Monday, December 15, 2014

Mod1

..And it’s done
Having not left my room for approximately 24 hours and running on less than 4 hours of sleep, I really started to despise myself for thinking it was fine to put off the assignment until the very end.
http://weknowmemes.com/wp-content/uploads/2011/11/procrastinator-no-i-just-save-all-my-homework-until-the-last-minute.jpg

http://weknowmemes.com/wp-content/uploads/2011/11/procrastinator-no-i-just-save-all-my-homework-until-the-last-minute.jpg
The more I wrote the more I realized the complexity and level of analysis required for this report. The assignment required careful planning to be able to convey to the reader the significance and flow of this experiment. It really did not help when crunch time came that I had not been organized throughout the entire module. During the writing, I realized that I had given a lot of attention to understanding the protocols but not necessarily grasping the why exactly are we doing this and what is significant about this.
Many times when I am in my UROP, my lab work I aimlessly follow protocols. I run the experiments because I am told to, but many times I do not stop to think what the results will allow me to determine, which is what 20.109 is allowing me to do. 
Writing this assignment was a scary process and moving forward for the next module, I will for certain start my report in advance. I see know that it is important from the very beginning to grab the big picture so that you can understand the significance of your data in this context. Also, do not leave everything for the last moment! Hopefully, I will apply these experiences from the module, so that the upcoming module report is a much smoother proces

Bioengineering is..

Before Module 3, I had never heard of being able of utilizing biomaterials to construct things such as solar cells. I always assumed that bioengineering was limited to combining engineering principles and life sciences to address challenges in fields of medicine and healthcare specifically. To be honest, before 20.109, I could not actually tell you what it meant to combine engineering with biology except that it sounded cool. Many times, I had worried that I picked the wrong major because I did not know what bioengineering could be applied to and what I was getting into. It is somewhat scary that it was not until 20.109 and 20.320, my junior year that I have really gained an understanding of what it means to be in bioengineering! The modules presented in 20.109 showed that you could use a biological system for different applications outside of it natural function, such as even making solar cells. Bioengineering is the manipulation of biological responses, which you can design and analyze, to solve many problems. All in all, I think I made a good choice J

Proposal: Optogenetic Cochlea Implant

For my very last blog entry, I want to write about a project that I think can potentially become a theme for 20.109 future modules. It capitalizes on the rapidly developing field of optogenetics, which overlaps with both synthetic biology and DNA engineering. The really cool thing about optogenetics is that there are so many open problems to solve and there are many ways we can apply it to address bioengineering challenges. For brevity, I am not citing specific articles but want to acknowledge Dr. Richard Turner from the Engineering Department, University of Cambridge, and Prof. Edward Boyden, from the MIT Media Lab, for the lecture notes and amazing publications on this field.

Background: the way we hear sound relies on an intricate auditory system that can decompose different frequencies and selectively stimulate neurons at specific positions. Concretely, inner hair cells are in control of stimulating neurons aligned at certain positions around cochlea which encodes signal strengths of sound wave with specific frequencies. The loss of inner hair cells (IHCs) is a major cause of deafness and the current cochlea implant solves this problem by bypassing IHCs and directly stimulating neurons according to incoming sound frequency spectrum. The sensitivity of the current technologies is very low because electrodes cross-talk, making perceived sound for people with hearing aid extremely coarse. Light, however, is promising for this application because of its small directed beam width suitable for accurately targeting neurons at millisecond timescale resolution. There are labs at MEEI working on this technology but there hasn’t been papers published yet.

Idea: for the 20.109 labs, we can transfect auditory neurons with light-sensitive proteins and verify that they can be stimulated by light input. We can then align these sensitized neurons and program simulations for selectively stimulating neurons at particular positions (which correspond to perception to particular frequencies of sound) and evaluate how well they work (in terms of spatiotemporal resolution) as compared to electrical stimulation. In fact, to make things simpler, we can even use HEK293 cells instead. We can try to find the optimal light intensity/wavelength as well as the thresholds that can make light stimulation work on mammalian cells.


What’s Cool: open research problem, easy-to-get-on first step experiments, great literature, immediate medical applications, and potential collaboration with Prof. Boyden...

What Makes Presentations So Hard

So you’ve timed yourself a hundred times. You knew exactly when to say what in which way. You knew you’d have it all right, until you started your presentation.

I don’t think I have a stage fright. But every time during a presentation, I’ll surprise myself quite a bit by saying what I didn’t expect and skipping what I always wanted to say. For Mod3 proposal presentation, it took me more than 4’ (12’ averaged for each person) whereas during rehearsals I only needed 3’30’’. What makes real presentations so different?

Maybe the lighting wasn’t right, so that I couldn’t see the emphasized texts as clearly. Maybe the remote control wasn’t quite sensitive, and a lot of the animations were delayed. But I think the real reason is that talking to a group of audience is always different from talking to myself. For the real presentation, I need to maintain proper eye contact, and I need to engage them as much as I can. What this means is that I need to adjust my talk to align it with the audience’s interests and expectations. Apparently, if the audience is bored by my rehearsed scripts, I need to speak say something that doesn’t sound as rehearsed. If they had an inflection point judging from their confused looks, I should probably spend a bit longer explaining what I just said. For Mod3 presentation, I heard a little chuckle from the audience when I showed the 2,000 experiments that we were planning to do. I then paused and joked that this is what would suit grad students perfectly as science research is being done now. I don’t personally think this is a particularly well-thought-out comment, but this small spontaneity was completely not planned and helpful for engaging the audience. Also unexpected was Agi’s question about scaling up the experiments – we kind of assumed that doing these 2,000 experiments wouldn’t be a big problem if people had done it almost 10 years back. But not only were we able to suggest a few ways to automate the experimental procedures to further improve our proposal, we were inspired to look at what we neglected and think more deeply into the nature of our experiments.

To summarize, interacting with real people is always unpredictable; no matter how well prepared we are, there will always be a few moments where things start to deviate from what we originally planned. I think this is what makes presentations particularly challenging but particularly fun. From now on, instead of over-rehearsing my talk, I will also focus on ways to engage the audience and get ready for the pleasant surprises for my future presentations.

The Art of Scientific Proposals

When I was taking HPS (History and Philosophy of Science) Tripos at the University of Cambridge last year, I remembered having a hard time debating with friends and supervisors what are the best way to ensure that the “right” science gets public funding while the “wrong” one doesn’t. In the end, we had to agree that even though not a perfect solution, the current paradigm of proposing research ideas to funding agencies is the best way we can practically do. Indeed, not every research project entitles the same amount of resources, and it is our job as scientists and engineers to justify our particular choice of research. I therefore really appreciate the opportunity in 20.109 to develop our own proposal after learning the many useful experimental skills.

It wasn’t easy though. Three of us came up with 15 different ideas in the beginning and we were pretty lost after lab 2 when we met and discussed our common interests – there wasn’t any significant overlap, and in fact, we weren’t even very clear what we were interested in carrying out. Phage biotemplating was pretty cool, and so is rewiring signal transduction pathways. Maybe we should apply the same technique to other model systems or other pathways? Say a bacterial/mammalian system that can sense broad-band EM wave instead of light, or a capacitor (and hence memory device) that is constructed by phage? Or more concretely, can we apply a new enzyme recently synthesized in T-cells to our intestinal stem cells, or apply optogenetics technology to engineer not only neurons but also inner hair cells around our cochlea?

Over the Thanksgiving break, we read more than 50 papers on the topics we were interested in, and to our great surprise and dismay, all of these ideas have been developed or are being actively investigated by labs around the world. But the good news is, we now realized that we are interested in and also good at quantitative modeling of biological systems (since we found pure biology articles extremely hard to read), and after Shannon’s and Agi’s insightful suggestions we were able to identify two different types of modeling which we can connect to create new possibilities. After reading extensive literature, we were inspired by the fact that there isn’t a commonly agreed way to classify such a common disease like colon cancer, and the fact that there are still new proteins being associated with the colon tumorigenesis Wnt pathway despite extensive studies for the past 30 years. That is when we decided to focus on the Wnt pathway (with cross-talking EGF, Notch, and BMP pathways) in intestinal stem cells as our research project.


The preparation for our proposal went much smoother after we identified the problem to work on and learned a few key modeling techniques to use. We can now appreciate the importance of having a well-defined set of questions to answer and goals to achieve, as well as a set of essential tools to use in order to make a convincing proposal. We realized that it is never a bad idea to talk to people from different backgrounds and brainstorm new ideas before focusing on specific areas of interest. Most importantly, we also realized that proposing new research ideas is an art as much as it is science such that there is nothing to fear about being creative. 

Friday, December 12, 2014

20.109: A Class Full of Questions...

I started off 20.109 thinking that it would be a lot like working at my UROP.  In some aspects, my knowledge from previous lab experience carried over.  I knew some things about lab safety, a number of the techniques that we used I had done before, and I was familiar with some of the communication components.  I had an idea of what controls were, I'd done some cloning before, and I'd presented data in front of an audience.  That said, I think that 20.109 has been one of the technical classes that I've most enjoyed so far at MIT, partially because we did some cool science, partially because of the fun students and instructors, and partially because I actually learned a lot.

Laura and I asked a lot of questions this semester.  We were always wondering why we did things in a particular way in 20.109 when it always worked just fine when we did it another way in our past experience, and why and how certain techniques worked, and why we chose particular controls, reagents, etc.  From the answers we got, I felt like I became armed with a deeper understanding of the experiments and protocols that we ran, which I think will be useful later on when I'm running and troubleshooting more of my own experiments.

But protocol questions weren't the only ones I asked this past semester.  Through the communications assignments we completed, I interrogated my data, class data, and data in the literature.  Why did my experimental results turn out differently from everyone else's?  What kind of troubleshooting can we use to get this experiment to work the way we want?  What do these results mean?  Do I believe the results I'm getting?

Outside of class, I also asked myself lots of questions related to 20.109 and to life in general.  Why did I procrastinate this assignment?  How am I going to get sleep tonight?  Am I going to make it back from my lunch break on time for the lab treat?  Do I like wet lab work?  Do I want to do 20.109-like work for the rest of my life?  Do I want to do 20.109 work for the rest of this afternoon?

So, 20.109 got me asking lots of questions.  Some of them had straight-forward answers, and some of them I'm still working on.  I'm not sure I'll ever get all of the answers I was hoping for.  But I'll do my best to try!

Thursday, December 11, 2014

The end

Today during the feedback session, I was quite subdued compared to how many questions I usually ask. I guess I just didn't have that many suggestions for improvements. It's definitely one of the best classes I've ever had. I enjoyed pretty much every step of the way (well, in hindsight). Just to list a few things that were awesome and shouldn't be changed:
- Presentations on how to write research papers and give scientific presentations
- Teaching us how to make quality figures
- Feedback on the reports
- Coming up with a novel proposal (which was way harder than I thought XD)
- It's ok if we mess up
- The barrage of questions will be answered
- Having cookies at office hours
- ... and many more.

109 is a lab class, but it's really more like research training. We learned a lot of skills, and that's what it takes to be a researcher. From wet lab techniques and research design to paper writing and grant-proposal-esque presentations, we've covered it all. I feel much more equipped for future research. Even though it was sometimes painful, it was well worth the effort. I was chatting with my parents who are researchers in biology, and they were totally jealous of what we do in 109. I feel like a lot of what we learned people learn by trial and error in grad school. It's pretty amazing that we figure a lot of it out in undergrad.

109 was also great at giving us a sense of what BE actually is. Since several posts have elaborated on this, I won't belabor the point. Suffice to say that I'm glad I stuck with BE. Plus I have this to show off now:

After a few long summers of working in lab, I wasn't sure how I feel about research. But 109 has gotten me excited about doing research again, so that's pretty great :D

Also, most importantly, the safe environment that 109 set up was amazing. I've never felt so comfortable in a class. I'm usually pretty quiet in class, not asking that many questions. But in 109, I felt totally comfortable doing so, and that was a huge relief. Thank you, 109 staff!! I will miss that. A lot.

Looking back, we accomplished a ton. I should be ecstatic that 109 has ended, considering the amount of work that I am now excused from and how much additional time I now have, but really, I'm getting nostalgic already. It's bittersweet. I'm a music nerd at heart, so here's something to take a listen to: Ashitaka and San

Peace out.

TIS DONE!!! The story of a glorious feat


I thoroughly enjoyed and learned a lot in 109 despite entering with little wet lab skills. Although the material was magical (bio-templating and two component systems), I credit the success of this class to the amount of dedication, knowledge, and passion seen in the 109 instructors. When things didn’t go as planned, I could always count on the instructors to be the first ones to know yet the last ones to leave; they were with us each step of the way -- and in an optimistic fashion too. 

Something that I am guilty of pertain exactly to what Camilo suggested today: having a module make sense as you are writing the full report. Only until then did it strike me… “Oh! This is why we collected this data or took this picture or had this lecture.” Honestly, I dreaded starting the module papers because I knew it would require me to relive the memories of previous lab days. I didn’t realize that the end result would be a tighter understanding of the material. I also didn’t realize that I would eventually start to miss these days in lab.


Eventually hasn’t happened yet, but there will be a time after college J. So if you ever receive a random email from me in 10+ years, it’ll be because I’m feeling sappy and nostalgic for these good times. Until then, devout readers.

Messing up my Circadian Rhythm? Ain't nobody got time for that (esp. when it's Kyle)

Please enjoy this video: How I felt after the presentation


This research proposal or more specifically my investigation on engineering a microorganism to combat Coeliac’s (yes, Kyle, I did spell it the British way. You can’t impose your brutish American spelling on me now) Disease was fruitful. For the first time, I was required to actually do research on previous and current news wrt CD. I mainly chose to proceed with CD because one of my close friends has CD, and I constantly worry if he's eating enough. This interest, hopefully, was obvious in my overall enthusiasm and energy during the presentation. Purely for the sake of friendly rivalry -- all these positive aspects helped me deal with Kyle as a partner, who wanted me to shift my sleep schedules to align with his. It's a useful skill to adapt to teammates, but when they expect you to pull an all-nighter with them...


Exactly, Sweet Brown: ain't nobody got time for that.


You find that it's beneficial as a person to stand your ground and go to sleep at 5am while your nocturnal lab partner works diligently on your futon. To be fair, he was working on his part. I'm not actually a terrible person.

Fun fact: my favorite factual tidbit encountered during the slash and burn process of researching was definitely understanding why gliadin (compound found in gluten) is so resistant to natural human enzymes: high amount of proline residues in primary structure -- 7.05 (and 330) do have their merits! This also came in handy for the mod 2 paper discussion in predicting a potentially more efficient mutant for our photography system! 


Reflections


After spending so many hours working on assignments, it is hard to believe that this class has come to an end. Even though my journey with this class has been difficult, I have gained a great level of respect and admiration for this class. I feel like I have grown tremendously by being constantly forced out of my comfort zone with writing and public speaking, while at the same time not feeling alone throughout the process. With the small assignments that build upon each other and the feedback, the 20.109 instructors did a great job in allowing me to see the big picture and to communicate my ideas more effectively.

With all the modules, especially with the very different aspect of Module 3, I was able to see how bio-engineering is so greatly applicable and has such great potential even in areas I would not have thought about before. I love bio-engineering because it is so multi-disciplinary!


But as 20.109 has taught me, to be able to share the awesomeness of bio-engineering you need to be able to communicate! As, I reflect back on this class, I am left with a feeling of joy to know I have improved and learned so much over the course of this semester. Thank you 20.109 for giving me this wonderful tool-set that will be applicable for the rest of my career!



12 minutes goes by faster than you think

I've always been fairly comfortable with giving presentations, but don't think I've ever been critiqued to the level I was during the journal club presentations. It was probably one of the most useful aspects of 20.109 for me. When I first started putting together that presentation, I thought it would be a breeze. Little did I know how much time it would take to decipher the paper to gain an in-depth understanding myself, and then how much longer it would take to figure out how to best convey that information to my peers. What made that latter part much more difficult was the time limit. 12 minutes is not a lot! Constructing that presentation really forced me to figure out what was important. I also learned a great deal about how to put together effective slides.

Going over the video of the presentation greatly informed the way I went about the research proposal presentation. During the second round, I knew specifics such as the importance of clear and informative titles, and how to walk people through a narrative. I had also never used additional slides, and my partner and I ended up with about the same number of additional slides as what was in our actual presentation. While that might have been overkill, it's an aspect of presenting which I now really appreciate, because even if we didn't use those slides during presenting, the act of simply putting them together gave us different perspectives on the points we were addressing, and helped us formulate our thoughts.

Done with 109!

Coming into this semester, I was pretty sure I'd be switching majors. If I went through with this change, I could opt to take 7.02, a rumored 'easy' class, instead of 20.109. Due to various factors, however, I decided to commit to taking 20.109 despite having heard how hard it was. There were definitely a lot of moments when I wanted to slap some sense into past Bria (i.e. while writing the Mod1 report), but now having finished the course, I could not be happier with my decision to stick with it. 20.109 has given me more experience and skill in communication and writing than any class I have ever taken. I can say now that I know how to both construct an effective and clear scientific report, but also think critically about biological design. Although at times 20.109 was incredibly time consuming, I now see that every assignment we were given was relevant and helpful for me to learn as a student. So for that I thank you all! 20.109 has truly been a pleasure :)

You can do anything!

Modules 1 and 2 were fun... but module 3 of 20.109 was something else! This module not only introduced the completely new field of biomaterials to us, but it also was a great short coverage on innovation resulting from re-contextualization.

I had heard that Prof. Angela Belcher had revolutionized the fields of materials and energy before this class, but I had no idea how. When we were told that we were going to use bacteriophages to construct a functional solar panel, I thought it was a joke. The idea of using a biological structure to create a long-lasting functional electronic made no sense to me whatsoever. But as the module progressed, and we went through each step of the solar cell construction, I started to think "This is so simple, yet so smart!"

Prof. Belcher's work was inspirational not just due to its innovative nature, but also in the fact that she was able to actually implement it without giving into doubt. This confidence definitely reflected on our proposals. For our final presentation for 109, Alyssa and I decided we wanted to stick with the whole bacteriophage-nanoscale-fabrication thing. And what field other than neurobiology would benefit the most from nanoscale technologies?! (OK maybe a lot of other fields, but we came up with this application, because we're still fascinatied with biology). Our proposal entailed the use of phages to assemble nano-scale multielectrode arrays for neural recording in brain-machine interfaces.

Now this idea was really cool at first. But the more I thought about it, the more implausible it became... Eventually I found myself thinking "There is no way we can make this work". So when we initially pitched our ideas in class, I had zero confidence in what I was saying. It blew my mind when Prof. Blecher was so supportive and confident in this lousy idea. Was our idea actually plausible? I still had my doubts, up until I went to Prof. Belcher's office hours the day before the presentations. Both her and researchers from her lab started pitching in ideas and we started brainstorming like crazy as we watched all our problems evaporate to reveal solutions!

At the end, we had a pretty wholesome and (fairly) realistic idea that we presented on confidently! It was really cool to see that theres no point in being afraid of crazy ideas; theres almost always a way of implementing it.

Thank you Prof. Belcher and the whole 109 staff and students for inspiring me to pursue my crazy ideas!

And since I feel like this post was a little too serious, here's something relevant to lighten up the mood:




Thank you 20.109!

20.109, in conjunction with some of the other classes I’ve taken this semester, has really revitalized my appreciation of not only bioengineering at MIT, but the field as a whole. Maybe it’s blasphemous to say this here, but at this point last semester, I was very strongly considering switching my major to 6-7. I had even drawn up a courseroad and spoken to older friends in that major. But thank goodness I stayed!

My concerns at that point were that I would not graduate with an in-depth enough understanding of bioengineering, and that I wouldn’t have any discernable skills to bring to the lab. Now, I can just casually mention that I’ve used viruses to build solar cells, and manipulated bacteria to produce photographs. Do I have bioengineering skills? I think that’s an easy yes.
The point where it all really came together for me was actually not through a 20.109 assignment, but the realization heavily involved 20.109 without a doubt. My appreciation for bioengineering struck at around 4am as I wrapped up my design project for 20.320. We had to construct a pathway for a liposome-contained system of our design to detect and signal the presence of Ebola or Marburg virus (distingushing between the two), then mathematically model the system and implement it on MATLAB, while subjecting it to various conditions. Where is the 20.109 you ask? While I was trying to work out the last few bugs in my code and putting together my final report for the project, I realized that sure, it was really cool that I could design such a system, but if I ever wanted all of it to 
actually work in real life, I could also make that happen through what I’ve learned in 20.109!


Up until the class, I’d done several research internships and UROPs, but had gained fairly specific wet-lab skills. Now, not only do I see the wide array of applications for bioengineering and the techniques I now know for accomplishing projects in those areas, I’m able to communicate that information through writing and presentations. This may have been my most practical class at MIT so far. I also very much appreciate the clearly large amounts of time and effort put in by all members of the 20.109 staff. Not only did that help me in the class itself, but I feel that attitude was infectious to all the students too! 

Defining Biological Engineering

When I began the college application process I planned to major in chemical engineering with a minor in biology. When I toured MIT I was introduced to Biological Engineering for the first time and I immediately fell in love. I knew that if I came to MIT I wanted to pursue a degree in BE. Typically when I would tell people that I was studying BE, I would get the response of “Oh! Biomedical Engineering is great!” and usually I would just let it slide even though the fields in my mind are completely separate. BE is a field that combines theoretical biology concepts with engineering and design. It is a truly revolutionary venture. Engineering cells and biological organisms is not something that people fifty years ago could imagine. Another important component is BE is computational analysis, which I found I truly loved. Learning to analysis and assess novel systems has shown me the power in modularity and engineering. Because of this, I made the decision this semester to switch my major to 6-7 (Computer Science and Molecular Biology). Although I am technically no longer a student in BE I plan to keep learning as a BE student by incorporating as many course 20 classes as possible.

This stuff actually matters

I don’t think I can relay enough how much I enjoyed and appreciated the research proposal assignment. While I’ve had similar “come up with your own idea!” assignments in the past, in a variety of fields, this is one of the first times where I could really see the application of skills I now know I have or can relatively easily acquire, and come up with a realistic idea of how the project’s goals would be accomplished. I think that last point regarding how realistic the work needed to be really hit home for me when we were asked to think about how many grad students and post-docs it would take to accomplish the goals.

It certainly helped that the research proposal which my partner and I chose was one that was very important to both of us, given our interests. We are both heavily involved in global health work, and in particular, work with a system of HIV/AIDS clinics in Togo through GlobeMed at MIT (logo below - using our bacterial photography system!), to implement primarily technological capacity-building projects. We’ve seen some of the issues that the clinic staff and patients have to deal with, and some of the ways they overcome those challenges. Communities in low-resource settings have to deal with diagnostic techniques which are really only viable in well-off countries. Not only do they not benefit from the use of these technologies to the full potential possible given the tools, but that failing undermines credibility of the health care system overall. When a patient knows that health care worker whom they’re seeing will give them a diagnosis likely to be incorrect, they’ve lost faith in the system.



By developing the proposal for a rapid diagnostic test for TB, amenable to use in such settings, our team was able to apply that background in global health, and combine in with all we’ve learned in 20.109. We even got the chance to talk to experts in the field, including Angie’s husband, Dr. Bebinger, and Professor Dedon, also in the BE department. It was encouraging to see their positive responses, and their excitement at students trying to design such technologies. 

Learning how to write all over again

I feel that I’ve improved leaps and bounds as a science communicator since the start of this semester. I’m still able to recall fairly distinctly the overwhelming feelings I had when faced with starting the Module 1 report. Prior to actually starting on the assignment, I thought it would be a breeze. The topics of Module 1 were things that I had spent months working on through my UROP, and at no time during wet-lab time did I ever feel a dearth of understanding. Actually conveying that understanding and analysis turned out to be a different ball game altogether. One of the hardest parts may have been crafting a narrative for the results, and figuring out how to best put together my figures. I would say that I improved in both of those aspects a great deal as the course went along, and by the time we got to putting together the Module 3 report, I had my game face on and knew exactly what I needed to do. My science writing has become much more concise, which probably now helps with my writing overall.

My introductions and discussions are probably areas I could improve on, as I sometimes assume that implications have been conveyed when I should explicitly delineate those points. My abstracts also sometimes rely a bit too heavily on methods, and not enough on results. While these remain challenges, I’ve certainly improved in those areas, and appreciate the fact that I’m able to identify my shortcomings as opposed to blindly moving through the writing process.

I would probably appreciate more one-on-one time with the writing instructors on the WRAP team, or even one of the lecturers, TAs, or other 20.109 staff, perhaps after the Module 1 report. While I could have signed up for one-on-one meetings, I ended up not attempting to do so most of the time. When I did try, all the appointments had already been booked. This is all something that I could have taken upon myself to accomplish. However, I probably also would not have scheduled a meeting on the presentations had it not been required, and am now immensely grateful for having had that opportunity. Perhaps if I had been required to meet with an instructor on the writing portion, I would have realized the benefit of the resource and utilized it to a greater extent. 

"I'm good with math"

One of my pet peeves nowadays is when people assume I am a biomedical engineer, as opposed to someone studying bioengineering. I guess I can’t blame them, because I certainly equated the two pretty much up until I was applying for college and noticed that the programs were differentiated in terms of college departments. Even when I first saw that MIT had a “bioengineering” department instead of a “biomedical engineering” department, I told myself they were the same thing.

Oh how far I’ve come. While I pretty quickly realized the difference between the two topics after actually joining the department, 20.109 cemented that understanding for me. While biomedical engineers might look specifically towards medical applications, Module 3 in particular showed me how biological components can be harnessed to accomplish entirely non-biological functions. Never in a million years would I have imagined that I would be using viruses in creating a solar cell.

The modules we’ve explored in 20.109 are certainly examples I use when explaining biological engineering to my friends and families. (My younger sister now thinks I’m the coolest person ever.) I also look to examples of what we’ve done in classes like 20.320, particularly when distinguishing bioengineering from biology. I think back to the first day of that class, where we were told that while biologists might sketch out the schematic for a molecular pathway, bioengineers apply rate constant to the interactions, write out mathematical models, implement models on programs like MATLAB, and are then able to actually use the models and understanding garnered from them to inform applications such as drug development. (No offense biologists.) 20.109 takes that one step further by showing how to put all of that theory and modeling to the test in the lab. How cool is that!


With all of that in mind, what is biological engineering? For me, it’s taking an understanding of biology and applying that to pretty much anything, while still being able to model systems in a rigorous manner. And no, it’s not biomedical engineering. 


My Thoughts About 20.109

As I've mentioned in my previous posts, I learned a ton over the course of the semester. Not only did the modules contribute greatly to my overall understanding of science, but the class did a lot to improve my communication skills as well. Even incredibly groundbreaking research would go to waste if you are unable to communicate effectively.

In module 1, we modified the DNA of a cell to elucidate aspects of homologous recombination. I currently UROP in the Runstadler lab, which teaches the first module in 20.109 for the Spring semester. When I first learned that our module 1 was about a subject that I was unfamiliar with, I was initially a bit bummed out. If I had taken 20.109 during the Spring, I would have "learned" about a module that I was already very familiar with. But having taken the Fall module 1, I was very happy to have learned about DNA engineering in terms of homologous recombination. This was a subject that I had never really learned about, and significantly shaped the research proposal Xander and I presented. It seems quite cheesy to say so, but I was glad to have learned about something new in 20.109 this semester rather than stay comfortable with subject matter I already knew.

In module 2, we optimized a synthetic biology system by introducing single amino acid mutations. Although the mutants we actually generated failed to improve the system, this was probably my favorite module. Once again, the concepts of biological systems I learned about influenced the microbiome aspects of my research proposal. Research in synthetic biology has the ability to perform really awesome tasks with living systems. Although we investigated a seemingly trivial bacterial photography system, investigating the inner workings of biology and applying them to engineering was just really...cool, for lack of a better word.

Although the shortest one, module 3 investigated the ability for biology to assemble more efficient dye sensitized solar cells. I went into this module not knowing a thing about biomaterials and what the hullabaloo about carbon nanotubes was all about. After all the work we've accomplished, I learned a new aspect of a very common idea in the class: that with clever techniques, one can manipulate biological systems to perform certain tasks.

I think what makes this course particularly awesome was its interactive nature. Rather than a conventional lecture-recitation-exam format, it was so much easier to communicate with teachers and ask questions. I also really appreciated how many instructors there were. Everyone on the 20.109 staff really complemented each other to provide the best academic experience for the students. If you count TA's and guest lecturers, the instructor:student ratio turns out to be somewhere near 2:1. I wish all other MIT classes could follow this format. I feel that all of my peers that took this course gained a very similarly satisfying educational experience. Because of those reasons, 20.109 is probably the best class I've taken at MIT so far in terms of usefulness of material and overall learning experience. Once again, I don't have any images that can summarize my blog post. So here's a video of cute hedgehogs.


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Considering 20.109

Reviewing this past semester, I can say for sure that I enjoyed these modules. As 20.109 was my first lab class at MIT, I was initially somewhat worried about how interesting this class would be. In the end, 20.109 went above and beyond my expectations; I learnt a lot of necessary lab skills, while also enjoying the assignments. The skills each of us acquired- from pipetting to writing research papers- are undoubtedly applicable to situations arising in the near future (maybe next semester) for most of us. I’m really happy I took this class (plus, the staff members are awesome).

I was delighted and surprised to see that my fall classes were somewhat synchronized. 20.320, 7.06, and 20.109 all seemed to complement one another regarding topics, which was exciting and made learning this semester extremely comprehensible. Though the workload was a little rough, it was worthwhile (and certainly preferable to a semester with little work and dull material).

I think my most favorite module was the 3rd, mainly due to my personal interest in the applications of biology to seemingly non-biological related fields. Each lecture was thought-provoking, and I personally really enjoyed developing a research proposal based on fields we found interesting.

One of the things I enjoy most about being a Course 20 major is the wide applicability of this field. I learnt a lot during this fall about not only observing biological systems, but also how to modify and observe them. I also learnt more about both written and oral communication, vital to the field of research. Looking back towards the start of the fall semester, I know I can confidently say I’ve improved and learnt a whole ton of things.

I guess that’s all for now. Thanks for an awesome semester!

Nature's Engineer

Inspired by 20.109, I wrote an article for my writing class about how human beings have changed from being Nature’s apprentices to becoming her engineers. Indeed, using bacteriophage to construct solar cells was completely mind-blowing for me, and I am glad that 20.109 provided us with such an invaluable chance to interact with top-notch faculty and work on their cutting-edge research ideas. This experience itself is extremely rewarding.

Coming from an EECS background, I was fairly comfortable with the concepts of solar cells, and I even knew how semiconductors work and how the choice of materials would impact the efficiency of the device. But the biggest lesson 109 taught me (apart from writing and speaking skills) is that many of the most exciting innovations happen at the interface between many seemingly irrelevant areas. Synthetic biology is a great example, and bio-templating is an even better one. I really appreciate the fact that there are so many ways to study the DSSC system, from mathematical modelling to TEM imaging, from discussing the pros and cons of the many ways by which M13 phage could be engineered to bind to Au NPs, to investigating the effects of NP sizes on light scattering. Apart from the interesting lab skills (among which doctor blading is my favourite one), Mod3 taught me to be a more systematic thinker, a more rational engineer, and a more creative designer. I am thrilled by the interesting connection between biology, material science, and electrical engineering, and this interdisciplinary viewpoint will certainly be beneficial for the rest of my research career.

I am proud to call myself a Nature’s engineer now.

Reflections on 109

At the beginning of this semester, I wasn't overly excited about any of my classes (aside from my Senegalese drumming class, because that's cool). From what I had heard about 109, I was expecting it to be a lot of hours spent pipetting and completing busy work. Now that I've actually completed the course, I have to say it was my favorite class by a landslide. While there were a lot of smaller weekly assignments, each one always clearly pertained to the overall goal of the module and was helpful for understanding the big picture.

Even journal club, which I was originally terrified for (as described in a previous blog post), ended up being a fantastic learning experience. My ability to read and understand a scientific paper grew tremendously once the pressure was on to present it to other people, and the actual act of presenting was less daunting since I actually understood what I was talking about. Preparing for our final research proposal was made easier by the feedback we were given from our journal club presentations, and I was only minimally nervous when it was time for us to present.

And of course, my scientific writing has improved over the past few months. I spent the summer after my freshman year working on a paper at the NIH, which took me over a month to complete, so I was wasn't sure how I'd be able to finish the writing assignments in 109 in time. Luckily we had fantastic instructors who made sure I understood the point of each module and helped me make a story out of our research. I'm ending the semester with a new confidence in my ability to approach and understand problems from a biological standpoint, and it's a pretty awesome feeling. 

The BE Fellows as a Writing Resource

During the course of the term, I primarily met with Diana Chien, one of the BE research writing fellows. I met with her usually for the sake of revision rather than brainstorming, showing her a draft piece of writing and having her provide input. I was impressed by the power of the BE Writing Office and the fellows as a resource for writing. I was initially somewhat skeptical; however, the BE writing fellows were constantly prepared. Since they were all pursuing Ph.D.s or had Ph.D.s, they were very quickly able to understand the technical nature of the word and provide meaningful feedback.
Our meetings generally had three main parts. First, I would write down the “key points” I was trying to convey in a section while Diana read them and took notes. Then, Diana would provide any feedback she had. Finally, we would jointly create a plan to improve the paper. This three step approach was very helpful, and was a powerful way to brainstorm individually and then come together to discuss and synthesize feedback. In addition, having to write down the one or two “key points” of an entire section forced me to clarify my thinking and make the “important points” of my writing more visible.

Overall, the BE Writing office provided a strong resource. The only time they provided a small source of confusion was when their advice was inconsistent with the vision of the 20.109 staff. For example during M2, I was advised to broaden the scope of my project from “optimizing the photography system” to “a framework for optimizing synthetic 2CS systems.” While the second framework made stronger claims, it was beyond the scope of the work we had conducted in the module. After talking with the 20.109 staff, however, the “more correct” scope to utilize was made clear. 

Post 20.109 Introspection

20.109 was easily the most intensive class I took during my Junior Fall. Between spending ten hours a week in lab or lecture and then working on FNW assignments and completing the major assignments for each module, I spent (on average) about 22-26 hours a week on 20.109 alone. With so much time invested in the class, 20.109 also provided a good environment for introspection.
First, working with Marco was a tremendous partnership. While I prefer analysis to experimentation work, Marco preferred experimentation work to analysis. Similarly, my primarily interest lies in big picture thinking rather than experimental details; while the opposite is true for Marco. In this way, we formed a very complementary partnership and were able to best utilize both our interests and our strengths to bring each research module together.
20.109 further showed me that, while I enjoy research, my enjoyment primarily stems from the work that occurs outside of the lab. Reading the literature, finding gaps that can be explored, analyzing experiments and understanding how they fit into the greater scientific body of literature are the parts of research I enjoy most greatly. With that in mind, I want to look for a Ph.D. experience that focuses on these aspects.

Finally, the 20.109 proposal was the most exciting project I’ve done at MIT. I loved looking through scientific literature and trying to synthesize multiple ideas into a novel research project. I was also impressed by the quality of the proposals from my peers in 20.109! The ideas seemed truly novel and, in most cases, feasible. I only wish the experimental work was less labor and time intensive, such that like for computer science students, we could pursue these projects aside from our classes without making them our primary research focus.

Scientific Presentations and Theatre

In high school, I acted in four different plays. I was cast in a wide variety of role, at different times playing a monkey, a boy with schizophrenia, a 1920s gentleman, and an 80 year old man. Acting out the lives of characters on stage helped me quickly overcome stage fright and developed my stage presence. In Theatre, I learned how to project my voice, speak clearly and emphatically, and use gestures effectively.
When I entered 20.109 this semester, I felt confident in my ability to deliver an oral presentation. I was nonetheless amazed by how greatly 20.109 helped my ability to present scientific and technical work.
In Theatre, the work of the lighting crew is to illuminate different parts of the stage in accordance with the action of the play. Specifically, the lighting is meant to direct the eyes of the audience so they focus on the right details and the right interactions between characters. In 20.109, I learned how to apply this lesson without a lighting crew. Specifically, the use of arrows and small markers on slides greatly helps to direct audience attention to the right details. Similarly, using animations to bring on specific pieces of information at different times helps in clear slide understanding.

Finally, every great play can be broken down into a “three by three”: three sentences of three words each that capture the plot. For example, “boy likes girl”, “girl falls (for) boy,” “boy marries girl.” Having this “three by three” understanding is critical to seeing the backbone of the play. Similarly for oral presentations, having a clear view of one or two central research questions and communicating them is key to audience understanding. 

Writing about Research

I love writing. From essays to short stories, poems to letters, the ability to effectively and efficiently communicate fascinates me. While I had done extensive creative and personal writing prior to 20.109; I had done little scientific writing. Even in my technical writing experiences, I had taken a mostly ad-hoc approach to scientific writing: reading manuscripts and trying to imitate specific techniques I enjoyed rather than really delving into the principles of scientific communication.
Before 20.109, I had written two posters, one manuscript (unpublished), and given numerous research presentations. I felt confident in my ability to present before an audience; however, I looked at technical writing with dread. Concentrating months of experiments into a clear and concise summary frightened me. Specifically, I found it difficult to find the overarching story of the research and then present each experiment and finding in the context of the overall story. In addition, I consistently became lost when explaining experimental results. Figuring out ways to address the controls and experimental cases at the right level of detail was particularly difficult.
With the module 1 report, 20.109 taught me to boil down months of research into core concepts and questions to be asked. The phrase “Simplify. Simplify. Simplify.,” constantly came to mind as the staff pushed us to exclude extraneous information and always tie results back to the fundamental question the research was addressing. In this way, 20.109 taught me to both find and convey the story of research; a skill which I now deeply prize. Moreover, the “bullet-point” based nature of the module 1 report allowed me to simplify and clarify my language.
With the module 2 research article, 20.109 pushed me to analyze our results in the context of other scientific work. The module 2 research article was the first time I had thoroughly delved through related literature and compared results in order to derive conclusions beyond my experiments. I loved writing the discussion section for the module 2 research article. I thoroughly enjoyed learning how to synthesize results from multiple research articles and broaden my perspective of the scientific field. For the first time, I began understanding how each piece of scientific work contributes to the greater whole; and that vision inspired me.
Overall, I have most greatly improved my abilities to (1) see and convey the overarching story of a research paper, (2) describe results completely yet concisely, and (3) relate my experimental results to the greater body of scientific work. However, I still believe that seeing the overarching story is the greatest challenge. I usually find it relatively straightforward to interpret experimental results, but tying them together to generate a cohesive narrative that answers a question is difficult. One method I found that helped greatly was to read the entire module before starting the experimental work. I did this for Module 3, and understanding the “end product” and “end results” greatly deepened my understanding of why the initial work was critical. For future research experiences and classes, I hope to understand the full map of work and how each experiment contributes to the next as early as possible in the research process.

Overall, 20.109 helped me grow tremendously as a scientific communicator. My only suggestion is to consolidate all of the scientific writing presentations/slides/suggestions into a single place on the wiki. Currently, they are spread out across modules, and people pages, and FNW assignments. Having them in a single place would make the principles of scientific communication easier to reference for later work.