 miles regularly to go work at the public library instead of in my own room, or on campus somewhere. In any case, I decided that, having lived in Cambridge for two years, my knowledge of the area was pretty poor. To remedy this then, following a pretty good lunch with my roommate and another friend, my roommate went back to the room to the crash (he had just had his final final), while this other guy and I decided to take a walk, as it were. We wanted to go all the way to the end of the branch of the T (the metro here) that ran out of Boston in the direction of the Northern suburbs, i.e. where we lived. The results you can see here below:


View Larger Map

Now, thanks to (read: in spite of) my excellent navigation skills, we managed to stay for the most part on course. The astute observer might note that this is patently false, to which I respond, we covered equivalent distance and your face is probably very ugly. In any case, it was an interesting walk through the parts of Cambridge that clearly could not care less that their city contained two universities. It was really refreshing, seeing how similar and yet how different suburbs in different places can be (this directed at those who bash suburbia at every chance they get). In any case, I eventually realized, thanks to my phone's GPS service (phones have this now?) that we might have taken 1 (or 50) wrong turns, and so were almost crossing the river, without being any closer to the T line. We decided to turn back, stopping for frozen yogurt on our way. During the walk, I talked to this guy, who I had know well enough, quite a bit. During the course of conversation, I managed to convince him that biology was in fact legitimate (one of my favorite pastimes these days, also you guys should read this: http://protein.bio.msu.su/biokhimiya/contents/v69/pdf/bcm_1403.pdf, I'm not sure I agree with everything in it, but it's pretty good). All in all a very worthwhile experience, and a great excuse for learning how to make routes in google maps. In any case, I'm set to leave Boston in another 6 hours. Sunday is reserved for family, but weekdays are free, so let's do something please!

Until then,


~jnub

Outlook

"It's impossible to really understand somebody, what they want, what they believe, and not love them the way they love themselves." - Ender Wiggin, Ender's Game

"...But when it comes to human beings, the only type of cause that matters is final cause, the purpose. What a person had in mind. Once you understand what people really want, you can't hate them anymore. You can fear them, but you can't hate them, because you can always find the same desires in your own heart." - Ender Wiggin, Speaker for the Dead

Talking is always interesting. Sometime it's fun too, but overall not so much. The more you talk to people, the more you understand, the more you realize just how different everyone is. Of course, this is not as scary as it sounds - after all, a discussion in which everyone agrees is at best an ego boost, and at worst a waste of time. But I'm not talking about views on this issue or that. I'm talking about how people think, how people analyze the world around them at a fundamental level. People with very different methods of analysis can still argue and talk in a more or less uniformly logical language, even though it seems like they shouldn't be able to communicate at all. This leads, as you might expect and have probably realized yourselves (at some level) to very interesting exchanges.

Most (if not all) of you are familiar with my reverence of the Ender Series. This, in and of itself, is not particularly special – I follow a fair number of things avidly. But this goes somewhat deeper. I can appreciate and even sympathize with many of the characters in the shows I watch and the books I read. Through Ender’s life story, however, I gained something much more powerful, an approach to living in some sense. Don’t get me wrong, I am not crediting a series of novels with shaping the entirety of my person. Nonetheless, these books, and in particular the sentiment quoted twice above, has become a critical part of my personality.

This has been rolling around in my head for the last two days, and after much examination I think I can truthfully say that I don’t actually hate, or even dislike anyone. There are people I don’t know well of course. Of the people I do know well, most do not think even remotely like I do. Nonetheless, without exception I like and respect them. Truly, when you know someone sufficiently well, even if you don’t quite understand their justification for certain actions, you can always understand their base desires, their underlying motivations, and you will always find these same things within yourself.

It became clear to me that this belief, this attitude as it were, is not as widely held as I had thought. I was talking with a friend of mine, and the conversation turned to a mutual friend. I use friend here to mean “person that you know well”. It quickly became clear that, while I enjoyed the company of both friends, they were no longer friends, in the colloquial sense of the word. It seemed as if they had had a falling out of sorts. Typically this is caused by some misunderstanding, or else some unforgivable offense that has not been justified or explained to the victimized party. In this case, however, there seemed to be no such event. The two had simply grown to be annoyed at each other. They could not, or were not willing to, consider that perhaps the other party had some justification, some understandable motivation for which they had acted in a certain manner.

As I was having this conversation, I began to feel strange. I grew more and more uncomfortable, without understanding why. Finally it grew unbearable, and I simply walked away. Thinking about it later, I realized what was bothering me. I didn’t understand how two people could come to know each other so well and yet miss this essential underlying truth, that everyone wants the same things. I have thought about this some more, and I have been unable to resolve it, but I am fairly certain that if this is a fundamental difference between people, i.e. if I am somehow strange in my appreciation of everyone I know well, then people who do not have this strangeness must (on average) be much more unhappy than I am. I feel that I am still somewhat shaken by this, though, so it’s possible that I’m not thinking clearly. In any case, your thoughts on the subject would be greatly appreciated.

Perhaps someday I’ll start writing about things that actually happen again.

Till then,

~jnub

Independence

There is a strange thing about independence, something intrinsically appealing about standing on your own two feet, that makes us all crave it. I'm not talking about independence from parents and teachers, or the right to make my own decisions; to be honest, I've never cared much about what I am allowed or not allowed to do in this respect. Rather, the independence that has enthralled me all my life is the independence of ability, knowing that you can do the things you want to do with minimal input from others. When I first truly discovered this independence in learning, it was one of the most exciting moments I can remember. An unfettered burst of productivity followed, and lasted perhaps a good two years before the excitement began to fade and laziness overcame me. In the intervening years, I tried in vain to recreate this emotion, to excite myself to action. This summer I finally succeeded.

Early in high school, I found it that while it was easy to learn theory, be it math, physics, chemistry, or biology, it was also fairly straightforward to manipulate the theory in different ways to discover ideas that, while perhaps not new, were certainly interesting enough to keep you thinking. You all know what I'm talking about with math and physics, and admittedly, I wasn't as surprised that such manipulations could be performed in the these two domains. But theoretical biology, as it were, grabbed me early, and despite years of effort on the part of you, my closest friends, I didn't let go. Every time I despaired of some unsatisfactory aspect of my experience with the subject, someone would come along to argue with me about the possible nature of a certain disease, or different ways to approach a clinical problem, and my interest would be revived once again.

I never really liked experimental biology though. It seemed to consist of following detailed procedures that I never fully understood in order to perform manipulations that seemed fairly simple to me. At the time I thought that my discomfort was a result of those unknown details which I suspected were uninteresting. Despite this hindrance, I had resolved to cultivate the ability to perform at least the standard set of experimental procedures in order to conduct my own work, and so I insisted on learning these techniques that I thought I despised.

I found out this summer that this wasn't the problem at all. I was treating experimental biology as if it couldn't be decomposed in theoretical terms, but of course this was bogus. The truth, then, was that I had never seriously considered measurement when I thought about biology. Once I realized this, I attempted to remedy my error. I found that it was not so difficult, and this revelation has made all the difference in the world. Now, when I think of a project I would like to conduct, I can readily examine what I can actually measure, and if there is some small piece of information that I am lacking that is not easily accessible, I can simply design an experiment to pull out that information for myself. In short, I am ready to treat biological problems in the same way I have been treating math and physics problems throughout high school: without apprehension.

My intention here had actually been to describe my research this summer, and this had been meant to merely preface that. However, it would seem to merit its own post, and so you can expect a post on research and other summer happenings tonight or tomorrow morning.

~jnub

Switching Roles

At Mather House, where I'm staying for the summer, there exists a common room, equipped with a TV, couches, kitchen, table, and ping pong table. Often I had come back late at night after work, hoping to get in a game, but for some reason my card never got me in. I finally found an alternate route on Monday, and got in a couple of good games. Up till now, because of my schedule and my somewhat reserved nature, I had not met many people other than my immediate neighbors, and I didnt know anyone very well. It was nice, then, to meet these people, and I've since gotten into the habit of spending an hour or longer in the lounge after getting back from work. This means I sleep daily after 2, and wake up at 6 or 7, but that's not too much of a loss, and most of it is self inflicted time wasting anyway.

Anyway, one day, relaxing in the common room after a few games of ping pong, I met a student who happened to be working in the same lab as Fiona Wood, one of Lily's roommates for the upcoming year. When I told him that I was doing bioengineering, he asked if I had heard of biocomputing. As it happens, I did know about the field, but this was a huge fluke: as far as I know, there are only a few good books currently out about this work as a whole, and I had come across one of them accidentally. More than anything else, though, I was surprised he had heard of the field, given that he was an EE major. I asked him about it, and he told me that went to USC, and worked with Leonard Adleman during the year.

I'm not sure how many people have heard of Adleman before. Those who have, though, almost exclusively associate him with RSA, the encryption algorithm used extensively today (this algorithm is actually pretty cool, you should all take a look into it). His more recent foray into biology is not as well known, despite the fact that he more or less founded the field of biocomputing. Apparently he now spends his time working on analytic problems in pure math. Talking about Adleman's work, old and new, got my really excited about biocomputing all over again, and since I think most of you haven't read the books I was talking about, I wanted to just write a little about the subject.

Computational Biology is the use of standard computing to simulate and understand biological systems and their underlying processes. Biocomputing is the exact opposite, i.e. the use of biological systems to solve difficult computational problems. The underlying principle here is that biological systems are inherently parallel in nature. It's never just one process going on, there are always thousands proceeding simultaneously. Of course, it doesn't have to be this way, we could easily make a living system with very few processes, but the point is that we can have a massively parallel system of processes that do not get hopelessly tangled up. Since parallel processing can speed up recursive or iterative processes by an arbitrarily large factor, biocomputing, in terms of general notions, seemed to be an excellent approach to vast computational problems. All that remained were the specifics: for a given problem, how to encode information in biological molecules, and how to encode operations on the information that would be performed legally, automatically, and in parallel.

Despite the work that has been done in the field, no system of encoding information and operations has been successful as a general computing framework., and consequently a new system had to be developed to fit every problem the field chose to tackle. Here I'll just describe the way in which biocomputing was used to solve the N-Vertex Hamiltonian Path Problem, i.e. finding a Hamiltonian Path in a graph with N vertices. For each vertex, assign a sequence of nucleotide basepairs of length M, such that 4^M is at least as great as N. Then, for each edge in the graph, assign a sequence of nucleotide basepairs of length L, such that 4^L is at least as great as E, the number of edges in the graph. Now, for each edge, create two DNA fragments:

1. M basepairs for the vertex from which the edge originates followed by the L basepairs for the edge.
2. The L basepairs that are complementary to the sequence for the edge followed by the M basepairs for the vertex at which the edge terminates.

Finally, for each vertex, also create the DNA fragment corresponding to the M basepairs of the vertex. If these strands are all synthesized and then replicated many times over using PCR, then just by putting them in solution, due to complementary basepairing they will automatically recurse through paths in the graph, all in parallel, very quickly, and each recursion will terminate when the strand corresponding to a lone vertex (i.e. no edge) is incorporated into the growing strand corresponding to the path. Finally, by checking the length of each path strand formed, and by ensuring the presence of the DNA corresponding to each vertex, one can very easily find a solution to the Hamiltonian Path Problem in almost linear time.

Anyway, I hope that gave you a little taste for the subject. I did finish writing this at 4:55 in the morning, so if something doesnt make sense, just let me know and I'll rewrite/clarify.

~jnub

Connections

Ved recently wrote a blog post about television shows. It amused me that every single show that he mentioned was at core a comedy (we exclude Burn Notice because no one knows why we watch it). This is interesting: are we only capable of coupling emotionally with those who have pleasant lives? I think we can safely that this is false. So let's rephrase a little: can we only connect with those who are ultimately happy. This, too, I believe is false.

The reason these shows appeal to us, of course, is part of the reason for which we seek friendship: to be able to immerse ourselves in the lives of others, and to empathize with them. But this differs in a critical way from making the same connection with TV show characters: as we come to know our friends, we are constantly changing, but as we watch a TV show, despite the effect we feel it has on us in retrospect, we are much more static.

But I do not think this explains our (or at least my) preference for comedies. For if we are static while watching TV, is not the same true doing the reading of a book. Yet, I find that I more often connect with characters who have deep underlying regret and sorrow than with happy-go-lucky characters. And here, of course, is the true motivation for this post: I have finished, for what is at least the 10th time, the Ender Series. As has become the norm, I cried when Ender died, because I had come to love him, the small, broken boy who bore the guilt of a million murders, the man who spent his whole life trying to atone for a crime that was not his.

Why should a book be so different from a TV show in the way it effects me? And are these tastes peculiarly mine, or does everyone feel this way?