What is writing though?

There's a reason I don't have a blog and the reason is because I never have any idea what to write. So this should go well.

I think Mod1 was essentially a 50:50 mixture of this:

and this:

Sometimes I would be sitting in lecture like "yes, I know exactly what is happening this is so great" and the other half of the time, my brain would be sad and refuse to cooperate in my learning endeavors. Also, working with an experimental, newly developed assay that has yet to be studied to death by the other science people of the world? A+. However, having to use new technology that doesn't have a pre-set, fully established protocol for me to follow step by step? Not so A+.

A lot of the time during lab, I felt slightly dissatisfied by the focus on breadth rather than depth. Biology research takes time. So much time. This is just a given fact of life. I understand that the point of the module (and I guess this class overall) is to give us exposure to research techniques and an idea of what Real Science is like, rather than coming up with a cohesive, all-encompassing story and indisputable publication-worthy data. However, as someone who literally spent an entire semester in UROP repeating one experiment over and over again to get a singular figure, a lot of the time, I kind of felt like this:

because of how fast the experiments were moving. We also tended to run out of time a lot and Maxine/Leslie finished a large chunk of the experiments and analysis for us, meaning there was a lot of behind the scenes action that we weren't privy to, which may have contributed to my/Oprah's confusion.

The homework assignments, in my opinion, for Mod1 were extremely helpful in hindsight. When I was doing them, I was skeptical as to whether they would actually help with writing the Data Summary (like the instructors kept telling us) but to my surprise, they actually did! Wow! I would consider Mod1 a successful introduction to new technologies and a successful start on my journey to trying to answer the question "What even is biological engineering?"

Keep Calm and Continue the Module

Hello my 20.109 friends!

My first reaction to this blog post assignment was why… 
I understand the purpose of blog posting and it is definitely good to share everyone’s thoughts about the projects but having just figured out that the posts are not anonymous, I am too nervous to start. Being sleep deprived from finishing Mod.1 data summary revision and from studying for 7.06 exam 2, 

I hope I can remember Module 1 well.

First of all, learning the background knowledge during the lectures and having a pre-lab session at the beginning of each lab really helped me connect different sections of our experiment to the overarching goal of this module. The protocols and instructions were given in details and I was able to not make any mistake and to reassure myself that I was following the correct steps. Different experiments we did in the lab and 
doing the tissue culture for the first time, 

I really enjoyed being in the lab.

I guess the struggle hit me with the assignments we had outside of our lab. Writing the lab reports on benchling for each experiment helped me examine what I did and summarize what I got out of each experiment, but it was quiet time consuming. Ideally I should have completed the lab report after each class but that did not happen. I will try to fix that in Module 2.

Assignments for making figures/captions and writing the introduction to results and interpretation/future work sections were very useful in a sense that it helped me a lot to prepare what to expect for the data summary at the end of our Module. However, as mentioned earlier, we didn’t know what to expect as this module was very new and open-ended. Many of the data were either lost or calculated to be insignificant from the t-test that when we do further experiments on the CometChip assay, we definitely need to run the assays in more duplicates. Nonetheless, I found BE Communication Lab workshops to be also very helpful that I now feel a lot more comfortable knowing what each section should look like. 

Overall, I worried a lot about taking this class as my first CI-M, but it was a great start. I admit it took a lot of time to finish assignments with tight deadlines, but I’m learning a lot to think and write as a researcher. Lastly, I just want to say thank you to Prof. Engelward, our instructors, TA and my lab partner for everything they have done for this module J

Mod1 Thoughts

Oh dear, how does one start a blog post???

Anyways, I really enjoyed Mod1 as a whole because of how new everything was. It was so cool that we were using recent technology developed at MIT (the CometChip assay) and we were learning from the creator herself! It was also interesting seeing how so many sub-experiments could come from utilizing the CometChip. However this did mean that occasionally the sub-experiments felt very un-connected and irrelevant to one another.

Something I really appreciated was the fact that (perhaps because it was a completely new module) the results were unknown. In that regard it felt like what real "science research" would be like--a foray into the unknown with little knowledge of what to expect. Of course this meant that there were some struggles along the way. I sometimes felt like different conditions were chosen somewhat arbitrarily (especially for the cell loading optimization sub-experiment).

Also through this lab I learned that making mistakes is super easy. Like super easy. For example, when we were doing the Coriell cell experiment for genetic variation/BER capacities, we loaded the concentrations of H2O2 in reverse order, necessitating relabeling of the gel. It seemed like relabeling would be an easy fix... but flipping the gel over actually destroyed some of the macrowells so we had very little data for some of the conditions. But for the purposes of this class we could just pretend everything was ok :D

Because of struggles like the one mentioned above (and possibly because the module was so new), a lot of our data wasn't statistically significant. While unfortunate, this again made the module more realistic since success is far from guaranteed in real research.

Overall, I thought Module 1 was a great first module for 20.109. It got me excited that we were using super new technologies and also introduced (or refreshed me) on basic biology lab techniques. Not knowing the results beforehand was a new experience for me in a lab class and lent a sense of realism to the class. Even though the experiments weren't necessary successful 100% of the time, I still feel that I learned a lot. Thank you to all the instructors for a great module!

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