Tardigrades, writing research papers, and the dark side of Astronomy

Some interesting pieces from around the web:

Some ideas on putting together a research paper from Dr. Raul Pacheco-Vega. This isn’t directed particularly towards scientists, but there are some great ideas!

A neat piece of writing that reflects on the dangers of contamination in genomics work and the importance of rigour. The subject matter is tardigrades which makes the story even more interesting!

A depressing article from the Globe and Mail highlighting the gaps in policy at Canadian universities with regards to dealing with harassment complaints.

Yet another article highlighting the problem of sexual harassment in astronomy. I predict that it won’t be long until other disciplines start to clean house.

What happens when you complain about sexual harassment as a graduate student.



Using Games in the Classroom

At the beginning of April I went to an excellent workshop facilitated by Dr. Scott Nicholson called “Games Beyond Screens in the Classroom”. Scott is the director of the Brantford Games Network game lab and teaches and chairs the program in the Bachelor of Fine and Applied Arts in Game Design and Development. The program has been wildly successful and they are looking to hire another faculty member who focuses on digital game design and project management.

Scott took us through several games during the course of the workshop and each had elements that I could easily see incorporating into my classrooms. He made the important point that after you run a game you always have to debrief. There is no point in running an activity without exploring how it made you feel, what was experienced, how it relates to your world, how you could see incorporating it into your space, and learning from the experiences of other people. Failing to debrief after a game is a very common error.

The other take-home from the workshop is that games do not have to be fun and they do not have to be fair. You are perfectly within your rights to manipulate the game in order to achieve the learning outcomes that you’d like for your students. This was a bit of a surprise for me, but having seen it in action at the workshop, I can see how it would work.

This past Monday I shared what I had learned at the workshop with some colleagues who are members of our SCAFFOLD (Student-Centred Active Flexible Face-to-Face Online Learning Discussions) community of practice. At our next meeting in May we’ll be discussing how to bring fun into our classrooms.

Do you run any games in your classrooms in order to facilitate learning? What has worked and what has been a disaster?


Giving students some control over their own learning

There was an interesting column written by Jim Lang over at the Chronicle Vitae website this week. Any column that starts with a photo of Harrison Ford as Indiana Jones is alright in my book! The content of his post “Small Changes in Teaching: Giving Them a Say”  is part of a series that Dr. Lang has been writing over the past several weeks.

In his post he explains the two ways that students often approach their learning. Some students are oriented towards performance and want to excel on activities that result in a good grade (e.g. tests, assignments, etc.). Other students are mastery-oriented learners and enjoy learning for learning’s sake. I would prefer to have mastery-oriented learners in my courses.

One way to do this is to give your students choices and allow them some control over their own learning process. I tried this as an experiment in my course during the Fall 2015 term, but this was before I’d read Jim’s column obviously. I was looking to give my students options in terms of how they would be evaluated in the course in the hopes that it would lead to better engagement in class and with the material. It was my hope that students would self-select the evaluation method that would make them more comfortable and that this would be reflected in the course grades.

For this particular class I offered two evaluation options. All students had to complete one term test, five 10 minute in-class essays, and a protist trading card during the first two months of the term. During the second half of the term, students could either take a second term test (Option #1) or they completed a group case study presentation and two take home essays (Option #2). I think that this option allowed my students the ability to play to their strengths and perhaps avoid their weaknesses. Out of a class of 60 students, 36 chose Option #1 and 24 chose Option #2. Based on the written feedback that I obtained on course evaluations the students really appreciated having a say in the criteria used to evaluate them in the course. I consider this experiment a success and will likely use it again.

After reading Jim’s post I think that I could take this approach a step further and he gives some excellent examples worth thinking about.


April Showers…

There’s a saying here in Canada that April showers bring May flowers. The academic year ebbs and flows in predictable cycles from one year to the next. I’ve been a professor for almost 6 years now, but despite this fact, April always sneaks up on me. I always assume that April will be a quieter month since I’ve finished with my in-class teaching, but each year April is very busy and my calendar fills up with a plethora of appointments, committee meetings, seminars, and workshops. You’d think that after 5 years of April doing this sneak attack I’d wise up, but so far it hasn’t happened. It’s like the mud puddle in the Robert Munsch book…just waiting for me to come outside so that it can mess up my carefully laid plans.

April’s one redeeming quality is the start of Blue Jays baseball.

The Top 10 Things I Learned in Graduate School

1. How to “Manage Up”.

Graduate school involves working with a supervisor/advisor and a large number of other researchers (e.g. fellow grad students, committee members, research technicians, etc.). In order to complete your research, you need to secure the help of all of these people and frankly you will not be their top priority. There is a skill in getting people to do what you need them to do without being demanding, rude, or ungrateful.

2. Strive for Good Enough.

Perfection is the enemy of getting things done. Aim to do your best, but understand that sometimes your research products and outcomes will not be perfect. It is better to have a strong finished thesis than an unfinished perfect thesis.

3. You need a strong support network.

This includes people who will support you both personally and professionally. They are rooting for your success and want you to finish your degree. They will celebrate your successes and will help lift you up when things are not going your way. Do not take these people for granted.

4. Leaving graduate school is not failure.

Graduate school isn’t for everyone, and if it isn’t for you, then is it better to realize that early on and make a change. It is not worth staying in a situation that is making you miserable for an academic degree. Leaving academia does not make you a traitor.

5. A few hours in the library/reading the literature can save you months in the lab.

Don’t reinvent the wheel. Science moves forward on the results of the people who have come before you. Heed their wisdom.

6. Be observant.

This goes for experiments in the lab as well as watching the people in your department. If something seems unusual or strange it is often an excellent opportunity to make a new discovery about the world or yourself.

7. Don’t accept paradigms and rules blindly.

It is good to think for yourself and challenge the status quo. If you would like to one day be an independent thinker and come up with your own ideas, you will need to get comfortable with getting outside of your comfort zone.

8. Science is not the only important aspect of your life.

Work on constructing an identity that does not include being a scientist. You will thank yourself later and it will make you a much more resilient and happier person. It is important to have friends, family, hobbies, sports, etc. that you enjoy.

9. Ask for help when you need it.

There is no shame in asking for help. Spend some time on your own trying to come up with a logical solution to your problems and if you are still stuck then get some assistance.

10. Have multiple mentors.

Asking for and receiving advice is not one stop shopping. It’s better to have multiple people that you can approach and rely on in order to get different perspectives.


DoctorAl Digest 18

For those looking to better inform themselves about gender bias in academe, here is an excellent resource of recent studies in the primary literature.

Some views on the biggest problems facing gender equality in STEM from several scientists in ecology and evolution.

A disturbing article on classroom sexual harassment and the fact that it can start before students enter university or college.

A tongue in cheek “field test for identifying appropriate sexual partners in academia”, but it makes several excellent points, especially the last four paragraphs.

The process of evolution is amazing and nature always finds a way…bacteria capable of metabolizing polyethylene terephthalate (a common type of plastic).

And finally, the perils of academic fashion sense.



Book Review-The Martian by Andy Weir

My husband read this book last year and was raving about it, but I didn’t get around to reading it until this week. The book is excellent and very engaging! It tells the tale of an astronaut stranded on Mars when his crewmates leave him behind after an accident because they believe him to be dead. The writing style is very different in that it changes between the first and third person throughout the novel. During portions of the book narrated by the astronaut Mark it is written in the first person as a personal log, but for scenes involving NASA headquarters on Earth or the other astronauts it is written in the third person.

Two things that I really liked about the book is that it manages to make science interesting and I think that this would be the case even if I wasn’t a biologist. I love fiction books that make science accessible for everyone. The second thing that makes this a great book is that there were several points when I laughed out loud while reading it!

This book is a great read and I hope that the author will write more books in the future.


DoctorAl Digest 17

Some great pieces from around the Internet this week!

As scientists we often don’t think about data management until it’s too late and we end up losing data due to a computer crash or catastrophe! Don’t let this happen to you! Excellent advice from Melanie Nelson over at the Beyond Managing Blog on data management.

An honest and frank appraisal of the challenges faced by working moms. Funny and heartbreaking at the same time. (Not for the squeamish!)

An excellent piece by Hope Jahren that needs to be read by all scientists. Lots of people have been talking about it on Twitter and blogs this week.

The excuse that all male panels at conferences “just happen” has been busted by a mathematical analysis.



Lab Freezer Organization

My freezers at home are fairly well organized. The one in my fridge is pretty full, but we have a good sense of what is in there. The chest freezer in the basement is very well organized after we did a purge last year and decided to organize by main ingredient. We can tell quickly when we are running out of something and need to buy more.

I’m in the process of doing the same for my lab freezers. We have a -20°C chest freezer in the lab that we use for storing various biological samples. I recently purchased 2 additional vertical racks and a bunch of 2 inch tall freezer boxes since the samples from my students’ projects have massively increased in the 5 years that I’ve been working here. These boxes work great for samples that fit in 1.5-2 mL tubes, but aren’t so super for biochemicals that I need to store at this temperature. I’m currently experimenting with various plastic containers in order to find a system that works for us.

We currently store our more sensitive/long-term storage samples in a rack in a shared -80°C freezer. A fellow faculty member has been very kind in letting us squat in the freezer for the past 5 years. Last week I was able to purchase a freezer of my own (oh, happy day!) and am proactively planning how we will store our samples. Our current set up is a rack that holds 16 2 inch boxes which has worked well for samples, but isn’t so great for several molecular biology kits that we regularly use. I’m happy to be getting our own freezer as I’ve been dismayed by the storage behaviours of other researchers who share the freezer. Pro tip: unlabelled baggies are not an effective storage tool! I’m also quite territorial when it comes to my freezer rack. I’ve been really angry when others have taken my boxes out of my rack and replaced them with their own boxes. Not cool!!

We will also be switching over to a labelling system that actually uses freezer safe labels. Previously we had been writing on our tubes with extra-fine Sharpie markers, but this is difficult. I’ve recently purchased various labels from GA International and I’ve been impressed with the quality and performance so far. The colour dots in particular will save us lots of time when locating DNA vs. RNA vs. protein samples in our storage boxes.

A logical freezer organization system will save you valuable time. I think that we’ve all had that experience where we got lazy or sloppy and are then cursing ourselves later when we can’t find that important sample in the freezer. It can sometimes take hours, days, or weeks to generate a biological sample depending on your experiments. It makes sense to store the sample so that it maintains integrity and you know where to find it when you need it.

What approaches have other PIs taken to storing your biological samples in freezers?