Tuesday, November 18, 2014

Deja Vu With Module 2

As I was starting to construct my research article for module 2, I couldn't help but feel as if I have done this before. Sitting in the reading room with my headphones in, trying not to procrastinate while I have this empty word document in front of me. It all just seemed too familiar. Although I had done the data summary for module 1, writing the research article for this module was definitely not easier. I had a better idea of what to expect and what to write, but the effort and time commitment had to be even greater. In the end, I probably got even less sleep trying to finish the research article than I did finishing my data summary for Mod 1.

The biggest advantage I felt that I had in module 2 was definitely the feedback from the 20.109 staff on my FNW assignments, as well as the feedback I got for my Mod 1 data summary. I had a much better idea of what I had to include on my research article because the teaching staff was able to answer all of my questions and give me advice on my intro and materials/methods sections. Specifically, the in-depth comments on my FNW assignments and Mod 1 data summary guided me in a better direction this time around. I felt like I was better able to concisely explain the overall project and the methods used by omitting unnecessary info and including things that I forgot to include in my Mod 1 data summary. I was also afraid that I would not know how to structure my results section because of the unexpected results we had in the module. However, we were given very clear and helpful suggestions to organize our data, and that made my life ALOT easier. Although I spent more time overall this time around, I was less stressed and more confident in my final paper (It did help that it was only a rough draft).

This might sound corny, but I really didn't find any thing to be unhelpful. I used so many different resources to help write my research article, and everything only helped. Sometimes when you look at so many different sources for help, you might get get conflicting advice which can make things very confusing. However, all of the sources provided by 20.109 were pretty consistent with their advice and made things a lot more clear for me. Overall, I think I learned a lot from writing the research article but I am so so so happy that we don't have to write another one for the semester. More sleep for me!

On to Module 3!

That kid who brought bread to journal club

I have never understood why people try to picture a naked audience before giving a presentation. For me, I like to relax myself by telling a corny joke and providing treats to my audience. Surprise surprise! That's exactly what I did. Although I feel comfortable presenting to my classmates and teachers, I always get a little nervous before any presentation. Bringing a loaf of sourdough to my presentation and telling a corny joke about it definitely eased my nerves a little. Thankfully, the audience laughed, or else it would have been really awkward.

In terms of the presentation itself, I found that the most difficult part of it was finding an overall application to my project. Knowing more about bacteria that live in sourdough bread is pretty cool, but so what? I spent hours just to think of further applications to the findings of the research. In the end, I was still very vague about what benefits the research can provide to the world. The thing that surprised me the most was how often I would say "ugh" or "um" between each sentence. I didn't realize this until I met with Atissa to go over my presentation. I must have said "um" at least 50 times during the whole presentation. It was frustrating to watch. I think that I could have rehearsed more, so that I wouldn't have to pause between each sentence. It wasn't easy to find time to rehearse because of the design project due the day before my presentation, but no excuses here!

Overall, I had a great time presenting the research article I read. The thing I feared the most was the Q&A session after my presentation; I thought the teaching staff would just completely grill me with questions. However, they asked questions that I was mostly able to answer (except for certain methods- I need to familiarize myself more with the methods section). The whole audience was also just very respectful in giving me their full attention and asking me questions that weren't too hard (thank god). Maybe next time, I will present research on Pumpernickel....

Friday, November 14, 2014

Not so bad!!

Much to my surprise, compiling the Module 2 report gave me a huge sense of gratification. After writing the Mod 1 report, I never thought I’d enjoy scientific writing, but this time it was unexpectedly pleasant. I was able to plan out my approach and instead of attempting to write the whole thing in a cramped 48 hour period, I began a week early and stuck to a strict plan of finishing a section a day. I think this is honestly the first time I’ve ever completely avoided procrastination and boy did it feel good.
The second module was designed very well in that we were assigned to write drafts of smaller sections and given very detailed and thorough feedback for improvement. This definitely helped make the final task of compiling everything a much less daunting task because there was at least the foundational draft of the introduction and methods section. Helpful feedback from both Agi and the BE communications lab made the writing process much easier. The overall reduction in stress made the experience enjoyable and incredibly rewarding. Now that I have completed the draft of my first ever journal-like manuscript I look forward to scientific writing in the future. Bring on Mod 3!!!

*ding ding* Round Two!

                An article that I recently read about time management mentioned the use of the Pomodoro Technique. In essence, using this technique, one should effectively break their day down into 25-30 minute chunks. During these intervals, only one task is targeted and no distractions whatsoever are allowed. The idea is that these short intervals allow for optimal focus, while also introducing an element of time pressure.

                I frequently run into the issue of viewing these assignments as monumental tasks that are too large to begin or finish in one sitting. It’s much easier to knock out smaller assignments and busy work with definitive ends. Hence, I end up chronically delaying these larger assignments. I was speaking with Atissa about potential solutions to this ever present problem, and the best advice that she offered me was in line with the idea behind the Pomodoro Technique. Though these assignments may be easy to push aside, it is important to designate small personal deliverable goals for each day. For instance, instead of aiming to write the entire paper in one sitting, it is more effective to allocate specific days to work on only one individual section of the entire research article. By focusing only on one section at a time, I will mentally be able to view the task as more digestible and reasonable to complete. Winning these little victories ultimately results in a more pleasant and manageable way to finish large assignments, such as the Module 2 research article.

                A specific resource that I utilized to aid in my writing for this module was the BE Communications Lab. During the beginning of the module, I met with Georgia from the BE Communications Lab on how to write the introduction for a research article. It was helpful to hear feedback from someone who had plenty of experience with scientific writing. She offered insightful tips that I had not considered before, such as using other existing published research articles as a model with which to base my writing. Though this seemed obvious, it was something that I hadn’t considered before and found particularly helpful. I will certainly be visiting the BE Communications Lab again in the future for help.

                All in all, I have thoroughly enjoyed my time in 20.109 so far. These modules have been both relevant and fun! I must say that, as a lab introducing the fundamentals of biological engineering, 20.109 has been a fantastic experience.

Thursday, November 13, 2014

Extending our bacterial photography system across engineering disciplines
Jessica Sandoval

For Module 2, we combined the beauty of a biological system with programming. We created our own bacterial photography system and later tuned the image quality by modifying the phosphorylation events of a photoreceptor kinase, much like tuning the knobs of an instrument. We were able to not only create a new system by combining two well-studied pathways in cyanobacteria and E.coli, but create photographs from plated engineered E.coli.  

Module 2 was my first exposure to synthetic biology, but the thought process was analogous to macroscopic engineering principles. We first generalized the engineered system to two black boxes, a signal sensing box and an output generation box. The signal sensing box functioned to detect photons from a red light source.  The output generation box took in the signals from the light sensing box and outputted a black precipitate. Unpacking the black boxes, the first box contained a modified photoreceptor with kinase activity. The second box involved the transcription/translation of a B-galactosidase enzyme. We were able to next “reach into” these black boxes and fine tune the phosphorylation events that regulated their outputs. By generalizing the engineered system to black boxes, we created a fundamental signals and systems problem. This thought process used to approach our system can be extended across all engineering disciplines, not just to synthetic biology.  

In fact, we applied the logic flow of the engineered bacterial photography system to electronics. Within this example, we created a simple system of electrical components that would simply amplify an input signal and turn on an LED. However, instead of playing around with E.coli, we tinkered with much more robust components: resistors, OpAmps, switches, and LEDs. This electrical engineering approach allowed us to modify our system and generate an output immediately, as opposed to waiting for incubations. It was a really exciting demonstration of the applicability of our biological system for other engineering disciplines. For me, this was one of the most important lessons from Module 2. The fact that the mechanisms underlying any engineered system, whether it be as small as a programmed cell to as large as space flight systems, all serve similar roles. Regardless of scale. Regardless of media. And that is truly fascinating to me.   

The Struggles and Achievements of Article Writing

Just finished writing the research article for module two! But I wasn't too sure what to think about it. The entire document ended up as a 3,400 word, 20 page beast that took me hours upon hours to complete. For many people, this assignment would seem to be easier, especially after Module 1. However, I found this article to be just as difficult as the last one. There is this sort of scientific language that many other papers use, but I still have yet to pick up on it. Even after reading other articles, I still find it difficult to incorporate that type of language into my writing. The concise and definite method of writing conflicts with my education as a writer in the past, which has been overwhelmingly based on humanities. I know that science and liberal arts can absolutely live together, but adapting my writing style from one subject to another has just been hard for me.

Another issue has been the type of research completed in Module 2. Near the end of the research effort, things didn't go exactly as planned and our results were less than ideal. In the real world, this would simply necessitate a re-trial of our protocol, taking extra care not to mess up this time. But in the strict time span of the Module, we had to carry forward and complete the experiment with reagents from other sources. Natalie suggested that we frame the first part of the experiment as a "pilot study" for the rest. I wasn't too sure how to accomplish that, but I looked at the mutants we generated and the amino acid mutations were identical to two strains that the teaching faculty provided! It turns out that the T541Y and T541L that we created were also represented as NB487 and NB491! So being able to smoothly incorporate our mutant strains in the article was especially rewarding. The mutants we created were kind of a happy accident, but I'm completely okay with taking advantage of the situation. For now, I don't really have a clever photo to finish up my blog post. So here's a gif of a hamster eating a burrito.

Moving up in the (module report writing) world

The process of writing the module two report was as different from the first round as possible – in a good way! While I did not go into it expecting a great experience, given that many of the results we were looking for in this module did not materialize, I found myself really enjoying compiling the report. I think the main difference between this report and the last was that I spent a lot of time mapping out the different components of the experiment. Whereas last time, I pretty haphazardly started creating figures and writing paragraphs, I forced myself to walk through each day of this module to make sure I knew why each step was important. Ironically, it was the fact that we had to modify some of experiments and that certain aspects of the original protocol were changed that prompted me to take this approach. I also had to closely look at the results and make sure I knew exactly what was going on, since they didn’t turn out as we expected. During module 1, I actually had a pretty good handle on theory behind each of the steps taken given the cloning I had done previously, and that, combined with the results turning out as desired, made me overconfident as to how easily I’d be able to write the report.
In addition to getting off on a better foot in writing this report, I benefited from the various resources we were provided with. Presentations by the WRAP faculty were very helpful in determining what to include in each section, and the degree of conclusions to be drawn in each. For example, I caught myself writing out conclusions in my figure captions, as opposed to reserving that material for the results text. Shannon’s lecture helped a lot on the statistics used to analyze the data. I used the feedback on the module one report, as well as the FNW figure 1 and materials and methods section drafts to pare down my writing to the essential information. The feedback we’ve received overall in 109 has definitely helped me focus my scientific writing and make it more efficient. I found it really helpful to read the background literature on the EnvZ-OmpR two-component system to supplement the material presented in lecture and pre-lab, if only to get familiar with the terminology used to describe the system.

Now that I know what works when writing a report, I look forward to applying that knowledge to any Module 3 write-ups we put together, and scientific writing beyond this class. 

Biology is Art, and Biology is an Art

In the year before I came to MIT, I took an art history class for the first time.  Though previously I had very little interest in the visual arts, the interface between art and culture really struck a chord with me.  Another art history class and many trips to the MFA later, my appreciation for art has only grown.  As a biological engineer, I think that advancements in biology will help to shape the future of our culture.  And, based on the technologies that we have learned about so far in 20.109, biology also has the potential to affect the future of the visual arts.

Imagine a painting made out of bacteria that could change shades in response to the amount of light in a room.  Imagine fluorescent trees that not only saved energy by lighting walkways at night but astounded passers-by with their combined natural and man-made beauty.  Imagine colorful stained-glass windows that captured solar energy.  Two out of three of these projects are possible based on technology that we learned about in 20.109, and the third is in the process of being developed through a crowd-funded project.

Biology can be art.

That said, biology can also be an art.  As we've learned so far in 20.109 (particularly in this module with our less-than-ideal beta-galactosidase assays and Western blots with many bands), getting experiments to work sometimes seems more like an art than a science.  The best way to get better at art is practice.  I think the same can be said for lab techniques.  I look forward to mastering the arts we've studied so far.  Even if repeating experiments can be tedious at times, the results are subtly different every time, just like with art.

Even though biological techniques might not be as predictable as the scientist in me says that they ought to be, now that engineering biology is feasible, designing with biology is a real possibility, and I'm excited to see how "bio-artists" give cells and viruses visual appeal.  Maybe by showcasing the beauty of biology, the public will become more comfortable with the idea of using biological systems to solve problems in everyday life, from GMOs to cellular- and viral-based therapies.  I look forward living in a world where biological engineering can have a real impact, and I'm hopeful that I'll be part of the change to see this happen in my lifetime.

My Confused Grandma

My grandma is 76 years old and still very with it.  She reads books, does crossword puzzles and is up to date on the news.  In fact, she's so with it that she often reads my facebook posts and comments on what I put up.  Recently I added a picture of Kathryn and me holding our bacterial photograph from mod 2.  A few minutes later, she asked me what I had won and why I was holding a metal.  I responded that I was actually holding a plate of photoreceptive E.coli, she got confused and asked again what I was holding.

That's when I realized that the research we're doing for a lab class at MIT is so far outside of what people consider mainstream, that the average person doesn't understand it.  No matter how many times I tell my grandma that I'm holding a plate of bacteria, she can't wrap her mind around it. Instead of growing algae or dissecting organisms, we're engineers. We're working to change what millions of years of evolution has been working towards, and that's awesome.

It's easy to forget that MIT is more than grueling psets, tests, and all too frequent all-nighters. It's more than the 3am panic when your code isn't running.  MIT is an opportunity.  It's the chance to work in top notch research labs as a freshman in a UROP.  It's a place where everyone is motivated and excited about science.  It classes where professors don't assign textbooks because you're learning from the primary research.  It's a community where you can totally geek out about biological pathways or organic structures and find people who are just as weirdly excited as you.


The Chaos of Biology

This may have been my first research article, but I’m pretty sure it’s not a good thing to write a paper about an experiment that didn’t work out. After such careful creation and screening of our two mutants, it was pretty sad to see our beta galactosidase assays fail. Also, our first sequencing data was atrocious. We couldn’t even find a sequence alignment with the original Cph8 plasmid, and we had an excessive (to say the least) number of ‘N’ nucleotides. Our western blot looked more like a tie-dye pattern than a protein gel. I’d show a picture but it’s embarrassing. Our hope was renewed when we learned that we’d be testing mutants isolated from an earlier class, but those didn’t work out very well either. This module has taught me to come to terms with the chaos of biology. Sometimes things don’t work, even when we really think they ought to. Making even one small mistake can have huge consequences. The weird data definitely made writing the report pretty awkward, but thank goodness for four-day weekends.

When all is said and done though, it was pretty neat to write a whole research article. At the beginning of this class, I couldn’t even tell you the parts that make one up. This class has definitely furthered my understanding of science. 

Mod2 reflection

Writing this module 2 report was a definite improvement from the module 1 report. Having the four day weekend also helped make the writing process less stressful. My failures with module 1 taught me a lot of how to structure this report. Even though a lab report is different from a research article, a lot of the portions were similar. From the feedback of module 1, I gained a lot of feedback about how to structure and introduce the key concepts succinctly with topic sentences.

For this module, I went into it more prepared. Throughout, I attempted to understand how all portions of the experiments came together. My classmates and instructors really helped clarify protocols and any questions. Furthermore, all my FNWs, I tried to go into as much detail to be able to get as much feedback as possible.  Knowing how to better focus on this paper helped me take advantage of my resources to be able to produce a more coherent paper.

Finishing, this module 2 report made me feel more confident about myself as I could feel my improvement. I appreciate how 20.109 is allowing me to improve my writing and analysis abilities and giving me the hope that in the future I will be able to  I definitely feel that in the future I will be able to write another scientific paper! :) 

Module 2 in Review

   Probably the scariest part about module two was the results. As far as I know, no single group was definitively able to improve the photographic bacteria system, much less my own, and I know only one group which obtained a mutant that may have worked. The results were somewhat disappointing; and, I was initially very confused at how I could turn them into a compelling paper. In fact, this one dilemma kept me from even beginning to write until I realized that this is 20.109, and I had to write something. I sought help from Agi, and with her and Shannon's guidance I managed to pull off the paper, and module two itself.

   Module 2 overall was much more enjoyable than the first. Not only had I become more accustomed to the format of the course, but I also feel that having accomplished the first data summary, I improved greatly as a scientific writer. I had never been so temporally strained with an assignment, and perhaps the shock of completing it permanently burned my accrued writing knowledge into me. I feel the difficulty of the first module made it comparatively easier to handle the assignments given out in the second.

   The first big assignment of the second module, the oral presentation, initially posed a challenge to me. But having done the module one data summary and given a journal club presentation with only one day of preparation (my schedule was crammed due to the data summary) to members of my lab at my UROP, I realized that this assignment was not so bad, and it wasn't. As I am writing this I am not sure exactly what grade I received, but I felt confident in my preparations and during the presentation itself, knowing that I had been through worse. Also, the paper I was presenting was pretty awesome. It pertained to using proteins which dimerize in the presence of light to control biological pathways, and I particularly enjoy papers like this which propose novel and fundamental methods, since not only are they interesting research in themselves but they can help increase the rate of interesting discoveries. Therefore, this assignment was exciting overall, despite my initial fears.

   Moving on to the next and final big assignment for the module, I was initially uncertain. I did not know from what angle I should attack my paper, but the instructors gracefully incited an epiphany in me: the best thing to do is be blunt and honest. The mutants we isolated diminished the contrast obtainable with the system, but we can still obtain valuable information on them in designing future optimization experiments: this was the essence of my paper, and it is the truth. This realization was crucial, and writing became very natural and enticing. Writing the paper, and watching it come together was like watching a sculpture slowly take shape. The creation of each new feature propels the artist to follow through, and in the case of my paper, the creation of each new figure and paragraph compelled me to write further. My paper was a self-sustaining fission reaction, and it progressed all the way to its completion.

Round 2: Easier? No. Better? Yes.

Although I would not say the module 2 paper was easier to complete than the module 1 abstract and data summary, I will say that I felt much better prepared for it and it was nice to have a whole four day weekend to devote to it. Things definitely would not have run as smoothly if I didn’t have the great support of the BE Communications Lab, 109 instructors and my peers.

I met with the Communications Lab to discuss the introduction section of my module 2 paper. I went in specifically for my introduction, but the general advice I received extended to my whole paper. The key concept that was pointed out to me by Jen was the importance of topic sentences. I learned how to write a literature paper long time ago, but writing a scientific paper is very different than a literature paper and somehow (embarrassingly) I forgot that topic sentences should still encompass the whole content of the paragraphs. Jen also gave me a great tip that taking the topic sentences out of the paper and reading the topic sentences alone should tell an almost-coherent story.  

For the rest of my paper, I really could not have done it without my classmates and office hours (thanks Agi and Shannon!). I turned to office hours and my peers for questions such as how many t-tests to run, how to analyze my western blot and even some simple questions about areas of the lab protocols that were a bit confusing to me. It was very nice having the support of the 109 instructors and my classmates to talk things out and overall helped me write a stronger paper.

The Module 2 writing assignment left me with an overall feeling of accomplishment, not necessarily because all of our experiments went according to plan, but because we have learned how to draft a scientific paper. Writing a scientific paper, or even being able to draft one, seemed like a very far-off task until 20.109. I really appreciate all of the guidance and support of 109 instructors, the BE communications lab and my classmates. 

The art of reading scientific literature

I have a (terrible) habit of printing out all the papers (and lecture notes, psets, etc.) that I’m going to read since I hate reading on the screen. For Mod2 journal club and report writing, this proved to be a very motivating exercise. The papers that I read or skimmed through literally piled up to 10cm high, and as I was drafting my slides and writing up the discussion section on my research article, it felt great every time I finished a paper, put them into the “used” pile, and watch the pile grow.

The most important lesson I learned for Mod2 is in fact how to read papers. I have always been complaining about the esoteric expressions journal articles use to convey their results. There aren't many captivating sentences, and all the numbers are usually packed together in a super space-efficient manner. What usually happened before was that I didn't know what kind of information to look for when all of a sudden I was presented with too much of it.

Now that I learned how to write concisely and professionally in 109, and how to analyse a paper to present it to a group of colleagues, I realized that there is in fact a common standard of scientific communication and an inherent logic of each paragraph within an article. The Mod1 M&M assignment prepared me for not only writing my own M&M in Mod2, but also digest the very dense information presented in the published M&M sections and recreate the experimental conditions. I also learned to dissect each section of introduction, results, and discussion into a purpose statement, context, findings, and implications. This was an extremely useful tip for me to parse the technically challenging information in many papers that I read for such a new area of synthetic biology. In fact, I think I am now ready to read literature completely on my own by following these general guidelines inspired by the writing and oral presentation experience.

Of course feedback is important. Agi, Shannon, and Natalie’s office hours have been extremely helpful for me to appreciate which points are relevant from other papers, what conclusions can be drawn from our experiments, and how to put our project into the bigger context of published literature. I think the main reason why I enjoyed reading these papers is not because I understood all the technical details (in fact I don’t) but because I was able to relate the overarching themes of these papers to what I know or to one another, thanks to the great help from the instructors and from my lab partners. Reading and writing (and speaking to a lesser degree) are intimately related and I am glad that I can start to better integrate them in Mod3 and future studies.

The Art of Presenting Failiure

When I saw that we were using the bacterial photography system developed by people in Chris Voigt's lab for module 2, I was pretty excited. I was actually familiar with this system from freshman year, when we generated images using the wild-type strain during the biological engineering FPOP (shout out to my awesome first ever lab partner, Ellie Laukaitis!) So when we started the module, I was confident about the performance of this system. Plus, from our experiments in module one, it seemed like results in 20.109 were fairly predictable.

This didn't quite turn out to be the case... Module 2 was also very well organized similar to module 1, and there was an unified goal for the experiments we were performing: optimization of the photography system. But the biggest difference was that experimental outcomes for each group were meant to be unique. And since not all outcomes can be successful, some groups were bound to get results that did not fulfill the projected goal.

But even before reaching different (and potentially inconclusive) outcomes, we-as the whole TR section- faced a few fundamental "road blocks":

After our whole section got results that completely contradicted any expected outcome, we realized that there might be an anomaly either in our bacterial strains, or in our methods for mutant generation. So all the results we had until this realization were suddenly deemed erroneous.

But there was hope! We ended up running experiments testing system performance using  mutants strains generated successfully by a former 109 section. So my lab partner Alyssa and I picked 2 of these mutant strains at random and set up our experiments.

It turns out our mutants didn't result in system optimization. But that was fine! There was a large amount of class data  to analyze, and I was expecting one mutant strain in particular to definitely improve the system. Guess what: this strain was also unsuccessful in reaching our goal for the module.

So there I sat at the beginning of the long weekend, with large amounts of data demonstrating how we had failed at optimizing the photography system. How was I supposed to base a WHOLE research article on failed results?

Well, it turns out, there are actually whole journals dedicated to experimental failures (Check one of them out!) I had heard people in lab mention these, but up until this weekend, I thought it was a joke. But after actually taking a look at some articles, I understood that presenting failed results could actually be quite beneficial for the scientific community. People can learn from the mistakes of others, and save time by avoiding experiments they know will fail.

Also, presenting failed results is significantly more difficult than writing about expected outcomes. But it is absolutely a very useful skill, as it allows researchers to see their experiments and results in a more objective manner. So even though things didn't go as planned, and we didn't get the results we wanted in Mod 2, we definitely acquired new skills we will need for better scientific writing. And on that note:

Wednesday, November 12, 2014

Multiple Support Beams for Effective Scientific Writing

As a full research article, the module 2 major writing project introduced a series of additional challenges to the scientific writing process. As an article, we were expected to interpret our results in the context of the scientific literature, present the broader significance of our work, and find a unifying story for the experiments. The WRAP presentations, BE Communications Lab, and Agi’s Office Hours helped with different aspects of these challenges.

As an overview of a scientific paper, the WRAP presentation provided critical guidance in how to structure a scientific article. Specifically, it helped me understand where to put specific information about the module as well as how to surround that information to maximize its effectiveness. The most helpful portions of the WRAP presentation were the sample scientific articles which were dissected to show the structure. Understanding such structure greatly illuminated my understanding of scientific writing.

In understanding the unifying story for the experiments, Agi’s Office Hours (including questions I asked in class) were tremendously helpful. Beyond asking guiding questions to help me understand the data, Agi helped me understand the overall story of the module and the unifying thread between experiments. For this module, framing the results was particularly difficult since we were not actually able to optimize the contrast present in the bacterial photography system.

Finally once a full draft of the paper was compiled, the BE Communications lab (specifically Diana Chien) helped me revise the overall focus of the paper and make sure that each section fit in logically with the others. Diana helped me restructure my introduction to fit the actual experimental questions answered by our work, and was thus a tremendously valuable resource in ensuring unity within the overall article.

Overall, the WRAP presentations, BE Communications Lab, and Agi’s Office Hours were all valuable in drafting the module 2 article, especially at different stages of development and I thus plan on continuing to use all three. As an early stage resources, the WRAP presentations helped me understand the theory behind the structure of a good scientific paper. Agi’s Office Hours helped me interpret data and create a unifying story. And the BE Writing Lab helped me polish and tighten the story for maximum effectiveness. I felt significantly more confident writing the Module 2 article and could see how quickly 20.109 is improving my capacity for scientific communication. 

Great Expectations

After submitting my lab report last night, I breathed a big sigh of relief. I had been stressing out long and hard about this paper because throughout the writing process, I kept coming to the conclusion that nothing really worked. Looking at our team's Western blot was depressing, only one of the "mutants" that we selected from the MacConkey agar screen actually had a mutation, and our team's B-gal data for NB486 and NB487 was a magnitude higher than we would have expected it to be. Our numbers were so ridiculous that I excluded them from my own data analysis. It was pretty humiliating to create a figure that had the sole purpose of showing how wrong our data was. After the last module where everything went more or less smoothly, writing this report made me feel angry and disappointed in myself.

I understand that no scientific study is perfect. You have to learn from your mistakes and try again in order to get meaningful results; it's all part of the scientific process. But being the perfectionist that I am, it was hard for me to put down on paper that some of  the experiments we performed simply did not work. I think my disappointment stemmed from the fact that we were doing these experiments in what I considered to be a "fail-safe" environment. I had the mindset that within the walls of our 109 lab, nothing could really go wrong. That's probably why instead of giving me closure, writing this report made me want to do the module all over again. Even after our experiments didn't work, I still pictured 109 as a safe place where things couldn't fail.

Yesterday as I was finishing my report, I came to terms with the fact that just because we are doing these experiments in a classroom setting doesn't mean they are going to work. After all, the whole point of this class is to give us experience working in a realistic lab environment. For our next module, I am going to take this lesson in stride and go into lab with the mindset that if our experiments are successful, then that's great. If not, I just have to dust myself off and try again (shout out to Aaliyah).

Thursday, November 6, 2014

Journal Club Nerves

I really, really don't like giving presentations. I seem to have inherited an attractive trait from my mother that involves my entire face turning red within a minute or two of me addressing an audience of more than two people. You could even call it positive feedback since as soon as I feel myself turning red I get more embarrassed and the redness grows. I have a lot of other unfortunate habits related to public speaking such as speaking incredibly quickly (and I've been told that I already talk unnaturally fast to begin with) and fidgeting with my clothes, but at least I've been able to improve on those with time. The red face, not so much. So needless to say, I was less than thrilled when we were told that 109 involves not one, but two oral presentations.

That unpleasant butterflies-in-stomach feeling only increased the weekend before journal club, as I took notes on the paper I'd chosen and tried not to think about how impossible it was going to be for me to coherently explain all of the interesting work this lab had done. But, the paper was really interesting - it described a new method to screen for gene expression when composing large or complex genetic systems. The project I worked on this summer also involved optimizing synthetic biology, a different aspect of it, but it definitely gave me an appreciation for the kind of research that isn't necessarily proving anything incredibly exciting but can be used to improve the field as a whole. The fact that I was actually intrigued by the work presented in the paper made the act of relaying this information to a group of peers a bit less terrifying. Also, I was really pleased when I realized that being in the smaller lab section meant I only had to stand in front of seven people (plus the teaching staff, but that was unavoidable).

Overall, I think it went better than I expected. I still got red, and I still spoke a little too fast - I cut off a solid minute from when I timed myself practicing to when I presented to the class - but I managed to get the general gist of the paper across without having a panic attack, so I'd call that a success. In the future I'll keep working on improving my bad habits, and I also want to do a better job of synthesizing the information presented by other people as they speak so that I can contribute to the Q+A more. 

Wednesday, November 5, 2014

Pre-Mod 2 Assignment

I plan on starting my Mod 2 assignment later today, I'm nervous already. I wasn't as familiar with the material and scientific background that we applied on this module, and since I had trouble writing the first paper, I worry that the lack of background knowledge will make this paper even harder to write than the first one. It's safe to say, these scientific papers stress me out, also science reports are definitely not my strength in science, in fact, writing has never been my strong suit, I'm pretty bad at words, but such is life.

In this module, it was interesting for me to see Jess, my lab partner's, interest and passion for circuitry and larger scale biology that I had never really been interested in. I'm glad that I got to work with Jess in this module because she definitely taught me and explained things to me that I probably would not have asked about had she not offered up her knowledge. It was nice that I saw first hand learning how learning from my peer could help in ways that a teaching staff could not, simply because they have more things to do than sit next to me and repeat everything four times when I don't understand it the first three times.

In regards to the journal club presentations that we did this module, I found them pretty interesting, the parts I could understand at least. I have trouble synthesizing information that quickly and following along with a presentation if they dive into the specifics too quickly because then I'm just lost and everything flies over my head. But then again this was also good practice in trying to understand and interpret data that I have not had time to analyze myself, because that certainly is also an important skill in science and engineering and just life in general. Public speaking is not my favorite thing in the world, which I think was apparent from my presentation (jump back to my problem with words), but I know that speaking in front of people is inevitable and something I'm going to need to get used to, no matter what field I end up in.

Before and after the fact, its really easy to see how much 109 is helpful in the long run, but whilst working on an assignment, thats another story.

Tuesday, November 4, 2014

Some Thoughts Following Journal Club!

So last Thursday, we completed one of the most exciting parts of 20.109: Journal Club!

It was a good experience. I've done some presentations for science competitions in the past, but they've mostly been for a single audience, and not based on research done by others. For this journal club, we presented research projects somehow correlated to signaling systems to our lab class.

Here’s the paper that I discussed, about constructing a more complex genetic circuit to detect image edges: http://www.ncbi.nlm.nih.gov/pubmed/19563759.
When making the slides, what concerned me about preparing the visuals was the content that could be cohesively covered within the time limitation. Initially, I included a ton of graphs and differential equations explaining the mathematical models that were developed in the paper. The complexity of the mathematical equations took a long time to explain properly; when I finally got around to timing my practice presentations, I kept going beyond the time limit by a few minutes. And that was by talking extremely quickly. In the end, I decided to focus on highlighting the theories and physical circuit construction over the mathematical/theoretical aspects, since it seemed more associated with what we've been learning during Module 2. As someone who enjoys visual art, the slide designing was fun to do.
My thoughts sometimes process at a different rate than my voice, so what comes out can be an incoherent jumble of words. What I expected was something along the lines of this (time stamp at 3:36, https://www.youtube.com/watch?v=4gXfdzs-S9Y, from Avatar the Last Airbender). 
What surprised me most was how the actual delivery went by a little better than anticipated. It was kind of like a positive feedback system, where input = power point slide, output = words that led to the next slide through positive regulation (shoutout to 20.320 here).

(from http://pespmc1.vub.ac.be/feedback.html)
After practicing a few times, and becoming more familiar with slide contents, making a cohesive presentation became easier; it was certainly better than memorizing a word for word script. I think I could have fit in some of the mathematical modeling, since I realized that I had some time left after reaching the discussion aspect of the presentation. I was also somewhat worried about the questions following the presentation; but I realized that regardless of knowing the correct answer, the most important part of having this aspect was the learning process for both the audience and the presenter. What things should we, as readers, consider when looking at research papers? What are some important take home conclusions should the reader draw, and what are some possible limitations not covered in the paper discussions? The questions that were asked by fellow 20.109 peers and staff helped me consider alternative perspectives on the research I presented about, which is something really great about having Journal Club.
Now that that’s over with (along with the second 20.320 exam, which was today), off to take a quick nap, and then get to work on the module 2 report!

Monday, November 3, 2014

Biological Engineering is Witchcraft

(I have a title now!!!)

Yes, I said it: witchcraft. But then I realize MIT, and magic is just possible here.

Coming here, I can confidently say that I’ve looked at everyday things differently. I think about heat transfer when things melt, energy transferred through friction to erase, where I can sit on a table to minimize torque, et cetera; this developed by the end of my sophomore fall with 20.110 (Thermo). Hmm, now that I think more about it, it all came from Professor Griffith lectures about ice cream crystal thermodynamics and honey’s medicinal properties. What can I say… food speaks to me.

This second module has had a similar effect on how I view the world. How? The possibility of manipulating normal cell processes for desired products (purified extracts, scents, even photography) astounds me! It never occurred to me that a single cell could be 2+ LEGO®  pieces; I always thought of it being just one piece. We can change the color or shape of several pieces giving us something aesthetically pleasing and/or functional -- or regrettably something that will fall apart. It’s nice to know that it’s possible to engineer biological systems, but at the same time it’s quite irritating we don’t have one universal design to rule them all. We’re still in the stage where we need to devote countless hours and energy, troubleshoot and debug many a time for one confident system.  

In the end, it’s comforting that we will soon have the confidence to tap into a repertoire of efficient E. coli systems for [insert something awe-inspiring] and, with just an overnight incubation, harvest our intended product in surplus without much effort. By that time, I’ll be an old, crusty man thinking about how wonderful it is that we can bio engineer everything now -- but most importantly its implications on food, such as how wonderful my lobster tastes because of a certain rare extract in my butter derived from cell systems.

Gifs from Big Bang Theory and Easy A (please talk to me about them)

Sunday, November 2, 2014

Public Speaking is a Thrill!

I had a brain fart. It was terrifying. Thirty minutes before my turn to present, I looked down at my notes, only to realize that I had entirely forgotten what the research was about (*slight exaggeration*). It seemed like I couldn’t make any sense of what the project was or what the conclusions were again. My mind was going blank. It was as if a subconscious part of me was telling me to stop over-thinking, avoid the unnecessary stressing, and calm my thoughts down. After all, I had read the research article multiple times and pored over all the minute details. I had rehearsed the PowerPoint presentation. And I had anticipated potential questions that might have been asked and thought of about insightful ways to answers them. I was certainly ready.

For me personally, the fear right before a big speech or presentation is what drives my enjoyment in the art of public speaking. Despite having many experiences confronting large audiences, I still get the jitters and uncomfortable palpitations, where I can hear and feel my heart trying to jump out of my chest. I am prone to the anxious anticipation that slowly escalates as it gets closer and closer to my turn. And then I make the realization that I’ve reached the point of no return once I’m standing at the podium. But the trick is to be confident; to make it seem to the audience that you are the expert of your topic. Though my hands were shaking, my face and voice exuded confidence. I smiled and made direct eye contact. The nerves slowly disappeared the longer that I kept talking.

(Funny side note: I had to keep reminding myself to use “they” instead of “we” when talking about the project, since I didn’t actually take part in any of the research…)

Surprisingly, when the Q&A began, I was actually able to come up with answers based on the knowledge that I had accrued from preparing for the journal club presentation. It felt great to know that I could provide the answers to the questions that my peers were curious about. Occasionally, I wouldn’t know how to respond, but the best I could do was provide my most reasonable conclusion based on what I did know. It was all in all a great learning experience.

These feelings all aggregate into the reason why I enjoy public speaking so much. It's a way for me to challenge and place myself outside of my comfort zone. And I know that the more I do it, the better I will get.