Mar 31, 2008

science education

I'm going to graduate from MIT in a few months. My imminent release in to the Real World (out of the frying pan and in to the fire, really) has got me looking back on my scientific education so far. As it turns out, until I came to MIT, my schooling contributed almost nothing useful to my body of scientific knowledge - an interesting observation indeed.

I should define by what I mean by "nothing useful", or, in other words, I should state what I consider to be useful knowledge. It's actually a difficult task. Since a lot of scientific knowledge builds upon previous knowledge, I don't want to trick myself in to thinking I learned nothing in school, if in fact I was learning basic principles upon which later learning depended. So I'll have to dig deep in to the memory banks and figure out where I learned about truly essential stuff, like the scientific method, gravity, careful observation, the existence of cells, and so on. Once the absolute basics are accounted for, I can define useful knowledge more precisely: knowledge which, at some point after learning it, I needed. For example, when I was one or two, I began asking my parents how electricity works. (There's a note in my baby book that says I was "quite good at remembering explanations of what it does", although I still had to ask all the time, apparently!) It has mattered many times in my life that I understand how electricity works. So that information is useful. (Incidentally, it's also something I was never taught in school.) On the other hand, I learned about grasshopper anatomy in high school biology. I still remember it, but it's never mattered.* That doesn't necessarily mean it shouldn't be taught - but I think it's reasonable to assume that at least some of the things you learn in school ought to be useful later on, or else schooling has failed to accomplish its goal. The question is: did they fail?

*One might say, at this point, that learning grasshopper anatomy was a vehicle by which I learned deeper scientific lessons about comparative anatomy, dissection, and so on. I've considered this possibility, but I must conclude that the only reason I learned about grasshopper anatomy was because it was tested on the New York State Regents exam. The content was certainly not presented in any way which would lead me to gain greater understanding about comparative anatomy or anything else.

So. Like everybody else, I really started learning about science the day I was born, since one really can't help but learn while living, but in this post I'll be looking at the more concentrated chunks of scientific education in my life - momentous occasions in my learning, if you will. Where did it all begin?

When I was 7 or so, I was given a copy of the Dorling Kindersly Science Encyclopedia. It instantly became my favorite book. For years, until I'd read it cover to cover several times, my parents would come in to my room in the middle of the night to find me asleep on the open book, lights still on. As far as I can tell (and actually, somebody has commented on the Amazon page saying the same thing), the encyclopedia covers everything that is generally taught in grade-school science class. It also covers a whole lot more - there's a lot of detail in there that I didn't see in school until high school, at least.

Because of the encyclopedia, I can say fairly certainly that although my school did present some interesting and/or important science topics in class, very few of them were new to me. In first grade, I did learn a great deal about astronomy because my teacher (whom I loved - I have very few complaints about first grade!) had me draw charts of every constellation in the night sky and memorize them all - and to this day I can see that drawing in my mind every time I look up at the sky. In third grade, my teacher assigned me an "independent research project" while the other students did I-don't-remember-what (this will be a theme in this post, you'll see) and I learned a lot about puffins and presented my findings to the class, which was fun. But other than those two things, I don't think I learned anything in science in grade school that I hadn't already read. And furthermore, the amount that I learned in grade school was a *tiny* fraction of what I had read. So that encyclopedia was one major teacher.

(Not every kid likes reading a science encyclopedia, obviously, but this post isn't about every kid. Just me.)

In fourth grade, a friend of mine mentioned that her father, a mathematician, had taught her how to do a word problem with algebra. I had heard of algebra from my encyclopedia, but I didn't know much about it, especially since neither of my parents know any algebra (they're musicians). That afternoon, during recess, my friend showed me that you could use letters to represent numbers, and then move them around in equations. Similarly, another couple years down the line, another friend of mine (with a mathematician father again!) mentioned the quadratic equation in a sort of off-hand way one day. I asked what it was, and she told me - just like that. I have a feeling that a lot of learning goes on this way - under-the-table conversations between peers, fueled by curiosity - even when schools think that they've done the teaching.

The third way I remember learning a lot in grade school was from my parents. My mother especially has always been very interested in nature, and she taught my sister and I to identify birds, trees, and bugs. We never had lessons of any kind - we just went to parks a lot (especially this one), went to museums, and went walking in the woods. I never felt like I was being forced to learn anything. I was just having fun.

The encyclopedia, conversations at recess, walks in the woods - the three most memorable ways I learned in grade school. None of them happened in the classroom. Moving on to middle and high school... did school take over as my primary informant as the subject material became more and more complex? Did I find school indispensable?

Nope. I'm actually going to leave school classes out of this bit almost completely, because the only important thing I actually learned was how to identify minerals. Almost everything I learned came from a string of obsessions that I had, in to which I would throw my self whole-heartedly until something new caught my fancy. The first obsession was ham radio, which isn't particularly typical of 10-year-old girls, but hey. I took my operator test, which required me to know how antennas worked, which required all sorts of other knowledge about energy and waves and electricity. I was so in to it - and then all of a sudden I was in to dolphins and marine biology - much more typical of young girls! I had dozens of books on dolphins. I wrote letters to children's magazines about the plight of the Indus River Dolphin. It was my thing. And then in a flash my thing was astrophysics. I read Kip Thorne's "Black Holes and Time Warps". I rented Carl Sagan's video series about the cosmos (think "billions and billions") and was glued to the screen. I was terrified of nuclear war. I stared at the sky all the time and begged my parents for a telescope (it took 10 years, but I got one for my 20th birthday)! I was fascinated by black holes. Eventually, an awesome organization in Ithaca called The Learning Web set me up with an internship at Cornell's Spacecraft Planetary Imaging Facility. My job was to work with a cool guy called Rick on organizing all of the pictures that came in from orbiters and satellites. Which meant that I got to hang around with astronomers and play with the computer and use Adobe Photoshop, which I thought was the most exciting thing in the whole world. Even more thrilling was when the group allowed me to come to the midnight party that they held when the Pathfinder touched down on Mars in 1997. I showed up in my pajamas, having already slept for some time, and the grad students gave me grape juice and let me sit in the front so I could see the TV. It was incredible.

That same year, I was assigned a "research paper" in my 8th grade earth science class. I was supposed to research any topic of my choosing, write a paper, and present to the class what I had learned. I wrote a paper explaining what black holes are (with an analogy to a trampoline, which I think was actually moderately clever), how they form, what they look like, etc. I had a blast. I wrote this 8-page paper that I was really proud of, and I made a presentation to give to my class. I got up there and talked for my allotted 10 minutes, after which my teacher told me... that I wasn't allowed to present on topics that nobody understood. I was absolutely crushed, mostly because the entire point of my paper had been to explain black holes from the bottom up.

After I worked at SPIF, I got more and more interested in particle physics. I read Brian Greene's "The Elegant Universe", a book about string theory. I didn't understand any of the math in it, but luckily the internet could offer some insight. I even wrote Brian Greene a letter asking him some questions, but unfortunately he never wrote back, though I waited for a response for months and months.

Eventually I got involved with the Learning Web again, and they set me up with an internship at the Cornell Wilson Synchrotron. I worked for a guy called Rafael, a retiree who'd gotten bored with retired life after only a week, and who'd returned to lend his considerable expertise to the operation of the particle accelerator. He was one of the people who helped build the synchrotron on the first place, and the only person still working who knew its deepest darkest secrets, so he was invaluable, but since he was technically retired, he didn't have specific duties. Which made him a great mentor - he had plenty of time to show me around. The facility is absolutely incredible. If you've ever been inside a particle accelerator tunnel, you know how cool it is - enormous bending magnets, cavernous detectors, massive boxes of electronics - it all looks like some fabulous science fiction paradise. I was a little out of place there, granted, being the only person under 25 around, and one of only 2 females, the other being a professor in her 60s, but physicists are known for being kind of aloof, and nobody seemed to mind too much.

Rafael had been a well-known lecturer in physics and electronics, which was absolutely to my advantage. When I first started working for him, I didn't know enough physics or electronics to build anything useful for the sychrotron, so he had to teach me. Which meant that I got private lessons in two-hour chunks from this guy. It was a great way to learn, especially since my new knowledge was immediately applied in the context of the project I was working on.

Later on in high school, when it came time for me to start taking normal physics classes, I found that I just didn't have any patience for sitting through dry, boring lectures with no fun projects in sight (neither did anybody else, I bet). I had also already taken calculus at that point, which made it a bit silly to take the physics class that my school offered, which attempted to bypass the calculus with long-winded, fuzzy explanations that obscured the math. So for the last couple years, I actually took physics, and later math as well, from a distance-learning program called EPGY. It worked out pretty well, because I could work at any pace I wanted, and it let me leave school after only 2 hours of morning classes.

Since I'm getting a degree in bioengineering, one might wonder why so little biology has appeared so far in this overly-lengthy narrative. It may just be blatant cynicism, but I think the reason is actually directly attributable to one person: my 9th grad biology teacher, whom I won't name.

Early on in the year, were were assigned a research project (oh no, not another research project...). I can't exactly remember what the constraints were, but I decided to test whether or not vegetables and fruits that had a bright red color had more vitamin C in them than paler vegetables and fruits. I did some very simple test (I think it involved iodine and potato starch), and found that indeed, the red fruits and vegetables I tested had more vitamin C than the others. My teacher refused to believe me. She hadn't heard of it being true, and not only was she was totally unwilling to believe that I had done a sound experiment (which is a legitimate concern in the context of a sloppy high school lab), she didn't even believe that I was telling the truth. She honestly thought I was fudging my data. We never got along after that. (Also, in her class, I was bullied pretty ruthlessly by 3 guys who sat at my table, and she refused to move my seat. So that didn't go over well either.)

(In case anybody's curious, my results were actually correct for at least one of the vegetables I tested. I had used orange and red peppers, and red peppers are now known to have 50% more vitamin C than orange ones.)

My interest in biology lagged for quite some time after that disastrous class. It only picked up when I was 16 so when I began to get interested in cancer research. When I first began reading about cancer biology and treatment, I became totally obsessed. I'd stay up all night reading. I'd download articles and read them on my laptop whenever I had a free moment - which I now realize is exactly my style. Complete immersion until I have the basics down, and I feel ready to ask questions, and talk to people, and understand the whole thing on a deeper level. (As it turned out, the way to understand things on a deeper level in the case of cancers was to get involved with the ACS and participate in the Relay for Life, which, if you haven't ever done it, is an incredible experience.)

After I had recovered from my bad introduction to biology, I started reading a lot more of it, and I got in to neuroscience and cognitive studies. And then I ended up at MIT, where I floundered around for my first year, unable to choose between physics, bioengineering, electrical engineering, and neuroscience. I feel that my education here has been very good. I certainly can't sum it up here, since it's really a whole 'nuther beast, so I won't try, but that's not the point of this post anyway.

The point I'm actually trying to make is that when I look back on my education, I find that I was incredibly fortunate to have opportunities to learn science in interesting and diverse ways. I am fairly sure that if I hadn't had the opportunities I've mentioned in this post, I would feel pretty negative about science. It would probably be lifeless and dull. I'm not even sure who I'd be today if these experiences hadn't been such a big part of my life...

Which really makes me wonder about education in this country. And if I had to answer my own question from the beginning of this post, I would say that yes, the schools did fail to educate me in science. Anybody who reads this blog knows that I have a lot of gripes about education, but I promise I won't go in to them all. Let's just say that public science education is... well, it's no fun. It takes a subject like physics - which is responsible for the Mars rover, and that magical party I attended in the middle of the night - in to an emotionless subject that exists between the cardboard covers of a (badly-written) textbook. It removes science from the forces that motivate it, all the emotion, passion, and urgency that scientists feel to discover and innovate, and isolates it in a small world of petty facts. It's sad, really - astronomy is so grand and humbling and biology is intricate and delicate and physics is full of explosions and bizarre theories... I'm beginning to think that we shouldn't separate science from science fiction, really. I don't mean to suggest that we should teach people science THROUGH science fiction - I'm all for keeping the facts accurate - but I think public science education has lost sight of the fact that science is what sends us to the MOON and builds mushroom clouds and saves peoples' lives. Where's the glory?

Mar 21, 2008


Because it isn't published yet, I can't say much about the work I did last summer on an HIV vaccine. What I can say is that the work wasn't particularly glamorous. I spent a lot of long hours mixing and measuring tiny amounts of clear liquid in tiny plastic tubes, which isn't quite as exciting as rocket science, but hey - that's bioengineering. Things that bioengineers think are exciting are generally about as thrilling as watching paint dry.

But damn, if it works... Imagine how it would change the world. Just thinking of it gives me the shivers.

HIV is a tricky monster. It attacks CD4+ T cells. Those helper T cells are supposed to activate B cells, which then produce antibodies, which bind to the virus, causing them to be endocytosed by macrophages. So if you don't have any T cells, you don't have any antibodies, which means that your specific immune responses are... zilch.

When it enters cells, HIV unpacks its (tiny, efficient, scary) RNA genome, uses an enzyme called reverse transcriptase to translate the RNA in to DNA (all the better to mimic human genes), and then inserts itself in to the human genome. There it lurks for years.

The virus can only replicate if certain transcription factors (molecules which bind the DNA such that transcription to RNA can occur) are present. (For example, in the case of HIV, one of the factors it needs to jump out of the human genome is NF-kappa-B. Sadly, NF-kappa-B is upregulated (produced more) when T cells are activated.) When such a transcription factor comes along, the viral genome is transcribed to RNA and translated to protein unwittingly by the body's machinery. The completed virus assembles, bursts out of the host cells, and goes on to infect again.

It's awful.

HIV is only made trickier by its tendency to mutate extremely quickly. The virus can change significantly within one person, within one month (this is mostly because the virus doesn't package its own proofreading enzymes, so when it transcribes its own genome, it makes a lot of mistakes). Which is part of the reason that no vaccine has been made so far - it's incredibly difficult to fight against a mutating enemy.

Therapy for HIV basically consists of anti-retroviral drugs right now. They work in a number of ways - they can inhibit reverse transcriptase, they can inhibit some of the viral proteins necessary for viron assembly, they can inhibit the protein that allows HIV to insert itself in the human genome, etc - but all of them focus on blocking the virus from doing what it wants to do. This means that all of them are dependent upon the virus not mutating so much that it becomes unrecognizable to the drug - and that's unlikely, given how fast HIV mutates. So lots of people become resistant to treatment, and then there's very little that medicine can do.

Most of my understanding of HIV and AIDS comes from a very scientific perspective. I know a lot about HIV surface proteins. I can go on about immune response. But the epidemic hasn't come too close to my life. It started just before I was born, and by the time I was old enough to know anything about it, it was a pandemic. Friends watched friends waste away. AIDS orphans were suddenly everywhere. The disease reared up from nowhere, ugly as hell.

I've never personally known anybody with HIV or AIDS. I've never even met anybody with HIV or AIDS (that I know of - though I probably have). Sometimes it makes AIDS seem so surreal. I've been hearing about it ever since I can remember, this hellish disease, for which we have no cure. I even forget, sometimes, that the disease is only a couple years older than me. How can it even be real? How can it have changed the world so fast?

Once in a while, I get a flash of understanding. Maybe I read something (like Susan Sontag's "The Way We Live Now" - not for the faint of heart), or overhear something on the T... Today, in a restaurant, just as I was leaving, I heard a group of people make a toast to a man who had died of AIDS. In those moments I'm reminded how blissfully untouched by AIDS my life has been, and how little I really know about it. And how very, very far we have to go before it can be forgotten.