Thursday, April 28, 2016

The Magical 20.109 Staff

Going into Mod 2, I wasn't worried. Most of the people in the class had never written a research paper before, but I had. That combined with the lessons I learned from the Mod 1 report was sure to put me ahead of the game for writing the Mod 2 report. As the time got closer to the due date, I started to realize that the peak of my semester for all of my classes and extracurricular activities centered around that day. I freaked out in the middle of my philosophy class and could not focus for the rest of the time. Luckily, we're allowed to use computers, and so, I sent an email to Noreen listing out all of my other commitments and asking for an extension... and I didn't get one.

I was horrified. She claimed that I had enough resources and time to do it. I didn't believe her of course,

but I got to work on a comprehensive schedule that would allow me to finish in time and sleep each night.

I worked though it slowly, day by day. I began to realize that all of the tedious homework assignments that we did in preparation for this assignment were incredibly helpful. I knew exactly how to fix those sections to make my paper better. Not only that, but I could use the feedback from those sections and apply them to other sections that I was writing such that I did not make the same mistake twice.

I also heavily relied on the feedback from the Mod 1 report. Normally, I don't even read feedback (I don't usually take criticism very well).

I also honestly could not see how writing a bulleted paper without a methods section was going to provide much help in writing a full-length paper. However, the feedback I got was incredibly helpful. I found it very useful to look back at the Mod 1 report to see what information was supposed to go where, how detailed the information needed to be, and what general writing mistakes I had made that I could make better. 

There were still times when I didn't know what to do. Most of them consisted of me frantically typing an email to Leslie at 11 PM claiming that I had no idea what was going on.

She is the resource that I most appreciated. If she did not answer my questions right away, she was sure to answer them early on the next day. She helped to clarify everything and settle my constant anxiety.

Overall, I don't think any of the resources were really unhelpful. I do wish that the feedback on our last round of homework was returned a little earlier, but other than that, it was incredibly helpful.

In the end, I did finish my paper by the deadline, and it was actually something I was proud to hand in. It was hard, but Noreen was right, I did have all of the resources I needed.

Wednesday, April 27, 2016

When In Doubt, Roll It Out

Today our lab protocol was titled "Cathode construction." Assemble a cathode--piece of cake right ? It's one of those things easier said than done. My lab partner called texted in sick, so it was just me and the phage-plated-iron-phosphate-and-gold-nanoparticle active material that we had created days before. Pearl vs cathode construction protocol= story time!

1) Weigh the dried active material that you prepared during the previous laboratory session. Calculate the amount of Super P and PTFE you will need to add to your active material.
Easy enough. Jifa taught us how to use the weigh boats correctly and use the anti-static gun (which looked like something out of a scifi movie and looked like it would shoot needles at you).

2) Transfer your active material into a mortar and grind by pressing the pestle into the material while moving it in a circular motion.
On my way from the weighing room back to the labspace where my mortar & pestle were, I happened to trip on a box that was lying in the hallway. Wheeee there went .0002mg of active material and super P into thin air.

3-9) Transfer your active material into a mortar and grind by pressing the pestle into the material while moving it in a circular motion. Add Super P to the mortar with your active material and grind to mix. Transfer your active material + Super P mixture to the center of a steel plate. Add the PTFE to the top of your piled active material + Super P mixture. Use the roller to incorporate the PTFE into the active material + Super P.
This required some elbow grease. I saw Jifa pipetting some ethanol to another group's powdery mixture to make it easier to roll so I thought I'd do the same. But, in typical Pearl fashion, I overestimated and added too much ethanol. I rolled and rolled..

but realized I needed to wait for some of the ethanol to evaporate in order for my grainy puddle to congeal a bit *tick tock*

In the end, despite my minor mishaps, I managed to roll and punch out six cathode circles, enough to make six coin batteries! I gained troubleshooting experience and was even able to give pointers to the yellow and pink team on their cathode construction. All is well that ends well :)

Sunday, April 24, 2016

Keys to Success

Halfway through my preparation for the Journal Club article presentation, I had a soul crushing realisation. I was a one trick pony.

My topic of choice was male fertility. My Module 1 topic of choice? Female fertility. I was all about the baby-making, and it was... Kinda weird, mostly coincidental.

But try as I might, I couldn't bring myself to switch my article choice. The more I read, the more engrossed I became. I realised that despite my hang-ups about the research topic, I was happy to spend time learning and talking about the issue of fertility, and the many ways in which it genuinely interested me.

I took my time perusing my Journal Club article, annotating where necessary, looking up related articles and topics whenever they came up. I carefully animated my slides and savoured the story I was constructing. And when the time came to present all I had learnt, I was cool, calm and collected.

Okay, that last bit isn't true, I was kind of a nervous wreck, like most of us amirite? But my point is, Journal Club was a truly enjoyable experience, and I'm so happy to have invested my time in learning about human fertility. The best part of 20.109 is being able to sample the various aspects and fields of bioengineering, until you find one that suits your palate. And don't be shy to stick with it! Passion is the key to BE (and life!).

Thursday, April 21, 2016

Ooooh, We're [More Than] Halfway There..


✔ Mod 1: Protein Engineering
✔ Protein engineering mini presentation
✔ Journal Club presentations
✔ Mod 2: System Engineering article

Now let's talk about that last one--the (infamous) Mod 2 report. We were told about it WAYYYY in advance; I had it penned into my calendar since the beginning of the semester. And yet, it snuck up on me. There I was, indoors on Marathon Monday, trying to ignore all the festivities I was missing as I worked on the report with Olivia in the student center. Sometime over the weekend, after office hours (just my luck), I had hit this writer's block:

And that was when I was still on the Results section of my paper. There was still the Abstract, Intro, and References...As I looked at the clock, I internally felt like this:

BUT WAIT, it got better worse. I'd hastily written an abstract and introduction that was based on homework assignments we'd completed previously, but my discussion section was half written by 4:58pm, two minutes before the deadline. I realized I couldn't hand in a 90% finished report and lamented to Olivia. She suggested that I take a full late day, because it'd be worth the 3 point penalty if it meant I could hand in a more complete report. And that's what I did that--I took a late day (and felt like this for the rest of the day):

I worked on the report again after dinner, but the figures I had initially chosen for my article didn't fit together. I had forgotten why they made sense in the order that they were. So naturally, I turned to Leslie and Noreen for help. Thankfully, Leslie agreed to let me come into her office hours on Tuesday. Guess what? I was there for five hours straight. Her office became my second home for the better part of the day. We'd sat down and reoutlined my report and I'd felt more confident about my story, but around 4:30pm, I ran out of time again. (Sense a trend going on here?) But in the end, I finished my Mod 2 report and never looked back.

Jk.. I went to Noreen's OH and told her of my suffering that day in Leslie's office. THEN I never looked back at that report again.

Wednesday, April 20, 2016

We always expect the opposite of what we should, don't we?

If I could choose one picture to summarizes how writing this paper went, it would consist of entirely unrelated things being thrown at each other in the hopes of forming a cohesive structure with some semblance of logic. 

If this paper were a poncho and I were a man.

This all started innocently enough. I was googling “Men poncho” because a) I am a grandmother and enjoy spending my free time crocheting (I have yet to collect the necessary cat population though) and b) I fervently believe google does not recognize nor require the addition of possessives to search queries. Then I stumbled upon that gumball man that might be James Franco with a fuzzy on his head. Then I thought “wow that mess really makes me think of what a mess I’ve been lately.” As that thought flitted though my head, I realized with sudden doom that I had to complete the final piece of Mod 2 – this blog post.

And here we are.

So, here we go. 
Since "are" is past tense and it is past the time I should've done this. 

If I were a joke I'd be a dad joke

Anyway, here we go, to the last memory I have of the Mod 2 report. 

There was something strangely satisfying about closing all the tabs I had open, one by one, after I sent the email on Monday. All the articles I had used as references, the research I had done on our research, all the identical little green images that I couldn’t quite discern, each a different day’s lab protocol. Each tab I closed felt like a weight lifted.

Which one of you made this? 

I had felt intimidated by the report that kept getting described as a beast, something to tackle and battle, but in the end, it wasn’t the report that was the monster. We had everything we needed – the data, the resources, the help – the problem was really that we had too much. As I was writing the report, I was constantly struggling between “How do I fit all this in here??” and “I don’t see what else I could possibly say about this…” In the end, it was the sheer volume of data and resources that was overwhelming and monstrous.

The report itself was more or less like this kitten. Getting the data organized though? More like the hidden fleas in its fur carrying Bubonic plague. 

It’s always the little things that we overlook, isn’t it? Hands down, there was one part of the report that I had by far the easiest time with of any paper I have ever written: the citations. Thank. The. Lord. For. Zotero. Honestly, that thing is magic. It’s like someone took all the kindness in the world and put it into an app. Like someone tried to atone for every instance in which a door was held open for an ungrateful individual, every time a toe was stubbed, every puzzle piece accidentally lost. I always thought about how convenient it would be to have something like Zotero, and I still can’t get over how happy I am that 20.109 introduced me to it. It’s like Pinterest, but for things that aren’t food!

So in the end, although nothing really went as expected (not even going to mention the actual data we got...), things weren't all that bad. In fact, they were barely even somewhat bad. And, now that the fearful anticipation of a looming due date is over, I can fully feel the lack of anticipation for the end of the semester. Sure, there's stress around every corner, but the thought of no longer having 4 hour lab blocks set aside on my Tuesdays and Wednesdays leaves me strangely empty... 

A Sciencetale (like a fairytale, but not really)...

Once upon a time, there was a princess wannabe (I really am a princess, they just haven't figured it out yet), who came upon a dragon called Mod 2.

Journal club was the first time I had spoken in front of a large group of people since the summer and the first time I'd ever presented work I hadn't done. It was daunting because at every turn, I wanted to say "I" or "we" because that's what they teach you in high school for the science fair - make sure your judge knows how much of the work was done yourself. Unfortunately for journal club, that was none. It was tough learning what someone else did and trying to get in their minds. I tried testing out my psychic abilities to see if I could figure out their logic and predict what they did next. It appears I didn't make it out of the psychic academy :( 

I read the paper. And I read it again. And again and again and again. (Not again, then I couldn't stand to read more about high-throughput screening, sorry Goglia). I presented. And then it came time to watch the presentation. I had a nice solid break between presenting and watching that I had basically pushed it out of mind. Journal club? What journal club? Things turned out okay in the end - I got some very helpful feedback that'll help make me into a better scientist but I don't think I've recovered from having to watch myself and I really hope that file gets deleted so that posterity can be saved from that D:

Just when I thought Mod 2 couldn't get more intimidating, the report came along...(dun dun dun).
Writing can sometimes be a challenge. Going into my mod 2 report, I felt a lot like Spongebob writing his essay for boating school - I really didn't know where to start. 

I had the homework from class that I put together - a few bits and pieces of the report. But how to put everything together? How was I supposed to make a story? I remember doing the analysis to determine NHEJ repair efficiency and opening the spreadsheet and being lowkey (read: highkey) overwhelmed by the volume of numbers on there. 

I felt like as I wrote my report, the story I wanted to tell kept changing. I'd begin writing about what my results told me and then as I thought about it, it slowly made more sense and then I started thinking about it differently, and before I knew it, I had a NEW best-seller about NHEJ to write. 

So I wrote a nice generic story until I was able to decide what direction I wanted to take with my report. I was also out of town this past weekend for a Camp Kesem retreat which was super packed with activities (which meant using my 2am inspiration to write my report :( ) and then volunteering at the marathon raising money for CK. So before I headed out to the wilderness (which actually turned out to be quite nice), I basically played 20 questions (times like 3) with Maxine, to figure out how to make this report sound good. I wrote a little by each day so when Sunday came around, only some editing and adding a beginning to my paper was left. Office hours helped me a ton! Before, I was very unsure if my story was coherent or made sense to someone besides myself (stream of consciousness??). But, everyone's help allowed me to craft my story such that it flowed well. From the protein engineering summary, I knew how important office hours were and I made sure to make the most of them on this especially busy weekend. And as you would have it...(*drumroll*)

It turned out okay in the end! Sometimes you just have to trust your instinct and not be afraid to get help when you need it! 

Tuesday, April 19, 2016

Something Has to Go Wrong

I knew going into Mod 2 that it was going to be rough. Mainly because I had to give a 10 minute long journal club presentation all by myself. Don't get me wrong, I love talking, but I hate presenting. I'm always self conscious about how I'm speaking, what information I'm delivering, if I'm making enough eye contact, if people are even listening to me. I also don't enjoy reading papers, especially biology papers. I get so lost in the acronyms and the common terminology that I don't know. So, needless to say, I was not looking forward to the journal club presentation.

I signed up for the first journal club day, even though I had a test the day before because I knew that it wouldn't be as packed as the second day. I made my presentation slides early, I made notecards, I practiced multiple times while timing myself, and I submitted my slides way in advance so I wouldn't have to worry about not getting to present in the order that I wanted to.

Of course, none of this helped on the day of the presentation.

I was so nervous that I was pacing around the room before I started. Generally, I like to let myself feel my emotions as it usually helps me identify the cause and get over them more easily. That was not the case for this. Of course I knew the cause of my anxiety. I was going to have to talk to a room full of my peers and professors, all of whom know much more biology than I do and probably already think I'm ridiculous for being in a bio lab when I'm a Course 2. Letting myself feel this anxiety only made it worse. I could see people around the room getting irritated with my pacing and whatnot, which also exacerbated the problem.

Eventually, I sat down and tried to breathe. I thought about all of the work that I had put into my presentation and how prepared I actually was. It worked a little.

Then, I got up to present. It wasn't awful. I was saying the things I wanted to say; I felt confident; it seemed like I was going at a reasonable pace. Just to be sure, I checked the timer and I was horrified at what I saw. I forgot to start the timer. Of all the things that could've gone wrong, this was probably the worst and the most unexpected.

I froze. I've given presentations with time limits before, but never such strict time minimums. But regardless of the time requirement, I now had no idea how long I had spoken for. I tripped up on my words while trying to think of a possible solution, some way to determine how much time I had left. There was none, so I just kept pushing through. I think the shock made me speak faster and distracted me, causing me to leave out some of the information. When I finally finished, I could tell that it was not the appropriate amount of time.

I tried to ask Leslie how much time I took, but she didn't want to tell me initially. That's when I knew it was bad. She eventually told me that I was under time by 1:30. That's not that much time, but relative to the length of the whole presentation, it was a lot. That was all that I could think about for the rest of the presentations. It made it difficult to focus on other people's presentations enough to ask intelligent questions.

When I finally watched my own presentation, I was fairly impressed with it. It appeared as though I did much better than I felt I was doing in the moment. When I got my grade and comments, there wasn't anything too unexpected. I did not do as well as I had hoped I would do, but I did much better than I thought I actually did.

In the end, I guess everything worked out okay. I hope to do better on the next presentation. Hopefully my lab partner will remember to start the timer.

Down in the DM

If I had to guess how many scientific papers I've read in my lifetime, I would say "one helluva lot". But despite the exposure I've had to research articles of all shapes and shades, when the time came to write one of my own, I felt like a literal fish out of water. 

We're talking hyperventilation and muscle spasms.

Not actually, but I was pretty lost.

It's a tale as old as time, and I had to learn the lesson same as everyone else... Synergy ain't easy. I never knew how difficult it could be to take the numerous and scattered ideas, data, analyses, bits and pieces of research that I had been compiling over several weeks, and turn them into a comprehensive, 12 page whole.

I thought that I was doing everything right. I started early, I went to office hours, I dutifully employed the improvements recommended by my instructors and my peers. And in the face of all of that, I still struggled to pull together my Module 2 Research Article.

My salvation slid into my DMs like**, "Hey girl! Have you started the report for 109?" It was my beloved lab partner, reaching out with a question about the assignment. Fast forward 5 days, we're seated together, working on our individual research articles, but frequently piping up to resolve each other's queries, big and small. In those moments, I realised that my most valuable take away from this module, and from this class, would be how to collaborate with a fellow researcher, while still crafting a final product that I could call my own.

To be able to bounce my thoughts and worries off of another person, without fear of judgement or sounding silly, was integral to my successful completion of this module. I know now that "individual completion" does not have to mean "afraid and alone", and everything is easier with a friend.

**Please see the following examples of how it went down in the DM: 24 Extremely Smooth Ways To Slide Into Someone's DMs

Uphill Battle

Before starting to write my report, I thought that the activation energy required to simply begin writing the report would be far greater than the energy required to write the report itself and once I started it would be an easy roll down the mountain. I was completely wrong. It was an uphill battle every moment up until the point of submission. 

Make no mistake, I was fully prepared for the momentous amount of work that would have to go into the report, but what I was not prepared for was having a quite drastic life-changing event the Friday before the report was due. My study space and environment was totally turned upside down and I struggled to find a place to work where I could focus and be productive without a gloomy cloud lingering over me. And so the battle became even worse, where not only was I climbing a huge mountain but I was going uphill with chains around my ankles. 

I usually love scientific writing and I generally enjoy making scientific reports and generating data. There is something soothing about organizing all my numbers and generating aesthetically-pleasing graphs and whatnot. I think if I would have dedicated more time to the report and not been blindsided by the events from Friday, I would have actually really enjoyed writing this report as well. It was great to think about crafting a story to tell with our data, and I felt like a real scientist gathering all the bits and pieces of the puzzle to get a look at the bigger picture. 

However, the report in combination with the Friday events totally drained me of energy and ability to focus. I searched desperately for places to focus and work because my normal environment was flipped on its head. Despite this I forged forward with my armor ready for any battles ahead, charged through everything and made it to the end.


With this report, I just faced a huge challenge in terms of dealing with adversity in the face of huge assignments and academic load. I feel stronger for having overcome everything and successfully finishing this mammoth assignment. 

Coming to Inconclusions

In writing my introduction, I read several papers about the surprising anticancer effects of loperamide (or Imodium, commonly.) Several labs have found that the humble antidiarrhea agent induces apoptosis and sensitizes cells to radiation and chemotherapeutic drugs by impeding NHEJ. This is a big deal! Loperamide is cheap, it's already FDA-approved, it has low toxicity, it's readily available, and it'll spare you your indigestion while you're at it.

But not so fast.

My single-replicate dose response assay begs to differ! I found that loperamide, in fact, *decreases* sensitivity to ionizing radiation.


It does seem a bit odd that an antidiarrhea drug would be an NHEJ inhibitor. Imodium works by specifically targeting epithelial cells in the digestive tract. These cells are constantly sloughing off and being replaced, and thus are among the fastest dividing cells in the body. You'd think you'd want them to have pretty darn good DNA repair.

But the scientific community doesn't seem to agree. So I and my dose response assay set off to change the world, hinting that *maybe* we should reassess our enthusiasm about loperamide the Anti-Cancer Agent just a tiny bit... or, you know, I could consider replicating my assay, say, 14 more times. I wrote twelve pages about it, with some figures to boot.

Lessons from Journal Club

The journal club project was quite the experience. We were given a large variety of papers, even though they all shared a common idea. They all suggested tons of add-ons to NHEJ’s mechanism and uses, and showed just how extremely complicated science is. However, in all this complication, there is so much that can be learned. Giving the journal club presentation taught me a lot more about science than reading 100 papers would.

               The reason I say this is when I read papers, it’s much more of a skimming than actual analysis. The main reason is that most papers can be boring. They’re extremely formal, can be written with excessive complexity, and not always directly related to what really interests me. But there is a remedy to this. To a certain extent, you can almost pretend a paper is interesting, and that alone can help you get through it. Having a reason to read the paper beyond it being mandatory is the big help. For my paper, it was the one that sounded potentially the most interesting, besides CRISPR which had already been claimed, so going in with the mindset that I will enjoy this paper helped the reading part of this project.

               Another reason this presentation does more than reading a bunch of papers is because you’re going beyond reading and basic understanding. You need to be able to understand this paper so well that you can re-explain it to a group of very intelligent people, who will ask some extremely intriguing and complex questions about it. Due to this, you have to re-read the papers and memorize the figures. When you look at all of this as an assignment, a grade, mandatory, required, etc… it sucks. But when you look at it as an opportunity to learn, to teach, to motivate others- then it becomes so much easier.

               Putting these together, I’ve relearned the power of perspective. The way you look at a problem can totally alter your experience in dealing with it. By actively engaging in a project, you can get so much more out of it than you do if it is just another grade.

               My takeaway is to make everything an experience, not just another requirement in your never ending journey.

Two Roads Diverged in a Mod 2 Report

The mod 2 report was one of those assignments that you hear about in advance, make a point to write down the deadline (on your google calendar, corkboard, post it notes, forehead – you know, whatever works), and then watch as the days approach much too quickly. It seemed like this huge obstacle that would be impossible to climb.
In mod 2 we had done a variety of different experiments, and there seemed to be a multitude of ways to organizes these results into a story. The sheer number of potential paths was daunting so I narrowed it down and decided to give one direction a shot.

But it ended up seeming disjointed, as if it were two different ideas, which made me wonder…
Why not just go with the new idea instead of clinging to the old one.  (Ha! sunk cost fallacy, you won’t trick me [this time]!) It was a freeing realization, but there was just one little problem. I now had to sift through the work I had already done and see what I could salvage.
Then some words advice from an old English teacher came to mind like the voice of Yoda during a Jedi battle. “Eat your elephants one bite at a time.” These goofy words of wisdom prompted me to sort through each section at a time, rather than worrying about getting the whole report done in one brain frying sitting. 
It you ever have to eat any elephants, I really recommend doing it one bite at a time. The results are rather sweet.