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.

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Logbook of Australia’s ancient megafauna

20 11 2019


Australia is home to some of the most unique species worldwide, including egg-laying mammals, tree-climbing, desert-bouncing and and burrow-digging marsupials, and huge flightless birds. While these animals are fascinating, the creatures that used to roam Australia’s landscape thousands of years ago were even more remarkable — these included wombat-like beasts as big as rhinos, birds more than two metres tall, lizards more than seven metres long, and a marsupial lion as big as a leopard.

Just how and why these animals went extinct has been challenging scientists for decades. But examining dated fossil records is one of the primary ways we can look into the past. The ever-increasing number of fossils and the advances in dating techniques have produced a wealth of material we can use to reconstruct the long-lost past.

DiprotodonEven with these data, it has been a struggle to gather enough fossils for large-scale analyses because reports of these records are usually scattered across the scientific literature, with no standardised quality control to make them comparable to each other. Designing a way to standardise these records is therefore important to avoid misleading conclusions.

The FosSahul database was first established in 2016 to try to alleviate these problems — it gathered all the fossil specimens for large animals (excluding humans) from the Late Quaternary (up to ~ 1 million years before present) across the region known as ‘Sahul’, the combined super-continent that included New Guinea and Australia when sea levels were much lower than they are today.

While FosSahul was an important step, the database needed to be updated. First, the quality rating of the fossil dates in the original version was a little subjective and lacked transparency in some cases. This is because the database did not capture enough detail to be able to reproduce all the steps leading to a particular quality rating. Second, given that new fossils are discovered regularly, updates are necessary to include the latest research. Read the rest of this entry »

Bad science

10 02 2016

Head in HandsIn addition to the surpassing coolness of reconstructing long-gone ecosystems, my new-found enthusiasm for palaeo-ecology has another advantage — most of the species under investigation are already extinct.

That might not sound like an ‘advantage’, but let’s face it, modern conservation ecology can be bloody depressing, so much so that one sometimes wonders if it’s worth it. It is, of course, but there’s something marvellously relieving about studying extinct systems for the simple reason that there are no political repercussions. No self-serving, plutotheocratic politician can bugger up these systems any more. That’s a refreshing change from the doom and gloom of modern environmental science!

But it’s not all sweetness and light, of course; there are still people involved, and people sometimes make bad decisions in an attempt to modify the facts to suit their creed. The problem is when these people are the actual scientists involved in the generation of the ‘facts’.

As I alluded to a few weeks ago with the publication of our paper in Nature Communications describing the lack of evidence for a climate effect on the continental-scale extinctions of Australia’s megafauna, we have a follow-up paper that has just been published online in Proceedings of the Royal Society B — What caused extinction of the Pleistocene megafauna of Sahul? led by Chris Johnson of the University of Tasmania.

After our paper published earlier this month, this title might seem a bit rhetorical, so I want to highlight some of the reasons why we wrote the review. Read the rest of this entry »

An appeal to extinction chronologists

2 06 2015

u7Pi3Extinction is forever, right? Yes, it’s true that once the last individual of a species dies (apart from insane notions that de-extinction will do anything to resurrect a species in perpetuity), the species is extinct. However, the answer can also be ‘no’ when you are limited by poor sampling. In other words, when you think something went extinct when in reality you just missed it.

Most of you are familiar with the concept of Lazarus1 species – when we’ve thought of something long extinct that suddenly gets re-discovered by a wandering naturalist or a wayward fisher. In paleontological (and modern conservation biological) terms, the problem is formally described as the ‘Signor-Lipps’ effect, named2 after two American palaeontologists, Phil Signor3 and Jere Lipps. It’s a fairly simple concept, but it’s unfortunately ignored in most palaeontological, and to a lesser extent, conservation studies.

The Signor-Lipps effect arises because the last (or first) evidence (fossil or sighting) of a species presence has a nearly zero chance of heralding its actual timing of extinction (or appearance). In paleontological terms, it’s easy to see why. Fossilisation is in fact a nearly impossible phenomenon – all the right conditions have to be in place for a once-living biological organism to be fossilised: it either has to be buried quickly, in a place where nothing can decompose it (usually, an anoxic environment), and then turned to rock by the process of mineral replacement. It then has to resist transformation by not undergoing metamorphosis (e.g., vulcanism, extensive crushing, etc.). For more recent specimens, preservation can occur without the mineralisation process itself (e.g., bones or flesh in an anoxic bog). Then the bloody things have to be found by a diligent geologist or palaeontologist! In other words, the chances that any one organism is preserved as a fossil after it dies are extremely small. In more modern terms, individuals can go undetected if they are extremely rare or remote, such that sighting records alone are usually insufficient to establish the true timing of extinction. The dodo is a great example of this problem. Remember too that all this works in reverse – the first fossil or observation is very much unlikely to be the first time that the species was there. Read the rest of this entry »

Dawn of life

18 05 2015

Looking east toward the northern Flinders Ranges from Ediacara Conservation Park. © CJA Bradshaw

Looking east toward the northern Flinders Ranges from Ediacara Conservation Park. © CJA Bradshaw

I’ve had one of the most mind-blowing weeks of scientific discovery in my career, and it’s not even about a subject from within my field.

As some of you might know, I’ve been getting more and more interested in palaeo-ecology over the past few years. I’m fascinated by the challenge of reconstructing past communities and understanding how and why they changed. It’s a natural progression for someone interested in modern extinction dynamics.

Most of my recent interests have focussed on palaeo-communities of the Late Quaternary, and mainly in the range of 100 thousand years ago to the present. We’ve started publishing a few things in this area, and I can confirm that they’ll be plenty more to come in the following months and years. Despite plenty more to do in the youngest of palaeo-communities, I’ve now been bitten by the deep-time bug.

The giant Dickinsonia rex - a flat, worm-like discoid animal. © D. García-Bellido

The giant Dickinsonia rex – a flat, worm-like discoid animal. © D. García-Bellido

When I write ‘deep time’, I bloody well mean it: back to 580 million years, to be accurate. This is the time before the great Cambrian explosion of life popularised by the late Stephen Jay Gould in his brilliant book, Wonderful Life1,2. I’m talking about the Ediacaran period from 635-541 million years ago.

I’ve lived in South Australia now for over seven years, but it was only in the last few that I realised the Ediacaran was named after the Ediacara Hills in the northern Flinders Ranges some 650 km north of Adelaide where I live, and it wasn’t until last week that I had the extremely gratifying privilege of visiting the region with some of the world’s top Ediacaran specialists. If you have even the remotest interest in geological time and the origin of life on Earth, you should make a pilgrimage to the Flinders Ranges at some point before you die.

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