Category: Graduate School

Common Problems Experienced during Graduate Student Theses and Defenses

By this point in my career, I’ve been on both sides of this scenario; I’ve written and defended 3 theses (undergraduate, M.Sc., and Ph.D.) and I’ve evaluated a number of theses and presentations from my own students and those from other labs. Here’s my 2 cents on common problems that I’ve experienced, or have heard about from others. I’m focusing on issues that can occur after the thesis has been written and submitted to the committee members up to and including the oral defense of the thesis.

Challenges for the Student

  1. Figures in the thesis aren’t as good or robust as those used in the presentation.

I’ve been in several defenses where many concepts that were challenging to figure out while reading the written thesis have been cleared up by the inclusion of additional figures in the presentation. It would be great if students just included these additional figures from the get-go as this would really improve the experience of the reader.

2. Figure and Table captions are not sufficient.

I always recommend to students that figures and tables should be able to stand on their own without any help from the written text of the thesis. This can be achieved by including an appropriate level of detail in your captions that explains what the reader is seeing as well as making any jargon and acronyms clear.

3. Interpreting questions or concerns as a personal attack.

It is very hard not to take concerns or questions about your writing, data, or presentation personally. While you should definitely not be a doormat, you should be respectful and thoughtful when receiving the feedback and opinions of your committee members.

4. Lack of knowledge on the basic theories, techniques, or information of your field.

Often committee members will ask what we see as very basic questions about your project and your field of study. If you mention something in your thesis or presentation, expect to answer questions about that content. Be sure that your focus has not narrowed so much that you neglect to explore and understand the theory or basic tenets of your research area. For example, if you are showing images of Western blots, I will likely ask you to explain the theory of how this technique works. It looks very bad if you can’t explain technique that is in your thesis.

5. Absent or inappropriate use of statistical analyses.

I’m not a statistical wizard, but even my Spidey senses start tingling when I can’t understand why you’ve chosen particular approaches, whether they are appropriate, and what they are telling you about your data.

Challenges for Examiners

  1. This is not the time to retaliate for a slight that occurred in 1999 from another faculty member on the committee.

Focus on the student’s work and accomplishments and let it go. Stop being so petty and giving professionals a bad reputation.

2. Come prepared and be on time.

Respect the time and efforts of the student and other committee members. Come with useful and insightful questions and suggestions.

3. Clearly communicate the student’s strengths and accomplishments that impressed you.

Be kind and sincere in your praise. A thesis degree is a tough slog and we don’t compliment our students enough and should celebrate their successes.

4. It isn’t about you.

Check your ego at the door. We all know that you are smart. You don’t need to convince us of this by your preambles to a question, your expositions on a particular theory, and your recently published work. Keep the focus on the student where it belongs.

What other insights can others offer about the thesis and defense experience? Leave your answer in the comments!


DoctorAl Digest 20

A great new website with blog posts targeted at research supervisors is The Supervision Whisperers. An excellent piece on stress and self-care for graduate students was posted several days ago.

Terry over at Small Pond Science is an insightful blogger. His latest on The deficit model of STEM recruitment is bang on.

If you’ve ever had the feeling that you are alone in having your manuscripts rejected from multiple journals, this post over at Scientist Sees Squirrel will be reassuring! The snazzy title is Persistence in publishing: the Tubthumping strategy. Now I have a 90’s ear worm


DoctorAl Digest 19

An exciting article in University Affairs about Laurentian’s new MSCom (Master’s in Science Communication) program launching this fall.

Samantha Oester’s (@samoester) Twitter feed from yesterday drives home the fact that it isn’t just harassers that drive women out of science; the clueless and unsupportive other members in the community also contribute.

I’m really enjoying the Period Podcast by Dr. Kate Clancy.  You’d think as a middle aged woman I’d know all that there is to know about menstruation…but you’d be wrong.

When I became a principal investigator of a lab I began managing people for the first time. I’ve found the Ask a Manager website an amazing resource. Some of the stories are so wild that you’d think that they can’t be true! A great source of examples of how not to manage, and excellent advice from Alison on how to solve problems and effectively manage your staff.


Book Review: Lab Girl by Hope Jahren

Hope Jahren’s book has been on my “to read” list since it came out. Many of her blog posts have really resonated with me as a woman in science. Several high profile reviews have been very positive and so I placed it on reserve at my local library.

Overall, I liked the book. It’s mostly a biography that covers the lives of Hope, and her partner in lab crime, Bill. The biographical bits are interspersed with quick vignettes that talk about major aspects of plant biology in a very relatable way. Readers who are not biologists will come away having gained some knowledge about how scientists think and operate and that is a good thing. I really enjoyed the beginning of the book, disliked the middle of the book, and thought that the reflections in the latter half of the book were poignant. I was especially touched by her descriptions of her experiences as a woman in science, her mental illness, and motherhood.

One major thing that I didn’t like about this book is that I found myself being very judgemental about several incidents described its pages. This likely says more about me as a reader, than it does about the author. One area that is treated very cavalierly in the book is lab and field safety. She describes a glass explosion incident in the lab and two car crashes (one very severe) that all involved trainees in an off-hand manner that I found disturbing and appalling. This may be how she has chosen to deal with what are traumatic events, but it leaves the reader feeling that scientists operate as cowboys who are answerable to no one. She also describes a few hazing rituals that she’s used on trainees in her laboratory to separate the wheat from the chaff which rubbed me the wrong way. A lot of time is spent referring to her obsessive and excessive hours spent in the lab. My personal feeling is that maintaining those kind of hours is unsustainable and unsafe and just serves to reinforce the masochistic aspects of science.

She peels back some of the mystery of what it means to be a scientist, warts and all, and perhaps that is what made me so uncomfortable with the middle of the book. She pulls no punches and this is a very honest book based on her experiences as a scientist. Many observations in the book made me laugh out loud, and some stories made me tear up. Books should make you feel and think and in this the author has succeeded.

I recommend reading this book to scientists and non-scientists alike. I think that it has something for everyone.


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.



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.


Figuring out what to do with the rest of your life

Having options is generally a good thing, but there can be such a thing as overload. Students today are presented with a myriad of choices that they have to make each year that will have a direct impact on where they end up in their lives and careers. That’s a lot of pressure to deal with in addition to any pressure being applied by family to ensure that you are making good choices.

When I was doing my undergraduate degree many years ago, I knew many students who were doing their degrees because they thought that it was what they were supposed to do, because their parents had told them they should/must be a doctor, or because they really didn’t know what to do with their lives and this seemed like a good default. Living your life in default mode is not really living your life.

We often tell students that they should work or study in a field that they are passionate about, but passion alone will not put food on the table or a roof over your head. The opposite is to do something that provides a steady stream of income, but I’ve seen that option lead to burnout and depression. I’d suggest that the healthiest option is a compromise; attempt to find employment that you enjoy and find interesting and that provides enough financial compensation for you to live comfortably. The other way to look at this is to avoid doing things that you hate. Completing an undergraduate degree is a useful way to figure out tasks and subjects that you hate and in the future you can do your best to avoid these as much as possible. You will probably never get through life completely avoiding things that you hate, but you can certainly design your life to minimize it.

Each situation is obviously different, but life is too short to be unhappy or to allow someone else to make your choices for you. When you are young you have lots of time available to try new experiences and see how they make you feel. There really is no rush to get on with the rest of your life, but it is better to make conscious choices about your future than to ride the tides of apathy.


Public Service Announcement: Don’t Date Your Students

With all of the recent news about PIs who sexually harassed their students, this piece by Janet Stemwedel is important and timely. It is excellent.

Do not use your students as your dating pool.

If you have romantic or sexual feelings about one of your trainees, then transition them out of your lab to another lab before you remotely entertain the idea of acting on those feelings.

I know many couples who met in graduate school, and in some cases one was the PI and one was the trainee. If the relationship started before the student transitioned or moved out of the lab (or if the student never left the lab during the relationship) this means that I give the PI the side eye for the rest of their career. It also makes me wonder what other boundaries they are violating. I will never trust that person.

Love can wait in order for you to do the right thing.


Attention Undergrad Students: Why Doing an Undergraduate Thesis Project is a Great Idea!

Doing a fourth year undergraduate thesis project has been one of the best experiences of my life. To say that it was life changing is not an exaggeration; it is the reason that I am a scientist today! I’ve always been interested in biology and during my second year of undergrad I heard that our department offered opportunities for students to do an independent research project in the lab of a faculty member in fourth year. The application process took place in third year and was very competitive. Many students wanted to do projects, but a limited number of project slots were available. The application consisted of making appointments with various faculty members to discuss the potential projects that they had available and in order to determine whether your research interests were well matched. You then listed your top three choices for placement and hoped that you would have a faculty member pick you as a thesis student. I was very naïve going into this process and had not laid much ground work in order to increase my chances of success. I was devastated when I didn’t get selected for a project.

Fortunately, my teaching assistant at the time for Plant Physiology thought that I showed promise and arranged an interview with her graduate thesis supervisor who hadn’t had any students apply to his lab. The meeting went well and I accepted the spot in his lab for my undergraduate research project. I spent 10 months designing and executing experiments, analyzing results, and presenting those results orally and in a final thesis document. It was an excellent experience overall, I really enjoyed myself, and it led to my decision to stay in science and obtain my M.Sc. and Ph.D. degrees.

Many of the undergraduate students that I talk to are unsure about whether to do an undergraduate thesis or not. It’s often perceived as a mysterious experience and I do my best to outline why I believe that it’s a valuable opportunity for many students. Here are some of the things that I say to students as to why they should consider doing a fourth year thesis project:

1) You are taking an undergraduate biology/biochemistry/health sciences degree. Presumably you are doing this for a reason; whether it is because you like the subject, you might want to go to graduate school, you want to get admitted to dental, medical, or professional school, or maybe you really don’t know what you want to do with your life. Doing a thesis can help to clarify your future plans. Perhaps you will love doing a thesis project and will have found your calling by the time you finish your time in the lab. Maybe you will hate doing lab work. Either way, by doing a thesis in 8 months you will have more information available to you in order to make an informed decision about your future plans. If you perform well, your supervisor will be happy to write you reference letters and to serve as a mentor in order to help you succeed in your future goals.

2) A thesis teaches you a lot of transferrable skills that you can go on to use in other areas of your life in the future. Other schools and employers are looking for people who can manage and complete projects, manage their time, work independently and as part of a team, problem solve, present information to a variety of audiences, write, and see the bigger picture. Your thesis should provide you with practice in all of these skills and many more.

3) Doing a thesis is an opportunity to put into practice what you have learned during your undergraduate degree. It is also really cool to discover something for the first time! You will also meet some interesting people in the lab and through the course of doing your project. It is amazing to contribute to the creation of knowledge!

4) You may have opportunities for travel by attending conferences in order to present your work. You might collect information through networking at these events that will help you to make choices in the future about your life and career.

These are the first few advantages of doing an undergraduate thesis project that come to mind. If you are a scientist who supervises undergraduate researchers, what other positives do you use to encourage students to take advantage of this opportunity?


Having Difficult Conversations

I would guess that 99% of the interpersonal issues that cause problems in laboratory environments are due to communication issues. The vast majority of these problems are due to the fact that many people in this world are conflict averse or avoidant and therefore refuse to deal with issues when they first arise. This allows the issue to escalate, expand, and lead to general dysfunction between people. It often starts small, but over time can turn into a huge deal.

I have found that the best way to avoid interpersonal issues is clear communication. This takes a lot of work and a great deal of self-awareness. Other people cannot read your mind in order to know that constantly borrowing your transformation solutions in the lab and using them up until they’re gone is driving you bananas. They may not realize that playing country music in the lab is making you want to take a hit out on Jason Aldean. They have no idea that hogging the centrifuge at all hours of the day is leading to resentment. These are the types of irritations that I experienced as a graduate student and a post-doc. All were resolved by a frank conversation about what was bothering me (and I framed it as my problem) and talking with the other person to come up with a solution together to address it. People made their own transformation solutions and stopped using mine, I accepted that country music was going to be played often in the lab and I brought in my own MP3 player and headphones to listen to my own music, and a booking sheet was developed for the centrifuge. When you have these conversations early, they aren’t a big deal.

As a PI, some of the conversations that I have to have with trainees and colleagues are more challenging and the stakes are often higher. Most commonly I have to talk to students about their research progress, writing, and professional development and offer constructive feedback. This is part of my job as an advisor and mentor and sometimes I have to deal with a performance problem. Doing this effectively and humanely is a skill that takes time to develop, but you do your students no favours by dancing around performance problems and not addressing them. Sometimes trainees do not have the skills or awareness to address interpersonal issues that they are having in the lab and it is my job to help them to do that; not to look the other way and allow resentment to fester and hope that the problem will go away. It is my job as a PI to manage my laboratory trainees and staff. I wasn’t trained as a manager, so of course this is going to be difficult at first. Difficult conversations are never pleasant, but with preparation they can go well and be productive and useful. I find it helpful to make a list of issues that I’d like to address and a bullet list of points that I want to communicate during the conversation. The other important skill to develop is the ability to listen to what the other person is saying. You may not have all of the information about a situation, or you might be working using false assumptions. I find that being tactful, professional, and honest goes a long way towards making these conversations go more smoothly.

In my job as a professor, here are a few examples of difficult conversations that I’ve had to have:

1) Informing a group of students that I was notifying the chair of my department and my dean that I suspected them of academic dishonesty. I also had to interview several students in that class in order to collect evidence and facts to support my initial suspicion. I was correct and then had to have 3 separate conversations with 3 of these students to outline the process and consequences.

2) Informing a graduate student that their progress in our M.Sc. program was insufficient. This involved transitioning the student out of our program after an honest assessment of their academic capabilities.

3) Informing a faculty colleague that their graduate student was constantly interrupting female faculty during committee meetings and asking whether they would like to communicate this as a problem to their student, or whether they wanted me to have that chat with the student instead.

I take notes during these conversations for my own records and I encourage the other person to do the same. I sometimes will also send a follow-up email to the person to document my understanding of what was discussed and agreed upon in the meeting if I suspect that my view point will be forgotten or disregarded. Depending on the nature of the difficult conversation, it may be helpful to have an impartial witness present if you suspect that the chat might turn volatile or abusive. It is also worth thinking about your personal safety if you think that the other party might respond inappropriately. It is usually appropriate to keep your office door open during these conversations in case you need to get assistance from another staff or faculty member.

I still dread having difficult conversations, but I have learned that they are necessary and most effective if done as soon as a problem is identified. Dealing with problems as soon as they arise greatly decreases the cumulative stress that the problem will cause you and frees up your mental energy for more useful pursuits.