Monday, April 28, 2008

You don't really exist

So I just finished reading Steve Grand's book, Creation, which was a really interesting exercise in looking at the world through a different lens. Although he aims the book toward the construction of artificial life, the insights he has are pretty cool as to what is actually real and what is not (here's a hint: everything is real, and nothing is real). The book was definitely a score from the discount shelf in Chapters. *self-congratulatory pat on the back*

An interesting point he brings up (pretty sure it wasn't his original statement, but I have no idea who its from) is that within the span of several (seven?) years, you as a person will have completely exchanged atoms with your environment. As such, we are all merely organization of atoms in space, that in turn direct the movement of other atoms, and eventually recycled to the external environment.

Within a certain amount of time, all of the original scaffold is gone and you are now made up of all the new atoms you have inhaled, eaten, and absorbed. Grand states that we are thus made more of energy than matter. Think about it. Think harder. It's sorta crazy, eh? Remember that wild party ten years back you remember having a blast at - well turns out you weren't actually there. The you that sits reading this now, anyway. Cue eerie twilight zone music.

Now of course, the you that was there in the past is the same organization of matter, and so there's little chance of a case holding up in court of a criminal stating he wasn't at the scene of a crime because the collection of cells and molecules that robbed the bank don't exist anymore. It does give reason for pause, however, and should maybe change our view of how we interact with our environment, as we're constantly in flux with it, and not separate from it.

Next week: How as much as you may think you ate bacon and eggs for breakfast this morning, you actually just had toast.

Wednesday, April 23, 2008


So, I'm going to be spending almost 4 months in Germany this summer. I'm starting to think I'm crazy; as this is a huge move. :S Alas, I am pretty much locked in to the trip now, and there's no turning back. So now, I must prepare, and hope that I have put enough thought into this trip to make sure nothing bad happens.

Plane ticket - Check
Rail pass - Check
Accommodations - Check first 2 days, Check next 2 weeks, and Check for the rest of the summer.
Work info - Check
Packing - Check having everything, just have to pack it all

I look at this, and apparently I've got my bases mostly covered; why does it keep feeling like I'm gonna go and completely forget something?

Monday, April 21, 2008

The problem with pre-med

Those who know me know that I like to complain about students in other majors. A lot. It's largely justification for picking the major that I did, and a bit of arrogance and snobbery on my part. I fully own my jerkliness in this regard.

In part due to this, this article on Wired magazine's blog recently caught my eye (Top 5 reasons to dislike pre-med students). The author states that he is trying to stir up a discussion, so I won't come down too hard on him for his sweeping generalizations.

A lot of his statements ring true to a lot of my feelings about lots of other students (see here, and here), but picking on pre-med students in particular just plays to the stereotype. There are students like this in all majors, and there are also many students studying pre-med that don't ascribe to this particular philosophy. That being said, there is probably a higher proportion in pre-medical, but I contest that you see the same thing in pre-law, pharmacy, pre-veterinary, teaching-oriented programs, many business and marketing degrees, and other technical or professional programs where good grades means getting a good job following graduation.

Our current system is broken, and really could use a reworking. In many programs, especially those mentioned above, the undergraduate degree is a means to an end and not the enrichment of knowledge that it was created to be. It does serve as a good meter of your persistence, tenacity, and adaptability, which is valuable from a potential employer's point of view. However, it seems more and more that a degree really doesn't say much about what you actually learned. The title of the degree no longer means that the student actually has passion for their subject; sometimes it's just what looks best on their resume. This is really frustrating to any student (read: me) who values knowledge and works hard to educate themselves.

Ah well. I just have to hope that someday what goes around comes around, and those that don't care to learn will see it come back to bite them. Failing that, voodoo dolls are always a cheap backup plan.

So for now I'll sit and whine. Grade 3 taught me that whining makes me feel like a bigger person, so that's what I'll do. However, I will continue to do my best; its the only way I know, and so far has not let me down. I will be honest and demonstrate integrity, I will strive to uphold the tenets of acadaemia.

After all, someone's gotta do it, and I guess I've just volunteered myself. :S

Friday, April 18, 2008

The Immunologist - slave to discontinuous thinking

Everyone's favourite militant atheist Richard Dawkins talked about the "tyranny of the discontinuous mind" in his book The Ancestor's Tale. This concept involves the natural tendency of us, as feeble humans, to try to divide everything into categories. We try to place all that we see as this or that, but never something in between. Or rather, when we do, the something in between becomes a new category, and not just a statement of the continuum between. Often you can find statements that prove this point.

"There are three types of phenomenon X:
a) extreme A
b) extreme B
c) some combination of the two "

Instead of setting up anything so stupid, all we need to say is that X falls between A and B, and ignore all the silliness of that list. However, our natural tendency is to try to divide continuous phenomena into groups of some sort or other. Reality gets forgotten and replaced with a model that categorizes whatever phenomenon we're talking about. This is the gist of the argument Dawkins presents, along with ample evidence of why it can suck.

I've seen first hand how this method of thinking can really harm the scientific process, at least the teaching of it. While In Dawkins' book he used ring species as the example of the limits of this method of thinking in phylogenetics, I have seen it in the context of immunology. This science is still working through its growing pains, still newborn with respect to its old-timer colleagues microbiology, cell biology, and chemistry. But in addition to that, it is a unique science in that the discontinuous, reductionist model no longer applies very well. There are specific instances where in vitro models have been helpful, but the science as a whole suffers from a lack of simplification usually possible in other subjects, that build from the ground up.

Immunologists classically try to break down all aspects of the immune response into discrete categories, but unfortunately, the harder you look, the more often you find that those distinctions are really just fuzzy boundaries, if not just two extremes of an continuum. I ran into trouble when trying to divide up cell lineages at one point because everywhere you try to define a complete group, you find that there is an exception. And in each of those exception groups, there is an exception to the exception. Big fleas have little fleas and so on. This tells me that maybe we're going about this the wrong way. A real revamp of how we look at this system is in order.

This isn't to say that divisions shouldn't be made, but they should never be presented as absolute divisions, as many the instructor seems wont to do. As soon as you start saying "This pathway applies here unless A of B or C or D happens", you're just asking to be proven wrong once E shows up to wreck your day. Its better to explain more of how the pathway actually works, and so predictions can be made. You can say, well based on what I know, if E happens, then I can expect this result. Take that, E.

Immunologists, take note. You're not going to get anywhere until you drop the reductionism and gain a better appreciation of (or respect for) the system you're dealing with. In fact, scientists in general should check themselves for this from time to time. Its all too easy to get caught in a cycle constantly breaking things down into groups until you reach a point where the groups themselves lose all meaning. This is the discontinuous mind at work, and in this case working against you.

The next time a biologist tells you that something falls into one of several categories, tell them they're lying. I dare you. No, double-dog dare you. Given enough time, you'll be proven right. You'll thank me. And to express your gratitude, you know where to send the cheque.

Thursday, April 17, 2008


So somewhere in between enzymology studying and preparing for Germany and everything else, for some reason, I got this image of the enzyme of study in the class and how the function of it might look if you were to look at it in 3D-space. I came to realize that although manufacturers of textbooks like to define proteins as

a) circles
b) ovals
c) ellipsoids
or d) oblong

and better textbooks show them as ribbon diagrams (one of which you can see at the top of this page), all of these pictures paint a really static picture of enzymes and proteins, and we really don't do them justice.

I came up with a better analogy than circles for proteins.* Transformers. Thousands of moving parts, all coordinated to align together for perfect function. In the case of allosteric enzymes, you have a complete transformation form one form to another. One form can perform reactions, but nowhere near as well as the others. Just like Optimus Prime can fight the Decepticons as a truck, but he's much badder ass in battle mode, complete with sword and all. My adrenaline is rising just writing this. You laugh, but just you wait.

Do you see what I'm doing? Combining science (boring) with a summer blockbuster movie (exciting!). I should teach this stuff. Or maybe I could turn it into a business. You pay me, I give you a sweet-ass analogy. We need more of me running the show when it comes to this stuff.

Patting myself on the back is the funnest thing ever.

Seriously, though, the reductionism that biochemists use to study proteins in many ways loses sight of the dynamics of the system. It becomes all to easy to forget that you're talking about a system that is extremely complex in its entirety when you're looking at what Asp36 binds to and how His253 is protonated and .......zzzzzzz.....

It may be time for a better, more holistic (though I hate that word) approach to biochemistry. And why stop there? molecular biologists get really hung up on the concept of genes and particular, specific functions of them, evolutionary biologists spend ages reflecting on relative rates of evolution and other mundane details, ignoring the big picture. We need a little more Hollywood in science.

Let's get Michael Bay in on this, he could make it happen.

*rather, it came to me in a bout of inexplicable inspiration

Tuesday, April 15, 2008

This is a study area. No popped collars allowed!

So every time exams roll around, a bunch of students I haven't seen before seem to come out of nowhere and invade my study space.

Where were they before? Studying somewhere that didn't infringe upon my right to study in peace? Did they have the misfortune of all beginning their semesters 12 weeks late? Or did they materialize from thin air, some psychic byproduct of my intense concentration on my studies?

Seeing as the school's population manages to remain roughly constant throughout this happening every exam period, I'd say option 3 is out (ignoring the possibility that they spontaneously combust as soon as I'm out of sight). And #2 seems pretty unlikely, so that leaves the first option, studying somewhere else. Except based on their attitudes, probably minus the studying.

An interesting tangent to the question of where all these students come from is why all of the invaders seem to loooooove the popped collars. There's also been a real increase in the usage of the terms "sup", "bro" and "dude" of recently. My daily quota of Chad exposure has recently been getting used up within about 10 minutes at the start of the day.

I'd tell these guys to leave the Abercrombie at the frat house and when you're at school to study, shut up and study. Its they least they can do, as their presence alone disturbs those who have come to rely on having a reasonably peaceful, quiet study space.

I would say that, if I wanted a quick trip to the hospital to get my face reconstructed.

Instead, I will mock from afar, and write derisive comments on the internet. Take that, Chads.

Sunday, April 13, 2008

Craig Venter on playing God

"Oh, we don't play"

Now if I've ever heard an argument against biotechnology, this is pretty much it in the superlative. Craigger needs to keep his ego at bay if he wants to win over the general public on this one.

For some reason when Venter comes up in class or discussion, my blood boils. Maybe it's because he's such an arrogant ass. Probably it's envy. Whatever the cause, I can't help but get mad because he seems to have got fame in the scientific community and even to a degree the mass media just by throwing money at things instead of the traditional method of systematic scientific discovery. This actually says something important about my bias of how I think science should be done. And not in a good way. Also, because I know I'm not alone, you can extend this to much of how the scientific community thinks as well.

I have stopped criticising Venter for saying he can do what seems impossible, Those people who do criticise him keep getting proven wrong. I have to respect the people that can actually deliver on their promises and while he's a egotistical, pompous jackass, he produces results. And does so in a way you'd never find an academic able to do, be it a question of resources or willingness to take risks.

So while Venter pisses a lot of people off, he's accomplished a lot already and shows no sign of stopping or even slowing down in his endeavours. He seems to have filled a void where the scientific community could not or dared not go. While he seems to lack a certain respect for the enormity of the research he undertakes, it may be that quality that seems to keep allowing him to push the envelope at the frontiers of molecular research. A shoot first and let the ethics committees clean up the mess later approach.

I have to respect his accomplishments and that he has driven science to new levels in the last 10 years. But while I'm forced to respect him, I don't think I'll ever be able to actually like the Craigger.

Unless his next big scientific undertaking involves making himself more likeable, that is.

I dunno though, next to making Venter agreeable, synthetic life seems like a walk in the park. Even the best science has its limits.

Saturday, April 12, 2008

I should be allowed to design final exams

So currently I'm done 1 of 5 of my second-to-last round of undergrad exams. woo.

This is, of course, a time when all the students I know, myself included, make a habit of complaining about every small detail of their classes, picking apart marking schemes, figuring out if-I-get-this-mark, I'll-finish-the-course-with-this, etc., etc., etc.

Somewhere in this process (or before it), we lose sense of what we're actually doing. I'm of the understanding that as much as it may seem like we're at university to get good marks so we can get into a good job, the actual philosophy behind higher education is (surprise!) learning.

If you've got a good professor, they will test you on your understanding and make sure you have actually learned the material. Those that genuinely get it and have understood the material should have no trouble, where those who haven't will suffer as a consequence. Unfortunately, truly good professors are few and far between.

From the professor's point of view, constructing an exam that genuinely tests that students understand is a very time-consuming endeavor when you can just pull a pile of multiple choice questions off some random database, stick them in a test, run off a bunch of copies, hand them out to the class, watch students struggle for two hours, then go home and pretend you're a good teacher. In fact, when tests are designed like this, some students can and do do well. Unfortunately, it's quite often the students who have no f*ing clue what they're doing that do well cause they've trained themselves to vomit up whatever random fact the professor asks for, where those that understand it lose out because they don't waste time studying irrelevant facts. Am I bitter? You bet.

So after 6 times thorough this cycle coming up 7, I've learned pretty well to gauge my instructor and anticipate what will be on my final. If the prof is a tool and will just ask random questions and mundane details that bear no relevance to the actual themes and objectives of the course, then those mundane details I will study. However each time I do this I feel like I sell a bit of my soul. Instead of learning the material in its entirety as I'm supposed to, I study for the test specifically, and then come out no better for it, having learned essentially nothing. Instead of pursuing the ideals of higher education and enlightenment, I am bowing to the economic machine that revolves around getting good grades.

As such, I am just as much of the problem as anyone else. Honestly, I am not willing to give up my career prospects and waste money that both myself and my parents have invested in this university to not get the best marks that I can. I see many other students in a similar situation (though there's many others that rank education somewhere below Guitar Hero on their list of priorities).

There is no incentive in place for students to actually learn material for the sake of learning unless they actually care that they do. We come to learn and in the end the only students that do learn are the ones that do it on their own time. This is a serious flaw in acadaemia, and it seems to be getting worse as education gets more and more commodified (is that a word?).

My solution: I get to decide what goes on my test. In fact, screw the paper sit-down-and-write thing altogether, and just let me have a meeting with my instructors and demonstrate my understanding. None of this stupid nitpicking over marks and weighting schemes and yadda yadda yadda. I prove that I'm a genius and know the material inside and out, and the professor gives me 100%. It's that simple. Is my arrogance showing?

If only I had control over the system. Things would be different, I say.

For now, I'll continue to jump through the hoops the instructors set up for me like the good little circus monkey student that I am.

But I won't like it one bit.

Friday, April 11, 2008


YHN signing on.

So after a bit of thought, and then a friend* mentioned about starting one of these for my summer abroad, I've decided to open up a blog. Besides, if Roger M. Phillips** has one, why shouldn't I?

So, if you're reading this, you're either
a) Friend or family member who I've directed here. Apologies for making you read my rants and groanings. Thanks for coming out.
b) An interested reader. OK, ok, I'm reaching here. No one is interested in what I have to say. Perhaps "someone who ended up here cause they clicked the wrong link" is more appropriate.
c) My future self, reflecting on the past. I sincerely hope that you haven't tried growing that goatee again. Some mistakes should never be repeated.

Welcome one and all, we'll try to have some fun. Stay tuned.

*I think he was joking. I played it off as such, because admitting in person that I'm starting one would be way past my comfort zone. I'm not secure enough in my nerd-ality to do so. I'll remain in the closet for now.

**Look for the Jan 15 episode, "Last guy to get his own blog"