Thursday, August 30, 2007

Peter Breaks In

Wendy locked the front door from the inside, waving goodnight to her coworkers with half a smile. Mr. Darling had told her there were a lot of bills to take care of and the budget needed balancing; from the looks of the ramshackle filing cabinet in the back room, Wendy had a full night ahead of her. Darling Toys was thriving; it seemed like they couldn't keep the toys on the shelves, but for some reason they were still barely in the black. When Mr. Darling had promoted Wendy to assistant manager last week, he told her that her first job was to find out why.

She pulled one of seven tea bags out of her purse at random - it was apple-cinammon black tea - and took a mug off of the shelf, filling it with steaming water from the coffee machine. She set the tea to steep and turned to the sheet of plywood, balanced on a filing cabinet and a massive old computer, that Mr. Darling called a desk. It was covered in children's toys - dolls and wooden trains, a remote control car, and even one of the heavy-duty, high-quality lightsabers. She cleared the desk, booted up the computer and held her mug of tea up to her face, breathing in the cinnamon-flavored steam and leaning back into the folding chair. She wished that Mr. Darling hadn't been so very... frugal with his purchases for the administrative part of the store. But perhaps there hadn't been much of a choice, if things really were as bad as he claimed.

Mr. Darling founded Darling Toys with his wife, twelve years prior, when they realized that they would not be able to have children. The Darlings loved children, and wanted nothing more than children of their own, but they hadn't even met until Mrs. Darling was thirty-five and past her reproductive prime, and so by the time they were ready to make the commitment to eachother that a child would bring she was forty and simply too old to conceive. Even the adoption agencies turned them down as too old. Mr. and Mrs. Darling fought the decision, sent calm petitions and angry diatribes and everything they could think of to nearly ten agencies, but simply could not get results. And so they sat down one night, and Mr. Darling looked Mrs. Darling in the eyes, and said to her, "My dear, why don't we just start a toy store, and spend all the rest of our lives making children happy?"

And so they took a loan out of the bank - for while having a child is much easier when you are twenty, getting enough money to start a store is much easier when you are fifty - and they rented a space and they began to sell toys to children. Of course they struggled in the beginning, because Mr. Darling had to scale back his psychological practice and Mrs. Darling was only a school teacher, but they squeaked by just barely and slowly grew their inventory and the store until they could move to a bigger location, which they did on the fifth year of the store's history.

And so they came to their present location, a friendly little corner store taking up the basement of a red brick three-flat, and until Wendy came it was just the two of them and their customers. Wendy walked into the store, a bit tentatively, two weeks into her first term at a nearby University and desperate for a job. It being a Saturday, Mrs. Darling was working the register and she took one look at the nervous girl in front of her and knew, instantly, that the girl would be just the right fit for the store. It didn't take long to convince Mr. Darling, and it took even less time to fill out the proper forms and hire Wendy officially. The Darlings came to look at her as a surrogate daughter, and she admired their love. Mr. Darling wasn't sure they would be able to pay her at first, but he and Mrs. Darling went into the back room and calculated expenses and insurance and decided that they could give her nine dollars an hour.

After Wendy, John, a boy who grew up in the neighborhood and was going to the local highschool, was hired (with much the same fuss). John was followed everywhere by his younger brother Michael, but no one really minded except John, because little Mike had too sweet a disposition to be much of a problem to anyone, and besides, he swept up and reshelved the toys for free.

There had been marginal raises and bonuses over the years, and Wendy was now managing to get by, in her third year at the University, working as many hours as she could at Darling Toys.
John was due to leave at the end of the summer, and Michael was already a freshman in highschool. Wendy realized now, of course, now that she was privy to the account book, that Darling Toys had only ever just squeaked by by the very skin of its teeth before, and that it had perhaps not been wise to move into the larger space, or take on any employees at all. But they had made do, and they formed quite the little happy family to the passer-by, and truth be told it was a very good place to work, if Wendy's judgement was to be trusted.

Wendy took a gulp of her tea while the computer finished booting up. It was a relic, a dinosaur, but all Mr. Darling asked it to do was run Microsoft Excel, and so it managed to limp along. Wendy opened the accounting spreadsheet and tapped her fingers against the keys of the keyboard, thinking.

The accounts were a mess, scrambled and unintelligible. Wendy sighed and opened a new file, and then pulled the bills and inventories from the past year out of the filing cabinet, spreading them on the floor. She began to categorize them; into regular expenditures she placed rent, electricity, the phone line, costs for advertising, her salary and John's. The security system she put in a different pile, resolving to investigate if perhaps there wasn't a better system available. She sorted the inventory by company and calculated the rate of return for each toy company, which jumped off the shelves and which they ended up giving away at a loss. She noticed that they lost toys regularly, but not so regularly that anyone would see anything amiss, and not with any pattern. She assumed that it must just be random teenagers or small children stealing on occasion, and was tempted to write it off as simply a regular expense. By the time she was done, she was down to two tea bags. She took a sip of her tea - mango green - and rubbed her eyes and back. Then she turned to the computer and began to set up a new spreadsheet.

There was a soft clatter in the front of the store, just barely enough to hear over her typing, but audible nonetheless. She froze, looked around for something to use in case of an emergency. She wasn't sure if she should call the police or if the security system would automatically do that, but she guessed that the security system would call someone, who would know better than Wendy what to do. Then she heard laughter. It was one person, alone, and with such a charming and innocent laugh that she felt her fear melting a little. She could, perhaps, explore, she decided, and so Wendy grabbed the heavy toy lightsaber from the ground by the desk and made her way to the front of the store. "Who's there?" she called, cautious.

The person fell silent, but she heard another soft clatter as something fell to the floor, and then footsteps moving towards the door. "Stop! Thief!" she shouted, and ran to catch him, but all Wendy saw was a bright green hooded sweatshirt before he was out the door. She turned back to the shop and began to check the shelves. As far as she could tell, nothing expensive was missing, although she would recommend a full inventory the next morning. The only disruption appeared to be pieces from the wooden train set scattered on the floor.

She told Mrs. Darling about what had happened the next morning, and Mrs. Darling told Mr. Darling, and together they reached the consensus that Wendy must have been dreaming. Michael and John helped with the inventory but nothing was missing, and it was impossible for someone to get into the store after it was locked without setting off the alarm system. And so it was settled, and left at that, although there always were the train pieces picking at the back of Mrs. Darling's brain, just unlikely enough to have fallen out of their box that it made her wonder.

In truth, it made her wonder enough that a week later she spent the night at the store, bringing an air matress and sleeping on the floor behind the register. She dreamed that night that someone had opened a store across the street from hers, and that all the children in the area preferred this other shop, and that Darling Toys was going out of business. But somehow, she was calm in her dream until she saw Wendy, John, and Michael peering into the windows of the new Toy Store with awe. She woke with a start to see a face through the window by the door, a boyish round face surrounded by a cotton sweatshirt hood. He looked her straight in the eyes, as if he knew she was there although it was dark in the store so he couldn't possibly, laughed in audibly through the glass, and then walked away.

Wednesday, August 29, 2007

This week's Futures

Is awesome. In part because it's clever and creative, in part because it tells something about humanity and life, and in part because it's based on really really real science. My mom told me about those parking-lot things, and some of the kids in her class have the high-pitched ring tones. She got lucky; even at age 54 she can still hear them, but most teachers can't and her students were shocked when she would go up to them and tell them to give her the ringing cell phone. They would actually say "But you can't hear that!" And she would stare and answer "Yes I can." So it's not very futuristic, I guess, which is what some people like about science fiction - wacky and futuristic - but I think I like this better.

In short, everyone should read it because I really like it. Here it is.

Edit: I think that I have a post about sexuality in mice, and possibly a short (Doctor Who related?!) story about it too (it's going to be awesome) but it bears some more cogitation. *cogitates*

Edit 2: I am victorious over fear. I got blood drawn today. On friday I will know if I have mono or if my immune system is just insane.

Monday, August 27, 2007

Science and Magic!

This is an awesome article. I like most of its ideas.

Saturday, August 25, 2007

My grandmother and the kitchen floor

According to my mom, my maternal grandmother would say that if you can't sleep, you should scrub the kitchen floor. If you feel antsy and anxious and can't do anything about it, at least do something useful and clean the house. As I was scrubbing the floor today with Cake playing loudly in the background, I thought of her, and my mother, and the days I would spend as a kid with my mom and brother cleaning the house. We would always scrub the floor by hand; we only got a mop when we hired cleaning ladies. As a result, I am perhaps more comfortable getting down on my hands and knees and scrubbing than I am weilding a soapy mop.

Which isn't to say that I don't want a mop in the apartment.

Friday, August 24, 2007

False Alarm

Never mind the joy of the last post. I'm still in cloning hell. And playing hooky today to not deal with it. I'm good at that; not dealing with stuff. It just might be one of the few things I am good at. Unfortunately, you can't make a career out of ignoring problems.

Thursday, August 23, 2007

Thursday is still full of meetings

But won't be next week.

This week's meeting was not as awesome and hilarious as last week's, but I did not bring a notepad to take notes, so I cannot blame myself for it. Julie made a big deal out of it being the last meeting for some people, and Steve said, utterly unconvincingly, "I'll really miss you all." When we laughed, Julie said that he really did mean it, to which Steve responded, in the same tone of voice, "Yes, I'll really miss you all." We laughed again. Then Steve said "I'll miss the lunch," which was kind of even funnier.

In personal science news, I *finally* have the construct which I have been working on off and on since December made (it's a long story involving being sent the wrong plasmid, a postdoc not doing what he said he would and us having to change plans three times in the cloning process)! At least, I think so. I am sending it off to be sequenced on Friday morning, and I have one more diagnostic digest to do tonight to verify the previous two semi-positive results. But that is exciting; I might not have to do much more cloning! Hoorays! Because, as Chauncey said at lunch yesterday, cloning sucks.

Wednesday, August 22, 2007

The Scarlet Letter

Richard Dawkins has Atheist tee-shirts for sale. They have bright big, scarlet, As written on the front. I think the comparison is fitting.

Sam Harris in Nature

I quote: "There are bridges and there are gangplanks, and it is the business of journals such as Nature to know the difference."

Here's the article.

His argument is an argument that I have heard before (I think it's his standard argument); that religion - any religion - is out of keeping with science, and as such the battle has to occur. Tolerance on the part of either side will simply end with that side being taken advantage of. Namely, in Sam Harris' case, the atheists have to take a strong view espousing reason at all costs - and particularly at the cost of God - in order not to be abused. To be utterly honest, it is a tempting view especially after seeing atheism blasted in various forums, and being told that I am not a good person or am going to Hell. Of course not all of my religious friends have told me that, and in fact a few of them have told me that they don't believe it, but it is a striking statement that the fact that some of my religious friends have told me that or things like it does not mean that I am not friends with those people anymore.

(P.S. Please don't read this as a plea to have my religious friends tell me I am not a bad person. It isn't. After a lot of deliberation I have decided that I couldn't care less what someone else thinks of my actions. At this point in my life, I can honestly say that I regret none of my actions, and that I do not think I behaved poorly in any major occasion and did not at least try to make up for it. Except that time I shot four men in Vegas. But you know what they say; what happens in Vegas stays in Vegas.)

In any case, the man brings up some good points; basically amounting to the fact that at least in a scientific journal, we don't have to lower ourselves to the kind of politically correct "Of course there are no contradictions between science and religion" that we do in other forums, and that since we do not have to stoop to that sort of, well, lying, we shouldn't. For example: "In his Commentary, Sardar seems to accept, at face value, the claim that Islam constitutes an "intrinsically rational world view". Perhaps there are occasions where public intellectuals must proclaim the teachings of Islam to be perfectly in harmony with scientific naturalism. But let us not do so, just yet, in the world's foremost scientific journal."

I think a nicer way to phrase his point, in general, is that religion never constitutes a rational world view, but that it doesn't even attempt to. It is impossible for religion to be rational because its agents are by their very definition arational or superrational. And perhaps there shouldn't be a value judgement attached to that.

The problem is where to draw the line. If you let someone believe something of which there simply cannot be any evidence or something which is simply a personal opinion (such as the existence of God or when life starts, respectively), you aren't saying that when faced with contrary evidence they should deny it. The existence of God or a Universal soul or merely something cannot really be proved or disproved, and so there is nothing requiring someone to deny reason and evidence simply because they believe in God. So we can say that the belief of God is perfectly in harmony - or could be perfectly in harmony - with the practice of science.

Then you get to things that we simply don't know yet. They are potentially knowable, but we don't know them. I'd put things like the physical cause of "the soul" (will and consciousness), here. There are a lot of people trying to figure it out, and it's possible that in the future some religious belief will be contradicted by evidence and reason. But at the present time, we don't know - all anyone has right now is a belief or a hunch or a gut feeling. In this case, perhaps, most people who lean towards atheism lean towards one answer and most people who lean towards religion lean towards another. But that's all there is - a lean - there isn't a clean line and there isn't a clean disharmony between the two views, at least in principle.

Of course, there are quite a few things that we do know, and that are hard to contest using reason and evidence, but are still contested issues simply because religious people make them so. For example, evolution. We've seen evolution take place in petri dishes (see here) and the paleontological and genetic evidence of relation between humans and other primates is huge, but there are still crackpots and religious nutters saying that all of that means nothing, because of a passage in the Bible or the Koran or whatever that says God created man in his image, period, end of story. Or who are masquerading as scientists saying that life is "too complex" to have developed through a process of natural selection (something which is, it seems to me, complete bullshit). This one, in my opinion, comes down pretty clearly to religion versus science. Either you believe what is written in the Bible or you believe in what we have learned and theorized and figured out. You can't believe both. Here, religion and science are directly at odds. There are religious people who believe in Darwin's theory of Evolution through Natural Selection, but they are choosing which parts of their religion to believe. And that's a slippery slope, because if you only believe some parts of the Bible literally, then why should you believe any of it? If you don't believe the Bible when it tells you that the ratio between a circle's circumference and its diameter is 3, why do you believe the Bible when it tells you that homosexuality is a sin, and why do you believe the Bible when it tells you that Man was Created in God's image?

But the point is that it's a continuum. There are plenty of things that the scientific community isn't quite certian of and religious views push you one way or another on. There are all sorts of intermediates. And you have to draw a line somewhere, except there's absolutely no clear place to do it. And so 44% of Americans say they judge atheists harshly, and people like Sam Harris say that the "forces of unreason" are attacking science, and we have to fight back or we will be defeated.

To prove that I am not that sad

Article: Peace in the Middle East through surfing

But of course it doesn't do that much immediately. Which is unfortunate but not surprising. It brings to mind a few things; how much someone can do and how little it can matter. How a common activity brings people who hate eachother together and builds unity. And how the zen state you acquire when you're concentrating fully on your body and not on anything else -- a state that is easiest to acquire through athleticism in my opinion -- can wash away anger and hatred and frustration. But not for very long.

Also, the fact that now that Hamas is a governmental organization, the rest of the world has to start treating it as such or cease helping the people of Gaza. It's sort of like the Cuba problem (although arguably much more severe). The United States' boycott against Cuba was meant to destabilize Castro, but instead it simply hurt the Cuban economy and through that the people. It didn't shorten Castro's reign at all - it is very likely that he will officially be president until he dies of natural causes, although his duties will be (and are) carried out by his healthier brother Raul. I don't know how accurate the parallel between Hamas and Castro's communism is, I'll have to think about that some more.

It would be interesting to ask that surfer again and see how much he likes Hamas now. I don't think that he has much reason to change his mind, though. I also think that one critical step in acheiving peace in the middle east is for Isreal and the West to convince Palestinians that they should not feel threatened. I think that in large groups people act with gut instinct, in a sort of animal response, rather than with logical, calm reasoning. And hence, since Palestine as a state is probably threatened, Palestinians feel threatened and violence ensues - just like a bee will sting if it is scared, or a dog (no matter how well domesticated) bite.

And so maybe things like this - uniting specific people with specific other people through common interests, charity, and friendship - is the most that anyone can do to help the situation. Perhaps in some ways that has more of an effect than any official state action, because it gets people to look eachother in the face and say "Well, I hate their leader, but I don't hate that person." And in my mind it isn't far from "I don't hate that person" to "I don't hate that kind of person" and from there to "If I take this action against that institution, it will hurt that kind of person, and I don't want to do that."

And once you're there you can start talking about peace.

Tuesday, August 21, 2007

A la recherche du temps perdu

Someone once said that of all the senses, smell was the most entwined with memory. I think it was Proust, but that might just be an image of madelaines and sadness. A la recherche du temps perdu. I smell like chlorine now, and it's bringing back all sorts of memories, good and bad, all of them lost now and covered in a fine layer of dust. I have been avoiding them, but the smell brings them back, whether I would or no.

It's that smell, and the feeling of the tight, disinfected and dried skin on my face, the feathery quality my hair takes on, and the rubbery tinge to my legs as they get used to walking on land again instead of kicking against water. That and the electric buzz of cicadas that forever will remind me of summer, and being at Glenwood, and belonging; what is summer without cicadas?

I went to Ratner today. I swam because they would not let me dive. I wanted to dive. I can't tell if that's a good thing or a bad thing, if it is prudent or foolhardy for me to step on a board again; whether it will give me comfort and pride, or sorrow and longing, whether it will lead to increased confidence or another injury. I can't tell. I don't know what the future holds, but I want to try it, and the ache in my legs and my stomach when I see a diving board and forbid myself from standing on it, feeling it move beneath my feet (because it's such a tactile sport, such a rhythmic sport), and then launching myself off of it into the air, well, I can't take it anymore. I want to be younger, I want to be freer, I want to fly.

I always have.

It's a peculiar feeling to float. Relaxation is key -- for whatever reason, a clenched muscle sinks to the bottom of the pool but a relaxed muscle responds and stays afloat. You start out level, and then slowly your hands and feet sink down, pulling your arms and legs with them and your torso. Your chest pauses at the surface before sinking too, and then all that is left is your head. If you kick, your feet stay above water and you can stay floating by slowly, gently kicking your feet so that they don't sink. Some people float better than others. I do not float as well as my mother.

The water gets in your ears, plugs them up so you hear the gentle rush of water leaving the pool by the drains and being replaced at the vents, the tinkle of your feet and hands splashing as they enter the water, and nothing else. If you close your eyes and float, it is perhaps like being in utero again; except colder, and when your face starts sinking less receptive to life.

If you sit at the bottom of a pool and look up, you feel like you are at the bottom of a bowl; the index of refraction is high enough that the light bends around you and the walls look like they swoop up. Apparently the atmosphere in Venus does that too. So walking on Venus would be like walking on the bottom of a pool, but much hotter and more sulfuric (I think?).

Since your vocal chords are open to air and not water, you cannot be heard if you shout underwater unless you shout very loudly. Instead, you make vague noises and expell bubbles through your mouth; it looks like the words escape in the bubbles and if someone was to sit up above you and put their ear to the bubble, they would hear what you were saying. I don't think it works that way in real life. But it would be awesome.

The floor in the Ratner locker room is made up of many small-to-medium sized white tiles arranged in a grid with dark brown mortar between them. The shower curtains fold and sway on them in some complex curve. I don't think I could model it, but I'm sure that you could write a series of sinusoidal functions whose sum was the path of the shower curtain on the tile grid. I only know this because any curve can be expressed that way.

Today I stared at the floor of the showers and thought; this is the shower I warmed up in after the accident. These are the tiles that I couldn't focus on then. The thought made it hard to focus today. Several times today tears came to my eyes, but they mixed with the chlorine and the water and neutralized themselves as they ran down my face or I submerged myself to keep from making a scene.

People don't appreciate pools. They go to pools and swim laps, and think about their days or their bills or work or their families. They don't empty their mind and stare up at the perfectly white rafters and think; how does one clean rafters so high up? For surely they must be cleaned every now and again, just like everything else in this world. They don't find all the little dots in the windows that block some of the light. They don't match those dots to the dots in the ceiling. They don't see the curve of the roof or the lines of the bleachers. They only see the black cross on the wall that marks where they should do their flip turn. They don't listen to the vents and the drains, to the splish-splash of their own strokes. I know this because when I was a swimmer, I didn't think about any of that; except perhaps occasionally about the shape of a cloud as I did backstroke -- I told myself that one day there would be a message in those clouds, and I would decipher it and it would mean I was special. I sang songs in my head, I counted strokes, I counted lengths, I futzed with my goggles and my cap.

But a swimming pool is a thing of beauty -- water just deep enough to being to turn blue of its own accord, smooth white tiled walls and floor, or rough concrete instead. In a swimming pool, you can escape into your own bubble and not notice someone until the wake of their strokes disturbs your own. You don't have to hear, or see, or feel or smell or taste anything other than the cool clear water that surrounds you, and you have no choice but to hear and see and smell and taste and feel it, immediately upon entrance and constantly thereafter. Perhaps the only exception is sight, but the sting of chlorine in my eyes is enough to convince me to close them usually unless I am wearing goggles - and goggles are such a sign of the quotidien, of the lap-swimmer, that I usually avoid wearing either of my two pairs.

I went to the swimming pool today, and sunk to the bottom to let myself think for a while. There, in the cool and clean and quiet water, everything was calm, and I couldn't afford not to be. I came of age in a swimming pool; I grew from a small child into an adult in a swimming pool, and like a mother's womb when I was finally ready for something else, I was rudely shoved away from its waters. I tried to return today. But it didn't feel the same. It wasn't home, it wasn't comfort. All that is left are memories. And I think I was the last person to figure that out.

Monday, August 20, 2007

My non-science post

I was going to post about not-science. It was going to be novel. However, I started writing the post and then I started reading the post and it was rambly and discontinuous and not well argued or thought out. So I'm putting it on the back-burner, and maybe I'll post it when I've thought about that stuff some more. But I'm pretty pre-occupied with my biology stuff now, so maybe I'll just keep talking about that.

So. This New York Times article is neither exciting nor news, but it is interesting. Better than this New York Times article which is just plain silly (and which we discussed last night over pizza and beer, hah).

Article #1: Americans have to drastically rethink two things: the label "Dumb Jock" and the idea that your brain stops developing at an early age. It turns out that in mice and in humans, excersize stimulates the hippocampus and prompts the development and maturation of new neurons. Aerobic excersize is better than stretching in the elderly. So take a jog, and you'll be able to do that problem set better!

Other things that supposedly increase bloodflow to the hippocampus and prompt the regeneration of neurons are: moderate alcohol use (although too much and you're hurting your brain), marijuana, a social life, and chocolate. Things that hurt your brain are stress and fast food.

Article #2: If you accept the "reasonable" hypothesis that some civilization reaches a point when they can create computers capable of modelling thousands of brains, then it is likely we are all simulated. There are several problems with this idea, and more problems with it being in the science section of the New York Times. Really, it is dubious that the assumption that thousands (or really millions) of brains will ever be able to be well modelled in a computer simulation. Especially not well enough to lead to the complexity and diversity we see in nature. At the moment, we have trouble modelling three electrons on the largest supercomputers. AI is incredibly basic and does not come anywhere near an actual sentience or even a facsimile of sentience. We can program supercomputers to play chess and solve checkers, but in the end we cannot make a computer that can have a normal conversation. Imagine not just the processing power but the skill in computer science necessary to overcome that barrier and model not just one being, but millions.

It's funny that one of the explanations given as to why this was a reasonable assumption to make began with the phrase "assuming a planet-sized computer" which is another assumption that I hope is self-evidently absurd. People can imagine planet-sized computers, but imagine trying to build one. And that ignores all the problems of finding a place to put such a computer where it would stably remain and be easily accessable but wouldn't interfere with life on earth. Basically, to do that it seems we would need faster-than-light-speed data transfer, unless it wasn't really a planet-sized computer but rather a moon-sized computer, and even then it would be incredibly unweildy to make and position and so on. Again, not only do we not have the technology, but we are nowhere close to having the technology.

We really will need to reach the technological singularity before any of this will happen. And given that the human race has a maximum of 7.8 million more years to live, and 1794 more years to travel in space, (taken from this, another nice pseudo-scientific article by the same dude) well, we'd better hop to.

This is all ignoring the fact that, well, presuming that some society did make it to a point where they could model the world, they wouldn't have come to similar conclusions as ourselves and realized that modelling sentient beings is, well, kind of sadistic. And if the question comes down to "Are we sentient or do we just think we're sentient?" well, then I ask you why you are asking such a silly question. Because in the end that is a bit meaningless.

Besides, the only conclusion you can really come to from the idea that maybe we're all just simulated in a computer is the fact that, okay, maybe we're all just simulated in a computer, but that doesn't have any repercussion on my every day life, what's right or wrong or in between, and so forth.

Friday, August 17, 2007

Rather than supporting Ethanol powered cars...

Why don't you just plant a tree? You will probably do more good for the environment. (See Science news article here.)

Basically, forestation of a piece of land X will sequester (take out of the atmosphere) 2 to 9 times the amount of carbon dioxide that we avoid producing by using that piece of land for production of corn, sugar cane, and other ethanol-producing crops, using a variety of estimates. Plus forestation helps with loads of other things, like not driving animals to extinction by taking away their habitats, keeping soil fertile, and apparently even stabilization of regional weather patterns. Which implies that to best fight global warming (and all sorts of problems that we cause in the environment), we should convert the farmland that is not being used for food into forested land rather than farmland being used for ethanol production (of course, there are even more complicated elements here because adult forests take a very long time to grow; plant succession and all of that). BUT! The point is, supporting industries like solar/wind powered electricity to reduce carbon emissions and planting more trees will (in the long term certainly and the short-term probably) do more good for the environment than supporting research into plant-based substitutes for gasoline and diesel fuel.

In conclusion; what you were taught in elementary school was right at base -- if you want to help mother nature, plant a tree. Or, if you can, plant a forest.


I just signed up for the GRE general test. It was pretty terrifying.

But what is more terrifying is that it won't let me sign up for the GRE Biology online. Wah!

Thursday, August 16, 2007

Thursday is full of Meetings

PCBio for lunch and NSF for dinner. Which means I am up two free meals today. Which is pretty awesome. And they were fun, funny meetings too. Which is even more awesome. BUT since I had lunch and dinner at meetings, I am at work after dinner, which is less awesome. But it won't be too late, so that's more awesome again.

PCBio was full of projects I have trouble really getting into on their own merits: Computer modelling of protein folding, mapping energy surfaces for small molecules found mainly in the troposphere, and determining conditions for crystallizing proteins. So two out of three were certainly bio related, but in the very chemical-biology or computational-biology sense. But that's okay. Because the presenters were really good and got you to see the merits and excitement behind their projects, and Steve was in a great mood, actually, so it was absolutely hilarious.

I should really start taking notes, because there were a lot of absolutely hilarious things going on. But here are the few I remember, in the order I remember them and not the order they took place.

To the physical chemist (EmJ) who proclaimed, somewhat guiltily, "This project has zero relevance to biology, so I am not going to try to give it any," Steve responds: "That's a challenge."

Later in the same presentation, EmJ mentioned coal. Steve: "Where does coal come from?" It was followed by awkward silence, because everyone knew where it was going but no one really wanted it to go there. Finally someone responds that it's compressed oil, and Steve says that oil comes from compressed plants, and it's all well and good. He asks where the Sulfur in EmJ's molecule comes from, and got Methionine and Cystiene. "That's your biological relevance," Steve said. "The true meaning of plants, which is to eventually make fuel for our cars."

Later on in the same presentation, EmJ confides that her molecule is incredibly reactive, reacting even with the teflon that she used to coat her reaction vessels. She's going to try glass next. Maybe that will work better. Steve makes her flip back to an earlier slide which has a picture of her molecule on it, and asked why that molecule would react with teflon. There were a few people who answered seriously; Sulfur is particularly unstable with four bonds, etcetera, but the best answer is that MeOSOCl is "Smokin' hot." For the rest of the day, everything was "Smokin' hot." In fact, Julie decided that it was her new word. So "Smokin' hot" is "Smokin' hot."

Steve brought up the interesting idea that protein crystal structures do not, in fact, show a very accurate picture of that protein in action. In fact, NMR structures often have many equally valid solutions -- many different possible structures for one protein. Which is an interesting way to look at it; if a protein has multiple conformations that are valid, and in fact equivalent in terms of energies of atoms and the other things measured by NMR, a crystal will exclude those structures which are different -- thereby giving you a static picture of something which is actually dynamic. I'm sure that's not an actually particularly new opinion, but it is interesting nonetheless. There was a very funny dynamic when for about a minute or so Steve kept interrupting Alexander (the presenter for that bit) about random things and making witty remarks. I cannot replicate that exchange, but it was priceless.

I know there are other things, but I cannot remember them all today. Maybe next week I'll take notes. But if I bring things with which to take notes, it won't be as funny, I'm sure.

Oh well.

Wednesday, August 15, 2007


I have just returned from Alaska! I saw Orcas and Dolphins and Seals and Otters and Eagles (lots of Eagles) and a Porcupine. It was tons of fun. I think we got the only 5 days of sunny weather all year, which was awesome. I could post a long story all about everything that I did in Alaska, but I think that in the end that would be boring and repetitive. You should instead ask me. I will tell you all about whatever parts I remember at the time. But Alaska was awesome, although not as much fun as Cuba. (It would be hard to be as much fun as Cuba without involving Swaney, seven of my best friends, and the whiff of fear whenever Costello would shout "DONDE ESTA FIDEL?".) In any case, I definitely recommend it, especially in August when it is miserable anywhere else.

Thursday, August 02, 2007


Is a segment in Nature where they publish a short science fiction story each week. They select them for a wided variety of reasons, obviously, but I would hope that not least among these is realism or something like that. A nice balance between realistic science and creativity. These are scientists who are going to be reading it, after all.

In any case, I read it every week because it's a cool idea, and most weeks I really like what I read. I went through the archives a bit ago and found this amazing story. Creepy and awesome at once. I really love it. In the new issues of them, this and this are my favorites. Enough wacky to keep you wondering and for it not to seem too mundane, and enough normal for my scientist part not to rebel. (Of course the first is very Matrix, and the second very... There's a word for it but I can't place it).

In any case, this week's futures story is about genetic engineering -- sort of. And I don't like it. The idea that we could mistakenly turn a person into a fish rather than simply cause a miscarriage is, to put it bluntly, patently unbelievable from a biological standpoint. I do not believe that we will be able to turn people into fish until we really want to and really know what we are doing.

In other words, merpeople are still a long ways off for genetic engineering. And that's the problem -- the practical procedures that are cited in the story (replacing all the junk DNA with markers) haven't been developed in the slightest, while the key idea that the scientists came to too late (junk DNA isn't junk at all) has already been reached. It would perhaps work in an Alternate Universe where we are very slow to pick up on all the various signals and miRNAs and so forth that are in "junk" DNA, but since the segment is called "Futures", well, I always took it as "This is a potentially plausible future if we're really cool."

Which is something that has always frustrated me about science fiction in general. Science fiction writers are not, by and large, scientists really. (For example, the guy who wrote "Junk".) The writers who are scientists are, in my opinion, better writers because they actually take the time to research the science, even if they are writing outside of their area of expertise. There is little more frustrating to me than "serious" science fiction that disregards scientific discoveries that are easy to find online or in a text book.

If you want to write fiction, great, wonderful, awesome. If you want to write weird and wacky speculative fiction, great, wonderful, awesome. If you want to write science fiction, you have to remember that half of that name is science. So maybe you should take out a subscription to Nature or Science or at least regularly read the NY Times science section. If you aren't at least vaguely interested in science (not doing it, but reading about it and thinking about it and wondering about it), why are you interested in writing science fiction?


It's a little bit like grammar and poetry. Poets who break the rules of grammar are rampant and cool. But poets who don't know the rules of grammar are lame posers. You have to know the paradigm in order to break it in meaningful ways.