Saturday, May 14, 2016

Why do I always think the words “suggested” and “possible” imply “optional”?

So, technically, they do. But it always evades me that an assignment being “suggested” is like hearing “I suggest you don’t leave your dog’s crap on my lawn.” Technically it’s optional, but… you also might end up staring at flaming dog poop at some point in the near future questioning at what point your life took this turn. Here’s to hoping my blog posts actually satisfied the suggested topics and weren’t just humorous sentences that left the instructors wondering, “Okay but where’s the actual assignment?”

I’ve also learned to triple check due dates. Just because you swear everyone has said “5 pm,” it’s equally likely everything is due at 11 am and you’re going to be the sad individual copying and pasting things that were done days ago into a box at 4 pm hoping you don’t end up staring at flaming dog poop in a week questioning the meaning of life.

My internal dialogue

Fairly often, I find myself thinking back to the saying “time flies,” but not just when you’re having fun. Judging from the number of times I’ve heard things along the lines of “those four years are just gonna fly by,” I think we can all agree that if we could take the derivate of time, its second derivative would be positive. Not to beat sayings we’ve all heard before to death, but it’s like we’re on a bus going downhill and the brakes don’t work and all of a sudden there’s no such thing as friction and the road is life and welcome to the struggle bus.

Sometimes I take a moment to admire the beauty of it.

Sometimes I pause, take a breath, and just stand there thinking about the game it feels like life is playing with us. Don’t get me wrong, I do not complain about the going being rough or having too much work. I know what I signed up; we all do. We wouldn’t be here if we hadn’t made an active choice to do so. But I bemusedly contemplate my outlook on life, how I desperately cling to the thought “next week will be better” or “these two weeks are tough but it’ll get lighter soon,” and I think a lot of us feel that way. Or when that moment to breathe finally comes, we find ourselves scared to actually relax.


I guess I should be frightened by the realization that this is probably never going to go away, but the truth is I don’t want it to. Life would be boring otherwise, at least for me. These blog posts are worth maybe 1% of my final grade, but there’s something strangely relaxing, pleasantly calm, about sitting down and having an excuse to get my thoughts together. Not “how am I laying this essay/paper/report out” thoughts, but straight up “what am I actually thinking” thoughts. It’s easy to get lost in your head but it’s also so easy to lose yourself in your head, to forget you are a person who exists in there and have your own thoughts and desires and needs and wishes. It’s so easy to forget how valuable you are as a person, that you’re more than all the assignments you have to do, more than that list on your calendar of things you need to accomplish today.

And even though I wrote 95% of this three or four weeks ago, it’s no less relevant now than it was when I sat there for two hours procrastinating on a Tuesday night. Bring it on, life. Although in a week I hope to be staring at a flaming grill, I’ll take whatever is thrown at me in stride, as I have and as I always will. And maybe I’ll learn to actually pay closer attention to not only the due dates, but also the times.  

Some things get better, some things never change

“Huh, journal club?” I remember thinking.

“What in the world is a journal club?”

I bemusedly considered the similarity between the words “journal club” and “babysitters’ club” – I vaguely recalled that might have been a book series I had never read not intended to read.

Fast forward a little bit to me thinking, “Oh, public speaking? That’s totally fine!” And no, that wasn’t sarcasm – I genuinely have never really minded public speaking, although I don’t necessarily reallyyy like it. “How hard could this be?”

It was not the public speaking that was difficult, nope, it was finding time to prepare. In my defense, I got stuck with my presentation day, and the week I did my presentation was absolutely jammed with assignments. Going into it I knew I wasn’t prepared well enough, but alas, what could I do? I had put as much time as I could into making my slides flow with the points I wanted to hit, I added an animation here and there, and I practiced… once.

Oh my Jesus, I thought, this is not going to end well. But it didn’t end terribly, and in the end, I was really pleasantly surprised by how fairly I felt I had been graded. However, I wanted a second chance. I needed a second chance. I wanted to prove I could do it better. I eagerly awaited the final assignment, the research proposal, and when it came around, I discovered that – some things change, others don’t.

I had expected to have more time to work on the presentation, but even though I objectively did have more time, somehow it got lost (in the research, I’m 98% sure) and I ended up feeling the same sense of foreboding and “I wish I had more time to prepare.” Luckily, I practiced more than just once, which truly paid off, but I think there was a much bigger factor leading to my improved presentation performance – I realized how to make presentation slides.

Although my questionable allocation of time may not have changed much – I still spent way too much time deciding on how to lay out figures and pictures and too little practicing – my preparation was drastically better because I realized you need to figure out what you’re saying first.

I know – surprise!!!

You’d think it’s common sense, but I find that what is common about common sense is how commonly we entirely forget it exists.

Now, this might not work for everyone, but writing down what you’re saying before making your slides is the ultimate time-saver and the best way to prepare. Your slides are there to supplement what you’re saying, not to guide your speech. You’re presenting an idea with the help of slides – not presenting slides with the help of an idea. Having first written out a speech and made slides to supplement it, I was able to go into my presentation feeling confident in what I was going to say and not feeling like I relied on the slides to guide me. When I realized just how much this strategy had helped me, I almost wanted to look at my slides and go “Who’s the boss now????”

But PowerPoint is still intimidating and the understanding of how its themes work still evades me, so maybe I’ll hold off on antagonizing Microsoft Office for a little while longer. 

Sometimes what you discover about yourself is neither particularly new nor surprising

- and a heartfelt thank you to Bremy for being an amazing lab partner.

~ ~ ~

I have this really bad habit of leaving things partially undone, in this sad state of 90% completion, for all eternity. Like for example, blog posts. I have no less than 4 blog post drafts that only require a final pass through, and of course, I waited until the very last day to finalize my last couple of blogs and post them. And, of course, in classic me fashion, I decided to sit down and just start a new one from scratch.

The same thing happened throughout the whole semester… I sit down and plan things out, get a ton of pieces done, and then just kind of push it aside at the final step when all the pieces just need to be glued together. Now, although technically this is something I learned about myself this semester, it’s also neither new nor surprising – my mom has been telling me this my whole life. The number of projects I’ve started only to lose interest right before completing them… It’s enough to drive just about any mother insane. So Leslie – I swear I wasn’t lying when I turned in homework late and said it was because it was almost finished just scattered in pieces through a few Word documents on my computer!

A questionably accurate representation of what Leslie saw at one point during the semester

Now, this ties in really well to another character trait that I learned some new things about – my teamwork abilities. In this case, I myself have worried on many occasions that I may never be able to be a good team player because I’ve always tended towards the alpha side in situations requiring cooperation. As you can imagine, this, when combined with the tendency for my attention to fluctuate, doesn’t make for a good teamwork situation… Enter: Bremy!

Bremy and I were both skeptical of each other, to be honest. Unlike most other groups, we just kinda… happened. I was the odd one out and he happened to join our section on the second day. But it was like a match made in lab partner heaven. While I oscillate between crazy, hyper, psycho cat thing and demure, is-she-still-alive blob, Bremy is a consistently calm, determined, motivated workhorse chugging along – so we perfectly filled in all the roles a good partnership needs. I had the excitement to get the ball rolling and brighten the day, and he could push me forward when my excitement waned. He never lost his patience when I would pull up ten different Word documents with thoughts all over the place as he pulled up one well-organized file. I never stopped annoying him with my outbursts of “Oh! I just had an idea!!” And I never tired of sighing “Bremy, let me take that paragraph and rephrase it into a sentence,” and luckily, he never had any hard feelings!

Once a high school newspaper editor, always an annoying "wait I can rephrase that" connoisseur 

So in the end, although when it came to learning about myself I didn’t discover mind-blowing new abilities or crazy hidden weaknesses, I did discover the magic of finding a work partner with whom you just… work. I definitely gained a brand-new appreciation for working with another person, something I had never been able to do well in the past, and I finally found myself being able to whole-heartedly trust the person I was working with. For once, I don't agree with these pie charts for haterz: 

20.109 - dispelling every preconception you've ever had and making you question the fabric of reality

20.109 definitely taught me more about the real world than any other class I have taken ever.  Not only was it the most useful and practical class I have taken, it was one that made me finally understand what biological engineering really is. Trying to come up with a topic for the research proposal presentation was the most interesting yet challenging task we had yet faced. There were just so many possibilities, so many interesting topics, and the fact that the sky was the limit when it came to fields of science that bioengineering can be applied to made it so difficult to narrow it down.  No seriously you can go into neuroscience, molecular biology, bioinstrumentation, medicine, biochemistry, biomechanics, ecology, genetics, the list goes on and on. And that's the best part! Now when someone asks me what bioengineering is, I know it can be anything I want it to be, there is no set one answer that encompasses all the possibilities. I truly have to say thank you to all of the instructors for making me confident in being a course 20, and making me love my major. 

Thank you for a great semester, all the time and hard work you guys put into engineering the modules and fixing all the things that went wrong after hours, all the weekend office hours for hours on end with endless snacks, and most importantly for helping me improve my skills as a researcher so drastically in such a short amount of time.  I couldn’t have asked for a better experience, and 20.109 will truly be missed (even Friday afternoon labs :D).

Evolution of my Writing Experience in 20.109

Mod 1 Protein Summary:

  • I write too much
  • Why does everything have to be in bullets?
  • Seems kind of choppy
  • What on earth am I supposed to say about this?
  • At least I have my partner
  • Promised myself I would revise on the flight home
  • I didn't necessarily lie to myself
  • But we still did most of the revision the night before
  • Sorry for the somewhat sassy revision cover letter

Mod 2 Research Article:

Now I was all on my own. There was no Nicole to help me with some miraculous new idea. Not only that, but we would not be given a revision step with feedback. Also, my thoughts actually had to be written down in concise sentences, which was still a skill I didn't possess. I spent many hours writing my report, finding peace and quiet either at Stata, the Stud, or one of the mini lounges in four east. I spent over 32 hours working on that report. The funny part is that I still don't have any closure: Nicole and I received each other's graded articles and have yet to exchange them.

Mod 3 Mini Report:


Money on my mind...

Of all the times I have been asked to come up with the kookiest, craziest, most ambitious research project I could think of, I've never before had the task of constructing it into a grant proposal. In Module 3, we were asked to go beyond the bounds of our imagination, while maintaining a real-world-applicable structure. With time and resource constraints to be considered, the kookiest science I could come up with became a lot more real.

Because now we're training to be real live biological engineers. And it's not just the money that was on my mind. Going through 20.109, especially focussing on the grant proposal in Module 3, has taught me that research is more than just what happens in the lab. There is no lab fairy to magically replenish our supplies, and no matter the outcome of the project, our science must have relevance to the wider scientific (and human!) community. The world informs our science, and our science informs the world. And no matter where I go, or what I do, the lesson of this consideration will remain with me throughout my biological engineering life.

Thank You For Everything

Yes, I'm going to write a completely cheesy post. My roommate would say that I'm being a total "cheese sandwich." However, I think a few very special people deserve my immense gratitude.

Dear Leslie,
Thank you so much for being the main person I could go to for any questions. I swear, we have these long email chains that mainly consisted of me frantically asking for advice or clarification on a major assignment. You always took the time to ease my anxiety as soon as you could. I know that looking over slides I sent you or some of my questions took time away from your family. I know how valuable that time must be for you and I'm very grateful for that. Thank you for making yourself so approachable and such a great professor to work with!

Dear Noreen,
Thank you for being such a positive force. Every morning you would always smile and say good to everyone who walked into class. You'd ask how our week had been and if there was anything going on the next weekend. Although someone might consider those things small or just being polite, those actions can really change a person's day from a bad start to a good one. Thank you for listening to my embarrassing story when I was worried about the journal club presentation and sharing your own. Thank you for coming in on a Sunday so I could make up the protein purification lab. You're truly a kind person!

Dear Maxine,
Thank you for going the extra mile. On multiple occasions I had heard you had prepared something for our lab the next day or was told "Ask Maxine, she's the expert on this." There were many times during lab that I would be struggling with a calculation and all I would have to say is "Hey Maxine, could you help me with this?" and you'd come over, check our calculation, double check your calculation, and offer me any help you could. Thank you for suggesting research articles for possible explanations in our Mod 3 mini report. Thank you for being supportive and taking the extra step to help me understand something better.

To you three lovely ladies, thank you for all the time and effort you have dedicated to this course and to our success. I hope you all have a relaxing and amazing summer! Perhaps I might see you around?

Best Regards,
Liz Strand  

20.109 Commencement

In three weeks, the MIT class of 2016's Commencement activities will begin. As of two days ago, the Spring 2016 20.109 class came to end. Although we don't receive diplomas or get to dress up in fancy caps and gowns, there exists the same sense of achievement in finishing something that compelled its students to learn and do so much. We wrote protein engineering summaries, gave elevator pitches, created scientific articles from scratch, presented on journal articles, and gave mock-grant proposal presentations. There were long hours and late nights, a bit of sweat (figuratively) and tears (maybe not so figuratively), and tons of Q&A email threads. The teaching stuff was with us every step of the way, whether it was remotely to answer questions that we had about our assignments, or physically in the form of project office hours and the open-door policy.

, thank you for promptly responding to every single one of my 103929 questions about assignments that I had. And for letting me spend an entire 5 hours in your office when I took a late day for my Mod 2 report.

Noreen, thank you for being such an understanding lecturer and working with me when I had that absence in the beginning the semester. And for having my back during TR journal club presentations while I tried to keep my compsure. And for assuaging my concerns about my Mod 2 report (even though you never gave me your preliminary comments on it haha).

Maxine, thank you for being a ray of positivity and knowledge in the lab. You had answers for almost every question we came up with (and quickly Google'd the answers you didn't already know) and helped me with those flow cytometry normalization formulas when I was being a complete Excel rookie.

Diana, thanks for being such a great resource for us. Each of your workshops taught us material that we could not only apply in lab, but for communication in general. Also, your sense of style is cool!

Leona, thank you for bestowing upon us just a piece of your immense knowledge on bioengineering and journal articles. I enjoyed learning about Jeggo and all the effort you put into those sound effects in your lecture slide animations *pow*

Belcher, thank you for being such a cool human being (*casually mention: you worked in the black pearl industry, founded several companies, and are the brain behind the phage-plated electrodes). I am so proud to be your advisee.

Jifa, (he may not see this but) thank you for being such a great help during the times we crashed your lab with our probably-trivial-seeming cathode construction projects. You were always patient and ready to assist at a moment's notice. We almost took for granted all the time that it took for you to discharge and charge each of our coin batteries for 10 hours each..

Liz's Declassified 20.109 Survival Guide

Now that we've all successfully completed and survived 20.109, I feel that we should impart our wisdom to the upcoming class next semester. Here are my tips to help you survive 20.109:

Tip 211: Get a jump start on the next major assignment

This is something we all tell ourselves we're going to do before each assignment. Do me a favor and don't just tell yourself, actually do it. Take advantage of the homework assignments; if you do a thorough job, you'll be able to use them to construct most of your major assignment. Trust me, you'll be one of the few that gets a full night's rest the night before the assignment is due and you can walk into class the next day looking like this:

Tip 109: But if you're a procrastinator, invest in some caffeine

You're going to need the boost when you're hard at work the night before the big assignment is due. However, if the procrastination lifestyle works best for you, who are we to judge? Warning: consume in moderation 

Tip 856: Makes sure to always check the wiki

The wiki contains all of the due dates for assignments, quiz dates, and protocols for every lab day. Make sure you take the time to look over the wiki so you're not caught off guard

Tip 11: If you get unexpected results, don't freak out

We do real science in this class. Every result has a some sort of significance to it, even if your results indicated nothing changed/ everything became nonfunctional. Just because your project wasn't the best, doesn't mean you don't have something to contribute. 

Tip 673: Have a problem? Don't be afraid to ask for help

The professors for this class are phenomenal. Ask questions in class, send an email, go to office hours. They will try their best to answer your question as soon as possible and answer it thoroughly. They are very patient and genuinely want to see you succeed. Don't be afraid to say something!

Tip 900: Take the time to talk to other groups

Over the semester, you will be seeing the same group of people for a few hours every week. Don't make the mistake of getting through the whole course and not knowing anyone other than your lab partner. Great friendships are waiting to be made!

Tip 435: Be prepared for a lot of research and writing 

This class is a CIM and is listed as a 15 credit class. This class will consume over 15 hours of your time each week. You will have over fifty tabs of research articles on your internet browser at any given time and you will spend hours trying to make your writing sound more 'scientific'. It takes hard work and determination to be a 20.109 geek.

Tip 20109: Relax, breathe, and enjoy the class 

This semester will go by quickly and before you know it, it'll all be over. Take some time to enjoy the new skills you'll be learning and the people you're working with. 

With these tips, you should be all set to survive the next semester! Good luck!

To Be Your Own PI (kind of)

My idea for an addition to 20.109 isn’t so much to replace a module with something else but more like an addendum for after the class. I think the notion of getting more experience in experimental design was touched upon during our class wide feedback, and is something I also wish there was more of in 20.109. The research grant proposal was a really awesome way of getting us to think more creatively about the stuff we had been exposed to in the class, but because it wasn’t actually going to be ever acted upon, I think there were some parts of the experimental design that I kind of brushed off. But more importantly, my project is something that I think would have been really cool to pursue in an actual lab setting (and even emailed the author of the base paper after the end of the project). I’ve heard rumors about being able to take 380 in the fall and pursue the project in the spring, and I think a smaller scale version could be done with 109. Maybe in a UROP type setting that allows us to use the resources in the 109 teaching lab in the semester following the class. Because part of our assignment was to incorporate techniques used in 20.109, I think creating a UROP to actually do the experiments could be feasible within the equipment available in the teaching lab. 

Thanks to 20.109 we might have some idea what we're doing.
Given that our projects were on a much smaller scale than 380 projects, I think a UROP setting could be appropriate as opposed to a full class. Obviously, a proposition like this would require much more detailed plans for the students beyond what was done for the research proposal, but I think it would allow students to get much more invested in their research proposal projects as well as given them a taste of doing research on a topic entirely of their choosing instead of being dropped into a predefined UROP. I was lucky enough to go to a faculty dinner with Professor Belcher yesterday, and she was talking about how exciting it is to be your own boss and to really think and develop the ideas that excite you. I think a post-20.109 UROP set up like this would be an excellent opportunity for students to try that out.

Too Much of A Good Thing...

I came into 20.109 feeling pretty confident about my scientific communication abilities. I had been doing science fairs for years and was pretty used to poster-style presentations. I was honestly super na├»ve about the other forms of scientific communication and I’m so glad I got exposure to them through 20.109. I think with both verbal and written communication, I struggled (and continue to struggle, but less so) with including way more than is necessary. In our first min-presentation in Mod 1, I had a hard time cutting down all the stuff we did into 3 minutes and in the journal club I was rushing through the whole presentation because I had just included way too many things for a 10-minute presentation. I never thought I would feel like a 10-minute solo presentation would feel short, but at the end I was left wanting much more time to speak. 

But this was a product of my own doing, I definitely could have presented the contents of that paper really well within those 10 minutes had I just omitted some of the repetitive and unnecessary stuff. Which is what I tried to keep in mind for the grant proposal presentation. Too much detail was definitely a bad thing. I was constantly trying to strike the right balance between actually providing the needed information but not going overboard in the details that I included. It felt a little bit like the process of methods writing, which is still an area that I need to get much better at (I have this compelling desire to include every single step because I’m just constantly worried that the reader won’t be able to actually discern what the experiment was). I know writing methods sections are super boring and I’m sure are super boring for the teaching staff to read, but I think it might be beneficial (at least for people like me) to have one or two more homework assignments that have us write just one subsection of the methods section. It’s a little daunting to do a half of a full module, but I think it’s a skill I need to develop further and that might have been achieved by smaller methods section homeworks spread throughout the semester.

I know they told us 7 posts, but so hard to say goodbye

We spent so much time together, and on the class assignments. This will be deeply missed, I have no idea how to describe this feeling of achievement at the end of the course, mixed with the sadness of departing all the great staff, students, lectures and projects throughout the semester.

What I will miss:

1- The forest seen by my lab partner, Jordan Smith, while I kept my eyes on the trees. Complimentary skills combined and dedicated to the best performance.

2- The supporting space created by the teaching staff in office hours, and the additional office hours around major assignments.

3- The weirdest snacks that I have ever seen...

4- The students that we spent so much time with.

5- The interactions with the teaching staff that taught me an insane amount of knowledge and trained so many useful skills.

6- Our lab bench, as team orange, now the color orange sends a chill down my spine since this is over forever.

7- The list can keep going on, but I encourage the entire class to add more and more thoughts to the list. I am sure that the course staff will find use and feedback with this kind of information!

In the end, the people will always stay in heart and thoughts, and the skills will always be remembered and improved with the foundation established in this class. Best of luck everyone, always.

Though hopes to see you around,
Saleem Aldajani

Juiceboxes and Communication

Our meeting with the BE Communications Fellow was super last minute. We didn’t sign up until OH the day before, at which point there weren’t even appointments available in the afternoon of the next day (this was worrisome as our Grant Proposal Presentation was the day after). Thankfully, Maxine was sitting right next to us and offered to email one of the fellows to see if he could take a meeting with us.

The next day, me and Pearl met up ready for the meeting. I was kind of anxious because we hadn’t really practiced our presentation yet and there were even a couple of slides missing and I honestly just didn’t know what would happen at this meeting. But Diana invited us into her office to grab some snacks before our BE Fellow showed up, and juice boxes have a very calming effect.
Basically me.

Finally, our meeting with Bill started and it was a little bit of a whirlwind. We tried presenting for the first time together, and it went surprisingly smoothly. He had really great feedback for us afterwards, both regarding slide content and for our overall grant proposal. I lost my anxiety as soon as we actually started talking to him (equipped well with my juice box). We managed to talk for almost 45 minutes about our project, and I felt a lot better about it afterwards. Presenting the project to someone a little removed from the 20.109 bubble was really beneficial, and I wish we had gone sooner. I think adding a BE Communications requirement earlier in the semester would be super helpful for future students.

Overall Reflections As A Non-Course 20

Overall Reflections As A Non-Course 20

This class was definitely one of those classes that change your life. I found it more rewarding as a CI-M than the other CI-M that I took for course 10. The standards were higher, the class was more structured, and the assignments were super intense. If you ever have to do writing and presentations in other classes, you'd nail them after 20.109 skills. I experienced this first-handedly.

In terms of the science and how it taught, it is absolutely phenomenal. I felt no problems with my limited background and the lectures and pre-labs were more than enough to understand all of the material. I was caught up to speed very quickly and was able to perform with no barriers.

The pace was really fast, but it was fun. I really enjoyed it, and you also develop a great relationship with your lab partner. Lab periods become better and better as the 20.109 family gets closer and closer. The instructors and labs involved do a lot of work behind the scenes to make sure we are successful, whether it was redo-ing failed experiments, or doing the time-sensitive parts of experimentation outside of lab periods. That is something I do not commonly see in other classes.

These may be unique reflections since not many non-course 20s take this course. So I thought if I focused a post on it, it might spark a discussion that can potentially make constructive change. Please share your thoughts, and I'll try to update this with more content– as I am still processing all the skills I learned, all the feedback I received, and how to use them to improve my performance and enhance my preparation for what is yet to come.

-Saleem Aldajani

Thank You

All in all, 20.109 was a great experience. It had its ups and downs for sure, but the lessons it taught me were invaluable and I can't thank the teaching staff and my partner enough. From quick replies to emails, to giving us so much food (#figandolivecrackers), to crazy amounts of office hours, to coming in on weekends to fix our failed experiments, you guys were amazing. I’m so grateful to you guys for giving us so much of your time and energy. It’s part of what made this class such a good experience and part of what made me want to do well in it and improve as a scientist and communicator. 

I really appreciate the feeling of camaraderie that you all had with the students as well – it always felt like we were on the same side, whether it be about deadlines, grades, or even experiments. This is the kind of relationship I used to have with my teachers in high school, and I felt it was really missing after coming to college. Being one student out of a lecture hall of 150 didn’t really help. But I’m very happy to have found it again in 20.109 and I will really miss everything about this class. 

Learned More 7.05 In 20.109 Than In 7.05

Learned More 7.05 In 20.109 Than In 7.05

This was a thought I wanted to share since the beginning of the semester. I had limited biology background since I only took 7.012 three years ago, and was in 7.05 and 20.109. In 7.05, the concepts was taught so ambigously and was not clear at all. 20.109 it was all made clear and it was learned way faster and more efficiently in less lectures. Here is the list of topics that I think were the most prominent.

1- Binding Affinity & Cooperativity
In module 1.

2- Protein Purification
In module 1 and 2.

In module 2.

5- GEL Electrophoresis
In module 1 and 2.

6- The Central Dogma
In all modules tbh.

It would be great if other students who took both classes share their thoughts on this. I'm not sure if it's just me or if this is actually true. Please think about it and let me know!

Lessons learned

I learned many important things from 20.109. If I were to make a (short) list, it would look something like this:

1. Slide titles are actually important. I used to pay no attention to the way I titled my slides (usually a generic Background and Results would do it) but Diana and the rest of the amazing BE Comm lab showed me, well actually, there is a right way!

2. Figure captions vs Results vs Discussion: After many iterations of research reports, I think I can proudly say I can differentiate between these three. Considering how confused I was in the beginning of the semester, I think this is pretty incredible.

3. Tying results back to the "big picture": Coming into 109, I was not used to thinking about how my results would affect the overall issue at hand. Maybe because in a UROP, you have your supervisor to show you those connections, so you yourself don't have to think about them as much. Or maybe it was just me. In any case, at first I found it difficult to make more out of my results than what they show. However, 109 showed me how feasible, and in fact how fun this process is. The "big picture" connect your results to whatever problem you're trying to solve, so it is actually pretty important, and pretty exciting.

4. If you don't know the answer, someone will ask you about it. General rule of thumb. I realized that, while giving a presentation, if I (knowingly or not) evade a topic, it's because I don't know much about it to talk about it. Therefore, the audience does not have that information, and so they ask about it. And then it's awkward. This is a pretty scary cycle, but now that I know how it works, avoiding it should be pretty simple.

This is definitely not an exhaustive list of all the things I've learned at 20.109. Among all of the classes I've taken at MIT, this one has definitely taught me the most. About bioengineering, about communication, and about how to do science in general. I feel so much more confident and excited about this field now and it's great. Thank you everyone, it's been a great journey!

Nanoplatelets Templated and Stabilized by Phage

Nanoplatelets Templated and Stabilized by Phage

I already wrote four posts, but I realized I did not write about the funnest part in the course– the research proposal presentation. This one of main reasons to petition this course instead of 7.02 for 10B. A proposal from scratch with no particular prompt is a skill that is essential to success in science and engineering. Teamwork and team presenting is also important for success in any career one may pursue. I really wanted to rap/spoken word the entire presentation, but I really did not want to fail this course lol. So, I decided to do it here. I'll try to attach the ppt here, but its 30MB from all the videos, figures, and backup slides. I hope this makes it more clear to those who attended the talk, and present it to those who didn't! Well, here it goes.

Perovskites were discovered in the 1970s,
But listen carefully please,
These chemical chamellions can seize
More than half the elements eas-
ily, into its lattices, more importantly,
Hybrid organohalid perovskites recently
Have been reported to unbelievably,
Outperform current options and can be made easily,
A droplet of precursor to toluene and instantly,
They crystallize and emit at any frequency,
Two-dimensional thickness control with quantum confining, you see
And constituent control with easy chemistry,
Giving the tunability to cover the entire visible spectrum conviently,
White light for solid-state lighting, and remarkable tunability
For optolectrics lasers, LED, vis-a-vis,
The bulk crystal counterpart getting better for photovoltaics increasingly!

Enough perovskite detail, we are almost going off-topic here,
This can solve a deeply ingrained problem, it is clear
That current lighting technologies are a serious fear
Either resource-intensive or inefficient low tier,
But these 2D nanoplatelets can dissapear
From the moisture in your breath!
Heat, irradiation, bulk crystallization can also cause their death,

So we thought of using biology for the sake,
Of stabilizing these materials to make,
A solution for commercial uptake,
Engineer bateriophage so they don't break
In the solvents we need, then put in a plaque
Forming assay to make sure they can still infect,
Then we use a library to detect,
Phage that can collect,
The materials that we suspect,
To stabilize the nanoplatelets from we expect,
We biominerize to assemble and grow crystals then inspect,
X-rays that deflect to reflect,
The structures we select,

Then we assemble a scaffold of phage,
That bind polymer and make a cage,
For the nanoplatelets to age slower,
With electron microscopy we can gauge,
Whether we got networks and the crystals that look like a page,
If this can be accomplished, then we can reach a stage,
Where nanoplatelets templated and stabilized by phage,
Can be used in all the applications that we want to engage!

-Saleem Aldajani

The art of communication

One thing that I really appreciated about the communication component of this class was that each module had different assignments and with each one, I felt as though I progressing towards better communication skills.  For module 1, there was little pressure to get the elevator pitch right on the first try since we could film ourselves as many times as we wanted.  Although it was awkward talking to my self out loud in front of my webcam in my room, I didn't feel the same nerves as I would have if I was standing in a room in front of people.  The elevator pitch taught me how to distill what I had done in lab for over a month into just a mere three minutes.  In addition, it taught me to make my research understandable to someone with a general science background.

For module 2, the stakes were higher.  I was in a small room full of people, giving a presentation about a recent research article about a NHEJ mechanism.  Unlike Mod 1, where I could start over everytime I jumbled over my words, for the Journal club presentation there was only one chance.  The most frustrating thing about practicing for the Journal club presentation was that everytime I would jumble over my words, I would want to start over to the beginning again.  The result was me practicing the beginning 5 slides over 10 times and never actually getting to the last few slides.  Also unlike the elevator pitch, for this presentation, we needed to incorporate a Powerpoint.  And the scariest difference from the Mod 1 presentation?  It was the fact that people were going to ask me questions after.  There's always a fear that I won't be able to answer a question and I will just stand in front of the room saying, "Uh......"  But the reality is is that after reading my paper, making the Powerpoint, and writing some form of a script, I knew more about the paper I read than I thought I did.  The journal club presentation went well, even with the few times I accidentally clicked the button to shut off the presentation instead of the button to go to the next slide.

For module 3, the research proposal presentation required the most work.  At this point, we were pretty well-versed in making powerpoints and giving presentations.  After a lot of research to know what kind of project was innovative and feasible, the hardest part about this presentation was figuring out what to include in our presentation and making the progression of the slides clear and logical.  To do this, the BE Communication Lab was very helpful in helping us make sure our slides were not too cluttered and sent the message that we wanted to.

After all these different forms of scientific communication, I can say that while I will still be nervous while giving a presentation, I will no longer be daunted by the idea of having to give a presentation.  After all, I am proud of the work that I have done in this class and I should be proud to tell other people about it.

Research Proposal

Thinking of a novel research idea is a lot harder than I initially thought. There's so much out there, so many papers that have just been published, so many unanswered questions, so many areas for improvement. It didn't feel like it would be extremely difficult to pick an area or a problem and propose something new, that no one else has started work on yet. What my partner and I found, is that it's actually very time-consuming and difficult. In order to get any sense of what's already been found, what is yet to be discovered, what the problems are, we had to read so many papers, summaries, and reviews. Sometimes, after reading a couple papers and then identifying an idea, once we started reading more closely into topics related to that, we found that this topic involved way too much physics and math for either of us to possibly understand. Sometimes, we'd think of an idea, and then after reading a couple papers, realize that someone had already looked into it, and published about it. There's a careful balance between needing enough information in the field to be able to prove that the project is plausible and worth the time, and then choosing a project that isn't already covered by literature. We ended up choosing our topic by drawing from a couple different "Future directions" sections of different papers.

Once we had our research question and were trying to write out an outline for methods, we found ourselves caught between different methods from different papers, conflicted and confused about what would be best for our specific question. Would it be too much to just try each method and see which one worked the best? There were four different ways to synthesize the spider silk scaffold, each focusing on different mechanical properties or biological properties. Extra paper-reading went into each one, to try to figure out which one was the best for us. Ultimately, writing a research proposal is, in my opinion, much more complicated than writing a research paper on data and results that you already have.

(WF) Blue Crew, Best Crew

20.109 has by far been the best and most rewarding class I've taken at MIT (actually, probably ever in my life). This entire post is essentially going to be a shout-out to my lab group (honestly, they deserve it) for being the greatest ever! So at the very beginning of the year, before the semester started, Preksha and I had already decided to be lab partners (lol).

To give some background,  I've known Preksha since day 2 of FPOPs 2k14 (there's an interesting story to how we met, but I digress..). I've known Madi since day 2 of 20.109 (but apparently messaged her back in the day asking for a textbook....that I never bought, awk). But then we all came together in 109. And it was quite an interesting experience. We had many issues with our experiments...not working/giving us results we wanted/expected. Thus, we would often be sitting there very stumped. Thankfully, the great instructors helped us out many, many times. (Thank you guys so so much for everything - re-running our experiments, explaining everything to us, being super positive overall, etc. :)

From our long hours in the stud dealing with our very useless protein (woo I62D!) to the countless hours in office hours to getting microliters and milliliters mixed up to avoiding looking in the flask with the aspirated liquid waste to being the one group with a very odd yellow phage solution to planning out our "ground-breaking" idea and having dinner at Pika, it has been great! Thank you guys for making this class as amazing an experience for me as it was! Don't think it would've been nearly as fun without our shenanigans and mishaps (throwback to throwing away the foil and asking for more in the most indirect way ever haha).
pretty accurate gif of us in class


Notes to Self

Reflecting on my 20.109 learning experience, I realize that the most elucidating part of any lab has been the pre-lab lecture, where the rationale behind every step we take is explained on clearly laid-out slides. Effectively, the pre-lab is like pre-reading for a class, which is something that would be perhaps helpful for other classes as well, and perhaps something I should try next semester. 

Pointers like these are another thing that this class has taught me. While my thoughts about my own study habits are fresh in my mind, I will compile a list of reminders to my future self.


1) Ask questions. As my choreographer always says, it's always better to ask than to not know. And you will be so much happier once you understand what you are doing. Why wait until later to understand when you can understand now?

2) Pre-read short readings before lecture. These 5 minutes will be the most productive 5 minutes ever, best done not between the hours of 2am and 9am. You will be primed for the knowledge given to you during class. If time does not permit or your brain does not process, still do the reading after lecture to reinforce. 

3) Summarize what you have done each day in your head or on paper. This way, you will know exactly what you did and why. This allows you to maintain perspective of the big picture and is helpful for understanding the purpose of each step / not being a robot. 

And that is all for now, future self. You might be laughing at the callowness of a past Jacqueline who would write down such seemingly obvious points, but save that laughter for after a few classes, when you manage to do these things.

Science builds science

One of the coolest things I realized while working on our research proposal was how science evolves. As we looked at countless research articles about solar cells and photosynthesis and Photosystem II, we realized a clear evolution of the research over time: each paper contributed to the accumulated knowledge, and each new advancement used this to build up on it.

How cool is this???  We're not simply talking about collaboration among different research groups. We are talking about collaboration amongst generations, where people who do not know each other and perhaps have never met contribute to each other's work. Let me show an example:

How difficult do you think it is to figure out how these researchers purified Photosystem II?
Answer: very.

X et al 2016: PS II was isolated according to previous methods (Y et al 2004).
Y et al 2004: Isolation of PS II was performed as described in Z et al 1990.
Z et al 1990: PS II was isolated using (insert important components here), with F et al. 1986's protocol.

Until you finally find that one paper that dates back to the ice age, good luck figuring out how they actually isolated photosystem II. Spoiler: they used spinach. I want to imagine it looked something like this:

Anyways, back to the original question. As you can see, some guy in the Neolithic age discovered how to purify Photosystem II, and paved the way to incredible research on this protein, ultimately allowing its use as a source of electricity. This is amazing collaboration- not only across peers, but across history. 

Thoughts on the Field

Bioengineering is definitely one of the newer fields, both at MIT and in the scientific community. Consequently, sometimes it feels like it’s still figuring itself out a little.

I feel grape!

One of my previous blog posts was about how bioengineering opens up infinite possibilities for those who want to create something new. That's great. But then it got me thinking: how do you teach a discipline where almost anything is possible and there are very few limitations?

20.109 does a pretty good job of that, I think. We are introduced to some very basic techniques that will probably prove useful in a whole host of future experiments (site-directed mutagenesis, PCR, Western blots, flow cytometry, etc.) and walked through the process of writing a lab report as well as formulating a research proposal. 

Ultimately, though, it seems that each individual experiment requires tailored procedures, sometimes even new ones designed just for that specific experiment. There is always something to learn upon beginning an experiment, and that design and creative process cannot be hard-taught. In addition, each experimental design also rests very much on the background knowledge of the designer. One piece of random knowledge could come in very useful and greatly simplify things. I remember previous professors complaining that their grad students forgot to account for acid-base effects in some experiment. It's events like this that make you wish your brain could be like Google.

But I suppose Google exists for a reason, and that's where lit reviews come in.

Bioengineering seems to me to be organized around a lot of case-studies of successful experiments. I'm not sure if there is any fleshed-out underlying organization of concepts or areas in the field. In physics, for example, there is electromagnetism, classical mechanics, thermodynamics, astrophysics, etc. In bioengineering, there is...E. coli?

Perhaps someday there will be a more laid out curriculum for bioengineering. Or perhaps that's contrary to the idea of exploring all the possibilities, and it's better to just embark on individual experiments.

Directing Evolution

Directing Evolution

What inspired me to take this class was working in the Belcher group since Fall 2013. This vision motivated me to contribute in biological engineering of biological systems in context of real world, impactful applications. I will dedicate this piece to the instructors of this course, and of course Prof. Leona Samson and Prof. Angela Belcher for their devoted efforts to make us successful in this class no matter what. But I will focus on module three since I haven't written anything about it yet in my  blog posts.

I am sorry for the bias,
But this qualified us
To make virus nanowires, plus
Build batteries that discussed
The effect of using gold nanoparticles, smaller than dust
On the specific capacity of these biotemplated batteries, must
I say that I've done this before,
But I just learned more and more,
About what the bioengineers used to do, furthermore,

The writing experience is always a way,
To open doorways that relay,
Science and engineering anyday,
These aren't like essays,
The assays tell you about pathways,
A report about how to use electron diffraction,
For elemental mapping and imaging samples that lay,
Between an electron ray,
And a detector to relay,
Electron density to display,
Giving you resolution to play

To see the nanowires and atomic planes,
Jokes side, an experience that always remains,
In our brains, can you imagine these planes as lanes?
What was beyond imaginations always had these chains,
But using viruses for directed evolution is like controlling a hurricane,
To clean dirty meadows and plains,
Of sand, and sort the grains,
This fuels my veins,
To train with no pain,
For the visions of the reigns,
Of humanity, with one that can rein,
Biological systems to build grains,
Binding molecules forming crystals from atomic plains.

-Saleem Aldajani

Defying the Diffraction Limit for Biology

Defying the Diffraction Limit for Biology

For my journal club presentation I chose an article that uses fluorescence techniques to actually visualize NHEJ, step by step. Not only that, but in a beautiful depiction of a shing shiny phenomena of science. My main take away from the article was that this was a demonstration of defying the diffraction limit to see objects within 100 nanometers. Instead of using optical or electron visualizing techniques that must obey the diffraction law as beams, this method shoots a laser at a sample mounted on prism with full internal reflection. It seemed confusing at first that the laser fully eternally reflects that it can interact with your sample through the prison. Magnificently, I realized that this the laser interacts with the interface layer between the prism and the air surrounding to produce evanescent waves, that decay very quickly. This allows you to see even smaller objects than any imaging technique that are limited by diffraction of beams, defying the diffraction limit.

In the paper I presented they these evanescent waves to excite dyes on ends of DNA breaks so you can watch their fluorescence from a detector as they get closer. You end up knowing that the ends join when you flourescent resonance energy transfer happens between the dye on one break and the dye on another. First of all, I really think that it amazing to see the power of defying the diffraction limit. But that is not where it steps, then you see how the development of such a technique allows you to advance science further in ways that humanity has never explored.

*drops the mic*

-Saleem A. Aldajani

Here are Thank Yous!

Here are Thank Yous!

I wrote this piece reflecting on module two, it was unbelievable. It was definitely challenging, but also very rewarding. These are my real thoughts on my general experience in module two.

It's an opportunity that cannot be compared,
I had no idea how DNA was repaired,
And thought that I was not prepared,

The labs began with a flu,
But time just flew,
Counting the cells in brain tissue,
Staining the dead ones blue,
From desiging slides to peer review,
So little time, so much due,
I thought it's amazing
How about you?
And to the instructors who
Saved our experiments, thank you.
Western blot, how to do
Analysis on proteins too
Flow cytomertry, is how to
use laser to view
Shining cells going through
A tube, to quantify tru-
ly the efficiency of DNA repair, using a breakthrough,
Developed by the Samson lab, another thanks to you

Yours truly,
Saleem A. Aldajani

Friday, May 13, 2016

109 vs. UROP

Taking 20.109 made me drop my UROP. I'm still not quite sure if this is a good thing or a bad thing. Part of it was just the time. After spending 8 hours a week in lab for class, it was pretty hard to motivate myself to head into the Whitehead for even more lab time. I learned not to plan times for experiments on Wednesdays and Fridays.

When I've just gotten home from 109, and remember that I need to go back and check on something at my UROP

It felt like the experiments went by so much faster in 109, mostly because our wonderful lab instructors did so much behind-the-scenes work. But when running Northerns for my UROP, I actually had to do all the washes and strips and probing and more washes. Things that took us maybe 2 hours combined between a Friday and the next Wednesday, took me a 9-hour day in the lab and then an hour every day for five days after that for my UROP. It was incredibly frustrating in two ways. First of all, I never felt like I was getting the whole picture in 109. What I set down at the end of the day on Wednesday was not what I picked up at the beginning of class on Friday. Even though every step was written in the wiki, it seemed really intangible without having done it myself, or at least watched it being done. I'd gone from doing every step along the way in my UROP, from googling what amount of cells can be seeded in a certain sized dish or the pros/cons between different transfection reagents, to having it all decided for me or even done for me in 109. On the other hand, having a lot of the physical experiments streamlined for us allowed me to focus more on the data. I spent more time thinking about the results and the big picture.

Many 109 students are able to continue UROPing through the semester. Maybe they don't mind, or enjoy, all the lab time. Or they find it very exciting to see the connections and differences between their UROP projects and 109 projects. So, for me, it wasn't just the time commitment. Through the different 109 modules, my vision of the scope of bioengineering widened so much. I was working in an RNA lab, on a project to better understand the functions and mechanisms of a particular microRNA. Very much straight bio. I didn't really know what bioengineering meant in terms of the lab – I previously envisioned prosthetics, biomedical devices, 3D printed organs, things of a much larger scale. But there are so many other areas, scales, and applications. This class really did open my eyes to the possibilities and options available in course 20. I realized that while I did find my UROP project interesting, and I'd learned a lot from it, there are so many other things in Course 20 that I want to do, or be a part of. So, next semester, I will hopefully be doing exactly that.

20.109 Taking Names & Busting Myths


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.