Grappling with reproducibility in science?

As a lab, we’ve made it a priority to increase the standards of our code to align with best practices for reproducibility and repeatability of our science. In keeping with this goal, this week in reading group Saras Windecker and Hannah Fraser lead a discussion on the British Ecological Society’s Guide to Reproducible Code in Ecology and Evolution, measures on how we can implement these guidelines in our research and the barriers that limit their uptake within the QAEco group. Here is a brief summary of that discussion.

The BES guide details workflow and project structure, version control, and techniques for defensive coding. While many of us already implement all or some of these suggestions into our workflow, it is by no means universal. Moreover, the QAEco group has a steady intake of new students, for whom these skills are, for the most part, completely new.

Whether a beginner or a veteran at maintaining ‘good’ workflows, we found over the course of the discussion that there are two major barriers to the uptake of reproducibility recommendations: lack of availability of resources/time, and fear/sense of intimidation to taking the plunge in to the great unknown of workflows, version control and GitHub!

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Qaeco’s favourite papers of 2017

We asked our lab members to nominate a paper published in 2017 that they had enjoyed. Recommendations ranged from the skill-based (scientific writing, reproducible coding, camera-trapping) to global reviews (plant traits, climate change, size-based models) and some great case studies (questionable psychologists, waterbirds at Lake Eyre, Finnish foxes).  We hope you find them as interesting as we did!

– Kate & Bron, hosts of QAECO Reading Group

Natasha Cadenhead

Doubleday, Z.A. & Connell, S.D. (2017) Publishing with objective charisma: breaking science’s paradoxTrends in Ecology & Evolution32, 803-805.

At the risk of sounding a little too Eat, Pray, Love, 2017 was a year in which I decided to try and actively improve my scientific writing. Not only is there an inherent joy to reading a well-written paper, but it makes the scientific message within that much clearer. Doubleday & Connell’s (thankfully, eloquent) paper recognises the problem with much of scientific writing – we spend a lot of our time doing it, but we’re never taught how to do it in an engaging way. They run through some steps for bringing out that charismatic “Ingredient X” in your writing, without falling prey to sensationalism. On this topic (although less science-focused) I would also recommend anything by the excellent Helen Sword.

Dave Duncan

Watson, D.M., Doerr, V.A.J., Banks, S.C., Driscoll, D.A., van der Ree, R., Doerr, E.D. & Sunnucks, P. (2017) Monitoring ecological consequences of efforts to restore landscape-scale connectivity. Biological Conservation, 206, 201–209.

My favourite paper from this year is the culmination of a monitoring framework I saw presented by one of the authors back in about 2015.  The article sets out a framework for thinking about the design of monitoring activities for projects whose intention is to restore connectivity at landscape scales.

Now, you might be saying to yourself: does the world really need another monitoring framework? Sadly, apparently yes. Well that and some kind of institutional revolution on the other side of which we actually implement some of these great ideas.

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Modellers v.s. Experimentalists – why can’t we all just get along?

Are modellers trying to steal your data?

Field ecologists not bothering to read your equations?

If so, you’re not alone, because the authors in Heuschele et al 2017 share your concern. They reckon that ecological research is being limited by a lack of communication and collaboration between modellers and experimentalists.

QAECO is made up of a diverse bunch of researchers, who use many different approaches to skin a cat. So this week in reading group, I (Matt Rees) bought this paper in to see what everyone thought. Turns out, quite a bit.

The authors of this paper conducted an online survey of ecologists, a bibliometric analysis of highly cited papers, and examined the background of highly cited ecologists. In doing so, they identified two key aspects that seem to be preventing collaboration between modellers and experimentalists: journal articles being written in “cryptic” ways that make it difficult for their counterparts to decipher, as well as a lack of data being exchanged. They showed that the recipe for being a highly cited paper/author, was to model, or use a combination of experimental and modelling approaches (but not just experimental).

Despite a couple people not being convinced by their review methods (and they didn’t use any modelling… tsk tsk), these concerns did seem to ring true in our discussion. The majority of experimentalists they surveyed were keen to share their data, however, had reservations about modellers using their data inappropriately (i.e. not recognising the limitations of their methods) and wanted appropriate acknowledgement. These results prompted a debate amongst us about what constitutes authorship, should collecting the data automatically mean you are a co-author? Unsurprisingly, our modelling folks tended not to think so, and generally those who have conducted experiments did. However, we all agreed that it was context specific and that those who collected the data should at least get an opportunity to contribute to the manuscript. Regardless, it was clear that like the authors, we all agreed that collaboration and sharing data is essential to make sense of the complex systems we study. Although, this shouldn’t just be a one-way street of experimentalists handing over their data without apprehension, modellers should also seek to collaborate in the experimental design process.


Just a standard day for QAECO experimentalist Jessie Moyses

But hang on a second, what the blooming heck is an experimentalist and who is a modeller? We were a little confused with their definitions (for example, they excluded statistical modelling from the definition of being a modeller, yet classified papers using statistical models of non-manipulative experiments as modelling papers in their bibliometric analysis). We also felt that this paper tended to reinforce the stereotypes of being either a modeller or an experimentalist. These labels can stick very strongly in science and can dictate what you work on in the future. In some sections, the paper seemed discouraging of using both approaches – something that many of us in QAECO strive to do.

A particular concern we found from this research was that experimentalists do not seem to be drawing inspiration from modelling papers. Surveyed experimentalists stated that these papers were difficult to understand and that they were sceptical about the model being a realistic representation of the system. A key recommendation the authors put forward was to increase mathematical teaching in ecology, which is of course, well justified and often called for. However, a few of us also thought that there is more that modellers could be doing to bridge this gap that didn’t get mentioned in the paper (and rarely does). For example, modellers could head into the field to see how this data is being collected, talk to land managers, communicate their findings directly to experimentalists that would be interested (especially if your highlighting an information gap), encourage them to test your model and collect their data in a way that would increase the modelling opportunities.


The famous supermodel Jian Yen

This article promotes an important discussion about how we can improve our field. We feel very lucky at QAECO to have such a wide  spectrum of experimental-modelling approaches being used under one roof. It is clear that increasing collaboration and communication in ecology needs to be better encouraged, luckily there are feasible steps we can all take to bridge this gap (which are probably much easier than catching thousands of bandicoots or deriving new algorithms).

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Sense of place: the ecosystem service to align social and conservation values?

Many conservation issues are influenced by a complex mix of environmental, social, economic and cultural processes. At times, conservation decision-making can be complicated by opposing social and ecological values. In this week’s reading group, Anja Skroblin led a discussion on “sense of place”, focused on a paper by Hausmann et al. (2015).

The authors suggest that recognising the human concept of “sense of place” as an ecosystem service is an important link to help to resolve conflicts where conservation is at odds with human development needs. The authors of the paper develop a framework for how “sense of place” can be used to inform conservation decision making to benefit human well-being and biodiversity conservation in a seemingly win-win situation.

The Kimberleys

But what is “sense of place”?

The definition differs across the psychological, sociological, geographical and environmental management disciplines. We felt it was best summarised by the attachment and connections that people develop with, and the meanings they assign to, places.

Each of us could describe a location for which we had sense of place. Our places were all nature-based, perhaps because we were all ecologists with an outdoorsy bent: the bushland patches we played in as kids, the parks where we went camping with our families, the Otways, the Prom, the family farm…The common factor was that we were connected to these places by the webs of stories derived from lived experience, often in childhood.

We agreed that sense of place could be lost if the place was damaged, but also if the activities we associated with the place were no longer possible.


If you care for it, you will protect it! But is sense of place correlated to biodiversity?

The small sample of Qaecologists in this discussion generally agreed that having developed a sense of place with the natural world was a guiding factor in our conservation consciousness. We recognised that engendering a sense of place can be used as a tool to encourage people’s support for conservation related to that place. People who have strong connections to a place are more likely to advocate for it.

But we had some reservations about how sense of place could be used within decision making:

  • Firstly, can we (and should we) quantify the value of sense of place as an ecosystem service in decision making? We are not so sure. It seems very difficult to assign a monetary value to sense of place.
  • Is sense of place a double-edged sword for conservation? Sense of place can be based on connections that are misaligned with biodiversity. Brumbies in the Australian Alps is just one example we discussed. Many Australians have a strong connection to the Alpine country. For some, their sense of place is interwoven with the stories of Banjo Patterson’s “The Man from Snowy River” and the “Silver Brumby” books, where the brumby plays a central role in sense of Alpine place more than native biodiversity. Placing higher value on sense of place in this context isn’t going to assist biodiversity.


    Brumbies – iconic or feral? Image by Robyn MacRae/Flikr. Used under Creative Commons 2

  • Whose sense of place should be valued in decisions? It’s not an ecological example, but to make a point – should people climb Uluru? For the Anangu who are the traditional owners of Uluru, their sense of place and culture does not permit climbing. But for some other people, their sense of place is connected to the experience of being able to climb – their sense of place is diminished by not being able to climb. Where there is conflict, whose sense of place should take precedence in decision making? When it comes down to values, minority groups can be overlooked.


    Whose “sense of place” should take precedence in managing Uluru? Image by MelaLouise/Flikr. Used under Creative Commons 2

We suspect that sense of place, or connection to places, values and activities, may already play a substantial role in decision making. In our experience, decisions in conservation often end up being strongly influenced by values (monetary or other) as well as scientific evidence.  People’s attachment to a place may affect their decision to advocate for a management outcome (whether or not it benefits biodiversity).

Regardless, for us, having “sense of place” for our own special places has brought joy and meaningful connection to nature. Opportunities for people to connect with nature is always something to encourage.

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Culling animals “ethically”

kangaroos-1563624_1920In reading group earlier this month Linda Riquelme led a discussion on the issue of wildlife culling. This is something that relates to projects a few of us in the lab work on. For example, the management of endangered Buloke Woodlands in the Victorian Mallee, which involves an annual kangaroo cull at Wyperfeld National Park in north-western Victoria.

Not all wildlife management strategies involve culling, though it is used in many situations: kangaroo culls in eastern Australia to manage grazing, badger culls in the UK to control bovine tuberculosis, culling of exotic brushtail possums in New Zealand, the list goes on.

A paper published earlier this year by Dubois and colleagues proposed a list of seven stepwise “principles for ethical wildlife control”. These principles came about as a result of a 2-day workshop held in 2015 that brought together 20 international experts from academia, industry, and non-governmental organisations. The aim of the workshop was to develop a set of steps that managers could work through to determine whether it was possible to mitigate a problem by changing human behaviour, or if not, whether a problem was serious enough to warrant a cull.

These seven principles are: Continue reading

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Is there truly “no saturation in the accumulation of alien species worldwide”?

sea-water-port-industryIn reading group last week (May 11th) Hannah Fraser brought the group a paper reflecting a synergy between QAECO interests and her current role in the Centre of Excellence for Biosecurity Risk Analysis. This paper by Seebens et al. (2017) “No saturation in the accumulation of alien species worldwide” evaluates the trends in the introduction of alien species from 1800 to 2000. They have three hypotheses

  1. The rate at which taxa that are deliberately introduced (mammals, birds and vascular plants) should be declining
  2. The rate at which taxa are accidentally introduced should be increasing due to increases in trade
  3. The rates of alien species introductions should vary between countries depending on country’s history and biosecurity regulations

They show that, overall, the rate of introductions is increasing and that this increase is particularly stark for algae, fungi and invertebrates which are thought to be primarily introduced by accident. They note that the rate of mammal and fish introduction has declined in recent years, possibly consistent with their hypothesis that the rate of deliberate introductions is falling. Continue reading

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Life in corrupt science: when metrics become targets

Publish or perish’. The overused phrase describing career aspects in today’s academia. Whereas day-to-day work is rarely quite as grim, we all learn early on that our performance as scientists is very much measured by the number of publications, citations, and successful funding applications we produce.


For our latest Reading Group meeting, Heini Kujala had selected a paper by Edwards and Roy (2017) on the importance of maintaining scientific integrity in the 21st century climate of perverse incentives and hyper-competition. It is a depressing but engaging read addressing the current metrics-based evaluation of scientists, which, coupled with an increasing number of academics and stagnant funding budgets, has created a perverse incentive system that is pushing academia to the ‘normalisation of corruption’. Continue reading

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