Wednesday, October 29, 2008

Klaus Störtebeker

Legendary German privateer and pirate; seems a fitting name for a new aquatic friend.

He's about as surly and cranky as a weathered seafarer, too. Fits well.

Why I'm getting nervous...

Despite my earlier rantings on how annoying it is that Canadians seem more interested in American politics than our own, as the election down south draws near, I start to become quite nervous, much more than I was for Oct 14, in fact.

Perhaps it is because in Canada, the worst case scenario was returning the same party to power that already was, and in my opinion - even with my liberal-leaning tendencies - haven't done a bad job. More likely the real discrepancy is that as a student of science, Sarah Palin terrifies me. The Bush administration have been negligent with regards to science, but she goes further and insults the scientific process. And with a reported 22% chance that McCain could die in the next four years (as per an article in The Lancet), that makes things even worse. And that article didn't even take into account the very real possibility that by cutting funding to important studies on wild bear populations, he be mauled alive by angry Grizzlies.

Monday, October 27, 2008

Fettes Brot ist toll!

Since getting back home in late August, I've had more reliable internet access than I had over the summer, and so have been able to look into some bands I learned of this summer in Germany. By far my favorites, who I have listened to far too much over the last two months, are a Hamburg Hip-Hop group called Fettes Brot. König Boris, Doktor Renz, and Schiffmeister make up the group, and something about their style harks back to 1980's American Hip-Hop. If you're looking for upbeat stuff with the exotic-ness of being in a nother language, check these guys out. My favorite is a story about the heartbreaker Emanuela:

Was weißt denn du von Liebe? Von Liebe weißt du nichts.
Dich ham deine gefüle mal wieder ausgetrickst.
Du hältst dich für gefärlich, doch siehst nicht nie Gefahr.
Das hier ist die geschichte von Emanuela.

What do you know about love? You know nothing about love.
Your feelings are playing tricks on you again.
You think you're dangerous, but don't see the danger.
This here is the story of Emanuela.

Sunday, October 26, 2008

Trial and error .....and error......and error......

One of the hardest things I've had to learn to deal with so far in working in labs is the fact that not everything works on the first try. When I express frustration, others tell me that that's just the nature of lab work, and I shouldn't worry about it. The thing is, I can't help but let it frustrate me, as I view myself as a competent, capable and smart lab worker, and so when things don't work it ends up being a bit of a kick in the face.

I guess my problem is that I beat myself up for things that are not my fault and are beyond my control. Nevertheless, if I continually make mistakes and get nowhere, then eventually things start to look less like random chance and more like a systematic problem - a systematic problem known as me - and so I shoot to avoid this problem altogether. But when you aim for 100%, then even 95% is a failure.

The rational me understands that everything does not always work out when you run experiments, but the irrational me does not. The irrational me expects that I should be accomplishing everything perfectly from the start through to the end and so sets himself up for disappointment.

I have been known to actually blow experiments by rushing too much, often following one or two rounds of wrecked ones, as impatience begets errors. This sort of thing can turn into a dangerous spiral, and one must remind themselves that not all problems are their fault. My supervisor from this summer put it quite nicely on my review at the end: "Sometimes slow is fast enough"

I guess I just have to stop being so hard on myself. If not, grad school will be really interesting.

Tuesday, October 21, 2008

Who has time to vote, we have to see if Palin does something funny!

Now that the Canadian federal election is over, and we are back to where we started, it's time for conversation to turn again to why more people don't vote in this country. With a precedent-setting 59.1% voter turnout, I am ashamed in a way that 2/5 of my compatriots don't feel strongly enough about their nation to exercise their democratic rights.

Perhaps more so, however, is my frustration that more Canadians seem to care at present about the upcoming American election, than the one we just had here. Putting aside the comparison between campaign times, (this Canadian election took just over a month between being announced and having the result), it really bothers me that many Canadians seem to be much more interested in the politics of a nation that's not their own. A recent clip from The Hour quizzes Canadians on this on the street and shows it quite well.

Perhaps the best example of this problem was with the Canadian English-Language debate, which by unfortunate luck happened to occupy the same time slot as the American vice-presidential debate between Sarah Palin and Joe Biden. Many Canadians opted to watch this American showdown, instead of the more relevant Canadian leaders' debate, which was the only real chance to see the leaders speak this term for most people. t really concerns me that Canadians are more concerned with who is elected in the States when who is elected here will have a much greater impact on their day-to-day lives.

Perhaps for that 40.9% of voters politics are just entertainment. Or maybe they just don't care. Either way, it bodes ill for the future, as there will eventually come a day when this sort of thing matters. If we continue to be complacent about our government, we'll regret it sooner than some may think.

Friday, October 17, 2008

Reality at the atomic level

Reviewing my Protein Structure course notes, I came again across the slide in which the professor writes "Reality is quantum, but classical approximations are convenient"

He made a very convincing case for why, a hundred years past the development of quantum theory, we still think of atoms as "balls on springs" when in reality, they are nothing like that. They are grains of sand held at the appropriate distance from each other, with a fuzzy cloud of mist in between that manages to hold it all together.

The things is, it's really hard to quantify just how fuzzy that cloud is, and so it becomes difficult to know how the system will behave when you want to do something to it. In addition, even our fastest computers just can't seem to manage the calculations beyond the simplest of systems, and so it's not just that we're too dumb to grasp it, the problem really is hard to calculate.

So we use the balls on springs, but we must not forget how we know the world actually works at that level, because certain phenomena just don't work if we only think of things in terms of classical approximations. I'm perfectly happy to leave it to the real chemists and physicists for now, but should I need to explain something I don't understand, I will be sure that the first thing I do is throw the Dalton model out the window, and remember to embrace the world of the fuzzy at the femto scale.

Tuesday, October 14, 2008

Memorization and the amino acids

A student of biochemistry, I've often heard the complaint "I have to learn all my amino acids again?"

The trick is not to forget them. And this extends beyond my little corner of the academic world to the periodic table, taxonomic groups, irregular verbs, and schools of philosophy. One must be able to speak the language of their subject so that others can understand them, and so that one can effectively communicate in their discipline. But good luck convincing those who don't want to bother learning.

As much as I dislike the procedure of memorization for school, as I believe that it does not really test your ability as a student, there are cases where it is just plain necessary. At those times if you are doing it right, you shouldn't be working on memorizing each thing, because they should come with an understanding of the process. Past scientists may not have been the smartest when it comes to nomenclature and systematics, lacking the hindsight that we now have, but usually there is still a reason for the names and that helps to know what we're talking about. For example, isoleucine is an isomer of leucine. Did not see that coming. Histidine is the protonable ring. Cysteine forms bridges, proline forms kinks, and glycine is flexible because it's smallest. Glutamine is the amide of glutamate, asparagine is the amide of aspartate. Sure, they're not easy to know but the things that make each one unique are what makes them memorable, and by learning this way, it is a lot easier than beating one's head off the wall trying to figure out how to draw arginine again from thin air memorizing how the N, C, and H's line up.

Like my professor said a few years back, "You need to decide which amino acid you are like. Are you large and negative, like glutamate, or are you small and polar like serine? Maybe you're extremely bulky like tryptophan."

Wednesday, October 1, 2008

The Antigravity Gene

Ever since LOST hit the air back in my freshman year, I've been sucked into the character-driven serial drama shows like 24, Prison Break, Jericho, and most recently, Heroes. Unfortunately.

I can forgive Heroes the terrible wrap-up of their second season due to the Hollywood Writers' Strike, and even the lousy start to season 3 so far (Does any character ever stay dead?!?). What I have a much harder time letting slip by is the abominable attempts of the show to explain the superhero phenomena in the show through science.

I have no problem to watching a show that deals with paranormal effects and accepting the weird stuff that happens there, as I routinely do watching LOST. The time-travelling and craziness, while it messes with my head, is ok too. I can even let slide the concept of a "mutant gene" that supposedly gives wildly different results in every individual who carries it (I allowed it with X-Men, so I have to let it go here too).

Where I do draw the line, however, is the use real scientific terminology and imagery, in distorted fashion, to try and describe obviously fictional effects. Perhaps the show's creators hope to make the Heroes world seem plausible, but to anyone who knows much about science, their attempts just end up ridiculous.

When Mohinder, the scientist who narrates the show, points at a computer screen with what looks like bacteria tumbling around in solution in HD, and says "there's the gene!", it makes me confused. When he spouts off incoherence about enzymes and the bloodstream and adrenaline and genes, I get annoyed. When he works for 20 minutes and completes what would be 2 years of lab work in the real world, I get angry.

The icing on the cake is the perfectly arranged rainbow-coloured solutions that sit atop his bench. I wish my lab benches were ever that nicely decorated.

While I suspend my disbelief about superhero powers and the like that is central to the show, I have a very hard time stomaching their complete misrepresentation of what science is, and how it works. If they want to make it mad science, the scientist should be a mad scientist, and not the more-or-less rational individual Mohinder is. It's fine to have him sit there and mumble on in some incoherence about something the viewer can't grasp, but when the character talks about things you actually find in the textbooks, the writers of the show start actually lying by making fake connections between real things. It's the same as introducing Bill Gates to the show as a character and giving him a super-geek-ray power or placing the Eiffel tower in the middle of New York. Make something fictional, even take inspiration from the real world, but don't make lies about things from the real world.

The writers of Heroes obviously know nothing about how science works, and that is fine. They just need to stop pretending they do. Or at least do some homework, and find out what a double helix really looks like.