A Little Modeling Never Hurt?

Hey everyone!

Ah, Mod 1. I heard quite a bit about 20.109 from past .109ers before I signed up for this class. Everyone told me this class was worth 15 units for a reason. Everyone had some nightmare-ish story about 20.109 projects and deadlines that still scared them to this day. I remember coming in for the first day of lab and hearing Leslie give us a disclaimer about how this module was brand new and that we should collectively anticipate the bumps we'd probably encounter along the way. And I even though I smiled and politely chuckled at this, I immediately thought back to everything I had heard about this course. I kept it cool on the outside, but I kinda felt like this on the inside:

It's safe to say I was a little bit nervous. But honestly, I didn't realize how cool this class was going to be. It's super exhausting and time-consuming, but it really feels like the staff is right there chugging alongside us. You never feel like you're in this alone. This class already feels like the most intimate class I've been in at MIT. Module 1 went by surprisingly smoothly looking back on it now. Of course, there was a bit of a learning curve and it really felt at times like there was no end in sight to the work being assigned to us. But I've already felt like I've taken more away from this course than I have most courses I've taken so far here. So I'm pretty excited for what these next couple modules have in store for us!

Also, totally unrelated note here, but if anyone needs a model who specializes solely in lab settings, feel free to send me an email or follow me on Instagram. I specialize at looking at really small things super intently and making science look more complicated than it really is. I'm easy to work with and overly-enthusiastic about being photographed. If you're looking for references, contact the nice folks over at MIT admissions. I'm pretty booked right now, so the sooner you contact me, the better :)

--Sami K

Just Keep Swimming

It's been a tough semester. With 22 hours of class a week, 15-20 hours of soccer (Roll Tech!), and approximately 42 billion hours invested in putting together the 2016 MIT iGEM team's project, here's a live look into my life:


via GIPHY

Add in the Mod 1 Data Summary and I was definitely feeling stretched to the limit. There is nothing I procrastinate more than writing assignments – my roommate says she can tell when I have an essay due soon because I suddenly get really chatty. The advantage of being so busy is that I had no other choice than to get started! Setting up meetings with my lab partner was also helpful because it forced me to put aside time to work on the assignment. Being held accountable by another person kept me motivated – I'm all about being a team player.

It was a good thing we started early, because scientific writing is hard. Distilling complicated subjects into clear and concise statements was a challenge, especially since most of our report was written in bullet points. Writing the abstract was particularly tough because every word matters!

Another un-anticipated hurdle was creating figures. At first I was pretty exciting about making them; it certainly beat wrestling with Excel to produce graphs. It turns out that creating clear and informative figures is far, far more difficult than coaxing Excel into spitting out a graph. You have to a) know what you want to convey b) figure out how to visually represent this information c) actually make the figure

About two hours in, this is how I felt:

via GIPHY

But the end result was a pretty sweet figure, if I dare say so myself :)

I invested a lot of time into the Mod1 Data Summary, and at first I worried I might have put a little too much time into it – I kinda put off on work for other classes (oops) – but in the end I think it turned out to be a good decision. It was nice to only have a few revisions to make this weekend as iGEM hit major crunch time. I do wish I had spent more time on the mini-presentation – I felt like I really burnt myself out on the data summary and was a total wreck by the time it came to film which made me feel really disappointed with myself :(

Oh well, onto the next module!

via GIPHY

[Insert Witty Mod 1 Title Here]

Hey friends,

This assignment makes me feel so much nostalgia. I always told myself I'd have a blog or contribute to a blog. I've tried on several occasions, but never stuck with it. It's hard! It's like writing an open letter each week (or at whichever frequency you choose) and giving the world an open window to your mind. I don't know about you, but that is a little scary.

Anyways, I digress. I will walk you through my thought process (or what I can recall of it) through each day and assignment in Module 1. I will finish up with some overall thoughts and reflections on the way this module went. I am writing this before I write the actual content, so I will do my best to be brief and not take too much of your time.

Here goes nothing!

M1D1: Yes, here we go! We get to do science! Alright, gotta make sure I do all of my readings and set up my notebook on Benchling... Am I doing this right? Probably not. Crap, I hope they don't grade this tomorrow. Do they check these at the end of each day? It's going to be difficult to keep up with this while sciencing...

Okay... I already know I don't want to finish that for everyday. I'll skip to my general thoughts on the Module:

It felt like this one moved very quickly. I felt sort of lost at the beginning of each lab section, whether or not I read the Wiki before class. Once I was able to really get into the work, things started to piece together, but it often felt like catching up. I think it often felt like a race to get through the day's assignment when it really shouldn't have.

I did really enjoy working with the CometChip. This was a nice bit of exposure to up-and-coming technology. It provided a reference point for anything one of us may hope to someday invent that would make sciencing even easier. Using the somewhat janky binder clips and glass slides to put our CometChip together made it fun and reminded us that innovation has to start somewhere and you don't always need the fanciest tech to make or do something great.

Some of the experiments, I wish we had more time or materials to commit to them. Especially the one with Coriell cells. We did not have enough replicates of the various conditions and it made looking for statistical significance in our data very difficult.

Especially towards the end with the Data Summary Revision and the early assignments for Module 2, things started to feel piled on. It became hard to keep up with what assignments were due when and determining how to prioritize.

Overall, I feel like I've gained great exposure to the types of things I would have to do if I were to work in a lab. I feel a bit more prepared for the Research Article from doing the Data Summary, and the Mini Presentation was great practice for an elevator pitch.

It's been fun, Mod 1!

(BE)st,

Jasmin

Ode to Mod. 1

Greetings and salutations to the 20.109 community! Below is my poetic reflection on Mod. 1 (followed by a more substantial one):

Ode to Mod. 1

I wasn’t sure what I would find

On Mod. 1’s starting day.

We’re told to “keep an open mind”

With Comet Chip Assay.

By Day 2’s end, I realized

I’m thrilled for what’s in store.

Our Comet Chip was optimized,

Cell loading times galore.

And, oh, day 3 was quite a ride.

We damaged all the cell,

Induced with H2 peroxide.

It really was quite swell.

The Coriells allowed us to

Assess variation

(On day 4, in our lab coats true)

In the population.

Day 5 took quite a different path:

We learned a new technique.

And got to feel the IF*’s wrath,

As pictures we did seek.

And on day 6, the end in sight,

Wrapped up our IF life.

Made sure conditions were all right

And wouldn’t cause much strife.

Day 7 was a sullen time –

The last day of Mod. 1.

And to our timer’s shrill, quick chime

We’d finished what’s begun.

* immunofluorescence

In all seriousness, I had a blast with Mod. 1. I’d come in having familiarity with the biology techniques we’d be using in lab, but really liked getting to apply them in a way I was unfamiliar with (i.e. in assessing DNA damage using Prof. Engelward’s Comet Chip Assay). I also found the “flow” of the first module to be quite interesting, because Leslie/Noreen/Maxine/Prof. Engelward constantly stressed that this module is experimental, and we were effectively guinea pigs for it. Honestly, I found that this made the pace of the class seem a lot more genuine (i.e. similar to a real lab experience), because we didn’t necessarily know – and could only speculate – what would happen at certain steps in the experimental/scientific process. I really appreciated this aspect, and didn’t find this “not knowing” to be very daunting. My sole “critique” of the module would be that it seemed like we ran out of time in our experiments often, and Maxine/Leslie would have to finish our work for us; I would definitely agree with Aria in that I wished these accessory steps/techniques we didn’t get the chance to do in class were covered in prelab…

That being said, thanks very much to the teaching staff for a fabulous start to 20.109!

-Nicole  

If I'd had more time, I would have written you a shorter presentation

Replace “presentation” with “letter” and that title becomes a quote by the great Mark Twain (although it’s also been attributed to Blaise Pascal and Winston Churchill, depending on who you ask). This is more or less how I feel about writing and presenting: I always have so much to say.  So when we were given the mini presentation assignment, my first thought was something along the lines of:



Regardless of my concerns about length, I wrote a script, learned all my key points, and set up my laptop in my suite lounge to record. Realizing that all my suite-mates were probably going to walk by the lounge door and hear me ranting to myself about genomic instability (not that they don’t expect this of me by now), I resolved to try to get a good take quickly, perhaps within about twenty minutes or so.

One hour later, I realized this was taking a lot longer than I’d anticipated.

The problem was, with everything I wanted to say, the talk was just too long. And there was too much information. I realized, if I were the one listening to this for the first time, I would have a massive amount of trouble following what I was saying. There were too many terms, and too much data, and I was supposed to be writing an elevator pitch, not a comprehensive talk over absolutely every little piece of the puzzle. I decided to be more discriminating when determining what points were relevant to what I was trying to communicate. I omitted experiments that weren't specifically about variation in genomic instability between different cell lines, since I wanted my future directions to be about using the CometChip to assay individual genomes. With each take I would cut out some more extraneous information until I had a more succinct, understandable story.

After two hours, I had decent pitch: it was just a matter of getting a good take. I was a theatre kid for a lot of middle/high school, so I actually really like talking at people about things. I think presentations are fun. Filming myself, however, is really, really tough. It requires enough focus to speak eloquently for three minutes without messing up, which, in theory is simple, but in practice is super challenging. This is because, after multiple hours of staring at a screen talking to yourself, words stop having meaning anymore and you enter a sort of twilight zone where you forget how to speak and you slowly start to forget your own name. It’s true. Actually me during take 14ish:



After three hours, though, I managed to remember my name and I finally had a finished product that I was happy with. After I got the final take, I was really happy that I’d been able to explain a month’s worth of research in such a short time, and I felt like I understood everything better.

On the whole, I thought this was a really valuable assignment. I’m often asked questions like, ‘what are you working on?’ or ‘what do bioengineers do?’ or ‘can you tell me about your research?’ and sometimes I just sit there not knowing what to say.

“Uhhhh, well I’m growing cells to do this cool thing… wait, first I should tell you about… but actually first do you know what this word means….?"

Saying things succinctly is very difficult for me (which is probably evident from the length of this blog post), so I really appreciated the opportunity to work on this. And maybe all my suite mates learned something after getting to listen to three hours of muffled ranting. :D

Looking forward to more work presenting, and thank you to the teaching faculty for a great module one!

Mod1 Blog Post

Hello world!
Let me first say that I had to ask a former 20.109er to figure out how to write to this blog. Yes, technology is hard.
Secondly, I would like to share some thoughts about Mod1, which involved the use of the CometChip assay to measure genomic stability. I thought it was really nice spin on "classic" laboratory techniques since we got to use a technology developed right here at MIT. It's quite amazing when you think about it - all the groundbreaking work done on campus, and I'm just seeping in it! It was also very nice to have Prof. Engleward share her technology with us, and to even pop into lab to check up on us.
Overall, I thought the module lacked flow: different parts of it seemed to be jammed together, and the connecting factor was that it used the CometChip as a platform. It was sometimes difficult to understand why we were doing one thing one day and something else the next day. Specifically, I thought the loading experiment could have been optimized better. If I were to do this on my own, I would never set up an experiment with just 2 different concentrations: I would have instead, titrated the concentrations. I guess the mitigating factor is that everyone in the class was doing it, but they also chose different loading times, so deciding the optimal loading conditions felt very arbitrary.
I also wished that we got to see more of what happened behind the scenes: all the work that Leslie and Maxine graciously did to move our experiments along. Obviously, biology works at the pace of life, so the students with set lab times won't be able to do everything for themselves, but it would've been nice if during pre-lab lecture, we talked about exactly what the lab instructors did for us. I think this would've created a more continuous story.
Overall, I thought it was a nice intro to 20.109, and that the data summary did a good job of introducing us to scientific documentation and writing. I liked that most of the homework assignments could be used directly for the end report (unlike that catfood article we had to read for a Mod2 homework assignment...). The mini-presentation was also a cute and relatively chill assignment, especially after writing up the data summary.
Thanks teaching staff! You guys rock!

Module 1 in Review

Hi I just wanted to give a little summary about my experience in module 1! Thank you for being such great instructors and organizing everything for us! It was exciting to get the chance to work with the relatively new CometChip technology in this first module doing experiments with unknown results and having some say in the protocol was a new experience that helped me engage in the material and research process further. In writing the Data Summary it was fascinating watching how all the different days/experiments linked together and built upon each other to culminate in the final research into variability of Corielle cell repair.  Conducting research into real-world applications that could improve lives has gotten me really excited about the rest of my future in Course 20. Writing the data summary was a good way to get an introduction into scientific writing and having it be a partner project was valuable in exchanging knowledge and was helpful in that we could teach each other different things and work together to gain further insight into the research. I had a hard time with formatting and just trying to organize my thoughts and convey them in a formal sense that was clear and concise- the BE communication lab was very helpful with these issues and they were a great resource that I plan on using for the rest of  this semester and probably the rest of my MIT career. Overall I thought Module 1 was very well organized and flowed in a way that really maximized learning and hands-on work.  I'm excited for the rest of the class! :)