Ahh... 3 am after a fairly successful day.
I should have gone to bed about, oh, 2 hours ago. But i don't care. An early Happy New Year's eve to everyone.
Today was fairly productive. I was able to see where in the algorithm I was getting tripped up for my protein folding project, and I was able to redesign my code so it was much more simplified. Then, I found a standard for writing research papers in LaTeX and went about converting my Bird Flu pandemic report into it.
I should probably explain the two projects I'm working on these next few weeks.
The protein folding project I'm working on is really interesting. Pretty much, I'm implementing a modified Genetic Algorithm first mentioned in a paper written by Unger and Moult in 1993. What it does is simulates a "protein" chain, composed of hydrophobic and hydrophillic amino acids, folding on a 2-d plane. Hopefully this implementation will be faster than that done by Unger and Moult... but hey, we'll have to see.
The second project relates to influenza. I'm sure you've all heard about H5N1. Well, my partner and I did a research project over last semester for our Bioinformatics class, and we have reason to believe that H5N1 has very high pandemic potential.. we have to perform a bit more sequence analysis before our paper becomes more publishable ( according to our professor). Heh. That's all I'm going to say though... Theo (my partner) and I are trying to keep as mum on this as possible, since we are really excited about what we've found. So today I transcribed our paper into LaTeX... good Lord, what a beautiful formatting tool! Our paper is even more gorgeous than before. Tomorrow most likely I'll import all the images in. If I get the feedback from my other professor that I'm waiting for, I'll also do some coding.
Ah. So New Year's eve... should I relax? or continue working? maybe I'll relax for a little while... or work for a little while.. maybe I'll decide in the morning ^-^
Have a good night. It's way past my bedtime.
Saturday, December 31, 2005
Monday, December 26, 2005
Science, Religion and Research
Recently, there was a post on Slashdot on Writing Genetic Code. Apparently a research group has taken a shot at "coding" an artifical organism. Really cool. And guess who's heading off the project? Craig Venter. Even cooler :-)
For people who may not be familiar with him, Craig Venter founded The Institute for Genomic Research, or TIGR during the mad rush to sequence the human genome. While the Human Genome Project swung ahead, Venter developed a new shotgunning method to complete the sequencing even quicker. NIH wasn't impressed; they denied him and his group funding. However, Venter duped them all when his group sequenced the genome quicker and cheaper than the Human Genome Project. This had a large deal to do with skipping over the physical map creation step, needed in the BAC-to-BAC sequencing method (used by the Human Genome Project), and the use of software.
I take my hat off to you, Dr. Venter! I wish you and your group the best of luck! Maybe his group will succeed where others have failed.
Some slashdotters took the news fairly well (Soviet jokes aside); however, the discussion predictably started becoming one about religion. On previous stories like this one, atheists crowed at the project, calling it a "smoking gun" against those who favor the theory of intelligent design. The intelligent design crowd retorted (essentially reversing the direction of the gun) that the project only supports the theory of intelligent design. And the squabbling and squawking continued.
Just as a personal opinion, can't people just respect other people's choice of religions and beliefs? Is it necessary to forcibly impose one's own belief system on others? It's one thing to express an opinion, but the things some people do are ridiculous. Fundies are pretty bad (Hi Mr. Falwell!), but atheists can be just as bad. Some of them are really hilarious ("I hate you and you don't exist!"). How do you hate something you don't believe exists? Idiots. Hey, I respect the beliefs of my atheists friends (and they respect my Christian ones), but these smacktards walking around thinking that anyone who believes in God lacks intelligence need to seriously grow up. It seems that such people are atheist because it's what's "in" in rebel fashion now. Sinfest did a nice piece on this.
I honestly hope that one day that people will come to realize or accept that Science is not necessarily the antithesis of God. The answer to such a complex question such as the origin of life is rarely housed in any extremist wing. Like Stephen Crane once wrote:
"When the prophet, a complacent fat man,
Arrived at the mountain-top,
He cried: "Woe to my knowledge!
I intended to see good white lands
And bad black lands,
But the scene is grey."
Until then, I get to hear the fundies and the atheists of fucktardia duke it out on Slashdot and other online news sources. *sigh*.
In other news, I've started working on my protein folding research project again. The coding is going fairly slow, but I think that's mainly a motivation issue. I guess that's because I'm on winter break. Oh well. Adding a bit of discipline to my schedule should break me of that. I can't wait to get the GA done. Oh! And after that, I can start work again on my avian flu project. Muahahahaha.
For people who may not be familiar with him, Craig Venter founded The Institute for Genomic Research, or TIGR during the mad rush to sequence the human genome. While the Human Genome Project swung ahead, Venter developed a new shotgunning method to complete the sequencing even quicker. NIH wasn't impressed; they denied him and his group funding. However, Venter duped them all when his group sequenced the genome quicker and cheaper than the Human Genome Project. This had a large deal to do with skipping over the physical map creation step, needed in the BAC-to-BAC sequencing method (used by the Human Genome Project), and the use of software.
I take my hat off to you, Dr. Venter! I wish you and your group the best of luck! Maybe his group will succeed where others have failed.
Some slashdotters took the news fairly well (Soviet jokes aside); however, the discussion predictably started becoming one about religion. On previous stories like this one, atheists crowed at the project, calling it a "smoking gun" against those who favor the theory of intelligent design. The intelligent design crowd retorted (essentially reversing the direction of the gun) that the project only supports the theory of intelligent design. And the squabbling and squawking continued.
Just as a personal opinion, can't people just respect other people's choice of religions and beliefs? Is it necessary to forcibly impose one's own belief system on others? It's one thing to express an opinion, but the things some people do are ridiculous. Fundies are pretty bad (Hi Mr. Falwell!), but atheists can be just as bad. Some of them are really hilarious ("I hate you and you don't exist!"). How do you hate something you don't believe exists? Idiots. Hey, I respect the beliefs of my atheists friends (and they respect my Christian ones), but these smacktards walking around thinking that anyone who believes in God lacks intelligence need to seriously grow up. It seems that such people are atheist because it's what's "in" in rebel fashion now. Sinfest did a nice piece on this.
I honestly hope that one day that people will come to realize or accept that Science is not necessarily the antithesis of God. The answer to such a complex question such as the origin of life is rarely housed in any extremist wing. Like Stephen Crane once wrote:
Arrived at the mountain-top,
He cried: "Woe to my knowledge!
I intended to see good white lands
And bad black lands,
But the scene is grey."
Until then, I get to hear the fundies and the atheists of fucktardia duke it out on Slashdot and other online news sources. *sigh*.
In other news, I've started working on my protein folding research project again. The coding is going fairly slow, but I think that's mainly a motivation issue. I guess that's because I'm on winter break. Oh well. Adding a bit of discipline to my schedule should break me of that. I can't wait to get the GA done. Oh! And after that, I can start work again on my avian flu project. Muahahahaha.
Sunday, December 18, 2005
Words of Inspiration
I hope I will never, ever forget the following:
"It will not do you any harm whatever to think in original fashion. . . The odds that your theory will be right, and that the general thing that everybody's working on will be wrong, is low. But the odds that you, Little Boy Schmidt, will be the guy who figures a thing out, is not smaller. . . It is very important that we do not all follow the same fashion. Because although it is ninety percent sure that the answer lies over there . . . what happens if it doesn't?"
Also:
"It doesn't do any good if it just increases the number of guys following the comet head. So it's necessary to increase the amount of variety . . . and the only way to do it is to implore a few of you guys to take a risk with your lives that you will never be heard of again, and go off in the wild blue yonder and see if you can figure it out."
- Richard P. Feynman (excerpted from "Genius" by James Gleick).
What an excellent book, and an excellent lesson. I am off to bed for now.
"It will not do you any harm whatever to think in original fashion. . . The odds that your theory will be right, and that the general thing that everybody's working on will be wrong, is low. But the odds that you, Little Boy Schmidt, will be the guy who figures a thing out, is not smaller. . . It is very important that we do not all follow the same fashion. Because although it is ninety percent sure that the answer lies over there . . . what happens if it doesn't?"
Also:
"It doesn't do any good if it just increases the number of guys following the comet head. So it's necessary to increase the amount of variety . . . and the only way to do it is to implore a few of you guys to take a risk with your lives that you will never be heard of again, and go off in the wild blue yonder and see if you can figure it out."
- Richard P. Feynman (excerpted from "Genius" by James Gleick).
What an excellent book, and an excellent lesson. I am off to bed for now.
Saturday, December 17, 2005
First Post
I look out the window and it's snowing. Again. Such is Upstate NY. It's finals week of my seventh semester, and in a sudden act of frivolity I decided to create a blog.
"What on earth will you do with a blog?" My boyfriend had asked me.
"Err... use it to.. chronicle.. research?" I replied meekly.
"As long as you don't become one of those depressing goth teenager types who write nothing but dark poetry and talk about their pain all the freakin' time." He said, returning back to his book.
"Those people suck." I said, somewhat uncertaintly, bitingly reminded that I, too, was once a black-wearing teenager who wrote poetry. I never was a goth though. The Computer Science side must have cancelled that out. I hung out with the academic types, my best friend the "czar" of the Computer Programming Unit (CPU) , the high school's Computer Science club that he and I and our friend Tian had founded. Granted, it was mostly him and Tian. I had my own club to tend to. I was the editor-in-chief of the school literary magazine, Eidolon. Day after day I sifted through piles of poetry that could be classified into three main groups. a.) "Dark and Depressing with Suicidal Overtones" b.) "I love him/her but s/he doesn't love me back" or c.) "I rhyme so hard that I lose sight of what I was trying to write". We had good writers. But when we saw one that fell solidly in one of the above stereotypes, it usually was quickly moved to the reject pile.
Heading Eidolon was my greatest achievement, as far as clubs went. But I was painfully aware that if it wasn't for the C.P.U., my choosing of a major in college would have been a bigger bolt out of the blue to many than it already was. It was the same reaction, time after time again: "Computer Science? I thought you would be an English Major." or, "Why Computer Science? Aren't you better at English?" Yes. I was good at English. I had the touching story of a first generation American learning English in public school and excelling in all her English classes, going on to becoming the Editor-in-chief of the literary magazine for two years, and earning the English award in her high school, winning creative writing contests, etc. etc. The stuff that people would say, South Park style, "Oh that's so courageous", at absolutely nothing at all. So why wasn't I an English major?
Because it's English. Because I have better uses of my time and my intelligence. Because the world according to English majors is bounded by definitions and books, by words and naunces. Because with Science, I have no limits. English is a static field. But Science... Science vibrates with the unknown, it glows, it glimmers. I would be one of many souls, thousand-fold, shooting through the varied expanse of science and pushing at its frontiers. When given the choice, of living in swamps and consuming the most brackish of knowledge, and living by the instant and being sunstained by ones discoveries, what would you choose?
That and because when I thought of English majors, I pictured Raven from Penny Arcade.
Fast forward four years. It's the end of semester 7 of my undergraduate career in Computer Science, and I lean back on the bed, very happy with myself. I feel like a rebel - relaxing, instead of studying for my last final of the semester.
"Research. And the daily thoughts of being a researcher. That's what I'll use it for." I say, curling up to Dan, who discards his book. He holds me close.
"Well, if it makes you happy. And as long as it doesn't distract you in your work." He says fondly.
"It won't my love."
"What on earth will you do with a blog?" My boyfriend had asked me.
"Err... use it to.. chronicle.. research?" I replied meekly.
"As long as you don't become one of those depressing goth teenager types who write nothing but dark poetry and talk about their pain all the freakin' time." He said, returning back to his book.
"Those people suck." I said, somewhat uncertaintly, bitingly reminded that I, too, was once a black-wearing teenager who wrote poetry. I never was a goth though. The Computer Science side must have cancelled that out. I hung out with the academic types, my best friend the "czar" of the Computer Programming Unit (CPU) , the high school's Computer Science club that he and I and our friend Tian had founded. Granted, it was mostly him and Tian. I had my own club to tend to. I was the editor-in-chief of the school literary magazine, Eidolon. Day after day I sifted through piles of poetry that could be classified into three main groups. a.) "Dark and Depressing with Suicidal Overtones" b.) "I love him/her but s/he doesn't love me back" or c.) "I rhyme so hard that I lose sight of what I was trying to write". We had good writers. But when we saw one that fell solidly in one of the above stereotypes, it usually was quickly moved to the reject pile.
Heading Eidolon was my greatest achievement, as far as clubs went. But I was painfully aware that if it wasn't for the C.P.U., my choosing of a major in college would have been a bigger bolt out of the blue to many than it already was. It was the same reaction, time after time again: "Computer Science? I thought you would be an English Major." or, "Why Computer Science? Aren't you better at English?" Yes. I was good at English. I had the touching story of a first generation American learning English in public school and excelling in all her English classes, going on to becoming the Editor-in-chief of the literary magazine for two years, and earning the English award in her high school, winning creative writing contests, etc. etc. The stuff that people would say, South Park style, "Oh that's so courageous", at absolutely nothing at all. So why wasn't I an English major?
Because it's English. Because I have better uses of my time and my intelligence. Because the world according to English majors is bounded by definitions and books, by words and naunces. Because with Science, I have no limits. English is a static field. But Science... Science vibrates with the unknown, it glows, it glimmers. I would be one of many souls, thousand-fold, shooting through the varied expanse of science and pushing at its frontiers. When given the choice, of living in swamps and consuming the most brackish of knowledge, and living by the instant and being sunstained by ones discoveries, what would you choose?
That and because when I thought of English majors, I pictured Raven from Penny Arcade.
Fast forward four years. It's the end of semester 7 of my undergraduate career in Computer Science, and I lean back on the bed, very happy with myself. I feel like a rebel - relaxing, instead of studying for my last final of the semester.
"Research. And the daily thoughts of being a researcher. That's what I'll use it for." I say, curling up to Dan, who discards his book. He holds me close.
"Well, if it makes you happy. And as long as it doesn't distract you in your work." He says fondly.
"It won't my love."
Subscribe to:
Posts (Atom)