Explorer-in-training

Hi, I'm Imraan.
I'm an explorer in training.











By explorer, I mean the art of research, of finding new questions to analyze, new data to interpret.
Found myself with a bit of a problem as I was working on my abstract and data summary for Module 1. 

I had two roads ahead of me:

1. Gather as much data as I could, and puke different results and analysis of data into the data summary.

2. Carefully choose data that fit the hypothesis that I had initially come into the experiment with.

Both of these roads were fraught with traps that experienced travelers knew well, and the occasional moan in the distance indicated that there were inexperienced travelers walking these paths. As an explorer-in-training, I knew nothing of the complexities of those roads, of the benefits and negatives of each pathway. I could only rely on my intuition to see which path would lead to the "correct" destination.

In the end, I chose the second road. I plodded along this road, carrying my prior experience and the map, written by the master explorers that taught our class. Yet, a journey isn't just one decision, it's a collection of decisions combined into one big hopeful mess.

I ran into a caution sign. The caution sign seemed out of place at first, interrupting my thoughts as I meandered forward. It was rusted, words worn by the passage of several years. The words hinted at a sort of requirement, as you will, that one must have before they can pass.

Caution sign: "10 pages not including title/abstract/references".

At that time, I had created multiple figures, analyzed the results, and came up with a conclusion that I felt supported my initial premise. However, I had come short with respect to number of pages. I panicked, searching through the vast amount of figures that I could create, if only to increase the number of pages. As time passed, and my frantic thoughts slowed and congealed into a coherent and sane mix, I thought about what I was going to sacrifice in my work.

One of the first rules that was told to the explorers-in-training was to craft a narrative, a story that used data to ride to its natural conclusion. And in my panic, I had forgotten that one rule, about to ruin the narrative for the sake of an arbitrary page number. I had looked at the multiple UniFrac tests, I had created phylogenetic trees for the whole entire class, yet none of them seemed to fit with the story that I was weaving.

As an explorer-in-training, I had almost failed on my first journey. I had almost sacrificed one of the most important rules in this travel for the sake of convenience.

But, all was well in the end, I found other areas that I could expand on. In keeping with this "journey", I had completed the requirement in a method that didn't sacrifice the rules.

The destination was reached, and I'm still not very sure about what the key takeaway from this report was. However, I do know that the lessons that I learned from completing this assignment are applicable to any sort of "journey" that I might take in the future, and I look forward to learning more as an explorer-in-training.










-Imraan

PS: I feel like this Kirby right now.

Surviving 20.109 Particularly the Abstract and Data Summary

I'm not usually one to go to office hours. I find that I either don't really have important questions that I can't look up in the textbook, or other people usually chain link their questions and I never get to ask my questions. However, I strongly suggest going to office hours even if you think you understand everything. You should ask if what you thought was correct. I analyzed my data for the Mod 1 Abstract and Data Summary and went to office hours and asked questions to make sure my understanding of the graphs were correct and of course it wasn't. What I learned completely changed the conclusion of my entire paper.

Also I am one of many people who if I don't see the solution, I can't start working on a problem. I am trying to get in the habit of starting work in hopes that the solution will appear along the way. In some cases it is important to have everything planned out before you start, but when you are looking at your paper the day before it's due and you only have two paragraphs out of the ten pages, it's important to just start writing. It's much easier and faster to write something and then come back to it later to fix it than it is to try to get it perfect the first time. I spent several hours over the course of multiple days just staring at my topic sentences trying to figure out what to do next. Eventually I decided to just start writing. Once you start writing it usually becomes easier to continue.

Back to the topic of office hours. I, like some others, when I get stuck find it difficult to skip that portion and come back to it later. Working during office hours gives you the opportunity to ask about whatever you are stuck on and get a quick answer and immediately continue. So attending office hours just to work on your assignment isn't a bad idea even if you don't have any questions at the time. If you are working outside of office hours then you can just email one of the faculty members and get a quick reply. While you wait for a reply, you will need to force yourself to skip that section and come back to it, which is great if you know how to do that. I haven't yet mastered that art.

Besides the fact that you will probably learn a lot more, and be more productive, the course faculty are pretty awesome and are usually alright with you going in to just chat. And they won't yell at you if it's the day before your assignment is due and you haven't started yet.

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.

3AM

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.

6AM:

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…”

8AM:

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!

4PM:

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

Mod 1: How does one blog?

I've never quite done anything like blogging; I expect it shouldn't be immensely difficult since it is based on a stream-of-consciousness approach. Honestly though, if I were to truly do this blog in a stream-of-consciousness style, no one would be able to keep up with the wild tangents. I basically have the attention span of a puppy, but I guess I make do with it...
Now to what I am supposed to be writing about, the majestic Module 1 report. And, what do ya know, it wasn't even too bad after all. I would absolutely call it a reasonable assignment and I think we all can admit to gaining from it.  It really came down to conquering the initial road block and just starting to write things down, start to process the data, and get some thoughts going on the consequences of the study. I just had to make it past initially looking at that phylogenic tree, gel electrophoresis figure, schematic, and Unifrac data to really identify what these figures were accomplishing. Sidenote, one of the highlights of this module was Leslie mentioning that Unifrac kind of sounds like a bad word, and, to be honest, it deserved that connotation because I think inputting the data to those specifications might have been the most difficult part sometimes. I can recall an especially fantastic Friday afternoon in lab where Sonia (go Pink Team) and I spent way too much time going over every ID file and every data input to make sure Unifrac was happy with us and would finally show us the figures.
Anyway, I think another difficulty arose from making sense of such a small sample size in the analysis part. It was evident that there was some overlap in the microbiome, but it could have easily been a result of the locations being very close to each other and the minimal samples used. As others have noted, I sometimes felt like I was really pulling some conclusions out of basically nothing.
Overall, I think I have taken a step towards becoming a better scientific writer. I realize sometimes you have to cut the fluff and realize what is most important to tell the reader of the report. This is easy said than done because I've always been a fluffy writer. I know that I have a lot of work to do to really understand all the nuances of scientific writing, but assignments like these help push me in the right direction. Scientific writing is essential and I hope that with each module, I keep improving. Bring on Module 2!

The Transition from Neuroscience Labs to 20.109

After a week of juggling class, psets, papers, and various extracurriculars, the last thing I wanted to do was write an abstract and data summary. I consistently had to convince myself to continue working and stop checking Facebook. I'm proud to say that after hours of exhausting research and sifting through data, I have finished mod1.

As I sit here and ponder the assignment, I realize why I struggled so much. I'm a bioengineering major, but I constantly find myself at the heart of neuroscience research. In nature, neuroscience labs are drastically different than biology labs. In my current UROP, I spend hours watching rats wander around a stimulation box, reporting their behavior as stimulus is applied. I've learned how to implant electrodes into the PAG and MFB regions of the brain and how to solder those electrodes together. But when I got to the 20.109 lab, I was out of my element. Most of my peers have experience doing at least the basics, and I had never held a pipet.

As I got to the data section of the report, I was overwhelmed with the amount of figures and statistical analyses I had to understand. Wikipedia had become my best friend. But, as I studied, I seemed to be more confused. How was I supposed to recognize patterns and interpret this data? How am I to know if what I have found is even legitimate? These were the questions that haunted me as I  tried to write. The fact that there was not many data points didn't help. The patterns weren't clear and I'm not yet confident in my ability to analyze these tests. As I progress through this course, I hope to gain confidence in my ability to interpret data and convey results in a clear way. I feel that by the end of the course I will be able to write a publish-worthy article. And to me, that make this all worth it.

Thoughtful Thoughts: Mod 1 and That One Time I Tried to Knit

I've been staring at this pesky flashing cursor for over forty minutes now (although admittedly, I think I accidentally fell asleep for about 37 of those minutes while lying in bed) and I can't figure out why writing this blog post is turning out to be so difficult for me. I suppose on one hand, it's not surprising that my productivity has bottomed-out; after hours and days of wading through figures, trees, and colorful geometric dots, your brain begins to feel suspiciously less like grey matter and a lot more like a crusty bowl of banana pudding. Banana pudding is not very good at generating thoughtful reflections. 

On the other hand, the mod 1 data summary and abstract was the most pressing matter on hand for this week, and now that 5pm has come and gone, the only things standing between me and spring break are a couple of psets and the primer design memo. Not quite home free, but certainly nothing to complain about. I should be eager to wrap this up with some culminating final thoughts. 

Thoughtful thought #1: When trying something for the first time, don't get discouraged. 

I think the hardest part about the scientific writing required for mod 1 was actually just getting started. Although the data for all of the samples had been posted over a week before the due date, I didn't really start sifting through the data and planning out figures until Saturday night. It was more than just a bad case of procrastination though. What it really came down to was the uncertainty that I felt and the unfamiliarity I had with manipulating the raw data and translating that into a cohesive piece of scientific writing.

I have never had experience with scientific writing before, so every time I thought to myself, "hey, right now would be a great time to get started on your 20.109 assignment because, you know, waiting til the last day is a really horrible idea", I would open openwetware, maybe pull up a MEGA file, but would ultimately be too intimidated by not having the slightest clue as to what I was doing.

In the fifth grade, after a particularly riveting needle-point unit, my class delved into the wild, wild world of knitting. I was supposed to be making a scarf, but having never knitted before, and perhaps lacking a bit in the manual dexterity department, I ended up with a sad puddle of mangled yarn. In the fifth grade, I gave up. I got discouraged by my initial inadequacy and since then, I have never had even the slightest itch to take up knitting again. 

In 20.109, I didn't have the option of giving up. With the Monday deadline looming, I was forced to face my inadequacies and to learn, mostly by trial and error, what was definitely not the right thing and what (I hope) would be an acceptable draft. The drafts of the figures and topic sentences that we had to turn in throughout the module were extremely helpful, and for the most part, learning from this feedback, as well as from examples in established papers, I was beginning to pick things up bit by bit. 

The hardest part for me was getting over that initial roadblock. All parts of the assignment were new to me so no one section was particularly hard. They all were. But once I hunkered down Sunday morning, the work started coming easier. Not that it was getting any easier to know what to write, just that I was getting more comfortable with trying new things and pushing forward. 

If only fifth-grade Krystal hadn't been so easily discouraged, who knows, I could have been a world-champion knitter by now or something.

Thoughtful thought #2 (though I guess this is more a piece of advice for my future self): For next time, I would make sure I fully understood the data and what I was going to say about it before making all of the figures.

I started backwards this time in the sense that I made all of the figures first and then started playing around with them and trying to draw conclusions from them. Obviously the PCoA graphs and the UniFrac clusters etc. would have to be run first to even have data to analyze, but I was referring to the more tailored figures, such as pie charts or Venn diagrams.

If I had had more time, I would have made some changes to my pie charts in the figures section because I felt that after drawing my ultimate conclusions, there were certain characteristics of the data that I would have liked to emphasize more on the figure. However, I had spent an ungodly amount of time clicking away at a frustratingly slow Microsoft Powerpoint and by the time I realized I wanted slightly different figures, it was too late to go back and change everything. 

A little extra time planning can go a long way in making sure you aren't scrambling to fix wonky figures at the wee hours of the morning. 

Closing thoughtful thoughts (that are probably less thoughtful and more rambling): I think that there are a lot of things that I would have done differently if I could go back and redo module 1. My first experience with scientific writing was not necessarily my most enjoyable experience (I made a lot of mistakes and questionable procrastination choices), but I would say it was one of those experiences where you learn a lot through the struggles and by the end, you can't help but feel a little bit proud of what you've made it through. The pressing question I suppose then is do I feel prepared for Module 2 now? I certainly hope so. 

FINISSHHHEEEDDD!! With the Mod 1 report...

After a busy week and eventful weekend dealing with a bunch of cute little kids and their crazy parents, I somehow managed to squeeze in this Mod 1 abstract and data summary and crank out the goodies. I must say, that right now I feel both exhausted and liberated. Staying up late to finish this report, memories from freshman year came back in which all of us freshmen in my entry messed around while the older residents in classes like 6.005 stayed up until the early hours of the morning, finishing endless assignments. Now I'm the old person, wow that went by fast. On another note, I like how this assignment was due at the beginning of the week as opposed to the end; now everything else from here until spring break (yay sunshine and warmth!) feels like a cakewalk.

As for doing the assignment itself, I'll try and recall specifics as it felt like I was in one giant haze the whole time I was writing it (hopefully this doesn't show negatively in my end product). The most difficult part of this Mod 1 report for me was definitely the data analysis. Not having much experience with or knowledge on bacterial strains, it was hard for me to look at individual bird gut microbiota and come up with possible reasons for why the bacterial strains were present. I feel like suggesting some papers to read that give good information characterizing specific bacterial species would be helpful in analyzing our bird's gut. Secondly, as Will has already said, I found it hard to deduce patterns and correlations on compositions of the guts from only eight birds from two relatively close locations. Were these observed patterns significant or just the result of a small noisy, sample pool? At times I felt almost as if I was reaching so far that I was completely making things up out of thin air. Overall though, I definitely feel like this assignment helped prepare me for future scientific writing. The main guts of a paper were laid out and it really wasn't that terrible. Having done the majority of this assignment in one day and subsequently feeling proud of my end results, I definitely feel like in the future, I will be much more able to write a whole, legitimate, publisher-worthy paper. And that is pretty cool.