Tuesday, March 17, 2015

Watching the Sun Rise

Disclaimer: If you are a freshman or any undergrad planning to take 20.109, start your Mod1 first draft right now.

Okay, maybe not right now, but definitely five days before its due. This is coming from two sophomores who are very excited about 20.109 but also want to sleep. Like right now.

Juan: A warm blanket of reassurance fell upon me Friday night as I clicked “execute” on the FastUnifrac website. Within only a few minutes, I had filled my previously cleared desktop with a wholesome blend of data analyses, clusters, and phylogenetic trees. I began rummaging through the files, starting with the classic “Cluster samples” trees that the FastUnifrac site had generated for me. I leaned back casually and nodded as I perused the fairly simple-looking tree on my screen. With the speed (and not the accuracy) of a state-of-the-art data-analyzing supercomputer, I decided that the tree suggested that gulls were more likely to have similar microbiomes if they were from the same place and were of the same sex. “This is easy!”, I bleated as I bounced giddily out of my chair and into bed, “I’ll go to bed early, rest up after this taxing week, and have everything finished by tomorrow evening!”. A naive smile was smeared on my face as I peacefully drifted off to the sweet sounds of a man screaming profanity outside my window.

To my horror, when I woke up the next day, hours were going by as fast as minutes. By the time I had scrambled to eat breakfast and finish my background writeup, it was already time for me to go to sleep again. Disturbed and disoriented, I fell asleep hoping time would return to its normal pace by the time I woke up. When I opened my eyes and checked my phone, I found an invitation from my dear friend Kristina to work on the assignment in the same room to provide moral support for each other. I gracefully accepted the invitation.

Kristina: By the time I rolled out of bed on Sunday, I was facing an extra long theater rehearsal that wouldn’t end until dinner… and an, err, less than half done Mod1 draft sitting sadly on my laptop. The past couple of days had flown by in a blur of rehearsals and class planning and while I had already run all of the FastUniFrac tests and oogled at the pretty clustering trees and the principle coordinate analysis plots, I hadn’t gotten around to actually analyzing them. I looked at my draft, looked at the time, did the math in my head and started to feel a little anxious. I took a peek at the UniFrac tests and grew suspicious when I saw that there was no consistent set of factors that would produce significant differences between any two gull samples. This was going to be more complicated than I thought. And I knew there was no way this was getting done before the sun went down. Yay...

So what do you do when you anticipate yourself pulling an “almost all-nighter”? You text a friend in the same class and share all of the all-nighter excitement feels before your assignment is done at 5pm. And tell your roommate that you should both be back before she gets up… ha.

11PM Sunday

So we both looked at our papers to see where we were at...
Figure 1: An accurate depiction of our progress at 11PM 3.15.15
We definitely had more written down than this, but at 11PM with the panic starting to set in, it certainly felt like this was all we had done

12AM Monday

Kristina: I saw that pulling the trees and plots right off the FastUniFrac site wasn’t going to cut it. First off, they were just too long. Second, the font was miniscule on the PCoA. Who is supposed to be able to read that? Powerpoint… I love thee…

Juan: At this point I was really starting to develop an appreciation for the challenge of analyzing raw data and putting it into my own figure. I would continue to ferment this appreciation for the next few hours.


Kristina: 3AM is always a slump. I don’t know why. My brain turns to towel fuzz and writing a sentence feels. like. the. hardest. thing. to. do. And… I just realized that I screwed up the formatting for the jackknifing tree. And the PCoA graph is still unreadable. Maybe I should go and edit my background (again) for a break? After the umpteenth time of rearranging and reevaluating parts of the motivation, I finally get something that is smoother to my mental ears. I realized that doing even a little bit of analysis goes a long way towards a more comprehensive background. Now back to those figures…

Juan: As someone who has seen their fair share of late night battles with assignments, I greeted the 3AM exhaustion hump with a firm, polite handshake. I looked to Kristina, who seemed to be greeting her own 3AM slump. We took a quick whining break and promptly continued our work. Not long after three, I had produced two phylogenetic trees, a jackknife tree, and two minimalistic Venn Diagrams which I created to show the bacteria genera that gulls from different sexes and locations shared as well as the genera that they didn’t share. I thought that my paper should include at least one simple, minimalistic figure which was immediately understandable to the reader, although I deliberated for a long time on whether or not to include instead some sort of UniFrac distance matrix.


Juan: The sun rose, and time began to speed up as I received my post-all-nighter second wind of energy. I made my way deeper into my discussion of the results, finding that I had to keep repeating something along the lines of “We don’t have enough data to make sound conclusions” in the discussion of every figure. Only my rough draft grade will show if such redundancy was a bad idea.

Kristina: The sky was lightening up and I could see the horizon turning pink, but by then I was charging along on my 5:30am burst of energy and seeing that my suspicions from the previous day were confirmed. Eight gull samples were not enough to see any kind of correlation between gull gender/location and microbiome composition. I felt like a bit of a broken record by the time I hit Figure 6. “Unfortunately, more data is needed before… Only eight samples is not enough to…”


Figure 2: The Eating of Breakfast at 8AM.
Simmons dining hall food was eaten by Kristina* and Juan.
*this was the first time I had ever eaten breakfast this early this semester!


Kristina: 7.05 went by in a blur, and then it was straight back to the paper for the Implications and Future Work section. By now, I felt a lot more relaxed. The majority of my report was done and I just had to put my head down and work away until I had written the last word.

Juan: Suddenly, time sped up again. I took a break from work to attend 7.05 lecture, which I was able to pay attention to only to the extent which a person who has not slept in 24 hours can. After class, I calmly returned to polishing up my Mod1 assignment, and coolly turned it in at a relaxed time of 4:48. The situation had been under control the entire time.

In conclusion, our experience with the Mod1 paper was enriching in more ways than one. We gained an appreciation for how difficult and time consuming it can be to analyze and write up  data, a feel for the scientific method, and a hefty respect for the art of making figures. 10/10 would embark on such a learning experience again*.

*although maybe not the night before said experience is due

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