Monday, March 9, 2015

In praise of difficult questions.

There were a lot of people at my graduate institution who weren’t afraid to ask probing, thoughtful, difficult questions. They asked them seemingly without any concern about making the recipient feel bad, although students were more likely to receive kinder versions, and they asked them at departmental talks, committee meetings, student seminars, and at faculty interviews. I’ll admit there were times when this made me uncomfortable, and it certainly contributed no small amount of anxiety before giving talks there (and I’m sure I’m not the only person who felt that way).

These days I find myself missing those tough questions, not because I enjoy confrontation per se, but because they made an important contribution to my education.

To be clear, bullying questions or competitive questioning meant to highlight the questioner’s intelligence are a waste of time (e.g. two minutes of talking about your research followed by "what do you think about that?"). Critical thinking, while one of the most important aspects of a post-graduate education, can't be taught. But tough questions and questioners model critical thinking for students in the most direct way. Being at the front of the room talking does not automatically grant expert status: the speaker's ideas must be clear and robust to debate. 

Difficult questions benefit a speaker too - they are the clearest demonstration that the audience has engaged with their work. The most useful talks are those in which the questions are thought provoking for both the speaker and the audience. 

And finally, it can be refreshing when a questioner holds a person to actually answering the question. Science is built on debate and some times disagreement. Hard questions made me feel that the people asking them were expressing a preference for good science, even if the cost was some discomfort or social unease. And that feels like an important thing to express.

Friday, March 6, 2015

Distilling an ocean of theory and adding a few of your own drops

I recently completed my PhD qualifying exam at the University of Toronto-Scarborough for the Department of Physical and Environmental Science. Prior to going through the process the exam took on a sort of “black box” quality where I’d seen colleagues pass through unscathed but the depth of questioning that took place during the oral examination remained unclear. So I thought it might be of some value to comment on my experience with the process.

The format of these exams is fairly variable across departments and between institutions with some requiring the production of several essays in a short period of time, some based on an extensive readings list, some formatted as a proposal defense and others including some or all of these components. My exam took the form of a proposal defense which required submitting a 9000-word proposal outlining the theoretical framework & justifications for my research questions, hypotheses, objectives, methodologies, preliminary results, discussion and thoughts on the significance of the work, a 25-minute presentation of this proposal followed by an oral examination that lasted about an hour and 30 minutes. These exams are typically meant to be taken at the early stages of one’s PhD, but it seems that they often get kicked further down the road, as was the case with mine which I completed half way into my 3rd year of a 5 year program. This had its advantages and disadvantages where further progress allowed presentation and discussion of some interesting findings and a clearer picture of what my thesis is going to look like, but also came with the colossal challenge of organizing everything into what seemed like a miniscule 25-minute presentation. This was probably the most challenging academic exercise I have faced.

I finalized my presentation a few days before my exam, and felt that it had a nice balance between theory and my contributions, but this only after “throwing away” 100+ slides in the 2 weeks leading up to the exam… And while that might sound like a total waste of time, it actually forced me to distill what seemed like an “ocean of theory” to the essential elements that grounded my work. Further, developing slides that can visually communicate complex theory is a great form of study that can serve you well during the oral exam; even if you can’t show the slides you will know the material. Also, I can’t overstate the importance of peer and supervisory assistance here. I was extremely lucky to have my presentation lovingly torn to shreds by my lab mates. This can be a terrifying process as we know that imposter syndrome is alive and well in academia (http://irblog.eu/impostor-syndrome-phd/). Yet, we of course survive these practice talks and our presentations benefit greatly.

Once I was happy with the content and flow of my talk I decided to inject a little humour by photoshopping some images and spattering in a couple silly animations. This was probably some kind of self-defense mechanism where I was hoping that by putting a smile on the face of an examiner I might be able to ease my own nerves and the general tension that goes along with a comprehensive exam. Of course, whether this succeeds or not will depend on the demeanor of your examiners, your delivery and probably the general quality of the rest of the presentation. In my case, I found that the humour worked and offered a nice lull in the tension. I highly recommend trying this, once you’ve nailed down the meat of the talk of course. Beyond attempts at humour, you should know the talk. You shouldn’t be reading off any notes and should only read out points on the slide that are essential theory items or specific research questions, hypotheses or findings. There will be an upcoming blog post on presentation tips, so I’ll stop there… Just remember that in this exam, your presentation sets the tone. It is your opportunity to articulate your comprehension of the subject and the novelty of your work.


The written component of the proposal, on the other hand, can seem to be propelled by a perpetual motion machine generating an endless sprawl of “conceptual axes”, “synthetic approaches” and “novel perspectives” about your thesis topic. Here, you can definitely produce a fairly comprehensive picture of the subject and your perspectives but you’ll still have to tug the reigns so as not to irritate your readers with a bloated document. If you find yourself delving into the linkages between your thesis and systems theory, and you’re not in physics, odds are you’ve gone too far. Everything in your written proposal is essentially fair-game for the oral examination, so don’t let it disappear from your desktop once you’ve submitted it. You will most certainly get questions about the methods you’ve proposed or have employed, and you will need to be able to justify your choices and situate your studies within the literature.

The oral examination will surely be one of the most unnerving experiences of your academic life, but you can minimize your unease by continually drawing those links between your thesis and the literature in the weeks leading up to the exam. I found the oral exam to be a very fair process where I was tested on the biophysical interactions that I was examining, the measures that I used, and the conceptual links between my thesis components and the trends in the literature. Now, my thesis is fairly atypical in that it takes a multi-disciplinary approach to a larger topic, and this definitely generated some questions about the linkages between the various components. But beyond that challenge I think any questions about the “grand scheme” of your thesis can be addressed by highlighting those initial motivations that you included in your application to your program. In my application, I was required to write a page about why interdisciplinary perspectives are essential in the field of environmental science, and I was able to pull from that motivation to answer these kinds of questions. Odds are that your initial reasons for engaging with a certain research topic will ground a lot of your answers during the oral examination. One question that I didn’t anticipate was essentially “where do you see yourself in 10 years”?  I think in our PhD’s we can easily get tunnel vision and forget that there is an end to the process at which point we’ll move on to something new. So don’t forget about that light at the end of the tunnel during the exam. Think about your future aspirations and how far you’ve come since you became fascinated with your topic. Your examiners want to feel that engagement and passion. And you will get questions about the theory that are right in your wheelhouse, so take advantage when they appear and highlight both your understanding of the unanswered questions and how your work is not just adding to the complexity but is helping to bridge those gaps.

In the end, after all the late nights of writing, pecking at bowls of nuts (because cooking takes too long) and re-arranging your presentation slides for the 100th time, you’ll most likely find that this process has probably been the most constructive thing that you’ve ever been a part of.

Wednesday, March 4, 2015

Graduate students- employees, scholars, or something in between?

Graduate school has always required that students balance research, classwork, and teaching activities (perhaps with some time for complaining). Though many aspects of graduate school are unchanged, there can be a tension between grad students and their employers driven by a shift in both these groups’ expectations, and the complex nature of STEM graduate school.

This is illustrated well by the current strikes of teaching assistants (primarily graduate students) at University of Toronto and York University – both major Canadian institutions. [And even more extreme cases exist]. The union at U of T has become a defacto union for graduate student issues as well, and the primary sticking point appears to be graduate student stipends, which are far below the poverty line. The students there are striking as teaching assistants (so research work can continue) but their main issue is a holistic “graduate student” issue.

Supposing the components of graduate school have remained similar over the years, why might tension be increasing between what graduate students and faculty/departments expect? Partly because so many other things have changed-–the economy, the workforce, cultural expectations. I think that in the past, it was easier to consider graduate school as a place of passion and intellectual curiosity, where one would make a lousy salary, but consider it “worth it”.  Today, the cost-benefit analysis for getting a PhD is considerably less positive – it takes longer to get a PhD, on average, and the payoff in terms of obtaining a faculty or other job, makes this less clear. The cost of education, particularly in the US, is immense: the possibility of student loan debt from 4-8 years of postgraduate education is fairly unpalatable.

From Nature.
As the realities change, so too do the expectations. That on its own would be the source of some tension. But the dual nature of graduate school compounds the tensions since it is difficult for graduate students, faculty, and department heads to evaluate what reasonable expectations are for things such as pay, hours, vacation time. For most students, graduate school has aspects of both a clear job (usually teaching duties—running labs, marking tests and assignments, sometimes lecture duties) and a clear studentship (class work, appraisal exams, all culminating in a defense). It also includes research, done in a lab or the field, which may vary between being a job (doing tasks primarily for the PI, monitoring undergrads, ordering supplies) and an intense learning experience. Employment involves contracts with expectations and restrictions, set hours and wages; being a student lacks the same expectations but is often associated with greater freedom and personal growth. The extent to which faculty and graduate students see the position as “student” or as “job” may well differ.

The interaction of economic realities with the duality of graduate school is an important issue. Should graduate school be considered the start of one's working life? If so, is it equivalent to an entry-level position? After all, TAs do a lot of grunt work -- marking, marking, and more marking, run simple labs and tutoring sessions -- and many universities hire undergraduates to do similar tasks. On the other hand, graduate students are also high-achievers doing complicated analyses for research, and have reasonably high education levels. Graduate school may come with opportunity costs  - peers with similar educations tend to have jobs and retirement funds. In contrast, the pure academic path usually means you will live frugally for many years before your first "real" position (and you may be in your 30s or later before you get it).

There may be some generational changes as well. It is suggested that Millenials/Generation Y have different priorities than previous generations: they strongly desire fulfilment from their work, but also competitive compensation and job flexibility (e.g.). The downsides of graduate school are greater and perhaps more obvious to this generation: if it is a job, it is poorly paid and entry-level, if it is a studentship, it comes with an opportunity cost. But how to evaluate it when it is both? It is undeniably easier to go through graduate school for those who don't have to deal with the dualities - such as through having a fellowship that allows a student to do research and classes only. Most people are still in graduate school for the same reasons as they always have been - love of science and learning. That hasn't changed. But the meaning of graduate school itself may well have changed. There is no one or easy solution to the issue. But no doubt a recognition by both sides of the realities of being a graduate student (and a supervisor) and honest communication about expectations on both sides (and sometimes, perhaps a little pressure) would go far. 



The real truth about graduate school according to the Simpsons...

**I just want to note that this is inspired by--but not addressing--the U of Toronto situation, and any comments that simply want to debate specific circumstances in particular universities will be deleted...
Larger discussion of the general issue always welcome.

Friday, February 27, 2015

Going natural: biological control of insect pests

*Guest post by Sheena Fry

Damage caused by agriculture pests is one of the most important factors of crop yield reduction (Cramer, 1967; Oerke et al., 1994) and can cause billions of dollars worth of damage each year (e.g. in Brazil, insect pests cause up to US$ 17.7 billon year-1 of damage, Oliveira et al., 2014). Due to its economic impact, controlling pest populations is a priority for agricultural scientists. Chemical control is the primary method of pest management due to its relatively low costs and high effectiveness (Cooper and Dobson, 2007). Despite the widespread use of chemical controls, the health and environmental risks associated with their use are well known (Pimentel et al. 1992; Pimentel, 2005). The risks associated with pesticide use, as well as the evolution of pesticide resistance, has lead to a surge in interest in the use of biological control for pest management over the past 50 years.

The most important decision to be made in a biological control program is which biological control agent to use against a pest. Success rates for biological control of insects are low, with only 24-35% resulting in the establishment of the introduced species (Hall and Ehler 1979, van Lentern, 1983) and only 16% resulting in complete control of pest species (Hall et al., 1980). What determines the success of colonization and establishment is a key question in biological control research and must be answered in order to make predictions about establishment and success of introduced species. In 1965, Debach attempted to identify characteristics of successful colonizers but found that neither success nor failure could be explained by the presence or absence of a common characteristic. Over the past 50 years, several attempts have been made to list characteristics of successful invaders (e.g. Murdoch et al., 1985) and while they seem logical, there are too many exceptions for them to be used as a reliable indicator of a species’ potential to colonize and establish in a new area. DeBach saw “no possibility of predicting the fate of a purposely colonized imported entomophagous insect” and at present it remains an elusive goal (Fischbein and Corley, 2015).
Paul Debach 1914-1992


The environmental and health risks associated with chemical controls of insects (see references above) are not an issue when using biological controls. In addition to this, successfully established biological control species will be able to maintain stable populations without the need for additional investment by humans (unlike chemical controls, which must be applied each season). Despite the obvious benefits of biological control, there are also risks associated with the use of insects in biological control, such as the risk to non-targeted species (Simberloff and Stiling, 1996) or host switching. In order to make decisions about biological control we need to understand the evolution of introduced species in new environments, which can increase the efficiency of biological control (through post-colonization adaptation) or can increase the risk to non-targeted species. “The Genetics of Colonizing Species” (1965) brought together evolutionary biologists and ecologists (theoretical and applied) to discuss the evolution of introduced species. In DeBach’s chapter, he focused on colonizing entomophagous insects and, using biological control case studies, looked at the relative influence of pre- and post colonization adaptation, a key question in evolutionary biology. One such case study was the introduction of a parasitoid wasp (Comperiella bifasciata Howard, Figure 1), which was introduced to control a citrus pest, the California red scale (Aonidiella aurantii Maskell). The parasitoid wasp was released throughout southern California but initially was only able to establish at one location. It slowly spread and increased in abundance and, by 1957 was found at various locations throughout southern California. DeBach interpreted the poor initial establishment of the parasite followed by intense colonization as an indication that genetic adaptation had occurred.

Figure 1. A female parasitic wasp (Comperiella bifasciata Howard) infesting a California red scale (Aonidiella aurantii Maskell), from Forester et al. (1995).

Fifty years have passed since the publication of “The Genetics of Colonizing Species” (1965) and understanding the relative effects of pre- and post-colonization adaptation has remained an important issue. Phillips and colleagues (2008) examined the relative effects of genetic drift and selection in the frequencies of two asexually reproducing, genetically distinct parasitoid biotypes. This South American parasitoid wasp (Micrictonus hyperidae Loan, Figure 2) was introduced as a biological control for a pasture pest (Listronotus bonariensis Kuschel, Figure 2) in New Zealand in 1992. Phillips and colleagues recorded the relative frequencies of each biotype over a 10-year period and found that changes in biotype frequency were consistent with strong directional selection, favouring one of the parasitoid biotypes. This resulted in parasitoid populations being better adapted to New Zealand conditions than those originally released. 


Figure 2. A female parasitic wasp (Micrictonus hyperidae Loan, right) infesting a South American weevil (Listronotus bonariensis Kuschel, left). © Copyright AgResearch

There have been significant advance in the tools (statistical and molecular) available for the study of post-colonization success and adaptation since the publication of “The Genetics of Colonizing Species” (1965). These tools allow for better understanding of the post-colonization process of introduced species but, despite these advances, there has been little progress towards being able to predict the success of introduced species.


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