Colors are Hard

From my AP Chemistry days jotting down the colors of flames as they irradiated different metals, to 20.109 where EVERYTHING is color-coded, I am all too often reminded of the unfortunate inadequacy inflicting my X-chromosome. Although I absolutely love everything about colors and the roles they play in biological imaging and other techniques, I have an incredibly difficult time pointing out exactly what colors I am looking at.

Sometimes I wish biology was colorless:


But most of the time it really isn't an issue at all! Either I've had phenomenally patient lab partners (like Julia) who are glad to help me out along the way, or I've been able to get away without really knowing what color I'm looking at. In either case, everything works out in the end. (In all honesty, though, I do make sure to understand what I am looking at before moving on to something new: stained comets, for example).

The reason I bring this up is solely to explain how positive of an all-around experience 20.109 has been thus far. Regardless of any lack of previously knowledge -- color-related or otherwise -- the 109 staff is always ready and willing to clarify a difficult concept or walk through an unclear technique. This has been an incredible help for me because this is the first real entirely lab-based class I've ever taken, and knowing that the staff has my back every step of the way is remarkably reassuring.

I can think back to Sean's BE Comm Lab discussion about creating presentation slides as a particular instance of this. Oftentimes science professors or teachers will blow past the concept of presenting with the specific audience in mind. Not here. He even mentioned to keep us color-blind folk in the back of our heads :) (Small gesture. Meant a lot.)

So while looking at the following gifs (a pulsating culture of stained cellular stuff and a swirling array of deadly colorful teardrops) might give me a headache and some minor anxiety, I can rest assured knowing my peers and teachers in this lab are there to support me through any challenge that has and will come my way...with colors, with CRISPR, and with anything in between.





<3 David

Student subjected to 20.109 experiences high levels of both stress and joy

(A)(B)

Fig. 1 – The idea of the CometChip assay blew Samantha’s mind. (A) Gif image of Samantha as she reacts to the CometChip assay experiments ahead of her. (B) Statistically significant levels of bewilderment, excitement, and stress were detected in comparison to control levels measured during 20.320.

In an initial survey (taken after a 50min dose of 20.109) it was found that Samantha was stressed and bewildered by Module 1 (the first stage of 20.109). These feelings were registered at 60% and 80% respectively, however notable levels of excitement were also detected (85%). Upon further examination, it was determined that even though Samantha had worked in a wet lab before, her comfort levels in this type of environment were lower than one would expect.

(A)(B)

Fig. 2 – Changes in Samantha’s feelings occurred as exposure time to 20.109 increased.
(A) Samantha and two other Life-As-Bioengineers (LAB) partners are observed celebrating successful results. (B) Changes in Samantha’s feelings in response to 20.109 as compared to baseline 20.320 levels.

As the exposure time to 20.109 increased, noticeable shifts in Samantha’s feelings were observed. Bewilderment and stress levels dropped, while excitement increased to a maximum level of 100%. It is also worth noting that these shifts are very distinct when compared to 20.320, where excitement plummeted to a mere 2% as bewilderment increased from the original 10% to 50%. These results were found to be statistically significant as determined by t-tests that the authors definitely (cough) computed.

(A)(B)

Fig 3. – Samantha ending Module 1 with a feeling of confidence. (A) In the process of writing the Disorientation And Total Anxiety (DATA) summary, Samantha was visibly challenged. (B) Gif data show that Samantha successfully survived initial exposure to Module 1.

In conclusion, while Samantha's initial 20.109 feelings seem to have been unfounded and gradually shifted from "OMG" to "it's actually ok," it is to be noted that changes in response may occur once she is exposed to Modules 2 and 3.

Future directions:

Time to up the 20.109 dosage and proceed to the next stage: Module 2!

Taking things slow... (Coriell #10 doubling time slow)

Greetings and Salutations 20.109 friends!

At the beginning, Mod1 really intimidated me. By some coincidence I knew a lot about CometChips, but mammalian cell culture was super new. For reference, I don't believe I have a green thumb, and I'm scared to watch pets just in case I accidentally neglect them, so being responsible for living things, however minuscule, scared me. This, for example, is not me:

I also felt a little disconnected at the start since I've never cultured cells, and felt I'd be slow on the techniques, but with MOD1 at the beginning of the semester, I felt super eager!

 And not yet drained by 20.320....

I soon realized that I had no reason to be worried. Lectures really delved into the mechanisms behind our cellular observations, and in the lab, I could double check my thoughts with my partner, then second guess our answer, then rethink, ask Leslie/Maxine, and go on. Thus, the idea that Mod1 was taking things slow, like taking all of class time. 

Somehow, Mod1 still managed to feel like it flew by. I was always surprised it was a Tuesday or Thursday and how quickly we built to the next logical experiment in the progression. Things were really thought out - mostly by the instructors! Still, I felt like I caught up to the point of the experiments by the time we started arranging Mod 1. (We started really early with the homework assignments, actually). I'm glad I had some feedback on my figures, background, and future implications especially before making the data summary. The preparation was definitely necessary:

I feel like the best part of this module was having unlimited help in understanding the material and additional hands behind the scenes to make everything possible. I also gained some confidence in my ability to keep living things alive(!) and that's a plus past the knowledge I gained in general cell culture, DNA damage, and CometChip technologies. I'm really grateful to the 20.109 instructors for both.

2 paragraphs and a list

Mod1. 20.109. Let’s see…

New! Shiny! Science! Working with the CometChip was a fun experience. It was a good platform for exposure to basic cell culture, DNA damage, and electrophoresis concepts. These interesting but fairly standard topics were made more exciting by working with the new technology. I forget that all of the technologies that make science work – centrifuges, pipettes, fluorescent proteins - haven’t always existed. Thinking about the process of developing a new technology is fairly amazing and I also enjoyed hearing a few tidbits about how the CometChip is being commercialized. It’s another side to the oddly shaped field that is biological engineering.

So when you put together information and tools you hopefully get results. And when you have results… You have to communicate them. Oh my. Here I have included my nearly foolproof instructions for making a diagram, as well as some tips for spending a little less time making it.

How to make a diagram (ft the BER pathway and Mod1 Data Summary):

+ Handy dandy tips! (some of which I did and some of which I most definitely should’ve)

            Step 1) Realize you don’t understand the system nearly as well as you thought you did

            Step 2) Sort through the google images results for explanatory figures that are all much more                  
            complicated than they need to be.

            Tip 1: Search through that towering stack of powerpoint printouts. Google is, as            
            always, a great friend, but the class information has been simplified a bit

                        Tip 2: Don’t move on to Step 3

                        Tip 3: Don’t do it

                        Tip 4: Sketch out on paper  a diagram with pieces important to you

                        Tip 5: Write out point you’d like to make and see if paper diagram matches 

            Step 3) Make 302 white boxes and 40 black lines

                        Tip 6: Nope. Wrong. Go back. You are not ready for Step 3.

                        Tip 7: Show your beautiful paper sketch diagram to the teaching faculty

                        Tip 8: Now you may go to… Not step 3. Okay. Maybe step 3. Provided you’ve added 
            in revisions from talking to the instructors (and said nice things to the instructors. 
            You should do that too. They deserve it)

            Step 4) Now, spend the approximate life span of a blue and gold macaw (about 30-35 years in
            the wild) attempting to line up the black lines and white boxes

                        Tip 9: Line up the lines and boxes into building blocks. It’s like building with legos
            versus sculpting marble. If you can make your diagram in pieces, then when you need to
            change part of it (which you will) you don’t have to start completely over.

            Step 5) GROUP EVERYTHING

                         Tip 10: Caps means IMPORTANT. Group the things. Group. Save often. Screenshot
            the figure so the white boxes can never move again. Send the figure to a cryogenic company.
            Whatever it takes.

            Step 6) Decide to also use some red arrows. Line those up.

            Step 7) Learn that your figure is incorrect/doesn’t convey your point/looks like the Nazca
            lines/is possibly made by aliens

            Step 8) Line up more boxes
            Step 9) Repeat

May this help me next time I need to make a diagram. 

Looking forward to Mod2,

Sarah

Wetlab for Dummies

Having never worked in a wet lab before, I can definitely say Mod 1 was… an experience. While most people were probably bored out of their minds, wondering why they had to practice the most basic techniques such as pipetting, I was slowly discovering a whole new world.

Thankfully my partner has tons of lab experience, and didn’t mind answering thousands of questions about what pipette to use, what exactly happens when I do this versus that, and tolerating my terrible pipetting technique (“cells don’t like bubbles Yvi! Stop making them unhappy”).  

I never thought that after just a couple of weeks, I would feel somewhat comfortable culturing and growing cells, inducing damage and then being able to visualize and interpret their repair by using cutting edge technologies that are still not even available for broad use. I find it amazing how the Engelward Lab was able to take a simple idea and reinvent the comet assay to create a new device with such a extensive range of uses. 

Despite messing up some of the experiments (are negative doubling times a thing?), knocking over the pipette tips (multiple times), and even having trouble finding the incubator on the first days, I found the lab part of the class to be very enjoyable. I love learning through hands on experiences and it is very satisfying to use the knowledge from lectures and past classes to understand the experiments you are doing and try to make sense of the results. Thankfully, I learned that I'm not alone in my "voluntary stupidity," and that not knowing what you're doing or what to expect is all part of the process. 

I also think the homeworks and the Mod 1 Data Summary improved my scientific writing skills. I noticed early on that I did not really understand the idea of writing papers around figures, the amount of thought that has to go into creating the slides, and how you have to think about presenting your data in a logical, clear way. The amount of support we receive from the BE faculty is amazing, and the amount of time and patience they put into guiding us to becoming good researchers, scientists, and writers is unbelievable. 

Looking at the new skills and experiences I gathered from Mod 1, I can definitely say they will be useful in the (near) future as I look for labs, internships and even jobs later on. Thank you to the 109 team for making this potentially very stressful and overwhelming experience into a very enjoyable one! 

Thoughts from an unexperienced "scientist"

Hi guys!

So here are some thoughts on all the experiments/hard work we did on Mod1 (but let’s be honest most of the hard work was done by the instructors so thank you guys!)

I really enjoyed being eased into the world of Bioengineering lab with the CometChip assay. Here I was, a barely third-year student, thinking I knew something about Bioeng lab because I had UROPed in a bio lab for the past two years. Reality check: I didn’t. It was amazing to learn that part of bioengineering is coming up with these amazing technologies that we use everyday now in other research, and these things happen on our very own campus. The CometChip assay seems like such a simple thing now that we have it, but no one thought to take a spin on the very traditional comet assay until the Engelward lab did it.

Before I was in 20.109, people told me that science was harder than anything else and that most of your experiments would not work. I didn’t believe them. Little did I know that this was going to happen to me. In the cell loading/doubling time experiment, we ended up loading WAY to few cells, so few that we got negative doubling times for some of our conditions. In addition, while trying to graph the data for the cell loading, we got such noisy results that our confidence intervals for number of cells extended into the negatives. All in all, we were getting a lot of negative numbers, and these made no sense biologically.

Anyway, after being amazed at all the things we were able to do, and kind of annoyed at our data, it was time for the hard part: writing up this Data Summary.

Now let me start by saying that I haven’t written anything like this before. The closest I’ve come is high school lab reports, and that was like 3 years ago. Honestly, for a couple of days, Yvi, my lab partner, and I stared at blank pages of our Google presentation and had no idea what to write. Yeah, we had some parts that we’d done for the Homework but these were not in the shape we wanted them to be for our Data Summary. Finally, about 3 days later, we had our figures mostly done, confidence intervals and all, and internally celebrated when we even had some significant differences in our H₂O₂ vs. MMS experiment.

We started writing and once this happened, it all kind of flowed from there. Yvi and I looked at each other at one point and we marveled at how our pages finally started to look full of information, rather than the blank pages that reminded us of our failure to come up with conclusions. 

Frustrations and all, it has been a great Mod1. Looking forward to the rest of the semester!!! 

The Magic of 20.109

Mod1 was an interesting time.  On the one hand, this felt like the first time any of my classes did science that I thought actually related to what I wanted to do.  Cancer is a very exciting topic that has concrete applications in the real world.  I could finally see how everything that I had been learning for the past few years was going to help in the real world.  I felt like I was an actual MIT student working with experimental assays and learning about real science.

But on the other hand, there were times that I had no idea what I was doing.  I understood most of the experiments well enough, having done something similar in my UROP, but because we were limited by time, Leslie/Maxine did a lot behind the scenes.  I really appreciated them finishing up experiments when we ran out of time, but this made it feel a bit like magic when our experiments suddenly had concrete results within the next couple of days.

Because of the “magic”, sometimes we had to take a bit of a leap of faith and hope that everything would turn out all right in the end.  But, for the most part, everything did turn out all right.  Leslie and Maxine were always super helpful whenever we had any questions about the experiments.  Professor Engelward’s lectures also tied in well with our experiments and helped explain a lot.  Everything was always made clear in the end, even if it seemed a bit like magic at first.  By the end of Mod1, I learned that science is a lot like magic, and you sometimes have to take a leap of faith.  You just have to trust that people before you have understood what will/should happen and that they can help you understand and see the magic.