BioBuilding: Synthetic Biology for Teachers: Design Assignment

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PDF of this page Teacher Considerations Using the bacterial photography system as inspiration, this assignment asks the students (individually or in groups) to use their imagination as they propose a design for a genetic system. The emphasis is on the decisions made by engineers during the planning of the design process and not on the genetics. The students are asked to consider existing technologies, risk, reward, and testing. Of course, they are expected to imagine a genetic system that will make a significant contribution to life on earth. You can worry about its feasibility later. You may also find this design assignment useful for an iGEM team as it develops an idea for a project. Although the assignment itself is written for an individual student, it can be adapted for a group. The brainstorming exercises below lend themselves quite well to a group process, such as is needed within an iGEM team. Guiding your students This assignment is open ended and can be adapted in many ways by you and your students. However, it might be helpful to take them through some exercises to help them to think about biological engineering design. These four questions, and the associated material, can help the students focus on a problem and begin designing a solution: Question 1: What is your focus area? This table will help you pick broad areas on which to begin your design project. A word doc of this table may be found here. Question 2: What particular problem do you want to address? Think about any topics in your area that you find especially interesting. These could be motivated by an article you've read, a personal experience, a research project you know about. You might want to have a couple of possibilities as you go forward. Question 3: Can you imagine a biotechnology to address this problem? Bacteria too smelly? Make them smell like bananas. Composting too slow? Make a living additive to accelerate the process. Need to fight cavities? Make a yogurt that sticks to your teeth and heals them. You get the idea. Question 4: How will you narrow down your choices? It might help to compare all your favorite ideas along these five lines: What precisely is the problem or opportunity you are focusing on? How clear are you on an approach to make a dent in the problem? What if your project is fully successful? How big a difference could it make? What concerns will it raise? What other technologies can be used/have been used to address this area? What don't you know? How big are the gaps in what you know? How much is completely unknown or unknowable? Going Further You may want your students to take the design assignment further by breaking down the systems they design into devices and then, perhaps, the devices into parts. This will be particularly helpful for an iGEM team. Systems to Devices: Think back to the bacterial photography system. There are two parts to the system: The sensor, which senses the light, and the actuator, which produces the pigment. In simple terms, the system requires two genetic devices. One device is needed to create the Cph8 sensor protein, and the second is needed to create β-Galactosidase protein that makes the pigment. A block diagram might look like this: When designing a system you should think about what components are needed. It is helpful to think in terms of inputs and outputs. Let’s try thinking this through with some practice problems. Practice problem I: Bacterial Buoy The 2007 iGEM Melbourne team wanted to build a 3D, floating mass of bacteria that adhered to one another when the cells detected both blue and red light. In other words: at the intersection of an incoming red light beam and blue light beam, a solution of bacteria would clump and remain suspended in its growth media. As a class we'll watch the first 5 minutes of the Melbourne team's iGEM presentation. Next you should work out a high level overview of this system's behavior. Make a list of cellular inputs and outputs then write a block diagram that connects them. In other words: What inputs will the cell have to sense? What two ways will the cell respond? Don’t worry about getting the clump to disassemble when the lights are off. Just think about what the cells needs to do to make the clump and make it float. And don’t get bogged down by what really exists. If you need a floater device, you can have one. Practice problem II: Polkadorks Let's try a more dynamic system. The 2004 IAP team wanted their engineered cells to "form, diffuse, and form again in random areas on the plate. Our system should thus form time-varying patterns based on local random time-varying symmetry breaking." Check out the Polkadorks animation. Then make a list the devices needed to implement such a system (for example “coin flipper” to generate the random decision to turn red) then connect the devices with arrows to indicate the logical information flow pattern. Your Challenge: Now think about your system. What devices would you need to create it? Again, don’t get bogged down by what already exists, but do keep it realistic. You are engineers. You may be able to make whatever device you need. So, if you need a “floater device” or a “garlic smelling device”, go ahead. Resources (just a sample) Here are some background readings and videos that teach about synthetic biology, its goals and projects. You may wish to provide your students with these resources. Decoding Synthetic Biology (YouTube) What is synthetic biology?( pdf) A Life of Its Own ( pdf) Our Synthetic Futures Handmade Biology Synthetic Biology: Tools to Design, Build, and Optimize Cellular Processes Video on design and synthetic biology by James King (Hastings Center) Explanation of the Engineering Design Process Design criteria Teacher's Domain video and essay on the Engineering Design Process You may wish to see the type of projects that college synthetic biology students have designed as part of the iGEM Competition. Please keep in mind that these projects put a much greater emphasis on the actual design of the genetic system than is intended by this assignment. plus some links to older articles: How to Make Life Life Reinvented Assessment Grading Rubrics Design Assignment Rubrics and Scoresheets (pdf) Survey To help us improve the labs, you can send the students here where they can offer anonymous feedback. 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