Active Learning Exercises for Teaching: Photosynthesis

I teach a 3rd year Plant Physiology course and a 4th year Environmental Stress Biology of Plants course. In both of these courses I go into quite a bit of detail about photosynthesis. This is material that my students have been exposed to in previous undergraduate courses, but in the context of these two courses my aim is to show students why the process of photosynthesis can be a double edged sword. I think that most people assume that plants love any level of light and that the more light that plants have access to the better. We often talk about photosynthesis as a steady-state pathway when in reality plants are constantly acclimating to their light environment likely on the timescale of milliseconds. I use an active learning exercise in my classroom in order to teach my students that photosynthesis is a dynamic process fraught with dangers for plants.
For this exercise I bring in a bag of soft plastic balls. These were left over from a ball play-set that my son had when he was younger (think the ball pits that you can find at IKEA or that used to be present at indoor play areas). I also bring in a large metal bucket. I ask for 6 volunteers from the audience to participate in the activity. Each student represents a complex/mobile carrier involved in the photosynthetic electron transport chain (e.g. photosystem II, plastoquinol, etc.) and the last student in the row is the enzyme ferredoxin-NADP+-reductase. The balls are used to represent electrons. The first student’s job is to accept the balls that I pass to them and then pass them to the next student. The other students in the chain in turn accept the balls and pass them along the chain. The last student in the chain aims to deposit the balls in the metal bucket. The bucket represents the ability of the plant to use the electrons to produce NADPH and ATP and to fix carbon.
The first time through the exercise I put balls into the chain at a very low rate. This shows the students that sometimes plants can have difficulty generating energy and fixing carbon if light is limiting. This would be similar to severe shading effects for example. I then put the balls into the chain at a reasonable rate. This represents a “steady-state” for photosynthesis where the process is running efficiently. For the last part of the activity I put the balls into the chain at an extremely high rate; as quickly as I can pass the balls to the first student in the chain. Inevitably the balls get dropped frequently at various parts of the chain and many of the balls do not make it into the bucket, or the bucket overflows. I use this to demonstrate over-reduction of the electron transport chain and to explain the generation of reactive oxygen species during photosynthesis.
Based on previous course evaluations, the students enjoy this exercise and claim that it helps them to remember key aspects of the photosynthetic electron transport chain. I’ve found it to be an engaging and effect way to teach about photosynthesis in my classroom.

See You in September

I’ve always liked September because it signifies new beginnings. I think this way because I’ve been in school in some form or another since I was 5 years old; first as a student for many years and now as a professor. September means super deals on school supplies in store flyers, like the fancy pens that I like and my favourite notebooks. I must admit surprise upon seeing that paper hole re-enforcements are still being sold. Whenever I think of September, I always think of freshly sharpened Laurentien pencil crayons (Peacock Blue or Cherry Red anyone?) I could spend hours happily walking the aisles at our local Staples store…
At my university September is also when the campus comes alive again. Although many of us have been on campus all summer, September is when the vast majority of our undergraduate students return to school. There is a feeling of nervous energy and anticipation that exists in the air during the first week of September that is comfortingly familiar.
My children also returned to school this week and the list of required supplies hasn’t changed much since my times in elementary school with the exception of one item. Evidently it’s no longer called Liquid Paper; it’s now correction tape.
Best wishes for a great first week of the semester!

Self-Promotion as a Female Scientist

Over at the Dynamic Ecology blog there’s an interesting poll and commentary on the topic of self-promotion in science. Many of us in science are introverts. Self-promotion is therefore unnatural and uncomfortable. In conversations that I’ve had with scientists over the years it seems that biologists are quite divided on whether self-promotion is a good or bad thing. Regardless of how you feel about it from a personal or ethical standpoint, I would make the argument that self-promotion in science is necessary in today’s funding climate. Some trainees and early researchers that I’ve talked to recently still seem to harbour the mistaken belief that if you publish well and do good science, your science will speak for itself, and the meritocracy of science will see fit to reward you. I think that this is a dangerous fallacy that has hurt many a career. Similar to networking, it seems that many scientists see self-promotion as dirty or unseemly behaviour. As universities continue to realize the importance of community engagement and knowledge mobilization in recruitment and advancement the pressure on scientists to self-promote will only increase. Whether you agree with this or not, in order to survive and thrive, you’ll need to learn how to promote yourself, your trainees, and your work.

 

I can reveal the importance of self-promotion in science by sharing a personal anecdote. When I was a Ph.D. student I made a discovery that was a big deal in my field of research; I discovered a new bio-energetic pathway in animals. I wanted to share my results with animal biologists and I felt that the best way to do this was to present my results as a talk at the annual meeting of the Canadian Society of Zoologists (CSZ). I put together the best talk that I could, wrote an effective abstract, and went to register for the conference. Going to this conference was a big deal for me because most of the work that I had been doing was in plant biology; I had only recently started working in an animal system. I therefore had a gigantic case of imposter syndrome. Each year the CSZ holds a competition for the best student presentation delivered at the annual meeting, but in order to compete you need to self-nominate by ticking a box during registration. I did not tick the box. After all, who was I but a plant biologist invading the domain of animal biologists? Long story short- I gave an amazing talk that likely would have won me the award, but I had taken myself out of the running. It was an epic fail in self-promotion. The next year I put my hat in the ring and won the honourable mention for the award. It was an important lesson to learn early in my career.

 

I am also conscious of the fact that some of my hang-ups about self-promotion are due to the fact that I’m a woman. I’ve been socialized to keep my head down, do my best, and hope that I’ll be duly rewarded. It’s taken a lot of work to get to the point of realizing that I need to toot my own horn and be proactive about telling others about my research. I can’t afford not to.

 

Aphids, ants, ladybugs, and wasps! Oh my!

We have a strange phenomenon occurring in our backyard. It started a few weeks ago when I noticed a pair of wasps engaged in a death match on our deck in the back yard. This event happened with regularity over the next few mornings, but I didn’t think much of it at the time.

Later that week we ate outside on the deck and were impressed by the huge numbers of wasps visiting our maple tree. I should say that my husband and I were impressed; our kids were very uncomfortable.

Fast forward to last weekend when I went outside to do some internet surfing on my tablet. The first thing that I noticed was the huge number of black ants running around our deck and all over the patio chairs and table. Being a biologist I also noticed that the table was covered with aphids and that the tree was infested with them. As I sat there for several minutes, it felt like a very mild rain shower was taking place. I realized that the aphids were excreting excess sugar in the form of honeydew and that there were so many of them that the screen of my tablet was covered in aphid poo in a matter of a few minutes! I’m guessing that the ants were going wild for the honeydew and that explains why they were running frantically all over the deck and furniture. Once I figured this part of the mystery out, I was also able to see a large number of ladybugs and their eggs in the maple tree. Ladybugs love to eat aphids and were taking advantage of this buffet opportunity.

But what’s the deal with the wasps? I’m not an entomologist, but there appear to be two species visiting the tree: the common yellow jacket wasp and something that might be a bald-faced hornet. Be doing some quick reading I discovered that the adults of both of these species eat nectar, tree sap, and fruit pulp. Perhaps the aphids have made tree sap readily available by feeding on the maple tree, or perhaps the wasps are eating the honeydew waste of the aphids deposited on the leaves. The other possibility is that the wasps are preying on the aphids and chewing them up to feed to larvae back at the nest. The wasps don’t appear to be a parasitoid species preying on the aphids.

It’s very cool as a biologist to see a food web occurring in your own backyard. This phenomenon has also served to remind me of the importance of observations in solving biological mysteries and testing hypotheses.

 

Flipboard: Finding current science news stories for use in your classroom

In the courses that I teach I’m always on the look-out for current news stories that are directly related to course content. One source that I’ve found to be a great source for these particular stories is the app Flipboard. They have a science section which is a great source for stories being covered by the popular media. Below are a collection of stories aggregated by the app within the past 24 hours.

If you teach a virology course, spending some time talking about the recent discovery of vials containing smallpox in Maryland  would be directly applicable to the course content and will likely grab the attention of your students.

Talking about plant dispersal in your botany course? EarthSky has written a great summary of an article about how migrating Arctic shorebirds are spreading mosses and liverworts  to new areas of North and South America. The plants may hitch a ride in the feathers of the birds.

Really into amphibians and conservation biology? Check out this Associated Press article on the hellbender; a giant salamander that is rapidly declining in population in the United States.

If invertebrates are more your thing, you’ll be amazed to watch the video of a purple siphonophore in this article from the Huffington Post.

I do a section in my Endosymbiosis class where I talk about all kinds of amazing and gross parasites. Talking about how a targeted eradication effort has almost wiped out the guinea worm in Africa  would be a neat way to talk about how public health efforts are changing our ecosystems and the natural world around us.

I’ve just given biological examples above, but the app collects stories related to many areas of science and engineering that could be used to bring your course content to life.

Feel free to share other news story resources that you use for course material or for general interest in the comments below.

 

 

Using Popular Sci-Fi films to Illustrate the Concept of Endosymbiosis

I teach a fourth year undergraduate course on the origin of life on Earth and endosymbiotic theory. I use my first lecture as an opportunity to highlight some of the interesting material that we will be covering that semester and to get the students hooked on the class. I do this by talking about several examples of endosymbiosis that are present in popular science-fiction movies.

 

I have a very broad definition of endosymbiosis. I classify it as two organisms living together where one organism lives inside of or is contained by the other organism. Endosymbiotic relationships exist on a spectrum of whether they are inert (e.g. not harmful or helpful), mutualistic (e.g. helpful to both parties), commensal (e.g. helpful to one, but not hurtful to the other), and parasitic (e.g. detrimental to one and beneficial to the other).

 

The first example that I discuss in class is from the 1979 classic film Alien. I didn’t see this film until I was a teenager and by then several sequels had been released. The first film in the franchise is a great example of how to use suspense effectively to really scare your audience. There is a classic scene in this movie that will ensure that you never look at eating in a mess hall or cafeteria the same way ever again. Long story short, the humans in this film serve as very effective incubators for the alien in a grisly endosymbiotic relationship. The relationship comes to an end in a very messy way. Unfortunately using this reference dates me a bit; usually only 2 out of 44 students have seen the film when I ask for a show of hands. I do have several students tell me after a few lectures that they ended up watching the film and liking it, so Ridley Scott’s royalties continue to serve as a revenue stream for him.

 

The second example that I use is from the 2009 film Avatar. The aliens in the film, the Na’vi, ride dragon and horse- like creatures. There are several short scenes in the film where a direct interaction between the Na’vi rider and direhorses or banshees is achieved by cilia like structures and a neural interface is created. I talk about this type of cellular interface as an interesting example of communication between two different endosymbionts.

 

The last example that I use in class is from the 1999 film The Phantom Menace. There is a scene in the film where Qui-Gon Jinn is testing Anakin Skywalker’s blood for midi-chlorians. Midi-chlorians are described as intelligent, microscopic life forms that allow their hosts to detect and use the Force if present in high enough quantities. Anakin’s midi-chlorian count is the highest ever detected and we all know how that turned out!

 

I use these fake examples of endosymbiosis from film to illustrate and discuss some of the concepts involved in endosymbiotic theory. They represent an interesting way to bring popular culture into the classroom and hold the interest of my students.

 

I’m always on the look-out for other examples of endosymbiosis in film or television; please leave any ideas in the comments!

Transferrable Skills

I generally think that graduate students under sell their skill sets to employers. Many graduate students think only of technical skills when they are putting together their CVs or resumes and it’s a real shame. They are failing to capture many great skills that they have developed during the course of their graduate degree and are not effective in highlighting these skills in job applications. Many researchers are competent in running gel electrophoresis protocols, but not as many have competencies in project management or leadership. It is these “soft skills” that will make one applicant stand out from the crowd.

I also think that many principle investigators (PIs) don’t realize that transferrable skills are absolutely required by students in this economy in order to get a job. It is no longer enough to be technically competent; employers are looking for what additional value a researcher can bring to the job. I’ve always been dismayed by hearing stories from students about how their supervisor discourages them from attending professional development workshops. I think that this “chained to the bench” attitude has no place in science.

It is for this very reason that I encourage my graduate students to participate in professional development workshops, go to conferences and meetings, collaborate with other scientists, and take part in student government or organizations. These are opportunities that I took advantage of as a graduate student and post-doctoral fellow and they have served me well over the years. Frankly, these experiences (and the skills that I acquired participating in them) have provided me with an edge over the competition at every transition that I’ve faced in my research career.

Let’s talk about some tangible examples using the case study below. This is a case study that I’ve made up, but many graduate students would be doing these activities during the course of their degree.

Janet has just completed her thesis based M.Sc. degree in the laboratory of Dr. Jones. Her thesis involved the identification and cloning of a gene involved in the biosynthesis of digestive enzymes in mouse saliva. She also characterized the enzymatic activity of the protein encoded by the gene. During the course of her project, Janet was assigned two undergraduate summer research assistants by Dr. Jones to assist her with data collection. Janet’s research has led to the publication of 2 peer-reviewed research articles and 3 conference presentations. While in graduate school Janet was employed as a Teaching Assistant for a 3rd year undergraduate biochemistry course laboratory.

Here is a list of the obvious soft skills that Janet has acquired during her degree:

i) Ability to plan, execute, and finish a multi-year project

ii) Ability to supervise and manage staff

iii) Scientific writing skills

iv) Ability to present information in oral/written format

v) Networking skills

vi) classroom management

v) Ability to evaluate the performance of others

vi) Ability to work effectively with a supervisor

 

Some other skills that Janet might have gained along the way:

i) Teaching skills

ii) Ability to manage a research budget

iii) Ability to receive and use constructive feedback/criticism

iv) Ability to work as an individual and part of a team

v) Troubleshooting and problem solving skills

vi) Ability to adapt to new challenges quickly

You can see that the potential soft skills that could be developed by Janet during the course of her degree are diverse and that I have not included any of Janet’s technical skills (e.g. molecular biology skills, enzymatic characterization techniques, etc.) in this list. Obviously when you are putting together your CV or resume as a student you only want to list soft skills that you believe are relevant and that are your strengths. You also want to think about tailoring your application package to the specific job for which you are applying. When you think about your soft skills in addition to your technical skills, a larger range of job opportunities become available. Casting a wide net in terms of identifying potential employment prospects is a smart move these days.

Book Review- Lab Dynamics: Management Skills for Scientists

The hardest part of being a research academic is not the lab work. By far the most challenging part of this job is maintaining effective interpersonal relationships. This holds true whether we are talking about relationships with colleagues or with trainees. When I started my own lab I realized that I hadn’t had any formal training on how to manage scientists and that I’d better get up to speed as quickly as possible if I wanted my research group to be successful and thrive. One book that I found incredibly helpful was Lab Dynamics: Management Skills for Scientists by Carl M. Cohen and Suzanne L. Cohen published by Cold Spring Harbour Laboratory Press. I have the first edition of this book as a paper copy and the second edition of this book in electronic format.

The book starts by asking readers to do some self-assessment in order to identify their own personality type and to identify personal blind spots that you might therefore have in your interactions with other personalities. This is accomplished through several exercises and requires taking some time for personal reflection. They make a strong argument for why you need to manage yourself first before you attempt to start managing others. There is an excellent chapter on negotiation with great “real-world” examples that serve to effectively illustrate the main points.

I’ve often heard it said that managing scientists is like trying to herd cats.  Most laboratory research these days is done in teams; gone are the days of the lone wolf scientist. As such, it’s important to master the skills involved in effectively running a lab group composed of scientists with different personalities and motivations. The problems that I experienced or saw while a graduate student and post-doc were almost always due to interpersonal conflicts.  Often the strategy of many scientists is to ignore the problem and hope that it goes away. This book contains an excellent chapter on addressing these issues head on in order to avoid escalations and lost time and effort on projects. The book also contains great chapters on managing up (i.e. how to manage your boss) and managing sideways (i.e. interacting with peers). There is a very eye-opening chapter on the various types of dysfunction that can be found in academia based on how the reward system is set up and how to become a better mentor and how to survive as a trainee under these conditions. A great chapter is present in the book that describes the transition to industry for those looking to leave the ivory tower. The final chapter encourages readers to shape their workplaces for the better using the techniques learned in the book in order to improve the culture of academia for everyone. The second edition contains an additional chapter on leading team meetings and a new section on how to deal with difficult people.

I think that any scientist could learn a great deal from reading this book. I have referenced it several times since starting on the tenure-track when I’ve run into a sticky interpersonal situation or when I need a refresher on a particular aspect of mentoring. I believe that it would also be incredibly useful for graduate students and post-docs who are navigating academia.

Dismantling the Stereotype of the “Crazy” Scientist

What comes to people’s minds when you say the word scientist? Chances are most people picture a middle-aged white man toiling away in a dark, mysterious laboratory. He’s likely wearing a lab coat (either pristine white or covered in who knows what) and has crazy hair in need of a good brushing. This is the image of the scientist most often portrayed in film and TV. The socially awkward misfit who is rude and abrasive to everyone he meets and clueless about the real world around him. He’s often up to no good and has no moral compass. If this is what most people really believe about scientists then it is no wonder that scientific progress is under attack in the US and Canada.

I have two kids who like to play with LEGO. I was therefore happy to hear that LEGO would soon be putting out a new series called “Research Institute” that features female scientists. I can only hope that this will serve to counteract the “Crazy Scientist” that appeared in the Series 4 set of minifigs that hits on all of the stereotypical characteristics that I just described above.

I was again reminded of this stereotype this morning when looking at my Twitter feed. It turns out that a Greek yogurt company Chobani has been putting messages under the lids of its products. One read “Nature got us to 100 calories, not scientists.” Understandably many scientists saw this as a direct attack on themselves and on science and mobilized an effective campaign to get rid of the offensive slogan. The company would do well to remember that many scientists are involved in the making of their product, whether they are engineers working to improve efficiency of the production line, biologists working to improve the texture, flavour, and development of the yogurt, or chemists involved in synthesizing the plastic containers that it’s packaged in.

Guess what? Scientists are people too. We have friends and family. We have hobbies. We have morals and beliefs. The person sitting next to you on the bus is a scientist. The person voting in the same poll as you is a scientist. The person coaching your child in little league baseball is a scientist. When I teach and train students in my laboratory I am showing them that the stereotype is incorrect. I specifically address and dismantle it in one of my courses.

I think science is awesome, but then again I am a scientist. I see the beauty and wonder of science all around me every day, and I appreciate that science allows me to live a healthy life by providing me access to clean water, sturdy shelter, nutritious food, and effective health care. What can we do as scientists to halt the disturbing trend of vilifying science and scientists that is in full swing in our neighbour to the south and is starting the sweep north into Canada? Perhaps the place to start is to deconstruct the stereotype of what it means to be a scientist.

McDonald Lab: Applicants wanted for the Banting Postdoctoral Fellowships program

The McDonald lab is seeking applicants for the Banting Postdoctoral Fellowships program for Fall 2014. The award is valued at $70,000 per year (taxable) for two years (non-renewable). Further details about the program and eligibility requirements can be found at: http://banting.fellowships-bourses.gc.ca/home-accueil-eng.html

Our lab focuses on the electron transport systems of photosynthesis and respiration. Our particular interest is alternative proteins involved in putting electrons into or taking electrons out of these systems. Current research projects focus on the alternative oxidase, plastoquinol terminal oxidase, and alternative NAD(P)H dehydrogenases of bacteria, fungi, plants, and animals. We use various techniques to study the molecular, regulatory, and functional properties of these enzymes. Trainees receive training in bioinformatics, molecular biology, protein biochemistry, and respirometry. We strive to do excellent science and have fun while doing it! I take a strong interest in my trainees’ professional development and encourage them to maintain a positive work-life balance. Further information about the McDonald lab can be found at: http://www.wlu.ca/homepage.php?grp_id=12358&ct_id=2893&f_id=4.

Wilfrid Laurier University is a growing institution in Waterloo, Ontario. The city of Waterloo is a thriving community and technology hub centrally situated in southwestern Ontario with access to other large metropolitan areas including Guelph, London, Hamilton, and Toronto. The Biology department is a tight-knit community and offers many opportunities for collaborations and research support. Research at Laurier is question driven and uses a variety of techniques and approaches to answer hypotheses through investigation at multiple levels of biology (e.g. molecular, cellular, physiological, ecological, evolutionary). Our trainees leave with a solid biological background, the ability to use critical thinking to address important challenges and issues, and are prepared to succeed in a variety of career paths.

An application package consisting of a CV, all postsecondary education transcripts (can be unofficial versions), a one-page description of career aspirations and rationale for your desire to pursue a postdoctoral research experience at WLU with me (highlighting the benefits expected with respect to fulfilling career aspirations), and a 3-4 page research proposal must be sent to Dr. McDonald at amcdonald@wlu.ca by midnight on July 18, 2014.

The successful candidate will be expected to put together a complete application for the internal competition at Wilfrid Laurier University and submit it by August 22, 2014. Further details are available at: http://www.wlu.ca/page.php?grp_id=36&p=24457.  Applicants will be notified of the pre-selection results by September 3, 2014.  Successful applicants will be asked to submit their final application by September 24, 2014.

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