Using BioBuilder to Teach Biology
For the last decade, teachers have introduced genetic engineering techniques to students. It is becoming commonplace for students in biology and AP Biology courses to conduct a standard set of “experiments” using gel electrophoresis and bacterial transformation techniques. Students who perform these experiments learn several basic techniques, but that is where the laboratory experience ends. There is little room for student inquiry or creativity. The students are more technicians than scientists.
A solution to this problem comes not from biology, but from the relatively new field of Synthetic Biology. Synthetic biologists apply engineering principles and extend genetic engineering techniques to construct new genetic systems. The synthetic biology approach provides teachers and students with a means to learn molecular biology, genetic engineering and microbiology methods in an engineering setting. The students learn while designing, or testing designs of, engineered biological systems. In addition, this approach provides science teachers with a means of exploring numerous state and national technology standards that are hard to address in most science classes.
Like genetic engineering, synthetic biology makes use of techniques such as gel electrophoresis, polymerase chain reaction(“PCR”), restriction enzymes, and cloning. For decades now, these techniques have been used to transfer genes that exist in one organism into the genome of another, and most students are familiar with human insulin producing bacteria and genetically modified organism used for food. However, synthetic biologists are not limited to moving existing genes into existing genomes. By constructing new genetic systems, they have designed bacteria that can change color upon contacting toxins and produce a drug to fight malaria. While it would be impossible for all students to design bacteria like these, they can follow the work of the iGEM competition. This is an annual competition among synthetic biology undergraduates from around the world. Recently, MIT iGEM students have engineered bacteria that can smell like bananas and yogurt that can clean teeth. The banana smelling bacteria are an inspiration for one of the labs you’ll find here.
Using BioBuilder to Teach Engineering
The engineering approach taught here relies on numerous enabling technologies such as DNA synthesis and focuses on two important principles: abstraction and standardization. These principles and technologies provide biology teachers with a means to extend the teaching of molecular genetic techniques into real world, authentic applications. In the way that physics teachers can have students create functioning circuits and computer teachers can have students create 3-D animations, biology teachers can have students safely design, construct and analyze engineered biological systems.
Importantly, though, biology teachers can use these available materials to conduct engineering challenges with students. For example, existing devices can be altered to meet a new design criteria, and the differing designs and their results can be compared. Students gain first-hand experience with the engineering paradigm: Design–>Build–>Test. Of course, since the engineering activities are performed in the context of living systems, the students will have to understand the underlying science. For instance, to rationally design and measure protein output, students need to understand what a promoter and a ribosome binding site are, and how to evaluate a population growth curve. Through synthetic biology, students can learn these concepts within an authentic context of engineering challenges. These tools of synthetic biology provide biology students with a means to be more than technicians; they can be engineers.
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Craig Venter unveils synthetic life TED talk
Authentic teaching and learning through synthetic biology, by Natalie Kuldell
Explanation of the Engineering Design Process
Teacher’s Domain video and essay on the Engineering Design Process
Download poster for the lab
Download Quick Guide for the lab
Download Eau that Smell comic strip
Lab VideosStreaking Cells Overnight Cultures Growth Curves
Experimental VariationsCan fruitflies be used to measure intensity of banana smell? What is effect on smells if growing the cells at different temperatures? If you are using the McFarland standard, would more precise or subtle standards be useful? Rather than telling the students which strain is which, can they identify the strains based on their smell patterns?
Download Colorful World poster
Download Colorful World Quick Guide for the lab
Download Colorful World comic stip
Download Teacher’s Lab Manual (color)
Hints and Tips
We generally observe strain 4-1 produces large, light green colonies and dark purple colonies, while strain 4-2 usually produces dark, small green colonies and no purple colonies.
We generally observe transformation efficiencies around 1*10^3 colonies/microgram of DNA. However, variations on the protocol, such as incubation at room temperature, may produce different results.
To achieve high transformation efficiency and clear color differences, it is important that students be precise when conducting the transformation protocol. For instance, a water bath in excess of 42°C or leaving the cells in the bath for more than 90 seconds may damage the cells and adversely affect the transformation efficiency.
As a control for this experiment, some teachers like to plate a “no DNA” control on an LB petri dishes (you’d expect a lawn of cells). Some like to plate the “+DNA” samples on LB also, in which case you’d see a lawn but ~none in that lawn will be colorful since the frequency of transformation is so low.
Download poster for the lab
Download Quick Guide for the lab
Download iTune Device comic strip
Hints and Tips
All of Part 2 can be done in one lab period and the reaction mixture is stable once the reaction has been stopped. You can store these tubes overnight in the fridge and read the OD 420 the next day once the tubes have reached room temp.
If a spectrophotometer is not available, the cell density and β-gal activity can be easily measured using the McFarland Turbidity methodology.
Abilities of technological design
- IDENTIFY A PROBLEM OR DESIGN AN OPPORTUNITY. Students should be able to identify new problems or needs and to change and improve current technological designs.
- PROPOSE DESIGNS AND CHOOSE BETWEEN ALTERNATIVE SOLUTIONS. Students should demonstrate thoughtful planning for a piece of technology or technique. Students should be introduced to the roles of models and simulations in these processes.
- IMPLEMENT A PROPOSED SOLUTION. A variety of skills can be needed in proposing a solution depending on the type of technology that is involved. The construction of artifacts can require the skills of cutting, shaping, treating, and joining common materials–such as wood, metal, plastics, and textiles. Solutions can also be implemented using computer software.
- EVALUATE THE SOLUTION AND ITS CONSEQUENCES. Students should test any solution against the needs and criteria it was designed to meet. At this stage, new criteria not originally considered may be reviewed.
- COMMUNICATE THE PROBLEM, PROCESS, AND SOLUTION. Students should present their results to students, teachers, and others in a variety of ways, such as orally, in writing, and in other forms–including models, diagrams, and demonstrations.
- We’re always looking to hear back from you if you’ve thought about a BioBuilder activity, tried it, or stumbled across it and want to know more. Please email us through BioBuilder, info AT biobuilder DOT org.