Monday, October 17, 2016

Reviewing peer review: gender, location and other sources of bias

For academic scientists, publications are the primary currency for success, and so peer review is a central part of scientific life. When discussing peer review, it’s always worth remembering that since it depends on ‘peers’, broader issues across ecology are often reflected in issues with peer review. A series of papers from Charles W. Fox--and coauthors Burns, Muncy, and Meyer--do a great job of illustrating this point, showing how diversity issues in ecology are writ small in the peer review process.

The journal Functional Ecology provided the authors up to 10 years of data on the submission, editorial, and review process (between 2004 and 2014, maximum). This data provides a unique opportunity to explore how factors such as gender and geographic local affects the peer review process and outcomes, and also how this has changed over the past decade.

Author and reviewer gender were assigned using an online database ( that includes 200,000 names and an associated probability reflecting the genders for each name. Geographic location of editors and reviewers were also identified based on their profiles. There are some clear limitations to this approach, particularly that Asian names had to be excluded. Still, 97% of names were present in the database, and 94% of those names were associated with a single gender >90% of the time.

Many—even most—of Fox et al.’s findings are in line with what has already been shown regarding the causes and effects of gender gaps in academia. But they are interesting, nonetheless. Some of the gender gaps seem to be tied to age: senior editors were all male, and although females make up 43% of first authors on papers submitted to Functional Ecology, they are only 25% of senior authors.

Implicit biases in identifying reviewers are also fairly common: far fewer women were suggested then men, even when female authors or female editors were identifying reviewers. Female editors did invite more female reviewers than male editors. ("Male editors selected less than 25 percent female reviewers even in the year they selected the most women, but female editors consistently selected ~30–35 percent female").  Female authors also suggested slightly more female reviewers than male authors did.

Some of the statistics are great news: there was no effect of author gender or editor gender on how papers were handled and their chances of acceptance, for example. Further, the mean score given to a paper by male and female reviewers did not differ – reviewer gender isn’t affecting your paper’s chance of acceptance. And when the last or senior author on a paper is female, a greater proportion of all the authors on the paper are female too.

The most surprising statistic, to me, was that there was a small (2%) but consistent effect of handling editor gender on the likelihood that male reviewers would respond to review requests. They were less likely to respond and less likely to agree to review, if the editor making the request is female.

That there are still observable effects of gender in peer review despite an increasing awareness of the issue should tell us that the effects of other forms of less-discussed bias are probably similar or greater. Fox et al. hint at this when they show how important the effect of geographic locale is on reviewer choice. Overwhelmingly editors over-selected reviewers from their own geographic locality. This is not surprising, since social and professional networks are geographically driven, but it can have the effect of making science more insular. Other sources of bias – race, country of origin, language – are more difficult to measure from this data, but hopefully the results from these papers are reminders that such biases can have measurable effects.

From Fox et al. 2016a. 

Thursday, October 6, 2016

When individual differences matter - intraspecific variation in 2016

Maybe it is just confirmation bias, but there seems to have been an upswing in the number of cool papers on the role of intraspecific variation in ecology. For example, three new papers highlight the importance of variation among individuals for topics ranging from conservation, coexistence, and community responses to changing environments. All are worth a deeper read.

An Anthropocene map of genetic diversity’ asks how intraspecific variation is distributed globally, a simple but important question. Genetic diversity in a species is an important predictor of their ability to adapt to changing environments. For many species, however, as their populations decline in size, become fragmented, or experience strong selection related to human activities, genetic diversity may be in decline. Quantifying a baseline for global genetic diversity is an important goal. Further, with the rise of ‘big data’ (as people love to brand it) it is now an accessible one: there are now millions of genetic sequences in GenBank and associated GPS coordinates. 
Many of the global patterns in genetic diversity agree with those seen for other forms of diversity: for example, some of the highest levels are observed in the tropical Andes and Amazonia, and there is a peak in the mid-latitudes and human presence seems to decrease genetic diversity.

From Miraldo et al. (2016): Map of uncertainty. Areas in green represent high sequence availability and taxonomic coverage (of all species known to be present in a cell). All other colors represent areas lacking important data.
The resulting data set represents ~ 5000 species, so naturally the rarest species and the least charismatic are underrepresented. The authors identify this global distribution of ignorance, highlighting just how small our big data still is.

Miraldo, Andreia, et al. "An Anthropocene map of genetic diversity." Science353.6307 (2016): 1532-1535.

In ‘How variation between individuals affects species coexistence’, Simon Hart et al. do the much needed work to answer the question of how intraspecific variation fits into coexistence theory. Their results reinforce the suggestion that in general, intraspecific variation should making coexistence more difficult, since it increases the dominance of superior competitors, and reduces species' niche differentiation. (Note this is a contrast to the argument Jim Clark has made with individual trees, eg. Clark 2010)

Hart, Simon P., Sebastian J. Schreiber, and Jonathan M. Levine. "How variation between individuals affects species coexistence." Ecology letters (2016).

The topic of evolutionary rescue is an interesting, highlighting (see work from Andy Gonzalez and Graham Bell for more details) the ability of populations to adapt to stressors and changing environments, provided enough underlying additive genetic variation and time is available. It has been suggested that phenotypic plasticity can reduce the chance of evolutionary rescue, since it reduces selection on genetic traits. Alternatively, by increasing survival time following environmental change, it may aid evolutionary rescue. Ashander et al. use a theoretical approach to explore how plasticity interacts with a change in environmental conditions (mean and predictability/autocorrelation) to affect extinction risk (and so the chance of evolutionary rescue). Their results provide insight into how the predictability of new environments, through an affect on stochasticity, in turn changes extinction risk and rescue.

Tuesday, September 20, 2016

The problematic effect of small effects

Why do ecologists often get different answers to the same question? Depending on the study, for example, the relationship between biodiversity and ecosystem function could be positive, negative, or absent (e.g. Cardinale et al. 2012). Ecologists explain this in many ways - experimental issues and differences, context dependence. However, it may also be due to an even simpler issue, that of the statistical implications of small effect sizes.

This is the point that Lemoine et al. make in an interesting new report in Ecology. Experimental data from natural systems (e.g. for warming experiments, BEF experiments) is often highly variable, has low replication, and effect sizes are frequently small. Perhaps it is not surprising we see contradictory outcomes, because data with small true effect sizes are prone to high Type S (reflect the chance of obtaining the wrong sign for an effect) and Type M (the amount by with an effect size must be overestimated in order to be significant). Contradictory results arise from these statistical issues, combined with the idea that papers that do get published early on may simply have found significant effects by chance (the Winner's Curse). 

Power reflects the chance of failing to correctly reject the null hypothesis (Ho). The power of ecological experiments increases with sample size (N), since uncertainty in data decreases with increasing N. However, if your true effect size is small, studies with low power have to significantly overestimate the effect size to have a significant p-value. This is the result of the fact that if the variation in your data is large and your effect size is small, the critical value for a significant z-score is quite large. Thus for your results to be significant, you need to observe an effect larger than this critical value, which will be much larger than the true effect size. It's a catch-22 for small effect sizes: if your result is correct, it very well may not be significant; if you have a significant result, you may be overestimating the effect size. 

From Lemoine et al. 2016. 
The solution to this issue is clearly a difficult one, but the authors make some useful suggestions. First, it's really the variability of your data, more than the sample size, that raises the Type M error. So if your data is small but beautifully behaved, this may not be a huge issue for you (but you must be working in a highly atypical system). If you can increase your replication, this is the obvious solution. But the other solutions they see are cultural shifts when we publish statistical results. As with many other, the authors suggest we move away from reliance on p-values as a pass/fail tool for results. In addition to reporting p-values, they suggest we report effect sizes and their error rates. Further, that this be done for all variables regardless of whether the results are significant. Type M error and power analyses can be reported in a fashion meant to inform interpretation of results: “However, low power (0.10) and high Type M error (2.0) suggest that this effect size is likely an overestimate. Attempts to replicate these findings will likely fail.” 

Lemoine, N. P., Hoffman, A., Felton, A. J., Baur, L., Chaves, F., Gray, J., Yu, Q. and Smith, M. D. (2016), Underappreciated problems of low replication in ecological field studies. Ecology. doi: 10.1002/ecy.1506

Wednesday, September 7, 2016

Where the wild things are: the importance of urban nature

Cities represent our ultimate domination over nature. They are landscapes that are completely modified to meet all of our needs and desires. In cities we drastically change the vegetation, reroute rivers, seal the Earth’s surface in impermeable cement, and often change the chemical composition of the air around us. For most people, this unnatural state of affairs seems completely natural. Its how we grow up.

What we don’t notice is all that is missing. The trees, the birds, and the mammals are largely absent from big cities. But not all cities are equal in this missingness. For those of us that live in cities like Toronto, Nashville, or Sydney, seeing birds and mammals is part of our normal life. In my back yard in Toronto, I am likely to see racoons, skunks, possums, red squirrels, eastern grey squirrels, chipmunks, deer mice, and a plethora of birds, and just down the road, foxes, coyotes, and deer are not uncommon. One morning I heard a ‘thud’ come from our sunroom window, and outside was a stunned red-tailed hawk (he was fine in the end). These cities are evidence that nature can persist and coexist with urban development.

However, there are other cities where nature is almost completely absent. While living in Guangzhou, China I saw just cats, dogs and rats, and barely any birds –shockingly no pigeons. Recently in while in Montpellier, France, it became obvious to Caroline and I (the two EEB & Flow contributors) that besides a small lizard species, pigeons and a few sparrows, we were not going to see any wildlife in the city. Guangzhou and Montpellier are very different cities in terms of size (16 million vs. 300 thousand), density, building height, pollution levels, etc.  But one way they are similar is that they are old. People have living and changing the landscapes in these regions for thousands of years. Of course the same could technically be said of North America and Australia, but the magnitude and intensity of human modification has no parallel in North America and Australia. Long-term intensive human activity removes other species in the long run. Is this the natural endpoint for our younger cities?

Cambridge, England. While quite beautiful, it is a typical old european city with a lot of stone.

Why we should celebrate raccoons

Toronto has a war against the raccoon. To most Torontonians, the raccoon is a plague –vermin that get into garbage cans and pull shingles off of roofs. Their density in Toronto is about 10 times higher than in wild habitats and many people in Toronto support removing them all together.

I have a different stance. We should be celebrating the raccoon. Yes raccoons cause problems; yes they carry disease; yes they damage property; yes their density is unnaturally high. But the same can be said of people (I don’t think I ever caught a flu from a raccoon). If raccoons were to recede to distant wilds and disappear from Toronto altogether, we would be no different than all those other cities where nature has completely lost. Raccoons give hope –hope that nature can flourish under the repressive and cruel dominion of urban centres. Raccoons remind us that nature has a place and can thrive in cities, and that we can share this world. They give me hope that Toronto’s destiny is not prescribed and we are not bound to the same fate as so many other cities.

I have a couple of new Chinese scientists visit my lab each year, and the differences between Toronto and say Beijing or Shanghai could not be more stark for them. To see deer, squirrels and raccoons in the city is a marvel. Every time one of these visitors comments on the wildlife in our city, I am reminded that we are really fortunate and have something that should be cherished.

Raccoon family –not an uncommon sight in Toronto (CCBYgaryjwood

Need to rethink urban nature

The problem is that Toronto, and most other cities, is continuing to grow and become more densely packed, making it more difficult for nature to endure. We need to rethink how cities grow and develop, and we need to keep a place for nature. There is no reason why new developments can't accommodate natural elements and green space –this often does not happen in most cities. Singapore is unique in this sense, new public infrastructure projects explicitly incorporate novel green space and infrastructure. I toured green sites there recently and saw a new hospital where it was impossible to tell where the park space ended and the hospital started (see picture below). There I saw patients tending gardens on the roof, nearby residents strolling through the forested courtyards, and turtles, wading birds and a large river monitor in the neighbouring pond. Also, Singapore's new large pump house infrastructure that reduces flooding in the city has a full sloping lawn on the top that is used by picnickers. In most North American cities this type of building would be grey industrial cement with little other function than to house pumps.

Singpore's Khoo Teck Puat hospital -the world's greenest hospital? 

Large old cities devoid of wildlife need not be the natural endpoint for a city.  Smart development and accommodating nature needs to be woven into the tapestry of cities. Toronto’s raccoons are great, and I wouldn’t want to live in a Toronto without them.

Tuesday, September 6, 2016

Examples of pre-interview questions

Last year, several postdocs at my institute (including me) were applying for faculty positions at North American institutions. Frequently, before on campus interviews, a 'long' list of people are asked to take part in phone/Skype interviews before a short list for campus visits is decided on. Since this step is now so common, postdocs put together an informal list of all the questions people had been asked during this initial interview*.

I found the list helpful. The usual caveats apply - different types of institutes and search committees will have different priorities and focus on different types of questions (e.g. teaching vs. research). Thinking about the answers to these questions ahead of time can be helpful for developing a vision of how you approach teaching and research, and being clear in how you communicate that.

(*Thanks to Iris Levin for originally curating this list)

Big picture questions:
Why X institution?
What do the liberal arts mean to you? Why are you interested in a career at a liberal arts college?
Tell us about contributing to XX college’s emphasis on liberal arts in practice, interdisciplinary and/or international aspects of education
How will our Biology Dept enhance your teaching and research?

Teaching focused questions:
General approach
What courses are you best suited to teach and how would you teach it?
What does a typical day in your class look like?
What do you feel you would add to graduate and undergraduate training in the department?
What is the biggest challenge in teaching?
You will teach X course every semester, how would you keep it exciting?
How would you teach a lab differently for introductory, intermediate or advanced students?

Specifics about courses
How would you teach X class?
What sort of interdisciplinary and/or first-year seminar course would you teach?
What sort of non-majors course would you teach? How would you teach it differently for non-majors vs. majors?
What new course(s) would you develop and how?
Tell us about your approach to teaching an XXX course for students who have had one introductory biology course
Tell us about incorporating quantitative and analytical reasoning into an XXX course
Tell us about using open-ended, inquiry-based group work in an introductory biology course

Research focused questions:
Approach and interests
Briefly summarize your most significant research contribution.
Tell us about your research program
You work on xyz – how would you conduct your research here?
How do you see your research complementing that of others in the department, and what do you view as your unique strengths?
Where do you see yourself in 5 years? Where do you see yourself in 10 years?
Who would you collaborate with here? 
How would you collaborate with faculty and bridge different fields?
What sort of projects would you do with graduate students? 
How would undergrads be involved with your research and what would the outcomes be?
Tell us about your approach to mentoring undergraduates in research

What sources of funding would you pursue to support your research program?
What grants would you apply to? 

Integration with teaching?
What contributions would your research make to these courses?
How would you involve students in your research outside or inside classroom

Misc (what type of colleague would you be?):
How would you contribute to the larger campus community?
How do you address diversity in your teaching and research?
What do you feel you can contribute to efforts to cultivate a wide diversity of people and perspectives at XX College?
Describe what you know about X college, how you would fit in, and any concerns.
How do you deal with conflict?
What has been the biggest obstacle in your professional development?

If you have more to add, please comment!

Friday, September 2, 2016

Science in many languages.

The lingua franca of biology is English, although through history it has variously been Latin, German, or French. Communication is fundamental to the modern scientific landscape, and English dominates the international ecological community. To be indexed by SCOPUS, a journal must be written at least in part in English. All major ecological journals are published in English, and clear, understandable writing is unquestionably an advantage in having work published. Large international conferences are usually conducted in English. Sometimes there is no translation for a key word and the English version is used directly, regardless of the language of the conversation. Even base commands in coding languages like R are in English. There is an undeniable but some times unmentioned advantage to being a native English speaker in science.

A common language is inevitable and necessary to communicate in a time of global connectivity, but it is also necessary to acknowledge that many scientists speak English as a second (or third, or fourth) language and barriers can arise as a result of this. The energy activation to move between languages is high for people, and it can take longer to read and write. But sometimes the costs are more subtle: for example, students may be less likely to give oral talks at conferences as a result of concerns about being understood. Even if they are relatively proficient, the question period after talks is difficult, since questions are often spoken quickly, are not clear, and are expressed in a variety of accents. That’s a difficult situation to address directly, but there are ways to facilitate communication across a variety of English proficiencies. And many of these are simply good practices for communication in any language.

First: slow down. Some of us are guiltier than others, but if you speak too fast, you lose listeners. This is another reason to consciously try to breath and relax during presentations and lectures. Some people speak so quickly that even the native English speakers have trouble following along. Now imagine listening to that talk while needing a little extra processing time.

When you give lectures and presentations, make sure that the slides and the verbal component both provide the overall message. I’ve followed talks in French and Spanish before, because the slides were well-composed (and in English). If someone misses something you say, it should be possible to follow the important points by the slides alone. And vice versa. This is good advice for any talk. Don’t be boring, but also be aware of when overuse of idioms or culture-specific references prevent understanding.

Sometimes fluent English speakers unknowingly dominate conversations because they speak faster and may be more confident in expressing themselves. In group activities like workshops and meetings, allow breaks in the conversation so that non-native speakers (or just less dominating personalities and quieter people) have a chance to express themselves as well.

An ear for accents comes from practice listening. Practice speaking improves accent. It’s a mutually beneficial relationship.

Also, remember that culture and language interact. English is interesting in that we have no pronouns differentiating between formal and informal relationships (we have ‘you’, not ‘tu’/‘vous’, etc.). This can make English speakers seem informal and friendly, or disrespectful, depending on the context. Keep this context in mind when interpreting interactions.

Thursday, September 1, 2016

#EcoSummit2016 The internationalism of ecology –variety is the spice of science

To look around at the faces, or to hear the languages at any science conference is to see the world in a single place at a single time. Science is one of the truly global enterprises, involving people from all regions. Of course this is not to say that science isn’t disproportionately dominated by some countries and regions, but geography does not have a monopoly on ideas. In my lab over the past seven years I have had 15 graduate students and postdoctoral researchers come through my lab from 9 different countries. The question is: does this internationalism influence science? Or does science happen in the same way regardless of who is doing it?

Caroline and I have had a couple of conversations on this topic, and we have both noticed that there seem to be cultural differences in various aspects of how science is done. Of course there is substantial variation among people regardless of their geographical origin, but there are important and maybe subtle differences. From how many hours a day people work, to how professors interact with students and junior researchers, to how quickly new ideas and tools are adopted, there are noticeable differences among geographical regions.

This geographical variation results in different priorities and emphases, and different rates of scientific production, but there is no ideal way. As students move around, international collaborations grow, and people meet and talk at conferences, the best parts of these cultural differences are transferred. I can say that from my year in China, how I view certain elements of my science has changed, and I suspect my Chinese students would say the same about their interactions with me.

The Ecosummit conference we are at is a very international meeting with 88 countries represented. This makes for fertile ground for the sharing of not only scientific ideas and methods, but also learning and sharing notions of what it means to be a successful scientist. This variety is the spice of good science.

Wednesday, August 31, 2016

#EcoSummit2016: Conferences –the piñata of ideas.

One of the greatest benefits of attending conferences is that they represent learning opportunities. I don’t necessarily mean learning about new techniques or analyses, though you can undoubtedly find out about these at conferences, but rather conferences are opportunities to hear about new concepts, ideas and paradigms. In some ways conferences are like a piñata of ideas –they are chalk full of new ideas but you never know which you’ll pick up.

Ecosummit is not the typical conference I go to, it is much more diverse in topics of talks and disciplines of the attendees. This diversity –from policy makers, to social scientists, to ecologists, means that I am exposed to a plethora of new concepts. Here are a few nuggets that got me thinking:

  • Knowledge-values-rules decision making context. Policy decisions are made at the interface of scientific knowledge, human values (what is important to people –e.g., jobs), and rules (e.g., economic laws). This seems like a nice context to think about policy, though it is not clear about how we prioritize new knowledge or alter values.


  • Adaptation services. I work on ecosystem services (e.g., carbon storage, pollination support, water filtration, etc.), but I learned that ecosystems also provide adaptation services. These are aspects of ecosystems that will help human societies adapt to climate change (e.g., new products).

  • Trees and air pollution. The naive assumption most of us make about trees in urban areas are that they improve local air quality. However, I saw a couple of talks where this may not necessarily be the case. Some species in North American (red oak, sweet gum, etc.) release volatile organic compounds. Spruce plantations may not take up nitrogen oxides, and in fact might release it. Thus we need to be careful on how we sell the benefits of urban trees.

  • Transformative. This is a term I have certainly heard and used before, but in listening to a wide variety of talks, I realize it is used in different contexts to mean different things. I think it best to avoid this term.

  • a-disciplinary.  I heard a guy say in a talk that he was a-disciplinary and so was not bound to the dogmas and paradigms of any discipline (I already have a hard time wrapping my head around interdisciplinary, multidisciplinary, transdisciplinary, etc.). He then presented a new paradigm and a number of prescribed well-formulated tools used to move from idea, communication, to action. I think the irony was lost on him.