Goldilocks and the Three Ideas

Between iGEM and 20.020, I am beginning to feel a little like Goldilocks.  I am also feeling that a love of reading is a necessity. To put it more accurately, a love of skimming. Over the past few weeks, I have read what feels like countless papers. Coming up with ideas for a synthetic biology project sounds like it relies on creativity and knowledge of biology.  Although both those aspects are necessary, so are Google and PubMed and Google Scholar and many other databases full of scientific papers as we need to have a better understanding of what genes have been sequenced and what types of proteins and cell actions can help us accomplish our project's goal. Although I have just started this process for 20.020, iGEM has at least partially prepared me for the search for papers pertaining to our cancer detection project that are to come. Bring on the abstracts, fancy graphs, and really long names of proteins that I cannot pronounce! (Speaking of things I cannot pronounce, we has our presentations on Wednesday and, despite practicing, I still messed up pronouncing the names of a few proteins. That really frustrated me because I really did not want to let down the people on our team.)
Now all these papers are what make me feel like Goldilocks.  When creating a synthetic biology project, you have to find the project that is just right. If there has been a lot of research done on the topic, other labs are probably working on the project. If there has not been enough research done, that might be because the project is not feasible, profitable, or there is just not enough known about the causes or treatment of the issue for a synthetic biology approach to be taken yet. (In iGEM, all four of our groups have had panic moments when reading papers that began to reveal both ends of the spectrum.)  When we decided on our three ideas, we dealt with this issue.  The biological sunscreen was really cool, but it might not work because people would be hesitant to use viruses to change there cells.  Rapid wound sealing would be a really interesting project, but we are not really sure how we could put something to clot blood in the blood without causing clots and there had not really been enough research done yet about the techniques we were investigating.  Luckily, the cancer detection and treatment idea was novel and exciting.  Regardless, we are still working on modifying the idea as we discover what is actually possible (like do we really know exactly how to tell which cells are cancer cells) and what may have already been done (like tagging them with something like GFP).  Regardless, I think playing the role of Goldilocks and reading all these papers is worth it as we come closer to developing a focused project.

A Turtle with a Strawberry

      Wow, time really seems to be flying by.  It seems like we've just barely started the semester and yet we're already through our three ideas presentation and on our way to specifying our final system.  Among my team's 3 ideas - early cancer detection, biological UV protection and rapid wound sealing - we decided to move forward with the early cancer detection system.  I felt pretty good about each of the ideas but I think we made a good decision in the end.  Cancer is definitely a "hot" subject area plus, I might be able to use some of the immunology-related research I've been doing for my iGEM project to help with the sensing/localization side of things.  This weekend will likely see a lot more research for each of us and I'm excited to see what we come up with; especially because we can be a little more optimistic  as far as functionality goes since we won't actually be building the final system.
      I'm still really enjoying the class.  Everyone - Natalie, 20.385 mentors, other 20.020 students - have been great to work with and it's cool to see how people approach these kinds of problems that we're setting out to solve.
      On a slightly less academic note, I would like to give a huge shout out to Natalie for making presentation day a little less intimidating by getting us all Chipotle.

3 Ideas Later...

Well we have finally made it through the "Three Ideas Presentation", and as of yesterday, have finally narrowed down our many ideas to one topic.  The presentation itself allowed for myself, as well as the rest of my team, to further explore particular areas of synthetic biology in hopes to find a project area to explore.

Many ideas were tossed around, but eventually we settled on a cancer detection method, more efficient wound sealant, and a biological sunscreen.  The eventual single idea we settle on had to do with the search for innovative cancer detection methods, to better detect cancerous cells at an earlier stage in development.  Although all ideas posed plausible areas of expansion, we decided that the project pertaining to cancer research had the widest range of possibilities available.

In the next few weeks we will see where our initial ideas will take us.  In addition to this, we must consider all ethical, societal, and environmental concerns which will inevitably arise as a result.  The coming weeks will be very enlightening to say the least, and will more than likely create complex thinking among our group en route to proposing the best final presentation we can.  I'm sure looking forward to it!

From Proposals to Presentations

The past two weeks haven't felt the same in terms of the activities and procedures we went through, but I suppose that makes sense; we've been intently proposing and researching ideas, culminating in the 3 ideas presentations this past Wednesday. This open agenda of proposals to research to presentations felt quite different, seeing how we were now entirely responsible for the direction of our time and energy, but that isn't necessarily a bad thing. I suppose this is the kind of thing grad students do, albeit with more experience in their field and insight into how to solve the world's problems... This is the thing innovators do, right? They surely don't come up with these things overnight... it's much too difficult!
I think I enjoy presenting a lot, but I'd much rather have material rehearsed and ready to go rather than talking from a tablet; I just wish I had more time to invest in the preparation of the presentation.

Team Salty Microbial Helix is Forced to Change Names

This was a fun week in 20.020! I had a good time coming up with our three ideas and I’m excited to see where our project (plastic decomposition) goes next. We also need a new team name now that our project has nothing to do with salt, microbes, or helices... suggestions?

I learned to be concerned about the environment from my mom, an environmental engineer, so I'm glad we picked a topic that will help the planet. I was always the one turning off all the lights in our house and making sure to recycle and compost as much as we possibly could. Although a complete solution to the plastic problem is probably a pipe dream at this point, it is so cool to imagine that I could design something with such a big impact on the world… sigh.

Scientists have developed thousands of different kinds of plastics, so figuring out how to take them into account is the first puzzle that I’m trying to wrap my head around. Right now we are envisioning an immune-system-like approach that can respond to different types of plastic the system encounters, similarly to how the body’s immune system can ward off foreign antigens. This is really cool to think about even if it is pretty crazy. I think we’re going to have a hard time making it work for every kind of plastic on the planet, so we have to prioritize. Should we focus on the most harmful plastics? The most numerous ones? The ones that can’t be recycled? All things to think about. If building a plastic decomposition system that can attack multiple variants of plastic proves too challenging, our fallback plan is to focus on Styrofoam. It’s a big problem and I think it’ll have to be narrowed down at least a little bit before we can really tackle it, but I’m excited to start designing!

Team 99 Bottles

Excitement.

My team and I just finished our presentation about our 3 ideas, and I'm starting to feel a real sense of direction for our project. Although everything is just speculation right now, the preliminary research that we conducted online shows that others have done concrete things with the decomposition of plastic, and that gives me hope that our project can accomplish something substantial.

Of course, this is probably the point in the project when the hype is most real, but still.

So we've decided to focus on the decomposition of plastics, and we're going to do more research into the different types of plastic, the bacterial methods out there, and the possibility of involving sensor cells. There are a ton of possibilities for where this could be headed right now.

On another note, this is my first project-based class at MIT and I'm loving it. I love the sense of creating something with a team, even if it is just a powerpoint presentation.

I'm definitely looking forward to launching into the project.

We chose a project! Go team!

This week we presented our three ideas: water desalination, plastic decomposition and stress reduction via the microbiome. The presentation went pretty well, and then we decided to look at plastic decomposition. I'm excited!

Digression: I wrote a song about our project:
99 bottles just floating around
99 bottles of plastic
Add some cells, stir it around
98 bottles just floating around

Having watched the video last week about labs in Cambridge (and neglecting to blog about it), I think it's important that we consider the ethics and safety of our project.

Ethically, how much can we manipulate our environment? Is it alright to use organisms to fix the problems that humanity has created? I would say yes, as an engineer, but a lot of people might say we have to leave nature alone for the same reason they may not eat meat.

Further, is it ethical to displace current organisms in landfills and/or the ocean? I would argue that as long as our organism primarily consumes that which other organisms cannot (therefore, is a niche organism), then our organism is not trespassing on the territory of current organisms in a morally wrong way.

Moving now to safety, what could go wrong? First, we need to make sure that our solution is non-pathogenic. That shouldn't be too hard, as long as we just steer clear of any infection vectors.

Second, how do we contain our solution? If we contain the process in some kind of vat, we might need to sanitize the vat before releasing the degraded plastic, but that might reduce the benefits of our process. If we use the process in some kind of landfill, we might need to make sure the cells won't drift off on an airborne plastic bag.

One possibility is to embed our solution in the microbiome of an animal. Hopefully, by making our solution dependent on the animal, we reduce the difficulty of controlling the solution to an animal-control problem, which is fairly well understood (see: mouse-trap, rodent exterminators, fishing nets).

Third, if everything goes wrong, what do we do? Another idea I've been toying with is making the solution dependent on some chemical that they can't self-synthesize, so if we stop providing that chemical, then they all quickly die off. Additionally, there should be a chemical that causes the cells to instantly commit suicide, and hopefully a feedback reaction would cause a small amount of this chemical to quickly propogate and kill off the entire species of our solution. After all, no one can predict exactly what will happen, so we need to build a big, red button into our system.

I'm looking forward to taking a more detailed look at our project in the next couple of weeks! There should be some really cool engineering going on.

Colin