Biochemically Inclined

Na Na Na Na

So, it’s been a while. It’s been a long time actually, but I am in fact still I alive and I’m doing just fine. Classes ended up turning out about as well as they possibly could have and I walked out of finals with an 8.5 GPA. Hooyah. Since the classes have been over I’ve been taking a rare opportunity to take a deep breath and… Do nothing. Absolutely nothing. I’ve been sleeping in, I’ve been taking naps, I’ve been playing video games and reading books. I’ve spent these last couple weeks doing nothing but enjoy life. I’m back upstairs in the Mortimer house and Colson has moved back in. The newest addition to the house is Ben, and I have to say that the current 5-man composition of the place is probably the best that we’ve had yet. Another friend of ours named Biagio might yet move into the final room, but I have mixed feelings about that whole situation since we’d be running the risk of having the universe implode due to the incredibly high concentration of awesome in the house. To summarize, life is good.

On the other hand, I’m having my first ever, “Shit, life is real” situation. A good friend is going through some things right now and I’m still really working on wrapping my head around how it could affect him and our friendship. That being said, I’m pretty optimistic about the whole situation. At the end of the day, especially based on what an outstanding person he is, I feel as if life will go on more or less unchanged. I love the guy to bits.

In other news, Chelsea FC is in the final of the Champion’s League. I get knots thinking about it right now because I’m so nervous/excited. We’re facing off against Bayern Munich and both teams are missing quite a few key players through injury, so it’s a tough one to call, but I’m envisioning Drogba taking apart a depleted Bayern back line. Or Torres. Literally nothing would make me happier than Torres scoring a hat trick in the final. Oh my goodness.

Anyways, I’m just trying to get this thing going again. I’m not nearly as busy these days and I’m actually doing something interesting with my life again. Much like last summer I’ll be writing about the research I’m helping out with, only this time I’ll actually be talking about lab work rather than discussing the pro’s and con’s of hydrostatic tractors. Woof.

Vava Voom

Classes are done for another semester and that means that once again have to win this biannual war of attrition against fun. Over the next 15 days I’m faced with 3 finals, a short excursion to Vancouver to take in some theatre, and 14 other days that will undoubtedly be sunny. There will be fun things happening. The beach will be tempting. But I must somehow persevere. I have confidence though, because this year I have a few things on my side.

1. Molecular microbiology is not cumulative. This is huge. Up until yesterday, everyone in the class was under the impression that we had to somehow memorize the myriad papers we looked at as a class, right down to the experimental conditions and positive/negative controls. I was concerned, but confident. Now? I’m laughing. This is a big midterm now. If I do really well here, I could turn around the worst midterm I had this semester into my best final grade. 

2. Biochemistry 300B. There’s no final. I’m done. Four midterms. Boosh.

3. Biochemistry 300A. This could be annoying, but I just essentially need to read a few chapters, take a few notes, and go over a couple of papers again. It’s a test from Dr. Briant, so I think it should be just fine. Also, this is only for the second half of the course. That’s right, not cumulative. Living the dream. 

4. BCMB 301B. This has the greatest potential to suck. Memorize a few lab procedures. Memorize a few really specific mutations and rare strains of bacteria. Stellar. 

I’ve taken one afternoon to do nothing, and this morning I’ve not done a lot either, but I think it’s about time to crush some studying in the library. These next couple weeks are going to suck, but then I have two branching paths for my future. Down one path I start work fairly quickly and I fast become a leading expert in the field of x-ray crystallography. Down the other path, I go to Australia for a couple of weeks, and then I start work and fast becoming a leading expert in the field of x-ray crystallography. Both seem pretty good to me, although I think it’s pretty clear that I’d rather go to Australia.

I’m going now. Things to do. 

It’s Only Life

Most of the way through March and the inevitable has occurred. I’ve hit the wall. I’m finding that dredging up the motivation to hit the library and put in the hours that I have been is more difficult than before. I suppose I should say that finding the motivation has been really tough, because after this weekend I feel like I’ve hit the reset button. A Friday night out for some sushi with all the guys, followed by a full on day of drinking and debauchery on Saturday, and I’m feeling pretty ready to write a lab report.

Not really a lot to add. Just saying, we had a slight dip, but we’re back.

Again.

It’s another drizzly Friday morning and I’m once again enjoying the break between my lab and my lecture by relaxing in a comfortable seat while watching ducks scoot around on the pond outside. Americano in hand, and a pumpkin scone sitting beside me; this is, without a doubt, a very pleasant way to enjoy the morning.

Since last updating I’ve managed to write yet another exam, and once more my professor managed to return it in pretty impressive time. Yet another A+. I realize that advertising your grades to the world is frowned upon by a lot of people, but to hell with that. I feel like the hours upon hours I spend taking notes from my notes, taking notes from my notes from my notes, making summaries of said Inception like notes, drawing and labeling diagrams, and finally simply just poring over all of my work completely justifies it. I work pretty darn hard, and I don’t think I should have to be sorry about being proud of my well earned achievements. Then again, there’s a lot of social norms that I don’t really care for… Most of which somehow involve shielding the delicate emotions of others. Whatever happened to the whole sticks and stones thing? Remember? The saying we teach children when other kids are being shitheads? Funny how that goes out the window at some point.

In other news, Stacey has been gone foralmosta month and a half now. That first month seemed to fly by pretty quickly, but the last two weeks? Not so much. We were both hoping that after the first little while we might get used to being on the opposite side of the planet, but thus far there has been no such luck. I do need to take a moment to just appreciate the hell out of technology though. Thank you, Skype, for existing. It’s pretty amazing that even while my girlfriend is on another continent, I can see her face, hear her voice, and get to speak to her every day. I can’t even begin to imagine what kind of brutal trial a long distance relationship would be 20 years ago. Trying to organize phone calls? Whatever kind of primitive semi-useful e-mail there was? I shudder to even imagine. So yeah, technology. You rock.

I’d also like to gush for a second about the coolest thing I’ve discovered in the last little while. Fitocracy. This website combines my love of fitness and video games. Log your workouts, track your progress, and in the process you accrue points. Get enough points, and you level up. Complete challenges and quests… It’s got it all, and it’s all centered around being healthy and fit. Stacey and I are both currently using it to track our workouts, and competing against each other to see who can be the highest level when she gets back is pretty fun. The only problem is that swimming, in which she used to compete at a varsity level, is worth an absurd amount of points. Time to start hitting the ergometer, it’s my only hope! If you’re looking for a fun way to motivate yourself to exercise, I would certainly recommend Fitocracy.

Unfortunately, with all the schoolwork that I’ve been doing, I haven’t had much time to consider writing anything very interesting or remotely thought provoking… I had imagined that I might write some little pieces on cool regulatory systems and whatnot in bacteria, but I’ve since realized that my primary readers would probably have no clue what I was talking about. It’s pretty funny how easy it is to forget that the basics of genetics and cell biology aren’t really common knowledge.

Once again, there is a duck that looks like he’s got a problem with me. It could be the same arrogant looking mallard as the last time.

Oh dear. A seagull has just moved in. We could have fight on our hands. Just as is so common in street fights these days, nobody is trying to break it up. People are just pulling our their phones to record it. Society, man.

Lull.

It’s been another busy one. It’s been real busy. Reading break is well and done, and we’ve actually gone through another week of classes already somehow. Midterms for both 300A and B were written on the same day again Tuesday and somehow were both marked and returned on Wednesday. That is a level of speed that I have never before experienced as far as tests go. I’m happy; no, overjoyed to say that I’m throwing a couple more into the win column for this week. A pair of A+’s will always feel good on the first week back from reading break though. What did I learn from this experience? Spending your reading break actually reading has some pretty huge benefits. 

So now what? Well, right this second I’m enjoying a well earned break between the second half of my BCMB lab and my first biochemistry lecture of the day. I’m enjoying the morning light, the rain drops falling on the pond in front of me, and the ducks splashing around looking for some good eats. On a longer timescale, I’m really just gearing up for yet another midterm next week while trying to ignore how long 5 months really is. I’ll come back to the 5 months, but I find it strange that in a semester where I only have 3 lecture courses that I’ve already had 5 midterms, and I have to yet write another 3. Crazy.

But 5 months. I suppose I shouldn’t really say 5 months anymore since on Sunday I’m only looking at another 4, but still. It’s a pretty long time. It wouldn’t even be that bad, but when someone you care about is on the other side of the planet, living in a country populated by a whole lot of scary/mean/extremely poisonous animals, it’s a long time to worry. It’s funny though, because I can now totally relate to things that my mom has said before… “Oh, I’m really enjoying it out here”, is answered by “But you aren’t enjoying it too much. You have to come home”. I get that now. I’m on board. Oh well. If I’m being totally honest, it feels like this last month has flown by pretty fast. It definitely helps that I’m so busy with school.

… 

Except for right this second, and I’m going to continue to savour this for now. I currently have a duck staring at me through the glass, so I’m going to go and make faces at him.

Schadenfreude.

Most people who’ve known me long enough to have a night out on the town with me are well aware of the fact that I do not like going to clubs. I’m a pub guy. Give me some warm lighting, a solid table, a good group of friends, and a handful of pitchers. To me, that is the ideal night out. The drinking game you play? It’s called drinking. You just drink, and then you drink more. In between you can tell stories, reminisce, enjoy some laughs. This is not the experience you get in a club. In a club, you get the experience of no lighting, paired very nicely with a combination of sweat soaked “bros” attempting to gyrate their pelvises on complete strangers butts, absurdly overpriced drinks, and music so loud that you have to yell at someone a foot away from you so that they can hear you. That doesn’t sound fun to me, and generally when I do somehow get convinced to come out, it isn’t. Sure, I had a couple of years where I thought it was a blast, and I honestly could not get enough of it; however, now that I’m a little older (a very very little) it’s not really my bag. That is, I thought it wasn’t, until last night.

Last night, I realized what I had been doing wrong in the past year or so of going out to clubs. I was trying to have fun, and I was trying to meet girls. Well, let me tell you, I was doing it all wrong. Now that I’m locked into a pretty awesome (albeit temporarily long distance) relationship, I have no interest in trying to meet girls, so was that the thing that was holding me back? Now that I’m not trying to meet girls, I can focus on just having a good time? Not quite. You see, last night I was the only male in the group of friends I went out with. Being the only male, and a male who is not in any way interest in picking up girls, gave me an interesting perspective. When I say interesting perspective, I mean I got to hang out and dance while watching guy after guy creep up behind my female friends to try and carry out the aforementioned gyrating. Initially, I thought it was hilarious, but then I realized both the frequency of the approaches, and how literally not one of them tried to actually talk to any of them. So, being the only male in our group, and a physically large male at that, I got to play life raft all night. I just got to casually dance guys off of my friends, gently shepherding them away towards the rest of the sweaty dance floor. It was awesome. I might have felt bad if any of them asked my friends’ names or, really, if any of them did anything other than try to essentially dry hump them, but they didn’t. So, what was I doing wrong in clubs? I was trying to have fun, when what I should have done was just stop really creepy dudes from having fun at the expense of my friends. So yeah. Schadenfreude and all that. It’s my favourite. 

Nope.

Nuh uh. I refuse to let this thing die. It’s happened all too often in the past, and I won’t stand for it. So, why haven’t I written anything in here for a while? I suppose I’ve been pretty busy with school, but I don’t know, I certainly could have found time to write something. It’s probably that now that I’m in school there really isn’t that much that I’m doing other than study, which isn’t exactly the most stimulating topic of discussion. Actually, I’m writing in this write now in an act of blatant procrastination. Although, because I am my mother’s son I am able to rationalize anything, thus I am allowed to take this study break since I just finished a review session for biochemistry with Dr. Boulanger. Boom. Segue. I swear I didn’t even mean to do that. Dr. Boulanger? Who is this guy? Well, he happens to be the fellow who I will be working for/with over the next two years fairly extensively. I’ll be spending the summer in his lab as a co-op student, followed perhaps by a directed studies project with him in the fall, and after that he will be the supervisor for my honors thesis, as well as my co-op employer for next summer as well. Yup. It’s pretty damn awesome, I’m not going to lie. He works on elucidating the 3D structure of proteins and characterizing them (kinetics, mechanism, etc.). He also happens to work fairly closely with my favorite professor thus far in Victoria, Dr. Wulff. Dr. Wulff works in medicinal chemistry. Where is this all leading? This is leading to my two favorite professors teaching me about drug design, i.e. the general field in which I would like to spend my scientific career. I honestly could not have lucked out more; however, I do like to think that, at least to a certain degree, this has come about as a result of the hundreds of hours I have spent studying over the last few years. To a certain degree. A little.

…

Okay, it was mostly my brown nosing. I’ve come to terms with it, and now you can too. I’m pretty much all set to go and do some studying now though. I feel like I should get an A+ on this next exam so that Dr. Boulanger doesn’t think he’s made a mistake in choosing me. Enzyme kinetics here I come.

BALLS.

BALLS. Balls, balls balls. I’m so eloquent it hurts. Seriously though, I’m taking a short break to let anyone who cares know why they won’t see or hear from me over the next little while. I’m usually a guy who doesn’t do a lot of looking ahead as far as when tests are coming up. Usually I just study every day for a while and when it turns out I have a midterm in a few days, it doesn’t take much more than a little bit of “maintenance” cramming to get everything in my brain that’s necessary. This time I did look ahead. This time I am glad I looked ahead.

Biochemistry 300A and B will be the most difficult classes that I have taken at university thus far. I mean that from an objective stand point, because obviously any class that has ever involved numbers has been a pretty huge struggle for me, but that is not the point here. The point is to build up how big and scary these courses are. Let it sink in. Let it marinate. Has it marinated? Are you really feeling to your core how difficult they are? Excellent. We can move on. 

As I said, I looked ahead. I took a gander; a little peak. Turns out that my biochemistry 300A midterm is at 12:30 p.m. next Tuesday. Woe is me. I have not been keeping on top of things too well thus far, so I’ll have to spend some time on that in the next little bit here. Naturally I moved on to look at when my biochemistry 300B midterm is. Well, that would be approximately one hour beforehand at 11:30 a.m. on the same Tuesday. Remember what I said before? Balls? It’s making sense now. Moving on to the Thursday, we have a nice little molecular microbiology midterm as well. Then there are the BCMB lab reports.

What I can’t decide right now is whether I’ve forgotten how to be an effective student, or if this semester is really as bad as I feared it was going to be. Oh well, the coffee will flow and I will lock myself into the library, and I will prevail. It probably doesn’t hurt that I happen to know a pretty young lady who happened to get approximately, give or take 0 marks, 100% on the first biochemistry 300A midterm last semester. I suppose approximately is the wrong word, but then, I’m well aware of that. I just really enjoy approximating numbers. 

Stupid numbers. 

THIS IS A SUMMARY.

Woah. Been a while. I made a liar out of myself again when I didn’t end up writing a single thing whilst in Calgary, but whatever, I had family to spend time with. Christmas was lovely and I was given the most excellent present: a new Chelsea FC kit. Man, they’re nice this year.

New Year’s went well. Being in Nanaimo was nice and I got to see a lot of people from high school that I hadn’t run into in ages. I also had a friend come over from Vancouver for the occasion and I think it went well all around. 

Back in Victoria now, chilling out in Mortimer House again; the old Bunker. Brand spankin’ new 50 Mbps internet connection is pretty delectable as well. Unfortunately things are a little hectic settling back into school, but I’ve decided I need to get A+’s in all my courses, just to try and stay on par with this one friend of mine. The friend from Vancouver!

Oh. Right, I guess girlfriend. My girlfriend from Vancouver. Yup, that happened. Will I elaborate? Probably not. This is a place for my own vain opinions and whining, not for mushy emotions. Just anger, frustration, and all that other jazz. I will probably even write something meaningful at some point! Be prepared for me to get excited about different enzymes and pathways over the coming months. It’s going to be a blast.

Paradigm.

Well, I’m a liar. I went and told you that I would be completely silent until my glorious escape to Calgary and the west, yet here I am. Now, I’m partially breaking to silence because a friend recently inspired me to actually write something thoughtful again rather than continuing my barrage of insipid updates about life in Saskatoon, which generally could be summarized by saying “Wah”, but I also decided to break the silence because I had a realization this morning whilst laying around in bed determining how to break down my day Note: I’ve determined that “whilst” is far superior to “while” because not only is it more fun to say, it also sounds very whimsical. Who doesn’t like things that are whimsical? Probably the same people who don’t like dogs. Terrible. 

I know you’re all just dying to know about this moment of insight, so I won’t delay any longer. This morning, whilst laying about in bed, I was thinking about DNA extractions. More specifically I was thinking about what steps I had left to complete on my last gasp attempt to get high quality DNA from a pesky canola line that my last primer set is meant to amplify. Except, this time I didn’t think about the physical steps I needed to take in order to complete it, i.e. centrifuge, remove supernatant, wash, centrifuge, remove supernatant, re-suspend. This time I thought about what I needed to do with the actual molecules. This time I thought that I needed to separate by DNA from my ethanol. That I needed to wash away excess salts. That I needed to ensure the pellet dried to enough to ensure that ethanol (a PCR inhibitor) wouldn’t mess around with experiment later in the afternoon. Now, this line of thinking may seem like it’s pretty straight forward, but it’s actually the exact converse of how I’ve been thinking up until this point. I guess it’s easier to illustrate what I mean if we go back to the beginning of the extraction. In previous times I would have thought about how I needed to the incubate my material in CTAB buffer before adding chloroform and vortexing. Now, this is a completely accurate description of what I would be; however, I now think of it in terms of my need to lyse the cells, solubilize my DNA while breaking up lipids, and to separate my nucleic acids from proteins.

I suppose it’s less of a new way of thinking and more a new order of thinking. What I’m getting at is that before my time in the lab here I would think about the steps taken in a protocol I was following  in terms of reagents added or actions taken first, and I would then remember why I was doing it. Now I think of what needs to be accomplished first, and then think about what reagents or physical manipulations I could use to achieve my task. This may seem like a pretty simple thing, but to me it feels like a pretty profound shift in the way that I think and in how I analyze situations. I feel that this can only need to positive things in the future. And that’s all until Calgary.

Probably.