… some (models) are useful

8 06 2021

As someone who writes a lot of models — many for applied questions in conservation management (e.g., harvest quotas, eradication targets, minimum viable population sizes, etc.), and supervises people writing even more of them, I’ve had many different experiences with their uptake and implementation by management authorities.

Some of those experiences have involved catastrophic failures to influence any management or policy. One particularly painful memory relates to a model we wrote to assist with optimising approaches to eradicate (or at least, reduce the densities of) feral animals in Kakadu National Park. We even wrote the bloody thing in Visual Basic (horrible coding language) so people could run the module in Excel. As far as I’m aware, no one ever used it.

Others have been accepted more readily, such as a shark-harvest model, which (I think, but have no evidence to support) has been used to justify fishing quotas, and one we’ve done recently for the eradication of feral pigs on Kangaroo Island (as yet unpublished) has led directly to increased funding to the agency responsible for the programme.

According to Altmetrics (and the online tool I developed to get paper-level Altmetric information quickly), only 3 of the 16 of what I’d call my most ‘applied modelling’ papers have been cited in policy documents:

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Cartoon guide to biodiversity loss LXVI

29 05 2021

Here is the third set of biodiversity cartoons for 2021. See full stock of previous ‘Cartoon guide to biodiversity loss’ compendia here.


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Killing (feral) cats quickly (and efficiently)

20 05 2021

I’m pleased to announce the publication of a paper led by Kathryn Venning (KV) that was derived from her Honours work in the lab. Although she’s well into her PhD on an entirely different topic, I’m overjoyed that she persevered and saw this work to publication.

Here, killa, killa, killa, killa …

As you probably already know, feral cats are a huge problem in Australia. The are probably the primary reason Australia leads the world in mammal extinctions in particular, and largely the reason so many re-introduction attempts of threatened marsupials fail miserably only after a few years.

Feral cats occupy every habitat in the country, from the high tropics to the deserts, and from the mountains to the sea. They adapt to the cold just as easily as they adapt to the extreme heat, and they can eat just about anything that moves, from invertebrates to the carcases of much larger animals that they scavenge.

Cats are Australia’s bane, but you can’t help but be at least a little impressed with their resilience.

Still, we have to try our best to get rid of them where we can, or at least reduce their densities to the point where their ecological damage is limited.

Typically, the only efficient and cost-effective way to do that is via lethal control, but by using various means. These can include direct shooting, trapping, aerial poison-baiting, and a new ‘smart’ method of targeted poison delivery via a prototype device known as a Felixer™️. The latter are particularly useful for passive control in areas where ground-shooting access is difficult.

A live Felixer™️ deployed on Kangaroo Island (photo: CJA Bradshaw 2020)

A few years back the federal government committed what might seem like a sizeable amount of money to ‘eradicate’ cats from Australia. Yeah, good luck with that, although the money has been allocated to several places where cat reduction and perhaps even eradication is feasible. Namely, on islands.

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Everything you always wanted to know about conservation (but were afraid to ask)

14 05 2021

While some of us still might imagine the conservationist as a fancy explorer discovering new species in a remote corner of the world, or collecting samples while drowning in mud, a growing portion of conservation science nowadays consists of asking people about their ideas and behaviours.

Needless to say, this approach produces a fair share of awkward, if not dangerous, situations. After all, who likes the idea of completing a questionnaire from the fisheries office, asking about compliance with harvest limitations or licence fees? Or, even worse, who fancies being asked about the possession of illegally traded wildlife? 

Many conservationists would really like to have this valuable information, but at the same time it is clear that these questions put people at great discomfort. This leads to biased estimates of important behaviours affecting conservation. This is where specialised questioning techniques can help.

Specialised questioning techniques aim to prevent researchers, or anyone else, to trace back individual answers. Many do so by adding noise with a known distribution to individual answers. Then, when all answers are pooled, this noise is ruled out with statistical approaches. Noise can come from a randomising device (e.g. a die), like in the randomised response technique:

Individual answers can also be masked by asking respondents not to indicate if they engaged in a certain behaviour, but by asking them, out of a list of sensitive and non-sensitive behaviours, to indicate the number in which they engaged. This is the case of the unmatched count technique (a.k.a list experiments):

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Attack of the alien invaders: pest plants and animals leave a frightening $1.7 trillion bill

19 04 2021

Shutterstock


They’re one of the most damaging environmental forces on Earth. They’ve colonised pretty much every place humans have set foot on the planet. Yet you might not even know they exist.

We’re talking about alien species. Not little green extraterrestrials, but invasive plants and animals not native to an ecosystem and which become pests. They might be plants from South America, starfish from Africa, insects from Europe or birds from Asia.

These species can threaten the health of plants and animals, including humans. And they cause huge economic harm. Our research, recently published in the journal Nature, puts a figure on that damage. We found that globally, invasive species cost US$1.3 trillion (A$1.7 trillion) in money lost or spent between 1970 and 2017.

The cost is increasing exponentially over time. And troublingly, most of the cost relates to the damage and losses invasive species cause. Meanwhile, far cheaper control and prevention measures are often ignored.

Yellow crazy ants attacking a gecko
Yellow crazy ants, such as these attacking a gecko, are among thousands of invasive species causing ecological and economic havoc. Dinakarr, CC0, Wikimedia Commons

An expansive toll

Invasive species have been invading foreign territories for centuries. They hail from habitats as diverse as tropical forests, dry savannas, temperate lakes and cold oceans.

They arrived because we brought them — as pets, ornamental plants or as stowaways on our holidays or via commercial trade.

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The biggest and slowest don’t always bite it first

13 04 2021

For many years I’ve been interested in modelling the extinction dynamics of megafauna. Apart from co-authoring a few demographically simplified (or largely demographically free) models about how megafauna species could have gone extinct, I have never really tried to capture the full nuances of long-extinct species within a fully structured demographic framework.

That is, until now.

But how do you get the life-history data of an extinct animal that was never directly measured. Surely, things like survival, reproductive output, longevity and even environmental carrying capacity are impossible to discern, and aren’t these necessary for a stage-structured demographic model?

Thylacine mum & joey. Nellie Pease & CABAH

The answer to the first part of that question “it’s possible”, and to the second, it’s “yes”. The most important bit of information we palaeo modellers need to construct something that’s ecologically plausible for an extinct species is an estimate of body mass. Thankfully, palaeontologists are very good at estimating the mass of the things they dig up (with the associated caveats, of course). From such estimates, we can reconstruct everything from equilibrium densities, maximum rate of population growth, age at first breeding, and longevity.

But it’s more complicated than that, of course. In Australia anyway, we’re largely dealing with marsupials (and some monotremes), and they have a rather different life-history mode than most placentals. We therefore have to ‘correct’ the life-history estimates derived from living placental species. Thankfully, evolutionary biologists and ecologists have ways to do that too.

The Pleistocene kangaroo Procoptodon goliah, the largest and most heavily built of the  short-faced kangaroos, was the largest and most heavily built kangaroo known. It had an  unusually short, flat face and forwardly directed 
eyes, with a single large toe on each foot  (reduced from the more normal count of four). Each forelimb had two long, clawed fingers  that would have been used to bring leafy branches within reach.

So with a battery of ecological, demographic, and evolutionary tools, we can now create reasonable stochastic-demographic models for long-gone species, like wombat-like creatures as big as cars, birds more than two metres tall, and lizards more than seven metres long that once roamed the Australian continent. 

Ancient clues, in the shape of fossils and archaeological evidence of varying quality scattered across Australia, have formed the basis of several hypotheses about the fate of megafauna that vanished during a peak about 42,000 years ago from the ancient continent of Sahul, comprising mainland Australia, Tasmania, New Guinea and neighbouring islands.

There is a growing consensus that multiple factors were at play, including climate change, the impact of people on the environment, and access to freshwater sources.

Just published in the open-access journal eLife, our latest CABAH paper applies these approaches to assess how susceptible different species were to extinction – and what it means for the survival of species today. 

Using various characteristics such as body size, weight, lifespan, survival rate, and fertility, we (Chris Johnson, John Llewelyn, Vera Weisbecker, Giovanni Strona, Frédérik Saltré & me) created population simulation models to predict the likelihood of these species surviving under different types of environmental disturbance.

Simulations included everything from increasing droughts to increasing hunting pressure to see which species of 13 extinct megafauna (genera: Diprotodon, Palorchestes, Zygomaturus, Phascolonus, Procoptodon, Sthenurus, Protemnodon, Simosthenurus, Metasthenurus, Genyornis, Thylacoleo, Thylacinus, Megalibgwilia), as well as 8 comparative species still alive today (Vombatus, Osphranter, Notamacropus, Dromaius, Alectura, Sarcophilus, Dasyurus, Tachyglossus), had the highest chances of surviving.

We compared the results to what we know about the timing of extinction for different megafauna species derived from dated fossil records. We expected to confirm that the most extinction-prone species were the first species to go extinct – but that wasn’t necessarily the case.

While we did find that slower-growing species with lower fertility, like the rhino-sized wombat relative Diprotodon, were generally more susceptible to extinction than more-fecund species like the marsupial ‘tiger’ thylacine, the relative susceptibility rank across species did not match the timing of their extinctions recorded in the fossil record.

Indeed, we found no clear relationship between a species’ inherent vulnerability to extinction — such as being slower and heavier and/or slower to reproduce — and the timing of its extinction in the fossil record.

In fact, we found that most of the living species used for comparison — such as short-beaked echidnas, emus, brush turkeys, and common wombats — were more susceptible on average than their now-extinct counterparts.

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One trillion dollars!

1 04 2021

Or thereabouts.

Let’s step back to 2015. In a former life when I was at another institution, I had the immense fortune and pleasure to spend six months on sabbatical in a little village just south of Paris working with my friend and colleague, Franck Courchamp, at Université Paris-Sud (now Université Paris-Saclay).

Sure, I felt a bit jammy living there with my daughter in a beautiful house just down the street from two mouth-watering pâtisseries and three different open marchés. We ate well. We picked mushrooms on the weekends or visited local châteaux. We went into the city and visited overwhelmingly beautiful museums at our leisure. We drank good champagne (well, I did, not my eight-year old). We had communal raclettes.

But of course, I was primarily there to do research with Franck and his lab, despite the obvious perks.

While I busied myself with several tasks while there, one of our main outputs was to put together the world’s first global database of the costs of invasive insects, which we subsequently published in 2016.

But that was only the beginning. With funding that started off the process with insects, Franck persevered and hired postdocs and took on more students to build the most comprehensive database of all invasive species ever compiled — InvaCost.

I cannot stress enough how massive an undertaking this was. It’s not simply a big list of all the cost estimates in existence, it’s also a detailed assessment of cost reliability, standardisation, and contextualisation. I’m not sure I would have had the courage to do this myself.

While the database itself has already been published, today we are pleased to announce the publication in Nature of the main results — High and rising economic costs of biological invasions worldwide — led by Christophe Diagne (one of the nicest people I’ve ever met), and co-authored by Boris Leroy, Anne-Charlotte Vaissière, Rodolphe Gozlan, David Roiz, Ivan Jarić, Jean-Michel Salles, me, and Franck Courchamp (of course).

Herein we described how the economic costs of invasive alien species accumulated since 1970 are tremendous, and that they have been steadily increasing over time.

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How to avoid reduce the probability of being killed by a shark

31 03 2021

Easy. Don’t go swimming/surfing/snorkelling/diving in the ocean.


“Oh, shit”

Sure, that’s true, but if you’re like many Australians, the sea is not just a beautiful thing to look at from the window, it’s a way of life. Trying telling a surfer not to surf, or a diver not to dive. Good luck with that.

A few years ago, I joined a team of super-cool sharkologists led by Charlie ‘Aussie-by-way-of-Belgium shark-scientist extraordinaire Huveneers, and including Maddie ‘Chomp’ Thiele and Lauren ‘Acid’ Meyer — to publish the results of some of the first experimentally tested shark deterrents.

It turns out that many of the deterrents we tested failed to show any reduction in the probability of a shark biting, with only one type of electronic deterrent showing any effect at all (~ 60% reduction).

Great. But what might that mean in terms of how many people could be saved by wearing such electronic deterrents? While the probability of being bitten by a shark is low globally, even in Australia (despite public perceptions), we wondered if the number of lives saved and injuries avoided was substantial.

In a new paper just published today in Royal Society Open Science, we attempted to answer that question.

To predict how many people could avoid shark bites if they were using properly donned electronic deterrents that demonstrate some capacity to dissuade sharks from biting, we examined the century-scale time series of shark bites on humans in Australia. This database — the ‘Australian Shark Attack File‘ — is one of the most comprehensive databases of its kind.

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A perfect storm of global ineptitude

18 03 2021

Given the ‘success’ (i.e., a lot of people seem to be reading it) of our recent Ghastly Future paper, I thought it would be interesting to go back and have a look at what we wrote in our 2015 book Killing the Koala on the subject. I think you’ll find that if anything we were probably overly optimistic.

An updated digest of that material follows.


When your accountant tells you to reduce expenditure, you do it or risk bankruptcy; when your electrician tells you the wiring in your house is dodgy, you replace it or risk your family dying in an avoidable fire; when your doctor tells you your cholesterol is too high, you cut back fat intake (and/or take cholesterol-reducing drugs) or risk a heart attack.

Yet few with any real political or financial power heed the warnings of environmental scientists. It is not just a few of us either — globally, ecologists, conservation biologists and environmental scientists are united in telling the world (for decades now) that growth in population and consumption cannot go on forever. They have been united in telling us if we do not clean up our planet, our life-support systems could ultimately fail.

There are now nearly eight billion people on Earth, and median projections suggest that the population will grow to ten billion or more by the end of the century. Some analyses indicate that with present technologies, Earth could only sustainably support indefinitely some 5 billion people under best-case scenarios, but assuming similar proportions of poverty and suffering as we have today. Others imply that 5 billion could be many too many.

As a result, humanity is entering that near-perfect storm of problems driven by overpopulation, overconsumption, gross inequalities, and the use of needlessly environmentally damaging technologies. The problems include the intertwined dilemmas of loss of the biodiversity that runs human life-support systems, climate disruption, energy shortages, global toxification, alteration of critical biogeochemical cycles, shortages of water, soil, mineral resources and farmland, and increasing probability of vast epidemics (as COVID-19 poignantly exemplifies).

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Cartoon guide to biodiversity loss LXV

10 03 2021

Here is the second set of biodiversity cartoons for 2021. See full stock of previous ‘Cartoon guide to biodiversity loss’ compendia here.


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Recreational hunting, conservation and livelihoods: no clear evidence trail

2 03 2021
Enrico Di Minin, University of Helsinki; Anna Haukka, University of Helsinki; Anna Hausmann, University of Helsinki; Christoph Fink, University of Helsinki; Corey J. A. Bradshaw, Flinders University; Gonzalo Cortés-Capano, University of Helsinki; Hayley Clements, Stellenbosch University, and Ricardo A. Correia, University of Helsinki

In some African countries, lion trophy hunting is legal. Riaan van den Berg

In sub-Saharan Africa, almost 1,400,000 km² of land spread across many countries — from Kenya to South Africa — is dedicated to “trophy” (recreational) hunting. This type of hunting can occur on communal, private, and state lands.

The hunters – mainly foreign “tourists” from North America and Europe – target a wide variety of species, including lions, leopards, antelopes, buffalo, elephants, zebras, hippopotamus and giraffes.


Read more: Big game: banning trophy hunting could do more harm than good


Debates centred on the role of recreational hunting in supporting nature conservation and local people’s livelihoods are among the most polarising in conservation today.

On one hand, people argue that recreational hunting generates funding that can support livelihoods and nature conservation. It’s estimated to generate US$200 million annually in sub-Saharan Africa, although others dispute the magnitude of this contribution.

On the other hand, hunting is heavily criticised on ethical and moral grounds and as a potential threat to some species.

Evidence for taking a particular side in the debate is still unfortunately thin. In our recently published research, we reviewed the large body of scientific literature on recreational hunting from around the world, which meant we read and analysed more than 1000 peer-reviewed papers.

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Conservation paradox – the pros and cons of recreational hunting

20 02 2021
The recovery of species such as mountain zebra (Equus zebra) was partly supported by the economic benefits generated by trophy hunting. © Dr Hayley Clements

Through the leadership of my long-time friend and collaborator, Enrico Di Minin of the Helsinki Lab of Interdisciplinary Conservation Science, as well as the co-leadership of my (now) new colleague, Dr Hayley Clements, I’m pleased to report our new paper in One Earth — ‘Consequences of recreational hunting for biodiversity conservation and livelihoods‘.


My father was a hunter, and by proxy so was I when I was a lad. I wasn’t really a ‘good’ hunter in the sense that I rarely bagged my quarry, but during my childhood not only did I fail to question the morality of recreational hunting, I really thought that in fact it was by and large an important cultural endeavour.

It’s interesting how conditioned we become as children, for I couldn’t possibly conceive of hunting a wild, indigenous species for my own personal satisfaction now. I find the process not only morally and ethically reprehensible, I also think that most species don’t need the extra stress in an already environmentally stressed world.

I admit that I do shoot invasive European rabbits and foxes on my small farm from time to time — to reduce the grazing and browsing pressure on my trees from the former, and the predation pressure on the chooks from the latter. Of course, we eat the rabbits, but I tend just to bury the foxes. My dual perspective on the general issue of hunting in a way mirrors the two sides of the recreational hunting issue we report in our latest paper.

Wild boar (Sus scrofus). Photo: Valentin Panzirsch, CC BY-SA 3.0 AT, via Wikimedia Commons

I want to be clear here that our paper focuses exclusively on recreational hunting, and especially the hunting of charismatic species for their trophies. The activity is more than just a little controversial, for it raises many ethical and moral concerns at the very least. Yet, recreational hunting is frequently suggested as a way to conserve nature and support local people’s livelihoods. 

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Ancient bones — how old?

22 01 2021

Radiocarbon (14C) dating was developed by Nobel-Prize winning chemist Willard Libby, and has become the predominant method to build chronologies of ancient populations and species using the Quaternary fossil record. I have just published a research paper about 14C dating of fossil bone reviewing the four standard chemical pretreatments of bone collagen to avoid sample contamination and generate accurate fossil ages: gelatinization, ultrafiltration, XAD purification and hydroxyproline isolation. Hydroxyproline isolation is perceived as the most accurate pretreatment in a questionnaire survey completed by 132 experts from 25 countries, but remains costly, time-consuming and not widely available. I argue that (1) innovation is urgently required to develop affordable analytical chemistry to date low-mass samples of collagen amino acids, (2) those developments should be overseen by a certification agency, and (3) 14C users should be more conceptually involved in how (much) 14C chemistry determines dating accuracy. Across the board, scientific controversies like the timing of Quaternary extinctions need not be fuelled by inaccurate chronological data.


Megafauna bones from the Quaternary fossil record. Top: excavation of a partial skeleton of a short-faced kangaroo Procoptodon browneorum at Tight Entrance Cave (Western Australia) [1]: these bones are close to the limit of radiocarbon (14C) dating in a geological context 43000 to 49000 years old. Middle: metacarpal of the extinct horse Hippidion cf. devillei from Casa del Diablo (Peru) 14C dated at 11980 ± 100 years before present (BP) (CAMS-175039) following XAD purification of collagen gelatin [2]. Bottom: collection of skeletal remains of (mostly) red deer Cervus elaphus from El Cierro Cave (Spain) 14C dated at 15520 ± 75 years BP on ultrafiltered gelatin (OxA-27869 and OxA-27870 average) [3].


Scientists have widely been interested in the present and future state of biodiversity. Ecologists (the main audience of this blog) have also looked into the past with pioneering investigations addressing the composition of ancient forests and the origins of agriculture in layers of fossil pollen accumulated in lake sediments [4]. But it took us decades to see the fossil record as a useful tool (combining biological, geochemical and molecular techniques) to answer basic ecological questions. Some of those questions are critical for conserving today’s biodiversity [5, 6]: for example, when did human impacts on ecosystems become global or what extinct species have best tolerated past environmental change and what that means to modern species? [7].

The study of (pre)historic biological events relies one way or another on our ability to time when a certain animal, human, or plant occurred and what environmental conditions they experienced, and relies on concepts borrowed from archaeology (past human activity), palaeontology (fossils), palaeocology (species responses to past environments), and geochronology (age of fossils and/or their geological context). Among the range of chronological methods available to date biological and cultural samples [8], radiocarbon (14C) dating has become the most important for dating bones aged modern to late Quaternary (last ~ 50,000 years). Hereafter, ‘bone’ comprises antler, bone, ivory and teeth. 14C dating of bones is appealing at least for four reasons: 

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Worried about Earth’s future? Well, the outlook is worse than even scientists can grasp

14 01 2021

Daniel Mariuz/AAP

Corey J. A. Bradshaw, Flinders University; Daniel T. Blumstein, University of California, Los Angeles, and Paul Ehrlich, Stanford University

Anyone with even a passing interest in the global environment knows all is not well. But just how bad is the situation? Our new paper shows the outlook for life on Earth is more dire than is generally understood.

The research published today reviews more than 150 studies to produce a stark summary of the state of the natural world. We outline the likely future trends in biodiversity decline, mass extinction, climate disruption and planetary toxification. We clarify the gravity of the human predicament and provide a timely snapshot of the crises that must be addressed now.

The problems, all tied to human consumption and population growth, will almost certainly worsen over coming decades. The damage will be felt for centuries and threatens the survival of all species, including our own.

Our paper was authored by 17 leading scientists, including those from Flinders University, Stanford University and the University of California, Los Angeles. Our message might not be popular, and indeed is frightening. But scientists must be candid and accurate if humanity is to understand the enormity of the challenges we face.

Girl in breathing mask attached ot plant in container

Humanity must come to terms with the future we and future generations face. Shutterstock

Getting to grips with the problem

First, we reviewed the extent to which experts grasp the scale of the threats to the biosphere and its lifeforms, including humanity. Alarmingly, the research shows future environmental conditions will be far more dangerous than experts currently believe. Read the rest of this entry »





Time for a ‘cold shower’ about our ability to avoid a ghastly future

13 01 2021

I wish it need not have happened in my time,” said Frodo. “So do I,’ said Gandalf, “and so do all who live to see such times. But that is not for them to decide. All we have to decide is what to do with the time that is given us.”

Frodo Baggins and Gandalf, The Fellowship of the Ring

Today, 16 high-profile scientists and I published what I describe as a ‘cold shower’ about society’s capacity to avoid a ghastly future of warfare, disease, inequality, persecution, extinction, and suffering.

And it goes way beyond just the plight of biodiversity.

No one who knows me well would mistake me for an optimist, try as I might to use my colleagues’ and my research for good. Instead, I like to describe myself as a ‘realist’. However, this latest paper has made even my gloomier past outputs look downright hopeful.

And before being accused of sensationalism, let me make one thing abundantly clear — I sincerely hope that what we describe in this paper does not come to pass. Not even I am that masochistic.

I am also supportive of every attempt to make the world a better place, to sing about our successes, regroup effectively from our failures, and maintain hope in spite of evidence to the contrary.

But failing to acknowledge the magnitude and the gravity of the problems facing us is not just naïve, it is positively dangerous and potentially fatal.

It is this reason alone that prompted us to write our new paper “Underestimating the challenges of
avoiding a ghastly future
” just published in the new journal, Frontiers in Conservation Science.

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Cartoon guide to biodiversity loss LXIV

7 01 2021

As the pandemic rages globally, and the fragility of the American political system goes on full display, I give you the first set of biodiversity cartoons for 2021. See full stock of previous ‘Cartoon guide to biodiversity loss’ compendia here.


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Influential conservation papers of 2020

19 12 2020

Following my late-December tradition, I present — in no particular order — a retrospective list of the ‘top’ 20 influential papers of 2020 as assessed by experts in Faculty Opinions (formerly known as F1000). See previous years’ lists here: 201920182017201620152014, and 2013.


Life in fluctuating environments — “… it tackles a fundamental problem of bio-ecology (how living beings cope with the fluctuations of the environment) with a narrative that does not make use of the cumbersome formulas and complicated graphs that so often decorate articles of this kind. Instead, the narrative and the illustrations are user-friendly and easy to understand, while being highly informative.

Forest carbon sink neutralized by pervasive growth-lifespan trade-offs — “… deals with a key process in the global carbon cycle: whether climate change (CC) is enhancing the natural sink capacity of ecosystems or not.

Bending the curve of terrestrial biodiversity needs an integrated strategy — “… explores different scenarios about the consequences of habitat conversion on terrestrial biodiversity.

Rebuilding marine life — “The logic is: leave nature alone, and it will come back. Not necessarily as it was before, but it will come back.

Towards a taxonomically unbiased European Union biodiversity strategy for 2030 — “… states that the emperor has no clothes, providing an estimate of the money dedicated to biodiversity conservation (a lot of money) and then stating that the bulk of biodiversity remains unstudied and unprotected, while efforts are biased towards just a few “popular” species.

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Need to predict population trends, but can’t code? No problem

2 12 2020

Yes, yes. I know. Another R Shiny app.

However, this time I’ve strayed from my recent bibliometric musings and developed something that’s more compatible with the core of my main research and interests.

Welcome to LeslieMatrixShiny!

Over the years I’ve taught many students the basics of population modelling, with the cohort-based approaches dominating the curriculum. Of these, the simpler ‘Leslie’ (age-classified) matrix models are both the easiest to understand and for which data can often be obtained without too many dramas.

But unless you’re willing to sit down and learn the code, they can be daunting to the novice.

Sure, there are plenty of software alternatives out there, such as Bob Lacy‘s Vortex (a free individual-based model available for PCs only), Resit Akçakaya & co’s RAMAS Metapop ($; PC only), Stéphane Legendre‘s Unified Life Models (ULM; open-source; all platforms), and Charles Todd‘s Essential (open-source; PC only) to name a few. If you’re already an avid R user and already into population modelling, you might be familiar with the population-modelling packages popdemo, OptiPopd, or sPop. I’m sure there are still other good resources out there of which I’m not aware.

But, even to install the relevant software or invoke particular packages in R takes a bit of time and learning. It’s probably safe to assume that many people find the prospect daunting.

It’s for this reason that I turned my newly acquired R Shiny skills to matrix population models so that even complete coding novices can run their own stochastic population models.

I call the app LeslieMatrixShiny.

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Citizens ask the expert in climate physics

24 11 2020

In the first of two consecutive interviews with climate-change experts, authors, editors and readers of the Spanish magazine Quercus have a chat with Ken Caldeira, a global-ecology researcher at the Carnegie Institution for Science (Washington, USA). His responses attest that the climate system is complex, and that we need to be practical in dealing with the planet’s ongoing climate emergency.

PhD in atmospheric sciences and professor at Stanford University (USA), Ken Caldeira has pioneered the study of ocean acidification and its impact on coral reefs (1) and geoengineering solutions to mitigate anthropogenic climate change by extracting carbon from the atmosphere and reflecting solar radiation (2, 3). He has also been part of the Intergovernmental Panel on Climate change (IPCC) and assessed zero-emissions scenarios (4, 5). To the right, Ken manoeuvers a drone while collecting aerial data from the Great Barrier Reef in Australia (6). Source.

SARS-Covid-19 is impacting the world. In our home country, Spain, scientists argue that (i) previous budget cuts in public health have weakened our capacity to tackle the pandemic (7), and (ii) the expert panels providing advice to our government should be independent of political agendas in their membership and decisions (8). Nevertheless, the Spanish national and regional governments’ data lack the periodicity, coherence, and detail to harness an effective medical response (9). Sometimes it feels as if politics partly operate by neglecting the science needed to tackle challenges such as the covid pandemic or climate change.

Having said that, even if a country has cultivated and invested in the best science possible, people have difficulties coming to terms with the idea that scientists work with probabilities of alternative scenarios. As much as there are different ways of managing a pandemic, scientists differ about how to mitigate the ecological, economic, and health impacts of a high-carbon society.

Thus, a more and more common approach is to make collective assessments (elicitations) by weighing different points of view across experts — for instance, to establish links between climate change and armed conflict (10) or to evaluate the role of nuclear energy as we transition to a low-carbon energy-production model (11). The overarching goal is to quantify consensus based on different (evidence-based) opinions.

The questions we here ask Ken Caldeira could well have different answers if asked of other experts. Still, as Ken points out, it is urgent that (of the many options available) we use the immense and certainty-proof knowledge we have already about climate change to take actions that work.

Interview done 23 January 2020 

We italicise each question and the name of the person asking the question and cite one to three relevant publications per question. For expanding on Ken Caldeira’s views on climate change, see a sample of his public talks here and here and newspaper articles here and here.

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Cartoon guide to biodiversity loss LXIII

26 10 2020

The sixth set of biodiversity cartoons for 2020. See full stock of previous ‘Cartoon guide to biodiversity loss’ compendia here.


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