30 May 2014

On A Year Of Being A Research Assistant. Or, Yay! Science.

Hello! If you were, at any point, expecting me to update the blog, I am sorry for the delay. A lot has changed since the last post. I'm no longer a college freshman, for starters. More on that later (maybe). Here is a very informal and candid reflection on my first real job. It's mostly written for myself. I ramble a bit, sorry for that.
Background: I worked for a biology professor for a year. Let me add that I am not a biology major (math and chem!), and have, in fact, not taken a single biology course in college. I officially ended my job yesterday (May 9), and felt unexpectedly disappointed. Painfully disappointed, actually.

More background: My professor is one of the sweetest people you could possibly meet. He has an adorably silly sense of humour, runs marathons, and makes bad puns all the time. He works with haloarchae, which are organisms that love really salty conditions. These organisms basically thrive in conditions most other organisms die in. Do you remember any of those look-bio-is-super-cool-the-lake-is-pink-because-of-living-things images on the internet? Yeah, that is what he works with. He has worked them for almost two decades now. He loves them and is offended if you tell him that the cells stink. Would you like it if anyone told you that you were emitting foul smells? Cells have feelings if you work with them for long enough.

Some more background: The lab technician for the Archae-ology Lab (get the pun?!) is a stereotypical science person. And is pretty strict. Well, that’s an understatement. She has very high expectations, believes that dumb questions exist (even I do, but my cut-off is way kinder), and is a perfectionist. I was terrified of her. But, I was also really glad to have her around. My lab technique and understanding of lab protocol increased substantially because of her ridiculously high standards. And because I was always mildly scared of asking her questions, I often figured out things myself, often the hard way. It also meant that the few times she praised me, it made me irrationally happy.

And some more background: I was the only freshman working in the lab for most of the year. Each student in our lab works on a separate project, and projects are interconnected. My job was to find what this one specific gene did to Halobacterium salinarum. This gene (henceforth referred to as my gene) was next to some pretty essential genes and therefore, it was believed that my gene also did something important. And by something important, I mean that it affected bacteriorhodopsin (it’s a protein, gives these cells their cool colour) production.

And the last bit of background: So fun fact, my gene does do something. It doesn’t exactly affect bacteriorhodopsin production as much as we would have liked it to. But, it significantly seems to affect bacterioruberin (another protein, cool colour) production. Here, you should ask if this is statistically significant. (Random aside: you should do that everytime someone uses the phrase “significant change in <insert x>”). I don’t really know. We were testing for bacteriorhodopsin, not bacterioruberin. My professor says that this project presents some interesting results that he would take up in the future. I really hope he does.

I think the first thing I realized was how easy it was to become attached to the organisms you worked with. Within a few weeks, I called the cells “my cells.” I had dreams about gel electrophoresis and nightmares about centrifuges. Not joking there. If my cells actually grew after ten days in an incubator, it made my day. And, just like my professor, I don’t like saying my cells stink. They don’t. (Well, they do, but I have just become really used to the smell). I think my happiest moment in lab was when cells with my genetically modified plasmid were added to my professor’s database. It’s this really cool database he has where he records every cell variation his lab has (successfully) created. Mine is now listed as number 121. It’s stored at -80ÂșC in the second shelf of the freezer. And I think someone just added a 122. I was stupidly happy that my strain number is a perfect square of a prime number!

The second thing I realized is that science is slow. It’s not as if I didn’t know that; it is just that I truly appreciated it after working in a lab. It took me three months to simply delete my gene. Cells need time to grow. Sometimes they don’t and you have to start all over again. Sometimes they grow wrong. Sometimes you hate them, and then sometimes you feel that they hate you. But, with enough patience and agarose, things always work out. I believe things would have been significantly faster (yes, statistically) if I wasn’t a starry eyed freshman. But even then, I have spent countless afternoons transferring liquids from one microcentrifuge tube to another, running PCRs, staring at gel images and sterilizing lab benches.

I am going to digress a bit here to recollect some hilarious lab stories. You remember I told you how strict my lab tech was? There was this one time when I was using a new chemical, and had no idea about its disposal protocol. My lab tech’s instructions: “Read the MSDS. Don’t throw it down the drain. Figure it out yourself.” The MSDS for the chemical gave disposal instructions only if the chemical was in a certain state. I didn’t have it in that state. I spent a lot of time figuring out ways to dispose the chemical safely while she amusedly watch me struggle. It took me a while to come up with a plan, but I did come up with one, and it worked. It wasn’t the most efficient solution and in retrospect, I was really dumb, but I am never going to forget how to correctly dispose this chemical now!

And then, on the last day I was working in lab, this is what happened: My professor was going to show me the entire protocol himself. He did not have it written down, had never done it since coming to this college, and had two beers without eating anything. Joy. It turns out that if you are working with the same organisms since graduate school, remembering the protocol isn’t that difficult but using Excel to make graphs is still a pain.

But the most amusing set of memories I have are my own blunders. I told you that me being a starry eyed freshman significantly slowed the process. Here is how: I once ran a gel in the wrong direction. If you know anything about science, you should be wondering just exactly how stupid I am. Rite of passage--achievement unlocked. I once forgot to put my plates in a bag before placing them in the incubator. Let me rephrase that. I did not realize that I needed to put my plates in a bag. Fun fact: my cells died. A few billion of them. And then, once I labelled test tubes in the form of a math joke. I had multiple samples and multiple controls. I decided to label them as terms of a sequence. I am not really sure why I did that (I mean, I love math but this was just dumb). The problem was that two months later, I had no clue as to how I had chosen the order of my terms in this wonderfully stupid sample sequence. I did eventually find that I had described my naming protocol in my lab notebook. Oh, and then there was this one time I set ethanol on fire. I promise, though, that wasn’t a big deal. Even my lab tech wasn’t mad at me. Honestly though, my learning curve was a really steep one. I did make some embarrassingly awful mistakes, but I made them just once. I think I learnt from them. And I promise, most of my mistakes weren’t a by product of carelessness or stupidity but were a direct consequence of a sheer lack of experience.

There were also times when I did not really understand what I was doing. I should have. It would have made life better. I mean, I have an intuitive understanding of my work. But there are bits where I can't really give you an exact scientifically accurate description of my work. My friend thinks that is totally acceptable--I am a lab minion and am not expected to uncover the depth of my professor’s archaeal empire in one year. Maybe, that is true. I hope it is. On the other hand, one thing that is definitely true is that I should have maintained my lab notebook better. It isn’t incomplete or inaccurate, but it is ridiculously messy and hard to follow.

Oh, I should have added that I am no longer working for my professor next year. You remember that I haven’t taken a single biology class in college? Exactly. He wants someone who is more into biology. The fact that I am not formally and actively adding biology knowledge outside of lab is affecting the research. And so, I am fired. Honestly, I don’t even feel bad about it. He is right. I don’t have enough biology knowledge to continue. But the super sweet person that my professor is, he told me that as my academic advisor, he felt that I should join a lab in my major field as that would be better for me.

I have read enough about scientific research to know that failure is common. Biological research is notorious for being nearly impossible to replicate. Most things in science don’t work on the first try. I knew that going in. Cells died, but that was okay. I went in with full acceptance of the fact that things wouldn’t work. This did not mean that I did not complain or feel bad when they didn’t work. It’s just that I never gave up hope when that happened. Yesterday was the ultimate ending. I had this unrealistic and stupid wave of optimism throughout that my gene did something important (which it actually does), and that I would identify what exactly it did. My project ended on an ambiguous note: my gene does something important but not exactly what we thought it would do. Let me put it this way: I don’t feel satisfied or successful, when I think I deserve to feel both because I don’t have proper closure. What does my gene really do? I was supposed to find that. I didn’t really fail, but now that’s going to be someone else’s job next year. I also am childishly upset that these cells are no longer “my cells.” Well, they’ll always be my cells in the sense that I created the specific strain. But beginning next year, someone else will call them their cells. I know I am being irrational here. But I spent 108 hours in lab over the year. And I spent a lot of time thinking and talking about my work. I was also the only student working on the project, and it was my first one on such an intense level. I am allowed to feel for the cells. Yes?

Oh, and as a true math major, I signed off my lab notebook as if I was completing a proof. Maybe my professor is right. I need to work in my actual major field. But, if you ever work in microbiology lab, here is what I learnt:

1. Never transfer anything to or from an unlabeled test tube. Ever. The first thing my professor told me.
2. Cross contamination does actually spoil experiments. Want to run a gel repeatedly because the buffer was contaminated? I don’t think so. So, stop being awful, sterilize your bench before and after each session. The first thing my lab tech told me.
3. Things can always go wrong. There are many possible reasons. The most likely one is that you messed up.
4. There is a correct angle to hold the micropipette at. And never be stingy with tips.
5. Label things properly. Always. Math jokes aren’t appropriate names.
6. Respect enzymes. The delicate darlings can make or break your experiment.
7. If your lab uses mm/dd convention for dates, follow it. ¾ means that it is March 4, not April 3.
8. Autoclaving is science’s way for getting back at all the awful memes you have created on the internet.
9. Centrifuges are scary. Follow instructions exactly. Nightmares ensured.
10. Don’t hide your mistakes. Admitting them is always the better option. Even if you think you have corrected them just in time.
11. Love your cells. They are beautiful and adorable. And they don’t stink.

16 July 2013

Why film adaptations fail

EDIT: This particular answer on quora.com does a good job of describing why film adaptations usually disappoint readers: http://qr.ae/Ihtpz 

I recently watched To Kill A Mockingbird, the movie. Made two years after the book was written, the movie is Robert Mulligan’s take on the book. I was pleasantly surprised with the initial part of the movie. The first 45 minutes were wonderful. For all my dislike for film adaptations of popular novels, I loved these 45 minutes. Scout from the movie seemed very similar to Lee’s Scout; Jem was just as defiant; Dill was just as innocent and, Atticus was just as Atticus-y. 

But from that point on the movie, in my opinion, was a straight downhill ride. Tom Robinson’s court case is an important part of the book; but clearly, not the only part of the book. The film completely forgets Aunt Alexandra, Uncle Jack and many other things, which, contrary to popular opinion, are an integral part of the book. 

I was disappointed by a film adaptation yet again. Why is it that movies based on books always fail to impress the original readers? 

For example, every Harry Potter fan agrees to the fact that the movies are a very sad, sorry version of the books. They do a very poor job of conveying the complexity of the books. To a person who has only seen the movies, well, the good guy killed the bad guy and that is that. But for people who have read the entire series, there exists a long interval, which is filled with events, characters, and emotions. 

On a very fundamental level, I want the movie to stay true to the book. I want it to maintain every aspect down to the finest detail. I want the director to completely borrow the author’s vision. I want the movie to be a perfectly aligned track of the book. But that, rationally, can never happen.

Because basically, these movies strip down a book to its functional core, eliminate any part which doesn’t directly contribute to its understanding and then dramatize it. The worst bit is that the director enforces his creation onto viewers: his interpretation against that of the author, his imagination against those of the readers. I don’t want my image of the Great Hall tarnished by what someone else visualized it to be and I am sure others agree. The Atticus Finch in my head is not irritatingly pensive. A movie forces onto me its vision with an absolute air that is hard to shake off. Despite countless attempts, my mental Harry Potter resembles Daniel Radcliffe a bit too much for my liking. 

I know the simplest solution is that I choose not to watch further film adaptations of novels I enjoy reading. And that is why I am not watching The Fountainhead movie anytime soon.

12 July 2013

Wimbledon 2013

Thoughts post Wimbledon 2013:

I am a Federer fan. An all-out, no holds barred Federer fan. I sometimes wonder whether I follow tennis or whether I follow Roger Federer. So you can imagine my disappointment and my surprise when he lost in the second round at Wimbledon. Wimbledon, to me and to many others around the world, is the Holy Grail of tennis. It is tennis at its purest, sincerest and finest. Something about those grass courts, that dress code and the years of tradition brings out everyone’s best.

But before you knew what was happening, Federer lost in the second round. The unthinkable had happened. Before the first week was out, some of the finest names in the game were ousted by relatively obscure names. It has been called the ‘weird Wimbledon’ because of the sheer number of top guns who lost before the fourth round. I thought that probably this year, the Wimbledon was rigged. Could it be possible? But then, I rather have Federer lose than have Federer be accused of cheating. So, bad idea.

With my sole tennis hero being out of contention for the game’s finest honor, I was stupidly hoping that both Andy Murray and Novak Djokovic also lost. I mean, it was only fair: Nadal and Federer lose, so Murray and Djokovic should follow suit! A completely unexpected, new man wins. But that didn’t happen. Instead, we had them play the final.

I decided to support whoever swore less during the finals (see, I seriously am a hardcore Federer fan—I don’t know whom else to support in his absence!). So I watched the ‘Gentlemen’s Final 2013’ without supporting either players. I watched for tennis’ sake. I cheered whoever played better, which meant that I was praising both players’ shots and strategies. Oh, and for once, my brother and I didn’t fight during a Grand Slam final.

That, I realize, is the beauty of the game. One then begins to appreciate skill for skill’s sake; see sportsmanship in its purest and enjoy a game beyond its winners. The gates to the Centre Court are inscribed with lines from Rudyard Kipling’s historic poem: 

“If you can meet with triumph and disaster
And treat those two imposters just the same”. 

In today’s match, I felt that. I appreciated the pressure under which Murray played, with a constant reminder of 77 years of history. I appreciated Djokovic’s magnamity to praise Murray for handling this pressure and playing the way he did.

It is not just Wimbledon. Every game in its highest form exudes an aura of excellence, perfection and sportsmanship. It is just that today, in the absence of the compulsive habit to take sides did I appreciate it. So, as always, the Rolex ad has got it right: Wimbledon is where legends are made.

PS: No one can match Federer’s grace and dignity though. End of the day, it is peRFection for me!

As I post this I realize, that a lot remains same. The things I appreciated about Wimbledon last year are also what I do this year. I guess that's the thing with being one of the oldest tournaments!