20.109 Taking Names & Busting Myths

*ka-pow*

DID YOU KNOW...contrary to popular belief, "lemmings do not commit mass suicide. During their migrations they sometimes do fall off cliffs, if they wander to an area they are unfamiliar with."*

Here's an adorable picture of what a lemming looks like:

Now that I've got your attention, I'd like to shift the conversation toward more relevant myths that were debunked during my time in 20.109 #enlightenment

1) I should only visit the BE Comm lab at the end of the course when I'm working on my research proposal grant presentation with my lab partner. Nope nope nope. It was only when I finally scheduled an appointment with a BE Comm fellow (shoutout to Bill!) the day before our mock-grant presentation that I realized how awesome of a resource the BE Comm lab was. Sure, Diana had reminded us during each of her workshops how we were free to schedule an appointment anytime for any questions about science writing in general or any 20.109-specific project inquiries, but it wasn't until my lab partner met up at 56-211 and realized:

- this consulting service is free
- they offer you a PLETHORA of snacks when you check in to your appointment, whether it's the "salty" bin that happens to call your name or the "chewy" bin that catches your eye
- THE COMM LAB FELLOWS ARE SO FRIENDLY. they have years of experience under their belts and know just how to point you in the right direction for your project

2) Bacteriophage are boring and don't do anything useful besides infecting bacteria. Prior to Mod 3, I defined bacteriophage as "viruses that attack bacteria, not humans". They're so measly that they can't even achieve their one goal of reproduction without some outside help (i.e. their host victims). 'Cause without host reproductive machinery to hijack, phages aren't much more than a protein polygon enclosing some genetic material. Our cathode construction module completely changed my perspective on the usefulness of phages and I have 20.109 to thank for that.




























*Businessinsider.com

Real Nanomachines, Son!

At times, it’s hard for me to imagine that we pulled it off, but it’s absolutely true. We learned to use viruses to make working batteries. How incredible is that! Our biomaterials module was the third and final module of 20.109. We used an engineered M13 bacteriophage to assemble an Iron-Phosphate/Gold Nanoparticle cathode for a battery. The cathode material would coat the viruses and the gold nanoparticles would space themselves along the viruses to conduct electricity. The crazy important detail is that we were able to arrange 5 nanometer diameter gold particles within 5 nanometer precision! Modules like these confirm my personal belief that mankind is capable of producing the smallest machines imaginable, specifically using biology.

     Many folks dream big about technological miniaturization, especially with regards to nanotech. Now more than ever before, exposure to science fiction media usually inspires these dreams. Hollywood films such as Transcendence (2014) like play around with swarming nanobots. Video games like the Metal Gear Solid franchise use nano machines as a plot device to handwave the fantastical abilities of its iconic bosses and playable characters.

Of course, to fully enjoy these stories, it’s necessary to suspend your disbelief. Yet, there are those out there who do have reason to believe that nanotech level miniaturization is inevitable. They may have faith that Moore’s Law is alive and currently bringing human-designed nanomachinery closer to the present day with exponential speed. They point to the explosion of solid-state electronics and micro tech that we currently know and love as the historical evidence. Who could have predicted single atom transistor? Who could have predicted the Macbook Pro 100 years ago? Who could have predicted how fast information sharing would be in 2016? 

While our technology has blown our minds and the wildest possible dreams of our ancestors, I want to be fair to these big dreamers and offer the idea that such nano systems would be hard to optimize further. According to some sources it would be outright impossible to get ANY smaller than nanometer-length wafers, such as Intel’s Sandy Bridge. Anything smaller runs into really bad interference with ambient electromagnetism and temperature effects. For instance, the single atom transistor needs to be kept around the same temperature as liquid nitrogen. Any nanobots using these revolutionary transistors would not feasibly work on our warm earth.

Biology on the other hand, works on the nanoscale all the time, and in ambient temperature conditions. Enzymes process chemicals on the nanoscale. Our Electron transport chain complexes conduct electrons across nanometer-scale gaps between electron carrier ions by exploiting quantum tunneling. Viruses are actually self-assembling nano-sized machines that replicate from harvested (bio)materials. Really, we can all benefit from understanding  that science fiction’s most unbelievable plot devices are actually all around us, ready to be engineered to realize the big dreams of humanity.

We're Talking About Practice.

For our second module of 20.109, we modeled an academic journal club, where members of a lab present research in the field to the rest of the group. 

Presentations are my life. I had lots of practice presenting and performing from high school band and oral assignments. The rush after a presentation is one of my favorite feelings in the world. Stage fright escapes me. I love presenting so much that whenever I’m not careful at parties, dates, or casual conversation, my contributions get way out of hand and turn into one-sided seminars. There are few situations where I feel as natural as i do in front of of a large stage, the larger the audience the better. I try to complete at least one big speaking gig each year, just to enjoy the moment that presentation entails. My favorite speaking gigs were Terrascope 2016 and First Annual BAHFest! at MIT.  As such, the 20.109 journal club was a super fun assignment, and I would truly do it again.

My presentation focused on the results of this article, which described the regulatory role that RNF-138 protein performs in switching between DNA repair pathways. Very neat stuff, but the challenge is to fit an entire study’s work in 10 precious minutes. It is pretty common to plan out one’s talking points or the script, run through several times and practice for live audiences.

However, did none of those things. I got surprised by my own slides and found errors in transitions that caught  me off guard and tripped up my flow. Just like rap, presentation is all about the flow. 

My advice to all involved in the rap and research industry is to practice, practice, practice your work before you debut!

Grandmother Nature

Bioengineering as a subject is both humbling and empowering. It’s humbling because you are constantly witnessing the elegance of nature. It’s empowering because you are using processes that have evolved over millions of years to your advantage for your own purposes. It's pretty amazing.

 

Purposes like growing an ear, maybe.

It's interesting to think that we use nature's process of evolution on two different time scales. We take advantage of evolution that has happened for millenia when we utilize techniques such as bacterial reproduction to reproduce certain plasmids or proteins. We take advantage of evolution on a much smaller time scale when we use techniques such as yeast display to search for favorable mutations. Yet all of it relies on the power of nature. Nature is like the patient grandmother who you see slowly knitting away everyday. You don't think much of it until you find that one day she is suddenly holding in her hands a brilliant scarf - one that can maybe mess up the world or salvage something.

Some Final 20.109 Reflections

20.109 is by far the most useful class I have taken thus far in my life. After reflecting over my experience in this class, I have realized how much I have grown as a communicator and as a researcher. With respect to my writing for example, I have usually struggled with being verbose. Although I definitely need to keep working on that, this class has helped me to become much more aware about the ways in which I can be more concise and still convey a significant amount of information. This was particularly the case with the methods section. I have never attempted to write a legitimate methods section with the same components you would find in real research papers (which I always skipped while searching for the discussion or conclusion….). I never would have thought that I would actually develop a level of comfort writing a section that always seemed to be mumbo jumbo to me.

Furthermore, learning how to develop schematics and diagrams, as well as how to appropriately describe them whether you were writing its associated caption, results, or discussion section was also invaluable. I again, have never really had the opportunity to try consolidating the important parts of an experiment in a schematic, or to put together and interpret results that I helped to generate myself. All of these technical writing skills were difficult at first for me to get used to. Thanks to the super useful feedback that I constantly received from my professors, however, I was able to learn how I could organize myself in order to start writing those components, and learned what I needed to look out for while revising my writing. I now feel confident tackling any other Module 2-type of research papers that lie ahead in my future.  

Another aspect of my communication skills that have greatly improved is my ability to give a presentation in front of a crowd. 20.109 wasn’t the very first occasion during which I gave a powerpoint presentation in front of a class. However, the stakes have never been as high as they were here. The simplicity of some other projects I had presented in high school, and the lack of a real Q&A session after those presentations made them look like a walk in a park compared to what I went through this past term. Although my Journal Club presentation was a nightmare for me, I was able to get ahead of my work and prepare much earlier for my second class presentation in order to work on my communication skills. Going to the BE Communication Lab was also very useful in setting my partner and I up for performing better on our final presentation than we had individually before.  

Time management issues and not spending as much time preparing for my assignments as I wanted to were certainly recurring themes in the blogs I have posted the past few weeks. The difficulties I had in these areas made preparing assignments for 20.109 and fulfilling my commitments in other classes pretty stressful. In an attempt to  save others from following the same tracks I did, I will continue to emphasize to start assignments and seek help EARLY! If you find yourself in a vicious cycle of sleep deprivation and the inability to finish assignments on time, don’t be afraid to ask for additional assistance from professors or other MIT faculty whom are there to give us a hand.

I would like to that this moment to also give a shout out to my great lab partner, Skirma.  I am really grateful to have collaborated with her, and for the patience she had even when I messed up badly during lab. I wouldn’t have made it through the tough moments of the semester without her. 20.109 did a great job of making us work in teams, where we had the opportunity to develop communication and collaboration skills that will be useful in any occupation we choose to pursue.

Last, but certainly not least, I want to thank the best professors I have ever had. This class could have been terrible without them. I really appreciated their time and dedication, and for helping me to really see what it means to be a Biological Engineer. I will always remember them and will cherish all of my experiences in this class. 20.109 was definitely a lot of work. But I would have never grown so much as a scientist without that work and the presence of all of the professors. Once again, thank you!

Oh yeah I know how to…I mean I thought I knew...

The day that I heard we were doing mini preps for the first time in 20.109, I suddenly felt pretty confident. “Hey that’s something I’ve done a million times in my UROP!” I even assured my lab partner, who had not performed mini preps before, that she didn’t need to worry about there being any issues with the protocol since I pretty much knew the steps by heart.

Now nothing actually went wrong with the mini-preps that day. However, it was in the prelab prior to performing the purification that I realized I how little I actually knew about mini-preps.

I may have known what buffers I had to use, when I had to use them, and how much I needed to add of each kind. But I had never gone out of my way to understand what each buffer was actually doing. Furthermore, I didn’t even know how those nifty columns actually purified DNA. Despite that initial deflating feeling which arose when I realized I couldn’t answer most of the questions about each buffer, by the end of the prelab I felt like I had been enlightened by Leslie. I no longer was merely adding Qiagen’s P2 buffer after P1 because the protocol said to do so. I was now adding P1 (which is not just some magical chemical but I now know it should have Tris, EDTA , and RNase) in order to resuspend the pellet, weaken the cell membranes of the cells, and to eliminate undesired RNA. I was then adding P2, an alkaline solution containing SDS and NaOH, in order to lyse the cells. That NaOH is able to denature the DNA. But why add SDS now? Ahhh, since later when we add N3 in order to neutralize the alkaline solution, SDS will precipitate out of the solution in the neutral pH, carrying with it the dissolved proteins and lipids that we want to get rid of. 

This is an example of one of the aspects of 20.109 that I truly appreciated the most. It was extremely useful to be able to learn new protocols while gaining an understanding of what you were actually doing along the way. Even when you may have thought that you knew a protocol very well from your previous experiences, this class also gave you an opportunity to brush up on or even learn for the first time why things worked out the way that they did. This information is of course crucial for troubleshooting if anything funky appears to happen during lab. Furthermore, this experience I just shared was a wakeup call, which made me realize that it is never a good idea to satisfy yourself with simply memorizing steps in a protocol. Many robots out there can do that just as well. Taking a few extra moments to look up the chemicals you are using before going to class or your UROP, and asking questions when you are in doubt will definitely pay off on the long run.

BE Communication Lab Meetings? 10/10 Would Recommend!

When I first heard about the BE Communication Lab, I thought it sounded like a pretty nice resource to have available. Unfortunately, things sort of ended there. The Protein Engineering Summary was an opportunity to receive feedback on one of my first major assignments in this class- but nothing happened. I was reminded about how helpful the Communication Lab could be for our Journal Club presentations. “I should probably make time to go to this one” I thought. Well, in case you haven’t read my other blog about how that presentation went for me, let’s just say that not much about my preparation for that presentation went well…. How about for the Systems Engineering Research Article- that assignment that is worth a modest 25% of my grade? “Wouldn’t it be nice to get feedback on all of this writing that I am uncertain about?” I’m sure it would have been nice. But no, Bremy once again didn’t find time to go and ended up working the entire weekend and most of Patriots day on it.

So I’m setting things up for you to predict whether or not I went to the Communications Lab for my final presentation project in 20.109. Your prediction may have been right. Except that now, our professors decided to make going to the Communication Lab a homework assignment for this final module. “Okay, I guess I really have to make time to go now.” I thought. Even then I kept pushing off the meeting, as I continued to feel pressed for time. I finally decided to follow up with my lab partner about scheduling a meeting. To my luck, she had already scheduled a meeting for that same day.

As soon as our instructor arrived, we got right down to business. After she had a gist for the project that my partner and I were trying to complete and what we wanted help on, she read our proposal ideas quickly and instructed my partner and I to draft our presentation slides. Our instructor was very helpful in pointing out the strengths and weaknesses of our proposal. She then helped us to connect our flow of ideas to how they could be organized onto the slides (which we hadn’t really started prior to the meeting) and proposed how we could go about best preparing those slides around the things we would actually say when we presented. I was amazed by the quality of the feedback my partner and I received in such as small amount of time. We went from not really being sure how to approach organizing our slides to having a solid plan early that allowed us to prepare better for the big day. I totally agree with the opinion some of my peers have that the homework assignment requiring us to go to the BE Communication Lab should have been given earlier. I likely would have benefited from multiple trips to this lab if I had realized earlier just how effective the grad students and fellows from this lab can be.

If you feel like you are going to be very busy around the time that you need to write your next 20.109 report, certainly avoid distractions:

But don’t avoid going to the BE Communication Lab!