Category Archives: Academia

Scientific journals should be judged, not ranked

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Aspiring scientists quickly learn that where they publish their hard earned data is important for career progression. A paper in a prestigious journal pushes them up the professional ladder faster than the same paper in an obscure one.

This has led to an obsession with quantifying the prestige of a journal using impact metrics. Over at Conservation Bytes, Corey Bradshaw presents a RShiny App to rank ecology and conservation journals using a composite of different citation metrics. His app is based on a published paper, so you can be sure that it technically sound. It is not my intention to criticise these efforts; if you want to rank jounals, then this composite approach is definitely the way to go.

However, I don’t think there is much to gain from ranking journals based on their impact metrics. Moreover, scientists – especially early-career scientists – would be better off judging journals based on whether is will ensure that their paper reaches the right audience.

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Training well-rounded and work-ready ecologists

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Over at the Ideas for Sustainability blog, Chris Ives wrote an excellent overview  of a recent paper about developing a translational ecology workforce. Briefly, the paper states that we need a work force that has the right combination of (1) multidisciplinary knowledge, (2) practical skills and (3) personal aptitudes.

Multidisciplinary knowledge focuses on traditional academic disciplines, like ecology, law, economics, governance, ethics and sociology. It emphasises T-shaped knowledge, where a deep understanding of a narrower sub-discipline (the vertical line of the T) is married to a more general appreciation of a wider range of topics (the horizontal line of the T).

Practical skills refer to the ability to actually get things done. This includes skills like effective communication, risk assessment, conflict resolution or project management.

Finally, personal aptitudes are those – often intangible – personality traits that make people good to work with. These aptitudes include things like patience, humility, trustworthiness, leadership, punctuality, reliability etc. Continue reading →

Boasting about backyard biodiversity

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The easiest way for an aspiring naturalist to explore wildlife is by stepping out into their own backyard. Try it yourself. As I write this, I can look through my window at a Karoo Thrush hopping about my garden. But this post is not about the tiny garden surrounding my current apartment, but rather about my childhood home. I was tremendously fortunate to grow up on a 60 hectare farm, where  first discovered my love for nature.

Between wrapping up my PhD and starting my current lecturing position, I spent a few months of unemployment back in the house I grew up in. During that time, I discovered the thrill of recording unobtrusive nocturnal critters using a camera trap. Every afternoon, I set up the camera trap and eagerly explored the footage the following morning. It was so much fun.

After enough time, even I was amazed by the variety of species that lived on this relatively small farm. Perhaps, I should rephrase that last sentence. You see, calling it a farm is not accurate because it hasn’t been used for agricultural in more than ten years. The last cows were removed back in 2004 and since then the land was left dormant and only managed to minimise the risk of wild fire.

Still, I captured footage of 18 different mammal species, which is remarkably high for such a small area. Moreover, the camera trap is unlikely to capture any footage of bats and small rodents, so the total mammal diversity is probably even higher. I decided to write up these observations and the results have just been published online in the African Journal of Ecology. Continue reading →

I work at a university, and have know idea what I am doing!

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I meant to post this much earlier, but I just haven’t found the time. You see, I started a new job a few months ago– my first full-time academic position – and I been struggling to keep my head above water ever since.

The last year has been a whirlwind for me. Within a few months, I finished my PhD, moved back to South Africa from Belgium, spent two months of unemployment living in my childhood home before taking on the position I have now. Needless to say, I embarked on this new career path in a unprepared and frazzled state.

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The “true nature of the university” as told by John Williams

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I’ve been appointed as a lecturer a since the beginning of March; my first real academic job. In my short time in the ivory tower, I’ve wondered about my role at the university and how it complements my own career ambitions. This form of navel-gazing rarely results in any meaningful epiphanies, but it does push me towards interesting sources of guidance.

One such source is the novel Stoner, by John Williams (It’s excellent. I highly recommend it). Below is an extended excerpt on the ‘true nature of the university’, which struck a chord with me. I can relate to all the characters and especially to the closing paragraph. It’s a beautifully written novel and I wouldn’t want to spoil it, but, for those in a rush, I annotated the best bits in bold.

To set the scene: three young English lecturers, Mrs Masters, Finch and Stoner, are having a casual conversation after work when the following exchange takes place. Continue reading →

The scalability of macroecology

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Russian Dolls

No matter at which scale you look at it, nature is remarkable.

Like many others, I was taught ecology in a very hierarchical way: individual organisms are part of a wider populations of species, collections of species form communities and communities come together to make up ecosystems. Similarly, single trees are nested within forests, which aggregate to form biomes. I’m sure you can come up with many comparable examples.

The trouble with such neat spatial hierarchies is that they lure us into believing that if patterns appear similar at several different spatial scales, then the processes leading to these patterns should also be similar. It’s so easy to assume that nature is like a set of Russian Dolls: each daughter exactly the same as its mother, only slightly smaller. But this is not necessarily the case.

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Species distribution modelling is not as simple as you think

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One of the most fruitful sub-fields in ecology is using climate variables to predict species’ geographic distributions. For the uninitiated, species distribution modelling assumes that species are limited in their distributions to suitable climate zones. By studying the environmental conditions where species are known to occur, you can infer the total geographic distribution by calculating the suitability of unsampled regions based on the environmental. Furthermore, using the same principle, species distribution modelling can forecast the effect of future climate change of the distribution of life on earth.

Unfortunately, studies have shown that these fancy climate-based techniques cannot consistently outperform much simpler ones based on spatial phenomena. For instance, spatial interpolation between point occurrences outperforms sophisticated climate-based predictions. Similarly, elaborate climate-based predictions perform no better than expected from random chance.

The trouble lies in the spatially-structured world we live in. Species distributions, especially at large spatial scales, are spatially-autocorrelated due to constrained dispersal. Similarly, climate variables are also spatially structured because the meteorological processes at proximal regions are generally more similar than those at distant sites.

When trying to link species distributions to climate conditions, the challenge lies is separating spatial and environmental correlations in species distributions. Specifically, we should identify three patterns in the geographical species distributions.

  • We must first identify ‘true’ correlations with the environment, which are independent of spatial patterns (E|S).
  • Next, we must identify the environmental-associations that also have a strong spatial structure (E∩S). This is known as exogenous spatial autocorrelation because it is due to autocorrelation is the underlying variables.
  • Finally, we need to identify spatial patterns that are completely independent of environmental conditions (S|E). This is called endogenous spatial autocorrelation because it supposedly stems from spatial processes, such as dispersal.

In our latest study just published online at Ecography, we set out to quantify the degree of environmental correlation, exogenous and endogenous spatial autocorrelation in the distributions of 4 423 species of amphibians, reptiles, birds and mammals in Africa. Continue reading →

Some motivation to get you through your PhD

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If there is one thing I hate, it’s the stereotype that PhD students are pathetic, dependent, helpless creatures bogged down by self-doubt and self-pity. It annoys me even more that PhD students are responsible for perpetuating this myth. We laugh along with popular websites like Piled Higher and Deeper (a.k.a PhD comics) and What Should We Call Grad School, which regularly make jokes about the futility of grad school.

Sure, these sites are funny because there is an element of truth in them, but I believe that they cause more harm than good. Although they are well-meaning and try to foster a culture of solidarity among students, they are more likely to cause complacency than empowerment.

We don’t need another shoulder to cry on, we need a kick in the arse!

As I am nearing the end of my PhD experience, I thought I’d share a bit of motivational advice I found especially useful. It is the final chapter of Adam Ruben’s book, Surviving your stupid, stupid decision to go to grad school. Some of you may be familiar with Ruben’s writing, because he also writes a monthly column in Science Magazine, Experimental Error.

Here it is, enjoy.

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MacArthur and Wilson’s Radical Theory wasn’t actually radical (even great ideas in ecology go unnoticed)

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Most ecologists know about the Theory of Island Biogeography; the theory that diversity patterns on islands are the consequence of dispersal from a mainland source. Robert MacArthur and E.O. Wilson presented this theory first as a research paper in 1963 and then as a monograph in 1967. The rest, as they say, is history.

The Theory of Island Biogeography is remarkable because it suggests that patterns of species co-existence are the consequence of chance, history and random dispersal. Before its publication, community ecologists generally assumed that species co-existence was due to deterministic niche-assembly, where the number and relative abundance of species were a result of ecological niches and the functional roles of each species.

The theory placed randomness at the forefront to community ecology. It also paved the way for Stephen Hubbell’s Unified Neutral Theory of Biodiversity and Biogeography; one of the most influential ecological theories in 21st century. In fact, the introductory chapter of Hubbell’s monograph (like this blog post) was titled “MacArthur and Wilson’s Radical Theory” in reverence to their path-breaking work.

Like the theory itself, MacArthur and Wilson have also reached cult-like status. Perhaps a most telling way of illustrating this fact is not by listing the prizes awarded to these two men (and there were many), but rather by listing the academic prizes named after them! The Ecological Society of America, for instance, awards the ‘Robert H. MacArthur Award‘ to eminent mid-career ecologists and the American Society of Naturalists grants the ‘Edward O. Wilson Naturalist Award‘ to mid-career researchers who make significant contributions to a particular ecosystem of group of organisms. Similarly, the International Biogeography Society has the ‘MacArthur & Wilson Award‘ for notable contributions to the field of biogeography.  Needless to say, MacArthur and Wilson are very influential and well-respected by contemporary ecologists (well, in most cases…).

The funny thing is that their paradigm shifting idea was actually proposed two decades earlier, by the less well-known lepidopterist Eugene Munroe. Continue reading →

Handling cumulative impacts during the environmental decision-making process

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Although ecology doesn’t have many general laws, one most likely to qualify is the species-area relationship. If you walk through a field in a straight line and count all the different species you come across, you’ll notice that the total number of species increases as you progress along your straight path. After a while, however, you’ll start seeing the same species over and over again until you eventually find that you’re no longer spotting any new ones. This is the asymptotic species-area curve. While the exact mathematical form of the relationship is still hotly debated, it is safe to assume that it is an increasing function that reaches a plateau once all the species have been encountered.

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