Education

PHB Simulator

One of the projects we took on this year was to see how we can use software tools to make the complex processes in synthetic biology a bit more accessible to the public. Several team members did not come from a biology background, so we decided to create a visual simulation that would demonstrate the pathways and enzymes involved in PHB production to a nonacademic audience. We were inspired by the Swarm Design lab lead by Dr. Jacob, which used game engines such as Unity and UnReal to create visual and virtual reality models of the entire human body.

PHB Simulator arose out of a preexisting project that demonstrated the Lac Operon in an E. coli cell. We took the cell and instead of using it for the Lac Operon, used it to simulate the Beta Oxidation and Glycolysis pathways, and the enzymes that are used to create PHB. In the simulation the user can explore in two different ways. First, the two pathways are isolated in glass jars which contain just the enzymes responsible for turning VFAs into PHB or acetyl-CoA into PHB. At each of these jars, the user is able to spawn either VFA or acetyl-CoA molecules and then watch the sequence and order of enzymes that it takes to transform it into PHB. Like in our real life system, once a molecule is transformed (indicated by turning a pale blue) it floats around in the medium, implying that some method of post processing, like the electrocoagulation method, is applied to the media.

The second option is for the user to actually view this process inside an E. coli cell. Here, there is an additional educational component in that the user can select any molecule and learn more about it. For example, when selecting a floating enzyme, the user will receive the name, graphic, which gene this enzyme comes from, as well as a brief description regarding where in the process it falls.

The cell view also has buttons that help guide the user through the glycolysis and beta oxidation pathways. This is because the VFA or acetyl-CoA molecule will change after each enzyme interaction, meaning it turns into anywhere from three to four other molecules on its way to becoming PHB. We recognize that a user might not realize this or be able to catch the molecule in one of its intermediary stages, so this function is intended to educate on every part of the system, not just those are the obvious and always present.

We have used our team and mentors as beta testers on the program, and in future steps would like to incorporate it into a virtual reality experience with the Oculus Rift. Unfortunately, due to the very large file size of the simulation, the wiki servers were not able to upload it. However, we will be demonstrating it at our poster during the course of the Jamboree if you are interested in taking a look. It comes in both a Windows and Mac executable file (just like an application).

Access to Synthetic Biology

Synthetic biology is an important tool to explore new worlds and improve our own. If people all over the world shared an equal (and robust) understanding of the principles of synthetic biology, multinational collaboration on synthetic biology projects would be possible – this could improve quality of life across the world through the development of synthetic biology-based novel pharmaceutical therapies, environmental remediation, and materials manufacturing processes. The open-source nature of synthetic biology and the close connections between the synthetic biology and information technology sectors would suggest that people all over the world are able to take part in synthetic biology projects, yet work in synthetic biology is largely undertaken by academic institutions in North America and Western Europe, and these geographic regions are overrepresented in international conferences such as iGEM.

Synthetic biology has been compared to computing in that the structure of the synthetic biology community is open-source. This is not limited to information sharing within and between academic institutions; the public is already aware of synthetic biology and synthetic biology will become more and more relevant to the interests of the public, much like the field of computer science in the latter half of the twentieth century. The open-source nature of the field allows, in theory, for increased access to information and increased opportunities to participate in knowledge creation. Thus, the barriers to accessing synthetic biology are not innate features of the field itself, but are the result of other external factors.

We examined the literature on synthetic biology (and anecdotes from iGEM teams in China and Pakistan) and found two barriers which were present in geographic regions which were seemingly underrepresented in the synthetic biology field (and some regions which were well-represented)

1. Prohibitive cost
2. Social conceptions of synthetic biology: deemed “unnatural” or unethical

Solutions:

The social, political, and economic differences between the different regions in the world which are underrepresented in the synthetic biology community should be considered while implementing these solutions:

With regards to cost:

• researchers could take advantage of lower-cost alternatives to traditional laboratory equipment
• participation in conferences such as iGEM could occur via the internet rather than requiring teams attend in person (this would require a change to conference structure)

• implementing a strong curricular focus on synthetic biology: responsible uses, biosafety
• public outreach campaigns

iGEM Manual