Meeting My Match

            I think I’ve finally met my match with respect to doing lab work in my UROP. Over the summer, I was in a happy little bubble of being able to do everything nicely, as long as I wasn’t doing stupid things and messing up what reagents I was using. While I knew this wouldn’t last forever, I had hoped it would last slightly longer than it did. Alas, it was not meant to be. As it turns out, I’m really good at getting qualitative results. But if you ask me to get anything that needs to be analyzed numerically, it’s a whole different ball game.

            For the past few weeks, I’ve been running RT-PCR reactions in an attempt to analyze the genetic expression of certain genes in the cells that we’re testing. Let’s break this down a little. The way RT-PCR works is that you mix a bunch of reagents (which is a fancy term for chemicals that make reactions happen) together in a test tube, and then add some of each reagent mixture to a 96-well plate that looks like this:

Along with the reagent mixture, you add some cDNA, which is DNA that’s been transcribe from RNA. Basically, the way it normally works is that DNA is transcribed into RNA, which is then translated into proteins, which are used throughout your body for various functions. In this case, RNA is used to transcribe into a form of DNA called cDNA, or complementary DNA, so called because it’s made by putting together the bases that are complementary, or match with, the RNA strands. In general, this is useful because the genome contains a lot of DNA sequences that don’t actually code for anything, and aren’t all that useful. These sequences get removed, through a process called splicing, before the RNA is translated into protein. The theory is that since you’re making cDNA from RNA, the splicing will have already occurred, and only the useful DNA sequences will be put into the cDNA.

Whew. That was a lot of technical stuff... unfortunately, we’re not quite done with it yet. When you mix the cDNA with the reagents and load everything into the 96 well plate, you then stick it in a machine that modulates the temperature such that the cDNA replicates over and over again, creating the piece(s) of DNA indicated by the primer sequence that you put into the reagent mixture. These pieces of DNA are your product, and the computer program records how much of the product there is over time, and does a bunch of calculations with it. (Don’t worry, I’m not going to bore you with how the calculations work.)

Okay. Now we’re done with technical stuff. The fact of the matter is, this test requires a level of precision that qualitative tests don’t. I have my days where my precision is good, but it’s surprisingly difficult to stand for 2+ hours at a lab bench, doing nothing but pipetting reagents and samples together, and still be accurate at the end of the 2 hours when you’re trying to load everything into the plate. And since this is a computer program, it has levels of precision that I couldn’t even hope to achieve. Granted, this means that there’s some amount of flexibility in the test, but not a whole lot.

SO, I’ve basically spent the last few weeks trying to be computer-level accurate, which seems to be more or less impossible. But it can’t actually be impossible, because people run these RT-PCR tests all the time... so there’s got to be some way to do it well, right? It’s mostly just frustrating because things went well over the summer, more or less, and now I’ve found one test that I just can’t conquer. For whatever reason, and despite the fact that I’ve run the test multiple times over the course of the semester so far, it refuses to work. My grad student keeps telling me that it’s just a matter of practice though... so I’m going to keep going with this and hope that it eventually works. And not just for the sake of my sanity, but for the lab’s sake as well- the reaction plates and reagents aren’t cheap! :P (Not that I think my using a few more reaction plates is going to break the bank or anything... but you never know.)

In other news, I do actually occasionally have a life outside of schoolwork and UROPing, as evidenced by the Roadkill Buffet show I went to with a couple of friends on Friday night. Roadkill Buffet is our improv comedy group on campus, and they’re really, really funny. Improv comedy basically works by setting up a couple of scenarios, with audience input, and having the actors act out the scenes. Since they’ve never seen these scenarios before, they have to think on their feet and come up with possibilities while we, the audience, are watching. It’s not something that a lot of people can do, but when you can do it, it’s hilarious.

This week, I’m looking forward to seeing my family, who are flying out to Boston for my birthday. They’ll be here for about 2.5 days, which isn’t really enough time to see the town, but it’s probably enough to start. And they’ll be able to go out and look at Brandeis, which is one of the schools my sister is looking to apply to. So yay, I’ll get to see my family! :D Next weekend is going to be super crazy though, because my family will be here until Saturday, and then Sunday is Apple Bake, our annual cooking competition in the dorm. I’ve decided that I’m making three dishes (Apple Kuchen, Apple Cinnamon Roll Muffins, and Apple Cinnamon Pull Apart Bread). My suite’s kitchen is going to be a little bit insane on Sunday though... so we’ll see how we get through that. I figure if we can survive Apple Bake, we can probably survive just about anything. (The reason for the predicted insanity is that I think almost everyone in my suite is entering a dish, if not many dishes... so the kitchen will be crowded, to say the least.)

Anyway, I should go do homework, so that I can be prepared for the craziness that the end of this week will probably bring... I hope that you all have a good week!

HOCR Confessions

Full disclosure: my favorite part of living in Boston isn’t the fact that I go to an amazing school, or that the weather is occasionally crazy, or that I get to meet ridiculously wonderful people every day. My favorite part of living in Boston actually only happens once a year. You might be thinking, “Alycia... is it really worth living in Boston, 3000+ miles away from your family, for something that happens once a year?” And I’d probably reply to that by saying “Yeah... that’s probably true. But there’s a really awesome stuff that happens year-round; I just really, really love this one thing”. And now that I’ve totally talked around any point that I was trying to make, I’ll come out and say it: I LOVE the Head of the Charles.

This year was especially awesome because I got the chance to volunteer at the Head of the Charles. I was a back-up timer both days this weekend. This meant that I was helping run the manual timing that was meant to serve as a check for the computer timing (which sounded like a very complicated process, involving two cameras, some timers, and a whole lot of scanning images). On the first day of the regatta, I was timing boats at the start line, which was a relatively calm process. The way the Head of the Charles works is that boats are started at roughly 15 second intervals to each other, and then they try to chase down the boats in front of them over the three mile race course. As a result, timing at the start line was a calm, collected process- basically all we had to do was mark down the time that each boat started.

A picture of me volunteering at the finish line. The girl behind me is Grace, another volunteer from MIT.

In contrast, timing at the finish line, which I did on the second day of the regatta, was something of a madhouse. By the time they get to the finish line, the boats are no longer in the correct order, and they’re not spaced out in regular 15 second intervals. The system at the finish line involves a boat spotter telling a line of waiting volunteers what the next boat coming down the course is, a volunteer running over to the finish line, and waiting until the bow (the front of the boat) crosses it, and then coming back to the person with the computer to tell them the time. When you’ve got boats coming in in quick succession to one another, this can get a little bit hectic.

Despite the craziness, timing the racers made for one of the best weekends I’ve had in a while. It was incredibly awesome to be able to see my high school team finish the race (one of the boats even came in first!), to see my friends on the crew team here finish, and to watch Olympians, both past and future, rowing on the river that’s part of the city that’s become my home away from home. I only geeked out a little bit at the Olympians... but they were only about 50 feet away from me! And their boat moved so smoothly through the water! The poor lady who was timing with me didn’t row... so I don’t think she understood what I was so excited about. But it’s not everyday that you’re so close to world-class athletes racing in one of the biggest regattas in the world, so I think my excitement was justified.

Giving up rowing last year was a bit rough for me. Honestly, giving up anything that’s been a central part of your life for over five years is going to be difficult. The great thing about rowing though, is that it’s not necessary to be actively rowing to be a part of the community. There’s a language that you learn when you’re a rower- about erging, and 2k tests, the difference between a fartlek workout and steady state pieces, and so much more. And that doesn’t just disappear once you’re no longer on the water everyday. There’s still people that I share that language with, which allows me to still be a part of the community of rowers.

That being said, I have every intention of becoming an actual rower in that community again some day. I’ve never been a particularly athletically inclined person, but rowing offered me a way to stay in shape that I loved, and I felt more like ‘me’ while I was on the water. As crazy as it sounds, I really miss the feeling that you’re about to pass out after a 2k, knowing that you’ve given your all, and no matter how you did, there’s nothing more you could have done to improve it. I miss the long head races (anything longer than a 2 kilometer race is generally considered a head race). I miss knowing that my legs couldn’t possibly do any more, but also knowing that they were going to have to do more, because there’s still 250 meters to go. I miss having a coxswain yelling at me, telling the boat that there’s something more we have to give to beat whomever we’re competing against. I miss getting up at zero dark thirty to drive to the regatta site, so we can rig our boats in almost complete darkness. There’s a lot of things that I miss about rowing, and while I know that I made the right decision about taking a break from it right now, wild horses couldn’t keep me from going back to it someday.

With that said, I’d like to issue a standing invitation to anyone who cares to accept- Someday I’m going to race on the Charles again. It might be in 10, or 20, or even more years. But I got a taste for what racing in the Head of the Charles is like when I was in high school. And I watched some really good friends get a medal last weekend. I want to go back and compete on the Charles again. Whether it’s in a club 8 when I’m a master, in a single (if I ever figure out how to race in a single and not be terrified of hitting bridges), or in one of the Directors’ Challenge events that people view as less prestigious, since you pay your way in rather than qualifying, I’m going back to the Charles. And you’re welcome to join me.

Smiles :D

           Today we’re going to try something a little bit different (to go along with the new layout I'm trying out... Let me know what you think). I think it must get rather boring hearing a list of everything I do every week... and I try to make it fun, but there’s really only so much you can do with a list of events. So today, instead, I’m going to present you with a list of an entirely different nature: a list of things that have made me smile over the past week (not in chronological order, because it’s all a bit confused in my brain...)

The police officer cheering for runners this morning. 

This morning, after working my desk shift, I went into my UROP lab to run an

experiment (before you freak out that I’m skipping school, I’ll point out that we had a day off today, for Columbus Day, which is also a thing that made me smile). Since the test only took about two hours, I was on my way back to the dorm right when the Columbus Day 10k was passing by. At one of the intersections on my way back, there was a police car blocking the intersection so that cars didn’t try to get onto the race route. Standing by the police car, continuously clapping his hands and yelling encouragement, was the police officer that I assume was driving the car. He could have easily sat in his car, drinking his coffee and staying warm while he was waiting for the last runners to go by. But instead, he was outside cheering them on, shouting encouragements that probably got some of the women (it was a women’s race) past the evil halfway point and into the home stretch. It’s little things like that that remind how good people are, in general.

Skyping with my mom

It’s my mom’s birthday this week, and since I’ll probably be pretty busy on

the actual day of her birthday, and I’ll definitely be busy next weekend, after her birthday, we had a pre-birthday Skype session. It was super relaxing to take some time out to just talk about random things that had been going on in our lives (and it was nice to see her smiling face :P ).

Watching two utterly ridiculous, but wonderful, movies

On Saturday night, we were sitting around not doing much, so we decided to

watch a movie. I’m not totally sure how it happened, but we ended up watching Hot Fuzz, which is not exactly the typical movie for my friend group. However, it was totally awesome. It may have been because of the group watching the movie, because I’m pretty sure that the movie itself is not something I’d usually enjoy. But for whatever reason, Hot Fuzz was completely hilarious, and suspenseful up until the last minute, and I loved it.

           On Sunday night (which wasn’t a school night because of the aforementioned day off) I went to one of the other floors in Burton Conner to watch Pacific Rim with one of my course 20 friends. Again, Pacific Rim isn’t a movie that I would have thought I would enjoy, but I actually liked it a lot. I knew from various people over the summer that it was a good movie, but it was a lot better than I had expected. The graphics were amazing, and although it was mostly a giant-robots-fighting-giant-lizards-from-under-the-ocean movie, it actually had a good plot and message to it. In case anyone is planning to watch it, I won’t give you any spoilers, but we’ll sum it up by saying that I thought it was a very worthwhile movie.

Professors who are willing to make time to talk to students

This one requires a bit of explanation... My 20.320 (Computational Analysis

of Biological Systems) professor holds office hours at a time when I have another class. I wanted to discuss the problems I had missed on my exam with him though, so I emailed him to ask if we could set up an alternate time to meet. Even though he had gone to a meeting in Florida, and was probably super busy, he took the time to respond to all of my emails requesting a meeting, and we managed to set up a time that works for both of us to meet this week.

Fall weather

The past couple of days in Boston have been gorgeous, and exactly the type of

days you would expect of a stereotypical fall season- crisp temperatures that are just starting to require a jacket, bright clear skies, and gorgeous fall colors on the trees. It’s the kind of day that makes you want to curl up with a hot mug of apple cider and marvel at how crazy nature is.

Speaking of apple cider...

I had something of an incident with apple cider this week... I was trying to

make a mug of that powdered apple cider. Since I didn’t want to lose any powder when I opened the packet, I was shaking the packet. Usually, this goes off without a hitch. Usually, I have absolutely no problems, and I get all of the powder to the bottom of the packet. This time, not so much. As I was shaking the packet, the corner suddenly ripped off, and the packet went flying across the room. This wouldn’t have been a huge deal, except that the corner I was holding onto contained some of the actual packet, rather than just the sealed part, so the packet that flew across the room was open... and it spilled powder all over the room. I kind of cracked up at this one.

Creative people

In addition to being filled with ridiculous things and very little sleep, this

week was filled with creative people. So many people I know have been drawing, or writing, or making music (I went to an MIT Symphony Orchestra concert on Friday... it was pretty much amazing) or just generally creating. My favorite thing I learned this week though, was that one of the freshmen who lives in my suite spent a month this summer crocheting a mantis shrimp. For reference, here’s a picture of a mantis shrimp:

Source

The level of detail required is ridiculous... I was extremely impressed with the finished product. Also, mantis shrimp are incredible for many reasons other than that they're beautiful... there's a web comic that explains some of them here (Warning: there's a little bit of fish-y violence that occurs). 

The reminder that it’s actually really easy to make someone happy

Probably my favorite comment of the week happened on Saturday night,

after we were done watching Hot Fuzz. We were all squished onto the futon in my room, which is probably only meant to hold three people, but was holding four in this case. It was late, and I was tired, so I had my head on one of my friend’s shoulders. At some point, I realized that I’ve got at least six inches and several pounds on her, and it was highly likely that I was squishing her, or at least making her shoulder rather uncomfortable. But when I asked if she wanted me to move, she said something along the lines of, “It’s okay. It makes me feel loved”, which was pretty much the sweetest thing ever, and also reminded me that it’s the little things in life that matter. I doubt that this is a moment that we’ll remember five or ten years in the future, and in the grand scheme of things it’s a fairly insignificant moment. But right then, and remembering it now, it made me happy to think that it’s so easy to brighten someone’s day. We are, as humans, actually incredibly simple, which gets lost in the shuffle sometimes. This was a good reminder that happiness, and love, can be found everywhere, as long as you know where to look.

There’s a ton of other things I smiled about this week... but continuing on for longer would probably test your patience as readers, and my patience as a writer. :P Also, I’m Skyping with a friend in about 20 minutes, so I kind of need to wrap this up... I hope everyone finds a lot to smile about this week!

Super Late...

Okay. Hi again everyone! It’s been a busy 2+ weeks, so there’s a good amount of stuff to talk about. I actually had to go back and look at what the last things I talked about were. So, without further ado, here’s a look at what’s happened in the past two weeks.

            School stuff: I had my first two exams (in Genetics and Analysis of Biomolecular and Cellular Systems). They were not great, as far as I can tell without seeing all the grades, but probably not insurmountable (i.e. there’s still enough of the semester left that I can probably recover from any mishaps on these tests, especially since in the future I’ll be more prepared for how the tests are written). I also had a bunch of written assignments due for my two communication intensive classes (Spanish and my lab class). Writing isn’t generally very hard for me... but when it’s in another language, either literally or figuratively, it’s certainly not a walk in the park. Writing in Spanish is hard because I have to actually think about the grammar on a more frequent basis than just wondering if I’m supposed to use ‘who’ or ‘whom’. The conjugated forms of verbs don’t just magically pop into my head the way they do for English, so there’s a good deal more thought that goes into writing a paper in Spanish. Writing for my lab class is hard because there’s a larger series of constraints about what you’re supposed to write, and how you’re supposed to write it. There’s basically a language of science writing that they’re trying to teach us at the same time as we’re learning a bunch of new lab techniques... so there’s a lot of thought that has to go into those papers as well.

            UROP: My grad student has been gone from the lab for pretty much the past week, so he left me with a bunch of stuff to do while he was gone. In combination with the various tests and assignments that I had due over the past two weeks, it was a bit difficult to complete everything that he wanted me to do. There’s still a couple of things left to finish up, but I was able to get almost everything done, which was nice. I’ve learned that it’s extraordinarily difficult to work around other peoples’ schedules sometimes though... As an undergrad, I’m not supposed to be in lab by myself, so I have to work when other people are in the lab. On Monday, I intended to go do some work in the two-hour break I had between classes, but I ended up not being able to, because the lab had a meeting I didn’t know about. Other than scheduling issues though, everything is going smoothly so far, which is nice.

            Choir: Our pieces are actually coming along pretty well, which is awesome, since there’s only about a month until our first performance. There’s going to be tryouts for the solo parts next week, and I’m trying to decide if I want to audition for those. I probably won’t, since solo-ing will require being able to sing out loudly enough to be heard over both the rest of the choir and the orchestra... and although my ability to project has improved, I’m not sure it’s quite at that level yet. We’ll see though. I’ll probably practice the parts over the weekend and go from there.

            Non-school things: There’s not a whole lot to talk about here, since I’ve spent most of my free time not doing much besides putting around on the internet and hanging out with my friends. We did do a couple of fun things in the past two weeks though. First, the Great Glass Pumpkin Patch took place on the last Saturday of September. MIT has a glass-blowing class, and a lot of what they do is make glass pumpkins to sell at this pumpkin patch. It’s not just a small thing, either. The women in front of us in line woke up at two in the morning to drive three hours into Boston, to get a ticket for the pumpkin patch, so they could be first in line. Since I’m not quite so dedicated, and since I have the good fortune of living on the campus where the pumpkin patch is held, my friends and I didn’t have to get up nearly that early to get a good spot in line. And even getting up as early as we did was totally worth it, since we got some gorgeous pumpkins. I bought one for myself, that I absolutely love... here’s a picture:

            The other exciting thing we did was celebrating one of my friend’s twentieth birthday. We went to a Thai restaurant in Boston, which was pretty delicious. Dinner was a lot of fun, not least because a table near us was celebrating a 21^st birthday, and kept ordering the special birthday drink that came with strobe lights and the birthday song played throughout the entire restaurant. It was a little jarring when the dimly lit restaurant suddenly descended into green and red strobe lights and singing over the loudspeaker, but it was actually pretty fun. After dinner, we walked a little further into Boston to go to an Asian supermarket, which was really cool. I had to convince myself that I didn’t need a teapot, because they were all really pretty and I was very tempted to buy one. Since I don’t really have loose tea leaves, it wouldn’t make a whole lot of sense to buy a teapot though. :P I did end up buying some jasmine tea though, which is delicious. I may need to go back and buy some more soon, since I’ve been going through my caffeinated teas at a somewhat alarming rate this semester. Luckily, there’s a whole aisle to choose from, so there shouldn’t be any shortage.

            It’s late, and I don’t have class until 11 a.m. tomorrow, but I should probably still sleep... so I’m going to end this here. Have a good week everyone!