Team:Genspace/Practices
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Human Practices
Running an iGEM team within Genspace is itself an exercise in Human Practices.
We were the first-ever community biolab- opening our doors to the general public in December 2010. For the past five years we have been welcoming citizen scientists and the intellectually curious to our lab space to experience modern biological science hands-on. Our lab classes in synthetic biology won “Best Social Study in Synthetic Biology” at SB5.0 in 2012. We have several events (lectures, group labwork, workshops) every month that are open to all, and anyone over 18 can become a Genspace member and work on a project in our facility provided they comply with all safety guidelines and are working with organisms appropriate to BSL1. We believe that the best way to communicate synthetic biology is to engage as many people as possible in its hands-on practice.
This is exactly why we consider running an iGEM team in such a public space an exercise in Human Practices. Day to day our iGEM team was forced to engage members of the public who would come through Genspace. Our iGEM team often would find themselves explaining our project to visitors of Genspace. All this culminated in answering many questions about our project, addressing people's concerns, teaching people about the Gowanus and as well getting valuable feedback from the community. In this way our team worked day to day in an open lab setting, a lab literally open to the public.
iGEM Members working within Genspace
Testing of the Synbiota RDP System in a Community Lab Setting
Citizen scientists in community labs wanting to practice synthetic biology encounter unique barriers to access. The labs are often less well equipped than university labs, and may have less mentoring capabilities. Thus we welcomed the opportunity to test out a new, more user-friendly system for assembling a long string of DNA parts. The Synbiota Rapid DNA Prototyping (RDP) system owes its origins to BioBytes, a project which won the award for Best Foundational Advance for the Alberta 2009 iGEM team, The system was further optimized as an easy-to-use teaching kit, Genomikon, which was the Alberta 2010 team project. This updated incarnation (RDP) has the potential to radically improve the accessibility of synthetic biology. It seems only fitting that our Genspace 2015 iGEM team would evaluate it and suggest improvements as part of our Human Practices.
Genspace first receiving the Synbiota kit
Preparing a part to be used in the RDP system is similar to the biobricking process. Primers adding the RDP prefix and suffix are used to generate assembly-ready parts using PCR. However, we found the assembly process to be very much faster and easier with less equipment required. The only equipment required is a magnet and a pipettor. DNA parts are added sequentially to an anchor part tethered to iron beads, Parts are added sequentially with ligation and wash steps at room temperature, all in the same tube, and exch step taking less than half an hour. The completed construct is released from an iron bead by treatment with a base solution and is transformation-ready. As an example, the dual-plasmid system testing LsrR/pLsrA2r would have taken weeks to build by 3A assembly, yet we did it in a couple of days.
We strongly recommend this system to other community lab groups, and are planning to add a video tutorial of the process to the Genspace website.
In order to reach an even greater segment of the New York City community, we engaged in the following additional Human Practices activities during iGEM:
Public Engagement around Synthetic Biology at the NY Hall of Science
On the 23rd of August, we participated in the Building with Biology event at the New York Hall of Science in Queens. This event was part of the NSF-funded Multi-Site Public Engagement with Synthetic Biology (MSPES) grant. Its primary goal is to convene conversations around synthetic biology and its societal implications between synthetic biology researchers and the public. Our event was part of the prototyping cycle aimed at developing specific engagement activities around synthetic biology.. The grant will culminate in the creation of materials for these activities that will allow them to be implemented at 200 informal science education sites in a national "summer of synbio" to take place in 2016.
About half of our iGEM team participated in this event. At an orientation meeting at the NY Hall of Science we were allowed to choose between several types of activities for the demo to the public on the Sunday. Although the physical objects were provided, we had to develop our own dialogue with the public around synthetic biology, using the physical part of the activity as a starting point.
The visitors to the Hall of Science come from all over the New York metropolitan area. We felt that it had the potential to be a really valuable exercise in engaging with people who had never heard of synthetic biology before and who might be distrustful of genetic engineering. We presented a wide range of activities covering topics such as the use of synthetic yeast to generate vaccines, the types of lab techniques that synthetic biologists use, and 3D printing with synthetic biology-derived materials. Whitney, one of our team members, summed up what most of us took away from the event “We presented our demo on spreading cells on plates. Most of the audience were children who were interested mostly in playing with the model of the tools we would see in a scientific laboratory. My experience at the event was both good and bad. The good part was that we were able to engage the younger public about techniques in labs and encourage them to think of a future in the biological sciences. The bad part was that our topic did not specifically relate to synthetic biology, but it did give the audience a basic step in working with synbio. In addition, one way our topic we were presented could have been improved is by providing better plate models and examples of cells from different organisms for the audience to get a better feel of the technique of spreading plates. But in all, I believe that the public did have a positive view towards synbio and also asked many questions about the project our iGEM team was working on.” So the conclusion was that although the engagement activities we developed need improvement, we were able to have a meaningful dialogue with the general public around our iGEM project using the activities as a focus.
Meeting with Enquête Gowanus
In order to understand the environmental issues surrounding the canal, our team met with members of the Enquête Gowanus project, an ongoing collaboration between Genspace, Nelson Byrd Wolz, the Gowanus Canal Conservancy, and several academic laboratories at local universities to catalog the microbiome of the canal bottom sludge. Ian Quate and Matthew Seibert both from Nelson Byrd Wolz came to Genspace and spoke about the project's history, challenges and stakeholders in the community. We took the opportunity to ask about the proposed cleanup.
Enquete Gowanus Part 1: Collection from Genspace NYC on YouTube.
Presentation of our iGEM Project to Gowanus Canal Conservancy staff and volunteers
Our team was invited to present our proposal for biosensors along the canal at the Gowanus Canal Conservancy volunteers meeting. At the meeting we were able to explain that Biosensors like canaries in the coal mine. We explained that our project consists of creating a combined nitrate and quorum sensing biosensor that will detect nitrogenous wastes and E.coli present in human feces from sewage leakage into the canal after the dredging and capping operations. The biosensor would be an efficient way to detect whether sewage or nitrogenous wastes are present in the canal after it has been dredged and capped (with clay, sand and rocks) in the future. The biosensors would provide a visual output by the amount of red fluorescence displayed on the biosensor. we emphasized that at the moment the deployment was hypothetical, and that we had come to get their input about the desirability of our proposed sensor.
Individual community members had differing reactions to the biosensor. Some were surprising to us. There was an almost fatalistic feeling around the pollution in the canal, and one resident expressed the opinion that they had concern around “dumping something else into the canal” but that it would be “acceptable if it had a good purpose” and one commented that “ As long as the intention is not to dump harmful waste into the canal then we are fine” In general they were intrigued by the possibility of a real-time biosensor. Some suggestions were “maybe you would need to do some mktg so it does not get lumped into the GMO category” and “the design of the membrane is super important”.
When queried about what the ideal form of sensor would be, they asked if it could be made to sense different types of pollution, if it could be made “visually stunning” and if it would give real-time feedback. One thing that surprised us was that, given the choice between a sensor that was in the canal and a kit that they could use to pull a water sample out and test it (eliminating the potential danger of the sensor releasing genetically modified bacteria into the canal) they overwhelmingly preferred the deployment into the canal. The reason was that they felt a visual reminder along the canal of the polluted state of the waterway would more effectively drive community engagement and potentially move residents to action. It occurred to us after the meeting that perhaps if we had engaged a group that was not dedicated to political action and remediation around the canal we might have gotten a different answer.
When the second part of our project, mining the microbiome of the canal for organisms and pathways that might help with remediation efforts, they were both interested and positive.
Exploring the potential Impact of our project on the Biosecurity Community: Meeting with FBI Special Agent Martin Maag
Because New York is the city that experienced the 911 attacks, we engaged with the biosecurity community soon after the founding of Genspace. During our work on the Gowanus project we realized that New York waterways are potential terrorist targets, and that deployment of sensors might impact the work of the biosecurity community.We wanted to cooperate with Homeland Security, so we contacted FBI Special Agent Sara Wood, who has a long-standing cordial relationship with Genspace, and asked for a meeting with her or one of her team members. FBI Special Agent Martin Maag agreed to meet with us at Genspace. Agent Maag has spent 30 years in the FBI, worked on cases including Unabomber, Whitewater (Arkansas), Oklahoma City Bombing, and currently works in NYC (the biggest of the 56 FBI field offices in the US)
Regarding biosecurity on NYC waterways and general biosecurity in NYC, the first and most important questions in any investigation are:
Who, What, When, Where, Why, How
In the context of the present iGEM project, answering the who, why and how questions may be the most difficult for our sensor (and will be more the focus of any downstream investigations), but the where, when and what questions are more directly addressable. For example, by knowing the precise location of a network of sensors (perhaps updated by GPS), associating timestamps with trigger events, and characterizing multiple trigger conditions (nitrates, AI2 bacteria, AHL bacteria, etc.) The use of "negative" information (i.e., what sensors did not go off) can be as useful of "positive" information (i.e., what sensors did go off) in order to provide a holistic picture of any investigation. Other variables can be important such as water/air temperature, water flow direction/speed. It is also helpful to consider the observable events leading up to any incident.
In the wake of an event, the STOP approach can be employed:
Stop, Think, Observe, Plan
Regarding the deployment of sensors on NYC waterways (and sampling in general), the question becomes one of jurisdiction with interactions and coordination across several departments including the FBI, the NYC Police Department (Water), the US Army Corps of Engineers, the Department of Environmental Protection and the Department of Health. The meeting concluded with questions from the iGEM team about FBI procedures and investigative philosophies.
Mr. Maag provided his contact information and encouraged us to reach out to him with any future questions.