Thursday, April 30, 2015

Seeing Course 20 in a Different Light

    This module is going by fast. It’s been not even two weeks of module 3 and already it seems as if it is coming to an end. With the mini report due next week and the research proposals due the following week, this module has flown by. To be honest, I wish this module was longer. I’ve never actually thought of bioengineering as a way to harness nature into making materials and devices. I’ve always thought bioengineering was used in a way module 1 and module 2 presesnted it—as a way to describe and study diseases and cellular functions. This module is the most interesting to me, especially since I’ve never been exposed to anything like this before. Learning about Professor Belcher’s research kind of blew my mind. 
    You may think I'm kidding, but I really think my brain exploded, much like the picture above, when I heard that bioengineering had applications in the manufacturing of materials and devices. I still can't wrap my head around the fact that phages can be harnessed to improve the electronic properties of a photoanode. I wish we could spend a little longer on this module so I can delve into this topic further. Can time just slow down so I can process this better? We spent so much time on module 1 and module 2, and I feel like it's a little unfair to spend so little time on module 3. This way of using bioengineering is harder for me to grasp and yet makes it so much more amazing to me. I definitely had a limited understanding as to what bioengineering could be used for before coming into this class. This biomaterials part of 20.109 opened up my definition of bioengineering and I’ve never felt prouder to be course 20.  The fact that people are constantly finding new ways to utilize biology for different applications in the world only makes me more excited to enter the field of bioengineering after college. 

Tuesday, April 28, 2015

Stubborn Collaboration

Exhibit A: Things Christian and Lyla say to each other as they’re beginning to work.
“Oh god, we’re so behind.”
“This week has been awful.”
“Did we ever get around to doing. . .” “Oh right. . . “
Exhibit B: Things Christian and Lyla say to each other when working.
“That’s false, that’s not a thing.”
“That makes no sense, let me explain.”
“Oh my gosh, Christian. Focus!”
Exhibit C: Things Christian and Lyla say when they’re done working.
“Wow, that was actually really productive.”
“Huh, I never thought we’d get this done.”
“I’m so excited for where this is going.”

For us, collaboration is the one thing that will simultaneously make us want to tear our hair out and keep us motivated as we work. There have been many times when we’ll disagree about something, start voicing our ideas, start discussing each idea, start arguing about each idea… still arguing… still arguing… (FYI our stamina is something to be envied).

Flash forward 90 minutes: we realize that we were too busy not listening to each other to see that we were both trying to say the same thing from the beginning. Yeah, it’s frustrating. Now imagine this happening at least five or six times in one sitting - that’s when the hair-tearing begins.

Bear in mind that our arguing activities don’t differentiate between important and unimportant issues. We argue non-discriminantly. We once spent half an hour debating whether it was better to center our presentation titles or to left-align them. Even as we’re sitting here writing this blog post, we’re arguing about what anecdote argument to talk about. Pretty inconsequential, you say? Well, we’re still arguing.

The thing is, it is this incessant arguing that allows us to generate our best ideas. It’s like natural selection - but for ideas. The weakest ideas get destroyed by our criticism and the best ones evolve to be better than they originally were.

We just keep arguing until one of us sees that the other’s idea is better... or we realize that both our ideas suck. But in the best case scenario, both of our ideas merge into an idea better than the ones we started with. So is all the arguing a necessary evil? Unfortunately, yes, because one person cannot catch every mistake or error, but with a good solid team and a few hours of heated debate you can turn one team member’s half baked idea into something a little more bulletproof.

Whenever you tell people that you’re considering getting into research after college, they give you that look that you know means “Are you sure you want to do that?”

Most people have this mental picture of the canonical scientist. Kinda strange, interesting sense of fashion, a head of hair that seems to be a creature on its own - yeah, you know what I’m talking about.

But the most distinctive characteristic of the cartoon-inspired scientist archetype is the fact that it works alone. You’ll be surprised (maybe not really) to know that you’re average scientist, while possibly clothed in interesting apparel and struggling to tame their unyielding hair, is highly unlikely to be one that works alone.

Collaboration is probably one of the most pivotal aspects of doing science. In our personal experiences, it is why we can keep working on that assignment due tomorrow even when both of us are too tired to think, why don’t end up flipping a table when our third trial of our UROP experiment doesn’t work, or why we don’t start crying when we try to read a paper that is 95% unintelligible words and 5% “the” and “and”. Collaboration is also the reason why we decided that science is the thing for us - why we’re willing to put up with the mad scientist stereotype for the next few decades.

- collaboration by Christian and Lyla.

Saturday, April 25, 2015

Limping Across the Finish Line

Around 5am the day that Mod1 was due, I sleepily told myself that Mod2 was going to be different. I was going to start writing it earlier, I was going to go talk to a writing advisor, I was going read all of the articles about NHEJ and our possible inhibitors, and understand this module inside out.

And then the ghost of overcommitments past came knocking on my door when the Mod2 deadline got moved up to the Monday right after CPW.

This year, I was the CPW chair for my dorm and performing in a musical during CPW. This meant I was busy 6pm-2am rehearsing and performing from the Sunday before CPW to the night of the following Sunday, when I would help deconstruct the stage. Any time I wasn’t in class or eating or trying to grab some sleep, I was running CPW events. Rooming for my dorm was also the Saturday before CPW.

I did the mental math in my head and realized that I had only the Friday night and Sunday morning of the week before CPW and Monday morning of the due date to start and finish writing Mod2. Not including sleep. And also not including a pset, an exam, and a UROP proposal I had to do the week of CPW. Cue internal freak out.

White cat has panic attack in bed

So, I got a two day extension and ran with it. In the tiny window of time before CPW, I finish making my graphs for the article. Starting the Monday that Mod2 was originally due, I crunched away at the results section and excitedly saw faint connections between the rate of NHEJ and the topology of the DNA breaks. I continued through a haze of sleep deprivation to flesh out my introduction and bring out the interesting points of my research for the discussion section. As I neared the end of the article and wrote about future plans, I saw that I had some idea of what we could do by the end of the experiment. What if I just tweaked the topologies… or change up the concentration of the drugs with the flow cytometry…? I had an idea of how to conduct a future experiment, and that was a first! I had never been able to do that before!

In short, I got very, very little sleep (most of which came from sleeping through my alarm and falling asleep at the keyboard while writing Mod2), and still didn’t turn Mod2 in time. But I finished. It’s done. And I know how to kinda figure out how to do future experiments! Hopefully.

Now I’m going to sleep like 1000000 hours...

Thursday, April 23, 2015

My thoughts on Module 2: That was fast

And I don't just mean that since the deadlines are approaching faster than the speed of sound you can't hear them.  This module seemed fast, I just got my class ring, so I feel like college is going fast, but biological engineering is moving fast.  I decided to focus my paper on genome editing and some crazy things have happened.  It started based on a hunch I got after going through my spam email from biology vendors (I went to a vendor fair during my urop and they got a hold of my email).  Now first, I have to give you some perspective on what fast is.  Physics has been around for a while.  Atoms were theorized by Greek philosophers around 500 BCE and proven some time after 1800.  That is what human history was like before modern science, things took a long time.  Now a common way to blow people minds is to state the fact that the first moon landing was 66 years after the first powered flight by the Wright brothers.  That's barely longer than it takes to retire from when your born, there were people who remembered both events.

Now lets talk about Cas9.  Cas9 happened fast.  I'll give you a time line.  In 2005, sequencing revealed that bacteria had viral DNA in their genome and it was theorized this was some kind of DNA based immunity.  In 2007, it was proved by manipulating these loci that there was in fact an immune effect.  In 2001 the guide RNA/Cas9 system was discovered and in 2012 site specific dna cutting was demonstrated.  Not long after, people started trying to use homologous recombination to edit genomes.  Things start to pick up right here.  In march 2013 zebra fish (multicellular and everything) had some genes modified and added with Cas9 (  That same year in December, Adult mice had a genetic disease treated by genome modification using Cas9(  Earlier this year, in April, Nature published an article detailing the ethical debate caused by a team in china editing the genome of non-viable human embryos (  As it turns out, our study in NHEJ capacity as a function of DNA break topology is highly relevant.  The email advertisement I got was advertising some premade genome editing package that used Cas9 directed nickases.  These cut a single strand, so you can use two different guides to have twice the specificity (based on something like  Conveniently, this also means that you can move the recognition site around a little but to get any topology you want (I think, if they kit they were selling didn't it wouldn't be hard to design one that does).  As it also turns out, since NHEJ competes with homologous recombination, down regulating NHEJ is desired (  I am pretty sure we should brush up this study and publish because if you have arbitrary choice over cut topology, using ends with low NHEJ is a free way to improve your genome editing efficiency.
I found that the following gif sums up what its like to do biological engineering, I hope it serves you well.

With the Setting of the Second Module

I have to say that sophomore year has been more taxing than freshman year, although I do feel like I'm learning and experiencing a lot more. The Mod 2 report was time consuming and there were times that I doubted that I would even finish.

What I thought about DNA Repair:
I was impressed by how much work had already been done in the field of DNA repair. When Professor Samson first introduced us to non-homologous end joining and homologous recombination, I was overwhelmed by the complexity of the mechanisms and the range of enzymes needed to fix damage caused by sunlight. I often enjoy the feeling of warmth that standing in sunlight can bring, but when I realize that ionizing UV radiation could be causing a great amount of DNA damage. Thankfully, cells are equipped with proteins that work to repair damage in DNA, although it's interesting to note that within the population, different level of repair can be seen across people.

How I felt about the experiments:
Having had only a few instances of working with cells, I knew that cell culture would require care in ensuring not to contaminate or confuse different CHO-cells. Although they were "immortal" cells, they would not be too happy if bacteria were introduced into the media. There was always a lot that needed to be done in each day of lab, but I realized that there was also a lot of work being done in the background by the teaching staff and others (cell splitting, preparing aliquots of solutions, treatment of cells with IR, etc.). While I greatly appreciate the care and work that goes into creating the 20.109 experiments, I sometimes feel like I'm missing out on some of the experiences. For example, I was excited to see the setup of the machine that ran LiCor Western Blot Analysis, but my partner did not have an opportunity to see it (and I missed out on some parts of gel purification of cut DNA). I also was a little curious about the flow cytometer because I read about the set up in pre-class notes, but never got to see it in person. Maybe it's just my slightly curious nature, but I would really like first-hand experiences of working with all parts of an experiment because I feel that it really adds to my understanding of how systems work.

Working on the report:
For the second round of practice in scientific writing, I thought the schedule was well made in that we developed several parts of the paper as we were experimenting. This way of splitting the work over a period of weeks seems very beneficial and I would like to utilize it more in the future because I have a bad habit of wanting to finish in one sitting (and often failing to complete something in this way). I realize that one of the hardest parts of writing for me is really knowing where to start with data presentation. I have a difficult time deciding what information is superfluous and what might be necessary; I believe this is due to the fact that I can get really nit-picky and feel that every little detail has some significance in the complete understanding of a topic. I find that the best way to overcome this obstacle is to write without being to particular about everything I have to say. Once I put my ideas in words, I can work on fixing errors on something that has structure rather than something abstract in my mind.

20.109 has been one of my more enjoyable classes in my MIT career. Although I feel under a load of pressure, I've gotten to better understand my major (and myself). One more module to go, can't wait to see the great lengths that I have crossed since the start of this school year.

Wednesday, April 22, 2015


Upon finding out that the lab report was due earlier than had been previously posted, I panicked. How was I supposed to finish it in time? Better yet, how was I supposed to juggle this lab report with CPW. I admit, I overcommitted myself this semester and that meant running a lot of CPW events. So, I started working on the module much earlier than I did for Mod1. I  thought that I would be able to finish and everything would be grand. I was wrong. I always underestimate the amount of time it will take to analyze all the data and write a nice, coherent story. It took me until Monday at 4 to complete it. But, I learned some things.
1. Starting early is wonderful. Although I didn't finish until Monday, I did finish. Had I started later, I might not have finished and that would bad.
2. Although it was a lot of work, I didn't mind doing it. Finishing the report actually gave me a sense of accomplishment.
3. I have great classmates. There were parts of the methods that I didn't quite understand, but my classmates were always willing to answer my questions and help me out.
Altogether, I think I improved from Mod1 to Mod2 and that is all I can ask for.
Only 1 more Mod to go! I think I can do this!

Finished with Mod 2 and on to Mod 3!

After being awake for almost 36 hours, I finally finished the report!  Today I’ve pulled my first all-nighter this semester…I think? Well hopefully I won’t have to do that again!

It’s been a crazy weekend...from being occupied with ROTC at 5:30am Saturday till Sunday afternoon, then coming back and immediately working on 20.109 in the free time I had Sunday afternoon…then heading to NYC for an interview Mon morning and coming back Tuesday night…and starting the bulk for the report.  I don’t think I’ve ever worked so long on one assignment for a consecutive period of time until now…it is both a very rewarding and stressful experience.

A random fact: When I was doing the report last night, I thought it’d be a good idea to have a Monster energy drink because apparently they help people study (I never drink energy drinks)…but I think I learned that instead of helping me focus, Monster gives me stomach aches…never drinking Monster again.

In any case, it feels good to be done!  Before starting the report though, it was pretty daunting to think that I would have to write around 10-13 pages, especially because I find it hard to write more than several pages for most of the writing intensive classes I’ve take so far.  But scientific writing is a different beast than creative writing…it’s easier to write a lot because a lot of the time you’re explaining data and results that you received from an experiment, so you don’t have to think too much about what you want to write about.  It definitely takes some getting used to, to be able to write in a scientific and technical style, but I think will all the practice I’ve been doing so far, I’m definitely improving. 

Even though I found it tedious at times to turn in the figures and methods drafts in incremental steps as homework assignments, it really prepared us for the mod 2 report.  I’m super glad about that because it definitely saved a lot of time while writing the report.  I cannot imagine how much longer it would have taken if we didn’t have those homework assignments.

After writing two reports for the modules we’ve done so far, I can say for sure that I’ve improved my writing skills in general, especially in the field of science writing.  

Time really flew by and we only have a month left till this year’s over! Wow!  I’m glad that it’s almost over because this has been a tough semester, but I’ll miss it at the same time!

Looking forward to mod 3 and the end of school!

-Joseph H.

Pressure Limits for Assignment Completion in SJ Cells

     The recently discovered SJ (stressed Juan) cells found in MIT environments play a vital role in the completion of assignments in academic ecosystems, but the circumstances under which the cells will occasionally cease normal function are not well understood. While SJ cells are adapted to high-pressure environments, their assignment completion capacity becomes inconsistent and error-prone when submitted to unusually high pressures for extended periods of time. In order to better understand the pressures at which SJ cells will experience significant productivity loss, SJ cells were transfected with Mod2-Assignment (the longest known protein) coding plasmid and examined for Mod2 expression under various high-pressure environments for a one-week time period. Our findings showed SJ cell assignment-completion capacity to be compromised after only five days at stress levels as low as 10 gigaRedBulls based on the production of Mod2 protein with a misfolded and truncated "Bibliography" C terminus and several errors in translation throughout the polypeptide chain. We suspect that producing altered versions of Mod2 is an SJ cell defense mechanism, as Mod2 protein is known to degrade and become increasingly toxic if kept within the cell membrane for long without being "turned in" to its environment. This data is extremely useful for future applications of knowing how much pressure to apply to SJ cells used the assignment-production industry, and can allow us to place cells in an environment with enough pressure to maintain productivity while allowing them to retain their function.  

Intricate metaphors aside, I can confidently say that during my 30-hour adventure with the Mod2 research article, I learned several useful lessons. I learned how fulfilling it can be to do an experiment from start to finish, gather a large pool of data, and pick from it something that can answer the questions that we asked ourselves at the beginning of the experiment. I also learned that it is easy to become lost in the pursuit of a beautiful, elegant analysis of your data and wander a dark, spooky forest of science for days crossing roads that you had already crossed, getting nowhere, and finally settling for your initial analysis after all. It was truly humbling to experience how much work has to go into writing a journal article, and although I finally submitted the paper in a crazed panic at 4:59 PM a day after the due date knowing there were errors in my paper, I feel enriched by the solidarity I found with my classmates, the lab experience I got out of this project, and the quality practice I received in interpreting data. I am excited to apply this experience to Module 3 and redeem myself. 

Module 2 Report

Alternatively Titled: Second Time's the Charm (?)
Writing the Mod 2 report was hard. There's no better way to put it. It was really, really, really hard. But so was writing the Mod 1 report, and that time, I had beyond no idea what I was doing. Here's a run down of some things that changed between then and now:

What I did better:

  • I went to office hours! I asked for help!!! Anybody who knows me understands that this is a pretty big step. Often times, I would just rather sit in my room chipping away at my work and feeling like a complete idiot when something didn't come 100% naturally to me. It's one of my worst traits as a student, and I was happy to take some steps to overcome it.
  • I carved out (a lot) of time to work on the report. Last time, I tried to do things more incrementally, but found that separating all my work into small, half hour pockets of time between psets led to one very long, moderately painful day of sewing together all the pieces that I suddenly realized didn't make sense at the end. This time, I devoted chunks of hours at a time over several days, and I found it worked very well.
  • I made all my figures before drafting the remainder of the results section that hadn't been completed in daily assignments. I found that this helped me to understand the "story" I was telling in my paper a lot better.
What I did worse:
  • In mod 1, we were given a built in revision period. In mod 2, I just assumed it would suffice to give myself a couple hours after I'd finish to look everything over. It didn't. I wished I'd carved out an entire day or two to go over everything so that once it was down to the wire, I didn't feel like there might have been things I could've tweaked or rewritten, if only I'd had more time.
So, there you have it! Two modules down, one to go.

Tuesday, April 21, 2015

Riding the Strugglebus

You would think that I'd have learned by now on how to manage my time. All the lectures from my parents on the importance of time management apparently have all flew over my head. I knew ahead of time that a lot of assignments and exams were going to coincide. From this research article to multiple essays and tests along with Ring Delivery occurring so close to one another I knew I was going to be riding the strugglebus, but did I do anything about it? Apparently not enough.

I tried writing parts of the research article ahead of time, but I kept being distracted by other things. Thank goodness for the fact that over the course of the module, it was assigned to us that we had to write drafts of methods and various figures and results. Although at times the work assigned to us can feel unrelentless, I really appreciate the fact that I had those done when I was writing the research article so close to the deadline. This time however writing came so much easier since we had so many notes from module 1 on how to write each section. I definitely spent most of my time on the introduction and discussion parts, trying to make a logical and coherent story. 

At office hours it was said that people can become addicted to procrastinating because of the adrenaline rush they feel when cramming so much work into so little time. Maybe my procrastination is actually a disease. I wonder if that warrants an extension for future assignments...Hopefully, I will avoid riding the strugglebus for the next module. But first, I still have to get off this one. 

Module 2 Report Reflection

After feeling rather rushed while writing the majority of my Module 1 report, I told myself that I would start writing earlier next time. So, when K Whang (Katherine) invited me to join her super organized life schedule for completing psets/studying for tests/writing the report, I thought I would join. Sadly, I think it only took me a day to fall off the schedule as I spent too much time studying for 20.310...but whatever, my report ended up getting written. Sadly I missed most of CPW and Marathon Monday, but I <3 Course 20. On the bright side of things, I am very happy that the majority of the methods section and a few figures were assigned as homework, because that made the assignment bearable.

I thought that the act of writing the last report made writing this report a little bit easier. However, I found new struggles with writing the Module 2 report that I didn't experience while writing the Module 1 report. I found it difficult to write a hypothesis that encompassed what I wanted to say. Because the topology experiments and the inhibitor study were kind of separate/kind of not, I struggled at first trying to figure out what "my story" was that I wanted to tell. Also, I struggled a lot more interpreting the data for Module 2. In Module 1, any difficulties I had were because I didn't understand the software or the statistical tests...But for Module 2, I understood what we were supposed to do, but the data that Joseph and I got was just very poor/inconclusive. I realize that science fails a lot, but the fact that our inhibitor seemed to display the effects of a promoter was a bit concerning. I found it very difficult writing such an important assignment on data that seemed like it should be torn up and thrown away. In the end though, I think I was able to draw a few solid conclusions from the results, so that is good :)

Even though I didn't realize it was raining on Marathon Monday until I submitted my report on stellar (I was sitting at my computer in a room with no windows until 5pm), I guess I am a little glad that we had the three day weekend to complete the assignment. Maybe in time I will become super fast and efficient at writing lab reports, but currently I work at the speed of a turtle. Maybe slow and steady wins the race.

Mod 2 report party

Well thank Jesus this report is over, now I feel like I can breathe. So even through all the complaining and countless hours of work put into this report, I feel like this went much better than the last one. With Mod 1 I had so many things going on, including my parents being in town, that I pretty much had  to squeeze in the report in the last four hours before it was due. Needless to say, it kind of showed in my final result. After learning from my mistakes with Mod 1 (not starting early enough), I really feel like I kept a much better plan with this Module, actually doing things in advanced and taking my time. I've realized that even if I think I have a whole day to do some work, it's really not best to cram it in; my brain gets fried and I put out my worst, most unproductive work. So now I do things in chunks, a little here, a little there, and I think it worked. After pretty much spending a day just on editing, I can say that I really put out my best, which I'm proud of. Also, I feel as if my scientific writing is getting clearer and more concise which has been tough for me to do. After years of AP English essays and writing like "I'm galloping through the fields of literature," science writing has been a huge shock. I'll think that something sounds good and then bam! It's actually crappy and no one knows what I'm trying to convey. You live and you learn, am I right? And though this report was a giant pain, all of us in 20.109 really bonded over it, looking out of our windows during the beautiful days of CPW or watching our friends throw marathon Monday daygers. We're all on this same struggle bus that's nearing its destination. Finally stretch, Mod 3!

Achieving My Goals (well, some of them)

               Writing the first mod 1 report was hard, and the ratio of sleep deprivation to quality of finished product was way too high. In an effort to expedite the second writing process for the mod 2 report, I told myself that there were quite a few things that I wanted to change: 1) NOT pull an all-nighter the night before the due date, 2) start working on bits and pieces early on so that I wouldn’t have to pull an all-nighter, 3) get feedback on my writing so that I’m not flailing around at 3am wondering whether or not I’m doing something right or wrong, 4) enjoy myself (possibly contingent on fulfilling numbers 1-3).

               As for 1), I technically slept 3 hours on Sunday night, but it was rather begrudgingly because I felt like I still had so much work to do. Sunday night I realized that I had signed up for an EMS shift from 5-11pm. If there were no calls, I would still be able to work on the report in the bunkroom, but if someone needed the ambulance, I’d be whisked away from my laptop. Of course, we had three calls that night and I was otherwise occupied between the hours of 6 and 11pm, prime work hours that I sorely needed. Sleep is important though, as I, and many others, can attest to the zombie-like inertia that overcomes you when you don’t get enough sleep. So I slept fitfully for 3 hours then worked non-stop from 8am to 5pm. This is only a technical fulfillment of my first goal. I consider this still a point that requires much improvement.

               As for number 2, I started the previous week off strong, revising and finishing most of my methods section and figures over a week before the deadline. Then I got slammed with psets and exams and all thoughts of “working ahead” were thrown out the window. My friends and I had made a googledoc that described an ambitious work plan for the week which would have ensured a complete draft by Saturday morning. But alas, after two days of struggling to stay on task, the whole plan fell through. 0/1 points for this goal.

               Number 3 is the only one that I think I fulfilled to some acceptable degree. Like last time, I went to the weekend OH and it was there that I was able to sort some things out in my head, mostly the narrative that I wanted to tell, as well as some technical and logistical questions about formatting and content etc. This was immensely helpful and I don’t think I would be able to survive this class without all of the helpful hints and constructive criticism that I get during hours spent sitting in OH and munching on snacks (word to the wise: eating too many chocolate donut holes is detrimental to your general wellbeing).

               What I am most excited about this time around was the I finally got to visit the BE Communication Center! I made two appointments, one on Thursday to force myself to finish some draft of my introduction, and another on Monday morning of the due date, to go over my final draft and polish things up. It’s so true that you only get out what you put in. The first meeting I arrived extremely unprepared. My introduction was weak and in all honesty had been cobbled together probably an hour before my meeting. When I arrived, I wasn’t entirely sure what I was talking about when I was trying to explain my paper, and I didn’t have any results or analysis to include in the intro, which I actually needed the most feedback about. Suffice to say the first meeting was not extremely helpful. However, on Monday, when I went in with a clear story in my head and a cohesive introduction, the meeting was extremely productive and I got some great feedback. It’s really helpful to have someone else read over your work because sometimes even though things make sense in your head, when other people read it, the readability is actually far lower than you expected. Although it was all very late notice and I do wish I had made a productive appointment earlier, the help was invaluable. After all, I’ve only ever written one other scientific paper and having the eyes of a PhD student, who has clearly read far more papers than I could possibly imagine, is beyond useful.

               Number 4 is a gray area. I can’t deny that I made myself miserable by working nonstop through Sunday and Monday, and not allocating more time earlier in the week. I feel tired and cranky and I have this weird craving for kettlecorn (actually, I always have a craving for kettlecorn). But on the other hand, I personally found this research topic far more interesting than the bird microbiome project and I enjoyed learning more about how this all applies to cancer research. In that regard, I had aa lot more fun, and there is something about suffering through a project with others that brings everyone closer.

               I would have to say I only really fulfilled 2 out of my 4 goals, but in the process, I’ve gained some insight into how I would better like to approach paper writing in the future. Now it’s time to actually get some sleep.  

The struggles of 20.109 coinciding with everything

After the struggles of completing Module 1 with barely a second to spare, I promised myself that Module 2 would be different. I had experience with cell culture and western blots, and I felt like I had a decent grasp of what this lab was about. The homework assignments were supposed to pace us with completing this module on time, and as much as I hated writing methods sections, I appreciated the homework that forced us to complete at least some of the report ahead of time.

But then, let’s fast forward to the week of Module 2 being due. If you read Katherine’s blog post, you’ll see that we had quite a plan to complete the report way ahead of time. Despite our 20.310 exam on Thursday night, we had weaved an intricate schedule to accommodate all of our work for the week.

Soon enough, the schedule fell apart (as always). Data analysis never got done, due to the 20.310 exam, and so our plans to “outline our discussion section” got pushed back as well. The introduction section went through rounds and rounds of rewrites, and by the time Friday rolled around, I still had no hypothesis. I was scrambling to finish a few psets, and by the time that was all done, I was looking at a blank screen with no progress.

Sadly, I had to skip out on all of my friends’ CPW events on Friday to work on the report, and then on Saturday, I was involved with a lot of my clubs’ CPW events. By Sunday, I was so burnt out from CPW that I had almost no motivation to continue my report other than the looming deadline that just had to be Marathon Monday.

Yes, Marathon Monday. My volunteer shift went from 5:30am to 9:30am, and I was freezing at my bus loading volunteer station. It was so bewildering to see these amazing athletes lining up to get on a bus to the start line, and I talked to a few of them about their running experiences. One said, “I’m actually running another marathon in 12 days, so this is just my long run.” I forgot about 20.109 for a while, and it was refreshing.

Once I got back and took the longest warm shower possible, I locked myself in my room and got to work. The only reason that I wasn’t devastated to miss the entirety of Marathon Monday was because it was so cold and wet. (Good thing the weather wasn’t any nicer, or else this blog post would be a much much much more bitter).

Of course, I hope that for next year’s students, this report is not due on a day like Marathon Monday. But to be perfectly honest, if this report were due on the original due date (April 24), I still would not have been able to complete the report peacefully. With ring delivery and a 7.05 test that week, the report might have been an even greater struggle.

So I guess there is no such thing as the “perfect due date.” Unless I were only taking 20.109 and no other classes, there would always be something in the way.

The story of the aspirational to-do list

Ahhh 109, or as I like to call it struggle-oh-nine.

I tried so so so hard to not procrastinate this time. The consecutive all-nighters induced by Mod1 did not make me a happy camper. At the same time, I had just kind of accepted that it was my own fault for not starting it earlier -- I got what was coming for me. So, a full week and a day before the Mod2 deadline, Tara, Krystal, and I decided that this time, everything would be different. Ahead of us was a week with a 7.05 pset, a 20.310 exam, and most dauntingly, the Mod2 report, but this time, we would be prepared to take everything in stride.

Screenshot of our overly-optimistic to-do list for every day of the week leading put to the Mod2 deadline

Guess how we did? Well, not that great. I think we all fell off by Wednesday of our to-do list. Despite our high aspirations of staying on track and finishing all our tasks with minimized stress, there were a few things that we did not take account of. These include: 
  • When I have an exam, it's hard not to spend at least the night before and day of obsessing over it, regardless of how prepared or how purportedly 'easy' the exam might be. This makes it difficult to achieve much else on those days.
  • The changing nature of feedback of the course. I attended office hours on Monday to see how I could restructure my introduction and check that off the list. I even went to BE communications lab on Tuesday to polish it even more! But then after asking some more questions on Thursday revealed that my current vision for the report was unfeasible by Friday = rewriting the whole section = sad Katherine. Even though finishing the introduction was slated for completion by Monday, it was not in a state even resembling the final draft until Sunday, and definitely not because I didn't try hard enough
  • CPW. Well, this did not really hinder my ability to complete assignments or anything, but it was definitely a lot harder to concentrate on studying for my exam when a gaggle of prefrosh decided to march into the same area and gossip about college. Also, interacting with prefrosh and telling them about how much I loved my major when I was in a state of mind of really not loving my major wasn't that great either. 
Even though I did end up having to stay up all night on Friday, Saturday, and Sunday night, the to-do list was useful in setting me up for a trajectory to complete the assignment. Because I had started data analysis early, I was able to receive definitive answers to my questions earlier, and thus, be in a place where I could be more self-sufficient in finishing a section (hypothetically). Unfortunately, this has its drawbacks (i.e. read above about my plight in writing my introduction). Still, breaking down the assignment into smaller, more easily tackled tasks made the Mod2 report less daunting. 

And with another (half) week filled with psets and exams, guess what we made? another to-do list!!!

Lab Funk

Well, I can't lie - this class has been tough.  It's been brutal.  It's been exhausting.  But heck, there's nothing like class bonding over a little hardship.  The material we learn is very intriguing (we're basically curing cancer!), but somehow I think the thing getting me through this 20.109 adventure is not the content we study, but the funky group of friends you end up forming through it.  We are almost officially a legit group now.  We have a GroupMe.  We have a snack rotation (P.S. who's bringing snacks next time, guys?!?!).  We even have a group Spotify.  There's just one thing missing.


Like this one.

or this one

In honor of my desire to have a funky-fresh tune for our lab, I began writing a music parody about CHO cells.  It's definitely not music video quality of course, but I still hope y'all enjoy it! 

****Sung to the tune of  'Uptown Funk'*****

'Lab class,
our lab squad,
Shannon Hughes -
that lab God.
This one, for them CHO cells,
them glow cells
straight masterpieces.
The quest, we test
inhibitors of gene repair.
Got plasmids with BFP,
got different topologies

The cells glow (glow bright).

Observed with flow cytometry.
The cells glow (glow bright)-
blue depending on topology.
The cells glow (glow bright).
What inhibits DNA repair?
The cells glow (glow bright).
Could it be an inhibitor?
Break it down.

Repair is inhibited (whuoo)
Repair is inhibited (whuoo)
Repair's inhibited (whuoo)
'Cause them drugs gon' inhibit it'
'Cause them drugs gon' inhibit it'
'Cause them drugs gon' inhibit it'
5pm and we in the lab
Don't believe us just watch (come on)
Don't believe us just watch
Don't believe us just watch
Don't believe us just watch
Don't believe us just watch
Don't believe us just watch
hey, hey, hey, oh!


Lab time, time to work, lab time, time to work (say whaa?!)
Lab time, time to work, lab time, time to work
Lab time, time to work, lab time, time to work (say whaa?!)
Lab time, time to work, lab time, time to work
Lab time, time to work, lab time, time to work (say whaa?!)
Lab time, time to work, lab time, time to work
Lab time, time to work, lab time, time to work (say whaa?!)
Lab time, time to work!