So this is why curing cancer is hard...

The idea that we were going to detect and treat cancer sounded difficult. Obviously no one has really "cured" cancer yet. So we should have expected that it would be a difficult task to take on.  First we looked as what makes tumors different from other cells in the body. We filled multiple whiteboards with different parameters that all had one thing in common: they work sometimes, but other times they create false positives or negatives.  Therefore, we had to narrow what type of cancer we were going to examine. We decided to look as GI cancer because we could report a positive result the same way it was reported in the blue baby project.
Then there were just more papers. I actually found looking for markers of GI cancer to be kind of enjoyable this time. Enjoyable is probably the wrong word there, but I think looking through papers is becoming easier.  I also liked how we were all working together and communicating about what markers we were coming across. Sometimes when we work in small groups in iGEM, we were all working on different aspects of the project and it was difficult to bounce ideas off of each other.  Regardless, through this process we have found something that occurs in many GI cancer cells and we now have a system designed that can detect it.
Designing circuits is also becoming more enjoyable. This is probably because I have a better idea of what we are doing.  Now that I have a general idea about the basics, the problem solving is really fun.   Now if I do major in 20 and ever read this blog post again, I will probably be shaking my head at that last sentence because I just have no idea how much I do not know right now. I suppose that it what is exciting though. Doing really anything with cancer is difficult and there is so much I do not know about synthetic biology and there is so much that is not known in general, but there is just that idea of potential cures and treatments and that is what makes it worth it.  On IB English exams at my high school, there were different writing prompts to choose from and my teacher always told us never to choose the prompt you look at and think "oh I can write everything about that quickly and in one paragraph".  Maybe innovation in general is based on the foundation of never choosing that type of "prompt", whether is be in science, english, math, or really any field.

waddap

We're more than halfway through the course and things are getting technical! It's the slightest bit stressful because I worry I haven't found enough parts to actually specify how to build our system, and I surely can't know all the mechanisms and pathways that go into those parts in the timeframe allotted, right? I don't know. Trying to actually put these things together in a cell correctly would be no laughing matter. I suppose that makes the successful transformations that much more rewarding, but I wonder how many failures will proceed that success, or if it'll ever be reached in the first place.

Tangible Progress

After working on this project for a couple of days, I feel like I have a much better grasp of what creating a prototype would actually entail. Breaking down our system into devices, and then parts, has been really helpful in making everything seem more plausible. It seems that if we complete the design and find the appropriate parts, we could just order a batch of products online and make our project a reality! Of course, I realize that things are not that simple: physical models don't always work the way they should in theory. But working with the theory has been really exciting because there are no physical impediments to limit our progress in designing the project. Our design only has to satisfy logic and previous knowledge of biological parts.

Having said that, I have been surprised at our progress. Instead of being steady, it seems to occur in bursts, when someone finds a part we can use. These bursts are then followed by periods of stagnation in which everyone is researching on their laptop. I wonder if this is what bioengineering is actually like.

And of course, I shouldn't neglect to mention that the team theme song, costumes, and bat signal also seem to be under development.

Still Trying to Cure Cancer...

It's still a work in progress.  Nevertheless we're heading down the right path for our Tech Spec Review next week.  We have settle on a more focused project, rather than blindly attempting to cure all forms of cancer.  We decided to attack gastrointestinal cancer, being that the detection method would be much easier than other forms of internal cancer.  The exact signal is unknown at the moment, but it will hopefully turn out to be much easier and less painful than the previous detection method of sticking scope down the patient's throat.

Our method revolves around the wnt pathway.  One main issue with this is attempting to delocalize the signal given off by one cell, to many, to allow for the patient to more easily detect whether or not they have cancer.  In other words, we need to find a method for the signal to be amplified from the original cell.

This is just one of the many problems we must confront when dealing with such a complex biological pathway.  Cancer sucks, and we're attempting to find not a way to fight it, but to recognize it.  This way, it can be more efficiently and accurately treated in the future.  I'm really looking forward towards how this project will turn out next Thursday; as of now it has a lot of promise.  Also, turtles are cool.

Preparing for the Tech Spec

Tuesday: I’m excited that our design for a plastic decomposition system is starting to come together! Breaking down the system into a device diagram and a parts diagram has really helped me to understand the thought process that goes into designing it. I never felt before that I could engineer something that hasn’t been made before, but this way of thinking has given me confidence that I can approach these problems in a systematic way. It is slow going; our group spent a long time coming up with a device diagram only to spend another long time re-doing it, and I suspect the parts diagram will be constructed the same way. We really have our work cut out for us before the tech spec.

Wednesday: We have moved on from the device diagram to the parts diagram, and now this project is starting to seem a little overwhelming. Where do we even start with finding promoters that work, or compounds that will bind to our plastics of interest? It looks like we may have to narrow down our sensing capabilities to just one plastic, and even that is complicated. The chances are next to none that we will find promoters specific to exactly the plastics we are looking for, but our task becomes more complicated with every step we add to the pathway in between. It’s a lot to think about, for sure, but I still think the project is worth taking forward. Even if our final design doesn’t work out, this experience has already been so valuable to me.

Moving forward, it looks like we will have to think more about our chassis and our sensing systems. E.coli can’t survive for very long in salt water, so we may have to switch organisms or focus on landfills instead of oceans. Sensors are difficult, because most plastics are too big to enter a cell, so we would need some sort of signaling pathway to get our promoters going. We’ll definitely need to address these questions before the Tech Spec next Wednesday, because I’m sure it will give us even more to think about!

Cure to Cancer--Coming Soon from a Group of 18-Year-Olds?

It had been a while since I was able to actually put in a decent amount of time and effort into a presentation, so I went “ham” on this last one. I also was pretty bad at using Google Slide before we made this presentation, so I went extra ham on the presentation so I could learn how to use Google Slides well. After spending 2 hours drawing my own pictures on the PowerPoint and making sure every picture looked just the way I wanted and everything was formatted well, I felt like I had picked up some nice PowerPoint making skills—score! Also, I felt the actual presentation went well for me. I didn’t stutter too much, and I made sure to project my voice loud and clear.

The day after when we had to pick our final project, I felt like I had to pick which child I loved most. This actually wasn’t hard because we all know parents secretly love one child more than the others (kidding). I wasn’t too sad to see the artificial wound sealing project go—it didn’t seem like it would be that successful anyway, and the competition was too tough. I was genuinely sad to have to kick my own project, the biological sunscreen, off the list. While I think it was actually very novel and something that was genuinely doable that would have a large impact on a lot of people, there were just too many bioethical issues that would come into play. No one would be willing to modify his own genome, even if it meant protection from skin cancer. On the one hand, I was very happy to see that we’re working on cancer because it’s so broad and we could help so many people if we were to design a successful system for detecting cancer, but I’m also perturbed at how slim our chances of success seem. Labs all over the world are working on things like cancer detection methods, and there’s no way a few 18 year olds would be able to do it better than them. The competition is fierce, so if we want to develop a significant project, we would either need a stroke of genius to find a unique solution, or we would need to target a very specific problem that few labs are working on.

This is important to me because something I decided when we started the project was that I wanted to make system that could genuinely help people, and I’m afraid that might be difficult to accomplish in the area we’re currently trying to develop a system for.

Curing Cancer and Other Daily 20.020 Happenings

The past two weeks have held lots of exciting developments in terms of our 20.020 projects. One of the most difficult things for me personally has been choosing between all of the incredible ideas that have come up during team brainstorming sessions. In the end, we decided to go the route of developing a cancer detection mechanism, but there were plenty of other ideas that would have also provided interesting opportunities for us to pursue.

That said, the cancer detection idea is one that I am especially enthusiastic about. I have been interested in cancer biology for a very long time, and it's exciting to finally be able to work with a team and think critically about a solution. Cancer is a disease that has very clear-cut knowledge surrounding it, but it is also enigmatic in many ways. As an example, scientists know how to kill cancer cells in vitro, and sometimes this translates well to patient applications, but cancerous growths are able to undergo angiogenesis and create their own 'microenvironment' of sorts that prevents many treatments from safely reaching them. This paradoxical nature of the disease is what makes cancer so deadly. You would also be hard-pressed to find someone who has not been affected-- directly or vis a vis a family member or friend-- by cancer. While our project is mainly theoretical, who knows where it could lead in the future? I know that I personally would love to partake in cancer research at some point, and research-based knowledge like what we're gaining through this project would be extremely helpful going in to something like that. 

Moving forward, it's important to go in with the understanding that this is a difficult issue. Researchers have been working on treating cancer for nearly a century now. It is a problem that has left many great minds in the dark. Granted, we are not trying to physically cure cancer, but from here on the project is no longer based on what looks interesting or fun to pursue. We need to get very critical and investigative about what makes this disease tick, and I am so excited to get started.