Category: Biological Musings

Cubic Wombat Poop

One of the many reasons why I love biology is when a great and weird story gets told about some kind of living phenomenon. This week I was surprised to learn that wombat feces are cubic. Evidently it’s been known for quite some time that the wombat’s poop is cube shaped and it is hypothesized that wombats use it to mark their territories and the fact that it is cubed means that it doesn’t easily roll away, but it more likely has to do with attempting to conserve water and the structure of their digestive tract.

Dr. Patricia Yang and co-workers investigated the physical properties of the wombat intestine and determined that variation in the amount of stretch in different sections (by using an inflated balloon no less!) resulted in the cubic feces. As you can imagine, the wombat poop finding is receiving a lot of attention in the popular media. In my opinion the best headline goes to Vice.

Fun fact: Dr. Yang won the 2015 Ig Nobel Prize in Physics for testing the biological principle that most mammals empty their bladders in about 21 seconds.


Doctor Al Digest 28

A few things that I’ve found interesting in the past few weeks:

A nasty case of alleged sexual harassment drives home the point the dangers that are inherent in a system where a graduate student has only one faculty member as their research advisor. It’s important as a grad student to develop a network of mentors.

In some cases, it is worth your time to improve a skill that you are poor at, especially if it is a required skill for your career. In many cases though, it is a better use of your time and efforts to capitalize on your strengths.

The “Dear HBR” podcast is excellent, but the Harvard Business Review “Women at Work” podcast is phenomenal! The podcast has recently returned for its second season and is better than ever! Honest, frank discussions of the challenges faced by professional women in their workplaces and practical advice on how to navigate this minefield. I can not recommend it enough!

I’ve written my second column for The Conversation Canada on the Venom movie that opened last night. The focus is on symbiosis and how an alien could go about hacking a human host.



Career Benefits of Blogging as a Faculty Member

I’ve been on Twitter and blogging since the fall of 2013. When I first started, I didn’t really have any goals other than that I wanted to help early career scientists navigate academia and I wanted to become part of some communities that I didn’t have access to in my daily life. Both of these activities have led to some unexpected positive outcomes.

I would say that the top benefit has been increased visibility of my research and my ideas to a broad community. This has involved interactions with other scientists, various academics, and members of the public. For example, a blog post from April 2015 called “The Advantages of Live Tweeting a Research Talk” led to an invitation to moderate a live Twitter chat comprised on Knowledge Mobilization officers across Canada and the U.S.

The second benefit is the honing of writing and communication skills. These skills are transferable to many other facets of my job and are valuable. I took a stab at writing an article for The Conversation Canada called “The Force of biology is strong in Star Wars” and my aim was to talk about mitochondria and cloning with a general audience. To date the article has received over 17,000 views; nothing else that I have written in my career has received so many reads.

The third benefit is that the blog allows me to share my opinions and to offer advice to early career biologists. The blog allows me to quantify some of my outreach activities and include them as part of my university service. My blog post on “Research Budgeting for Scientists” from March 2015 was re-published on the University Affairs website the next year. I’ve been interviewed for two articles for the journal Nature; one on networking in 2017 and one a few weeks ago called “Why science blogging still matters”. More recently I was invited to join the Science Borealis blog network that features Canadian bloggers who focus on various scientific fields.

I’ll point readers to this fantastic article written by several of my blogging heroes that explores this topic in more detail and talks about other impacts that science blogging can have for an individual and the broader community.


Mitochondria are hot!

There have been some very interesting developments in the field of mitochondrial biology in the past two months. This is very exciting for me as someone who works on bioenergetics in a variety of organisms.

The first paper made quite a splash in the community when it came out because the findings suggest that mitochondria operate at much higher temperatures than were previously believed. The paper by Chrétien et al. 2018 appears in PLOS and is entitled “Mitochondria are physiologically maintained at close to 50°C”. I will admit to being pretty open to this idea and it’s because of two reasons. The first is that I perform research on plants and have specifically worked on the enzyme alternative oxidase (AOX). Several plants are capable of shunting electrons through this enzyme and are able to heat inflorescences up to 42°C when ambient temperatures are much lower. Secondly, I’ve always been bothered by the fact that mitochondrial respiration assays using oxygen electrodes are often performed at 37°C regardless of what organism the mitochondria have been isolated from. It doesn’t made sense to me and I question the physiological relevance of assaying mitochondria using a temperature of 37°C when for example the study organism is a fish that has been acclimated to an external temperature of 5-12°C. Mitochondrial respiration is definitely more sluggish when you run these measurements at 5-12°C, but the mitochondria are still active. So for me, someone attempting to tackle the question of what temperature mitochondria actually run at is an important and highly relevant one.

The paper is an elegant one and what struck me in particular is that the authors have attempted to proactively counter the most obvious challenges that they would face from other researchers in the field. It hinges on the supposition that no energy transduction process in nature is 100% efficient and that some of the free energy of the electron transport system (ETS) must therefore be released as heat. They are obviously limited by the technologies currently available, but they have done an excellent job in using both positive and negative controls to validate their experiments and data. They have used the temperature-sensitive probe MitoThermoYellow to attempt to determine the temperature of mitochondria in a mammalian cell line background. As I read the paper, every few minutes I thought of another potential factor that could be responsible for their results, and in the very next sentence they addressed each of my particular concerns; it was a pretty surreal experience. The mitochondrial temperature is directly influenced by the level of operation of the ETS and what components are present (they do some very neat work with the alternative oxidase and uncoupling protein). They do some preliminary enzymology work on crude extracts to demonstrate that several ETS complexes exhibit temperature optima ~50°C, but that this is only true if the mitochondrial membranes are intact. A fascinating next step would be to examine the role of supercomplexes in these effects.

The authors themselves admit that one of the key questions that needs to be considered is whether mitochondria and cells can maintain temperature gradients, or whether any heat would immediately be lost to the rest of the organisms and/or the environment? Here we need to consider what is known about the physical shape, size, number, and localization of mitochondria in cells and what is known about the insulating capabilities of phospholipids, membrane components, and the contents and composition of various cellular compartments. Much of this information is lacking. These issues and other possible critiques of the paper are addressed by Nick Lane in his article “Hot mitochondria?”. Lots of new questions and concepts brought up by the Chrétien et al. paper which makes it a very valuable contribution to the field.

The second article is one by Cory Dunn entitled “Some Liked It Hot: A Hypothesis Regarding Establishment of the Proto-Mitochondrial Endosymbiont During Eukaryogenesis”. This paper was a lot of fun to read and presents a simple, but profound hypothesis: the initial usefulness of the proto-mitochondrion and the evolutionary driving force for its retention was due to its ability to generate heat and that it wasn’t until much later in evolutionary history that its ability to biosynthesize ATP could be harnessed. It’s a pretty neat idea and the figures in the article help the reader considerably. The premise of this article will be further supported if the conclusion of the Chrétien et al. holds up over time.


Doctor Al Digest #24

The #reviewforscience Twitter hashtag has been cracking me up this week. Highlights include gluing trackers on bees, using a body massager to attract spiders, nooses for lizard collection, and the winner: using nail polish for killing bot fly maggots prior to extracting them from your own body.

Looks like the #MeToo movement has caught up with Canadian politics and they’re clearing house (the House of Commons that is!)

Tooting my own horn a bit…myself and several other bloggers were interviewed by the Nature piece “Why science blogging still matters”

A very elegant and thorough study by Chrétien et al. that suggests that the mitochondria in human cell lines operate at ~50°C when at maximal capacity  and a thoughtful critique by Dr. Nick Lane . I suspect that some paradigms are about to be destroyed in the near future in mitochondrial and thermal biology.

Lady of the Flies: Attempting to ID the infestation in my office

A couple of weeks ago I started noticing a large number of flies in my campus office. They are a mild nuisance as they get trapped between my blinds and windows and the buzzing noise is distracting. The large number of fly corpses is also gross, but I’m a biologist, so I’m taking it in stride.

Due to the fact that I’m a nerd, I’ve been attempting to solve the mystery of where these flies are coming from and what type of fly is in my office. I was quickly able to rule out the blowfly, which means that my fear of a rotting animal in my ceiling is likely unfounded. So it’s a toss up between the common house fly and the cluster fly. Based on the fact that the flies are pretty sluggish and have golden hairs on the thorax my best guest is that they are cluster flies.

Cluster flies feed on earthworms as maggots and move into buildings when it comes time to hibernate. I’m guessing that because September was so warm, it’s only recently that the flies have started to move into my building and invade my office. I’m guessing I’ll see a second wave when they all wake up in the spring.


Doctor Al Digest #21

The Ig Nobel awards are always amusing, but they do make you think. You can go here for a list of the winners that were announced yesterday. I too have always wondered whether cats could be both a solid and a liquid.

A great post over at the blog Conditionally Accepted on Recognizing Emotional Labor in Academe

A powerful art exhibit reinforces the offensiveness and irrelevance of wondering what sexual assault survivors were wearing when they were assaulted. Trigger warning for sexual assault descriptions.


Impacts of Hurricane Irma on biology

The footage and news coverage of Irma has been amazing and serves to remind us that no matter how much we think that we have been able to engineer our environments we are no match for the power of Mother Nature. While much has been said about the impacts that the hurricane will have on human affairs, culture, and infrastructure, not much has been said about the long term effects that will be felt on the ecosystems in the path of the storm. This focus, when it does occur, will no doubt be on animals. My daughter was particularly disturbed by the Tweets that went out yesterday urging Floridians to not abandon their pets to fend for themselves during the hurricane. While this is certainly disturbing, it is worth taking a moment to think about the wildlife in these regions that will never be the same.

I find it amazing that birds are commonly found in the eyes of hurricanes and that they can be transplanted hundreds of kilometres by this process. Here’s a short article from the Miami Herald on the topic of wildlife and hurricanes. As a plant biologist, I’m really impressed by the ability of the palm trees to survive hurricane conditions. Here’s a quick article on the adaptations that allow them to do this.

I also found the emptying of the bays and the returning storm surge to be amazing. This phenomenon must kill a huge amount of aquatic life due to the changing water levels, salinity, temperature, and oxygen that results.


Good-bye to 2016

All in all, 2016 was a good year for me. During the first semester of the year I taught a course, mentored several students, and found out that my NSERC Discovery Grant was renewed. I also hit 100 followers on Twitter which I thought was pretty cool. In February I started Bullet Journaling as a system of time management and I really like it. The part that I think that I like most is that it’s a written record of everything that I was able to accomplish this past year and that the system can be modified to suit your individual needs.

The second semester during the summer saw me switch gears significantly as I was preparing for my first sabbatical in July. I attended two conferences in cities where I did my post-doc and Master’s degrees respectively, so it was a bit of a homecoming for me which was neat. At the end of June I left for Italy to attend a conference and then my family and I spent 3 weeks in Palma de Mallorca, Spain. That trip was a conscious effort to push myself out of my comfort zone, but I need not have worried as my hosts were wonderful! While I was working with a collaborator, my family explored the city and the island’s beaches. We then took a family vacation in August to Paris, England, Scotland, and Ireland which was fantastic!

The fall term found me getting a new groove and I was able to be much more proactive rather than reactive due to being on sabbatical. The biggest success that term was finally publishing a manuscript that was the result of 6 years of laboratory work. That was a huge win for me. I was happy to watch the Blue Jays in post-season baseball for the second year running; unfortunately they were eliminated by the team from Cleveland. The year rounded out with time spent with family and friends over the holidays.

I hope that your 2016 was productive and that you are looking forward to 2017!


The Sabbatical

I started my first sabbatical in July. It began with an international conference in Italy and then a three week research collaboration and visit to a colleague’s lab in Spain. It was a wonderful start to this academic year. I am discovering that a sabbatical allows one to be reflective rather than reactive. I am using the time to think, plan, discover, recharge, and appreciate aspects of this job that I have tended to take for granted.

My hiatus from the blog this summer was due to my travelling schedule in July and August and a September that saw me settling into a new routine afforded by my sabbatical. I hope to post more regularly in the upcoming weeks as I reintroduce blogging into my schedule.