Evidence

I'm giving a talk to the biophysics group on Wednesday about molecular rulers, which are little molecules that bacteria use like ropes to determine how long they should build their toxin injection needles. Most of the research I'm relying on for this presentation refers to how similar the toxin injection needles are to the bacteria flagellum, the little corkscrew motor that allows bacteria to swim around, and how this probably means that the injection needles are their evolutionary predecessor.

While reading this, I am reminded of how intelligent designers often cite the bacteria flagellum as evidence for creation. It is too complex a piece of machinery, and the individual parts are useless, they argue. I was intending to add this to my presentation as an introductory side note. When looking for a source for the intelligent design argument, I found these humorous google suggestions:

That's right. The evidence for the existence of Jesus is on the same list as the evidence for the existence of dragons and astrology.

Job + first quantum processing picture

I finally got another part time job to replace my post office job - with one month of Summer to go. I'll be working as a web editor/ assistant to the director of health for the International Student and Exchange Office. It pays more than any other job I've applied for (about %50 more than the Post Office) and continues during the school year.

I've also started putting the quantum lab's data into Processing. Click on the image to find out more.

Also, I've jumped on the bandwagon and joined Twitter. Since most of my work are office jobs now, it will most likely just be a monotonous outlet for my boredom/ computer related frustrations.

An Analysis of Disney Movies (by someone who is probably too old to still be watching them)

Ever since around the age of 13, when I decided I was too old to still watch them, I came to the opinion that most Disney movies suck. Of course, I still saw they occasional latest release from Disney, as I had my neighbor's kids and cousins to babysit.

Last week, after having the movie recommended by friends (Liam and Katherine) John decided to take me to see Wall-E.

Wall-E was amazing. It was cute, visually and sonically stunning. It was funny without being juvenile, smart without being pretentious. Even the ending credits (all 900 lines of them!) were interesting.

Encouraged by this, I decided to watch Enchanted, another Disney movie recommended to me by a friend (Laird). Enchanted also greatly exceeded my expectations of Disney movies. I also recently re-watched Mary Poppins with a couple of friends, and it seemed so much better than I remember it being.

I started to wonder - where Disney movies always this good? But then how to explain the crappiness of what about Robin Hood, The Haunted Mansion, The Pacifier or The Game Plan? Has Disney just been revitalized in the bast couple of years after a downward trend? In order to answer this question, I decided to graph the rottentomatoes.com ratings of major Disney releases (not the straight-to-DVD sequels like Pocahontas 2 or Mulan 2, I know those are going to suck) by year. This is what I found:

A few remarks:

Most of the first Disney movies ever made (Snow White, Pinocchio, Fantasia) are over 90%. The fraction of movies in what I'd call the 'excellent' category has been decreasing steadily with time. But this isn't a good measure of the quality of Disney movies, as Disney now produces around twice as many feature movies per year as it did in its first decade of existence. Perhaps Disney put more effort into its movies when it only produced one or two per year, or maybe now that there are more we're seeing a more normal distribution of ratings.

Pixar is Awesome Toy Story was the only Disney movie to get 100% in the 90s. Finding Nemo, The Incredibles, Monsters, Inc. and Wall-E were the top rated Disney movies of the 00s. Disney also rides high off of the imported Miyazaki movies (Spirited Away, Princess Mononoke). But...

Computer animation does not a good movie make. Disney's non-Pixar attempts at computer animated movies, such as Meet the Robinsons, The Country Bears, and The Wild, have all been suck-tacular.

Sequels are not meant for theatres. In 2003, Disney broke their rule that animated sequels being kept out of theatres by releasing The Jungle Book 2. It sucked. Movies that also sucked: the live action versions of 101 Dalmatians, and 102 Dalmatians. Children do seem to love repetition (most nursery rhymes use it), but sequels should only be used for television babysitting.

The main problem with children's movies are that they are made for children. Bad Disney movies pander a child's sense of humor or attention span. That's why we get movies like Dr. Dolittle. Good Disney movies are the ones that still capture childlike innocence and wonder without relying on slapstick comedy or constant action. My research supervisor took his 4 year old daughter to see Wall-E, and they left 20 minutes in to the movie because she was getting bored. There were no talking characters or people doing silly things, just a robot and a cricket on a deserted planet. I always got bored or fell asleep watching Mary Poppins as a child, these days it moves at just the right pace.

Disney hasn't made a decent non-computer animated movie in years. DisneyToons, the branch of Disney now making classic-style animated movies, is a recipe for suck.

Making movies used to take a lot of painstaking effort. Now they're relatively cheap, which means that Disney can produce a lot of them without too much quality control. They make movies that only stupid kids want to see. Because of this, we seem to have forgotten that movies can have a G rating and still be entertaining for adults.

Every Five Books: Religion is Scary

Since it's summer, and I have time to read, I'm back to cataloging all the books I read on my blog. This summer, I'm not allowed to cheat and read the really short young adult books. No, for this first entry of the summer, I read an 800 page book on evolution.

God is not Great, Christopher Hitchens - another atheist friend of mine lent me this book after being unable to complete it himself. I can understand. Though there are a lot of scary tidbits about religion - the rabbi in New York who transmitted herpes to around 30 babies because of the practice of sucking off a baby's foreskin during circumcision sticks out in my mind, though it definitely wasn't the worst example, Hitchens comes off as pedantic and pretentious. He writes like he speaks, and too often comes back to examples of his own life, as if he, too, is a genius persecuted by religion. It was a great vocabulary builder, though.

Omega - Jack McDevitt. I picked up this book because John picked it out of the library and I was looking for something to read on my trip home to Antigonish at the beginning of May. The basic plot is that there's an astronomical storm heading towards a planet with a primitive civilization, and so humans arrive and pretend to be their gods in order to save them. Sounds like the plot of a forgettable episode of Star Trek. It was well written, but the ending was kind of lame. I read 300 pages of the book before realizing that it was just one in a series and that because of this, the book would not have a satisfying ending by the last page. The quality of writing is enough to get me through one book, but not the entire series. It was also kind of preachy, as if the author was trying to convert his readers into believing in some great celestial god that most of his characters believed in.

Infidel - Hirsi Ali. This book is amazing. Ali was born in a Muslim political family in Somalia but ran away to the Netherlands on her way to an arranged marriage in Canada. She learned Dutch, got citizenship and earned a college degree in political science, eventually becoming a political leader in the Netherlands. She campaigned against the abuse of women in Islam, which makes her a constant target of death threats - she wrote the screenplay for Theo Van gogh's Submission. Now that she is in the united states, she mostly appears on talking heads shows to denounce Islam. Here's an example of two different styles of interview with Ali:

The first, the reporter from Canada, seems to refuse to believe that Ali had a difficult life in Somalia. He paraphrases her biography and insists that life in the west isn't as good as Ali says it is. In the second, Glen Beck nearly falls to his feet in adoration of Ali, but is it really respect for her life or just happiness that he's found someone to support his beliefs? Neither interview does a very good job of capturing Ali's message. Infidel is probably one of the best books on feminist issues ever written, and it's nice to see the message of female empowerment coming from a non social relativist, far left point of view.

Quicksilver - Neal Stephenson. This is probably the nerdiest book I've read in a while. It follows Daniel Waterhouse (the fictional founder of the Massachusetts Institute of Tecnickal Arts) who was Newton's roommate at Cambridge, but who later joined Leibniz in creating a difference engine after Newton turned into a crazy astrologer. Heavy on the science and history, low on plot. The only female characters were a dumb housewife and a prostitute.

The Ancestor's Tale - Richard Dawkins. The Ancestor's Tale is an 800 page book that could serve as a substitute for half of first year biology and earth science. I would recommend it to anyone who hasn't taken first year biology, as this book covers the parts of biology that I found interesting (I'm sorry Dr. Staicer, memorizing the Krebbs cycle or the phylogeny of a hundred different sorts of microbial life was not helpful). Dawkins writes a lot of his own life into the book, so even though I felt like I was reading what I already knew as gospel, every so often I'd read a little amusing tidbit about his childhood that made the book interesting.

Playing around with Processing

Through my work in visualization, I've come across this really cool program and programming language called Processing which is basically a nerdier version of flash developed by people at MIT. I played around with it today. I generated a list of random numbers ranging from 0 to 255 and grouped them into 3s. The three numbers are used to make up the colour of an ellipse, and then the same three numbers are combined again to make up the x and y coordinates of the ellipse and the width and height. so basically, each possible shape has only one possible colour, and the order of the stacking of the shapes is random. Here's the image generated by the code ellipse(first,second,third,first*second/third,)

and here's the same set of data, with the slight difference in code being: ellipse(first,first*second/third,second,third).

In other news, today I was assigned my own research project in the biophysics lab. So instead of having to help debug other people's code, I get to debug my own crappy code! I was also offered a job for September, but it's a bureaucratic job with lots of work and little pay, so I don't think I'll consider it. I also made coconut curry tonight. It was delicious.

Joe's big win

My cousin Joe won second place in a race in special Olympics in Ohio. I'm posting this mostly because this is now one of my favourite photos.

He's the kid with his hands in the air.

Birth of a Facebook application

I've just released my first facebook application out of development mode. Here's the about page:

and here's what it does to a profile:

Georges Island

Last weekend, I went with John, his sisters and his dad to Georges Island, a textbook-perfect glacial drumlin in the middle of Halifax harbour that housed a naval fortification in the mid nineteenth century. It is off-limits to the public, as it is still an archeological site and is currently too hazardous to be turned into a tourist attraction (dark, slippery tunnels and steep cliffs are just a lawsuit waiting to happen). Obviously, the archeologists aren't the only ones getting to the island, as evident by the beer cans lying around. But for one day last week, Parks Canada decided to divert a harbour ferry to the island and offered guided tours. It was pretty neat.

Looking back at Halifax from the ferry.

Looking back at Halifax from Georges Island.

Looking down one of the steep cliffs at the Georges Island lighthouse. The tall gray building in the background is Fenwick Towers, where I'll be living next year.

This picture was taken from where one of the cannons used to sit. I think it's cool because you can see the Halifax Citadel (the green hill in the background) from there.

Coding frustrations

For most of today, I've been dealing with two programming annoyances. The first is in my work. I chose to write my programs in Actionscript instead of Java, and I think I'm now paying the price. As far as I can tell, the only way to incorporate outside data is with XML, and Actionscript references XML in a very irksome way. Think of XML as storing data as boxes inside of boxes. For example, an XML document could be of the form:
<box1>
<innerboxa>
</innerboxa>
</box1>
<box2>
</box2>
<box3>
<innerboxb>
</innerboxb>
<innerboxc>
</innerboxc>
</box3>
Now, I think it would make sense to be able to reference the stuff in inner box c by going xml.box3.innerboxc . But no. Actionscript ignores the names of the boxes and instead arranges the tags by a family tree. To get to innerboxc, you have to go firstChild.nextSibling.nextSibling.firstChild.nextSibling.
Anyway, I've gotten used to the Actionscript family tree system. The problem I ran into a few days ago was that Actionscript didn't seem to be passing variables out of the xml scope into the global scope. At least, that was what I assumed was going on, from the forum threads I read. So I spent several hours trying out all the various solutions, and none of them worked. It turned out that my problem was that the functions using data from xml were executing before the xml data was loaded. A few minutes to write some timeline controls and it was fixed. So much for four wasted hours spent on the wrong solution.
I'm also working on a facebook application for the DSU. My second frustration is related to the facebook libraries that are required for facebook applications. They include files that don't exist, or are in another directory. It seems like a really easy thing to fix, and facebook has been allowing people to develop applications for at least a year now.

John's Website

I made John's website pretty. Aren't I the best girlfriend ever?

Introduction to Summer

Since I haven't yet described exactly what I'm doing this summer, I think I'll do it now. I'm subletting from one of my friends in my math classes, and living with four male friends who are all in engineering or physics in a house in a nice residential neighborhood of Halifax. I'm working as a clerk in a non-computerized post office (meaning I have to weigh and measure parcels, calculate the volumetric weight and then quote a price out of a binder! Now I know what my physics skills are useful for!). I vowed to never work retail again after my horrible experience in the smoke shop last year, but the post office is a better job. My customers are nicer - polite senior citizens and people from the medical offices upstairs rather than people addicted to pull-tab lottery tickets or who have lost their teeth from chewing tobacco. I'm getting paid a dollar more per hour than the smoke shop, and when it's slow, which it quite frequently is, I'm allowed to sit in a little office and read. Most of my co-workers are also university students.

But that job's nothing really to brag about.

Rutenberg, the prof I've been doing volunteer research for for the past year, told me yesterday that he will pay me to work for him this summer. This is despite not quite having the grades to get a summer research scholarship, and Rutenberg told me from the start that he probably wouldn't be able to pay me. But I guess my hard work has paid off, and he's managed to find the funds to pay me.

He's assigned me to the project of programming a computer visualization of peptidoglycan exteriors in bacteria. I'll be working with my friend and roommate Bobo, who was a co-author on my carbon nanotube paper.

So yeah. That's what my summer looks like. Hanging out in Halifax with friends, working two jobs, one of which is a fun/nerdy computer programming one, cooking my own food and waiting for school to start up again.

In a previous e-mail my mother expressed concern that my diet was not very nutritionally rich. Here's a list of the stuff I've cooked so far in order to dispel that idea:

Spaghetti
Chili
Pesto
Cabbage casserole
Beef stew
Spanikopita
Chicken tetrazzini
Chicken broccoli stir fry
Lemon chicken
Beef tortillas

... and of course everything is accompanied by a salad or a side of vegetables.

Registering for 3rd year

I've just finished registering for classes for next year. So far, here's what I've chosen:

Fall term:
Differential Equations I
Experimental Physics I
Quantum Physics
Electrodynamics
Mathematical Methods in Physics

Winter Term:
Differential Equations II
Experimental Physics II
Energy and the Environment
Advanced Classical Mechanics
Science and the Media

My fall term is going to be much more difficult than my winter term. Electrodynamics and Mathematical Methods are both 4th year courses, but I have to take them next year because the physics department at Dal is annoying and only offers half of its classes every other year. I'm excited about Energy and the Environment, which is a class comparing the financial and environmental cost of different forms of power, and Science and the Media, but they're both 2nd year courses which are math-lite. I would have preferred taking Materials Science over Advanced Classical Mechanics, but alas the physics department is screwed up and I can't take the prerequisite for that course because it isn't offered this year.

Huffman Encoding on a picture of David Huffman

For my second term of honours linear algebra, I wrote a paper on JPEG image compression. I was only supposed to write it about DCT and quantization, but reading about the steps involved in JPEG encoding, I found out that some JPEGs are encoded using Huffman encoding as a final step, and I figured I should include that in my paper out of respect for my genes. I even used a scan of an image of me and Uncle David together to compare images with Huffman compression and without.

I realize that I probably got a lot of technical things wrong in this paper, but in my defence, I'm a physics major, not a comp sci major, and I stayed up until 4 in the morning the night before handing it in to finish it. Regardless, after handing it in, my professor responded with an e-mail that read "Congratulations on your project. It is very good." and I think it's the reason I got an A in that class despite nearly failing the midterm.

How to move without a car

I am moved into my home for the summer. It's a nice big room on the second floor of a yellow house on Cherry St. It's about three blocks away from a supermarket and within ten minutes of the Dal campus. It has a dishwasher, non coin-operated laundry and a big screen TV. It's also one street over from where John is living.

However, moving in was quite a challenge. I had no car available as my parents are in Tucson. Residence kicked me out a week before I could move into my new place on the first. I was borrowing furniture from a friend, but the friend was leaving on the 29th. Luckily, John could move into his place a few days early, so we'd just walk all of my furniture and luggage to his new place and then move it to my new place on the 1st. Here's our original plan:

Then it turned out that John would not be allowed to move things into his apartment until the 29th, and that my friend would be moving out on the 28th. She was also concerned about her furniture getting hurt by being carried several blocks. Fine. I stored some stuff in residence and at John's place until I could move it into his place, and luckily my parents were friends with people who lived out in Clayton park. The furniture would be taken by my friend's parents to Clayton park and then my parent's friends in Clayton park would take my stuff to Cherry St. The plan was now as such:

The day that my friend was going to move out, another problem arose... her parents didn't want to drive the furniture out to Clayton Park. I don't think this was unreasonable, they had had a long day of moving. However, I had sent the address to them a week in advance. I compromised by storing all of the furniture and my luggage at John's old bachelor apartment overnight, and moved it to his new place on the 29th when he moved. This change in plan was probably the most stressful day of the move. After that, it was easy to move my stuff from Shirley St. to Cherry St. Here's what ended up happening. In the end, my luggage and furniture ended up going to two different locations before ending up where I wanted them, and John's bachelor pad was pretty crowded for a night.

All the gazette articles this year on my door

The title of this post is pretty self explanatory. Throughout the year I posted all of my gazette articles on my bulletin board and my door. I've been out of residence for two weeks but I'm late in posting this because my camera cord has been packed up.

End of Second year

I had my final exam on Wednesday. I moved out of residence that afternoon. (no more sharing a bathroom with drunk frosh! no more country music neighbor! no more watery, overly salty cafeteria food! no more shower flip flops! no more having to walk down the street every morning for breakfast!) Since then I've been chilling, catching up on Ugly Betty and enjoying the high speed internet and torrent access at John's place, making my own food, going to the pool and reading non-school related books. I've been working out the final details of my move on May 1st, although plans seem to be constantly changing. I have a few summer job interviews lined up for Monday, and I'm fairly confident that I'll get at least one of them. The grades I've been getting back for this term are so far pretty good - A- in journalism and A in Intermediate calculus. I got my hair cut above my shoulders again like at the end of last year.

And that's the state of my life in one long, messy sentence. My level of stress has gone down now that my exams are over and I've got job prospects, but I'll feel even better when I'm moved into my summer place and I have a definite source of income.

Oh, expendable red shirts

I have a calculus exam this evening. I only need a 60 on it to get an A, since I did extremely well on the midterm, but I'm still a little stressed out about it because it's on much more difficult material than the midterm - Stokes' theorem and series solutions to second order differential equations.

My final gazette article of the year was for the spoof issue, entitled "Scientists discover arts student gene". I don't think it will be posted on the website.

Gazette #44 - Hadron is an awesome word

The $10 billion experiment

I had an interesting conversation on Sunday. Upon hearing that I was a physics major someone asked me if I knew enough to understand the LHC experiments. I told them that I haven't really studied the standard model yet, but we were taught that neat things happen when you smash high energy particles together.

# 43 was about bad things humans have done to each other and gotten away with under the guise of it being 'science'. It was an extremely depressing article to write, but I got a bit of praise for it.

Late April Dilemma

I'm living in Halifax this summer. Don't know yet exactly what I'll be doing for work, but I know I want to stay here. Almost all of my friends are staying here and I can do research at the physics department here.

I'm subletting from one of my friends for a reasonable amount and living in a house with four (4!) male friends my age. The problem is that the lease starts on May 1st, and none of us can even move our stuff into the house until that date, and Dalhousie really wants you out of residence once you're done with the semester. I'm supposed to be out of residence at noon on the 24th, 24 hours after my Electricity & Magnetism exam.

I can't go home to Antigonish for this week because my parents are still in Arizona and our house is being rented.

Current boyfriend John has invited me to stay in his bachelor pad for that week and has offered to help me move. Assuming we don't break up before then, that's probably what I'll do. A bachelor pad is definitely the correct noun to describe his place. School, research (he recently presented a paper on evolutionary computation at a conference in Italy - and he's only 19) and being the president of the computer science society keep him pretty busy, so he doesn't have much time for chores. The first time he invited me over he had papers and books all over the floor, about a month's worth of dishes in his sink and a pathetically unoccupied fridge. Don't even get me started on the bathroom. However, I complained about it and he cleaned up his place really well. This does not bode well for living with guys my age.

Anyway, I suppose I should not prejudge my summer roommates. They may have more respect for their own place than what I have seen them to have of their residence rooms. Or maybe I'll have to lower my standards for the next four months.

Furniture poses another dilemma. I am borrowing furniture from one of my friends who is spending her summer in Calgary. She's leaving on the 29th, I can't move in until the 1st, leaving me with a mattress and table to deal with for two nights. I have three options: hope that the people moving into her place don't mind me leaving the mattress there temporarily, con a campus storage company into moving the stuff for me by paying for storage for two days, or, move the stuff to John's new place for the summer since he can move stuff into his place for the summer ahead of time and his place is a block away from hers, and then move the furniture a block again to my place.

Oh the joys of living on my own with no car.

Gazette #42 - explaining calculators to arts students

Divide and Conquer

42??? 42!!! This article was inspired by a classics major asking me how a calculator can solve a square root, and me not exactly knowing the answer. I learned a lot of interesting stuff along the way, and I only hope that the arts students reading this article also find it interesting.

Gazette #41 - The Gazette's intrepid science columnist

Grand Canyon Creationism

This issue was inspired by my recent trip to the Grand Canyon. It's funny, I thought I was going to write a stronger article about how republicans are trying to prevent the National Park service from talking about evolution in the public parks, but I found out that the information I was basing that opinion on came from a looney lefty lobby group who made stuff up. I guess you can get bullshit from both sides.

Gazette #40 - BRAINS!

How to use more than 10 per cent of your brain

This was a fun one to write. Aaron Newman was an interesting interview.

Free Wifi at the Denver Airport

As the title suggests, I'm at the Denver airport right now - about a third of my way back to Halifax. The flight from Tucson was beautiful - we flew over the Rocky Mountains. I've got three hours before my flight to Montreal leaves and right now it looks like I'm the only person at the gate.

I'm debating whether to blow some of my American cash on overpriced airport food. It's about lunchtime in Halifax but I'm not hungry and the only fast food I'd be tempted to eat right now would be Tim Hortons, which aren't overly abundant in Colorado.

For the time being, I guess I'll enjoy the free internet and the constant announcements of "Please to not leave baggage unattended. Unattended baggage will be destroyed." and "The department of homeland security has rated the current threat level as orange. Please report any suspicious activity.".

Gazette #39 - DINOSAURS!!!

A scandal by any other name

I'm sitting in my parent's apartment in Tucson right now.

Gazette #38 - The Sex Issue

Animal Sex: Fancy penises and explosions

BIG WARNING: this article was published in a student university sex issue newspaper so you can imagine what audiences this article will not be appropriate for.

Also, I didn't choose the image, title, or ending sentence that go along with this article - those were added by my editor. Yay picture of cows going at it right next to picture of my head. And I was not trying to say that ducks eat each other after sex.

Just another reason why I'm so happy to be moving out of the dorm in April

Exhibit A: the bottles of urine.

Note posted on the garbage room door by the cleaning lady.

My question would be: why? We live at most three doors from a mostly clean bathroom and I don't think anyone has a medical problem preventing them from using it.

Gazette #37 - not quite so controversial, but still sad.

Harper slashes Science Advisor Office

This was actually pretty boring to write. I don't really like writing about politics. Especially Canadian politics