Thursday, June 28, 2007

From Nature Genetics

The dangers of allowing geneticists to write poetry.


Sporadic Traits

SNP, SNP, SNP, so passé
CNVs are here to stay
One FISH three FISH red FISH green FISH
Inversions too, if you wish
Mechanisms? Don't know how
But arrays in clinics here and now
Is recombination what we're after?
Base-pair changes are not always the answer!

J.R. Lupski and M.E. Hurles
(Inspired by Dr. Seuss)"

Liberal Education

Duff points out this article, as being thoughtful and a good critique of the liberal arts education. Basic idea: large class sizes, instructor-centric education, and etcetera contribute to the percieved shortcomings of modern-day students as much as television, consumerism, and other problems do.

It puts me in mind of the core cirriculum here, which is supposed to be small discussion-based seminar classes. Even in my Hum and Sosc classes, I felt like actually thinking about the text in more than a superficial way and disagreeing with the professor was scorned and I often felt ostracized when I disagreed (my opinions on Aristotle and Freud were positive, gasp!). I still did - and I still will, because I think it's important, and because I have been having such conversations with my parents since I can remember. But it is often difficult, I think, for students who are taught throughout high school that the proper way to 'learn' is simply to listen and repeat what a teacher says to suddenly think for themselves and disagree when a professor says something that is, at base, opinion and not fact, or offers a biased view of the material. It is also hard for a professor to see the scorn shown towards other students when they are given almost too much respect and deference to their view.

For whatever reason, and my feeling of ostracism certainly played a part, I didn't really make friends in my core classes. (This is a second part of the author's argument -- that a more collegiate tone in classrooms would yeild more social interactions between students outside of the classroom.) There are a few people from my Hum and Sosc classes that I say hello to, and one person who I wasn't friends with in my Civ class that I almost was by the end of two quarters, but nonetheless I haven't really made friends through classes - with one notable exception, being PCBio.

Of course, PCBio isn't really a class, it's a weekly discussion session about research projects that goes basically all year. Usually Steve Kron is there trying to poke holes in our projects, find the chinks in our armour, and generally needle us into developing thick skins and vast repertoires of knowledge suitable for PhD committees, post-graduate seminars, and generally analysing data and making scientific arguments. But in addition to needling us to answer questions thoughtfully and put the best face possible on our presentations, his most common complaint is that we don't participate enough, that we don't ask enough questions, and that we let things slide that simply should not be allowed to slide. In the past, I have felt a little bit critical of his techniques for a few reasons; first, I think that his caustic approach scares away as many people as not (although it is possible and in fact probable that he could argue that the sort of person who would be scared away by the rough edges is not dedicated to the research and should not be in the program). Second, it seemed that the students didn't really want to ask questions; that they would ask questions when ordered to but that wasn't really indicative of a relationship with the subject matter.

However, Steve was absent from the PCBio meeting today (and for the second half of it, so was Harinder, so all of our tough-question asking faculty members were gone). And I was happily surprised by the level of participation. We stepped up, we asked questions, and we were talking about research until almost 2 pm (2 hours in total). One of the students from last year came back (although it is entirely possible that he is just weird). The discussion was really good, and we facilitated it almost without faculty assistance. It was the sort of discussion that the author on top appears to desire for his classes.

And the thing is, I'm closer to the PCBio kids than I am to kids in any of my other classes. I actually feel a connection to them, I actually feel a camraderie that means that when they ask me a question about my research or suggest things I don't take it as scorn, criticism, or one-up-manship. I take it as it is meant - an honest question or suggestion reflecting an interest in the research I am doing. The people from my physics class, from my biochem class, and so on that I want to invite to social gatherings, have coffee with and chat with outside of class are mostly PCBio kids.

I think there should be a way to foster camraderie and interest without the caustic, demanding, rough-hewn exterior that Steve often portrays and that I have seen put people off. However, in middle and high school my friendships were often forged through the difficulties in responding to a particularly demanding teacher - and maybe that has something to do with it. In middle school, we had a famously demanding teacher in the seventh grade (she taught every class of algebra and every class of IM 7, so every child in my program had to have a class from her). My class formed a cohort that stuck together throughout high school -- even the people who I was not friends with per se were people whose name I knew and whose general likes and dislikes I knew. There was almost no one who I would have been totally baffled to pick out in a class-wide Secret Santa.

My brother's year, the demanding teacher had left, and his class disintegrated. Whereas the majority (on one count, almost 80% I believe) of students in my class continued on to the magnet high school, less than half of his class carried over -- and he was among those who chose to go to a different high school. Of course, that wasn't a controlled experiment and there are many confounding variables involving the personalities of the people in the classes and so on, but similar things happened in high school. My friends were made, predominantly, in classes that were overtly challenging, classes that forced you to ask for help, and classes that I now look back on as particularly demanding and rigorous. I hated some of my classmates in Physics class, but when I had some of the same people in a Shop for Engineering class with a particularly demanding teacher, I recognized them for something more than obnoxious loudmouths.

Which brings me to I guess the one thing that I would add to the author's suggestions on how to rebuild the classroom and foster conversation and social interactions. The course has to be intensely rigourous and demanding. The professor has to be able to tell a kid, outright, that the kid is 100% wrong. He has to be able to discard his use of kid gloves and treat the student as an adult. However, the student can't take it too harshly when they are called out -- when Steve criticizes my research, I want to prove him wrong and show him that I can overcome the barriers he says are insurmountable, not go into a corner and bemoan the awful fate -- that my experiments won't work and my professor doesn't like me.

Which brings it to the front: It can't be about whether you like a person or not, it has to become about whether you respect a person or not. Classes today, I find, are all too often phrased in likes and dislikes - a student likes Plato but dislikes Aristotle, women don't like Freud.

But we can all agree that all of the three were great thinkers, even as we pick apart their arguments looking for faults. We can all respect them with that peculiar sort of academic respect that requires criticism.

Wednesday, June 27, 2007

Monkeys Guessing?

The New York Times yesterday ran a bunch of articles about molecular biology, evolution, and evo-devo. All of which are awesome subjects and you should read about. One of them in particular was interesting, because it was about the idea of the soul and its place in biology/science. That article can be found here. The point of the article in the New York Times is basically two-fold, and obvious.

First off, the idea of the soul isn't biological in nature and therefore the question isn't a scientific one to begin with -- if you want to believe that humans have souls, you will, regardless of any scientific fact or lack thereof. And if you don't want to believe in the soul, you won't, regardless of any scientific fact or lack thereof. Pretty much every scientist in the article says this, which is perfectly logical and somewhat obvious.

The second idea, however, is the one that interests me. It is based on the presumption (which may be a rather large one, and I would have no idea since I am so very much not an expert on religion or the idea of the soul) that the soul and the capacity for complex thought and reason are the same thing. Or rather, that while the soul itself is by nature a religious/spiritual thing and cannot be guaged by science, conciousness or the capacity to reason is not, and perhaps a physical manifestation thereof can be found. Hence, conciousness is science's soul - the closest thing to a soul that can be guaged scientifically.

The interesting thing is that neurologists and their ilk are increasingly able to isolate the physical manifestations of things like conciousness, aesthetics, sensory perception, and the like. (For a GREAT review of this with a wry wit and a thoroughly readable voice, I recommend V.S. Ramachandran -- who is unfortunately not the same Ramachandran of Ramachandran plot fame.) AND other mammals, like mice, and other vertebrates, like fish and birds, seem to have similar or analogous structures in their brains.

An example is an article in Nature this week. (Here it is for those of you who can get it because you have access to a university's subscription or something like that. If you would like me to e-mail you the pdf, feel free to send me an e-mail.)

Some background: (Ramachandran covers this very briefly in one of his books). The Lateral Intraparietal area (LIP) appears to accumulate visual cues to make a decision in humans. These decisions are often probabilistic -- i.e. there is no specific predetermined right or wrong answer, but merely a bias toward reward with one specific outcome. These people trained monkeys to be able to make such a probabilistic choice. They would see four shapes on a screen and then look towards a red dot or a green dot. Depending on which dot the monkeys looked at, they would be rewarded, and the correct dot was determined in a probabilistic manner based on the shapes that were shown. (Each of the 10 shapes had a weight, changing the probability by -infinity, -.9, -.7, -.5, -.3, .3, .5, .7, .9, and infinity respectively).

The researchers saw a few interesting things: first, the monkeys were trainable but different monkeys picked up the patterns to greater or lesser extents. Second, the choice the monkeys made appeared to be strongly related to the activity in the LIP when the choice was made. Finally, the activity in the LIP was proportional (roughly) to a log likelihood ratio that the red dot was correct based on the shapes shown.

The big selling point, for me, is that these monkeys were guessing. What's more, they weren't guessing at random, but rather they were figuring out a pattern and guessing in an educated way. They seem to have been using logic to make an educated guess. That's a very human action, not an instinctual action. I've had arguments before about will vs. instinct, and what the difference is. I guess what I would say is that because of neurobiological studies like this one, I am increasingly coming to the opinion that there isn't a difference between will and instinct, and that the only thing that necessarily separates us from other animals is a written language (and possibly a spoken one as well, but complexity in dolphin 'names', and some monkeys as well makes me doubtful of that). Mice laugh, monkeys lie, and dolphins have names. At the risk of being a little bit too "Doctor Doolittle", maybe the only thing that is keeping us from realizing that animals "have souls" - have conciousness and will - is that we can't communicate in their language.

Tuesday, June 26, 2007

Harry Potter and the End of Harry Potter

We have internet in the apartment now, but I am waiting for a digest to go to completion at work so I don't have much better to do than read online newspapers. (only 15 more minutes!)

Such as this article. Which I love, especially the last sentence; that this has probably been the most fun an intelligent person can have with clothes on in the 21st century. Partly because it's goofily true and partly because all the caveats are absolutely wonderful and make it better. As in, well, there might have been more fun things to do in the past, and there might be in the future, but in the 21st, it's Harry Potter. So far at least. And people who aren't clever and don't like discussions and analysing texts might find this fun, but we do. Of course, I think there are more exiciting things going on than Harry Potter, but more fun (in the sense of good, clean, fun)? Probably not.

Also, I am tempted to write down all of my theories so that I can consult back and see which ones are fulfilled and which ones I got wrong. But then again, maybe that's beside the point. People who have talked to me about it know what I think is going to happen, at least in general terms (and the more generally I couch my statements, the more likely they are to be true!).

Besides, I'm not as big a fan as I used to be - or I'm a calmer fan than I used to be, it's hard to tell - I haven't frequented fictionalley or mugglenet or the leaky cauldron for so very long. Part of me is proud of it. Growing up. Or something like that.

The one thing I'm certain of is that I won't want it to be the ending, however she ends it, and I will go through a process of denial -- it isn't really over, there are still so many stories to tell! -- until I just come to terms with the fact that she's moved on to bigger and better things. Which is all as it should be, I think.

And as much as I want to order online from Amazon and get sleep the morning of the 21st, well, it's the last book, and so there are certain things (like standing in a line to get my copy at 12:01 am) that simply must be done. To honor the fandom and my former place in it. Or just the fun that it is no doubt going to be. Because it will be fun. And once I have finished reading book 7, I'll probably check all the others out from a library and re-read those. Or rather, once I have finished reading book 7, and Day Watch, and the collection of short stories by Marquez on my desk, and probably a couple other books as well.

Because that's just how it goes.

And my samples are almost ready! So, I go!

Thursday, June 21, 2007

If I listened to podcasts

I would listen to Nature's podcasts. Just because I think it is funny they have them. It's probably an awful lot like Science Friday, I imagine. Just a little bit more specific.

Wednesday, June 20, 2007

My life is boring

Or at least not blog-worthy.

Sleep, work, dinner, sleep. That's pretty much a summary.

The culprit, it turns out, which was spoiling all my experiments, was bad BSA. Curses! At least it has to be, because it wasn't bad DNA, contaminated water, bad buffer, or bad enzyme. There are only so many variables in such things.

Or maybe God just doesn't like my experiments. That could be. I should pray for my PCR to work. Although I feel like if I prayed, I would want to pray for something a little bit less selfish and a little bit more important than my PCR working. I mean, I should be able to get that under control with a little bit of ingenuity and methodical work. God should be paying attention to bigger things, harder things, like stopping genocide or curing Alzheimer's. Or even making Kristy and Tamar's kids feel better. You know. The important stuff. If He's going to pay attention to a PCR, it had better be a PCR that could cure cancer or AIDS or something.

That was random.

Friday, June 15, 2007

I was at work today until 7:30 PM.

I am, in fact, just now leaving.

The Graduate student in my lab called me a nerd.

I responded that if it had taken him this long to figure that out, he was pretty damn slow on the uptake.

Also, my experiments worked! Hooray! This means I will have much more work to do next week! Also Hooray!

My Acro adventures, however, have been sadly delayed on account of the fact that it takes me significantly more than 5 minutes to get from here to there; and when I left work I had approximately 5 minutes until I would be 5 minutes late.

Perhaps next week. Perhaps next week I will borrow a car? That would be novel; and would involve approximately 1/4 of the time and significantly less sketchy train and bus rides through/into blue-light neighborhoods.

Thursday, June 14, 2007

Words of Wisdom

I saw Harinder on my way into work this morning, so we chatted for a bit. He said that he had seen a batman bumper sticker on a chevy, and it made him think about batman versus superman. The end-point of his reverie: Batman is a "normal" human who uses technology, while Superman just has super powers. I pointed out that Batman's ninja skills are certainly exceptional, and can be considered barely human, and also that Superman's fortress of solitude was made using alien technology and not super powers (at least as the latest movie would have it). Harinder just shook his head, and said that even so, the general trend holds.

The moral of the story: Old geeks never get less geeky.

Tuesday, June 05, 2007

I know Chimpanzees have wars,

But do they have genocides? Are they capable of that level of cruelty, or is that a particularly human thing? And if it's human, what has our intellect given us that hasn't been more than made up for with our peculiar brand of evil?

Perhaps Rousseau was right - our society, the very things that make us human, is only a breeding ground for inequality, brutality, and evil. We'd all be better off if we lived like gorillas. Or something.

Dolphins are the only other animals that have recreational sex. I think they "murder" and "rape" too. (Or at least there's stuff like it? How would you know if a dolphin raped another dolphin? I guess you can tell if one of them is trying to swim away and fails. It seems like it would be so rare that it would be hard to catch in the act. And it also seems like you would need to. It's not like you can talk to dolphins and ask them if they had ever been raped.) Do they have serial killers? Despots? Is our desire for recreational sex at the bottom of our cruelty and violence, and not perhaps our conciousness? We have libido to repress, and it comes out in violence. Whereas other animals do not have to repress their libido, so they can live in peace. That'd be... weird. Almost biblical in the twisted sort of way that my mind works.

According to Elie Wiesel, evil is a particularly human thing. Animals aren't evil, people are. Which brings it back to what started this, which is Hitler, and genocide, and what it says about our existence, our species, that we can create something like that.

On a happier note, the Hiesenberg Uncertainty Principle is awesome for the following two reasons:

1) It states that you need to take a finite time to get an accurate measurement of energy -- that you cannot know to an arbitrary accuracy the instantaneous Energy of a particle. Hence, you can have a violation of the laws of conservation of energy so long as it only lasts a very short while. I imagine this is like God keeping an eye on some meddling kids and looking over his shoulder to make sure they aren't messing with the laws of the universe - shouting "Hey! Quit playing with conservation of energy! That's important!" The kids can get away with it if they are fast enough. (On a side note, I TOTALLY want to be one of those kids when I grow up).

2) It applies to macroscopic objects like cars and people too. So the next time you are pulled over, you can definitely say that the police officer couldn't write you a ticket because if he knew exactly how fast you were going he couldn't have known where you were. (Except for the fact that the uncertainties intrinsic in our devices more than cover the necessary uncertainty, so... except for the fact that that would be totally false.) It would be a great way to get arrested for being flip to a police officer. You should try it!

The preceding has been Elizabeth after too much studying.

Impossible, you say?

I have condensed notes from an entire quarter of biochemistry onto one page. The writing is itsy-bitsy. Hopefully it will actually be useful for the exam.

Hah. That's a funny idea.

Friday, June 01, 2007

Mirror, Part 2

The wolves were howling. Not their normal cries of salutation, signal, hunt. Something more, this time. The forest was noisy tonight, and Joseph wanted nothing more than to get home. His stores of food, and tea, were dangerously low, and as he lived alone there was no one else to go to town. He had set the clockwork butler to guard the door and not let anyone in, and he had only been gone for a day, but returning at dusk with a heavy satchel on his back and the wolves howling noisily behind him, he could sense that something was wrong. He should get an assistant, someone to guard the homestead while he was gone – or to run the necessary errands for him. But it was too late for that.

He reached his ramshackle tower, taller than the trees and overgrown with ivy and moss. He took the last few steps to the door blind with joy, and only then realized that the door was hanging on only one hinge, askew. He held his breath as he pushed it in, revealing the clockwork butler taken to pieces all over the floor. “Damn!” he whispered, and carefully stepped inside, setting his satchel down and reaching for a heavy bludgeon, carefully avoiding the delicate gears that used to comprise his butler as he made his way towards the laboratory.

He crept to the laboratory and found it empty, but dismantled entirely. He cursed again, this time a shout. The tables were overturned, the floor covered with who-knew-what chemical or mixture thereof, the hydraulic shelving system was completely trashed, and pieces from his flying machine were scattered from one side of the room to the other. Everything was either singed or covered in ash, and the smell of the smoke remained thick in the air, and there was one window, crashed open either to allow entrance or escape. He shouted again.

It would take a long time to clean up the laboratory, but first he had to check the other rooms in the tower, to be sure that his burglar had left. He opened a cabinet to find his trusty crossbow, a net made of iron chains, and a few bolts. He picked up a mirror as well, and made his way through the tower. Carefully, he examined each room, and in each room he found the same destruction, until he came to the top of the tower. This balcony had been his sanctuary, and as he made his way up, he could hear sounds that someone was there. He knew exactly what to expect, then, and loaded the net into the crossbow to fire and entrap whoever was up there.

Joseph pushed the door, and it turned smoothly on its hinges. The balcony was deserted, except for one man, skeletally thin, sheathed in blue. That would be the upstart sorcerer, playing some game. “Who are you, and what are you doing here?” Joseph asked.

“Why are you so afraid of magic?” came the answer.

Joseph shiverred, but wouldn’t let it show. “I’m not afraid of magic,” he insisted. “I laugh in the face of the countless sorcerers I have killed. I am more powerful than magic, and therefore have nothing to fear.”

The blue-sheathed being laughed, the sound of dry leaves scraping across cobblestones. “You are afraid of magic, for although you are the most powerful sorcerer in the land, although you have killed so many magicians, there is not one item with any magical power in your possession. You have never, it appears, even touched magic. You do not know magic, and you must fear what you do not know.”

“If I’m so afraid of magic,” Joseph said with a chuckle, “Why am I not afraid of you?”

The skeletal man turned to face Joseph, and Joseph shuddered to see two blue eyes sparkling – almost glowing – beneath the hood. “You are afraid of me.” It was the intruder’s turn to chuckle. “You are afraid of me, for you know that I bring your death. Your time of reckoning has arrived, Joseph Daedalus! You are faced with your doom, and you are powerless to stop me! Never again will you sully the very name of magic with your existence; you will be purged and the title of sorcerer will be washed clean. Daedalus, prepare to meet your death.”

And then Joseph Daedalus realized it; if this man had come prepared to kill him, there would have been one quick spell and the deed would be done. Suffocation was easy enough, he knew, and there were stories of sorcerers powerful enough to stop a heart with the blink of an eye. Joseph laughed outright, a joyous laugh, and as it echoed into the forest the wolves began to howl again. “I’m not in the mood for fighting,” he said jovially. “Perhaps another time?”

“I have invaded your home!” The man shouted. “I have come to kill you, and you are not in the mood for fighting?!” The cloaked figure stepped toward Joseph. “I will not tolerate your impudence! You are a mockery to sorcery! Your very existence is a thorn in the side of magicians everywhere! It is my duty to relieve you of your mortal coil!”

Joseph laughed again, and the man in blue screamed in rage. “Relieve me of my mortal coil? Is that the best you can come up with? You really are new at this.” Joseph smiled at the sorcerer. “But really, I can go put a pot of tea on, if you’d rather that. I would have the butler do it, but you took him to pieces and I haven’t had time to repair him yet.”

The man in blue’s shoulders fell, like a disappointed child. “You aren’t afraid of me any more.”

“Nope,” declared Joseph, smiling broadly. “Not really.”

“I have powers you can’t imagine!” The cloaked man whined, petulant. “I found nothing of real value in your tower, so you must not know real power! I can make the seas boil, I can stop your heart just by thinking of it – you must know that, so why aren’t you afraid of me?”

Joseph just laughed again. “If you can stop my heart, why haven’t you already?” The cloaked man stuttered something, but Joseph just shot the crossbow and caught the sorcerer in its iron net. The man fell to the ground, shouting. He reached his hands through the net, but Joseph just smiled and walked over. “Who are you?”

“What?” asked the defeated sorcerer.

“Who are you? Why didn’t you want to kill me?”

“You know who I am,” the sorcerer spat. “You know all too well.”

Joseph sighed. “I thought as much,” he said, and then he pulled out his mirror, holding it in front of the sorcerer’s eyes. “Look at yourself. Look at what magic has done to you. Once upon a time you were healthy, happy, human, full of life. Now you’re a dying sheath, just like I said you would be. Look at what you did to yourself, and ask yourself if it was worth it.” Joseph felt a tear roll down his cheek.

“It was worth it,” hissed the sorcerer.

Joseph shook his head and loaded a bolt into the crossbow. “No, no it wasn’t,” he said, and aimed for the sorcerer’s head. He shot straight and true, and whispered, “I’m sorry,” to the night. It was necessary, Joseph thought. He didn’t have a choice.

The choice had been made long ago, when his opponent decided to open a book of magic. This was what always happened.