Genetic Engineering Workshop

The introduction of genetic engineering(GM) and synthetic biology to the layman has long been fraught with issues. Already, as evident from the organic and non-GM food movement, there exists a portion of the population that is distrustful of Genetic Engineering in their food, let alone for any medical treatment. As our project involves the use of a genetically engineered bacterial vector, this issue is of particular importance to our team.

We believe that this distrust stems from a misconception of synthetic biology amongst the general public; Genetic engineering is to many an almost mystical concept. It draws out terrifying images of science gone mad, of biologists tinkering with things far beyond their understanding. However, with the fundamental complexity of many synthetic biology concepts, their lack of understanding is somewhat understandable.

A Simpler Way to Learn
At first blush, genetic engineering and synthetic biology seems a wholly biological domain, due to the emphasis on ‘wet lab’ techniques, genes, and complex biological systems. We knew that many students have already been exposed to genetic engineering techniques such as molecular cloning techniques like gel electrophoresis and PCR. However, their knowledge often ends at the execution step, and students are not taught the theory behind synthetic biology.

We decided to address this lack of understanding of synthetic biology by creating tools to facilitate its learning. We designed and created highly simplified abstractions of flow control in genetic circuitry (Figure 1). The idea was that this way of perceiving genes and biological systems could help students better appreciate the level of control involved in circuits, as well as view genes as part of the larger system.

Figure 1 : Example of a genetic circuit representation of a biological system

To increase accessibility, we eschewed potentially intimidating circuit diagrams in favor of a simple color and shape based model to avoid overloading users with prerequisite biological concepts. Promoters, repressors, and the various control elements that govern the system were replaced with a basic, easy-to-learn representation (Figure 2). Importantly, the system designed was nonlinear, allowing for multiple paths to a solution.

Figure 2 : Representation of genetic circuit components

Putting It Into Practice
Ultimately, the value of this tool is in it’s utility as a teaching aid. To demonstrate it’s use, the SPSingapore team integrated this tool into a genetic engineering workshop for science students from different disciplines. The workshop was a one day course aiming to introduce participants to both theoretical and experimental aspects of genetic engineering. The workshop comprised of two phases: The theoretical phase and the experimental phase.

In the theoretical phase, we attempted to establish the fundamentals of genetic engineering, teaching them both the biology behind molecular machinery and introducing them to the theory behind it’s design. Participants were able to engage in hands-on design of genetic circuitry in the form of a set of puzzles designed with the tool (Figure 3). Following this, participants were invited to use what they had learnt in the experimental phase in a wet lab setting.

Figure 3 : An example of a genetic circuit puzzle (alpha)

In the experimental phase, participants performed Fusion PCR (Polymerase Chain Reaction) and performed bacterial transformation in the SPS Wet Lab. They also had a look at green fluorescent protein (GFP) expressed in E. coli, as an example of one of the methods that are commonly used to quantify protein expression (Figure 4).

Figure 4 Participants examining transformed bacteria

The workshop was designed such that people from different disciplines could understand it readily - a principle from our namesake interdisciplinary programme, SPS (Special Programme in Science). Our participants were mostly first-year biology students,with a good scattering of physics and math majors. Results of this workshop-cum-trial were positive, with most reporting improved conceptual understanding. More importantly, we observed that the participants enjoyed the puzzles and the workshop, with the puzzle component being most popular (Figure 5).

Figure 5 : Workshop participants indicated that the category of the workshop they most enjoyed in post-workshop feedback

The teaching tools and video recording are available for viewing under the page Workshop Materials, along with a detailed analysis of workshop feedback from the students.

Moving On
We have since received participant input on the tool, as well as insights from educators Dr Chammika Udalagama and Mr Lim Kim Yong. We’ve learnt much about user-targeted design and potential pitfalls in accessibility and have since attempted to resolve accessibility/usability issues with the system (Figure 6). For instance, Dr Lim suggested that red-green colourblind students might have problems with the way the puzzles were presented (Figure 7).

Figure 6 : The team acting as facilitators during the workshop

Figure 7 : Modifying the puzzles for the color-blind

While the framework is currently minimal, we believe it shows promise as a tool for teaching synthetic biology concepts across a wide range of skill levels. Furthermore, this activity ties in well with the BioBuilder curriculum educational materials, developed by the BioBricks Foundation. Though we did not know of the BioBuilder curriculum at the time of design, our inspiration for developing the tool aligns well with their goals - to teach students problem-solving, by allowing them to understand a system via design.

The tool is not yet publicly available, as we would like to further refine it. However, once it reaches a satisfactory state, we intend to release in an open manner for free modification and distribution.