IGEM Jamboree 2009

I arrived back in Waterloo from MIT about 15 hours ago now. I'm a little bit behind in school work right now, so I can't really do the Jamboree/conference/competition justice (not that I could ever do it justice in a single blog post), but I thought I'd type up some assorted thoughts anyway...

• Road Trip (1): It's a nine hour drive. A couple of the more experienced members of the team chose to pay for flights instead.
  
• Road Trip (2): Toll roads... everywhere.
  
• MIT vs Waterloo (1): I've had an unhealthy admiration for MIT for a very, very long time so a lot of the people who knew me assumed I'd be disillusioned by this trip.
• MIT vs Waterloo (2): They both have those ugly abstract sculptures that are just beams welded together and painted a single colour; however, MIT's are bigger, blacker, and placed in the open while Waterloo's are small, orange, and pushed off to the side. Lesson: if you're going to have a Big Ugly Statue, you might as well make it Big.

MIT has ugly statues too! Ours are still uglier.

• Hotel (1): The Marriott. Not to be confused with the other gazillion Marriott's in Cambridge.
• Hotel (2): Once we found the Marriott, it was surprisingly swank. I'm more used to hostels and motels, but the Marriott is a genuine hotel.
• Jamboree (1): We missed breakfast on the first day. Never miss breakfast if you want to be alert for six morning lectures on synthetic biology. It's painful.
  
• Jamboree (2): The Osaka team presented their work on gene art; Valencia mock-interviewed themselves about voltage-controlled light-emitting cells (that were controlled using a laptop sound card); Pavia, Wisconsin, and Uppsala Sweden presented various ways of using biology to solve energy/environmental problems.
• Jamboree (3): The lunches provided by MIT catering made up for the lack of breakfast. Never has grilled roast beef and pasta tasted so good (with a side of a bun and a godly brownie).
• Jamboree (4): I saw several talks in the information processing track on Saturday afternoon. I found them more understandable than the morning talks; being fed and interested in the information processing category helped substantially. The Bacterial Decoder project (Illinois) and Satisfiability problem sover (MoWestern Davidson) were particularly cool.
• Jamboree (5): The 4:30 PM timeslot on Saturday had a few interesting-looking presentations. I passed up the chance to see the MIT and Freiburg software presentations to go to the John Hopkins' talk about their Build-A-Genome course.
  
• Poster Session (1): Tom Knight's presence greatly excited a couple members of the team.
• Poster Session (2): I talked to a few groups about their projects. Nobody really discusses modeling.
• Hotel (3): Staff are dressed for Halloween. This is probably the only day when plastic weaponry can be freely brandished in the lobby. Then again, it is the States, so maybe they do allow rifles in hotels.
• Hotel (4): The team from Brussels meets us in the lobby and provide an audience for our practice presentation.
• Hotel (5): No. Cheaper by the Dozen is not a good movie.
• MIT vs. Waterloo (3): The campus is surprisingly dead. I feel like there's some cool stuff lurking around, but without any students around it feels like any other conference center. Also, our section of Cambridge is a ghost town over the weekend.
• Jamboree (6): I didn't see the Alberta presentation, but other members of the team were quite excited by it. They were working on a toolkit for artificial genome construction. This somehow included a "Lego DIY biofab robot". I'm not quite sure how this all worked, but I plan on reading Alberta's wiki soon.
• MIT vs Waterloo (4): Woke up really early to get breakfast on the second day. It was worth it. Bagels, muffins, hard-boiled eggs, yogurt parfait's, fruits... I can't believe they ran out on the first day.

The MIT nerd crossing sign.

• Jamboree (7): Another day, another twelve presentations. Waterloo's own presentation about our chromosome engineering project was an obvious highlight.
• Jamboree (8): Bristol's presentation, which immediately preceded ours, included some pretty cool modeling software. They eventually won the modeling award.
• Poster Session (3): More posters... it's a bit frustrating that they're all spread out, there were a couple of teams that I wanted to talk to that I just never saw.
• Poster Session (4): Technically, I could have found posters by looking up the teams in the provided poster list. I think I lost mine.
• Jamboree (9): the iGEM Canada meeting was quite interesting. It'll be interesting to see how attempts to organize the Canadian teams unfold. There's currently a Facebook group.
  
• Hotel (6): The hotel had no free wifi, but it did have a single room with three computers (the "business center") where I could check email and (more importantly) accept a job offer. Collectively, the iGEM teams hogged the business center.
• Social Event (1): More free food (hosted by Jillian's).
• Social Event (2): Also free pool, bowling, and ping pong. What type of a bar has a bowling alley?
• Social Event (3): There was also a dance downstairs. I have never seen so many dancing scientists and engineers in one place. More awesome.
• Jamboree (10): Finalist presentations. I liked Heidelberg's presentation about developing standards for mammalian synthetic biology. The biologists also swooned over the idea of a universal endonuclease (Freiburg) and Cambridge's pigment-producing E. coli biosensors.
• MIT vs Waterloo (5): The city and campus came back from the dead on Monday. MIT looks a lot more like MIT when it has students swarming over it.
  
• Jamboree (11): Cambridge won the grand prize. Heidelberg was the first runner-up and Valencia was the second runner up. Alberta won for "Best Foundational Advance".
• Road Trip (3): Parking cost a little over ninety dollars from Friday until Monday.
• Road Trip (4): The return trip was still a nine hour drive.
  

RECOMBINATRON!

I spent the whole day programming for Waterloo's iGEM team. iGEM, for anyone who doesn't know, is the International Genetically Engineered Machines competition hosted by MIT, the goal of which is to figure out ways to design useful things out of biological components.

There's a subtle but important difference between iGEM's philosophy and conventional biotechnology, and it lies in the issue of design. People have been able to do things like getting bacteria to produce human insulin for a while now, by taking the human gene for insulin production and inserting it into the bacteria. What we haven't been able to do is to really understand the genes that we're dealing with.

Biological parts have been impenetrable black boxes: if something comes out of that box that we can use, that's great, but more often than not we would like to get into that box and tinker. What's more, these parts don't tend to play well with each other, and all sorts of chaos ensues when you start mixing together genes.

iGEM's approach is to create new biological parts. Parts that are not massively complex genes, but simple, reliable, reusable components that have intended purposes and known effects with other components. The goal, really, is to allow for true genetic engineering instead of genetic experimentation.

This isn't to say that all genetic parts created for iGEM are simple or reusable and it certainly doesn't mean that all that many of them are reliable, but we're working on it. The project I was coding today, for example, is intended to allow the team to predict the results of certain biological reactions, the end goal of which is to develop a repeatable method of inserting genes into chromosomal DNA.

At least, I think that's what it's for. Biology hurts my brain.

How to Buy an Airline Ticket

Well, I can finally say I've attended an MIT lecture. Dr. Belobaba from MIT's International Center for Air Transportation (ICAT) dropped by today to give a guest lecture on the topic of airline pricing schemes and revenue management.

It was an interesting talk that did a good job of explaining why airlines feel the need to have multiple fares for the same flight and to sell tickets at different prices depending on when they're bought.

Basically, airlines want to sell as many high-priced tickets as possible, but they know that there are a lot of people who will only fly at lower costs, hence the need for differential pricing. Then of course, the people who were willing to pay more won't be quite as happy to part with their money if they know that someone else is getting the same service for the same price, which is why airlines introduced restrictions on low fare tickets including "Saturday night stay" conditions that prevent the type of quick round-trips that businesses require.

But on top of these differential pricing schemes, the airlines also use revenue management. That is, they reserve a certain number of the more expensive tickets based on statistical models for how many they believe they'll be able to sell. This is sensible enough, because if they know that they will eventually sell out a given number number of expensive tickets, they don't want those seats going to starving students who will only pay the cheap rate. Of course, they don't know how many tickets they'll be able to sell exactly, so that's where the probability comes in.

Technically, you look at the expected value of some probability function to do this, but all that means is that the cutoff for reserving a ticket of a certain class is the point at which you get the same number by multiplying the ticket's price by its probability of being sold as you do when you multiply the price of a cheaper ticket by its probability of being sold.

Anyway, what this all boils down to is that, first of all, you won't get the super cheap tickets months in advance, regardless of the probabilities, because airlines know they'll be able to unload those later relatively easily. The cheap tickets actually start appearing once the revenue management system kicks in and it realizes that the expensive tickets are being undersold. Now, if the expensive tickets are actually selling really well than you can forget about the cheap ticket and start wishing you had bought one before the prices tripled, however the upshot of all this is that given the statistical anomaly that is the current economy the model forecasts might be overshooting slightly.

On Engineering Blogs and Bluffing

I've always been a big fan of the blogs published on the MIT admissions page. Establishment propaganda or not, I imagine they do a really good job of getting young little MIT freshmen excited about their school and preparing them for their first year.

However, I am a Canadian engineering student in second year. This means that: (a) I don't go to MIT, (b) I've already passed the excitement that is first year engineering, and (c) I can't really relate to institutions that bleed money.

Hence this blog. This blog is for every student that wishes their school was just a little bit better, for every engineer that secretly loves arts, and every arts student who really wanted to be an engineer; most of all though, this blog is for whoever the heck can find it.

But enough of the manifesto! I'd like to take a moment to bring the non-engineers up to speed so without further ado I present to you The Majugi Guide to Bluffing Through a Meeting of Engineers:

• XKCD is awesome. (Also valid for meetings of mathies, CS students, or internet junkies)
• The engineering song: "We are, we are, we are the engineers / We can, we can demolish forty beers [alternatively: fix anything with gears]" after these two lines start mumbling but try to join in for the part that goes "and we don't give a damn for any damn [mumble] that don't give a damn for us."
• Lady Godiva is the mascot / patron saint of engineering. She got the gig by riding naked through town on a horse.
• Regardless of your gender, you believe there are not enough women in engineering.
• Engineers who have graduated from Canadian universities receive Iron Rings. They are meant to be reminders of engineers' responsibilities as the iron was originally taken from a collapsed bridge in Quebec.
• You cannot legally call yourself an engineer in Canada unless you have the P.Eng certification. Don't worry though, you can still blend in with engineering students by calling yourself a plummer (supposedly -- I've never actually heard anyone use the term).
• If you're really having trouble breaking the ice, flap your arms together like a seal and repeat "arts, arts, arts" in your best seal-impression voice. [I can't claim to have come up with this on my own, but it's a sure-fire way of amusing engineers.]
  

...and for those of you who knew everything on that list I present The Majugi Guide to Appreciating Arts -- ie How to Avoid Being a Complete Douchebag:

• Don't do that artsy seal impression in front of arts students.
• Pick up and read a campus newspaper every once in a while.
• Note that arts students actually have time, so they make great recruits for thankless but crucial roles in organizations such as Engineers Without Borders and student governments.
• Student film festivals are amazing... particularly if admission is free for students.
• Drama productions are usually surprisingly fun. Try to go on the last performance on the last day when they'll often allow heckling.
• You're not a computer power user until you've used it to compose music, draw, do some 3D modelling or animation, or something similarly artsy. A very elegantly coded hash sort does not count.
• To develop a quick appreciation for visual artists, try making your own graphics for a website, or a video game, or for the GUI of any fancy software project you might be working on. If you've tried this and you're smugly thinking it was easy, show your design to a non-engineer and watch as they recoil in horror.

Thanks for reading. Homework beckons.