Saturday, July 31, 2010

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

Saturday, June 26, 2010

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

Tuesday, June 22, 2010

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?

Saturday, June 19, 2010

A Revival of Sorts

Tonight, 450 miles from this room I sit in now, too lazy or tired to return to my dorm on the other side of town, 450 miles from here the Class of 2010 graduated. I don't pretend to know what it meant to them, collectively or individually, but I suspect it hasn't really hit them yet, what they just finished, what they're leaving behind more or less forever. As this new day begins, the first day on which they are no longer high school students, ANGP is in full flow. Hell, they have a whole summer to go, no need to get a jumpstart on the nostalgia.

It matters to me though. For one, I'm losing a huge anchor to a school that I love. I'll still visit, more often than most others I suspect, and there'll still be people I know, but at the end of the day I'm more or less detached at this point.

More importantly, it reminds me why I started this blog. I've been somewhat negligent, and I intend to fix that.

I've been back in Boston for nearly two weeks now. I'm spending the summer working on a systems biology project in Sean Megason's lab. We're looking at morphogenetic dynamics in the inner ear of zebrafish (the process is more or less identical to inner ear formation in humans, just at a different rate). At some point, I'll post a small summary of what we're actually doing, because I'm pretty excited about it. The project was part of an internship program in systems biology, and so my housing was organized through this program as well.

I'm also doing a part time thing from 6 PM to 10:30 PM or so on weekdays called iGEM. This is a synthetic biology competition, where each team basically decides to design a system of some sort and implements the system entirely biologically. For our project, we decided to make a touch screen that essentially produces a crystallized photograph of the pattern we draw. It's pretty neat, and I'll go into a little bit more detail on this in a future post as well.

Since I'm working pretty late on a daily basis, I don't really get a lot of chances to interact with the other people living in my dorm. I've met some pretty cool people, though, and I do have 8 more weeks to get to know them.

Anyway, today a group of us (Chris, Jessica, Five Other People, One Other Person, and I) went to watch Toy Story 3. I had already seen the first 70 minutes of this during the year at a free advance screening, but the ending was excellent, and definitely worth rewatching the first part of the movie. The first movie was obviously a classic, and the second one was excellent as well, but this one struck a chord in me that the other two missed. You should all go watch it.

Anyway, let's see how long the next hiatus lasts!

~jnub

Wednesday, February 10, 2010

The End of an Era

I suspect most of you aren't aware of this, but for the last 2-3 months, I have been fighting a battle with a crafty enemy. Actually he may not be crafty, but I'd rather not admit to extreme stupidity >_>

It was a close battle, with a lot of back and forth, and he always seemed to have the slightest upper hand. Nonetheless, I refused to retreat or surrender. Despite my best efforts though, I lost that battle today.

What am I talking about? My laptop, good sirs. Around winter break time, I caught a virus (I have no idea how) that started messing with and redirecting links on google searches. There was an easy enough workaround to this, but it irked me that I had this thing. With help from you guys (mostly Luke), I pulled together an assortment of anti-spyware/malware software and went after the bastard. Indeed, for a while, it looked like I had driven him out. Then one night, I found that I was wrong. As I was working, a series of error windows started to pop up as the virus tramped through my registry deleting critical files. I managed to turn the comp off and do a system restore, but I knew then that I was in for a nasty haul.

This sort of thing has been happening regularly for several weeks now. On Monday, though, without any warning, I lost everything in the Documents and Settings folder. Nothing crucial, but I was finally starting to get legitimately worried. I backed up everything (finished yesterday night) and was more or less content. Unfortunately, this morning, following a regular shutdown sequence, Windows fails to boot. To make matters worse, the virus had taken out both Safe Mode and System Restore. In short, I am completely shot.

It's kind of sad that I'm writing an entry on fighting a virus, but it's pretty valid. I've had the laptop since sophomore year of high school, and I value it a lot. I'm going to have to get a new one now, and it actually makes me kind of sad. Luckily, one thing won't be changing - my desktop background (yes, I saved it =P).

In any case, until this new machine shows up, my access is pretty much limited to computer labs here, so don't expect me to be online, and if you need to reach me, call.

~jnub

Thursday, February 4, 2010

Subject: Wow... okay, I wasn't sure if I was ever going to tell anyone about this,

but it's late and I'm sleep deprived so i guess I'll just write it now and
regret it in the morning

First of all, - just for some background: My mom died right when I was born,
(she was actually really, really hot- but this isn't about her. I guess that's
messed up to say, but whatever.) I actually grew up with my dad's family,
because my dad has all sorts of emotional issues and he bailed before I was
born. So you can see, my childhood was really kind of messed up.

Anyways, growing up I feel like there was always a lot of distance between me
and my sister. When I was about 17 or 18 I first noticed that my sister was a
hottie.

I don't want to go into to many details about it, but basically what happened is
that I accidentally found a video that she made of herself. I knew she didn't
make it for me- but I thought she was so beautiful that I watched it twice.
(probably would have watched it a hell of a lot more, except that like right
around the time I found the video, all this crazy :!: went down and I had to
leave home. (My dad's family who I was staying with got in bad trouble with the
law. I never talk about it).

Sooo... I was totally lusting after my sister at that point. She was also having
bad trouble with the law. She was actually in custody when I left home.

My friend and I went to go pick her up. When I saw her that day, after seeing
the video, I have to be honest, I just wanted to frak her brains out. Looking
back on it now, it's pretty messed up- but I think she had feelings for me too.
She actually kissed me right after we came to get her... and it wasn't a
sisterly kiss, you know? I mean, it wasn't like ridiculously sexual or
anything, but it definitely wasn't sisterly.

After we left, we all went to crash with my Sister's friends. On the trip there,
my friend sort of implied that he wanted to get with my Sister, and I got a
little jealous. He's a good looking guy- and even though she was my sister- I
just felt like he was competition. Not much else happened between us for a
while except some maybe-sexy hugging.

Pretty much everyone in my life at that point was wanted by the government, so
we all moved around a lot. I'm not saying that I'm proud of it or anything, but
it was kind of an awesome time.

My friend and my sister never hooked up I don't think- but I thought there was
some serious sexual tension going on between them. It was around that time that
I got really badly hurt in an accident. It was messed up. I almost died. But
when I was in recovery my sister came to see me, and out of the clear blue sky
she started gives me this awesome, slow, passionate kiss on the lips.

Sadly (although, I guess for the best) nothing ever came of it. We spent some
time apart... and I started to get really religious, so I tried not to think of
her that way. It was actually going well for a long time- like I was totally
over her. But I have to say, like a year or so after all that stuff went down,
we were out sailing (not like a date or anything romantic like that), and she
was wearing like the hottest bikini I've ever seen and it brought back all the
old feelings. Sigh.

A little while later she actually wound up with my friend from before (the
sexual tension guy). I can't say I was surprised.

But even after she was shacking up with my friend, there was one time we were at
a party... my friend was inside, and my sister and I were outside alone. It was
a really intimate moment. I think something might have happened, except that I
killed the mood when I told her that Darth Vader was our father and that I had
to go face him.

Tuesday, January 26, 2010

Opportunities

I'll preface this by apologizing to everyone who believed in me. I have betrayed your trust in the worst way possible: by selling my loyalty to the enemy. Or so it appears anyway. I hope to convince you someday that I am still pure, but that is a discussion for another day.

Some of you know exactly what I'm talking about; others not so much. To the former, know that I trusted you enough to reveal the dark patch in my soul. To the latter, know that I valued your respect and friendship so highly that I was hesitant to tell you of my treachery.

Here it is then: I am currently enrolled in a class entitled, "The Nuts and Bolts of Business Plans". There are a number of alleviating notes to this point, but as I said, that's for another day. For now, go ahead and bash me. In fact, if you don't, I promise I will bash you for being a business lover.

Now, to the actual post:

At the end of the lecture today, the speaker invited students in the audience to give an elevator pitch, either for a team to join their project or for funding from venture capitalists. One guy gets up and introduces himself as Nico from Harvard. The audience lets out a groan. Then Nico starts talking:

"Most of you watch TED Talks, right? Well, there was recently this one talk by _______ where he's discussing this assignment given to kindergarten students in the UK. The kids were asked to draw what they wanted to be when they grew up. Most of the kids made recognizable pictures of firemen, nurses, etc, but one girl was drawing feverishly in a little corner in the back of the room. The teacher asked her what she was trying to draw, and she responded, "God". The teacher stumbled and then responded, "But nobody knows what God looks like". The girl responded, "They will in a moment."

Just another example of the faith that kids have in their own ability. And they do, definitely. There's kids all over the country interested in and passionate about different things, and they have no way to funnel this passion. Some of them are lucky enough to have great parents, but parents can only offer support, not physical resources. And despite all of the potential these kids have, for one reason or another most of them lose their ambitions as life goes on.

I was one of these kids. I grew up in inner city Detroit, and I worked hard as a kid. I had dreams like all of them, but somewhere along the line things didn't go the way I planned. I dropped out of college after my freshman year and found myself jobless in San Francisco. I had no idea then what I wanted to do with my life, and I spent the next 7 years of my life selling books door to door while I tried to figure it out. I finally got it: I enrolled as a student at Columbia University to pursue an economics degree. While at Columbia, I served as President of student activities (something like that) for two years, and I had a experience similar to what these two VCs have been describing. I met with so many college students hoping to organize events and run programs that they neither had the money or the manpower to execute.

Something clicked. Shortage of manpower? But there are all these interested high school kids who can help! All we need is to give them the chance. What I'd like to do is set up a program to link a kid in Florida, interested in Global Warming, with a kid in Alaska, interested in Clean Tech, to a kid in West Virginia interested in eco-friendly coal tech, and link all of them to, say, the Environment and Energy Initiatives at Harvard.

A survey was recently given to pre-college students asking if they believed that there was a Bill Gates in their generation. More than 80% answered that they did. 62% answered that they actually knew this person, and 25% answered that they were this person. These kids are out there, waiting to make a difference and lead us forward. Let's give them the chance to do it."

I'm just transcribing from memory, and he sounded much better in person, but in any case, it was a very good pitch. I was sitting there the whole time listening to him, agreeing with everything he said, but at the end I was slightly lost. I mean, sure, it'd be great to pair all these kids up with Harvard, but aren't there universities with research and whatnot near their homes, at least comparatively? I mean, there are opportunities, if people are just willing to ask, right? What exactly is he trying to set up.

The answer is, of course, a point that was reiterated so often during the last 4 years of my life that it made me nauseous by the end of it. And yet, looking back, I can't see how it could have been overemphasized, it's so humongous. It's TJ. Partly the classes, even the less than stellar ones, partly the students, and partly just the place. How many college professors would honestly just hire high school students who show up at their office asking for a chance to do research. Don't get me wrong, it's possible, and there are definitely people who do it. But those kids have to work a lot harder to prove themselves. TJ, both by reputation and by actual education, gave us this unerring ability to just get research from the nearby universities.

It's not just that of course. Through math team and the satellites, we picked up so much stuff we just take for granted. Of course, there's a lot more, and the absolute attitude is rather useless, but it's interesting to think about once in a while. And the stuff I learned shows up so often, despite explicitly being taught as "contest math". It's helped a ton with research, from random generating functions manipulations on Boltzmann Distribution Functions to predicting folding of large DNA networks by analyzing the adjacency matrix of interactions between basepairs.

I guess all I'm trying to say is that I can't even begin to express how much I loved everything about high school. Not in a depressing, I wish I were still there kind of way. I don't like getting emotional, so I take a great deal of effort to remain emotionally passive. There are great days to come, but it's worthwhile to keep the past in mind.

Anyway, you guys made TJ what it was for me, and continue to make it so. I just wanted to thank you for that.

~jnub