Monday, March 23, 2015

Journal Club, Here Me Roar

To start out this blogpost, I think it is only fair that I tell you that no, I have no fear of public speaking. In fact, some might even say that I love public speaking. Why exactly? I have no idea. Maybe it stems from the fact that I come from a big family where everyone talks at once and thinks what they're saying is the most important thing to ever be spoken, so I consider the chance to get to talk freely with no interruptions a gift. Maybe it stems from the fact that I've always found I'm better at expressing myself through spoken words than words on a paper. Maybe it stems from the fact that I've been a generally ridiculous human being for the last 18 years of my life, and I basically feel no embarrassment or shyness when it comes to making mistakes in front of people. Or maybe I just like to talk. Either way, hand me that mic, I'm ready!
However, just because public speaking doesn't terrify me does not mean that this journal club presentation didn't terrify me a little. There's a difference between just getting up in front of a crowd of people and talking and getting up in front of a group of extremely intelligent people and presenting complex science. As I began to picture myself giving this presentation, the only images that kept flashing through my mind were a flurry of likes and ums, over-the-top hand gestures, and the color red. Let me break this down for you:

#1: Valley-Girl Syndrome
One of my biggest peeves when listening to a presentation is when people excessively use "like" or "um". However, this is not to say that I am immune to the use of these words. In fact, when listening to me tell a story, most people would probably assume I was a valley-girl not a Massachusetts native due to my atrocious overuse of the word "like". However, this is usually not much of an issue while presenting, but that didn't stop my mind from thinking that it could just happen and sending me into a panic.

#2: Interpreter Syndrome
Blame it on my Indian heritage. Blame it on my restlessness. Either way, I'm a gesturer. I always have been. I talk with my hands flying all over the place, sometimes in helpful ways and other times in relatively random sweeps. For my everyday life, this is passable; a person or two may comment, but it's generally just accepted for who I am. However, in scientific presenting, random hand movements can be very distracting. Every movement you make should be with a purpose because your viewers are acutely aware of everything you do. Hand gestures can be extremely effective, but only when used in moderation. I knew that the "moderation" part would be the challenge.

#3: I'm-not-good-at-associating-colors-with-feelings Syndrome
During our practice journal club slide presentations with Professor Runstadler, many comments were made involving the color choices that people made on their slides. What looked like just ordinary templates to me were ripped apart for the thickness of a line or the location of a square. The colors were acutely analyzed, and I was sitting there, thinking "Holy cow, who knew a square could be so insulting?" One particular comment that stuck with me was about the use of red. Black, white, and red are the three basic colors that I felt were often used when trying to highlight something without being too playful or unprofessional. However, during our practice presentations, I was informed that red was thought to be too alarming. It made viewers feel worried or like something bad was happening. I had never thought about it like that, but needless to say, the red titles on my slides were not feeling the love. Therefore, in preparing my real journal club presentation, every time a color appeared on my slide, a slight pang of fear would go off inside me, hoping that this color wasn't also one that elicited a strong emotional response. I went for a variety of blues and prayed that no red appeared anywhere.

Journal Club is frightening experience for  a variety of reasons, depending on the person, but what we all shared as a class is that we got up there, spoke for 10 minutes, and did awesome jobs in my opinion. Everyone climbed Journal Club Mountain, and now a 20.109(S15) flag is planted firmly at the top.

Saturday, March 21, 2015


I’ve learned a lot of things in 20.109. I’ve learned short snippets of information that make me feel more scientifically literate, like how to pronounce Pseudomonas Aeruginosa. I’ve also learned about some of the challenges in current scientific research, like consolidating data from different experiments in genomic databases. I’ve learned how to load gels, perform Western blots and do UniFrac Analysis. Which is all really really cool.

I guess these are the sorts of skills that I would mention in a resume or talk about in an interview, the kind of information that earns you units and degrees.

But at the end of the day, here are the most important things I feel like I’ve gained/am gaining from the class:

Embracing Uncertainty. 

No one actually knows the answers to the questions we are asking with our research. Not PI’s, not the people that have worked in science for their entire lives, and certainly not the students. Which is kinda terrifying. But it also makes me feel like I am going into a field where there is room for me to contribute. It is what makes me over-analyze our protocol, ask questions during pre-lab, and gets me excited about “doing science." 

Thinking outside the box

In our analysis, in the questions we ask, and in the way we deal with problems that come up in lab. 


Usually, on a weekday morning when I have eight hours of class to look forward, my reaction  is something like:

But thankfully, this is how I feel when I talk to my lab partner and the other awesome students and instructors in my section

(dramatic reenactment) 

I feel comfortable asking them questions and talking about school, or pretty much anything else. They've taught me how to communicate about science and how to share a lab space. And they are one of the best parts of my semester. 

My Love-Hate Relationship with Science

“Gosh, I haven’t had this much fun on a Saturday night in a while,” I thought to myself.
 It was 4 a.m. and I was standing, eyebrows furrowed, staring at the table of UniFrac distances I had made, in an empty 5th floor Student Center Athena Cluster. Yeah, not the kind of fun you imagine yourself having on Saturday nights, when you first come to college. But, I had finally gotten the mountains of data from our microbiome characterization experiment to tell me something, and I was excited. Maybe I’ll finally be able to reach a conclusion after staring at this data for the last 12 hours (give or take a few naps).
 But it wasn’t telling me what I wanted to hear.
 “What do you mean the UniFrac distances between birds who don’t have anything in common are smaller than between birds that share sex or location or both?!!”
 I look around to make sure the room is, in fact, empty. Good, no one’s around to hear me shout at inanimate objects.
 Now back to these numbers. I stand there, staring at the whiteboard, trying to think of a reason why this data would be like that. Did I analyze it wrong? Did I mix up the numbers when I was writing them? I go back to my computer. No, everything is where it should be. Could there really be an underlying factor causing birds who didn’t share sex or location to have the most similar microbiota? Are these numbers even significant? A few hours ago, I would have never imagined this thought crossing my mind but man, I wish we had more bird samples to analyze. Maybe, then we’ll get some real answers.
 Looking back at my journey through the Abstract and Data Summary, I found that it perfectly exemplifies my love-hate relationship with doing science. Being a fan of lists, making lists, reading list, reordering lists, and anything to do with lists, really, I decided to list some of the things I love and hate about doing science.
 Accidently deleting the data I had just analyzed from the UniFrac website without saving it was like that one time I aspirated the supernatant from my just finished miniprep. There goes the DNA I spent the last 45 minutes extracting…
 Uploading the spaced ID file instead of the underscored ID file and having nothing work was (though admittedly not as dangerous) like the first time I loaded a centrifuge and didn’t balance it and had it shake violently on the bench until I stopped it.
 Analyzing my data so that it gave me a conclusion and then realizing my analysis was done wrong. Working on an experiment for a week and a half only to realize that I forgot to add the essential reagent that makes everything work.
 Realizing the one little thing that was making my last ten experiments not give me any results, fixing it, and seeing my experiments begin to work again.
 Finally being able to reach a conclusion (based on correct analysis this time) and having that conclusion tell me something that I didn’t know before.
 Finally being able to reach a conclusion and having that conclusion be so completely unexpected that I have no idea what it could mean. Doing a ton of research and figuring out that some factor that I wasn’t even considering was giving me my weird results.
 A year ago, I would have never imagined myself being able to enjoy doing science. Spending ten hours a day pipetting clear liquids into other clear liquids. Working on a project for six months and having it not work. That’s how I go insane.
 Now, I feel differently. I look fondly upon the vast amounts of pipetting as the tribute we need to sacrifice for good science. Each obstacle is another puzzle to be solved. Every problem has a logical solution and when that solution hits you in the face, you immediately forget the frustration you felt before, bask in the beauty of your new solution, and then go on to the next obstacle. 

Friday, March 20, 2015

The Five Stages of Scientific Writing

Like many other life events there are five distinct stages to completing your first major scientific piece of writing. All of which I experienced on my journey to complete the 20.109 abstract and data summary, a daunting 10 page paper filled with data that, at first, I could barely comprehend. So without further ado here are the five stages of writing your first major lab assignment.


You've got plenty of time ahead of you! 2 days = 48 hours - 6 for sleep means you have 42 whole hours to work on this project if you have to. The deadline creeps closer and closer and all you can think about is how sunny and happy it is outside and how nice it would be to go for a run. The pain and suffering this will cause you later never crosses your mind.


The pain and suffering this will cause you finally crosses your mind. You're screwed! The deadline for the paper is only 12 hours away, you have no idea what all those numbers and charts you're supposed to interpret even mean, and on top of that, it's midnight, and you are exhausted from a full day of classes. Why couldn't you have started this assignment sooner? Why do you have to procrastinate so much? The regret for all those hours you wasted on the weekend starts to kick in and you make hollow promises to yourself that you will never procrastinate again.


After getting over your pre work tantrum, you start making deals with yourself. If you can finish two pages in the next hour you can take a 15 minute break. If you finish them in 45 minutes you get a 30 minute break. As your situation becomes more and more desperate, sometimes you will start making deals with the universe; if this deadline get's postponed I will never procrastinate again. Eventually you somehow manage to settle into a frenzy of productivity burning through the bulk of your assignment.


Somehow by a seemingly superhuman effort you've completed most of your assignment. There's only the abstract and the bibliography left but it's now 7 AM and you haven't slept a wink. You struggle to make it through the last few hours of work without passing out and it seems like the last few edits take longer than writing the piece in the first place. Eventually, you drift off to sleep hoping your paper is adequate, and that you set your alarm so you will wake up for class in a few hours.


The deadline is minutes away and you make a few last minute changes to your paper before you submit it online. You get it in mere seconds before the deadline. Somehow, you managed to comprehend all those confusing charts and tables. Not only that but you managed to write a ten page paper about all of the significant features of that data. After all the blood, sweat and tears you poured into this project you can finally claim victory. Despite your exhaustion you feel awesome. You wrote your first major lab assignment!

Tuesday, March 17, 2015

Module 1: The Abstract and Data Summary

Alternatively titled: There's A Reason I'm Not Course 6

I'm pretty bad with computers. I joke about it a lot because it seems ridiculous given the school I attend, but it's a sad fact of my life. One would think that by now I'd understand this personality flaw and learn to overcome it, or at the very least prepare for its inevitable interference with my work.

I started writing the background and motivation section in advance. I found some references, redid my topic sentences, spent time formulating my ideas. In the data section, I incorporated the figures we'd already turned in for small assignment, made my tree, and wrote some paragraphs (which I later frantically converted to bullet points after reading over my notes from the M1D8 your assignments carefully, kids), and even had most of the abstract ready. I don't yet know how well I did, but I know that although these parts of the assignment were time consuming and in a rather unfamiliar territory of writing, I completed them without much incident.

Perhaps it was my early Baby Boomer-like repulsive fear of technology, or maybe I'm simply masochistic, but I saved the data analysis bit for last. Yeah, the part where you have to create appropriate files and upload them to a website for analysis.

Of course, on the first try, I couldn't even upload the files. The button didn't work. How could the button not work? I took a deep breath. I was using Google Chrome, and sometimes websites where you submit forms or files don't like Google Chrome (don't ask me why, I'm not course 6), so I switched to Mozilla. Voila! The files uploaded. But when I went to run the tests, they either didn't run at all or output gibberish. I began to panic. Of course I left the hardest part for the last day. I tried uploading and re-uploading files, reformatting files, redownloading files. Nothing worked.

Then, a bright idea appeared: what if I restarted my computer? I turned the machine off, turned it on again, switched back to Google Chrome, and suddenly everything worked like a charm. Again, I'm not a course 6, so I have no idea why.

Overall, the assignment was difficult and more time consuming than I expected it to be, but I think it pushed me to more thoroughly understand what we've been doing in lab thus far and truly pushed my limits as a scientific writer. I'm excited to get feedback and see how I can improve upon the skills I've developed.

Module 1: The Journal Club Presentation

Alternatively titled: Conquering My Fear of Speaking on Something I Know Little About

It's no secret that I love to talk. My friends know it, my TA's know it, one of my brothers claims that I am never able to shut up. At parent teacher conferences through primary and secondary school, reviews of my academic performance were almost always followed by the phrase "and while I love Rachel's participation in class, sometimes she doesn't stop talking when she's supposed to." Public speaking isn't something that has me quaking in my boots.

No, for me, the cold sweat in the middle of the night comes from the idea of, quite frankly, looking like an idiot. One of my biggest fears is making a fool of myself in front of my peers, or worse, my professors. Naturally, the Journal Club assignment presented a bit of an anxiety-inducing predicament. Not only was I told to present a topic I initially knew nothing about, I had to learn about it from a scientific paper, which in some ways feels akin to deciphering an ancient manuscript written in a foreign language I'd only been taking for a single semester. What if people asked questions I didn't understand? What if people asked questions to which I didn't know the answer? What if I tried to answer a question and got the answer wrong?

I was terrified, to say the least.

After reading the paper a few times over and referring to my foreign language-to-English dictionary (thank you, biochemistry book and wikipedia), I found that I was actually understanding the material. Not only did I understand it, but I found it fascinating. Before this presentation, I hadn't even known that Simian Immunodeficiency Virus existed, let alone understanding the mechanisms involved in its infectivity. I buckled down and made my slides. I practiced, first in front of a mirror, then in front of an actual person.

The day of, I took a deep breath and dove in. It was still nerve-wracking at first, but I found that making eye contact with the people I know and mentally checking to make sure I was going slowly enough helped me through. In the end, people did ask questions, but I did my best to answer them, and the whole thing went much more smoothly than I expected. I now feel a lot more confident in my ability to interpret and present scientific material. And hey, I got to learn about something cool in the process!

Journal club fun times

The first time I heard the phrase 'Journal Club,' I was spending the summer before the senior year of high school at a university lab near my home (let's face it, high school research is not real.) I thought, "How quaint! Clubs are fun, right?" before a presentation on the migration of cortical neurons. Nothing like a dark room and a topic that goes completely over your head that just lulls you to sleep. This would be the first of many lab presentations I would embarrassingly nod off during.

But not in 20.109! I guess as I gain more familiarity with the skills and techniques that go into certain research fields, I find it easier to stay focused (and awake) during presentations. As a slightly wiser (maybe?) student, I can better see the value of learning about what is currently going on in the field of research and compare what's being done in your lab to techniques of other labs. And around three weeks ago, I had the opportunity to construct and give a journal club presentation of my own.

I'm not much of a presenter. However, equipped with a full set of tools on how, theoretically, one should give a presentation from Atissa, and a newfound love of making animations in PowerPoint, I set out. The first practice run took place in a deserted floor of Barker library and was remarkably choppy and jumbled as I tried for the first time to verbalize all these ideas in my head into words spoken out loud. A few times going through the presentation, I found it easier and easier to put words together, and finally, after a stressful 7.05 exam, I was ready to present.

When I came to college, I joined a dance team, which performs a show once a semester and a few times off campus. Since freshman year, I have definitely developed more of an attitude of having no shame when it comes to performances, which I think really helped me be more comfortable in front of an audience. Although journal club was a different environment, I wasn't 'scared' of presenting for this reason. Also, because I was the first presentation out of eight, I didn't get a chance to psych myself out beforehand! While giving my presentation, I felt fairly confident in what I was talking about, and hoped I was conveying information clearly to the audience.

Today, a few weeks after, I sat down with Atissa and watched myself giving the presentation. Even though I was prepared to hear it, there's always something quite jarring about hearing your voice in a recording. Nonetheless, watching myself was really informative, and I noticed particular things I did that I never realized during my practice, such as saying "and so..." for many of my transitions. Atissa gave me a few pointers about my presentation, which were really useful, and I definitely feel more confident that I can give an even better presentation for Mod3!

The Ups and Downs of Writing About The Microbiome

Subject: Me
Action: Writing about my perspective of writing the abstract and data summary and having gone through the first module of 20.109.

Motivation for me taking the class:

At first, I was really excited. All the work that had been done over the past few months from DNA extraction to gel electrophoresis to transforming competent cells would be culminated in a roughly 10 page report on our research. Although I have been working on a biological engineering UROP over the last summer, I was really impressed by how 20.109 labs worked: there was always big EMPHASIS on understanding the protocol and each step that went into task of understanding the microbiome and how our research was related to that. For example, I never really took the time before to understand chaotropic salts and their role in DNA extraction.

What did I want to write about:

For the longest time, I had convinced myself that our research pertained to the relationship between the seagull gut microbiome composition and host susceptibility to avian influenza virus. As a researcher, we would be doing the dirty work of dealing with avian cloacal samples that could somehow be related to avian influenza virus (although we were told that samples that contained human pathogenic influenza were excluded from the study). While the cause was worthy, the limitations placed on our research seemed to be due to our dearth of lab experience or because our class was only an introduction lab class or maybe because we needed to be specially trained to deal with infectious viruses... I sort of missed the purpose of the experiments.

What I ended up writing about:

There was a little disappointment when I realized that our topic covered what I felt to be a more simple scope of inferring characteristics of the host from the microbiome. However, I realized that all research starts at a foundation and builds up from there. My conclusions from our research focused more on the correlation between the microbiome composition and gender and geographic location of the host, but future implications of modulated microbiome therapies and microbiotic markers for disease susceptibility cause me to realize that there is a lot of potential in the field and study of microbiomes and phylogenetic analysis. How I got to these conclusions is another story.

Troubles I ran into with data analysis:

There was a lot of data collected from just 8 seagulls, an entire 109 16S sequences that were all roughly 1400 base pairs in length. While the hard work of filtering out the 16S DNA amplicon and running BLAST analysis was split among the class. The task of using and interpreting MEGA and UniFrac data and even individual parsing of the data proved rather tedious and led me to the realization that scientific research is difficult. Especially telling a story from the resulting data felt like being told to solve a 100-piece puzzle except instead of all the pieces being unique jigsaw pieces, all the pieces were identical 1''*1'' squares and you're told that some of the pieces are missing so you need to infer what the puzzle is a picture of without all the pieces. So I went to work: observing the strange trees and trying to make sense of what patterns and information could be parsed from each graph and whether the heat maps told any story at all.

"Brilliant" breakthrough:

I stared at my computer screen feeling utterly perplexed as to why none of the data seemed to be making sense. I saw some sort of relationship in the cluster sampling between male gulls from Worcester and female gulls from Carson Beach, but all of the other points seemed to be outliers or seemed to serve the only purpose of destroying any theories I had with regards to microbiome composition and host gender and geographic location. Having then exhausted what I could from the UniFrac website, I began to explore the 20.109 website to see if I had missed something that could explain my lack of tools in data parsing. Suddenly in a "Huzzah!" moment, I located the Spring 2015 tab-delimited text file containing all the results of the BLAST queries on closest matching strain to the 16S sequences and their corresponding gull number. If I could systematically organize the data, maybe I could have a better idea of the composition of the gull microbiomes being compared and make better inferences of the relationship that microbiota had with their host. Now how do you change a text-delimited file back into a excel file and how can I most efficiently sort and organize all these 109 results and how best could I represent this data in a figure and...

Finishing at the point of daybreak:

After an exhaustive process of chugging through and gaining better understanding of the microbiome, I looked at my report. After several weeks of weekly coming into labs and getting nervous that something could go wrong, (which it did, huge thanks to the teaching staff and assistants for being so awesome with troubleshooting) here was a paper that represented that work in the form of a schematic, an image of a 1400 base-pair band of DNA in a gel after gel electrophoresis along with other trees and figures that tried to tell the story of a class of MIT sophomores in course 20 who tackled the question of what a microbiome was and how to even quantitatively/qualitatively describe and interpret variation of microbiome structures as seen across coastal and inland communities of seagulls. There was a feeling of pride and satisfaction as I looked through my entire work. In a sense, I took the puzzle pieces, found more pieces and then started reasoning out a possible picture and started building towards that design and adjusting as needed until the final piece was crafted. Possible pieces may have been put in upside down or at the wrong angle, but that is hopefully where constructive criticism can come in to put pieces in more optimal places.

Expectations of the future:

As we head off to Module 2, we are again starting a new foundation where we will gain skill and learn knowledge that will really allow us to delve deeply into the problems and questions that researchers are trying to solve and answer. I hope to learn a great deal of interesting things about DNA repair mechanisms and the potential motivators for why we are so invested in understanding how it works. As for now, I feel that I have overcome a great hurdle and with that a fond farewell to the microbiome, although I'll keep my ears open for anything interesting that might come up in the future.

Summary of Abstract and Data Summary

I will now write a lovely summary of my experience writing the abstract and data summary for Module 1. :)

So...the week leading up to the due date of the Abstract and Data Summary was one of my busiest weeks with school work, UROP tasks, and life in general. On the Friday before the due date I had class straight from 9:30-5 and then I UROP-ed (I don't know if that is a word but whatever) from 5-7:30 plating more cells, yippee. I took a necessary mental health recovery break at Chipotle, and then prepared myself to start the abstract and data summary. I knew it would be a long weekend of writing.

Around 9pm on Friday with my lovely lab partner, we planned out a timeline for finishing our assignment and we began organizing data. I had grand plans of staying up until the majority of my report was done, but my eyelids refused to stay open and I succumbed to my tiredness. The next morning, I woke up and Joseph and I met to complete the UniFrac Analysis. Within a few hours we were done, and then we separately began writing. I spent a long time, probably too much of my time on Saturday just doing the Abstract. I am a writer who edits as she writes, so I have trouble writing a "first draft" because I want to make everything sound good before I move on. On Saturday I also edited the past assignments, began my introduction and thought about the overall structure of the assignment. I wasn't the most productive in terms of actual writing; however, I felt alright spending some time planning and organizing my thoughts.

Sunday, referred to by some as a "day of rest," involved no rest for me :(. With the due date looming around the corner, I knew I had to pick up my pace. So, I worked for most of the day, taking breaks for food/short conversation/bathroom/etc. and I eventually found myself done at 7:30am Monday morning. I am not typically a person who pulls all-nighters and actually, before this assignment I could proudly say "I have never pulled an all-nighter." However, I have lost the ability to truthfully say that anymore. But, what did I learn from this experience?

Overall, through the Abstract and Data Summary, I learned not only about the bacterial diversity in the avian microbiome, but I learned about scientific writing in general. I had never made figures before for a paper, and I found it especially hard to boil down all of the results into the most clear and meaningful figures. I kind of enjoyed playing around with PowerPoint and making the figures. Well, at least I enjoyed making the figures more than writing haha. I learned that the number of sentences in the Abstract is certainly not proportional to the time spent writing it. I thought it would be easy to write such a short blurb about the paper, but due to the required length of the Abstract I spent a long time trying to think of the most important words to include.

To anyone taking this class in the future, I would definitely recommend starting the Module 1 Abstract and Data Summary well in advance. However, many lessons are often learned the hard way, and sometimes you just cannot start assignments very early-- so anticipate sleeping very little, and keep your stock of K-cups high. Caffeine is wonderful, and will be your best friend throughout the writing of your Abstract and Data Summary. It will also be your friend immediately after you submit your Abstract and Data Summary and have a 9:30am class. Lesson learned: A four shot latte is a thing at Area Four (probably not good to drink on a frequent basis)!

Not a critique

I'm choosing not to talk about the abstract and data summary assignment until it's completely over, to prevent myself from putting my foot in my mouth when the first draft comes back and I've done everything wrong (well, hopefully not everything!). I decided to focus more on the scientific content of Mod 1 and I'll follow up about the writing portion later.

There are two ways to read this blog post. I'd recommend reading the non-ranty version first.

The first 20.109 module dealt with characterizing the gut microbiome in seagull populations from two different beaches, using sequence analysis. On the surface, this seemed pretty interesting and familiar.

My first UROP project at MIT involved some related material, looking at data from a human gut microbiome study and evaluating various community distance and similarity metrics. UniFrac, the phylogenetic distance measure we used in 20.109, was notably not one of the candidate distance metrics, for important theoretical reasons that weren't relevant in 109. The paper made it to publication, but I wasn't involved in it; my UROP mentor took this project as an opportunity to teach me a bunch of things while I essentially reanalyzed the data that had already been submitted for publication in search of more interesting conclusions. Rather than find something novel, I instead was only able to confirm the main conclusions of the study without adding much.


[I'll reserve judgement as to whether that's a good idea in undergraduate research. On one hand, that project took a summer and didn't result in much fundamentally new science. On the other hand, the project was entirely my own, and while the question looked promising in the beginning the situation turned out to be exactly what we expected. C'est la vie--sometimes there isn't something interesting where you think it might be. On the (other) other hand, I left it with what is perhaps a much better grasp of ecological theory than I might otherwise have. I realize now that this probably served me very well during this module, and will hopefully serve me well in life.]


Unfortunately, despite my high hopes for the module, snow days and the inherent time crunch associated with an academic class took a lot of potential value out of this module. While it served as a good introduction to molecular cloning skills and other wet lab techniques like primer design, the module didn't treat issues like ecological community analysis with a satisfying degree of depth.

[Disclaimer: what follows might read like a list of complaints, but I tried my best to justify everything]


UniFrac was the only distance measure described in class, and while it's not a terrible measure, other distance metrics like Simpson's Index, Shannon's Index, and generalizations thereof were never touched. I mention this because using UniFrac over, for example, the Simpson Index (which, for some subfields of ecology, is the index of choice--UniFrac is by no means a clear winner) is a methodological choice. Given this data, perhaps it's the best choice, but it's worth mentioning why. Making justified choices about your experimental or analytical methodology is an important part of research, and 20.109 is as good a time as any to talk about it.

Principal Coordinates Analysis and Principal Component Analysis were used in software without really emphasizing what they mean. Importantly, the difference between PCoA and PCA is huge, and significant (PCoA deals exclusively in pairwise distances, while PCA deals with inherently multidimensional data--the kinds of things you can do with the output are very different; for example, PCoA cannot be used to make predictions about a new sample, while PCA can.)


I'd like to emphasize again that the goal here wasn't to bash the first 20.109 module (as if I'm even remotely qualified to do so). Perhaps my "complaints" are nitpicks, and perhaps my hopes here were set too high. To some extent, I was hoping that going through Module 1 would make students more capable of working in the Runstadtler group, for example, than the average course 20 student, all else equal. That's likely not the goal of the module.

I imagine that executing a laboratory module that deals with current research but must also introduce students to fundamental techniques is a hard line to walk. The broader scientific scope of this module (which is fundamentally an ecological one) was quite far removed from what most students in course 20 will have been exposed to, even after mostly completing their degree, so that makes the task even harder. Given how hard it is to teach this module, I think this was very well run. However, I might question the inclusion of this module over an alternative module in future incarnations of the class, if only to make the job of balancing extraneous theory with laboratory fundamentals a little easier for everyone involved.

The timeline of my journal club presentation

T-minus two weeks: 
Two hours before Wednesday lecture, Krystal frantically waves to me during recitation to check my phone. “I’m going to sign you up for Journal Club presentations on M1D6,” the text reads. Oops, forgot about that. I check my schedule, and of course it’s the day of my biochemistry exam. All the spots are already filled up for Day 9 presentations, so I decide that I’ll just suck it up and start the presentation early.

T-minus 1.5 weeks: 
I realize that Day 6 presentations get to read journals related to disease detection, and I grow a little more content with presenting on Day 6. Although I’m a bioengineering major, I’ve thought about pursuing public health, being involved in preventive health measures and, like my friend nicely put it, “being a mother to the entire world.”

I wanted a journal article that was related to a disease that I’ve heard of, so naturally, “Comparison of the Sensitivity of Laboratory Diagnostic Methods from a Well-Characterized Outbreak of Mumps in New York City” was the best choice. I glanced over the abstract, and printed it out for further reading later.

T-minus 1 week: 
I read through the article for the first time, highlighting all the words I don’t understand. By the end of the article, my highlighter is practically dead (thank goodness for Wikipedia). The journal article talks about a particular outbreak of the mumps, which I find intriguing. Unfortunately, I find myself getting sidetracked, reading other articles about mumps outbreaks, and then an info sheet about the MMR vaccine, and then an article about people who don’t believe in vaccines.

T-minus 2 days: 
“What happened between T-minus 1 week, and T-minus 2 days?” you may ask. Well, I’m not entirely sure. It probably went to a little bit of biochemistry studying, and a heavy sprinkling of those random MIT things that pop up out of nowhere.

At this point, every minute of my day is blocked out—showering, eating, and sleeping included. My two hours blocked out for working on the journal club presentation are not nearly enough time to finish the figures in my presentation, so I siphon off a couple hours from “sleep” and continue working.

T-minus 24 hours: 
“Thank goodness I’m not in the T/R section,” is all I can think as I groggily get through my morning. Every free minute of my day seems to be consumed by biochemistry studying, or PowerPoint-ing. I’m scrambling to figure out why MMR vaccinated individuals would be less sensitive to IgM detection, even though the vaccine should result in IgM in those individuals’ serum samples. It just seems so counterintuitive. Finally, after thousands of Google searches (or maybe more like 20), I discover that it’s because IgM levels decrease after second exposure. I don’t know why the author of the journal paper wouldn't just explain that in the paper. 

T-minus 12 hours: 
It’s 1am, and my roommate’s asleep. I’m whispering to myself as I rehearse the presentation, deciding what to cut or keep for my precious ten minutes of informing the public about mumps detection methodology. 

T-minus 4 hours: 
Somehow squeezed that biochemistry exam into my schedule!

T-minus 0 minutes to T-plus 10 minutes:
I’m not terrified of public speaking, but I am still nervous because this is the first time I'm presenting on scientific research. I have to know the topic inside and out, and for once, the questions that people asked me had a right or wrong answer. As I reflect, I think that although I could have spaced out my preparation time better, I was pleased with the outcome. The nerves wore off as I started talking, and I went through the presentation just as I had rehearsed.  Someone even asked me a question about why MMR vaccinated individuals were less likely to be diagnosed with the mumps via IgM detection assays!

Especially after this journal club presentation, I have decided that I much prefer a presentation over a test. For me, the amount of work I put into a presentation correlates to my confidence when presenting, which then (hopefully) correlates to the overall success of the presentation. I loved becoming an expert on MMR detection, and it's inched me closer towards wanting to learn more about public health. 

Writing the Module 1 Abstract and Data Summary

Writing the Module 1 Abstract and Data Summary was very challenging.  It was the first time I had written a report for a scientific experiment that I had done.  In high school when we did science fair experiments, the “report” we had to submit was basically just a poster or a Powerpoint on the results we got and some simple materials and methods list.  Also, the science fair experiments were so much simpler than this experiment we did in module 1.  Rather than just spitting out the results we got from our experiments, we had to analyze the data and think in the grand scheme of things for module 1.  The results of our experiments had a real-world application.

When writing the report for module 1, I found that interpreting the data was much easier and quicker to write than writing the abstract, background and motivation, and implications and future works.  For these three written sections, I had to figure out how to best deliver information in the most concise fashion, especially because I was using a bullet point format.  I found myself many times just sitting at the computer thinking about how to say something in a concise way.  In hind sight, I think I should have just put pen to paper earlier so that I could get as much information out earlier, and then edit it to make it more concise.  For next module, I’ll try this method and see if I can write these sections in a more time efficient manner.

Regarding managing time, I tried to start writing the abstract and data summary as early as possible because I read a blog post about how one student from last semester really regretted starting the report one day before it was due.  I was able to start it on the Friday before it was due, but I still worked up to the last minute on Monday until 4:56 pm.  From first-hand experience, I can see why the student from last semester regretted starting it the day before.

All said and done, this report forced me to think critically about the experiments that we had done.  I am glad we completed the report in pieces before submitting the report (electrophoresis gel and schematic) because it definitely saved time while working on the report.  I also found it helpful to receive constant feedback on the assignments I submitted.  However with this report done now, I am excited for spring break!

For Your Own Good

I try to avoid public speaking as much as possible. When choosing classes for the semester, I try to choose classes without projects or presentations. I have managed to do this for over a year now, but school has a way of making you face your worst fear. It knows that communication is crucial to any job and life in general, and for your own good, school *makes* you take these communication classes. Apparently there is a length I won’t go to to avoid public speaking—dropping out of school.

Why do I hate public speaking so so so much? It’s because I don’t know what will happen when I get up in front of the classroom. No matter how much practice I put into a, the fact of the matter is, I can’t control every element of what will happen during the presentation. How will I react when I have so many eyes on me? What if someone asks me a question I don’t know? What if a freak tornado comes in the middle of the presentation and I end up having to present twice?!

Now, I know the last situation would probably never happen, but the other two were valid concerns that plagued my mind for the week leading up to journal club. When I get nervous, my heart starts beating, my hand starts shaking, and I tend to speak so fast that spaces in between words are pretty much nonexistent. To try to teach myself not to react in this way, I practiced in empty conference rooms, drawing smiley faces on paper and putting them on the chairs to simulate an actual audience. (Sad, I know, but it was necessary!) I practiced in front of my roommate to get a feel of presenting in front of an actual human being. I practiced anywhere I could, in front of anyone who would listen. I also read the article over and over again, each time thinking of questions I could possibly be asked and finding answers for those. Anything I didn’t understand I got it into my head that I would be asked that question. It’s easy to understand why we were assigned this project after looking at my annotated article. I learned so much, mostly out of paranoia, but I did learn.

All this preparation was put into a presentation that I don’t even remember much. I don’t know if my mind is just suppressing the memory, but I do remember feeling that I overthought this whole project. It wasn’t that bad to be up in front of the class. Maybe school has a method to its madness. Making us students take these classes forces us to overcome our fears. I’m not saying that I won’t get nervous next time I have to present, but it obviously won’t be as bad as this time. And if my pre-presentation jitters can decrease every time I give a presentation, maybe over time I’ll even welcome public speaking with open arms. 

Climbing the Mountain of 20.109

Coming into 20.109 has been like climbing a mountain - a mountain jagged with rocks you have to climb over and beasts you have to battle - but once you get to the top, the view is sort of worth it.  In this blog, I'm going to attempt to present a treasure map to get to the top of this mountain.

The Journey part 1:
You've just entered the lab.  You've found a lab partner and pick a team color.  Now to begin the journey up the mountain.  But wait, which way do you go?!  Well, lucky for you, like Dora the famous explorer, you have two helpful items:  a map and a backpack.  Vamanos!
Image result for dora the explorer backpack and map
This map of course is the information-packed Wiki that we so delightfully get to use.  Unfortunately, this map is sometimes very overwhelming or, if your a newb like me, it may not be clear enough, so that's when you can turn to backpack - Shannon or the other sections TAs.  Like Backpack, the TAs have everything you need.  And they can answer all your questions!  Now, I understand asking questions can be very scary; at least, it was scary for me as my lab partner and I needed to ask like 20 questions a lab.  We would look over the protocol and be like:
 Image result for spongebob question
So we needed to ask for further directions! But the TAs are here for questions, and though you may feel silly for asking some maybe very basic questions, at least you're that much closer to getting to the top of that 20.109 island mountain.

The Journey part 2:
Along the climb there are going to be lots of rocks to make you stumble and fall.  The point is to watch out for these rocks, and as long as you keep an eye out and stay on top of them, you'll be able to continue making those steps to get to the mountain top.  These rocks are the many smaller assignments of lab notebooks, methods papers, and data drafts that you get assigned for weekly homework.  Of course, we can't forget the boulder of a journal club presentation you have to climb either.  However, through this rock climbing (or stumbling) you slowly begin to develop the muscles you need to climb on the mountain.

The Journey part 3:
Wrestling the beast.  The beast of an Abstract and Data Summary.
  Image result for bear beast meme
This will not be an easy battle.  But hopefully, you've come prepared with strong muscles for scientific writing and knowledge from your friends Backpack and Map, and you're ready to rumble!  Do not try and defeat this beast in one day; it will take much longer than that.  And of course, you may not fully conquer it, but at least, you'll temporarily stun in and be able to reach the top before having to truly fight it as you turn in your final draft.

So now you're at the top.  You've done it, you've finished Module 1.  You've successfully learned all about gull gut microbiomes and designed a primer to detect flu.  Isn't that awesome?!?! Now go enjoy the view!
Image result for mountain sunset