Sometimes nothing works...and that's okay.

Hey guys :)

I know this post is long overdue, but the module 2 research paper took so much of my focus that I completely forgot about blog posts until this moment. I'm sitting in the corner of an 8 year old cousin's bedroom, hunched over my laptop as I pretend the members of the Cheetah Girls aren't staring directly at me from their 24"x36" theatrical poster hanging behind me.

Module 2 is finally over. It's hard to imagine how we managed to get so much done in such a short amount of time. I could have sworn just the other day, I was sitting in the third row of 20.109 lecture on the first day of class wondering how we were going to get through such an ambitious course load in such a short amount of time. And yet, here we are. Module 2 was demanding. But it never stopped being exciting. I was in a position where I could to take control of the direction my research went it. I got to select my targets and sequences and make decisions that would produce my own unique results. Having this responsibility is something I've always imagined I'd have in graduate school. But this experience came a couple years early, lucky for me ;)

I loved the journal club presentations. It's a skill I really never get the opportunity to practice in front of people. To be able to break down an academic journal, pull out all of the skeletal, important bits of information, and present them as clearly and concisely to a panel of my peers is something I want to master. When I got up to present on that first day of JC, I blacked out. I have no idea what I said or how I got through it. I really have no memory of presenting. I had rehearsed it so exhaustively the night before that I was able to go through this routine without really paying attention to anything I was saying. And I will admit, it was super cringe-worthy watching a tape of myself present. But I got to see I was good at a lot of things I didn't know I could do. And I got to see exactly what could use some work. And for that, I'm grateful of this experience.

Now, the Mod 2 report. That report was one of the most difficult things I've ever had to write. Having to capture weeks and weeks of thoughts and concepts and execution and data in a single assignment was so much easier said than done. I knew what I wanted to say deep down. But how do I organize my thoughts on paper to get everyone else to understand exactly what my partner and I tried to accomplish? Honestly, I've never gone through more writing blocks with an assignment ever before. And one of the biggest roadblocks I had to deal with? Our experiments did not work. Not even a little bit. All our data showed our CRISPRi system made no effect. I'm pretty sure in academia, no one would dream of writing a paper where nothing happened. The bulk of my writing had to be about why it should all work conceptually and what could have gone wrong here. But having to turn nothing (data that contradicts the basis of the study) into something (a quality paper) was so difficult. It was a draining experience.

Failure is a part of this line of study. Getting knocked down is a part of this line of study. Hitting as many roadblocks as I did is a part of this line of study. And ultimately, I'm happy I got a chance to struggle through it. Things aren't going to go right, regardless of how extensively concepts have been studied and understood. And the reality is, I'm going to have to communicate failures with those around me. It's exhausting, to be quite frank. But it's the good kind of exhausting. The right kind of exhausting.

-Sami K

Impact of Time on Improving Scientific Communication

Three years ago I attempted to write an independent research paper for the first time. I was lucky enough to have phenomenal resources at my disposal from a biological standpoint, but my knowledge of effective biological communication was incredibly minimal. My first step was, of course, to write the title and the abstract and work my way onto the methods, results, and discussion. I had no plan and went after the paper as if I was a hungry child on his birthday with a cake all to himself. Which bite should I take first...

Jumping ahead three years, I met Sean and the rest of the remarkable 20.109 staff who have aided me exponentially improve how I approach the process of communicating biological research. Module 2 was a really enjoyable one for me. I'll be honest in that I didn't always know what I was doing at first (i.e. Why were we taking reverse complements of certain sequences? Why did we add ampicillin to this culture?), but there was never a moment when I felt I didn't have a valuable resource at my disposal.

This was all the more true when it came time to organizing my data and work on paper. At first, I was entirely overwhelmed in much the same way I was my senior year of high school. The abstract seemed tantalizing. I mean it summaries everything I did, why wouldn't I write that first?? The title! Of course get that on paper. That's the easiest part! Turns out my brain was full of fallacies that took me until this Module in 109 to reverse and grasp completely. Every communications lesson gave me a clearer understanding of what an effective research paper should look like, and what I should be thinking about as I write.

By the end of the paper-writing process, I remember thinking back to my time senior year so much so that I actually pulled open the paper I wrote back then. After reminiscing for a minute, it amazed me how far I had come with the help of the instructors and professors in this class. This Mod contained a lot of different experiments, difficult molecular bio and cell bio concepts, and potential for misunderstanding 'why' and 'how' things were done. After the initial moment of bewilderment at how to collate all of this information in a clear format, I was excited to take on the challenge. I was excited to prove to myself that I had really gotten something out of the hours of the discussion we spent on effective communication. Mostly, I was excited to see the transition I had made from a high school science student to a more experienced one. The transition process won't really ever stop, but at least I know I'm making progress.

On CRISPRi, public speaking and fdr...

Although the experimental part of Mod2 was shorter than the one for the first module, I really enjoyed learning about cutting edge technologies such as CRISPR and the different variants it has. The idea of being able to specifically target and inhibit or activate particular genes in order to manipulate metabolism, and use a cell’s innate abilities to produce something we want is incredible.

I enjoyed hearing about current research being done in the field during the Journal Club presentations. It was great to see the extent of the impact this research has, and the innovative ways of using new technologies scientists and engineers come up with. Presenting wasn’t all that fun, since I am definitely not a fan of public speaking, but hearing the papers my lab mates presented was very enlightening, and presenting was a valuable learning experience.

I am also glad for all of the Mod2 homeworks we were assigned throughout the course of the module, since they made the Research Article a little easier to write. I can’t believe I’m saying this, but I sort of wish we had more of them, so approaching the final report didn’t seem as daunting or time consuming.

Despite not getting insertion of our frd gene, managing to mess up our standard curve, and getting very small ethanol values that could not be corrected for noise, my overall experience throughout Mod2 was very positive. I feel like I learned useful, current, exciting things about the field and the research being done, as well as the impact it can have in bioengineering and medicine.

-Yvette

PS. If the CRISPR module is taught again in the future, can the teaching staff target the frd gene? I’m still curious as to what the effect of inhibiting the TCA cycle has on ethanol production.

PPS. In case you were wondering.. number of times the following words appeared in my Research Article:

Ethanol-68

Product-67

gRNA-61

CRISPR- 60

Cell-54

Increase-44

Cas9-37

Successful-1

Pernicious CRISPRi refuses to cooperate with students’ metabolism manipulation plans

(A)                                                                                                

                                (B)

Fig. 1 – Samantha looked forward to implementing CRISPRi in Module 2. She did not look forward to Journal Club. CRISPRi is a very trendy gene-editing tool, and, like all trendy things, kids wanted to get their hands on it. This included Samantha. Moreover, Samantha and her lively, creative friends will probably come across CRISPR sometime in their professional life. Samantha knew that this first exposure would mark the transition from a before-CRISPR era (B.Cr.) to an after-CRISPR era (A.Cr.). However, hidden in CRISPR heaven, was the thing Samantha dreaded most: Journal Club. (A) Samantha getting Journal Club instructions. (B) Timeline of every bioengineer’s life.

                                 (A)

                                 (B)

                                     

Fig. 2 – Benchling is the worst. Samantha understood the general idea of CRISPRi and how to implement it. However, she had more trouble getting comfortable with using Benchling to build the plasmids with inserts, perform sequencing analysis and design primers. In the end, though, she grew accustomed to this, implemented her CRISPRi system along with her fellow experimental subjects, and was very excited to see lactate yield increase! (A) Samantha trying to understand Benchling. (B) Samantha watching her CRISPRi samples do their thing.

To Samantha’s dismay, CRISPRi stubbornly declined to do its job. Tensions between Samantha and CRISPRi grew, to the point when CRISPRi walked out of the room and refused to be part of the team, telling lactate to “go produce itself.” Samantha was a little disappointed in the lack of yield improvement because (1) it was her first experience with CRISPRi, and (2) she needed TO WRITE HER RESEARCH ARTICLE. Luckily, other teams had better success in cooperating with CRISPR and she could use some of their data. 

Now it’s time to move on to Module 3!

Fig. 3 – Samantha and her team members approaching the Module 3 Research Proposal Presentation.