Friday, May 15, 2015

How to trick yourself into thinking you’re writing the module report

I would like to share with you an amazing strategy I have had the pleasure of discovering via 20.109 this semester.

You see, through tireless effort, countless attempts, and endless hours dedicated to grinding out reports for this course, I have finally discovered the most optimal procrastination technique. It is so effective, in fact, that at times it will irrefutably convince you that it is not procrastination, but work of the utmost and immediate importance. It may seem difficult to implement at first glance, but believe me, once you train yourself to stop the urge to write your results down and get the report over with, you will find this technique very easy to master and even quite enjoyable. In the end, you might figure that is it too overwhelming or unnecessary to actually write the report anyway, and your problem is solved!

Curious? There are two key steps to for this process to work.

1. Read all of the related literature. ALL of it. Read it in depth and pay attention to all the details. Follow the tangentially-related references and whatever you do, don’t stop reading until you have learned the complete history and entire current state of the field.

Figure 1: Schematic demonstrating the process from a more relatable starting point. However, this is biological engineering research, so I recommend you begin the voyage from PubMed, or at least google scholar. (Xkcd 2007).

     I know, it sounds quite challenging at first. After all, you might just read a few papers and feel like you have a pretty good understanding of what is going on in general and how it fits into the experiments you did in class. DO NOT LET THIS FEELING FOOL YOU. I repeat, you have not learned enough yet. For example, you have to understand that it’s important to read beyond just all of the literature on “Ku80 related NHEJ-repair in CHO cells,” which is probably under 10 papers anyway. Have you at least learned everything on Ku80? Do you understand its crystal structure? What--you didn’t know the crystal structure was elucidated in 2001? How are you to possibly understand the molecular mechanism by which it resects double stranded DNA breaks? Aren’t you curious about the differential repair results of your specific cut topology? I mean it’s your precious, darling, unique break-site architecture for crying out loud! Once you sufficiently feel like you understand enzyme-DNA dynamics, you can move onto exploring the all of DNA repair, or at least homologous repair which you can frequently mentally compare. Don’t forget to really explore all the sub-branches, mechanisms, and implications. It’s also really important that you don’t have a system for organizing all the useful portions of the literature that you read—downloading entire pdfs and dumping them into a folder or bookmarking the tab (try to keep switching it up for fun) should work fine. If there’s anything you don’t understand, a method or a term, immediately open a new tab (Figure 1) and learn about that until your computer overheats or the deadline for the report has passed.

Take home message: Don’t feel limited in your exploration! Remember, the point of your MIT education is to learn as much as possible.

2. Make all of your figures before you write anything. Then continuously remake them. Generate many types of visuals from the same data set. Keep changing them as you find little errors or large mistakes in reasoning. This is the fun part, so give yourself every excuse to keep working on them.

       Ok, now that you have sharpened your critical reading skills, it’s time to move on to the artsy design skills you’ve dreamed of developing ever since you first used Microsoft paint in second grade. In fact, for nostalgia or for lack of more complex software, you should probably do all your figures in Microsoft paint. Sure you can plan them out in PowerPoint or Illustrator, but make sure to always drift back to Paint for any finishing touches. See how fun it is to manipulate each pixel? There is such a joy in eyeballing where things should be without those pesky guidelines always snapping and giving away the alignment solution! Make sure to spend a lot of time on font, text size, color palette, and especially about positioning the images into your report. This last step is particularly key because you have no idea how the text in your report is going to ultimately look like, so you might as well define it with images first. The text will then easily follow into the spaces you’ve confined. After all, if your report doesn’t look publication quality then how can it possibly contain useful information? So definitely make sure that the figures, and not the text, carry your research. This is also where many versions of the same image come in—if it doesn’t look “nice” then have you tried changing the significance threshold so your error bars are smaller? You might as well take off the bottom error bars that annoyingly cross the axis anyway, since your audience is scientifically literate and understands that the range is symmetrical. Also, try to log transform your data and otherwise deviate from any “overly-simple” representation to really show that you are a researcher concerned with presenting compelling and clear visual results. Oh god wait—is that a formatting inconsistency? Remake them and watch as they grow more beautiful and more plentiful! Hopefully someday research can progress where readers can follow the images and just read between the lines, you know? Then you don’t have to explain anything; just look at the graph people! After you’ve exhausted all possible data files and their representations, you should contemplate picking up the hobby as a children’s picture book author, which is perfectly suited for your visually-dominating, textually-minimalistic approach.

      Congratulations! After these steps you should have a lot more files on your computer than when you started! Wow, you really have done so much work on this report; you temporarily know everything ever and just look at all those figures!! In fact, at this point you should feel pretty finished, since the remainder of the report is just filling in the words—trivial.  In fact, it probably feels pointless to detail your results now anyway since you’ve realized it’s all mostly been done before, more carefully and much more impressively.

      So you should probably just go take a nap, since it took a lot of effort and time to truly master the most productive procrastination approach to large writing projects. You only lose 1/3 of a grade for late work, so I encourage you to continue implementing this process after the initial due date. Good luck! 

Thursday, May 14, 2015

Platinum and Titanium and Gold

The final written report for 20.109 was a summary of sorts, covering the construction and testing of our dye sensitized solar cells. Before I started this module, the idea that I could coax viruses into growing precious metals seemed ridiculous. How was I supposed to convince a tiny little phage to make gold and titanium nanotubes that would become part of a solar cell?

51 Corgi GIFs That Will Change Your Life
What? They can do that? I had no idea that they could do that!

The answer? Through a lot of cooling and mixing of the phage in nanoparticles of gold and titanium oxide. The nanotubes were eventually integrated into a dyed paste that became the heart of our solar cell. All of the 20.109 teams were able to test their solar cells in a solar simulator in the Belcher lab. We didn’t do too bad at all - our little solar cell had 2.8% efficiency (to put that number into perspective, one of the highest solar cell efficiencies in the history of 20.109 was around 4%)! We got a chance to see the titanium and gold structures under a TEM later on. While gold was hard to find, our solar cell had a ton of crystallized titanium, and even displayed some phage-length titanium wires!

51 Corgi GIFs That Will Change Your Life
We did it!!!!!!

But back to the Mod 3 summary. While we had been having fun assembling our solar cells and seeing them in action, we still couldn’t slide away into the summer without analyzing our data. We got all of the solar cell data and TEM images and started typing away. This was when I really was happy to have the Platinum team of three. Sure, we were that team in the back of the lab, the overflow team, the team that had to constantly re-divide tasks between three people no matter how awkward it was (cough, tissue culture hoods, cough), and the team that an extra set of samples to analyze in one module. We also didn’t know one another that well at the beginning of the semester. Like Will said, the first couple of weeks was a lot of tripping over one another and forgetting to grab extra buffers and water because we had another set of samples to run through. But as the weeks went on, we figured out a way to assembly line a lot of the procedures, and soon we weren’t always the last group to exit the lab. We subbed for one another when club trips happened and we always had things to chat about during the awkward 10min incubation times that came up. So when we had to write a report summary in 4 hours that last day in lab, we quickly got working away, automatically splitting the summary into sections due to our strengths, but also leaving time for all of us to discuss the results together and come up with a consensus on how to interpret it.

We saw that the size of the gold nanoparticles didn’t have much of an effect on the efficiencies of the solar cells and that the differences in dye absorption between the T/Th and W/F classes made a large disparity in the final solar cell efficiencies. We puzzled over the lack of gold in our TEM images and contemplated future changes that we could make to the solar cells to make them more efficient (Thinner doctor blading? Longer gold incubation times?). We finished and left early(!) and walked back home, ready to meet up later that weekend to work on our research proposal. We still had that last presentation to do but for a last day in lab? Not bad. And we came so far since the first day.

And with the leaves, we leave 20.109

In one moment, I was taking the pink laser pointer from Jenny and stepping forward to discuss the methods of our research proposal, in the next I was answering questions about the formation of G-wires, and then I was finally (shakily) taking a seat back in the audience for the rest of the WF 20.109 final presentations.

It didn’t hit me until I walked past the chirping walk signs across a green, leafy Mass Ave that it was my last official day of 20.109. Whoa. It’s been a long three? Four? Four months. And a ton has happened since the first day.

I admit it, I totally included leaves in the title of this blog post just so I could add this adorable gif

I wasn’t sure what to make of this class on that first Tuesday of spring semester. It looked simple enough on my registration form - a requirement for my major, a CI-M, and a class that included lab time. I thought it would be like any other class, except that I would trade the constant lecture hall for a lab bench and science articles for psets. It would be simple, walk in lab, walk out with data, and I would pick up some lab techniques on the way, riiiiiiight?

Happily enough, I couldn’t have been more wrong. I might have disagreed on the “happily” part while on the dark, stormy seas of writing the Mod2 report, but in the end, I gained so much more than I was expecting. I learned how to work with tissue cultures, how to not load a DNA gel, how to check for the probability of homodimerism and heterdimerism in primers, how to find a variety of species in a microbiome, how to commit viruses to “growing” precious metals, and much, much more. I learned how to write scientific papers and give professional proposals and presentations. Heck, I learned how to prepare to write papers and proposal and presentations (the number of times I would have been truly screwed on a mod report if I hadn’t been forced to write drafts earlier as homework is laughable). I learned the basics of what a life might be like in research. And I got a good course in how-to-deal-with-all-nighters 101… as well as what-you-can-do-to-avoid-all-nighters-101 and how-important-sleep-is-when-writing-anything-101.

I walked out of this class knowing that even if I got thrown into a new project with a few procedures and a topic to chase, I could work towards understanding the background literature and make some progress on moving the project forward through tests and assays. The wide range of topics we covered - from characterizing microbiomes with, to testing the DNA repair abilities of cells in the context of cancer, to designing solar cells - gave me a great snapshot of the different fields that I can explore in the future. Ultimately, this class taught me the steps I can take to learn how to conduct research, an important method for any engineer.

Thanks to all of the wonderful instructors and TAs and professors that made this possible! 20.109 was definitely a big surprise this semester (wait… this is not just a lab technique class… what?), but one that came out for the best!

Now, onto the adventure… finals. See you all on the other side!

The End is Just the Beginning

My days in 20.110 may be over, but the 2nd half of my MIT experience will begin soon enough. There's a pretty good chance I might not write my thesis on the seagull microbiome or work specifically on NHEJ DNA repair, but that (hopefully) doesn't mean that all the work I've done this past semester has been for naught. I've learned a lot about experimental design from the setting up controls and the prevention of variables that could confound the data. I've also learned some of the jargon of biological engineers and have become more experienced in scientifically writing about the introduction, methods, results and discussion of a lab report. These skills greatly help me to effectively communicate and investigate interesting biological systems.

The 20.110 experience also showed me how important (yet difficult) it can be to stay up to date with various innovations in the biological engineering world. The rate at which new technologies and experiments are being performed, there's so many interesting resources and ideas flowing to tackle several modern day problems. That being said, communication and discussion among peers is a great resource, and even asking for help and advice from mentors and experts can provide guidance about different ways to go about solving a problem. I really appreciate all the 20.109 staff for being open and making time to discuss ideas with the students, it was very reassuring to know that support was available even if at times, I went about doing assignment in my own way.

In the future, I hope that my experience at 20.109 will have prepared me for upcoming challenges of future lab classes as well as UROP work. I know I still need to work on my communication and hope to take the initiative to find opportunities to speak and present to others about interesting research going on in the field of biological engineering. One of the fields that I am currently interested in is synthetic biology, which incorporates cellular transcriptional circuits. There is still much about this field that is new to me, but I hope that as I learn more about the field, I can take some opportunities to share the exciting things that I am learning with others.

Wait, there's no Mod 4?

It's pretty hard to believe that my time in 109 is really over. Certainly, a lot has happened over this semester. Most importantly, I believe that I have taken steps in becoming a better communicator in regards to science. I am more confident presenting something like a Journal Club and I am even more confident presenting a research proposal of my own devise. I have made significant progress in my scientific writing throughout this class. I think each module uniquely supplemented the learning experience.

Mod1: This module had some pretty awesome real-world connections to the flu and it opened my eyes to the immense complexity and function of the microbiome. Now, to be honest, I could not see myself a lab studying the microbiome as a UROP or anything, but I can't ignore the numerous benefits of studying it. Mod1 introduced me to how to write a structured scientific paper. I had a little trouble analyzing the data because I felt like I was stretching, but I put a lot of effort into making important connections. It was nice to have a rough and final draft on that report as I really was just trying to figure out my scientific voice at that point. The primer design was a really cool part of the module and I think that is a lab skill that can be very important in other lab work. Professor Runstadler was a great help throughout the process and I think he did an awesome job as the figurehead of the module.

Mod2: Not to pick favorites, but Mod2 was my favorite module. More than anything, I think this can be related to the fact that I really understood the material and the processes. I could much more easily analyze the data and come up with better discussion points that conveyed how well I understood the material in general. I became way better at writing a methods section (thank goodness), although that's still my absolute least favorite part of scientific writing. My abstract was more clear and stronger. Attributed to a great understanding of the workings of this module, my results section was able to very clearly and concisely illustrate the data from this module and the discussion nicely provided the necessary depth to the overall project. I think Mod2 was a great leap in my ability to be a scientific writer, maybe it was a matter of being more comfortable in the class. All the practice and the reviews from Mod1 certainly helped. Professor Samson was fantastic.

Mod3: I liked the uniqueness that came with Mod3; the class definitely took a more engineering approach at this point with optimization and solar cell efficiency. I was introduced to very new concept with the material growing/binding phage. Also, getting to use the TEM was really awesome. It's amazing some of the things we are capable of seeing at the molecular level. No matter the efficiency of my solar cell, I really enjoyed constructing the solar cell and seeing that it actually managed to have some current, if only a little. My favorite part of this module, though, was the novel research proposal. I'm really excited about what Sonia and I were able to put together. It was so cool seeing it developing in our minds and then coming to life in the presentation. I felt really confident while presenting. It was actually a really fun process - great news for a person strongly considering grad school. Professor Belcher is awesome and it was so nice how much effort she put in coming to our lab class often and helping us through the research proposals.

Overall, I would definitely call the class a success overall. I met some really great people all around and learned a lot. It was rough at a few points, but it was also often quite fun.

Thank you immensely to all the instructors, Noreen, Leslie, and Shannon. It really meant a lot that you put so much effort into this class and were always so willing to help out. The TAs were also a great help throughout the modules.

Thanks 109. This is a big step in the Course 20 journey!

Final Words on a Final 20.109 Presentation

Hooray! I can't believe 20.109 is finally done. It was definitely one of the most interesting and time-consuming classes of my MIT career so far. From microbiome to DNA repair to virus solar cells, we've really come far. Especially the final lab class where we had our research proposal presentations, I saw so much improvement among my peers as well as myself.

Up until the day of the proposal I was so nervous. My partner and my research proposal was a proof of principle to test whether Antibody-KillerRed conjugates (AKRC) were an effective means for specific cancer therapy. I never realized how much work and research went into coming up with a novel idea (or even to build upon and optimize existing systems). Sometimes, I even worried that idea was too similar or not novel enough. At times like that, I realized the best thing we could do would be to continue scanning through literature to find ways to improve and develop our research ideas.

As well, with journal presentations being all the way back in module 1, I had butterflies in my stomach thinking about giving our presentation. So many details to not forget to include, not to mention the added element of having two presenters and the need to have a balanced pitch. As well, we had to compliment our slides because our styles of presentations were different, there needed to be constant dialogue about ideas. At one point, when we thought we were almost done, I found an error in one of experimental designs (our positive test would not work under our current test conditions) and we frantically sought a replacement to fix the problem. Then finally at 12:40 AM the night before, we put the finishing touches to our assignment, practiced our presentation a few times and rested for the coming day.

Presentation was scary, but I was glad that we went 2nd. I had enough time to calm my nerves without becoming more anxious in waiting. When we got up to present, I felt much different than I had in journal presentations. Although I might have still been nervous, speaking became much easier and when I did get stressed, I took a deep breath and was able to get back on track. In the end, I'm so thankful for all the support that the 20.109 staff and my peers provided. The 20.109 experience has indeed been a rich experience that I feel will have a lasting impact in the rest of my semesters here at MIT.

Mod 3 I messed up our solar cell

Even though Mod 3 was short, I really enjoyed it once I realized what was going on. Using bacteriophages to grow nanowires? That's like some real sci-fi stuff there. As I said, I was a little confused by everything first, as in which part did what but at some point during one of the lectures, I finally wrapped my head around it.

So all was going well at first, I even survived without Cortni one day and did the M3D2 experiments and calculations myself (#calculationstruggles). When it got to assembling the solar cell, we even doctor bladed pretty well as far as we could tell. Everything seemed like it was going smoothly. And then the final assembly took place and I ruined it. When putting the cover over the paste, I happened to rub off a decent chunk of the dye that was there. Whoops. Oh well. So now we had a semi-functional solar cell with a whopping 0.5% efficiency...

As they say, better luck next time. After reducing our area calculations though, efficiency went up to 1%, suggesting that maybe if I hadn't messed it up, our solar cell would've been fine and dandy. But as my dad says, not everyone can be a winner.

After this disappointment, the long-awaited TEM day arrived when we would get to see our beautiful nanowires. So the green team and platinum team cram into the TEM room waiting patiently to see the image on the screen and then the smart Asian guy pulls up the image. It looks like a gray blob. Prof. Belcher started to explain the different parts of the gray blob. This slightly dark blob was a crystal composite, this black blob was gold. I almost felt like we were looking at a baby in an ultrasound video. When my aunt was pregnant, my dad was somehow able to point out all the portions of my future cousin while all I saw was some blackish-blue background and white-lined curves. In the end though, this was our little baby. Though I couldn't really tell what everything was, I was proud that we had made this functional thing.