Teaching biology using video games, comic books and tattoos – Michael Pyne

Perhaps one of the most challenging and often overlooked qualities of a great university teacher is their ability to get students excited about their chosen discipline. As a teaching assistant for a fundamental first-year chemical engineering course called Engineering Biology, I take it upon myself to try and draw chemical engineering students toward the bio side of the discipline. I want to show to them that chemical engineering can entail more than polymers and petroleum. Continue reading Teaching biology using video games, comic books and tattoos – Michael Pyne

Biopunk – Michael Pyne

I like biology. I like it a lot. So when people ask me what field I am in, I usually respond by stating, “Biology!” But what does this tell them? Is this response too vague? Of course it is! And these days it is as ambiguous as ever before. What I have done is merely scratched the surface. An analogy would be showing someone a globe when they ask for directions to your house. The point is this: biology is expanding at an unprecedented rate and is blurring the lines that used to separate distinct fields. This has led to the birth and development of numerous diverse fields still in their infancy, including biotechnology and genetic engineering, biomaterials, bioinformatics, genomics and proteomics (and other omics), systems biology, synthetic biology, metabolic engineering and so on. It seems that nowadays anyone can bring a novel field into being simply by tacking the bio prefix onto any preexisting field. We’ve yet to hear about biovisual and bioperforming arts, biophilosophy (perhaps bioethics?), bioreligion (perhaps evolution?) or biolanguages but I suspect they are not far away. This bio trend likely has origins in the marriage of biology with both chemistry and physics, which occurred sometime in the 19th century. As a result, many of us are quite familiar with the disciplines of biochemistry and biophysics. Biotechnology (and genetic engineering), on the other hand, has thus far become known, at least to the general public, as a sinister sci-fi field (“Franken”-field) that should probably be left untapped until we can better understand the consequences of tinkering with nature.

To me, biology has always been lagging behind chemistry and physics. We have a very good understanding of atoms, molecules and forces, yet we have only begun to decipher the layers of complexity that make up even the simplest single-celled living organism, let alone the human brain and cancer, for example. Even viruses, essentially genetic material wrapped in protein (they’re not even living!), are able to outcompete our lackluster attempts at prevention, vaccination and treatment (think of the common cold, HIV, HPV, hepatitis, SARS, Ebola, avian flu and H1N1). The emerging line of thinking seems to be that, as humans we simply are not capable of fully understanding the intricacies and complexities that make up a living organism. We do not possess the brain power to compute or design the workings of a living organism. Enter the computer and Digital Age.

With the advent of petrochemistry and the global chemical industry, the 20th century is largely regarded as the Chemical Century. Now in the 2000s, however, it is time for chemistry to pass on the reigns, albeit extremely gradually, to biology. We are currently at the dawn of a worldwide biorevolution, one well-documented in the unsettlingly-titled 2011 book “Biopunk: DIY Scientists Hack the Software of Life.” The book’s author, Marcus Wohlsen, equates the current desire and need for open sourcing of biological information to the open source software revolution of the 1970s. Wohlsen envisages a world in the near future where eager DIY bionerds have access to all the necessary equipment, know-how and genetic information (i.e. DNA and gene sequences) to perform exciting genetic engineering experiments in the comfort of their own garages. In essence, biotech and genetic engineering experiments will no longer be performed solely in well-funded academic institutions and multibillion dollar biotech companies. Just as companies such as Apple, RIM, Google and Facebook emerged from basements, dorm rooms and coffee shops in the 70s, 80s and 90s, Wohlsen believes many of the future groundbreaking biological discoveries will grow out of kitchens, garages and abandoned buildings turned DIY laboratories.

Although I may have lost track, my rambling does have implications to teaching biology and all of its distinct fields, subfields and yet-to-be fields. Although biology is evolving at an unprecedented rate and is amalgamating with numerous other areas of science and engineering, it is almost impossible for our curricula to keep pace. With my undergraduate training in Biochemistry and Biotechnology only three years behind me, I feel that my research field is demanding I know more about coding, mathematics and bioinformatics than my undergraduate degree allowed. Since we now have a better understanding of metabolic reactions and fundamental cellular processes, biology is on the move toward life on a larger scale – I mentioned the rise of systems biology, the interdisciplinary study of complex biological interactions and their implications in biological systems, earlier in this post. However, many university biology programs are lacking sufficient training in omics, bioinformatics and synthetic and systems biology – the very fields that are most likely to define and shape the 21st century. But with the pace at which modern biology is changing, can we really blame our curricula for being a few steps behind? Perhaps a wake-up call will be in store in the coming years when undergraduates begin showing up for class with their own personal genomes, all 3.4 billion nucleotide “letters” that make up a person’s unique 25,000-30,000 genes, arranged nicely on an App on their iPhone. Or perhaps it is already happening around the world with a small army of resourceful Biopunks preaching their DIY gospel and putting on demonstrations by isolating the genomic DNA from strawberries using nothing more than water, rubbing alcohol, table salt, shampoo and a coffee filter – all items readily available in any common household. All I can say is that it’s a great time to be a biology student!


The Centre for Teaching Excellence welcomes contributions to its blog. If you are a faculty member, staff member, or student at the University of Waterloo (or beyond!) and would like contribute a posting about some aspect of teaching or learning, please contact Mark Morton or Trevor Holmes.

Why don’t you come inside and get some stale air? – Michael Pyne

Lately, I’ve been reflecting on what exactly makes a great engineer. Or, better yet, what traits and skills allow top engineering students to excel? I’m sure we would all agree that the best engineers are superb problem solvers, creative thinkers, innovators, and are as sharp as they come. But what I want to know is how did they acquire these traits? Although I like to think I possess many of these qualities, I am merely a half engineer at best. Perhaps a quasi-engineer or pseudo-engineer is more fitting. You see, I completed a BSc in Biochemistry and Biotechnology before joining the Department of Chemical Engineering at the University of Waterloo as a PhD student. Thus, my “expertise” lies somewhere awkwardly between applied molecular biology and chemical engineering.

While spending most of my waking hours in the laboratory with a mixture of talented undergraduate and graduate engineers, I have come to observe an underlying commonality between such students. What I am referring to is a hobby that many true engineers have grown up with. Many of them still actively take part in this hobby as adults. What I am referring to may frustrate or annoy some parents. What I am referring to, of course, are video games.

Despite the stigma that has plagued video games since the inception of Pong and Pac-Man, I am confident that they have helped me acquire important problem-solving, cooperation, strategy, and teamwork skills, in addition to a keen eye for detail; all things that are ever so important in a molecular biology laboratory, not to mention dozens of other disciplines. At UW, I continually observe much brighter engineers than myself who, as I am usually quick to find out, were also much bigger gamers than me growing up. Perhaps gamers are so drawn to engineering because they love challenges and are able to treat real-world problems not unlike the problems they solved in games as kids. I apologize if I am generalizing, as I am certainly not suggesting that to be a great engineer you must have clocked thousands of hours gaming as a teenager. I am also not implying that students who were non-gamers growing up will have trouble succeeding in engineering as adults. Indeed, I know many brilliant engineers who have never had much interest in video games and have likely acquired many important skills from a range of other activities.

Video games have always received a bad rap, particularly from parents who claim that they contaminate young minds, distract youth from more nourishing activities, and lead to aggressive behaviour. I think we have all been victims of the indefensible “Why don’t you go outside and get some fresh air?” argument. By the way, I never understood what parents meant when they said that. Was my Super Nintendo emitting some highly toxic gases which prevented me from playing beyond 2 or 3 hours at a time? Does gaming contaminate the air we breathe, thus requiring excessive ventilation? As a kid, I found out that this was not true – opening all the windows in the house, setting up an elaborate electric fan network, and even hooking up my system to an electrical outlet in my backyard on a sunny summer day still did not allow me to extend my playing time. But was I contaminating my young mind? Did I waste my youth playing video games when I could have been doing more productive things? Hardly.

Just as I am a quasi-engineer, I am also a quasi-gamer. As a child, my gaming interests typically did not venture beyond the realm of Mario, Zelda, and Donkey Kong; hardly games for parents to lose sleep over. However, these games were jam-packed with puzzles, obstacles, and a slew of problems just waiting for my young and developing mind to solve. While playing video games, I was able to explore, to discover, to figure things out for myself, all at my own pace. I was able to feel an immense sense of accomplishment, whether it was through beating a challenging level or an entire game that I had spent a great deal of time mastering. And these joys were often shared. My brother and I would play games together for hours on end, sharing, taking turns, and figuring things out together. Or I would play with a couple of friends and we would work as a team and collaborate. My love for video games was also coupled to an equal love for jigsaw puzzles and number and math games of all shapes and kinds. So it is no surprise to me that, come high school, I developed a strong interest in chemistry and biology, or more specifically, cells, DNA, and proteins. As a graduate student, the genetic engineering experiments I conduct in the lab can be thought of as puzzles in which I cut DNA into thousands of pieces and paste them back together to form new recombinant molecules. I feel that I was able to acquire so many important skills from video games that have helped me immensely as an undergraduate and graduate student, and also as a developing scientist and engineer.

Although many view video games as time wasters, even more worrisome to parents is the violent nature and mature content of many modern games. This is where my pro-video game stance crumbles. I will not deny that any game that is “rated M for Mature” is not suitable for anyone under 18. I will also not deny that there is an unnecessary amount of violence, sexual content, and gore in video games these days. Although Mario games continue to do well commercially, more violent games such as World of Warcraft, Grand Theft Auto, and Call of Duty have created much worse dilemmas for new parents than my parents likely ever faced. As my favourite comedian, Demetri Martin, puts it, “I like video games, but they’re very violent. I want to design a video game in which you have to take care of all the people who have been shot in the other games. ‘Hey man, what are you playing?’ ‘Super Busy Hospital 2. Please leave me alone. I’m performing surgery on a man that was shot in the head 57 times.’” Jokes aside, I believe that video games have done immensely more good than harm, so long as they are regulated and screened by parents. Also, as with most things in life moderation and variety are paramount. So if you find your children spending excessive time outdoors this summer why don’t you have them come inside and get some stale air?


The Centre for Teaching Excellence welcomes contributions to its blog. If you are a faculty member, staff member, or student at the University of Waterloo (or beyond!) and would like contribute a posting about some aspect of teaching or learning, please contact Mark Morton or Trevor Holmes.