Projecting global deaths from covid19

18 03 2020

covid

I know that it’s not the best way to project expected deaths from a pandemic disease, but being something of a demographer, I just couldn’t help myself.

I therefore took the liberty of punching in some basic probabilities into our world population model to see how many people could potentially die from covid19. But this is not an epidemiological model, so I’m probably vastly over-estimating the total death rates.

Nonetheless, the results were revealing.

I first took the expected mortality by age class based on the Chinese data so far. I then assumed a worst-case scenario of a 60% infection rate (i.e., 3 out of 5 of us will eventually catch the virus). I assumed these values across the entire globe (not taking into account greater or lesser susceptibility or probability of death among countries or regions).

I also considered two more scenarios: (i) double the mortality rate (in each age class), and (ii) the disease outbreak lasting two years instead of just one.

The graph below shows the four different outcomes based on these scenarios relative to the baseline (no covid): Read the rest of this entry »





Global warming causes the worst kind of extinction domino effect

25 11 2018

Dominos_Rough1-500x303Just under two weeks ago, Giovanni Strona and I published a paper in Scientific Reports on measuring the co-extinction effect from climate change. What we found even made me — an acknowledged pessimist — stumble in shock and incredulity.

But a bit of back story is necessary before I launch into describing what we discovered.

Last year, some Oxbridge astrophysicists (David Sloan and colleagues) published a rather sensational paper in Scientific Reports claiming that life on Earth would likely survive in the face of cataclysmic astrophysical events, such as asteroid impacts, supernovae, or gamma-ray bursts. This rather extraordinary conclusion was based primarily on the remarkable physiological adaptations and tolerances to extreme conditions displayed by tardigrades— those gloriously cute, but tiny (most are around 0.5 mm long as adults) ‘water bears’ or ‘moss piglets’ — could you get any cuter names?

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Found almost everywhere and always (the first fossils of them date back to the early Cambrian over half a billion years ago), these wonderful little creatures are some of the toughest metazoans (multicellular animals) on the planet. Only a few types of extremophile bacteria are tougher.

So, boil, fry or freeze the Earth, and you’ll still have tardigrades around, concluded Sloan and colleagues.

When Giovanni first read this, and then passed the paper along to me for comment, our knee-jerk reaction as ecologists was a resounding ‘bullshit!’. Even neophyte ecologists know intuitively that because species are all interconnected in vast networks linked by trophic (who eats whom), competitive, and other ecological functions (known collectively as ‘multiplex networks’), they cannot be singled out using mere thermal tolerances to predict the probability of annihilation. Read the rest of this entry »





Postdoctoral position re-opened in Global Ecology

18 10 2017

women-are-better-codersI believe it is important to clarify a few things about the job advertisement that we are re-opening.

As many of you might recall, we advertised two positions in paleo-ecological modelling back in July — one in ecological networks, and the other in vegetation modelling.

We decided to do something a little unusual with the vegetation modelling position by only accepting applications from women. We did this expressly to increase the probability of attracting excellent women candidates, and to increase the number of women scientists in our lab.

I’m happy to say that we received many great applications for both positions, and whether or not it was related, most of the applicants for both positions were women (83%). As it turned out, we ended up offering the network position to a woman applicant, but we were unable to find an ideal candidate for the vegetation modelling job (i.e., the one that was originally targeting women only).

Our decision not to appoint anyone in the first round of applicants for the vegetation modelling position was clearly not related to the fact that it a woman-only position, mainly because we had so many excellent women candidates for both positions (and ended up hiring a woman for the position that was open to both genders). In other words, it seems to be a just one of those random things.

That said, we are still in need of a great vegetation modeller (or at least, someone who has the capacity to learn this knowledge), and so we have decided to re-open the announcement to both genders. However, it should go without saying that we particularly encourage women to apply.

The full details of the position, essential and desired criteria, and application process are available here (Vacancy Reference Number 17115). Note that the application closing date is 15 November 2017.

Please distribute this widely among your networks.

CJA Bradshaw





Two new postdoctoral positions in ecological network & vegetation modelling announced

21 07 2017

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With the official start of the new ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH) in July, I am pleased to announce two new CABAH-funded postdoctoral positions (a.k.a. Research Associates) in my global ecology lab at Flinders University in Adelaide (Flinders Modelling Node).

One of these positions is a little different, and represents something of an experiment. The Research Associate in Palaeo-Vegetation Modelling is being restricted to women candidates; in other words, we’re only accepting applications from women for this one. In a quest to improve the gender balance in my lab and in universities in general, this is a step in the right direction.

The project itself is not overly prescribed, but we would like something along the following lines of inquiry: Read the rest of this entry »





Job: Research Fellow in Palaeo-Ecological Modelling

13 04 2017

© seppo.net

I have another postdoctoral fellowship to advertise! All the details you need for applying are below.

KEY PURPOSE 

Scientific data such as fossil and archaeological records used as proxy to reconstruct past environments and biological communities (including humans) are sparse, often ambiguous or contradictory when establishing any consensus on timing or routes of initial human arrival and subsequent spread, the timing or extent of major changes in climate and other environmental perturbations, or the timing or regional pattern of biological extinctions.

The Research Fellow (Palaeo-Ecological Modelling) will assist in addressing these problems by developing state-of-the-art analytical and simulation tools to infer regional pattern of both the timing of human colonisation and megafauna extinction based on incomplete and sparse dataset, and investigating past environmental changes and human responses to identify their underlying causes and consequences on Australia’s landscapes, biodiversity and cultural history.

ORGANISATIONAL ENVIRONMENT 

The position will be based in the School of Biological Sciences in the Faculty of Science & Engineering at Flinders University. Flinders University boasts a world-class Palaeontology Research Group (PRG) and the new Global Ecology Research Laboratory that have close association with the research-intensive South Australian Museum. These research groups contribute to building a dynamic research environment that explores the continuum of environmental and evolutionary research from the ancient to modern molecular ecology and phylogeography. The School of Biological Sciences is an integrated community researching and teaching biology, and has a long history of science innovation. The appointee will join an interdisciplinary school of approximately 45 academic staff. The teaching and research activities of the School are supported by a range of technical and administrative infrastructure services.

KEY RESPONSIBILITIES

The key responsibilities and selection criteria identified for this position should be read in conjunction with the Flinders University Academic Profiles for the relevant academic classification (scroll down to Academic Profiles).

The Research Fellow (Palaeo-Ecological Modelling) will work under the direction of the Project Chief Investigator, and will be required to: Read the rest of this entry »





Job: Research Associate in Eco-epidemiological modelling

3 03 2017
myxo-rabbit

European rabbit infected with myxomatosis

Earlier this week I advertised two new PhD scholarships in palaeo-ecological modelling. Now we are pleased to advertise a six-month Research Associate position in eco-epidemiological modelling.

The position will be based in the School of Biological Sciences at Flinders University. Flinders University offers a dynamic research environment that explores the continuum of environmental and evolutionary research from the ancient to modern ecology. The School of Biological Sciences is an integrated community researching and teaching biology, and has a long history of science innovation.

Project background

Since 1996, Biosecurity South Australia has been running a capture-mark-recapture study on a European rabbit (Oryctolagus cuniculus) population located at Turretfield (~ 50 km north of Adelaide). Now into the 21st year, this is one of the world’s longest studies of its kind. Approximately every 8 weeks cage traps are reset and the population trapped over five days, with the captured rabbits weighed, sexed, tagged and blood-sampled. The study was established to investigate the epidemiology and efficacy of the two imported rabbit biocontrol agents, rabbit haemorrhagic disease virus (RHDV) and myxomatosis. To date, from 119 formal trapping events and RHDV-outbreak carcass-sampling trips, > 4500 rabbits have been monitored with > 8700 cELISA RHDV antibody tests and 7500 IgG, IgM and IgA RHDV antibody tests on sera (similarly for myxomatosis), and 111 RHDV-specific polymerase chain reaction (PCR) analyses run on tissue samples of the sampled rabbits. This represents an unparalleled dataset on rabbit survival, population fluctuations and disease dynamics. Read the rest of this entry »





No evidence climate change is to blame for Australian megafauna extinctions

29 01 2016

bw spear throwingLast July I wrote about a Science paper of ours demonstrating that there was a climate-change signal in the overall extinction pattern of megafauna across the Northern Hemisphere between about 50,000 and 10,000 years ago. In that case, it didn’t have anything to do with ice ages (sorry, Blue Sky Studios); rather, it was abrupt warming periods that exacerbated the extinction pulse instigated by human hunting.

Contrary to some appallingly researched media reports, we never claimed that these extinctions arose only from warming, because the evidence is more than clear that humans were the dominant drivers across North America, Europe and northern Asia; we simply demonstrated that warming periods had a role to play too.

A cursory glance at the title of this post without appreciating the complexity of how extinctions happen might lead you to think that we’re all over the shop with the role of climate change. Nothing could be farther from the truth.

Instead, we report what the evidence actually says, instead of making up stories to suit our preconceptions.

So it is with great pleasure that I report our new paper just out in Nature Communications, led by my affable French postdoc, Dr Frédérik SaltréClimate change not to blame for late Quaternary megafauna extinctions in Australia.

Of course, it was a huge collaborative effort by a crack team of ecologists, palaeontologists, geochronologists, paleo-climatologists, archaeologists and geneticists. Only by combining the efforts of this diverse and transdisciplinary team could we have hoped to achieve what we did. Read the rest of this entry »





All (fisheries) models are wrong, but some are useful (to indigenous people)

1 08 2015

miracle_cartoonAnother post from Alejandro Frid. (Note: title modified from George Box‘s most excellent quote).

As an ecologist working for indigenous people of coastal British Columbia, western Canada, I live at the interface of two worlds. On the one hand, I know that computer models can be important management tools. On the other hand, my job constantly reminds me that whether a model actually improves fishery management depends, fundamentally, on the worldview that shapes the model’s objectives. To explore why, I will first review some general concepts about what models can and cannot do. After that, I will summarize a recent model of herring populations and then pull it all together in a way that matters to indigenous people who rely on marine resources for cultural integrity and food security.

Models do a great job of distilling the essence of how an ecosystem might respond to external forces—such as fisheries—but only under the specific conditions that the modeller assumes to be true in the ‘world’ of the model. Sometimes these assumptions are well-grounded in reality. Sometimes they are blatant but necessary simplifications. Otherwise, it would be difficult to ask questions about how major forces for which we have no historical precedent—such as the combined effects of industrial fisheries, ocean acidification and climate change—might be altering the ocean. For instance, due to our greenhouse gas emissions, the ocean is warming and contains less dissolved oxygen. These stressful conditions hamper the capacity of fish to grow, and appear to be on their way to shrinking the body sizes of entire fish communities1. If you want even to begin to comprehend what the ocean will look like in the long term due to these effects of climate change, it makes sense to assume, in the ‘world’ of your model, that fishing does not exist, even though you know it does. Of course, you would then acknowledge that climate change probably exacerbates the effects of fisheries, which highlights that you still have to examine the combination of these effects. And that is exactly what an excellent team of modellers did1. Read the rest of this entry »





Upcoming conservation, ecology and modelling conferences

7 03 2014

IMG_34271Our lab just put together a handy list of upcoming ecology, conservation and modelling conferences around the world in 2014. Others might also find it useful. Some of the abstract submission deadlines have already passed, but it still might be useful to know what’s on the immediate horizon if attendance only is an option.

Conference Dates Venue Call for Abstracts Deadline
Queensland Ornithological Conference 31 May Brisbane, Australia Open 10 Mar
Spatial Ecology and Conservation 17 Jun Birmingham, UK Closed 21 Feb
Asia-Pacific Coral Reef Symposium 23 Jun Taiwan Closed 5 Feb
International Statistical Ecology Conference 1 Jul Montpellier, France Closed 13 Jan
International Institute of Fisheries Economics & Trade 2014 7 Jul Brisbane Closed 31 Jan
World Conference on Natural Resource Modeling 8 Jul Vilnius, Lithuania Open 31 Mar
Society for Conservation Biology Oceania Section 9 Jul Suva, Fiji Open 7 Mar Read the rest of this entry »




Where the sick buffalo roam

28 10 2011

It’s been some time coming, but today I’m proud to announce a new paper of ours that has just come out in Journal of Applied Ecology. While not strictly a conservation paper, it does provide some novel tools for modelling populations of threatened species in ways not available before.

The Genesis

A few years ago, a few of us (Bob LacyPhil Miller and JP Pollak of Vortex fame, Barry Brook, and a few others) got together in a little room at the Brookfield Zoo in the suburban sprawl of Chicago to have a crack at some new modelling approaches the Vortex crew had recently designed. The original results were pleasing, so we had a follow-up meeting last year (thanks to a few generous Zoo benefactors) and added a few post-docs and students to the mix (Damien FordhamClive McMahon, Tom Prowse, Mike Watts, Michelle Verant). The great population modeller Resit Akçakaya also came along to assist and talk about linkages with RAMAS.

Out of that particular meeting a series of projects was spawned, and one of those has now been published online: Novel coupling of individual-based epidemiological and demographic models predicts realistic dynamics of tuberculosis in alien buffalo.

The Coupling

So what’s so novel about modelling disease in buffalo, and why would one care? Well, here’s the interesting part. The buffalo-tuberculosis example was a great way to examine just how well a new suite of models – and their command-centre module – predicted disease dynamics in a wild population. The individual-based population modelling software Vortex has been around for some time, and is now particularly powerful for predicting the extinction risk of small populations; the newest addition to the Vortex family, called Outbreak, is also an individual-based epidemiological model that allows a population of individuals exposed to a pathogen to progress over time (e.g., from susceptible, exposed, infectious, recovered/dead). Read the rest of this entry »





Webinar: Modelling water and life

27 08 2010

Another quick one today just to show the webinar of my recent 10-minute ‘Four in 40’ talk sponsored by The Environment Institute and the Department for Water. This seminar series was entitled ‘Modelling as a Tool for Decision Support’ held at the Auditorium, Royal Institution Australia (RiAus).

“Four in 40″ is a collaboration between The University of Adelaide and the Department for Water, where 4 speakers each speak for 10 minutes on their research and its implications for policy. The purpose is to build understanding of how best to work with each other, build new business for both organisations and raise awareness of activity being undertaken in water/natural resource management policy and research.

CJA Bradshaw





Long, deep and broad

24 08 2010

© T. Holub Flickr

Thought that would get your attention ;-)

More scientists need to be trained in quantitative synthesis, visualization and other software tools.” D. Peters (2010)

In fact, that is part of the title of today’s focus paper in Trends in Ecology and Evolution by D. Peters – Accessible ecology: synthesis of the long, deep,and broad.

As a ‘quantitative’ ecologist (modeller, numerate, etc.) whose career has been based to a large degree on the analysis of large ecological datasets, I am certainly singing Peters’ tune. However, it’s much deeper and more important than my career – good (long, deep, broad – see definitions below) ecological data are ESSENTIAL to avoid some of the worst ravages of biodiversity loss over the coming decades and centuries. Unfortunately, investment in long-term ecological studies is poor in most countries (Australia is no exception), and it’s not improving.

But why are long-term ecological data essential? Let’s take a notable example. Climate change (mainly temperature increases) measured over the last century or so (depending on the area) has been determined mainly through the analysis of long-term records. This, one of the world’s most important (yet sadly, not yet even remotely acted upon) issues today, derives from relatively simple long-term datasets. Another good example is the waning of the world’s forests (see posts herehere and here for examples) and our increasing political attention on what this means for human society. These trends can only be determined from long-term datasets.

For a long time the dirty word ‘monitoring’ was considered the bastion of the uncreative and amateur – ‘real’ scientists performed complicated experiments, whereas ‘monitoring’ was viewed mainly as a form of low-intellect showcasing to please someone somewhere that at least something was being done. I’ll admit, there are many monitoring programmes producing data that aren’t worth the paper their printed on (see a good discussion of this issue in ‘Monitoring does not always count‘), but I think the value of good monitoring data has been mostly vindicated. You see, many ecological systems are far too complex to manipulate easily, or are too broad and interactive to determine much with only a few years of data; only by examining over the ‘long’ term do patterns (and the effect of extremes) sometimes become clear.

But as you’ll see, it’s not just the ‘long’ that is required to determine which land- and sea-use decisions will be the best to minimise biodiversity loss – we also need the ‘deep’ and the ‘broad’. But first, the ‘long’. Read the rest of this entry »





Linking disease, demography and climate

1 08 2010

Last week I mentioned that a group of us from Australia were travelling to Chicago to work with Bob Lacy, Phil Miller, JP Pollak and Resit Akcakaya to make some pretty exciting developments in next-generation conservation ecology and management software. Also attending were Barry Brook, our postdocs: Damien Fordham, Thomas Prowse and Mike Watts, our colleague (and former postdoc) Clive McMahon, and a student of Phil’s, Michelle Verant. At the closing of the week-long workshop, I thought I’d share my thoughts on how it all went.

In a word, it was ‘productive’. It’s not often that you can spend 1 week locked in a tiny room with 10 other geeks and produce so many good and state-of-the-art models, but we certainly achieved more than we had anticipated.

Let me explain in brief why it’s so exciting. First, I must say that even the semi-quantitative among you should be ready for the appearance of ‘Meta-Model Manager (MMM)’ in the coming months. This clever piece of software was devised by JP, Bob and Phil to make disparate models ‘talk’ to each other during a population projection run. We had dabbled with MMM a little last year, but its value really came to light this week.

We used MMM to combine several different models that individually fail to capture the full behaviour of a population. Most of you will be familiar with the individual-based population viability (PVA) software Vortex that allows relatively easy PVA model building and is particular useful for predicting extinction risk of small populations. What you most likely don’t know exists is what Phil, Bob and JP call Outbreak – an epidemiological modelling software based on the classic susceptible-exposed-infectious-recovered framework. Outbreak is also an individual-based model that can talk directly to Vortex, but only through MMM. Read the rest of this entry »