Overview

The Peking iGEM 2017 team took part in three major aspects of Integrated human practice work.
First of all, we evaluated the possible impact of our work in the “real world” by visiting two distinguished synthetic biology companies, SynBioTech and Bluepha. We then visited both an electrical engineering expert and a synthetic biologist, creating an interdisciplinary communication environment. Based on their feedback, we further designed a handbook for synthetic biologists and a lecture for electrical engineering students. Since it is the 10th anniversary of Peking iGEM, we organized a series of activities to commemorate the culture and spirit of the team.

The ethical, social, legal, and environmental impact of a concept usually unfolds when it is transformed from a novel idea into a “real world” project, especially when it is applied to the practice of production. Sometimes it is too late to solve the problems at that time, which makes a thorough consideration in advance quite essential.

Teams concerned with theoretical projects of the iGEM competition are often limited to talking to other researchers about their work, and in a sense must ignore the application of their work in the “real world”. This is not to say that we do not need to consider wider implications of our work. We surveyed two distinguished synthetic biology companies, SynBioTech and Bluepha.

We focused on two questions during the investigation:

1. When an idea is converted into an application, what should be thoroughly considered?
2. What do we expect for sequential logic programming from the perspective of industry?

About the third question, Dr. Yin suggested two potential areas. The first is an automatic cell factory that can repress redundant metabolism pathways and shift to production once proliferation is completed. This procedure has the possibility to be triggered by the cell’s internal control circuits, in the absence of outside control. This is of central concern to BluePHA. He also suggested engineering cell cycles to let normal bacteria adapt to harsh environments, which need pollution abatement or environmental improvement.

We also discussed with chief information official Dr. Jiang Hao on software design. He suggested that we can incorporate deterministic model for prediction of sequence candidate performance during screening. Stochastic simulation can be used only in visualization of detailed sequence behavior. The talk inspired us a lot for how to convert our project into an application, especially in modeling and designing.

Interview

With synthetic biologist

We first visited Dr. Wei Ping from the center of quantitative biology, whose research interest mainly lies in reconsidering and programming important cellular signal-transduction networks. Dr. Wei carefully listened to our design principles and voiced his concerns:

1. The coding capacity of the system.
2. The connection between the clock module and the flip-flop module.
3. The necessity of a CAD system.

During the interview, Dr. Wei was at first slightly confused by several concepts from electrical engineering. As the conversation went deeper, he found our project interesting, since we based our design on the development of electrical engineering and introduced the design principles into synthetic biology. He further had several pieces of advice for us:

1. A good researcher should always be open-minded. Although we designed our project from the viewpoint of engineering, we can still consider applying the idea to fundamental research topics such as cellular differentiation on a population level. Never restrict our sight only to the purely technical side.
2. We can demonstrate the periodical changes generated by Repressilator through continual observing of colonies.

With electrical engineering expert

We then visited Prof. Chen Jiang from the Institute of Advanced Communications, who has been teaching Electronic Circuits (A) for years. We showed him how recombinase works and demonstrated our design of the system. Prof. Chen soon recognized that we are actually building a T-Flip-Flop in cells, and was keen about designing other types of flip-flops. His interests include:

1. The properties of the repressilator in synthetic biology.
2. The biological realization of cascading in synthetic biology.

Prof. Chen failed to realize the complexity of living systems in a cell at first. We then showed him that the entropy of the system can be much greater than in electrical systems. Thus, the requirements for design rules are quite strict. Prof. Chen encouraged us to further explore the topic, and inspired us to pursue signal noise reduction and a D-flip-flop.

Bridging

A great number of synthetic biologists have built and characterized a variety of logic gates in a number of organisms, and are familiar with combinational logic, Boolean algebra and design automation, which used to be terms of electrical engineering and computer science. On the other side, students and researchers focusing on electrical engineering and computer science gained a much deeper understanding of the models from biological research, such as neural networks. However, we found that such interchange between two subjects usually stops at some specific concepts, and lacks a general view of the development and the frontiers of the subjects.

Therefore, communication channels should be established and mutual understanding should be promoted. Through the interviews with two experts, we recognized that both sides showed a strong willingness to know the other domain more. This, however, was confronted with some barriers, from basic concepts to perspectives of analysis. We, as a team of mixed backgrounds, pioneered the bridging between two types of researchers.

1. We designed a handbook for synthetic biologists, which clarifies basic units as well as design principles in electrical engineering. We hope it will help inspire novel ideas, designs, and analytical views.
2. We gave the EE students several lectures on synthetic biology. We introduced the history and development of the subject and great past achievements of iGEM.

It has been 10 years since the first Peking team joined the iGEM competition as well as the iGEM community. We organized a series of Peking iGEM 10th Anniversary activities, such as a team reunion, reminiscence collection, trying to keep a detailed documentation of the culture and spirit alongside the developments of a decade.







The following is the invitation letter we sent to the former team members of Peking iGEM, from 2007 to 2016.





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