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Visualising the Invisible

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Published: 18 Jul 2019
Category: Education and training
By John Barrow

One of the hardest things to get across to students at any level is the idea of a concept. This is especially so in the sciences and even more so in the molecular life sciences where the processes discussed are often abstract in nature and unseen. I have taught biochemistry and molecular biology for over 10 years, and throughout all of that time I have tried to teach the subject in the simplest way possible. I have heard accusations of dumbing down the subject or creating ‘edutainment’ for the masses, but I fervently defend what I do as feedback from courses and student engagement in my classes would suggest the teaching approaches I take do work and do allow students to gain a better understanding than I ever did as an undergraduate student, even though the curriculum has remained largely unchanged. 

My teaching revolves around processes like glycolysis, the citric acid cycle, beta-oxidation, phosphorylation, electron transport…the list goes on. 

If you pick up a textbook and read about these pathways and processes, they will all show diagrams of ‘molecule A’ being converted to ‘molecule B’ via an enzyme catalysed reaction or some other abstract process that students struggle to understand. Through course feedback and engaging with students directly, I came to realise that the reason biochemistry is often seen as such a difficult subject is two-fold: 

  1. Students will view biochemistry as chemistry – this is not strictly the case as all of the processes are not entirely chemical in nature as there’s that thing called life that helps them work the way they do. The concepts underpinning a protein's function also provide a reason for the processes to work the way they do, and in turn gives context and meaning, which goes above and beyond pure chemistry. 

  1. Biochemistry is very abstract – this is exacerbated by the way in which the processes are portrayed in textbooks and other teaching materials. The reactions and mechanisms being discussed are often shown as static images that are not true to life, for example, enzymes may be shown as abstract shapes that have no link to their actual structure, or the processes are simply shown as a set of reactions. This means that students struggle to link what they see on the page with the molecular processes that are occurring in cells. 

With these ideas in mind, my teaching has developed over recent years to try and introduce visualisation into the subjects I teach. This initially started by introducing the Protein Data Bank to early stage undergraduate students in my metabolism-centred biochemistry lectures. The feedback was overwhelmingly positive because it allowed students to see the proteins and provided them with research-grade tools that they could use themselves to appreciate and understand proteins at a molecular level. This simple intervention allowed me to take lectures in a variety of directions depending on the interests of the class as we collectively explored the protein structures being shown on the lecture theatre wall. 

More recently, I was awarded funding to accelerate this molecular visualisation approach in my teaching, which has included public engagement in science teaching as well as my undergraduate biochemistry teaching. This approach utilises video game design software to create visualisations that can be delivered through augmented or virtual realities, as well as via more traditional animations or videos. 

Augmented reality allows digital models to be overlain on a real-world environment usually with a mobile device (see Figure 1). This was the approach used to create a simplified version of food digestion and insulin signalling for public engagement activities. I am also working on the creation of an augmented reality workshop that will aid the teaching of glycolysis to allow students to see the concepts of this ten-step process in action. The ability to blend the visual animations with physical worksheets (Figure 2) or objects will allow students to interact with the processes and concepts in a vastly different way from a standard lecture. As this is in progress, we have not trialled it with the students in classes, but I would envisage it will have an impact on their appreciation of the concepts I would normally talk them through using static imagery or at most a short video animation. 

My hope is that visualisation of these invisible processes that are so fundamental to life and medical science will aid students in their own understanding of the concepts involved. Further, I believe this approach could dramatically enhance engagement by allowing students to immerse themselves in their learning through the simple act of seeing a dynamic process in action, so watch this space! 

AR_App_in_Action.png
Figure 1. A screen shot taken from the augmented reality (AR) viewer as viewed on a smart phone device.  This is showing the pancreas releasing insulin into the bloodstream (far right hand side of the image). The AR marker is shown on the table and acts as the trigger to display the human figure and animations.​

AR_App_Flyer.jpg
Figure 2. The leaflet that accompanies the augmented reality app. Students can cut away the three AR markers and then use them to display the animations for digestion, insulin release and insulin action on muscle cells. The leaflet has extra information that allows the blending of traditional learning styles with the augmented reality animations.

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Published: 18 Jul 2019
Category: Education and training
By John Barrow

About the author

John Barrow  



John is a Senior Lecturer (Scholarship) in Molecular Biology and Biochemistry at the University of Aberdeen.  His research background is the understanding of gene regulatory processes and has spanned the fields of diabetes, stem cells, developmental biology and neuroscience, amongst others. He currently teaches biochemistry and molecular biology across a diverse mix of undergraduate programmes.  

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