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!


The Ultimate Guide to Being a Gracious (Non-creeper) Conference Attendee

An important post went up yesterday over at the Tenure, She Wrote blog on the topic of microaggressions towards female scientists at conferences. If you’ve never heard of microaggressions before, a quick overview is available at Wikipedia. These behaviours create a toxic atmosphere, a chilly climate, and drive women and other minorities away in droves. It’s often a long pattern of experiences caused by many different individuals and that is what makes it so hard to call out. The examples provided in the above blog post were very blatant, but no one stepped forward to stop it; not the organizers and not the moderators. In fact, the two women who were the targets of the behaviours banded together in an attempt to support each other through the ordeal. We shouldn’t expect the victims of the behaviours to change them.

Below are a few thoughts that I’ve had over the years of both organizing and attending many conferences over a span of 20 years.

1) Organizing a conference is a lot of work. Be appreciative of the efforts of your hosts. Not everything will be perfect, but most things will not make or break a conference. If you have organizational or safety concerns, bring those to the attention of your hosts in a firm and polite way. Don’t wait until the end of the conference, because at that point the problem often can’t be effectively addressed.

2) Encourage the conferences that you attend to have an official policy on civil, professional, and non-harassing behaviour. The past several years have seen massive exposé stories on a large number of conferences that had systemic problems involving harassing behaviour that might have been avoided had such policies been in place. If you are a big-wig in the community, an effective way to encourage conferences to implement a policy is described by John Scalzi. A recent survey of conferences in the area of Artificial Life done informally in June is interesting in that it shows how few conferences have a policy. Do the conferences that you attend have such a policy? Can you advocate for one?

3) One of the great things about conferences is catching up with friends and seeing what’s new in their professional and personal lives. Thanks for asking about my partner and my kids and how they are doing, I’m happy to share updates and news about my life. I do not however appreciate inquiries about who is looking after my kids so that I can attend the conference (I guess I’m a bad mother and/or a crappy scientist who doesn’t take her work seriously), implied judgements about my spouse’s ability to care for our children (he does not babysit his own children by the way, he PARENTS them!). These lines of questioning make me feel like an outsider who doesn’t belong. When four people ask me this in quick succession it’s demoralizing.

4) Be aware of personal space boundaries. Unless we are besties don’t hug me, don’t greet me with the kisses on both cheeks, don’t rub my back, arms, or shoulders, and sure as hell don’t pull or tweak my hair.

5) Be aware of power dynamics. Use your powers for good, not evil. To believe that the undergraduate who is new to the field has the same influence or power as a senior PI is absurd. Advocate and speak up for those who need it. Be an ally. Actions speak louder than words.

6) You are a professional. Act like one! I have a long memory; what you said or did reflects poorly on you, your department, your colleagues, your institution, and our professional society, especially if you’ve been getting away with it for a while. Don’t use a professional setting as your dating and/or hook-up pool. Hitting on or flirting with students at the poster session is inappropriate. Propositioning post-docs for sex at the conference banquet is harassment. These are not misunderstandings; they are predatory behaviour.

7) Help others network. Remember what it was like to attend your first conference? Introduce people to each other and be kind to everyone. You never know when collaborations and great ideas could spring to life!

8) Take the opportunity to educate others about some of the above issues. Most people will be receptive and invested in making the conference better for all attendees.

Project Management for Scientists

project management notesToday’s topic in my group lab meeting is project management. It took me a long time as a scientist to believe that research projects could actually be managed. I think that I felt this way given the uncertain nature of scientific research; you never know if an experiment will actually work and you often can’t predict in which direction the research will go next. I’ve always been an organized person and it turns out that managing a research project isn’t all that different from other projects that you do in your day to day life such as go grocery shopping, clean out the garage, and plant a vegetable garden. Once I started thinking about science in the same way it’s like a light bulb went on.

I don’t recall ever having explicit conversations with my research mentors and supervisors about project management. That may be because I was fairly productive and am a planner by nature, but these are skills that don’t naturally come to everyone and that can be learned and improved over time. As a purely ridiculous example, I explicitly tell students that they should do something else with their time while PCR is running or they are incubating a sample for an hour. I’d like to think that they know this, but I have heard stories from colleagues, of students who will literally sit there for the duration of the incubation thereby wasting precious time that they could have used doing anything else. It’s like the science equivalent of watching paint dry.

Here are some thoughts on how I approach project management in laboratory science:

1) My first step is to define the project clearly and to determine what success looks like. If you skip this step you’ll never know when the project is done, nor will you know if you did it well. You need to identify the full scope of the work, what resources you’ll need (reagents, people, literature, etc.), and the time that you have available to do it in. Thinking about these limitations up front will decrease the amount of frustration that you and others experience later. At the same time, there is room for flexibility, which I will talk about later.

2) My next step is to think about the major milestones that need to be completed in order for the project to be finished. For even the most basic science experiment this will include things like generation of hypotheses and predictions, experimental design, ordering of reagents, allocation of people, doing the experiments, data collection and analyses, data presentation and communication (i.e. making figures, tables, diagrams, etc.), and generating a manuscript, poster, or talk to communicate your findings. That’s a lot of stuff to complete in order to successfully finish your project! One of the major things that I struggle with is maintaining an interest in projects that span several years of work; I often get bored part way through and struggle with staying motivated to finish.

3) Up next is thinking about the flow of tasks and their relationships to one another in your project. I like to think of the major milestones in a project as parts of a puzzle that need to be put together. When I build puzzles, I always start with the edge pieces first, and then work my way in; this means that the connection of some pieces requires the presence of other pieces first. With your project you want to determine whether some of your milestones are interconnected and have to happen sequentially, or whether some of your milestones are independent and could be worked on in parallel at the same time. For example, if you wanted to clone a particular gene in your critter of interest, you would first want to obtain the DNA sequence from a molecular database, you’d then design and order gene specific primers, you’d then perform PCR with your primers, purify your amplified DNA via gel electrophoresis and a gel extraction kit, clone your DNA product into a plasmid, and sequence the plasmid to ensure that the DNA sequence matched the one in the database. These tasks are sequential and one needs to happen before you move on to the next. Other projects have milestones that could be completed at the same time because one doesn’t depend on the completion of the other. This is also the time to identify what could go wrong. Where might your project go off the rails? Can you come up with a back-up plan to get around the problem should it arise? Can you plan ahead to avoid the problem? Can you ask for help?

4) Now you need to break your project milestones into smaller mini-projects that contain a small number of discrete steps. Ideally, you’d aim to complete a few of the small tasks every day and one of the mini-projects each week in the lab. This will help to keep you motivated as you’ll be able to measure your progress on the project and you will build up lots of little wins and that will keep your mental and emotional state positive.

5) The final step is putting together a timeline for completion. I like to set a deadline that I think is realistic, but I usually add several extra weeks and expect that something will go wrong during the course of the project. I then work backwards from that date when planning my time. I schedule in my major project milestones, my mini-projects, and my smaller tasks at a level of detail that I’m comfortable with. Some projects are tricky and it will be difficult to easily identify all of the mini-projects and small tasks up front. Do your best and don’t get off target because that can lead to project creep where the scope of the project balloons out and doesn’t resemble the scope of what you originally set out to do. You need to be flexible because plans can sometimes change mid-project, but head back up to what you defined in Step 1 if you feel that your project is getting out of control. You’ll often find that you reimagined the scope of the project without really thinking things through because you got excited by a neat result or finding. Think extra hard about whether you really want to commit to expanding the scope or redefining the success of your project before you leap in! That being said, there will be times when you need to retool your plans and timeline due to the unpredictability of lab research, but hopefully because you’ve identified the possible trouble spots in advance (Step 3) this will be minimal.

6) Execute your project management plan. Enter specific tasks and mini-projects in your daily and weekly calendar and set deadlines for your project milestones.

Some great resources:

If you need help with bigger project management concepts, Melanie Nelson’s blog Beyond Managing is great!

If you find that scheduling, prioritizing, and keeping up with your to-do list is a challenge, I recommend reading David Allen’s book “Getting Things Done” . It will change your life – I kid you not!

What tips and resources do you give to your trainees in order to help them manage their research projects?

My first media interview as a scientist

Today I did my first interview with a large media organization. While I had previously done interviews with some campus print media outlets this was the first time that I was doing an interview with media that was external to a university. The topic of the interview was the under-representation of women in STEM (Science, Technology, Engineering, and Math). That’s a topic that is very personally and professionally important to me so it was extremely vital that the interview go well. I was therefore very nervous about the interview.

The first hurdle came up this morning when determining what to wear. I wasn’t sure whether the interview was for TV or radio. TV is a visual medium, so rightly or wrongly half of the message that you’re sending will be based on how you look. From previous conversations and photo shoots I’d learned that patterns are bad for TV. Stripes especially look awful and appear unstable when broadcasted. My husband thought that my original shirt made me look washed out and pasty, so I switched to a darker, solid coloured top for the interview. I did my make-up, hair, and accessories as usual and kept things simple. As it turns out it was a radio interview, so a tip for next time will be to clarify this piece of information in advance.

Since I’d never done something like this before I wanted to make sure that I was as prepared as possible, so I did what any reasonable person would do and I researched how to prepare for a media interview using a quick Google search. I’d also previously participated in a media training workshop as a post-doc and more recently as a faculty member at one of Informed Opinion’s excellent workshops facilitated by Sheri Graydon. I quickly learned that it’s important to have 1 key message that you want to convey and to use 3 points or examples to hammer home that key message. I spent about 20 minutes fleshing out my key message and 3 talking points that I’d like to convey during the interview and practicing how I could say them in response to an interviewer’s questions. I think that the interview went very well and was a positive experience. I learned a lot from participating myself and from watching two other people being interviewed for the segment.

Our interviews will be edited down to a 7 minute radio and web segment and will likely to live tomorrow or Monday. I’ll add a link once it gets posted.

I’d be curious to hear from more seasoned interview participants. What are your top tips for a scientist who is speaking to the media for the first time?

Science Moms

There have been some great articles on-line this week talking about the realities of being a female and/or Mom in science and technology.

Meg Duffy tackles the logistics of pumping breast milk at work and sending bottles to daycare in today’s post over at Dynamic Ecology . This is a practical post about an important topic that doesn’t get talked about a lot. I give Meg props for making this work. I found that after my kids started daycare we had to switch to formula during the day due to a lack of supports for pumping/breast feeding on my campus. I just wasn’t willing to pump in a nasty bathroom stall and probably would have gotten bizarre looks if I had asked about a lactation room.

An awesome article posted yesterday by Rebecca Schuman in The Chronicle of Higher Education on how Academe Is a Lousy Family Planner. Rebecca has articulated very well how I felt as a graduate student starting a family. Looking back I’m amazed that I was so strong (or naïve) to start my family during that phase of my career. It was tough, but I have no regrets and the timing worked out exceptionally well for me. Start your family when you are ready; do not let the academy dictate your reproductive choices.

Jessica Valenti has an interview in theguardian with Anita Sarkeesian about GamerGate and how it has changed her life. The comments kind of say it all and illustrate the point of the article quite effectively.

I’m also pleased to have taken part in @EdenHennessey’s display that highlights the challenges faced by women in STEM. The #DistractinglySexist exhibit is on display @LaurierLibrary for the next month.

Funding graduate student travel to conferences

This blog post was prompted by a disturbing post over at Tenure, She Wrote by a graduate student talking about the lack of funding for conferences. I am happy to say that my experiences of conferences as a graduate student were not like the experience that this student is describing, but I was horrified by the situation detailed in the blog post.

I’m now a PI and my goals with regards to graduate student travel funds are to be as transparent and fair with my graduate students as I can be. It is what I would like a supervisor to do for me if I was still a graduate student. Since starting my position 5 years ago, I have had an unwritten policy on this topic, but this student’s post made me realize that I should be more explicit in my policy and perhaps write it down so that there is less chance of a miscommunication with one of my students.

My goal for each of my graduate students is to send them to 1 conference per year of their program. Most of my students complete their program in 2 years, so this usually means two conferences. Usually the first conference is local and therefore lower cost and they usually present on work in progress at this meeting. These are smaller meetings where I am able to help them network and the attendees are friendly. The second meeting involves the presentation of the full story of their thesis work and I try to ensure that this is either a national meeting or an international one. This is my philosophy on meetings. I allow my students to present work in progress or partial stories at the first meeting and I know many PIs who don’t do this; I feel that the experience is worth it for the students even if the work doesn’t yet represent a full story. I tell my graduate students several times during the year that my goal is to send them to one conference per year. If students wish to attend more conferences, then we discuss their reasons for attendance and negotiate my financial contributions based on grant funds available.

I also have a very explicit conversation with my graduate students near the beginning of their program about how the costs of the conference will be handled. I pay for all travel, accommodation, meals, posters, and registration costs. If I can charge the cost directly to my grant (usually using an institutional credit card) I do so. If the cost gets charged upon arrival at the conference I either charge it in person upon arrival, issue the student a travel advance, or if the student is comfortable with it they charge it on their own credit card and get reimbursed. Fortunately our institution is fairly speedy with reimbursements, so students do not have to pay interest on the amount or carry the balance for more than two weeks after our return from the conference. I let the students tell me what they are comfortable with and I don’t judge. I let them know that if funds are tight, we will come up with a solution that works for both of us and that they should not place themselves in financial hardship to attend a conference. If the student wishes to pair travel to a particular location with a vacation and stay for a bit before or after the conference, then I still pay for the return trip, but during those extra days they are responsible for their accommodations and food and I explain that clearly before we make any travel bookings. I also ask my students to apply for all available travel grants that they qualify for to help support their attendance, but these funds do not make or break the trip.

As a graduate student I often had to share rooms with other students. At times this was fine and I expected it and at other times it was awkward (e.g. when I was pumping milk while still breast feeding). I initially ask students if they are comfortable sharing a room or a suite of rooms with other students. Residence and hotel options differ quite a bit and I ask my students to explore all options and let me know their preferences. I have had students who preferred their own room with a washroom, students who share a room and washroom with one other student, students who share a suite with other students (they have their own room, but share 1-2 washrooms with others), students who have their own room and share a communal washroom on the floor, etc. I respect the requests of my students and I assume that they have logical reasons for any limitations that they place on housing arrangements. I do not share accommodations with my students as I am not comfortable with that arrangement.

Affording all graduate students with the opportunity to participate in conferences is one of the commitments that I make to each student that I accept into my laboratory. Whether or not they can financially afford it should not dictate whether they can attend. I consider this philosophy one of the privileges and responsibilities of mentoring graduate students.

How do other people handle conference costs for their graduate students? Any horror stories that you’d like to share?

PhD Tree: The website that lets you see how incestuous research science is

Last week I received an unusual piece of spam in my email inbox. It was from a website called . Evidently someone thought that it would be an awesome idea to spam email addresses acquired from PubMed in order to publicize the site.

The concept behind the website is an interesting one. The idea is to follow the academia genealogy of scientists through their research careers. It’s an idea that I’ve joked about with colleagues at conferences and it’s therefore interesting to see someone attempting to make it a reality. It’s somehow been auto-populated as I haven’t added anything to the site, but two entries from my M.Sc. and Ph.D. degrees are present. Sort of a 6 degrees of Kevin Bacon for researchers. It would be interesting to identify people who are hubs in the network. Someone has even decided that it’s worth doing an Academic Genealogy of Nobel Prize Winners .

At the moment the tree and most of the entries are very heavily skewed towards one sex. It would be interesting to see if an analysis of the data could highlight leak points in the leaky pipeline or identify particular PIs that exhibit biases in the trainees that they take on.

Not sure if it will take off or not, but it’s an interesting idea.

On-line Storage of Lab Protocols

In the labs I’ve been in previously, common lab protocols were stored in a binder in the lab for reference. Usually I’d make a photocopy for my own use as a place to start and as I optimized the protocol for my experiments I’d mark up this copy. Once I had a solid protocol worked out, I’d generate my own copy of the protocol so that it served my purposes. When I started my own lab I wanted to make sure that my students had a binder of protocols that they could refer to for their own experiments. At the same time I wanted to prevent protocol drift (i.e. the inadvertent changing of a protocol over time). I thought about the common protocols that we would use in the lab and generated several binders for these that are stored in the lab. This approach works, but it’s a bit clunky and limited the students to looking at the protocols only while in the lab. I recently decided that it would make sense to generate a central, on-line repository for our lab protocols.

A quick search of the web showed that researchers do this in different ways. Some labs make their own Wiki to hold this information, others use cloud storage or an online protocol repository, and others used a campus intranet or password protected website. I’m currently in the process of evaluating all of the possible options. How does your lab store and manage experimental protocols? I’d love to receive advice and hear about options in the comments below!

Blogs that I read

One of the great advantages to using social media (e.g. blogging, Twitter) is the wonderful people that you can meet and the impressive knowledge that you can acquire in a short period of time. Before I began blogging I lurked for a long time on-line in order to examine the landscape and get a feel for how bloggers go about blogging and how scientists were using Twitter. I’m still learning, but for those of you who are new to the on-line world, or are looking for new blogs to read I thought that I’d share links to the blogs that I read regularly. I list them below in no particular order.

  1. Apple Pie and the Universe

I’ve been reading this blog for several years. The writer is a female astrophysicist who is balancing a professional career with family. She has recently gone back to school to become a teacher and has a strong interest in public science outreach.

  1. Ask a Manager

Alison Green dispenses straight shooting advice on how to manage people. I’ve found her blog very helpful for providing perspective on my role as a professor managing my lab and a group of trainees. The scenarios presented here are sometimes shocking, but the advice is solid.

  1. Beyond Managing

Melanie recently left a job in the information technology sector and has become an entrepreneur. She often posts insightful pieces on productivity, managing people, and women in science.

  1. Dynamic Ecology

I am not an ecologist, but I enjoy most of the posts on this site by Brian, Meg, and Jeremy.

  1. Eat, Read, Science.

Betty posts great summaries of recent, cool science papers! Always an interesting read.

  1. Female Science Professor

This blog was recently referred to as the “gateway” science blog for many women in science that led them into the blogosphere or encouraged them to start blogging themselves.

  1. The Simple Dollar

Trent provides simple ideas for how to manage your money and live a frugal lifestyle without turning into a humourless hermit.

  1. Get a Life Ph.D.

Tanya provides useful advice and perspective for graduate students and those starting out on the tenure track.

  1. Small Pond Science

Terry et al. talk about what it’s like to do research at a smaller, teaching focussed institution. The “Recommended Reads” posts are awesome!

  1. Tenure, She Wrote

A fairly new blog that covers a wide array of topics in frank and honest voices from multiple contributors.

  1. Isis the Scientist

This was one of the first blogs that I read that really spoke to me as a woman in science. Dr. Isis tells it like it is, but offers effective strategies for real world scenarios.

What blogs do you like to read as a scientist? Leave links in the comments below.

The Positives and Negatives of Conferences

I’ve been going to conferences for >17 years and many things have become much easier compared to my terrifying first conference experience, but some things will always stay the same. Below I talk about some of the positives and negatives of attending conferences.

  1. Travel

This can be both a positive and a negative. Getting to your destination is usually not a particularly pleasant experience. The first few times on an airplane, bus, train, etc. can be exciting, but after a while it gets pretty boring. I am constantly amazed by the bad behaviour of other people while travelling. Recent changes by air carriers in Canada has made this even worse by charging for checked luggage. This has led to a massive uptick in the number of passengers bringing carry-on luggage that has to be stowed in the overhead bins. If you can fit a small adult in your carry-on bag you need to check yourself…and your bags.

Once you get to your destination the fun can begin! Many locales that you travel to as a scientist are international and interesting; I consider this one of the perks of the job! I’ve been to Australia, England, Portugal, Spain, Austria, and various North American cities. After you’ve been doing science for a while, you may end up visiting the same locations which is not as stimulating. When the Icelandic volcano erupted in 2010, I got stuck in London, England for an extra 5 days. In that case the delay was somewhat positive as I got to visit Kew Gardens and the Victoria and Albert Museum , but the uncertainty of when I’d be able to fly home was pretty stressful.

  1. Meeting new people

The vast majority of the scientists that I’ve met at conferences have been awesome and amazing. I’ve started new collaborations, shared knowledge, developed new research ideas, and learned a great deal. These interactions are what make a conference worthwhile for most of us. I could certainly do without the creepers and the gigantic egos however.

  1. Oral presentations

Watching other people present is always an education. A great talk can be inspiring and offer tips on how to improve your own presentations. A bad talk provides you with a list of what not to do and can put you to sleep. I often come up with ideas for material to use in my courses, or slide layouts that are more visually appealing.

  1. Poster presentations

It’s really hard to put together a strong and effective poster, so I’m always on the look-out for great posters and what they have in common. I’m not a huge fan of poster sessions because I’ve often had the experience of having only a few people stop by my poster. I think that oral presentations offer better exposure and opportunities and therefore encourage my students to do talks if possible.

  1. Social events and field trips

These events are usually lots of fun. I look forward to them as a chance to catch up with friends and colleagues, recognize professional achievements, experience the culture and traditions of the host institution and country, and if I’m lucky- dance. I don’t enjoy being around scientists who drink to excess and make idiots out of themselves. I will remember that time in 2005 when you hit on that graduate student and refused to accept that she didn’t want to dance. It’s unfortunate that her first experience of being at a conference hosted by our society involved me tactfully removing her from the situation, making sure that she was o.k., and telling her that you were in the wrong. In retrospect I should have done more, but power differentials suck.

  1. Participating on the executive of your professional society

This is a great way to become involved and to meet new people. I’ve served on the executives of two different professional societies and I’ve gained a lot of transferrable skills and knowledge. Many societies have positions available for students and post-docs, so even if you are just starting out in science there are great opportunities available.

Overall, conferences are very positive, useful and fun experiences! I’d appreciate hearing your conference triumphs, tribulations, or disaster stories in the comments!