Friday, September 30, 2005

well the girl in the front row is leaving

K went to the bar, temporarily turning their square into her triangle. Their ears still buzzed. Her supposed date observed, “You have a thing for guitarists.”

She shrugged uncomfortably, knowing he played. Her friend caught this, cutting in to correct him, like a reliable doorstop. “No,” he asserted protectively. “She wants to be the guitarist.”

Maisnon, A N N A, Andrea, Chai, et al, this is not a lifetime commitment to recovering the satellites. I'm not good at keeping to my word (or a word count).

Thursday, September 29, 2005

watching the detectives

Dudes, I seriously need to be institutionalized. I have a stack of research papers on my desk that are completely unrelated to work. Oh yeah, I have over 100 pages of required reading to do for classes, but am I satisfied with getting all of that done this weekend? Hells no- I compound the pain by digging up another 100 pages worth of research to do a pet project. Crikey, I am turning into an utter kiss ass, complete with don't stand so close to me emails to the professor.

Having just decried my insanity, let me completely contradict myself by noting that I totally lurve all of it. Really researching a topic in science makes me feel like a private investigator. Gathering evidence, following the paper trail, putting it all together. I never used to be one of those people who wanted to take a clock apart to figure out how to put it together again. But I guess it's just that mechanics don't pique my curiosity the way other things do. It is way cooler than my job, I can tell you that much. Of course, that is not a big accomplishment these days.

Tonight, the bro-seph is heading out to South Beach to get himself into all kinds of trouble, I'm sure. When we talked yesterday to coordinate getting him to the airport, we reminisced about a family friend around the same age as my brother. When this kid was younger, in his early 20s, he told us he wanted to move from New England to Florida. When my brother pressed him for a reason, he confessed that it was because of Will Smith's Miami. Let me repeat that-- this kid wanted to move based on the portrayal of a city in a Will Smith song. We have lost touch with the kid, but we can only speculate that he's currently spending his time in dance clubs convincing everyone to do the Switch.

Maybe I'm not supposed to broadcast this to the world, but I doubt that many people read this blog anyway. We are having a mini-blogger meetup on Saturday at noon. I know what you're thinking- and by we, she means her and her pet rock. But so far, maisnon, oodles, and ads will be there. If you happen to be in San Francisco, be sure to wear some flowers in your hair. Oops. What I meant was, let me know if you would like to join us. Especially if your name is Sawyer and you just pulled a bullet out of your arm with your bare, beautiful hand.

Wednesday, September 28, 2005

stuck in a moment and now you can't get out of it

Today, it finally hit me why I have felt so off balance lately. There is an inherent weirdness associated with going after something you really want, while simultaneously maintaining your stake in something you really don't want at all. It comes down to being in a transition state.

When some molecules go through reactions, they start out at a certain thermodynamic level, a certain stability. Because I'm a cynic, I like to think of this as their level of dissatisfaction with their current state. It's this state of being- something better could be out there, but they're not in such an unbearable state that they would not even be to begin with.

If the molecules can get enough energy, can get excited enough about reacting, they can clear the Sisyphusian-looking hill they are staring up at their original state. They decide to ride that rollercoaster, but it takes a lot to get up there- that's the activation energy required to make a reaction happen. At the top of the rollercoaster, they're in the transition state- at this point, they resemble neither the original molecules, nor the molecular products they are destined to become. It's that point at the top of the rollercoaster, after the slow click, click, click as you make your way up the incline. You're at the very top, and you know you have a thrilling, effortless ride ahead of you. But there is still that moment of uncertainty at the precipice; your stomach hurts in anticipation.

Most molecules stay in a transition state briefly. After a short inhale, it's a wheeeee and they've found their new state of being, a happier place than where they started. They had to travel to a place where everything was difficult and uncomfortable in order to get to their promised land. I realized today I have a long transition state ahead of me. I'll just have to keep reminding myself that I'll be in a better place once the freefall finally begins.

Tuesday, September 27, 2005

but what would you change if you could?

This class is going to be the end of me, I tell you. I try to speak intelligently with the instructors, and I get all tongue-tied and twisted, just an earthbound misfit, I. Seriously- I am worried that I am just going to blurt out "I lurve you!" instead of talking about the articles I am researching for class. I left class last night flushed over chatting about RNA. Not good. This class is turning me into a friggin' sixteen-year old. And you know what? I kind of like it.

In days of yore, there was some thought that protein binding had almost everything to do with finding the right fit. In enzymes, this is known as the lock and key hypothesis. I won't bore you with all the details, but it supposes that a protein just has this void, this part of itself that it is yearning to find, and that's how it ultimately binds its specific substrate. Much like a lock and key fit together. Or like a hook and an eye.

Since then, layers and layers of complexity have been added to that initial model. It turns out that proteins are just fine on their own, and are not necessarily holding still, arms spread, waiting. What is more, it's not about a perfect fit. It is more to do with a series of perfect interactions. Proteins don't fuse (most of the time); they bind. The essential components of their individual parts remain the same. But the right part of a protein will come in contact with the right part of another protein's receptor, and the right interactions will trigger binding. And binding itself is a complex process. The right interactions induce the proteins to change their conformations just so, so that they fit together. And a bound protein quite often has a completely different shape/conformation than the same protein, in its unbound state, does.

These conformational changes, in general, are fascinating. Okay, to me, they are fascinating. "Oh," she says, "You're changing." But we're always changing. I mean, the idea that every interaction we have changes us in some way is not just amazing- it has to be true. It is why I rarely look back on things with regret- if you change one thing that happened, you disrupt the whole process of how you got to where you are now, who you are now.

A wrinkle in this notion, an idea that is a bit gloomy, is that a protein can have certain interactions, interactions outside of its binding area (or active site for you nomenclature junkies). Some of these interactions can trigger a conformational change that will render the protein inactive, unable to further bind anything. Something has happened, and the protein is closed for business. Movies have been made about this, but they always assume that the inactivity is reversible, that you can change back to your original conformation. I remain uncertain.

Monday, September 26, 2005

if I don't win, I'm gonna break even

Manohla Dargis perfectly captured something about Peter Sarsgaard that made me smack my head in realization, wondering why it had not been abundantly clear:
"All that the restless viewer can do is marvel at the snazzy production design and the strange elocution of Ms. Foster's co-star, Peter Sarsgaard (as a sky marshal), who serves up his lines as if he had studied at the John Malkovich school of cinematic expediency."
Yep, those snarky NYT reviewers are at it again. That said, let it be known that, despite the veracity of this characterization, I love me some Peter Sarsgaard. And no, I have not seen Kinsey, and that is why I only love me some Sarsgaard.

I spent the better part of yesterday at one of the loveliest cafes in my neighborhood. I rarely go in because I don't drink coffee and it is quite often too crowded to sit peacefully. When, on the other hand, I am trying to study, a din in the background does not trouble me. Somehow, it works like some kind of noise cancellation device.

When A visited last, he went to this cafe every morning and said the coffee was very good too, so I'm not totally talking nonsense about the quality of the cafe. However, I like the cafe because it is colorful. There's one of those water-pouring-down-stones devices that delivers the gurgling sound of sitting by a brook. They make great varieties of sandwich melts, and they do not use mayonnaise in said sandwich melts-- I hate mayonnaise. They also serve eleventy billion different teas. Finally, while I was there, they managed to play both K&D and the Amelie Soundtrack. This place may actually have no flaws.

Contrast that music with the soothing sounds of IKEA on a Friday evening (with the effervescent maisnon). Just after I prefaced our visit with a confessional on how Friday night IKEA trips were the thing to do in New Jersey, Livin' on a Prayer came on the loudspeakers amidst couches and coffee tables galore. This is not a joke. I have a witness for a change! Oh, also, you should be so lucky as to get maisnon to do the Axl-snake dance for you. Ha ha, suckers! Every once in a while, it's good to be me.

Finally, I'd just like to thank Steve Carell for putting me in a terrible quandary. I really can't remember an SNL episode since Will Ferrell left that was vaguely funny or worth watching, but now Carell has ruined it by agreeing to open this season. And he had to go and host when Whine-ye West is the musical guest. Damn you, Carell!! One thing is for certain- I will have the option to watch it, since I'll be spending most of the weekend nerding out with all sorts of biology. My future bf professor is hitting us with our first quiz today. Wish me some good juju.

Friday, September 23, 2005

everything I never liked about you is slowly seeping into me

It is a rare moment when I actually look forward to spending a Friday evening on the Peninsula. Berkeley on a Friday night is logistically taxing, but completely fine with me. Anywhere in San Francisco on a Friday night is a go. But the Peninsula is a place I usually avoid like the plague. I do not even know why. It is not as though the area ever caused me trauma of any kind (besides the hellish traffic that builds up at certain unfortunate hours on 101). But I do look forward to heading out to see maisnon this evening, regardless of place.

All of this reasserts something that has been happening with alarming frequency of late. I keep having these role reversal experiences- behavior I never understood in other people is now my behavior. My brother used to live in Manhattan when I lived in New Jersey. It was a 45 minute maximum train ride, but it always only happened in one direction- me hopping on the train to New York. He rarely could manage to drag himself out of the city. But now I'm on the opposite side of that coin, and I behave the same, exact way. I am always forcing people to come to San Francisco rather than meet elsewhere in the Bay Area. Hell, most of the time, I am forcing them to come to my very neighborhood. This is what happens when you truly like where you live and where you are: you have difficulty fathoming why anyone would feel differently.

Also when I was younger, I used to really get miffed at friends who did not keep in touch regularly. And wow, have I ever switched to the opposite end of that pendulum. I am the worst offender on earth these days of not responding to extended emails, not returning phone calls, and not letting people know where I am at with my life. I realize now that I am the bad guy of the situation that no one means for it to be taken so personally. If I get an email from someone I have not actively kept in touch with, and they are not experiencing a tragedy or emergency, more often than not, I file it away to respond to at a later time. Then, of course, time passes by, and the response would have to be longer and more involved, even more explanatory. And the amount of effort gets insurmountable. It is incredibly lazy, I know. I am not saying this absolves me of any reproach. The fact is, I am a bad friend, and probably will continue to be a bad friend for a number of years. But I know I'm a bad friend. Do I get any partial credit for that?

Did anybody else watch Everybody Hates Chris last night? I made a point of giving it a chance, but was not holding my sides from laughter. It was, however, sweet, and it taught me a great new threat-- "I will slap your name right out of the phonebook." Hee! I think I just ruined any chance I may have had of babysitting any of your future children.

Thursday, September 22, 2005

my aim is true

Oh, dudes, I feel guilt. You know I love my iPod mini. It was my first, and it will always be significant to me, if for no other reason than that it plunged me into the world of iTunes and basic tech-competency regarding music (okay, I'm still pretty woeful in that regard). And I will never give up my iPod mini, for it is beautiful in its blue hue and plays the pretty music. All of that said, as of this afternoon, delicately at rest in its wee box, is a new, sleek black gadget. I could not help but gasp upon seeing it up close and personal. It is my new precious. Will my iPod mini feel I'm being unfaithful?

Here's some stuff I have learned from the idiot box television lately:
  • Desmond is the new Ethan Rom.
  • Ethan Rom has decided to play Ethan Rom, but on Threshold.
  • Walt is the new kid from The Shining that kept popping up all "REDRUM"-like.
  • There's something magnetic about Peter Dinklage.
  • Extras is coming! Finally, Ricky Gervase can be seen weekly on my TV, even though I don't get the Beeb. Now is the time on Sprockets when we dance.
I also like how I convince myself that I'm actually reading journal articles while watching TV. Suuuuuuurrrrre.

For the last thirty minutes, I have been trying to get a little peace and quiet in my office so I can write something vaguely coherent. Instead, coworkers have knocked on my door continuously with the classic, "Can I pick your brain for a minute?" So, now, my brain is picked as clean as a carcass by turkey vultures. Come to think of it, that's a good characterization of my coworkers. It's also a handy excuse for why this post is even more nonsensical than usual.

I made a momentous move yesterday, but it is sort of silly in the scheme of things. Just as life is getting so hectic that I really wonder whether I should continue to blog, I confessed to my friend B, from my pre-blogging existence, that I have been engaging in this self-absorption fiesta. Instead of sending the men with the straitjackets, she was surprisingly understanding about it. I still do not know if I will ever tell everyone I know about this. B is a particularly non-judgmental person; it is not a random coincidence that I unleashed the blog on her before anyone else. But B, if you're reading this, thanks.

And thanks to everyone who has wished well to my family in Houston. They have driven as far as Katy, and are stopping there for the timebeing. If the highways get a little less congested, they may try to get out to Austin. If not, Katy will hopefully suffice. It's a very, very mad world, it seems.

Wednesday, September 21, 2005

minute hand, millenium hand and an eon hand

Is it possible that I have some kind of homing beacon inside me? Because now, for two weeks in a row, two different people have decided that it is perfectly acceptable to sit right next to me after walking into a completely empty room. If this happens again next week, I might have to quit the class. Okay, I am not really going to quit a class because my personal space is constantly invaded. Maybe I should just stop wearing deodorant.

Well, that very likely grossed out anyone still reading. Yesterday was a very odd weather day for the city. Thunder, lightning, and a sprinkle of rain are highly unusual in September in the Bay Area. By the time I was getting to class, the rain had just stopped. Smell is supposed to be a sense very deeply connected to memory. Yesterday, I became a believer- when I stepped out onto the sidewalk, a flood of the past overwhelmed me. There are times that this happens, and I start to believe time has more than one dimension. Something about the warmth of the air, the humidity, and the smell of the asphalt and moist earth, that smell that seems to make everything fresh again- something about all of it made me feel like every step turned me into someone else. At one step, I was me, at the next I was me at nine, waiting for the schoolbus. In the next step, I was me again, but with one more step I was me at nineteen, walking along the Charles River. Each step, I was someone else, different versions of me, in different places, different times. Maybe I need to ease up on the caffeine.

E used to say that, when he had trouble falling asleep, he closed his eyes and pictured himself in his room. Then he zoomed out and he was looking out above his house. Then he zoomed out again, and he was looking over the whole city. Then he zoomed out again, and he was looking at the whole planet. On and on, until he could no longer see himself even as a speck, so small was he in the vastness of the universe. And he felt quite at peace after that.

I find comfort from the two extremes. I think of a person, and then I think of all of the body parts that make up a person, how all the organs need to work in perfect harmony together for something as fundamental as breathing to continue. Then I think of all the cells that make up each of these organs. And then there is, within the cells, the complex machinery of proteins and molecules and carefully orchestrated interactions that must happen just so to maintain a body's current state of being. It feels like a work of art.

But on the other hand, I think of the timescale in the opposite direction. I think of this fury of activity that is going on inside the body every day at the cellular level. And then I think of the bustle of daily life, which seems very busy, but quite pales in comparison to those frenzied molecules. Then I think of a lifespan, which seems very long. But then I think of how long humans have been around, and a lifespan feels very short. And I think of how long archaebacteria have been around. And I consider how long it has been since life first started on this planet. I think of the timescale of evolution, and how change happens at such a slow pace. And it feels like I’m that tiny thing like E.

I don’t know why, but I feel like I need to know both- I need to know that my life and what I make of it is very important and I need to know that I am ultimately insignificant in the face of the larger picture. Perhaps some people need their life to feel one way or the other. But I like that balance.

I didn't realize it until I finished writing this, but I must acknowledge that these two posts triggered much of what I wrote today, so blame them, just as you might blame Eddie Vedder for Scott Stapp. Funny, the effects of the blogosphere.

Tuesday, September 20, 2005

how did they teach you to be just a happy puppet dancing on a string?

Yesterday in class, my future bf the instructor wore a t-shirt that said Stop Reading My Shirt. And then he mimicked preacher speech while singing the gospel of the central dogma of biology. It is quite surreal to hear an entire class yell, “I believe in RNA!” But also awesome. This dude is killing me, yo.

We also got to watch these videos. If you are a visual learner, these videos could be the difference between huh?!? and Ah, yes! when it comes to understanding certain biological processes. It is all pretty basic stuff, but it is the bomb diggity. We were all as giddy as wee school children while we were watching these.

Here’s a little something that has been haunting me lately- telomeres. Seriously, they are little somethings. They are a repetitive strand of DNA that cap chromosomes. The telomere really has one main purpose- it marks time. Each time a chromosome goes through replication, a little piece of the telomere is used up. The telomere gets shorter and shorter each time the chromosome replicates. Trees have their rings. Parents put a pencil mark on a wall at the height of their children. Chromosomes have the length of their telomeres.

Once the telomere gets too short, it signals that the chromosome is too old to be going through all this replication mumbo jumbo. As a result, shortened telomeres usually trigger cells to enter a phase called senescence. After that it’s just a matter of time before the cells decide to call it a day. The alternative is to go all Darth Vader, head to the dark side, and become an immortal cell. Everyone knows the dark side comes with a price- those immortal cells more often than not are cancer-causing little bastards.

This concept troubles me because I firmly believe that there is a certain amount of life that is dictated by willpower. Fate plays a hand, but I have to believe that I have some small lever of my own control. But every time I think of my cells and the amount of information that was given to my cells from the time I was an embryo, it gives me pause. Everything is marking time, and everything seems decided and destined. I could just be playing out a pre-programmed song and dance.

Monday, September 19, 2005

turned away from it all like a blind man

True sign of the apocalypse: the Donald in overalls, singing the theme song to Green Acres. I had to run out of the apartment for a solid hour after that.

Classes: causing me stress in a good way. Work: causing me stress in an anger-inducing, Milton-burning-down-the-building way. Blogging: causing me stress, in a guilt-ridden way. Should someone who has been blowing off friends & human beings still take out the time to drone on in a blog? I'm conflicted.

I have not forgotten my oath to bake every weekend, though I have already managed to be unfaithful to it. I had to do some preparatory work on Sunday for the next baking adventure, and have yet to locate one of the key ingredients.

Also, I knew the Pats were not going to fare well this year- I am glad that my studying prevented me from watching the debacle. Sunday was official Boston Area sports choke day.

Finally, Naveen, see what happens when you don't wash your hair?

Friday, September 16, 2005

get back to my city by the bay

Okay, let's take a break from the walk down Science Geek Blvd, and welcome the newest resident to the area. I do not have anything against other parts of the country, though I may poke occasional fun. There is something to appreciate everywhere. You might think me mad for saying that living in New Jersey had its benefits, but, truly, there are so many things I would have never done if I had not lived there. Of course, some of those things I should have never done, but... well, I'm getting off track, aren't I? Every place has its fine points, but this is my city more than anywhere else. Strangely, this is the place where I feel most at home, though I grew up over 3000 miles away.

When I come home from work every day, I have two roads to choose from. The first takes me up the 101, passing by the Bay, the less pretty part of the Bay. This is the part of the Bay where Candlestick Monster Park sits, where, if you get off an exit too early, you end up in Hunter's Point, praying that locking all the car doors won't be interpreted as an act of hostility. It is a fairly congested road. During the tech heyday, this highway used to be a nightmare from what I hear.

I get off the 101 right before the city traffic really starts to become unbearable. After that, it's nothing but local roads through the Mission to get home. But what beautiful roads they are. This drive cuts through the heart of the Mission, the very bowels of the Mission. Men in overalls splattered with paint trudge homeward. Women push strollers, and these are not the ladies who lunch- these are the ladies who make lunch for the kids before they leave for work in the morning. A group of teenagers congregate on a sidewalk, slapping handshakes with each other, laughing. Someone is drunk on the corner. And, the color. Oh, there is color everywhere. Houses are painted brightly. Murals are everywhere. This is the view as I am driving home on this route:

There is always a choice on how to get from Point A to Point B in San Francisco. Ask five people how to get from the Mission to Inner Richmond, and you'll get five different routes. Some times, I find it more enjoyable to drive the 280 on my way home. The whole experience is completely different. Instead of overlooking the Bay, 280 is nestled in a valley of lush green. As you pass through Colma and Daly City, the fog settles in, blurring all the edges. And you can drive to The Killers without actually getting killed.

But then, as you approach the city, on most days, you cut through the fog. The fog fades away, and quite often, sunshine awaits you. On the exit I take, the road turns off of the 280, and suddenly, emphatically, announces the city. There's a slight incline, and then a drop. And just before the drop, an amazing panorama of the city presents itself. For a moment, you can catch a glimpse of the skyscrapers downtown, occasionally even catch a glimpse of the TransAmerica building or the Bay Bridge. That moment is such a crescendo that I have never quite gotten used to it. After several years, I still find myself catching my breath when I reach that precipice. I tried in vain to capture it on camera. By now, you all know I can't take a picture to save my life, so you're going to have to use your imagination:

Maybe you cannot see it from the pictures, but this is what I love about San Francisco. It exhibits two types of beauty- beauty on a grand scale and on a small one as well. And I love both equally. I love the dirty Mission, and I love the pristine view from Dolores Park. I like the way you can get a severe stitch trying to climb one of the steep inclines, and I like the way the guy who works at the convenience store knows me. Instead of these differences being a dark contrast, they serve to illuminate each other.

Thursday, September 15, 2005

chemicals between us

You have Saheli to blame for triggering this one. I was really going to stop writing about science for the rest of the week, but she had to go and allude to my penchant for an appropriate distance in relationships. I have been resisting the urge to write about this for some time; it is probably one of my favorite science analogies of all time.

Above is a very poor representation of the oft-studied, famous (in my head) potential energy curve-- my primer. This is a very good mock-up of the handwritten potential energy curve I had hanging up in my dorm room in college. No, I will not provide you with photographic evidence of this, as I was going through some unfortunate apparel choices at the time.

The potential energy curve measures the change in attractive/repulsive forces between two atoms as they approach each other in space. When two atoms are far apart, this is termed the dissociative limit. They are so far apart that they just don't care about each other one way or the other. Long-distance relationships never work, do they?

As two atoms approach each other more closely, they gradually become more attracted to each other. They like what they see, they'd like to know more. They're a little cautious in their interest. Maybe this other atom is trouble, but maybe that is a little intriguing. But as the two atoms are moved closer together, they reach a certain, specific distance that is absolute perfection. They are in a perfect state of bliss there.

And yet, push them past this point, move them closer together still, and it is bad news bears. The repulsion grows at a hyperbolic rate. It passes the indifference stage, and goes into intense hostility. The thrill is not just gone; it has been replaced with annoyance. And isn't that how it should be?

I wanted to save this idea, so that I could write it when I had more time, when I could put it all together the way I envision it in my head. But, ultimately, I do not think it is necessary. This one is pretty obvious. What can I say, I am all about personal space.

Wednesday, September 14, 2005

how I get my ends and my beginnings mixed up too

A few things that puzzle me:
  • If you’re the second person to arrive in a classroom, why would you choose to sit right next to the only other person in the room? WTF? Am I the only antisocial misanthrope around here? What ever happened to personal space, and trying your best to leave at least one chair between you and the next person until there are no other options?
  • Likewise, if you’re already in a cramped setting, need you edge in even closer into my personal space? Is it necessary to look at my handout, when yours is exactly identical? I promise you, the meaning of life is not scribbled onto the margins of my handout- that’s just my way of processing information.
  • If you openly admit that you’re taking a class to improve your GPA, immediately upon graduating, would it not behoove you to take notes during class? I mean, at least pretend to be taking notes? Write love letters to your girlfriend or something, but at least write something down. If I were the professor, I would have kicked you out for that alone.
  • Speaking of the professor, hey, have you heard of this new invention? It’s this great version of the computer, making it brilliantly transportable… maybe you’ve heard the buzz? Laptop?!? Seriously, watching you behind what looks like a mainframe from the early 1980s is not conducive to learning.
Hey, but that doesn’t mean I’m not going to go all nerdy on you (sorry, oodles). On most Tuesdays and Wednesdays of the next several weeks, I’m likely to be blogging about science-related stuff. This is just a warning for the few people that mercifully read this blog regularly. Assuming such people actually exist, that is.

With that preamble, both the Roberts’ confirmation hearings today and class last night started me thinking about life and death, embryos and cadavers. Here’s the thing- from the very moment that a fertilized egg decides it wants to be something other than a mass of identical cells, from the moment that cells commit to what they want to be when they grow up, existence becomes a careful balance of life and death. During embryonic development, we’re growing where we need to grow, and dying where we need to die. For example, during fetal development, a fetus has webbed fingers, vestiges of our ancestry. But as the fetus develops, it kills off the cells that contribute to the webbing. When it doesn’t, when the cells our unfaithful to their commitment, you have birth defects like fused or webbed fingers. Or maybe you have two thumbs.

Whenever anyone takes a basic biology course, one is banged over the head with the concept of cell growth, mitosis, yada yada yada. But cell death gets short shrift. That is a shame, since it’s just as crucial to our survival. Cells die through two mechanisms- necrosis and apoptosis.

Necrosis basically means that a cell has died before its time. It’s unplanned. The cell is badly injured, infected, or otherwise traumatized by some external force. The cell can’t live, so it dies. And it does not go gently. It’s a messy death, and the signs of decay permeate the surrounding areas. Not pretty.

Apoptosis is cell suicide. It’s pre-meditated. The cell was born to die in this way. The cell could keep living, but it’s decided against it. The writing is on the wall. Maybe it’s no longer serving its purpose. Maybe it’s just tired. Maybe it wants to give the new kids the spotlight. Apoptosis is discrete. The cell starts carefully dismantling itself, packaging itself away, putting itself out on the curb for the trash collectors to pick up. The apoptotic cell bids adieu with dignity.

As always, I carry these things too far. The idea that bad traumas cause necrosis, but little faults we find with ourselves cause apoptosis- it’s a tempting idea. If you’ve been badly hurt, physically or emotionally, it leaves an ugly scar that might never fully recover. It’s unplanned, and you have to deal with it, and truly, doesn’t that stink? Correcting those little things about ourselves is more complex, requires a lot more work, but it’s what we were meant to do. Maybe we’re always meant to be growing where we need to grow, and dying where we need to die.

Tuesday, September 13, 2005

I won my own pet virus

No one knows for sure how viruses came to be. They are smaller than bacteria, just barely the size of some proteins. We’re talking small. You can’t see them with a light microscope. You're not likely to catch them in the fossil record. But we know they’ve been with us for a long time. Even in ancient Egyptian paintings, there is evidence of people afflicted with polio.

There are three main theories regarding how viruses became what they are today. The first is regressive evolution. This idea supposes that a virus was, once upon a time, a parasite, that enjoyed burrowing into cells and hijacking them. Eventually, the parasite decided not to maintain its independence. It sacrificed its ability to replicate by itself, so happy was it within the cell’s confines. There are proven examples of this in nature— chloroplasts and mitochondria. Both are essential to cell viability, but both were once independent organisms. A romantic theory, maybe- in sort of an I need therapy co-dependent way.

The second hypothesis is cellular origin. The idea here is that some component of a cell, a macromolecule or a protein of some sort, evolved over time to replicate by itself. The student becomes the master theory, if you will. Or more accurately, the student goes free-agent and decides to kick the master’s ass (see Crouching Tiger, Hidden Dragon for a demonstration).

The final hypothesis is independent co-evolution. This supposes that viruses have been around since the origin of life, and just proceeded along their own evolutionary chain, separate from cells. There’s a lot to love about this final hypothesis. For one thing, that these tiny things that defy the definition of life and not-life have been around from the very beginning is awe-inspiring. It’s like they’ve always played Lex Luthor to our Superman. What’s the point of superheroes without good villains? For another thing, the biology of viruses are complex, but in a completely different way than anything else you see in nature.

But what strikes me particularly is how, even though they could be considered separate from the rest of evolution, they may be intimately connected with our evolution anyway. Think about how viruses may have influenced evolution. Why do viruses, like the one during the influenza epidemic of 1918, infect many, but not all people? Is there not some sort of pressure being applied to the system by the virus? In some weird way, haven’t we needed viruses just as much as viruses have needed us?

No one knows the true answers to any of these questions. Some people may question the merits of even asking the question. But if you believe everything is about coming full circle, and a part of me does believe that, you have to want to know. How can we ever figure out how to definitively deal with viruses if we don’t know how they came to be?

As you may have guessed, I have a big crush on the class I just started taking. Okay, let’s take it a step further: I am hot for teacher. This is a problem, folks, and it is not my fault. You cannot stand there and lecture me passionately about viruses for three hours, and expect me not to melt. This does not bode well for my future endeavors. A little knowledge is a dangerous thing.

Monday, September 12, 2005

missed the saturday dance

Anything done perfectly moves me to some degree. I am always drawn to that which I am not. On most of my undertakings, I will settle for good enough over perfect. And yet, I am astounded by people who are meticulous, who take pride in getting things just right. For that reason, it was a bit difficult to watch Roger Federer the last two days. Federer did not play flawlessly against Lleyton Hewitt, Australian jackass supreme. He played less than perfectly yesterday against Agassi. His level of play is so ridiculously superior that, on a meh day for him, while Agassi is playing some of the best tennis of his career, he beat Agassi in four sets.

Usually, watching a one-sided match is boring because of its predictability. But I rather enjoy watching Federer when he’s in his zone, steamrolling through sets, because it’s an opportunity to witness perfection on the court. This time, Federer waited until the end of the match to exhibit perfection. He could have been bitter about the fact that the US Open audience was 99.99995% (the tiny percentage for him amounts to his girlfriend in the audience... and maybe Gavin Rossdale?!?) in favor of his opponent. He could have gloated about how he floated through the last set with complete dominance. He could have been puffed up by all the talk of how he will most probably be known as the best tennis player ever. Instead, after accepting his congratulations, he asked for a moment’s time on the microphone, having just glanced at a dejected Agassi who was failing to hide his disappointment. And out of the microphone, flowed Federer at his best, once again saluting Agassi for a match well played, encouraging him to stay in the game, hoping that they would meet again on the court.

I swooned. I told you I am a sucker for the sports stuff, even moreso for good sportsmanship. That said, I thought I was rid of Andy Roddick when he choked out in the first round at the US Open. But no. I have to watch him, tail firmly between legs, still shilling out for some credit card company, constantly during the Open. Gah! Someone sign Federer to some sponsors, quick- he might be Swiss, but that just makes him, unintentionally, even funnier. I can see him in Mentos commercials; he'd kill.

Yesterday, I didn’t speak to a single person, unless you count me shouting at the television during the tennis match. I’ve read that some people advocate fasting once a week as a way to cleanse your body of toxins. I don’t buy into that, mostly because I enjoy stuffing my face far too much to subscribe to such a notion. But I do think there is something therapeutic about silencing yourself. I like the idea of spending one day a week turning inward, in a little cocoon, only for me. I’m selfish like that. As penance, I baked a sour cream poundcake. Even that was more fun than usual, because nothing or no one prompted me to do it. No pictures- the vultures at work have picked it apart at this point. I'll take suggestions for next weekend's undertaking, however. I've decided I'm spending a portion of each weekend making something.

In much sadder news, Clarence "Gatemouth" Brown passed away this weekend. He was evacuated during the hurricane, lost all of his belongings, but was already ill at the time. I saw him perform twice in New Jersey, at this complete dump of a place in the backwoods of Northwestern NJ. My soon-to-be-bf at the time was a huge blues fan, and would drag me to these obscure performances, but it was easy to appreciate Brown on his own merits. Even then, he was an old man. But as soon as he started playing his guitar, he seemed fifty years younger. He seemed, in those lights, a young beanpole-like teenager, coaxing his guitar into singing. During a break in the set, you could go right up to speak to him. We did; E tried to convince Brown to hire him as a roadie. Brown told him that maybe he could drive the bus, but that he couldn't get paid for that. When E said he didn't expect to get paid, Brown laughed heartily at him and turned to me, saying, "this kid's crazy." I can remember his slim fingers resting softly on my shoulder. I remember, too, what that encounter told me about E, who had seemed so run of the mill until then. When I hear about a musician passing away, it always takes on this different level, because there is always some direct personal experience that is inextricably part of my awareness of their music.

Friday, September 09, 2005

I predict a riot

Well, so much for the Summer of George. This weekend marks the end of mental vacation for me. Inappropriately enough, I will commemorate my final weekend of freedom by destroying some brain cells tonight. It is clearly a mistake, but I am going to a trendoid place that is probably going to drive me insane. I hate bars that get so crowded that you feel like people are molesting you just to get from their booth to the bar. But, enough about me and my personal space issues.

After a brief trip to oodles’ lovely, charming abode yesterday, I reconsidered the fortress of solitude which I currently call home. I like the neighborhood; I love some aspects of my old, beaten-down apartment. But it’s not spacious by any definition. And that’s the reality of living by oneself in this city. It’s certainly enough space for me. A recent purge of clothes to goodwill revealed just how much storage space I have for junk. But it’s not the kind of place to throw soirees… or blogpotlucks (TM Saheli) for that matter. I’ll probably just continue to whine about this fact, rather than actually moving. I’ve been whining so much lately that it surprises me that I found something additional to whine about. Poor maisnon had to listen to a heaping helping of whine and cheese yesterday. It’s particularly uncool to complain to someone who is stressed for justifiable reasons. But I did it anyway, because I’m a jerk like that. Yeehaw.

There's the usual whining, which is an excellent cover for the energy wave I'm still riding. But then there's the unusual rage. Of all the outrageous things about Hurricane Katrina, there is one single quote that just infuriated me beyond all else. That quote was from one Barbara Bush, mother of He who I will not discuss here today so that I do not spontaneously combust:
"Everyone is so overwhelmed by the hospitality. And so many of the people in the arena here, you know, were underprivileged anyway, so this, this is working very well for them," Mrs. Bush told American Public Media's "Marketplace" program, before returning to her multi-million dollar Houston home.
I actually heard this quote on playback on television, and nearly jumped off my couch in, well, shock and awe. There is an audible amused laugh that can be heard from Mrs. Bush as she makes this remark. I mean, great, we've got people in the Astrodome, awesome! This is way better than the cardboard boxes some of them were living in. They should be grateful that they lost the only homes that they knew. What's even further astounding by this is the sheer lack of regard for people's sense of home. Personally, I never much cared for the place where I was raised. But I knew people who were deeply attached to their place of residence, more so than their actual residence in fact. That is a very human reaction to living somewhere for a long time, living in a place where generations before you may have lived. So, are only the economically affluent entitled to that feeling of attachment? It's okay for Trent Lott to rebuild his house, but the poor should simply be content wherever they've been shipped off? Ugggh... truth be told, I do not like to feel this angry, the Samuel Jackson furious anger type of rage. But that little soundbyte sent me over the edge. And no amount of FEMA head dismissals will quell me at this point, frankly.

It's a weird juxtaposition. I feel very lucky that I've recently somehow managed to meet a bunch of bloggers in real life who are cool, normal, genuinely good people. But at the same time, my faith in the good of mankind wanes when I hear the kind of blackhearted ignorance that spewed out of Barbara Bush's mouth without a moment's hesitation. I want to give everyone the benefit of doubt, but the cynic within keeps getting validated. Bring on the vodka.

Thursday, September 08, 2005

don't blame it on good times

If the Pats lose to the Raiders tonight, expect some gnashing of teeth, followed by kicking and screaming on the floor, followed by out and out wailing, by yours truly. Thanks to hermano, I was out at a sushi restaurant last night when I could have been watching, quite possibly, one of the best tennis matches ever. Maybe that is for the best, as I am quite certain that I would have taken a few years off my life with heart palpitations, had I watched the game in its entirety. Even though I am equal parts infuriated and enamoured of Agassi most days, today I am simply inspired by a 35-year old taking down a 25-year old in an endurance test, 5-set, final set tiebreaker match. And to be gracious and gentlemanly to boot. Andre, you've come a long way, baby. I remember when you were but a wee mulleted bumblebee.

The bro, pseudo-bro PG and I got into an argument yesterday about music. I was getting interrogated for my failure to use my iPod mini in the car. I have a fifteen minute commute. Though the music on the radio is less than fun (case in point- last night, I heard the cringe-inducing song J cited), I can stand it for a short period of time. PG made the statement that always drives me mad though-- there is no good new music these days. I could give the guy a pass if he had said there is no good new music on the radio these days. Mind you, PG is younger than me, which made the argument even more laughable. I'm the one that's supposed to be the cantankerous, old curmudgeon, not him! Certainly, I get nostalgic regarding certain old artists and classic music. But I just think you might as well send in for the AARP membership form and the Lawrence Welk DVD box set, if you're going to run around saying there are no new artists worth listening to.

Of course, PG wouldn't let me just box his ears without resistance. He started asking me to name new albums that I liked. That's when I realized that I have become way too sidetracked by mash-ups lately. Somehow, I convince myself I'm listening to new music, by listening to two old songs that have been mixed together. To further complicate matters, PG is a strict hip-hop fan, so any veering off that genre causes him to make the ugly grimace face. I shut him up with the new Common album, but I'm turning to the blogosphere for help- any other suggestions in the rap genre?

That reminds me of a random thing that JP divulged to me the other day- in Brazil, they call it hippy hoppy music, yo. I dare you to say that without laughing. I can't do it.

Wednesday, September 07, 2005

I belong anywhere but in between

three crooked hearts swirl

I'm starting to think I need professional help. I can't, as much as I sincerely try, follow a recipe faithfully. I'm a baking ho! I really tried this time, but the dark side lured me in, and even with something as simple as these cookies, I still had to fiddle by adding a dollop of maple syrup in the dough for no discernible reason. I'm also clearly a sucker for a gimmick, like caramel-chocolate chips. Ah well. Oodles, ping me- a portion of these can be on your doorstep by nightfall. Some are going to the ungrateful wretch I call mi hermano. Okay, he's not an ungrateful wretch; he just fell asleep last night when he was supposed to be picking cookies up from my place.

Something has infused me with vigor recently. I think that something might just be having a plan. Now, I have had enough spectacular belly-flops, enough run-ins with brick walls to know that life rarely proceeds according to plan. Still, as I heard a synthesis professor once say, "Homer's Odyssey is more about the journey than the destination. So it is with synthesis." He was Greek and spoke in that measured, gravitas-bearing manner.

In some ways, it is a shame that I need to have a foreseeable destination to really fuel me. If I was really enlightened, I would look at the whole of life as a journey, and find the destination wholly irrelevant. But I'm far more shallow than that. Without the wanting, I'm treading water, directionless.

Someone just walked into my office and quoted Before Sunset. I also just found out I'm being given one of these gratis. Life is not too shabby, and I should probably just STFU and count my blessings for a change.

Tuesday, September 06, 2005

on your hand his golden rings

I went to the Legion of Honor a few weeks back. For the record, I cannot say the name of this museum without immediately picturing a bunch of Superfriends flying out of it. It does not help that the museum perches atop a hill that overlooks the Golden Gate bridge. You can almost picture Wonder Woman's airplane coming in for a landing... well, except that you can't really picture it, since it's invisible.

There was an exhibit on Manuel Neri's work that had prompted the whole visit. Initially, I'd felt cheated. I thought I was going to see an overview of his collected works, and instead, the exhibition was in the tiniest room in the museum. The idea was to explore a specific facet of Neri's work- those instances where Neri collaborated with a writer. It's an interesting concept. Artists are always portrayed as so independent and free-spirited; how do they react when constraints are placed on them?

This reminds me of something I had heard about blogging- that blog writing is like writing without an editor, free-form and rambling. My writing certainly exemplifies this perfectly. Some people have enough of an internal editor to write well without imposed boundaries. But others react better to drawing such lines.

Neri's work made me think that constraints can be a matter of perspective. You could interpret the work he did in books as giving him structure. But what became quickly evident was that something was going on in the interface. He worked extensively with Julia Klimenko, a poet who wrote a book called She said: I tell you it doesn't hurt me. There is some sort of interplay happening between his art and hers. It's as though the energy of one art fueled the other and vice versa.

All of this came to mind when I read an article today on the collaboration between Nick Flynn and Josh Neufeld, and read a particularly heartbreaking comic/poem. I like the notion that everybody could win:
Flynn says of his collaboration with Neufeld, "It would have been almost impossible for me to explain to someone how the poem worked, but in order to create his response to the poem, Josh came to understand how I had put the poem together. That was satisfying for both of us." Flynn‘s reflections concur with Neufeld‘s concluding thought on the collaboration: "I found a more profound way to enter into the poem."
I know I'm in particularly weird (for me) territory right now. But I can't stop questioning why we have to be artists and fans? I mean... why does one person have to have the upper hand in a dynamic? How is that sustainable or even enjoyable? Why can't we, instead, be a poet and a painter?

See, this is where the editor would step in and write in dripping red ink, Wha?!? Don't quit your day job, kid. Indeed. I don't know- perhaps it's as simple as this: the idea of being bound together is far less appealing than the idea of being in a collaboration. The latter lends itself to the possibility of inspiration. Who couldn't use that?

Monday, September 05, 2005

I got my feet on the ground and I don't go to sleep to dream

On Friday night, LS was gracious enough to meet up with me, even though she was flying out the very next day to her wedding in India, people. I can't even meet up with people the night before I fly to places like Seattle for something as stressless as a mind-numbing business meeting. The inner calm she has going on is something that has to be witnessed to be believed. All through dinner, I had to keep reminding myself that she is younger than me. It's something I have going for me, my immaturity. LS also has this inner, nurturing quality that just encourages the dynamic of older sister giving sage advice.

I tried to mix hard labor into my Labor Day weekend, but kept injecting little flights of fancies to distract myself from the many tasks at hand. Like going to the Sausalito Art Festival, or going to Napa, or baking cookies. Still, here I am at work, having just spent four hours plugging away at the things I absolutely abhor and therefore put off until push comes to shove.

Thanks to LS, however, I lost myself in reverie at several points during this weekend. She and a trip through old college journals started me thinking of SN1 and SN2 reactions. These reactions are all about bonds breaking and forming. It's something of a soap opera- the substrate is one partner, the leaving group is the one that's about to get the heave-ho, and the nucleophile completes the love triangle, the new love interest.

SN2 reactions occur in one fell swoop. The substrate stays bonded to the leaving group, until the nucleophile shows up. The substrate stays connected to the leaving group, but it's not that interested. Once the nucleophile shows up, kiss, kiss, bang, bang, and it has displaced the leaving group. The substrate never spends a moment in solitude, stays bound to both the leaving group and the nucleophile weakly until the strong attraction to the nucleophile wins out.

SN1 reactions, on the other hand, proceed in steps. First thing's first. The substrate is just not that into the leaving group, or vice versa. So, even with no nucleophile to catch the substrate's eye, the substrate and leaving group part ways. The substrate is left behind as a cation; but this substrate forms a stable cation. It holds out until the right nucleophile shows up on the scene. Attraction is not the key; it's actually about what will result in the most stable bond. In certain instances, the cation is so stable that it will remain a charged molecule independently, indefinitely.

It's not random why reactions happen one way or another; it's something innate. SN2 reactions happen as they do because the substrate is the type of molecule that is unstable, that can't be sustained without being bonded to something else. SN1 substrates, conversely, are highly branched, complex, and therefore can handle the solo gig. In some cases, they appear simple, but, upon losing their leaving group, are able to rearrange into a branched version of their former selves in order to become stable on their own.

All of this reminds me of a total Excuse me while I kiss this guy blunder of mine from years past. I once thought the Talking Heads were singing "I'm just an atom looking for someone to share the same orbit for a minute or two." Say it with me now- NERD!?!

Friday, September 02, 2005

my cup is half full but his is empty

Remember a long while back when I posted this picture?

Yeah, me neither. That's why I never got around to revealing what it was, or what it was going to grow up to be. It presented itself to me in its entirety about a month ago. And due to early onset Alzheimer's, I forgot to present it here until now:

My friend R likes to call me Freddie Kruger when I happen to wear this sweater. I like to call him jacka$$ when he happens to say that. Can't you feel the lurve?

I did not post these pictures to show you how badly I take photographs, or how pathetically domestic I can be, or how navel-gazing these posts can really be. I think most of you already knew all that. It is the genesis of all of this that came to my mind today. I am not going to get into the details, because it quickly devolves into the maudlin. Sufficed to say, there came a time when I felt a sense of helplessness, profound helplessness. There was nothing that could be done, but I felt like I needed to do something.

I was trained to be an organic chemist. In some ways, I was born to be and always will be an organic chemist. It means I'm ultimately obsessed with making something. The obsession goes deep; it lies not only in the end product, but in the actual act of making, the steps, the process, the getting there. Today, I donated where it was needed. But money feels empty to me. I know that giving should not have such a selfish slant to it; I know that logically. But my senses frazzle at times like this, and the familiar nervous energy surges in me, demanding a task.

The television is some times a panacea for me, what with Tobias in cut-offs, and Jeremy Piven whispering tsetse fly. But in a time of crisis, the television is a weapon of mass depression. Last night, yes, I was struck by the awful devastation of the hurricane. But I was also equally gripped with sorrow at a sudden realization. These words, race and poverty, get bandied about all the time as linchpin to political arguments. The manifestation of those words was plain last night, however. Some of these people were suffering, but were long-suffering. Some of these people were impoverished before the hurricane swept away the last of their belongings. Some of these people needed our help years ago, and we didn't see it. We must have been blind.

Thursday, September 01, 2005

that girl is poison

First, a quick note:
Dear Paul RuddDavid,

After placing so much of my faith in you for all of these years, I am sorely disappointed in you. How could you make such a misstep at such a critical junction? You finally realized that you were down with brown, and I commend you for seeing the light. Still, when that bolt of lightning illuminated your brain, why did your eyes wander to the wrong girl?

Would I have been untrue? Would I have changed my phone number and moved so that you would stop stalking me? Would I have left you heartbroken only to encounter you at speed-dating one fateful afternoon? The answer is a resounding NO on all counts.

Oh Ruddy David, in the illustrious words of those crazy Swedes, honey I'm still free, take a chance on me.

For any of you shaking your head in horror or confusion, please note that you would have to have seen this movie to make sense of this (as an aside, the film sealed its genius for me by using the theme song to The Greatest American Hero perfectly). Then again, even if you have seen it, you still might be horrified and confused. Sorry. I know this is no time for kidding around, but all I can offer to the blogosphere is levity. I think there's enough sadness and angst out there already (understandably so), and I am not going to add to that with whining about nothing justifiable, not this week.

The company that currently pays my bills just announced that it will be donating a large amount of money for Katrina Hurricane relief. The company that used to pay my bills a few years ago has made a similar announcement. In addition, my current employer is matching donations that are made by us little peons as well, which means my dollar stretches a little further. You can turn your nose up at such things and mutter whatever, tax write-off, but I still feel happy to work at places that are responsive to this sort of thing. In the end game, I really do not care if companies get shelters or whatever else in this situation, because ultimately, it translates to people who need money getting it, now. To me, that's meaningful.

Also meaningful: Amardeep's post today on the flooding, featuring a poet I had to study all through elementary school, one of the few saving graces of growing up in EBF.