Team:XMU-China/Human Practices
The Escherichia coli colonies simulating the interation between groups is chosen to be this year’s theme after brainstorm. It should be significantly noticed that the content of our project is not limited to traditional synthetic biology, but also extended to traditional social sciences as Sociology and emerging interdisciplinary subjects as Molecular Anthropology. In order to ensure the rigor of our project, we refer to the classical sociological research methods to carry out our Human Practices which is combined with Wet Lab and Dry Lab organically.
Meanwhile, there’s also a wiki page showing what we have done in Public Engagement such as annual science-popularizing activities which aim to promote basic knowledge of SynBio to the public, especially kids and teenagers.
Fig. 1. 2019 XMU-China project’s workflow
This year, we have thought carefully and creatively about whether our work is responsible and good for the world. Specifically, three methods, “Literature Analysis”, “Interview” and “Questionnaire & Field Surveys”, were used to execute the Human Practices, which affected and corrected the design of genetic circuits and the progress of experiments.
What we have learned is indicated below in bold.
Literature Analysis
The team members have extensively read plentiful literatures of sociology and microbiology, which solidly established the foundation for our project. Some of the ideas that support our work were refined, which became the background and logical basis.
Using microbes for group interactions often gains interesting results. Japanese scientist Nakagaki (1) used slime molds to crack a maze successfully in 2004. In 2010, Tero (2) just spent 26 hours by using slime molds and sweet oat granules simulating the road map of Japanese Shinkansen which actually spent several decades to build. People wondered why slime molds without nervous systems can solve such complicated network problem in such a short time, but no wan can give a convincing answer so far. Shapiro (3) pointed out in 2007 that bacteria have cognitive, computational and evolutionary abilities. Meanwhile, they can utilize complex intercellular communication mechanisms to control the basic cellular biology functions of “advanced” plants and animals, which means that it is possible to use bacteria to simulate some basic social forms or interactions.
Bourke, an evolutionary biologist, gives an explanation for the biological evolution to social evolution. He believes that: genes form genomes, prokaryotic cells and protobacteria form eukaryote cells, eukaryote cells form multicelled organisms and multicelled organisms form eusocial societies or join with other organisms to form mutualisms (4).
In fact, observing the evolution of a stable species to another stable species can better help us understand the social structure. However, due to the consideration of time cost, it seems to be a more viable way by using synthetic biological method to create engineering bacteria with different functions that we need directly.
So, we abstracted group interactions into Mutual Benefit, Altruism, Spite and Selfishness. Our team prepared to build genetic circuits around these 4 relationships.
Interview
During different stage of our project, the team members communicated with professors from the departments like Molecular Anthropology, Bioenergy Engineering, Sociology and Public Affairs Management respectively, whose feedbacks helped a lot to determine the subject of the project and the track of the experiment design.
Chao Chen, assistant professor of sociology.
After the literature research stage, we preliminarily decided to carry out our follow-up human practice with the subject of bacterial simulated sociological relationship. For this reason, we visited and interviewed Dr. Chen, assistant professor of sociology.
After introducing the preliminary idea of our project to him, Dr. Chen gave his two suggestions.
Firstly, how to combine our subject, the synthetic biology with sociological theory. Dr. Chen mentioned that one of the cornerstones of economic theory construction - human is rational and self-interest, so he suggested that we should take the personality characteristics and environmental conditions of the subject as parameters, and use synthetic biology to carry out sociological experiments that strictly control the variables of the subject, which shares similarity to computer simulation.
Secondly, for the four kinds of social relations initially designed in our project, he gives some analogical historical facts or economic principles as the display carrier, and the corresponding relations are as follows:
Mutual benefit - comparative advantage of economics;
Altruism - crowdfunding;
Spite - Japan and Holland fought for colonies in World War II;
Selfishness - British colonization of India.
In the end, he also raised a question that the behavior of engineering bacteria is determined by genes. For engineering bacteria, they have no spontaneous motivation to drive a series of events, slightly deviated from the reality.
Xianhai Zeng, a professor from the college of energy in Xiamen University, his research interests are in biorefinery and bioenergy.
In our project, we successfully verified the secretion and positive enzymatic activity of Cex and CenA. However, during the experiments, we regreted to find that for unknown reasons, beta-glucosidase (Bgl1A) secreted outside the cell has no activity. For the design we originally demonstrated, this was the result we didn't want to see.
In desperation, we had to ask for help. In our communication with Prof. Zeng, we learned that E.coli itself has the ability to transport cellobiose, so we didn't need to secrete Bgl1A, and just to prove its intracellular enzymatic activity.
In addition, we got the relevant reference (5) shared by Prof. Zeng. Thanks to Prof. Zeng, we finally changed the design of our demonstration.
Linbin Zhu, an assistant professor from the school of public affairs in Xiamen University. He is a scholar with rich experiences and now works in a department of social science, while he got his bachelor’s degree in biochemistry.
We introduced Dr. Zhu our project of this year and showed him a paper about social biology which inspired us at the very beginning of the brainstorm. After listening to our introduction and briefly scanning the paper, he got a primary understanding of what we were doing this year.
“Can you explain your experiments’ results from the perspective of dynamic game theory? Can your experiments achieve multiple games from a single game?” Dr. Zhu made a brief description of the future development of our project. He gave us a lot of understanding and encouragement about the concerns we had felt about using the relationship between the flora to simulate the relationship between advanced human groups, “Maybe it doesn’t make sense, however, I think innovation and creation should be encouraged. Your project provides new ideas and methods for social science research, which is very valuable. And in my opinion, there is no problem that you abstract the relationship between groups into the simple ‘positive’ and ‘negative’ descriptions.”
In summary, Dr. Zhu gave a positive evaluation to our project. He advised us that we ought to read and refer more literatures about social group ecology and group dynamics as well
. Liang, another assistant professor from the school of public affairs as well. Dr. Liang also has a background of science, while he is studying the environmental policies and forest-protection policies.
“It will be more interesting to address in a longer historical dimension, I think.” He said. This sentence reminded us of the group evolution theory we have heard before. Dr. Liang figured that if we started from a perspective of group, our project might provide a possibility for the prediction of human society. Hence we introduced the carrier we would utilize to give a presentation to Dr. Liang, which is section of Gone with the Wind. In our opinion, a character in the novel or movie stands for a kind of people, even a group, rather than an individual. What we hope is to simulate a development of group interaction in a certain status of time by the plots in Gone with the Wind. Dr. Liang gave a positive assess to this, which was better than how we presented in the early time. In addition, we also extended to the theory of economic man. Dr. Liang sighed, “If you could reproduce the choice of economic man under certain special circumstances and point out the inevitable results in those situations, then your project would be very attractive and interesting!”
He continued, “To quantify human’s behaviors has always been controversial. As what I have just said, due to the subjective initiative of human, it’s actually a very difficult matter for us to quantify human’s behaviors.”
Through this talk, we have resolutely adopted the idea that the group interaction is our carrier of project rather than social relationship.
Chuanchao Wang, a professor from the school of sociology and anthropology in Xiamen University. Prof. Wang is an experienced scholar whose research fields are mainly molecular anthropology and ancient DNA research.
“Because of division of labor, people can form social structures from chaos. Is it feasible to research the birth process of social structure by simulating chaos with unmodified bacteria and introducing exogenous genes as division of labor?” Our teammate asked him. And he told us that the formation of social structure is a very complex process, which needs a long-time evolution. But E. coli can iterate quickly. And it would be meaningful to see how E. coli responds to imported foreign genes at genetic level, which somehow shorten the long evolutionary observation time.
Prof. wang also proposed an idea about our design. He suggested that we could give E. coli more freedom, and observe them when they are cultivated with unimproved bacteria, especially in the culture of restrictive conditions. This condition can better simulate the evolution process and reflect a kind of social behavior motivation to survive and transmit their genes. This interview had strengthened our confidence that we have identified the project’s carrier is group relationships rather than social relationships.
Questionnaire & Field Surveys
Speaking of the details of surveys, the questionnaire was elaborated by using social-science research method (6), and comprehensive investigation was conducted in iGEM Community and the public. The team members also attended various exchange meetings in China, and discussed with many teams. According to these activities, the ways of displaying the project were refreshed. Based on the results of the questionnaire and suggestions from other teams, the team members interviewed Prof. Li who is in charge of Marine Culture Collection of China (MCCC), which solved the problem about the classification of bacterial species.
This year's iGEM Southern China Regional Meeting was held in Shenzhen University. Some of our team members participated in this meeting. More than a dozen teams from south China introduced their project design during the meeting. The meeting prompted us to establish contact with several participating teams after the meeting.
During the brainstorm stage of our team, there was an idea that was promoting at that time: using alkaloids to kill fouling organism barnacles. This project was surprisingly similar to the design introduced by Greatbay_SCIE in the meeting presentation. We had more in-depth communications with Greatbay_SCIE team for genetic circuits. As we hope to construct innovative project, this stimulated us to explore more new fields through brainstorm. The meeting was a great impetus for us to turn our attention to the study of sociology using synthetic biology.
CCiC is the short name of the Conference of China iGEMer Community. This year, the sixth CCiC was held in Shenzhen Advanced Research Institute of the Chinese Academy of Sciences from August 19th to 23rd. The theme of this year’s conference was “Automation & Innovation”. XMU-China participated in this conference.
Through the poster session, we actively communicated with other teams during the conference. We gained a lot of experience and suggestions from other teams, which helped us to improve the experimental schemes and run experiments more efficiently.
By giving a presentation on stage to showcase the design, we received many questions and suggestions from judges and audiences.
There are three main doubts:
Firstly, some audiences questioned that the concept of “social relationship” should exist between the same species. It was difficult to judge whether the E. coli that was artificially introduced different foreign genes were still the same species.
Secondly, some judges pointed that the social relations in human society were ever-changing and diverse, so only four relationships we showed could not summarize them all.
Finally, the use of the word "social relations" is not rigorous enough and is too vague.
We conducted a questionnaire survey on the possible applications of our project in sociology.
After discussions, the questionnaire was divided into three parts: basic information, social relations and bacterial group relations. From the simplest ones, we use the most understandable way to convey our definition of the group relation of bacteria.
We have collected nearly 400 questionnaires, including students from various professional backgrounds. Now, we have selected some of the survey results of our questionnaire for display.
Question 1: What factors do you think will affect social relations?
It can be seen that stake as a factor affecting social relations is almost unanimously recognized.
Question 2: Do you think that social relations can be refined into certain types?
It can be seen that more than 60% of the students think social relations can be refined into certain types.
Question 3: Do you think there is a similar social relationship in the cells before the transformation?
It can be seen that more than 70% of students are optimistic about the existence of similar social relationships in the cells before the transformation.
Question 4: Do you think it is possible to simulate social relations by transforming simpler engineering bacteria and their external culture environment?
It can be seen that more than 70% of students are optimistic about simulating social relations by transforming simpler engineering bacteria and their external culture environment.
MCCC (Marine Culture Collection of China) is the national microbial resources platform.
We learned about the structure of the national microbial resource platform, the process of sample storage, the tools and equipment used in this process and the principle involved.
At the same time, we exchanged our topic this year with Mr. Li of MCCC, hoping to find our answer to the classification of engineering bacteria with his professional knowledge of classification of bacteria.
Mr. Li suggested that the classification of bacteria is based on the difference of 16srDNA. Even though we have carried out foreign plasmid input and transformation on the engineering bacteria, the genome of the bacteria itself has not been changed, so it still belongs to the same strain. In addition, from the perspective of ecology, we classify different bacteria into different roles, such as producer and consumer. But it's from a genetic point of view that we have different bacteria in species, which is a different concept, and it's not to be confused.
This visiting solved the problem that has been bother us, and gives us an understanding of the classification of bacterial species in different academic concepts.
The vitality in Human Practices of XMU-China is relayed this year, combining Wet Lab and Dry Lab with Human Practices activities. From the phase of Brainstorm to the ending of the project, the HP activities played an irreplaceable role in connecting with the iGEM community, faculty of frontier research areas in relevant disciplines and the general public. The maxim by Mr. Peter Carr, “Human Practices is the study of how your work affects the world, and how the world affects your work.”, is embalmed.
In this part, We integrated the investigated issues into our project and expanded on our silver medal activity.
These silver medal activities are indicated below in bold.
During the stage of brainstorm, our team was divided into 5 groups to explore different project directions for the 2019 iGEM competition. We initially constructed 5 alternative projects in 8 weeks, You can see all of our alternative projects in our Description page.
With these preliminary projects, we joined this year’s Southern China Regional Meeting, hoping this meeting could help us determine our final project.
During the brainstorm stage of our team, there was an idea that was promoting at that time: using alkaloids to kill fouling organism barnacles. This was surprisingly similar to the design introduced by Greatbay_SCIE in the meeting presentation. We had more in-depth communication with Greatbay_SCIE team for genetic circuit.
As we hope to construct innovative project, this stimulated us to explore more new fields through brainstorm. The meeting was a great impetus for us to turn our attention to the study of sociology using synthetic biology.
Then we did a pointed Literature Analysis and summarized some ideas that could support this project. Bourke, an evolutionary biologist, gives an explanation for the biological evolution to social evolution. He believes that: genes form genomes, prokaryotic cells and protobacteria form eukaryote cells, eukaryote cells form multicelled organisms and multicelled organisms form eusocial societies or join with other organisms to form mutualisms. (4)
It was the origin version of our project.
During the stage of design, we tried to design circuits for several social relationships, but they all stayed at the genetic level, which includes the secretion of antibiotics, group effects, etc.
When we discussed our preliminary design with sociology teacher Dr. Chen, he suggested that we should take the personality characteristics and environmental conditions of the subject as parameters, and use synthetic biology to carry out sociological experiments that strictly control the variables of the subject.
Inspired by this, we began to redesign genetic circuits from both environmental and genetic aspects. And the genes and environment correspond to the personality characteristics and environmental conditions.
In addition, we also expanded our activities and conducted extensive sociological literature searches to prove the rationality and feasibility of using personality and environment as control variables.
During the stage of experiment, our experiments at CenA, Cex, Bgl1A were in trouble.
In the experiment of CenA, we have some difficulties in characterization. So we communicated with UESTC-China team about the characterization methods of CenA and got the reference of the enzyme activity determination methods of CenA from them. At last, CenA enzyme activity was determined by using their protocol of Congo red test.
In the experiment of CenA, we met some trouble when determine enzymatic activity of our exoglucanase. So, we want to try more types of exonuclease, we had collaboration with HUBU-WUHAN. We received the plasmids of HUBU-WUHAN that are gene coding CBH I and Cc Exgs and determined enzymatic activities of CBH I and Cc Exgs in our method.
In the experiment of Bgl1A, we regretted to find that for unknown reasons, beta-glucosidase (Bgl1A) secreted outside the cell has no activity. We ask for help to Prof. Zeng, In our communication with Prof. Zeng, we learned that E.coli itself has the ability to transport cellobiose, so we didn't need to secrete Bgl1A, and just to prove its intracellular enzymatic activity.
During the stage of Refine Project, we actively communicated with other teams during the 7th CCiC meeting and gained a lot of experience and suggestions from others.
We summarize these into three questions:
Firstly, some audiences questioned that the concept of “social relationship” should exist between the same species. It was difficult to judge whether the E. coli that was artificially introduced different foreign genes were still the same species.
Secondly, some judges pointed that the social relations in human society were ever-changing and diverse, so only four relationships we showed could not summarize them all.
Finally, the use of the word "social relations" is not rigorous enough and is too vague.
For the first question, we visited MCCC and exchanged our topic this year with Mr. Li. Mr. Li suggested that the classification of bacteria is based on the difference of 16srDNA. Even though we have carried out foreign plasmid input and transformation on the engineering bacteria, the genome of the bacteria itself has not been changed, so it still belongs to the same strain. In addition, from the perspective of ecology, we classify different bacteria into different roles, such as producer and consumer. But it's from a genetic point of view that we have different bacteria in species, which is a different concept, and it's not to be confused. This visiting solved the first question that has been bother us.
For the second question, we conducted a questionnaire survey on the possible applications of our project in sociology. In question there: “Do you think that social relations can be refined into certain types.” more than 60% of the students think it is feasible. At the same time, we interviewed Dr. Zhu, he thought that is no problem about we abstract the relationship between groups into the simple ‘positive’ and ‘negative’ descriptions.
For the third question, we interviewed two teachers with sociological experience: Dr. Liang, Prof. Wang. Through the interview of Dr. Liang, we have resolutely adopted the idea that the group interaction is our carrier of project rather than social relationship. And through the interview of Prof. Wang, strengthened our confidence that we have identified the project’s carrier is group relationships rather than social relationships.
In addition, we also expanded our activities. We communicated with many sociology students and benefited from the conversation.
Working on synthetic biology in a lab is amazing, but sharing our enthusiasms can be even more wonderful. For the science education, we worked with people from all walks of life including teenagers, citizens, freshmen and XMU students.
You can see more details by click here.
Reference
1.T. Nakagaki, H. Yamada, Maze-solving by an amoeboid organism. Nature 407, 470 (2000).
2.A. Tero, et al., Rules for Biologically Inspired Adaptive Network Design. Science 327, 439-442 (2010).
3.J. A. Shapiro, Bacteria are small but not stupid: cognition, natural genetic engineering and socio-bacteriology. Stud Hist Phil Biol & Biomed Sci 38, 807-819 (2007).
4.C. E. Mouden, Life: social to its core Principles of Social Evolution. Evolution and Human Behavior 33, 79-80 (2012).
5. R. Sekar, H. D. Shin, R. Chen, Engineering Escherichia coli Cells for Cellobiose Assimilation through a Phosphorolytic Mechanism. Appl Environ Microb 78, 1611-1614 (2012).
6. X. Liu, et al, Questionnaire design method based on reliability analysis. Modern education 10, 78 (2015). (in chinese)