Team 99 Bottles Reaches Shore

So, the journey has finally come to an end. Throughout this semester, this project definitely has had its ups and downs. There were times when I got really excited and times when I got really frustrated, times when I questioned what the goal of the project was and times when I thought we could maybe save the world. But I imagine that’s all part of the journey. I suppose roadblocks and incompatibilities are occupational hazards of bioengineering, and fun and discoveries are the rewards. Maybe it’s because I’m new to the field, or maybe it’s because the field itself is relatively new, but it seems to me like the rules still have yet to be defined. It seems as if you can do whatever you want as long as you have access to resources and stay away from anything ethically controversial. The possibilities are endless, and that’s exciting but also challenging because that means there are fewer examples to go by, fewer guides to help you know what you are doing.

Indeed, I thought that the freedom of the project was one of the hardest things about this class, but also one of the most valuable elements of the class. It’s made me realize that although high school has taught me how to study for exams and maybe even how to learn, it hasn’t taught me how to do research. I think that’s why this class has been one of the most novel experiences since coming to MIT. It asks you to learn without a defined curriculum.

Furthermore, I loved getting to know the people in my team. Each and every one of them was amazing and brought so much energy, curiosity, ideas, and hard work to the table. We went through a ridiculous amount of changes together, from salt water to fresh water and E. coli to Vibrio. As I continue on in course 20, I really hope that I will gain skills that will make this type of work easier, so that one day I can maybe do something of this sort for real (if the rigor of research doesn’t scare me away). Overall, it was a great introduction to something I had never been exposed to before.

All the Feels

It's been a fun, informative ride. We got to experience synthetic biology techniques first-hand, transforming e. coli into banana scents and light sensitive printers. We examined the social problems our field can face, with relation to bioethics and public opinion on our topic. We played out the economical difficulties that can prevent the acquisition of other researcher's parts, which is apparently a huge barrier to bringing products to market. Most thrilling of all, we we're all placed in the shoes of a researcher and told to use our brains and synthetic biology to affect great change in the world. No other course at MIT offers the 20.20 experience, so I'm really glad I took the plunge.

The process of collaboration with Team 99 Bottles was pretty amazing, especially as members got comfortable and let their talents shine through. Colin emerged as the lead researcher, Lee was the organizer and editor, Jackie was secretary who'd catch our oversights, and I just kept my head in the clouds, blurting out novel ideas from time to time. I'm not sure if there's an ideal group of people to comprise a research team, but Team 99 Bottles was certainly on the right track.

I feel Course 20 knowledge flowing through my veins! The concepts and methods by which we manipulate bacteria seem much more familiar and accessible than they did before. Device diagrams and timing diagrams have actual meaning! And the process of researching and uncovering information? Not as terrible as a thought it'd be hahaha. On that note, experts are certainly an invaluable resource, reducing our research times by a tenth, at least. That must be a great feeling--to have mastery of a subject to a point where you can be consulted for your knowledge and help others accordingly. 

It's funny that I ended up declaring Course 2 when I was inclined to Course 20 at the beginning of the year. It has nothing to do with me being scared away our put off by 20.020, but more about the variety of options post-undergrad. Biotech is an emerging field and I'm not sure if I want to work in academia yet, and besides those two options, the Course 20 road seems a little limited. Course 2 on the other hand have a multitude of career options to choose from. I suppose I'll know if my decision was right in due time, but I'm so appreciative to the 20.20 experience for informing my path much more than I could have done alone. Natalie has been a wonderful teacher and mentor throughout the entire experience, guiding us with a gentle hand and a great smile. Between the senior mentors, my peers, and Natalie, I feel like I have access to a wealth of resources and informed people as I move forward in my college career, and I'm so grateful for that. 

To conclude, I no longer think bacteria are gross (as I alluded to in my first blog post :) ). There's great potential in synthetic biology to solve world problems and great potential in each and every one of us to see it through. Thank you everyone for your great collaboration to the very end! Thank you seniors for being so charitable with your time. Thank you Natalie for taking us on this ride and I wish you so much luck with your future endeavors. :,)

Final Thoughts

20.020 is over! I am happy and sad, and proud of what my group accomplished. It is so strange to look back at past blogs, getting a peek into my brain at that point in time. I almost don’t even recognize my own thoughts. Looking over the old blogs, I decided that 20.020 was one of the most worthwhile classes I’ve ever taken. It reminds me a lot of Terrascope, but taught in a smaller and more focused setting, which I preferred. Both projects I undertook this year were incredibly complex, much more so than I realized at first. In both cases, there was no way to account for all the possible variables; we just had to pick solutions that seemed like they might work and improve on them as we went. Improving—that was an enormous part of design. More so than for the other group, our project went through a number of iterations as we went. First it was some sort of plastic decomposer that we might use in the landfill or oceans or who knows where… It later morphed into an E. coli with a salt balance kill switch, then a cyanobacteria equipped with plastic degradation enzymes, and finally a vibrio bacteria that we used to decompose additives instead of plastics themselves. I could never have predicted our final product at the very beginning of the process, and from the end looking back at the beginning, our idea seems so simplistic and doomed for failure. I could probably come back next year and improve on our idea even further—I wonder how long it would take to crystallize into a project that a “real engineer” would actually work on. I put “real engineer” in quotes, because I don’t think of myself as an engineer. But really, I just need more practice. I never thought we would be able to come up with the project we did; it makes me wonder what else I can do that I think I can’t.

The Struggle was so Real, but so Worth It.

Seriously though, we have come so far since the beginning of this class!  Looking over the posts from the beginning of the semester really provided me with some perspective of how much more I now know.  Having very little experience in such a huge field coming into 20.020, I had no idea what to expect.  Although we only touched the surface of such a large science, I feel as though I now have a better understanding what biological engineering is all about.

This class, for me, was not entirely geared towards the introduction of biological engineering however.  It also allowed me to work in a small group for many weeks, constantly re-engineering, fine tuning, scrapping ideas, and thinking of new ones as we strove to come closer to our ultimate goal of making early detection of cancer more accessible.  The skills I have learned in this class including proper research techniques, efficient time management, and complex thinking in general will certainly benefit myself while at MIT.

Once again, looking back at my previous posts, I can see a trend of a much more focused approach toward the end of the class.  In other words, the first few weeks of the class were simply exploration, finding things that fascinate us.  As the course progressed however, I found myself becoming more and more immersed in the ever evolving problems at hand, of which there seemed to be a new one each week.

How far we have brought our project, from three adventurous ideas, to one finely tuned proposal in such little time brought tears to my eyes (not really, but it was still pretty cool).  Not only that, but having our final project be as detailed as it was, without even having access to laboratory equipment really highlights the power of in depth thought and problem solving.  This class was awesome (especially you Natalie), and although it was a race to finish everything at the end, the final outcome was well worth the struggle.

The Semester in Reveiw

It's strange to think that the semester has finally come to a close. It feels like it went by so fast! And yet, I reflect on the amount of work that went in to our final project and realize that we actually spent a long time developing this system. I kind of can't believe that we finally managed to understand enough to put together our project, and yet, here we are with a "finished" presentation (I'll get to why "finished" is in quotes in a second).

I looked back over my very first blog post a few days ago, and the general gist of it was along the lines of "haha what's a cell?" I knew absolutely nothing coming into this course. Biology itself was a foreign concept to me, not to mention the idea of applying biological concepts to engineering. I had no idea what I was doing. I am so happy to say that that has changed. I feel confident now that I understand the foundational ideas behind bioengineering, and I am excited to continue learning as my career at MIT proceeds.

I'm really amazed at how far our project came over the past few months. The night before our presentation, we all virtually met up and went over our documentation and systems until we felt solid about the design. Even though it was late and we were all tired, the enthusiasm about our system never deflated, and it was so exciting to see the minds behind the project continue to chug along until we were confident in it. It was then that everything we had learned over the semester was applied as we checked through the details of our work. Seeing it all culminate was an incredible experience and it really brought everything in the course together quite nicely.

Now, you will notice that I put "finished" in quotations in the first paragraph. If I can sum up my learning during this course into one lesson, it is to never assume that I know everything. It seemed like every time I got attached to an idea or concept, someone else had a novel approach that was even better. With the viral vectors, for instance, my attachment to EBV was shattered when Dr. Coen suggested seeking an alternative, leading me to find oHSV, an even better match for our project. This inability to know everything is definitely not a bad thing, don't get me wrong. It means that there is always more to discover. The field is ever-changing, and there is so much more we could do with this project. Sadly, the class has come to a close, but that knowledge and thirst for new ideas will continue on with everything I do at MIT. Thanks for an amazing course. It's been a blast. Team Turtle for life <3

... and this is why we have experts ...

      When I wrote my last post, I mentioned that we were adding an extra component to our system to detect another possible mutation in the Wnt signaling pathway.  After thinking it over for a bit, we thought that we'd come up with a pretty nice solution and it seemed like our system was well on its way to completion.  On Wednesday, we were scheduled to speak with some experts on some of the things we're working with - viral vectors and Wnt signaling - largely hoping to confirm our ideas and maybe get some thoughts on ways to improve moving forward.  We got quite the wake-up call; there's a reason we talk to experts.
      It turns out that the vector we were planning to use was not quite as well characterized as we had thought.  It definitely had the capacity we thought it would but Dr. Cohen (our virus expert) had not heard of it being used effectively without pathogenic effects.  Furthermore, this particular vector is not suited to be freeze dried and delivered by capsule as we had planned due to the weak lipid membrane that surrounds it.  Luckily Dr. Cohen was able to suggest some other possible vectors that Katelyn is doing some more research on.
      Still reeling from our first consultation, we prepared to speak with Dr. Xi He - an expert on the Wnt signaling pathway.  I tried to stay confident that we had done enough research for this second consultation to go well but then again, we had been really confident about our information going into the first.  Fortunately Dr. He was able to confirm much of our research into and reasoning about the pathway, and broadened our list to the 4 most common mutations in the pathway that lead to cancer (all of which seem to effect beta catenin activity).  We did run into some problems however when we proposed our entire circuit - that is, a system which only produces output in response to sustained high levels of beta catenin activity.  It turns out that because intestinal cells have such a short lifetime (all cells are replaced every 5 days), beta catenin is almost constitutively active in GI stem cells, meaning they would be tagged alongside any hidden cancerous cells.
      The problem we then faced (and will still be working on for a while) is how to tell a cancer cell from a stem cell.  We believe that one of the points Dr. He made may have given us the answer.  Although this pathway is almost constitutively active in both types of cells, cancer cells lack the ability to control when it is active.  Each of the four genes he mentioned, when functioning normally, can either increase the activity of beta catenin or reduce it (at least to a first approximation).  So our strategy at the moment is to try to use our position of acting within the cell to test whether those genes are working.  We are trying to think of each gene as a stop button, each of which is wired up to beta catenin in a different way.  We will wait for beta catenin to be active for a "long" period of time then press each of our metaphorical stop buttons and check whether the downstream circuitry is still functional by looking for changes in beta catenin activity.  Most of our research over the next week or so will likely center around figuring out what these "stop buttons" might look like (if they can actually be made at all), but overall I am very excited to try to get this system to work.

Project 2.0

So it seems as if the calls with the experts have prompted both groups to readjust their project goals pretty dramatically. If I learned one thing, it's that I prefer talking to people over researching online. The experts were just so informative and helpful in such a short amount of time. I kind of wish we had gotten to talk to experts earlier, so that we could have picked a more appropriate chassis from the start, but I suppose there's value in exploring the waters on your own first and learning from your mistakes.

Looking back, I feel like we were trying to piece together a system that was logically sound but not necessarily the most intuitive. A lot of choices seemed arbitrary and involved compounds that we happened to stumble upon and seemed to work. After running through the design process once and talking to the experts, I'm starting to realize the value of drawing from the experience of others to obtain a better sense of what tools and parts are available and appropriate in the bio engineering world. 

I'm treating this next phase as our project version 2.0. Vibrio seems like a very viable chassis, and I'm ready to see what the cyanobacteria expert suggests. 

On another note, something that really excited me was the fact that the bacterial expert had been contacted by industry to create something very similar to our project. That means that our idea is viable and in demand! This project has me seriously considering pursuing something similar in a lab as a UROP - I think that if I could work on a project like this in a team and have some control in the direction of the project, I would be working on my dream UROP. 

So Much Can Change in 30 Minutes

On Wednesday, we talked to experts on the topics pertaining to our topics. We thought we were pretty well prepared going into the meetings. We had several questions written out for each of the experts and knew how to present our project to them.  We even knew how to pronounce their names (this was a larger problem than we had anticipated though).  We had people ready to take notes and were open to any information we could obtain from these people who know much more about Wnt signaling and viral vectors than we do.  There was one thing we were not completely prepared for:
"Yeah that is not going to work."
Neither of the experts actually said those words.  They were much kinder and more scientific, but that was the takeaway.  We learned from he viral vector expert that our choice of a virus was not ideal.  When we asked him for suggestions for a replacement, we were again reminded on how much we do not know.  We need to know how long our sequence is and what cells and how many cells we need to infect before we can really decide on a vector.  From the Wnt signaling expert, we found out that one of our issues will be that many of the cells that cause GI cancer are stem cells and that intestinal cells have a life span of about 5 days. There are also four main causes of GI cancer and we had not considered two of them.  After the conversations with the experts, we discussed a new system and each have areas to research, so we have not lost hope.  However, I have definitely been reminded of how little I know and how much I just did not consider. Sometimes the enormity of the subject is frustrating because I know that I will probably never fully understand all of it, but I think that is why the impact of a project is so important.  Even though I know that we will never complete this project in a lab, I am still motivated to push forward with my ignorance and try to just learn whatever I can to create a usable system because I want to help people and for there to be a simpler early detection system for cancer.  Science is great and all, but the "why" matters.

Meeting with the Experts

This week was one of my favorite weeks in 20.20 so far! The experts we talked to were so helpful in answering our questions, probably saving us hours and hours of research. Up until this week, I had the vague notion that our system in its current form would not work, but couldn’t really come up with a definite reason other than that it was kind of a mess. (Natalie described it as a dam with a bunch of leaks that we kept trying to plug with our fingers, which I thought was pretty accurate.) While our system now has a less well-defined goal than before the meetings, I believe we are moving in a better direction now. Such is the iterative design process! It is a little frustrating to be possibly taking a large step backwards at this point in the process, but if it will help our design, that’s what we’ll do.

One of the most important points brought up by the experts was the harmful effects of microplastics and plastic additives. Although we knew we would have to worry about the by-products of decomposition, this concern wasn’t as high on the priority list as figuring out how to make our system work in the first place. However, I had no idea of scale of the real problem: the spread of microplastics to nearly every corner of the globe, their tendency to accumulate in the digestive tracts of marine life, and the detrimental effects of plastic additives such as BPA (which can mimic estrogen and disrupt the endocrine system). We may narrow down to a more specific focus, which we knew from the beginning was a possibility—our goal was so ambitious! One interesting idea we are discussing is to engineer some bacteria to live in fish and chow down on the microplastics they eat. It sounds pretty cool and I think we should run with it, but who knows whether it will work. I’m excited to talk to Danny Ducat on Tuesday, and to see what direction our project heads next!

Experts do know best...

This week was both the best and worst in the class.  We received much more information regarding our project--very helpful information that we never thought to research before talking with the two experts.  However, this information maybe wasn't what we wanted to hear (unhappy face).

Dr. Donald Coen first talked to us regarding our choice of viral vector.  He provided useful insight as to why EBV was good to use in theory, but it would be very difficult to introduce into the gut for a variety of issues.  He told us of the possibilities of other vectors (pox viruses for example) that may be worth our time to research.  After talking with Dr. Coen, we all felt as though we were back at square one--at least we had a wealth of new information to combine with our preexisting knowledge to create a perfect design.

Next, Dr. Xi He, an expert in Wnt signalling told us of the four most common mutations in the Wnt pathway that could lead to a cell turning cancerous.  This will be our other focus moving forward: finding out more about the big four mutations, and trying to implement them into our system.

The next few days will be full of us attempting to make last minute adjustments to our system with the suggestions proposed by the two experts.  I am confident we can get everything researched and implemented before the final presentation, and make the best system possible with the information we have thus far.

An Expert's Opinion and a Student's Shock

This week we had the opportunity to speak to two professionals doing work related to our GI Cancer study: Dr. Xi He, an expert on Wnt signaling, and Dr. Donald Coen, a virology department faculty member at Harvard. Both had incredible insight for our project and were able to provide a lot of great feedback for our team.

That said, speaking with them also made me wonder what on Earth we were doing.

Well, that is a bit of an exaggeration, but the point is that I had no idea how much we still had to cover for our project to even be close to a feasible solution. It's one thing to go online and read literature about a biological system, it's another thing entirely to hear from someone who has spent their entire life researching that system. Sure, both posed many questions we were prepared to answer, but many times their feedback led us to more and more that we still had to look into. For example, in my last post, I raved about the EBV virus. From Dr. Coen's input, it turns out that there are many far better options that I have to look into! Similarly, Dr. He outlined four clear cellular malfunctions that can lead to the development of GI cancer, which we had previously not looked into.

By no means is this a negative thing. Seeing how much work is still to be done was certainly shocking, but now we have the opportunity to improve our system significantly thanks to the opinions of the experts. Getting clear feedback was hugely important to making sure we were on the right track, and though we still have a lot to do, I think we are definitely getting there.