Tips for managing a research lab

/ Chris Buddle / Leave a comment

Running a research lab* isn’t easy. I learned this the hard way last fall when I performed rather poorly on my lab safety inspection. At the time it seemed to be a low priority: cleaning up the lab always seemed less important compared to, for example, having a lab meeting. We have since done a major lab clean-up, and we are back on track (phew!), but the experience has made me think about the skills needed to run a lab. Hopefully this is of interest to some of you, especially early career researchers (ECRs), but I would also like experienced researchers to wade with comments and tips. This post will be more about the “nuts and bolts” of running a lab, but perhaps a future post can be about broader philosophies around being the head of a research lab.

CleanLab

Part of my lab – AFTER cleaning.

Human resources

There are people in a lab. This means, as the head of a lab, you need to pay attention to human resources. This might be practical kind of stuff, like signing expense reports, or making sure students are getting paid when they are supposed to. But there are also many more complex things to think about, such as helping resolve arguments, or helping students through difficulties. You need to learn to listen, you need to navigate social dynamics, and be a good communicator. Make your expectations clear, and be sure that everyone is well aware of their roles and responsibilities. Work on ways to have a productive AND fun lab. Be sensitive to everyone’s different needs, and be open to change – operate on a principle of kindness. You will likely find yourself navigating some tricky situations so be sure to get help when you need it: there may be training available, or perhaps ask your Chair or a colleague about advice on being a good manager of human resources.

Organization

Running a lab is very much about being organized. There has to be a “plan” for all the different supplies, and space for everyone to store their samples, find the ethanol, or grab new Petri dishes. From the start it’s important to think about space needs in the long-term – anticipate how the lab might change in the future, and make sure there is room to grow. People need to feel that they have a “home” in the lab, whether it’s a desk or piece of a lab bench, and this requires careful assessment of space. I personally struggle with sample storage, and seem to squeeze old samples into various drawers, with a promise of getting rid of them (or putting them in long-term storage) after students have published their work. That promise is mostly broken, as it it easier to just store stuff and forget about it. ECRs: avoid this mistake! Stuff accumulates far too quickly. Be sure to label things too, including where to put supplies.

OrganizedLab

Safety and training

Don’t drink from the beakers; broken glass is dangerous. Stay on top of the safety rules at your institution: it’s easy to miss those emails, but as I learned, they are important. Top-down guidance about safety will show the lab members that safety is a priority not an afterthought. Know where to store chemicals, know about the eye wash stations, and make sure the first aid kit is stocked and ready. Know what needs to get stored where, and be ready when there is a call for hazardous waste disposal. Learn about MSDS, and be on top of the chemicals that may be present in your lab. As the head of a lab, you are indeed responsible for making sure your lab members have the appropriate training in the context of lab safety: whether it be WHIMIS, research ethics, or wilderness first aid, get your students signed up, and pay for the training. Don’t shirk this essential responsibility.

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Permits

As the head of a lab, your name will likely be on all the research permits, and depending on your field of study, this can be a very big deal, and complicated. From collecting permits to animal care to biohazards, you need to guide your students through the permit process, from application to final reports. You have to be aware of deadlines, and know the ins and outs of the different requirements, especially when your work might cross jurisdictions. This can take an inordinate amount of time, but it requires the time commitment: lacking a permit can stall an entire research program. It’s essential to be proactive and prepared for permits. I certainly get my students to write the bulk of their own research permits, but a manager of a lab needs to facilitate this process.

Budgets and supplies

Running a lab means making sure there is a budget (i.e., you need a research grant!) to buy light bulbs for the microscope, flagging tape for field work, or medium for the agar plates. You need the money, and you need to know the process. The latter is not trivial: at my University some supplies are best bought using an internal purchasing system. Other places need just a credit card, or perhaps a purchase order. There are so many systems to learn, and each one probably needs a different password. It’s confusing and frustrating, and you have to stay on top of it. I keep a special file with all the details written out, and a hard-copy folder with old invoices – this way I can make sure to but the right sizes of things. Consistency is supplies is rather important!

Troubleshooting

Here are some things that have occurred in my lab over the years: weird smells from the sink. Lack of heat. Leaks from the ceiling. Power failures. Spider escapes**. Failing fridge. Failing freezer.

And the list goes on… Running a lab can be a lot about troubleshooting – you need to figure out who to call for what problem, and find a speedy resolution – otherwise you let down your grad students. Make a list of key people to get to know, from facilities to the local safety officer. Even better, post the list up in the lab, next to the telephone.

 

Ok, so there are certainly more things to know about running a lab, but hopefully the list provided is a start. Here’s the catch: almost everything I learned about running a lab was learned on the job. Despite attending some required workshops at the start of my career, I did not learn any real skills about running a lab. I was not trained to run a lab. Scientists must be taught to manage a lab.

That is a problem because a failure to run a lab properly has significant consequence for a lot of people! My students depend on the supplies that I have to buy, and they need to know what to do if there’s a chemical spill. Thankfully I had some good mentors when I was a grad student, and I managed to figure a lot of things out. However, I do think Universities need to do a better job helping hone the skills needed to run a lab; in many research fields, a successful academic career really depends on having a smooth-running lab, anything that can be done to help prepare ECRs for this would pay off.

In sum, I’m certainly a work in progress. Although I have some skills in research, I know that running a lab can be a real challenge for me, whether it’s forgetting to order supplies or checking the eyewash station weekly. I have learned to delegate a bit, and my grad students help me immensely at maintaining a safe and clean lab environment. I sure hope some of you can learn a bit from my own trials and tribulations… And please educate yourself, plan ahead, and know what it takes to run a lab well before you get the keys.

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Here are some other resources I’ve come across, related to managing a lab: from Genome Web, ASBMB, a post by Matt Welsh, and a Reddit thread on the topic

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**Sometimes we work with live spiders, on various projects. There have been times when they haven’t been where we left them. Oops.

Will spiders bite my dog?

/ Chris Buddle / 1 Comment

I field a lot of questions about spider bites, and I have argued that spider bites are exceedingly rare (for humans). But what about our pets? Do our furry friends get bitten by spiders? If they get bitten, how do they react? Let’s look at this, move beyond anecdotes, and see what science has to say on the topic!

Can spiders bite my dog or cat?

The short answer to this is: YES. Some spiders are physically capable of biting mammals, including dogs and cats.

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This is my dog, Abby. Should she be scared of spiders?

The longer answer is that we really don’t know about this for the vast majority of spider-pet interactions, and even if spiders can bite mammals, I would argue that such events are relatively uncommon. Spiders certainly don’t hunt dogs or cats, and when bites do occur, they are likely quite accidental. Your puppy Ralph can be quite energetic and rambunctious, and stick his snout into a dark corner which may be home to an arachnid. I’ve certainly seen my cat “play” with insects and spiders, and ping-pong an arthropod across the kitchen floor. However, we certainly have to get a little lucky to see an actual spider-pet interaction, and dogs and cats can’t tell us whether they have been bitten by a spider. Proper verification of any bite requires evidence.

In some cases, the evidence isn’t in dispute, such as the paper by O’Hagan and colleagues who state quite clearly in their peer-reviewed paper:

“Two 9-week-old Chihuahua pus weighing 960 grams and 760 grams were seen to be attacked and bitten by a large black spider. The spider was killed” (O’Hagan et al. 2006).

Right: the puppies were seen to have been bitten by a spider, and presumably the pet-owners know what a spider looks like. Also, that paper was co-authored by a well-known Arachnologist, Dr. Raven – having an arachnologist involved in these studies is important, and gives credibility to the incident. This is a good example of a verifiable interaction between dogs and spiders.

There’s another detailed paper by Isbister et al., outlining spider bites (in the family Theraphosidae, a family of Tarantula spiders) in humans and dogs: their evidence isn’t in dispute either, and in two cases, the human was bitten just after the dog was bitten. That’s pretty clear!

Without clear evidence, however, it becomes tricky: there’s a case report of a Brittany spaniel being brought to a hospital, with “swelling on its muzzle, left of the midline” (Taylor & Greve 1985). This became a ‘suspected’ case of loxoscelism, and assumed by the authors to be caused by the brown recluse spider. However, diagnosis of loxoscelism is very difficult, and other more probably causal agents could be investigated. Stated another way: it may not be the spider. Don’t blame the spider without adequate evidence. As Rick Vetter states on his excellent website:

“There are many different causative agents of necrotic wounds, for example: mites, bedbugs, a secondary Staphylococcus or Streptococcus bacterial infection. Three different tick-inflicted maladies have been misdiagnosed as brown recluse bite…” (Rick Vetter, accessed Feb 9 2015)

It’s also very tricky to look at a ‘wound’ on a pet and determine whether or not a spider was involved. I would suggest if there are multiple wounds, or lacerations, multiple bumps and bruises, it is unlikely to have been caused by a spider, and other more likely causal agents should be investigated (e.g., punctures, skin reaction to something, or perhaps an insect sting, or fleas).

So, bottom line: although I think direct interactions between spiders and our pets are relatively rare, spiders are certainly capable of biting our dogs or cats.

Cat

Do cats and spiders mix?

What happens if my pet is bitten by a spider?

If there is clear evidence that a spider bit your pet, there are really only two outcomes: nothing will happen (or your pet may exhibit mild reactions that may not be immediately obvious), or there will be clear, definable symptoms, and these may lead to more serious consequences.

I think the first scenario is more common than the latter, largely because we just don’t have a good way of tracking the frequency of spider-pet interactions, and as is the case with humans, the vast majority of spiders probably aren’t venomous to our pets. Our pets certainly get ‘mildly’ sick all the time – I think of the times that my dog got an upset stomach, and I always assume she tracked down some ‘snacks’ when on an off-leash run (I think she is quite fond of rabbit droppings…).

Science does provide us some data about more serious reactions when our pets do get bitten by certain spiders. The paper by Isbister et al., from 2003, is quite detailed, and gives case studies of a number of verified bites by spiders on humans and canines in Australia. Here’s the alarming part:

“There were seven bites in dogs, and in two of these the owner was bitten after the dog. In all seven cases the dog died. In one case… the Alsatian died within 2 h of the bite. In two cases small or juvenile dogs died in less than an hour…” (Isbister et al.)

In this paper, the effects on humans were relatively minor, but this was not the case for our furry friends – reactions were severe and fast and resulted in death. The poor little Chihuahua pups mentioned earlier were equally unlucky, as reported by O’Hagan et al. Although both of these studies were from Australia, and involved only one family of spiders, it’s certainly scientifically interesting that canines were affected so strongly, and their reactions provide opportunities to further research the components of spider venom (e.g., see Hardy et al 2014).

There is also some evidence that cats may be affected by spider venom: research reported by Gwaltney-Brant et al, and Hardy et al, stated that toxicity studies result in fatalities of our feline friends:

“Cats are very sensitive to the effects of widow venom. In one study, 20 of 22 cats died after widow-spider bites, with an average survival time of 115 h. Paralysis occurs early in the course; severe pain is evidenced by howling and other vocalizations…” (Gwaltney-Brant et al.*)

That’s pretty grim. Interestingly, this case reports on envenomation by widow spiders in the genus Latrodectus (e.g., the genus that includes all the black widow spiders that occur in North America) – these spiders are relatively common in some habitats, and can certainly live in proximity to humans. Looking at Australia again, Hardy et al. state that cats are seemingly unaffected when bitten by female funnel-web spiders in Australia. So,  effects of spider venom on cats and dogs differs depending on the type of spider, and even our pets aren’t likely to respond the same way to different kinds of spiders. Clearly, it is difficult to generalize about any of this!

WidowSpider

Black widow spider – bad for cats? (photo by Sean McCann)

In sum, I have presented some details about spiders and how they might interact with our beloved pets. It’s fair to say that our pets certainly may get bitten by spiders, but overall I would argue such interactions are relatively rare. However, dogs and cats are certainly not immune to spider venom, and there is evidence to suggest they might have strong negative reactions to spider bites.

Despite this, I don’t see this as reason to panic or start stomping on any arachnid that wanders across your living room floor. The evidence we have is still relatively limited, and we just don’t have much information about effects of venom on pets, for those spiders that commonly inhabit our homes. I also think the lack of evidence is important to mention: if our pets were getting bitten by spiders on a regular basis, there would be more papers on the topic, and certainly more cases where anecdotes made the transition to evidence.

I think it’s possible to love your pets AND be an arachnophile. That’s certainly how I live my life.

[A BIG thanks to Maggie Hardy, Daniel Llavaneras and Catherine Scott, for helping point me to literature on this topic]

References:

Hardy, M.C., J. Cochrane and R.E. Allavena (2014). Venomous and Poisonous Australian Animals of Veterinary Importance: A Rich Source of Novel Therapeutics. Biomed Res. Intl. doi: 10.1155/2014/671041

Isbister, G.K. J.E. Seymour, M.R. Gray, R.J. Raven (2003). Bites by spiders of the family Theraphosidae in humans and canines. Toxin doi:10.1016/S0041-0101(02)00395-1

Gwaltney-Brant, S.M., E.K. Dunayer and H.Y. Youssef. (2007) Terrestrial Zootoxins. Ch. 64 in Veterinary Toxicology (Edited by R. C. Gupta).

O’Hagan, B.J., R.J. Raven, and K.M. McCormick (2006) Death of two pups from spider evenomation. Aust. Vet. J. 84: 291

Taylor, S.P. and J.H. Greve. (1985) “Suspected Case of Loxoscelism (Spider-bite) in a Dog,” Iowa State University Veterinarian: Vol. 47: Iss. 2, Article 1.

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*I was not able to access or read the original paper upon which this statement is based (Peterson and McNalley 2006 Spider evenomation: black widow, in Small Animal Toxicology, 2nd edition)

© C.M. Buddle (2016)

Expectations (of graduate students and supervisors)

/ Chris Buddle / 4 Comments

I have been running a research laboratory for close to 15 years, and I’m ashamed to say that I have not written down, formally, my expectations* of graduate students and their expectations of me. I regret this, especially since there are amazing resources out there to help with this discussion. I would argue that differing levels of expectation is probably a key source of conflict in research laboratories, and having a solid agreement between graduate students and supervisors is key for success.

Here is some context for my laboratory: I run a mid-sized laboratory (currently with three MSc and three PhD students and two undergraduate Honour’s students), focused on studying arthropod ecology.  As a Professor, my job involves teaching, research and administration. When running my research laboratory, the three tasks overlap – for example, I’m a lab ‘administrator’ in some ways, including ordering supplies, dealing with budgets, working on policies related to laboratory safety. I am also a researcher – perhaps doing research directly**, and certainly helping students with their research, from project design, to field logistics, analyses, and writing and editing manuscripts. I am also a teacher, and supervision involves different kinds of teaching, from leading lab meetings, teaching graduate-level classes, to taking parts in scientific debates, and sharing interesting literature. I assume my graduate students see my ‘roles’ as being varied, and sometimes fuzzy, because they really are! In recent years, my administrative duties at the University have increased, so I’m certainly not in the lab as much as I used to be, which can be tricky for everyone.

After a terrific laboratory meeting about expectations, my students pointed out that a lot of what is written below can be considered more as a philosophy about supervision, graduate school, and running a laboratory. This is quite true, and valid, but I think there are some concrete expectations that emerge from some of the bullet points, and the more vague and intangible expectations are a good starting point to the development of formal agreements with graduate students. With this in mind, I have agreed to work with my students (individually) to develop a “student-specific” document to outline a plan for meetings, communications, timelines, research priorities; that kind of living document will be a way to formalize specific expectations, plans, and contingencies when things don’t go as planned – such a document can give weight to the broader ideas around expectations, and allow for accountability (as that document develops, I’ll be sure to share a draft form on this blog).

For now… let’s get into some of the ideas around my expectations of graduate students, and their expectations of a supervisor.

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A lab environment… should be a team environment!

As a supervisor, my expectations for my graduate students are as follows:

  • Celebrate diversity, be respectful, be honest, and be ethical.
  • Be part of the team: I expect my students to be engaged and active members of the lab. This includes taking part in laboratory meetings, and being responsive to activities in the laboratory. This could include showing up for lab clean-up days, replying to emails related to lab events and activities, and generally working to be an integral and important member of the lab.
  • Be productive: graduate school is a full-time endeavour, but being productive in work does not necessarily mean working unreasonable hours; being productive is about working well. It’s about quality, not quantity. I do not expect my students to be in the lab all the time; if work is progressing well, and students are reading for comprehensive exams, or have other tasks that don’t require them to be physically present, it’s quite fine that students are not in the lab during regular working hours. However, at other times (e.g., when there is a lot of microscope work required), I do expect to see students in the lab on a more regular basis. I do not count hours, but if productively is not where I would like it to be, we will have a discussion about this, and determine ways to see that work is being done well. Related to this, I do hope that my students to have a life outside of graduate school and that ‘work-life-balance’ is happening, and hopefully this helps promote wellbeing.
  • Communicate: I expect my students to communicate with me, on a regular basis. I will discuss the importance of this at the start of the program, and establish a system that works for both of us. Communication includes (most importantly) keeping me in the loop on their project development, but also around issues they are facing, complications with their work, and certainly about their schedules (e.g., if they will be away for extended periods of time). I need to know when things are not going well – otherwise things can go off the rails rather quickly – being proactive on communications is essential.
  • Develop a research project: a core part of graduate school is developing a research project. I expect my students to do this, with me. The project will likely be a mix of my ideas and their ideas, done with knowledge of literature and ideas, from the broader scientific community. I expect PhD students to develop their project with less input from me (as compared to MSc project development)
  • Keep research as a priority: although I’m very keen on science communication, and outreach, and keen to have students that are engaged in many parts of the graduate student experience, at the end of the day, the research is a priority. “Keeping an eye on the ball” is important, as we are all working with limited resources (mostly time and money!), and the reason students are doing a thesis-based MSc or PhD is because there is an interest and passion for the research, and the current path involves this research-intensive stage. It must be the overarching priority.
  • Be organized: I expect students to be organized; successful students students use an agenda, plan ahead, and think ahead. I expect them to come to meetings with the appropriate documents (prepared and forwarded ahead of time) and with questions prepared. Being organized is a key step towards effective time management and that is essential for success in graduate school (and beyond!).
  • Apply for funding when appropriate: I will do my best to find funding for research, but at the same time, I expect my students to be on the lookout for any funding opportunities relevant to their program, whether it’s applying to a fellowship to get them through their final year, or applying for funds to offset costs for attending conferences.
  • Be responsible for the program: I am well aware of many deadlines, and overall program requirements, but it’s also the responsibility of students to know what courses they need to take, and when to take them. Being aware of deadlines is essential for supervisors and students.
  • Finish on time: I expect MSc students to finish in under two years, and PhD students to take around 4 years*** to complete all degree requirements. There may be exceptions to this, but these should be rare, and should be discussed well in advance. My role as academic guide is to help students through the program, and help design projects that are feasible within the time limits mentioned; the students are also responsible for trying to reach these deadlines and communicating when they cannot. I am a very strong believer in avoiding ‘extended’ MSc or PhD programs: it is seldom a good idea.
  • Publish: While I provide opportunities for joint-authorship with my students, I expect my students to publish their main thesis chapters, in suitable peer-reviewed journals. Ideally, (some of?) these publications should be submitted before the student graduates, or at least within a reasonable time frame after graduation. For me, this time frame is certainly within a year of graduating. I expect to be a co-author on papers that originate from a student’s thesis work, provided I have earned that authorship.
  • Be responsible for data: I expect my students to have good data management procedures, and any field books or raw data sheets be copied regularly. I expect data-back up to be happening on a regular basis. I also expect all data files will be submitted to me at the time a student graduates.
  • Collaborate and mentor: I model a collaborative research approach and expect my students to share what they are doing with each other, and work collaboratively whenever possible. I expect my more senior graduate students to mentor more junior members of the lab. I expect my students to seize opportunities to collaborate with other students (provided it complements their own research, and doesn’t distract too much from their own research!)
  • Read: Reading narrowly and broadly will help students become better scientists. I expect my graduate students to be aware of broader happenings in science, as well as the specifics related to their projects.
  • Do #SciComm: Communicating science is a central skill for scientists. I will give students opportunities to go to conferences and I expect my students to present their work at these conferences, and to spend time and energy on developing effective science communication skills. 
  • Be independent: I expect my graduate student to be independent. I’m a busy person, and I’m not in the lab all that much. I travel, teach and have a bazillion meetings to attend. Therefore, my students need to be able to work independently. I will not micro-manage; I will not be a ‘helicopter supervisor’. I’m hands-off, much of the time, although I will be available and accessible as needed.
  • Be creative, take risks, have fun: Graduate school is a wonderful time in a career, and I certainly do my best to create an interesting work environment for my students. I hope this is an environment that will allow for students to feel comfortable being creative and taking risks. Also expect there to be ‘play’ and ‘work’ and that in many cases, the lines between the two will blur.

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Being a supervisor can be like setting out pylons in a construction zone.

Here is what I will try to provide to my graduate students – this is what I perceive to be their expectations of me (note: my current students helped with this section):

  • Celebrate diversity, be respectful, be honest, and be ethical.
  • “uphold and transmit the highest professional standards of research and scholarship” (that one comes straight from my University)
  • Be supportive and human: I will develop a working relationship with students that will be based on the philosophy of being a good human! This means being supportive of my students, and to be there when they need me. A supervisor’s role is certainly to give advice (even long after graduation), and be a person they can depend on. I will strive to be compassionate, patient and empathetic. I recognize that everyone has ups and downs, and will have dark days as well as bright times: I will be supportive through all of this, and will work with my students to help them through their program, despite the challenges that will be thrown their way.
  • Be available: related to the previous point, I will be available to my students. I recognize this is a struggle at times, but when a student needs a meeting, I will help make this happen. I will answer emails, and meet face-to-face as necessary. They will know about my schedule, so it’s no surprise if I’m away on vacation, or otherwise unavailable. (as an aside: this is something I have to work on, and increasing face-time with my graduate students will be a priority going forward)
  • Communicate: I will do my best to have open communications with my students, from laboratory happenings, progress on research, troubleshooting, or just basic planning. The communication may be via different types of media (e.g., social media, emails or phone calls) but regardless, I will communicate.
  • Compromise: when discussing this document with my students, we talked about the power imbalance in Academia. It’s important to be honest about this power imbalance, recognize it’s there, and understand the stress it can put on students. Conflict can arise in part because of different priorities of students compared to a supervisor: for example, a supervisor may see a short-term gain by having another publication, whereas a student may need to devote some time to professional development activities, and see that ‘critical’ publication as being less time sensitive. This is further confounded by the power imbalance; therefore, a supervisor needs to be willing to see these differing priorities, in the context of potential power imbalance, and be willing to compromise.
  • Take the feedback: A supervisor has to be willing to be criticized, and be willing and open to comments from students. This becomes especially relevant when there are agreed-upon expectations!
  • Edit: A key role of a supervisor is to read and edit manuscripts, proposals, thesis chapters, etc. I will try to provide timely feedback on written materials. The definition of ‘timely’ is difficult to pin down, but optimally this will be within a 2 week window, provided there is advance notice and planning.
  • Provide funding: I will provide adequate support for research activities, from helping fund research assistants for the summer, to making sure students are not out-of-pocket for airline tickets or field supplies. My job is to make sure research can happen, and a big part of this is funding. We need open communication about funding, from the start, so that my students are supported, financially, in all parts of their work.
  • Help navigate graduate school: a supervisor has to help establish a research project, set-up committee meetings (help fill out the relevant forms), organize comprehensive examinations, sort out potential examiners for a PhD defense, and have good working knowledge about the policies and procedures at the University around graduate school. Although the program is ultimately a student’s responsibility, a supervisor has a key role to play in navigating the program. I will try to be organized on these tasks.
  • Leverage my network: Whenever possible, I will use my own contacts and network to help my students. At times, it may be necessary for students to get in touch with experts outside of their own network, and I will facilitate this as much as possible.
  • Help get jobs: I know my students, care about them, and recognize they will pass through the lab on the way to a career. I have a responsibility to help them with this transition, and as such a supervisor needs to be ready to write letters of reference for students (even at the last minute!), and send interesting job opportunities their way.
  • Troubleshoot: I will be there to help troubleshoot, whether it is issues with a collaborator or fellow graduate student, or laboratory equipment failure. I will make sure most stuff works and model steps to problem solving.
  • Provide a safe laboratory environment: I will provide a safe work environment by following the standards put in place by my University. I will ensure there is adequate training, dissemination of policy, and good practice. I will work with my University and my students to make sure any problems are dealt with in a timely fashion.
  • Space and supplies: I will work to make sure students have the physical space they need in the lab, and the equipment they need, from IT support to insect pins.
  • Send students to conferences: I will send students to conferences, and pay for these (in part****). For MSc students, this may be 1-2 conferences over the course of their degree, and these will likely be national-level conferences relevant to their field of study. For PhD students, this should include at least one international conference, preferably towards the end of their degree.
  • Sign stuff: I will sign stuff for my students, whether it is expense reports, or forms for scholarships.
  • Put out pylons: although I expect my students to be mostly independent researchers, this model does not apply to all students, and problems will occur. When necessary, I will play a more active role in direct supervision, have weekly meetings as necessary, and work in a more ‘hands-on’ manner with students. I like to see a supervisor’s role as one that involves setting up pylons in a construction zone: ideally a student can navigate this zone with just a few pylons, placed here and there, and I will help facilitate a route through the zone with as few pylons as possible. At times, however, more pylons are needed, perhaps placed closer together, and navigating through a graduate program may require more help for some students. Creating a laboratory environment in which it’s safe to take risks, and safe to fail now and then, is also important, so at times, veering into the construction zone is fine, and I may not stop a student, but I will help to find a way out.

I realize this is long-winded, and detailed, but it needs to be. Expectations are drivers of success in graduate school, and essential for good supervisor-student relationships. I encourage other Academics to develop this kind of document, and have this discussion with students, before they come to your lab, when they start, and during the program. It will benefit everyone.

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* To be clear, I certainly have discussions with students about expectations, but talking about it isn’t as good as having it stated more explicitly in written form.

** I don’t “do” all that much direct research anymore; although I try to get out in the field with my students, and certainly edit/write manuscripts, my research is not mostly at arm’s length to my students. I have traded field work for a desk job… 

*** Time for completion for PhD programs are more variable, and they should be. When I state ‘4 years’, it’s much more of a goal than a reality. However, I feel strongly that there are very few reasons why a MSc should take more than 2 years, from start to finish.

**** Funding for conferences will not come out of a student’s own pocket, but I do expect students to apply for relevant travel funds, or for departmental funding, to help offset costs to my research grants.

Spiderday (#24) – January

/ Chris Buddle / 1 Comment

It’s SPIDERDAY! As promised, this feature on the blog will be a monthly occurrence, so here’s the round-up of the best Arachnid-themed links and stories from the past few weeks.

To start off, here’s a lovely image of a wolf spider, by Christy Pitto:

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Bog spiders: a serendipitous research project

/ Chris Buddle / 1 Comment

This is a guest post, written by an Honour’s undergrad student in the lab, Kamil Chatila-Amos. It’s the first of two posts about his work, and the goal of this post is to introduce Kamil and his research project. 

Research can be serendipitous and spontaneous, and that’s certainly the story of how my honour’s project started! I spent last winter working on howler monkeys in Panama (which is a story in itself) and although I adored every second of it, it certainly made me out of touch with the McGill world. When I came back, most of my friends had found themselves a summer research job and even an honours supervisor for the upcoming semester.

So there I was, barely a week after my return, erratically filling out online job applications in the lobby of one of our buildings. I was looking at all kinds of opportunities: herbarium employee in Edmonton, ichthyology assistant in Wisconsin, plant surveying in Vaudreuil, bird surveys in Ontario, insectarium employee in Montreal. I was applying to anything and everything that was still available. Little did I know that the arthropod ecology lab is right next to the lobby… Chris walked by, saw me and stopped to chat. (Well it’s more accurate to say he talked to me while quickly walking to his next meeting)*. Turns out, a student of Terry Wheeler (another entomology Prof. at Macdonald campus), Amélie Grégoire Taillefer, was going to post a job online that very afternoon! She was looking for a field assistant to help her catch flies in bogs in the James Bay area.

A couple days later I was northern-bound! A 15 hour drive north of Montreal is the town of Matagami and about 30 km north of there is Lake Matagami, along which we were staying. In a yurt. A yurt!!! Basically, a large round tent of Mongolian origins. They’re big and this one had a minimal kitchen and shower. But the fact remains that it’s a tent with the isolative properties of canvas. It got pretty cold those first couple weeks and dropped below freezing a few nights. At least it had a fireplace. (It’s actually a great place for people wanting to explore that area of Québec and the owners are wonderful. Go check them out at ecogiteslacmatagami.ca)

Kamil_Yurt

The work itself was great. The first week, we explored the area for suitable bogs to install her pantraps. That’s when I realized how awesome bogs are. There are so many things to eat in bogs! Cattails, cranberries, Labrador tea, cloud berries, chanterelles, boletes, black flies…

For the remainder of the trip two days a week were spent visiting our five sites and harvesting the pantraps filled with flies, dragonflies, crickets, spiders and the occasional putrid mouse. The following two or three days we would sort through the samples, separating the lower flies (Nematocera) from the rest.

Kamil_Sweeping.jpg

Ready for some serious bog-sweeping.

After the first week I couldn’t help but notice just how many spiders we were catching. Mostly out of pity I think, I decided to sort out the spiders as well. I felt bad throwing them out… Fast forward to five weeks later and I’m heading back to Montreal with a bagful of vials filled with dead spiders. (My roommates were not very fond of having them in our freezer).

A few weeks later I set up a meeting with Chris and essentially barged into his office with the spiders to ask to work in his lab. It took a while (and quite a bit of convincing) but here I am, sorting through spiders and writing blog posts!

The research project we structured has two components. The first part will look at how the community composition of spiders varies between the five sampled bogs. Second, I’m lucky enough to have the opportunity to try DNA barcoding using COI markers. This part remains very blurry right now**, but I’m very excited to see where it leads.

Kamil_Microscope

Kamil hard at work in the lab!

If it weren’t for serendipity I would not have gone to James Bay this summer. And if it weren’t for being spontaneous, I would not have sorted out the spiders and would not be working in Chris’ lab right now. But spontaneity does have its down sides. I didn’t plan far enough ahead** and in hindsight, I should have collected some insect orders to be able to do a more in depth ecological analysis.

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* um, yes, I spend a LOT of time in meetings, and often have discussions and chats with student on my way to and from those meetings!

** for what it’s worth, research is often blurry, and planning ahead isn’t always possible!

Goodbye chalkboard! The opportunities and challenges of teaching in an active learning classroom

/ Chris Buddle / 7 Comments

This year I have the pleasure of teaching my Population and Community Ecology class in one of McGill’s Active Learning Classrooms – this one is touted as been quite exceptional, and I’m keen to put it to the test. Over the past 4-5 years, I have been teaching my quantitative ecology course almost entirely with chalk. In fact, I have actively argued about the value of teaching with chalk, and about a move away from technology can be beneficial to student learning, to my own teaching, and overall a very positive experience for all. Now I’ll be faced with this kind of environment when teaching my class:

Screen Shot 2016-01-10 at 11.14.36 AM

A view of two of the group tables in the Macdonald Campus active learning classroom; each “pod” seats 12 students (in three wings), and each is colour coded, and linked and adjacent to a screen and whiteboard

So why change?

One problem with the Chalkboard it that it doesn’t easily allow for ‘capturing’ the content from the board. Students need to write their own notes (which is good, in my opinion), but at times there may be specific equations, graphs, or other content from the board that they wished they could have captured, but failed to do so. The Active Learning classroom allows an easy way to overcome this – as the tablet/screen that is in the room has a smart pen, and acts like a chalkboard (or, rather, kind of like a smartboard, except that the instructor uses the screen at the podium in the middle of the room). I can therefore project this board, and teach as if I was using chalk, and everything I write is projected on one of the screens. The big benefit here is that I can save everything I write as a PDF (or other file type), and upload the notes to the online course management system. This approach still encourages students to come to class and take notes, but doesn’t put them in a position to rush with notetaking, and live in fear of missing something that I write on the board. Here’s an example from the first lecture (it’s a bit clunky, and I’m not used to writing on the screen yet, but hopefully will get more seamless as the term progresses):
Screen Shot 2016-01-10 at 11.17.12 AM

Another great benefit of the classroom is that it allows a second screen to be projected simultaneously as the first screen – I am thinking of primarily using this second screen to project graphs or equations directly from the textbook, through the use of a very high quality document camera. This saves me from having to hand-draw graphs (I do this very, very poorly – drawing straight lines is NOT easy!), and will allow the students to see the very direct ways that the content relates to the course’s textbook. This photo below shows how this looks: in that example the textbook cover is projected on the left screen and some ice-breaking questions are presented on the right-hand screen.

Screen Shot 2016-01-10 at 11.11.28 AM

I have been trying to transition my course into more of an active learning course, and set an active learning challenge last year. Overall I felt this was very beneficial, but the traditional lecture theatre (where I have taught in the past) is not conducive to active group work and student collaboration. I’m excited that the active learning classroom is ideally set up for this: the 84 students in the class sit at seven separate tables, each with 12 students, and the tables are designed into three wings of four students each. This is optimal for group work, and provides many opportunities for different sizes of groups. Next to each table is a whiteboard and screen, and each table can project (independently) onto their screen. Students then have many options to collaborate and work on problems. I’m excited about this, and look forward to having groups of students work on problems together, collaboratively. The interesting thing about this space is that it doesn’t seem that big, yet is a classroom that holds 84 students! It’s also designed so that the noise level isn’t overwhelming when students are working in groups.

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Students writing out ideas/answers to some questions, with their groups (from two different groups – notice the different colours?)

During the first lecture last week, I asked students how many of them had previously taken classes in the Active Learning classroom, and of those that did, many stated they did not enjoy the classroom. A little more discussion revealed that the students who disliked the classroom said their instructor used the room as a traditional lecture hall, and taught with powerpoint slides, from a podium. This clearly doesn’t work – the podium is in the middle, there are multiple screens (students say they are confused about where to look), and there are pillars that run right through the classroom (unavoidable since these are support pillars – and the classroom is in a basement); the ‘feel’ of the room, when used for traditional podium lectures, is all wrong. To use an Active Learning classroom means moving away from a podium-style lecture.

I certainly have a challenge ahead: in order to fully use the classroom’s potential, and make it engaging for the students, I have to ensure the technology and space is used properly. I’m only at the very start of term, so I will certainly report back on the experiences as the course unfolds. That being said, the combination of the technology and design is really promising for an active learning environment for my ecology class. It may just lead to the abandonment of chalk for a smart pen…

Frozen spiders

/ Chris Buddle / 1 Comment

Winter has arrived here in the Montreal area. Brrrrrr. Last night was below -25C, there’s a bitter wind, and about a foot of snow on the ground. I found my warm mitts and down jacket, but our arthropod friends don’t have this luxury! This time of year really gets me thinking about how spiders are handling the weather….

What do spiders do in the winter?

Some spiders don’t overwinter at all, and instead die at the end of the Fall, with their hardy egg cases doing the overwintering. Many other spiders, however,  do remain active under the snow, in a little zone called the ‘subnivean zone‘ – between the snow and the ground. Others hunker down, nestled in leaf litter, under bark, or in otherwise concealed locations. On slightly warmer winter days, spiders can also become quite active on the snow surface. But all of this is generally not enough to guarantee survival, because even subnivean zones and hidey-holes can get very cold.

Maybe they freeze, and come back to life after it warms up? You may be inclined to think so – it certainly happens with a lot of insects. And, check out this photo that popped up on Twitter a week or so ago, by Nash Turley. It shows a fishing spider under a layer of thin ice, and it was still alive after Nash helped it out of its icy tomb. What the heck?

Capture

A fishing spider, under ice.

Did this spider  ‘flash freeze’, and like a good science fiction movie, pop back to life once it warmed up?

Probably not… I think ‘flash frozen’ spiders probably won’t survive. The literature generally suggests that spiders are not freeze tolerant. In other words, their tissues cannot survive the process of freezing, and ice will cause irreparable damage. Instead, I suspect Nash’s spider was already prepared or preparing for winter, and got trapped under the ice, but hadn’t yet frozen. It’s physiological adaptations involve some nifty and super-cool tricks.

Spiders are generally thought to be freeze avoidant* (e.g. here’s a paper on this), and through the process of accumulating glycols in their blood (i.e., antifreeze), are able to supercool. This means their tissues remain unfrozen at temperatures well below freezing, because they have physiologically adapted via the production of special antifreeze compounds that stops them from turning into ice. It’s a neat trick, and one that is relatively common in the invertebrate world. Of course, supercooling alone doesn’t ensure survival at extremely cold temperatures, and that’s where other adaptations come into play. Spiders will therefore find their way to the relatively insulated subnivean zone, or deep down in soil or leaf-litter. These behavioural adaptations (i.e., selecting overwintering sites), combined with supercooling superpowers, helps them get through the cold seasons. 

For me, I’ll stick to my down jacket, and enjoy how Hydro Quebec helps keep our buildings warm!
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* actually, we don’t know nearly enough about spiders and their overwintering physiology. I should state that I assume most spiders are freeze avoidant, based on the current literature on the topic – there’s a LOT more species to study, though!