Tuesday, March 29, 2016

Pretty sure DMEM is actually Kool-Aid and we’re all just cell chefs

Alrighty well the hardest thing for me to tackle during Module 1 had to be the hunger. The consuming, soul-ravaging, lab partner’s patience-destroying, insatiable desire for snacks. No, my hands did not shake when pipetting because of nervousness, withdrawal from fishing or other drugs, the effort of resisting the urge to belt out folk songs, or whatever other things cause most people’s hands to shake. They shook because *heart beats faster* EHS must not find out *eyes dart around nervously* I have *the voices reach fever pitch* snacks in my purse. Except not really. I don’t know what I would’ve done all those times we were working together in the evening if not for Bremy pulling out random snacks, although I’m convinced he only did so because he got fed up with me constantly being distracted by recipes on Pinterest… Hehe. Fed up. Puns. 

Picture of me reclining on a couch (if I had my life together). 
Actual picture of me. 














But in all seriousness though, the hardest part of Module 1 was probably learning how to be concise. I feel like up until now we’ve been taught the exact opposite of scientific writing. Use big words, sound fancy! If your audience has to look up a word – perfect! The mark of a successful writer is having your audience get so caught up in your rhetoric that the point of your words is almost irrelevant. But all of a sudden for us, it’s about what you write, not how you write it. No longer are we trying to leave our readers thinking “This is beautiful, these sentences are like a river of shimmering rainbow sounds in my head.” Now the goal reaction is, “Wow, this is so simple a monkey could do it! Maybe even my UROP!” Or maybe the schools I went to had weird standards for good writing. 

The rubric at least three of my K-12 teachers used. 

Besides that, it’s also what we’ve taught ourselves. Honestly, it’s weird to not really have page requirements. For years in school we’ve been told “minimum 6 pages,” and we’ve become masters at turning simple ideas, words and paragraphs into superfluous, verbose conglomerations of nouns, verbs, prepositions, articles, unnecessary restatements, and perhaps the occasional kitchen sink for good measure (or even an entire kitchen if you’re prone to getting hungry when you should be focusing on work like some of us *cough cough* me *cough* *clears throat* *pops a cough drop because yum food stuff*). Totally staying on topic, if you’re amused in the slightest by my poorly executed joking, I highly recommend this stand-up comedy clip by George Carlin on soft language. Like go watch it right now. Everything else can wait. It’s just ten minutes of your life that you could spend looking at cats. Plus it’s a great illustration of exactly what I’m talking about. And it's way better than any meme I could put between these two paragraphs. 

To be completely honest, I miss the sort of superfluous, artistic writing that we’ve gotten used to in school. But as much as it’s an art to turn sentences into beautiful flowy creations, it’s an art to condense those same sentences into neat little packets you wouldn’t be afraid to let your kid play with.  It’s like comparing an idyllic autumn picnic to a fun-size candy bar you throw in your mouth on your way to lecture.  Sure both are sustenance/writing, but one takes ten times as long to get the same amount of calories/information. Imagine how many pieces of fruit would have to be lovingly fed to you by your hypothetical partner on this hypothetical romantic picnic to elicit the same caloric guilt as a handful of Snickers bars scarfed down in the infinite.


Then again you could also bring a romantic stack of chocolate to your fruit picnic. 
That’s what makes scientific writing so hard. It’s one thing to find some berries in the forest and have a picnic, it’s another to sit down, analyze the nutrition content of everything in front of you, break it down, put it back together, leave only the essentials, and in the end turn a perfectly nice meal into Soylent. Sure it’s more efficient… But who actually likes Soylent as opposed to a fancy five course meal with confusing names no one can pronounce? Oh wait, we’re talking about scientific writing. I guess there’s something to be said for not getting buried in metaphors and language. But are citations so much better? The number of times I’ve had to reread the same sentence five times just to understand which parentheses were separating what and which parts of the sentence were actually part of the sentence… I’m pretty sure 70% of the struggle in science is training yourself to see parentheses as an invisibility cloak.

The (quick brown fox jumped over the lazy undergrad) only (because foxes are cute) way (and fish are actually puppies) to understand (you’ll need 2 eggs, a glass of milk, a frying pan, and Wite-OutÒ) a methods (novel) section (the authors would like to thank Google, their pipettes, the Academy, reviewer 3, and their mothers) (in that order).

In the end, although it’s admittedly difficult to actually sit down and start working, it’s not the writing that I found to be hardest. It was how to write, what to include. I was constantly torn between “am I leaving out necessary details” and “did I add too many unnecessary details.” It’s easy to think “well if I added that detail this one should be added too,” and it starts this snowball effect of adding more and more details until you have three pages of methods written for how you did a Western blot. Something I learned, or more accurately, am in the process of learning, is how to let go. Me being an emotional sappy mess aside, I find it hard to let go of things I’ve written in favor of making my writing more concise. Over the course of Mod 1 I found that structuring my writing before beginning helped a lot with that problem; instead of going in and proofreading for brevity post-factum, I work best outlining my main points to myself before falling down the rabbit hole that is writing. Science is like cooking. Sure, you love mayonnaise and would put it on everything if the world was an ideal place. But is it really necessary? No, you don’t need ten adjectives in the meal name; if it’s lamb call it lamb. God no you don’t need to add anise. And do you really need to inform your audience that the chicken fell on the floor during prep so you had to substitute beef but it’s all still fine voila? I have learned the answer to this is no. Unless the chicken runs out of the kitchen and informs your guests that there actually are no cows and they are eating horse. In which case, maybe you should find a journal that actually proofreads things before sending out two packages of horse meat and labelling one of them “moo.”


 Clearly, learning how to be concise in my inclusion of memes is the next step. 




Weenies Don't Read Science

I entered MIT like most people do: unsure of what I wanted to study but confident in my ability to succeed in whatever major I chose, and blissfully unaware of what "real science" was. To better explain my mindset, let me backtrack a bit and explain my high school experience.
I attended a public high school is rural Wisconsin. My graduating class was just shy of 180 students. My AP physics class consisted of 7 students, and my AP calculus class was a mere 5. I was the only girl in each. I rose to the top of my class with minimal effort; I did little work outside of school, I never studied for tests (or even remembered when they were), and still managed to pass with flying colors. 
Although my laboratory experience consisted solely of lighting bunsen burners and using pH indicators, I assumed college (and grad school) would be just as easy. 

 Once I got here, however, the fire hose that is MIT showed me just how wrong I was.

In the spring of my freshman year, I began my first UROP. Trying to perform techniques I had never heard of--much less done--before taught me that science is hard. Lab-wide journal clubs and one-on-one meetings with my mentor taught me that reading science is harder. Lab meetings taught me that writing and presenting your own work is hardest of all. Nearly every paper I read felt a mile over my head. I could hardly comprehend what people were saying in meetings--I once dozed off in a meeting with my mentor and PI. All I knew was how to keep my cell cultures alive and measure mouse tumors. The summer after my freshman year, I almost abandoned course 20. I remember thinking: I'm a weenie. Grad school is not for me. I was unable to fathom reading--let alone writing--a scientific paper. The idea of carrying out experiments on my own in grad school was daunting; defending a thesis was unimaginable.

For some reason, however, I decided to stick with it for just one more semester. I continued taking course 20 requirements and doing my UROP in the fall. While I became much more confident in my ability to do science, I still shied* away from reading or presenting scientific literature (I once "nose-goes-ed" a question asked to the lab's 3 UROPs during a lab meeting). I was still convinced that I wasn't cut out for grad school. When my UROP ended with the fall semester, I comforted myself with the knowledge that at least I wouldn't have to read any more of those god-forsaken papers. 

*"shied":








Once again, MIT (mostly 20.109) showed me that I was very wrong.  But I also also learned that I was very right about some things. I guess you could say I've learned a lot so far. For example:
  1. You will never not have to read papers. Even if you aren't assigned to read and discuss them. There comes a point when you can't simple google your homework answers (Believe me, there is nothing worse than googling what you think is a "simple" concept that you just didn't understand in lecture and discovering that you have to read a paper to learn more about it). And even when you're not in school any more, chances are you'll still want to know what people in your field are doing (which means reading papers). 
  2. Papers aren't the worst thing in the world. If you you have a strategy, that is. I'm ashamed to admit that the article I presented for journal club was the first paper I've read and really understood. Shame on me for being so hesitant and stubborn. It turns out that if you know how to unpack a paper in the right way, it all seems much less overwhelming. Up until this semester, I sort of assumed that figures were like pictures in a children's book, adding some value but nothing essential. I also thought you could fully comprehend a paper by sitting down and reading it end to end like a book. Spoiler alert: those are horrible ways to go about reading scientific literature. 
  3. Science IS hard. It takes a lot of time (on several occasions over the summer, I spent 15 hours in the lab. We also spend a lot of time in the lab for 20.109, relative to other classes). Things break. A lot. You don't always get the results you were hoping for. Sometimes you don't get any results at all. Such is the life of a scientist. 
  4. Science is also very do-able. Even though it's hard, science is not impossible. And just like scientific articles can be unpackaged and broken down into smaller, more digestible pieces, so can other daunting tasks (like our Mod 1 report, the upcoming Mod 2 report, a presentation, a thesis, or a grant proposal). Having a plan, understanding what you are doing, and taking things bit-by-bit makes science a lot less overwhelming. 
  5. If you google the locations of enough lab supply companies, Thermo Fisher will start advertising on your Facebook newsfeed. 
    ....Need I say more?
    6. I am not a weenie. Although the idea of grad school still seems daunting, it is now something I could see myself potentially doing. I still have time to make the decision about what I want to do after graduation, but now my options have significantly increased (and so has my confidence in myself as a real scientist!). 

Every Protein has a Silver Lining


The cursor blinked on and off. We sat there on the second floor of the student center staring at an essentially blank screen. "Implications" it stated at the top. Good start, right? Not really, if you turned your eyes a little downwards, our slide read "None, to be honest. It's actually useless. Oops."

I remember a few days before when we were getting ready to see our results, Noreen was showing us how to analyze the curves we got from the Ca2+ titration assay data. She mentioned that one group in the past had gotten a flat curve, indicating they had abolished the ability of their sensor to, well, sense calcium. Jokingly we looked at each other and said that would be us. And, well...it was (funny how that works). 

So there we were staring at our results, thinking about what we could possibly say about our sensor. We could be #1 on the list of the top 10 things not to do in 20.109? 

Quite confused about what we could possibly say, we went to office hours*. Many of them. We were told to craft a story. One of the main things I learned was that all results are meaningful. Even though our results said our sensor was useless, it still meant something. We may have found that the region in which we generated our mutation was so essential that any mutation would destroy the function of the sensor or that the residue we mutated to changed the binding environment too much. Our results opened up a door of possibilities - our seemingly useless protein actually meant something. The most important part of any experiment is thinking about the story at the end and to not be discouraged if your results aren't what you expected. Everything has meaning, you just have to find it. 

When it comes time to prepare the report for Mod 2 - there are two very important things I'll keep in mind - go to office hours and expected or not, the results can always be used to tell a story (and not just warn future experimenters of what not to do).

* I highly suggest taking advantage of office hours! They're the perfect way to get focused on finishing (or starting) your report while having wonderful people there to help you when you get stuck. 

"What does Kd even mean?"

Greg and I agreed to meet at the Student Center Saturday, March 12th at 11 am to finish our Protein Engineering Summary due 5 pm the same day. That's 6 hours of non-stop working. Solid, right? Especially if we have some things done (sort of) (kind of) (not really)?

To be fair, we weren't completely in the dark. We had great ideas, a few bullets here and there, and a few graphs ready (credits to Matlab). But we still needed to come together to make something out of all of this. We needed a story, a clear start and a clear finish. That was the goal of that Saturday.

We met at 11 am full of hope and motivation. I had never been in the reading room of the Student Center on a Saturday before. I was shocked at the amount of people occupying the desks and study rooms. Turns out, people do study on a Saturday! Note to future self I guess?

Anyways, we sat down ready to work. We opened the shared document, and... blank. What's our game plan? How do we start? How to squeeze weeks' worth of information into these tiny blank spaces?

Just as we were figuring out how to get about to start, we ran into Ada and Ann from our lab section, who had -wait for it- worked with the same mutation as ours!!!!  Just like that, the reading room of the Student Center turned into a D23H party. They joined us in our study cave to work on their project, and we were ready to begin.

Greg and I decided on a sound game plan: division of labor, high efficiency, fast output. Like a small factory of scientific knowledge. Edit figures, write captions, make sense of the data. Slide after slide.

To be honest, progress was slow. As it turns out, looking at pretty pictures of graphs and gels becomes much more complicated when you actually have to account for what they mean and why they're important. They're just individual pieces of the puzzle, essential but not worth much unless they're linked together in a logical way. Only then do you get the big picture, the whole story.

Sometimes, we hit existential crises like "Why are we here?" or "What's the point of all of this?" or "What does Kd even mean?" but thankfully we had each other overcome these difficult times.

There are no words to explain how the last 30 minutes passed. We were trying to do 10 things at once: fix the bullets, check the text, fit the figures, subscript all the d's in the Kd's, send Snapchats... a real struggle. By 4:55, all four of us in the study room were simultaneously laughing and shouting and praying to the universe that we would be done on time. Once we were at the point of no return, we saved our file, gave it the correct name, and sent it to Noreen I don't know how. This was us right after submission:



However, this was us after we realized how this experience had brought us closer as friends than no other project ever can:



Long story short, my 7 hours in the reading room of the Student Center showed me that science does not end at the bench. You can have all the gel images, Matlab plots and titration curves you want, but at the end of the day, it's all about what you make of them. It's about paying attention to details, knowing what you're talking about, and keeping the big picture in mind at the same time. And, in that one moment when nothing makes sense and you forget what Kd means, it's about having labmates nearby to remind you again and again.

(Everyone in the photograph gave consent to having their names in the blog.)




Lets Start at the Very Beginning


The hardest part of any assignment is beginning. It can feel so daunting, looking at an open word document or blank power point presentation, the blinking cursor taunting you, as you struggle to craft the perfect first phrase. I can’t say how much of my life I’ve spent glaring at that open page, waiting for inspiration to come out of nowhere.

.

Unfortunately, writing rarely works that way. Most of the time, you have to put all of your ideas down on paper in this sort of haphazard way and then edit, edit, and edit some more. From my experience, this second method seems to be more efficient. (This may seem strange, but I have a hunch it’s because I don’t spend the first half of the time having a staring contest with a blank document).


Once I got my momentum, I found that it was easier and easier to write – sort of… The tricky thing with writing is that you can trip yourself up thinking of each paragraph or even each sentence as something new you have to start. If you do that, you can end up back at the beginning, looking blankly at your paper (like I had been prone to do).  Instead it is easier to keep trying.
        

With time and good editing everything will come together.


Working on assignments in 20.109 has taught me how to overcome the inefficient method of waiting for the perfect moment to get started and instead prompted me to jump right in.