Correcting times for light exposure across spatial extents

30 03 2022

The other day I was tasked with revising a figure for a paper (that should be out soon) where I had to figure out how to compare incident times in a biologically meaningful way.

Without giving away too many details, we had a long list of incidents spread right across Australia, covering all periods of the year and going back to the early 20th Century. The specifics of the ‘incidents’ isn’t important here — suffice it to say they were biological in nature, and we wanted to see if they were clustered around any particular times of the day.

Yes, we could just do a histogram of the time bins (say, every 2 hours), but this ignores a very important phenomenon — 17:00 in July in Hobart isn’t directly comparable to 17:00 in January in Darwin (and so on). What matters instead — from a biological/phenological perspective — is the period of day in terms of available light.

Fortunately, there are some clear definitions of relative light availability we can use.

‘Night’ is defined as the time between astronomical dusk and astronomical dawn, which are when the sun is 18º below the horizon. ‘Twilight’ is the period between night and sunrise/sunset (the latter being when the sun first appears/disappears above/below the horizon), further broken down into three periods: astronomical twilight, nautical twilight, and civil twilight. These latter refer to when the sun is 18º, 12º, and 6º below the horizon, respectively.

It’s still ‘dark’ in astronomical twilight, but light starts to be discernible at the start of nautical twilight. We can therefore define four major periods of relative light availability per 24-hour period: night (between the start of astronomical dusk and end of astronomical dawn), dawn (between the end of nautical twilight and sunrise), day (between sunrise and sunset), and dusk (between sunset and the onset of astronomical twilight).


So, after all that malarkey, now we need a way of determining when those transition periods occur on any given day in any given location. Sounds difficult, but, there’s a function for that!

Read the rest of this entry »

Be wise about what you put online

21 03 2022

While you have little choice these days about posting your data and code online when you publish, here are some things to consider when contemplating putting potentially sensitive data online (modified excerpt from The Effective Scientist).

One aspect of making your data publicly available is the prickly issue of whether your data contain sensitive information.

Of course, there are many different types of ‘sensitive’ information that might accompany the more basic quantitative measurements of your datasets, with perhaps the most common being personal details of any human subjects. For example, if you are a medical researcher and your data are derived primarily from living human beings undergoing some procedure, trial, or intervention, then clearly you are bound by your human ethics approvals not to publish information like names, addresses, or anything that could be used to identify the subjects in your sample. In fact, human ethics approvals generally prohibit any sort of public accessibility to medical data that has personal information included; thus, the scientists concerned are being pulled in two different directions — keeping their subjects’ personal information out of the hands of the public, while still making the data available to other scientists.

There are ways around this, such as publishing only generic information online (i.e., by excluding personal identifiers) that could then be linked to the more sensitive data via unique identifiers. In these cases, any other researcher requiring the additional information would have to seek specific permission from the primary researchers, pending additional human-ethics approvals.

Read the rest of this entry »

Can we resurrect the thylacine? Maybe, but it won’t help the global extinction crisis

9 03 2022


(published first on The Conversation)

Last week, researchers at the University of Melbourne announced that thylacines or Tasmanian tigers, the Australian marsupial predators extinct since the 1930s, could one day be ushered back to life.

The thylacine (Thylacinus cynocephalus), also known as the ‘Tasmanian tiger’ (it was neither Tasmanian, because it was once common in mainland Australia, nor was it related to the tiger), went extinct in Tasmania in the 1930s from persecution by farmers and habitat loss. Art by Eleanor (Nellie) Pease, University of Queensland.
Centre of Excellence for Australian Biodiversity and Heritage

The main reason for the optimism was the receipt of a A$5 million philanthropic donation to the research team behind the endeavour.

Advances in mapping the genome of the thylacine and its living relative the numbat have made the prospect of re-animating the species seem real. As an ecologist, I would personally relish the opportunity to see a living specimen.

The announcement led to some overhyped headlines about the imminent resurrection of the species. But the idea of “de-extinction” faces a variety of technical, ethical and ecological challenges. Critics (like myself) argue it diverts attention and resources from the urgent and achievable task of preventing still-living species from becoming extinct.

The rebirth of the bucardo

The idea of de-extinction goes back at least to the the creation of the San Diego Frozen Zoo in the early 1970s. This project aimed to freeze blood, DNA, tissue, cells, eggs and sperm from exotic and endangered species in the hope of one day recreating them.

The notion gained broad public attention with the first of the Jurassic Park films in 1993. The famous cloning of Dolly the sheep reported in 1996 created a sense that the necessary know-how wasn’t too far off.

The next technological leap came in 2008, with the cloning of a dead mouse that had been frozen at –20℃ for 16 years. If frozen individuals could be cloned, re-animation of a whole species seemed possible.

After this achievement, de-extinction began to look like a potential way to tackle the modern global extinction crisis.

Read the rest of this entry »

The integrity battlefield: where science meets policy

4 03 2022

Professor Ross Thompson, University of Canberra

On the whole, I am inclined to conclude that my experience of academia and publishing my work has been largely benign. Despite having published 120-odd peer-reviewed papers, I can count the number of major disputes on one hand. Where there have been disagreements, they have centred on issues of content, and despite the odd grumble, things have rarely escalated to the ad hominem. I have certainly never experienced concerted attacks on my work.

But that changed recently. I work in water science, participating in and leading multi-disciplinary teams that do research directly relevant to water policy and management. My colleagues and I work closely with state and federal governments and are often funded by them through a variety of mechanisms. Our teams are a complex blend of scientists from universities, state and federal research agencies, and private-sector consultancies. Water is big business in Australia, and its management is particularly pertinent as the world’s driest inhabited continent struggles to come to terms with the impacts of climate change.

In the last 10 years, Australia has undergone a AU$16 billion program of water reform that has highlighted the extreme pressure on ecosystems, rural communities, and water-dependent industries. In 2019, two documentaries (Cash Splash and Pumped) broadcast by the Australian Broadcasting Corporation were highly critical of the  outcomes of water reform. A group of scientists involved in working on the Murray-Darling Basin were concerned enough about the accuracy of aspects of those stories to support Professor Rob Vertessy from the University of Melbourne in drafting an Open Letter in response. I was a co-author on that letter, and something into which I did not enter lightly. We were very concerned about being seen to advocate for any particular policy position, but were simultaneously committed to contributing to an informed public debate. A later investigation by the Australian Communications and Media Authority also highlighted concerns with the Cash Splash documentary.

Fast forward to 2021 and the publication of a paper by Colloff et al. (2021) in the Australasian Journal of Water Resources. In that paper, the authors were critical of the scientists that had contributed to the Open Letter and claimed they had been subject to “administrative capture” and “issue advocacy”. Administrative capture is defined here as:

Read the rest of this entry »

The sixth mass extinction is happening now, and it doesn’t look good for us

2 03 2022

Mounting evidence is pointing to the world having entered a sixth mass extinction. If the current rate of extinction continues we could lose most species by 2200. The implication for human health and wellbeing is dire, but not inevitable.

In the timeline of fossil evidence going right back to the first inkling of any life on Earth — over 3.5 billion years ago — almost 99 percent of all species that have ever existed are now extinct. That means that as species evolve over time — a process known as ‘speciation’ — they replace other species that go extinct.

Extinctions and speciations do not happen at uniform rates through time; instead, they tend to occur in large pulses interspersed by long periods of relative stability. These extinction pulses are what scientists refer to as mass extinction events.

The Cambrian explosion was a burst of speciation some 540 million years ago. Since then, at least five mass extinction events have been identified in the fossil record (and probably scores of smaller ones). Arguably the most infamous of these was when a giant asteroid smashed into Earth about 66 million years ago in what is now the Gulf of Mexico. The collision vapourised species immediately within the blast zone. Later, species were killed off by climate change arising from pulverised particulates suspended in the atmosphere, as well as intense volcano activity stimulated by the buckling of the Earth’s crust from the asteroid’s impact. Together, about 76 percent of all species around at the time went extinct, of which the disappearance of the dinosaurs is most well-known. But dinosaurs didn’t disappear altogether — the survivors just evolved into birds.

Read the rest of this entry »

%d bloggers like this: