Tropical forest resilience depends on past disturbance frequency

16 07 2014

I’ve recently come across an interesting study that perfectly marries palaeo-ecological data with modern conservation philosophy. It’s not often that such a prehistorical perspective dating at least to the Last Glacial Maximum has been used so effectively to inform future conservation outlooks. I’m particularly interested in this sort of approach considering my own palaeo dabblings of late.

Published in Nature Communications this May, Lydia Cole and colleagues’ paper Recovery and resilience of tropical forests after disturbance is a meta-analysis of 71 studies covering nearly 300 disturbance events in tropical forests over the last 20,000 years or so. Using fossil pollen records as an index of vegetation change, they demonstrated the (somewhat intuitive) main result that the time to recovery following a disturbance generally decreases as the past disturbance frequency increased.

This appears to be a vindication of the idea that a system’s adaptive strategies evolve as a product of the local disturbance regime. More importantly, they found that recovery was faster following ‘large infrequent events’, which are natural perturbations such as cyclones and major fires. While most past disturbances were caused by humans clearing forest, the fact that tropical forest systems were most resilient to ‘natural’ events means that if we can’t stop human disturbances, at least we can attempt to emulate natural processes to maximise the rebound potential. Much like many modern forestry operations try to emulate natural disturbances to limit their damage, we should at least manage our impacts by understanding so-called ‘natural’ regimes as much as possible. Read the rest of this entry »

Be a good reviewer, but be a better editor

6 06 2014


Perhaps it’s just that I’ve been at this for a while, or maybe it’s a real trend. Regardless, many of my colleagues and I are now of the opinion that the quality of editing in scientific journals is on the downhill slide.

Yes – we (scientists) all complain about negative decisions from journals to which we’ve submitted our work. Being rejected is part of the process. Aiming high is necessary for academic success, but when a negative decision is made on the basis of (often one) appalling review, it’s a little harder to swallow.

I suppose I can accept the inevitability of declining review quality for the simple reason that there are now SO MANY papers to review that finding willing volunteers is difficult. This means that there will always be people who only glance cursorily at the paper, miss the detail and recommend rejection based on their own misunderstanding or bias. It’s far easier to skim a paper and try to find a reason to reject than actually putting in the time to appraise the work critically and fairly.

This means that the traditional model of basing the decision to accept or reject a manuscript on only two reviews is fraught because the probability of receiving poor reviews is rising. For example, a certain undisclosed journal of unquestionably high quality for which I edit does not accept anything less than six recommendations for reviewers per manuscript, and none that I’m aware of is accepted or rejected based on only two reviews. But I think this is the exception rather than the rule – there are simply too many journals now of low to medium quality to be able to get that many reviewers to agree to review.

I won’t spend too much time trying to encourage you to do the best job you can when reviewing – that should go without saying. Remember what goes around comes around. If you are a shit reviewer, you will receive shit reviews. Read the rest of this entry »

School finishers and undergraduates ill-prepared for research careers

22 05 2014

bad mathsHaving been for years now at the pointy end of the educational pathway training the next generation of scientists, I’d like to share some of my observations regarding how well we’re doing. At least in Australia, my realistic assessment of science education is: not well at all.

I’ve been thinking about this for some time, but only now decided to put my thoughts into words as the train wreck of our current government lurches toward a future guaranteeing an even stupider society. Charging postgraduate students to do PhDs for the first time, encouraging a US-style system of wealth-based educational privilege, slashing education budgets and de-investing in science while promoting the belief in invisible spaghetti monsters from space, are all the latest in the Fiberal future nightmare that will change our motto to “Australia – the stupid country”.

As you can appreciate, I’m not filled with a lot of hope that the worrying trends I’ve observed over the past 10 years or so are going to get any better any time soon. To be fair though, the problems go beyond the latest stupidities of the Fiberal government.

My realisation that there was a problem has crystallised only recently as I began to notice that most of my lab members were not Australian. In fact, the percentage of Australian PhD students and post-doctoral fellows in the lab usually hovers around 20%. Another sign of a problem was that even when we advertised for several well-paid postdoctoral positions, not a single Australian made the interview list (in fact, few Australians applied at all). I’ve also talked to many of my colleagues around Australia in the field of quantitative ecology, and many lament the same general trend.

Is it just poor mathematical training? Yes and no. Australian universities have generally lowered their entry-level requirements for basic maths, thereby perpetuating the already poor skill base of school leavers. Why? Bums (that pay) on seats. This means that people like me struggle to find Australian candidates that can do the quantitative research we need done. We are therefore forced to look overseas. Read the rest of this entry »

Putting the ‘science’ in citizen science

30 04 2014
How to tell if a koala has been in your garden. © Great Koala Count

How to tell if a koala has been in your garden. © Great Koala Count

When I was in Finland last year, I had the pleasure of meeting Tomas Roslin and hearing him describe his Finland-wide citizen-science project on dung beetles. What impressed me most was that it completely flipped my general opinion about citizen science and showed me that the process can be useful.

I’m not trying to sound arrogant or scientifically elitist here – I’m merely stating that it was my opinion that most citizen-science endeavours fail to provide truly novel, useful and rigorous data for scientific hypothesis testing. Well, I must admit that I still believe that ‘most’ citizen-science data meet that description (although there are exceptions – see here for an example), but Tomas’ success showed me just how good they can be.

So what’s the problem with citizen science? Nothing, in principle; in fact, it’s a great idea. Convince keen amateur naturalists over a wide area to observe (as objectively) as possible some ecological phenomenon or function, record the data, and submit it to a scientist to test some brilliant hypothesis. If it works, chances are the data are of much broader coverage and more intensively sampled than could ever be done (or afforded) by a single scientific team alone. So why don’t we do this all the time?

If you’re a scientist, I don’t need to tell you how difficult it is to design a good experimental sampling regime, how even more difficult it is to ensure objectivity and precision when sampling, and the fastidiousness with which the data must be recorded and organised digitally for final analysis. And that’s just for trained scientists! Imagine an army of well-intentioned, but largely inexperienced samplers, you can quickly visualise how the errors might accumulate exponentially in a dataset so that it eventually becomes too unreliable for any real scientific application.

So for these reasons, I’ve been largely reluctant to engage with large-scale citizen-science endeavours. However, I’m proud to say that I have now published my first paper based entirely on citizen science data! Call me a hypocrite (or a slow learner). Read the rest of this entry »

Alliance of Leading Environmental Researchers and Thinkers

11 03 2014

ALERTIf you’ve been following this blog or my Twitter feed over the last few weeks, you’ve surely noticed a few references to A.L.E.R.T. – the Alliance of Leading Environmental Researchers and Thinkers. You might also have asked yourself, what exactly is ALERT, and is it something I should pay attention to?

Today’s post attempts to explain this new organisation, and hopefully convince you that the answer to the second question is ‘yes’.

Several months ago, a slightly cryptic e-mail from eminent conservation biologist, Bill Laurance, arrived in my inbox. It asked – what do you think of this logo (see associated image)? A few e-mails later and a couple of minor tweaks, and we ended up with what I thought was a pretty cool logo for this new ‘ALERT’ thing. It wasn’t until quite some time later that I finally understood what Bill was attempting to create.

Is ALERT a news aggregator, a blog, an advocacy group, a science-communication resource or a science-policy interface? Why, yes it is!

Read the rest of this entry »

Biowealth: all creatures great and small

4 12 2013

Curious Country flyer“So consider the crocodiles, sharks and snakes, the small and the squirmy, the smelly, slimy and scaly. Consider the fanged and the hairy, the ugly and the cute alike. The more we degrade this astonishing diversity of evolved life and all its interactions on our only home, the more we expose ourselves to the ravages of a universe that is inherently hostile to life.”

excerpt from ‘Biowealth: all creatures great and small’ The Curious Country (C.J.A. Bradshaw 2013).

I’ve spent the last few days on the east coast with my science partner-in-crime, Barry Brook, and one of our newest research associates (Marta Rodrigues-Rey Gomez). We first flew into Sydney at sparrow’s on Monday, then drove a hire car down to The ‘Gong to follow up on some Australian megafauna databasing & writing with Bert Roberts & Zenobia Jacobs. On Tuesday morning we then flitted over to Canberra where we had the opportunity to attend the official launch of a new book that Barry and I had co-authored.

The book, The Curious Country, is an interesting experiment in science communication and teaching dreamed up by Australia’s Chief Scientist, Professor Ian Chubb. Realising that the average Aussie has quite a few questions about ‘how stuff works’, but has little idea how to answer those questions, Ian engaged former Quantum star and science editor, Leigh Dayton, to put together a short, punchy, topical and easily understood book about why science is good for the country.

Yes, intuitive for most of you out there reading this, but science appreciation isn’t always as high as it should be amongst the so-called ‘general public’. Ian thought this might be one way to get more people engaged.

When honoured with the request to write an interesting chapter on biodiversity for the book, I naturally accepted. It turns out Barry was asked to do one on energy provision at the same time (but we didn’t know we had both been asked at the time). Our former lab head, Professor David Bowman, was also asked to write a chapter about fire risk, so it was like a mini-reunion yesterday for the three of us.

Read the rest of this entry »

King for a day – what conservation policies would you make?

29 11 2013

CrownI have been thinking a lot lately about poor governance and bad choices when it comes to biodiversity conservation policy. Perhaps its all that latent anger arising from blinkered, backward policies recently implemented by conservative state and national governments in Australia and elsewhere that leads me to contemplate: What would I do if I had the power to change policy?

While I am certain I have neither the experience or complete knowledge to balance national budgets, ensure prosperity and maintain the health of an entire country, I do have some ideas about what we’re doing wrong conservation-wise, and how we could potentially fix things. This is not meant to be an exhaustive list – it is more a discussion point where people can suggest their own ideas.

So here are 16 things I’d change or implement (mainly in Australia) if I were king for a day:

Read the rest of this entry »

Making the scientific workshop work

28 10 2013
I don't mean this

I don’t mean this

I’ve been a little delayed in blogging this month, but for a very good reason – I’ve just experienced one of the best workshops of my career. I’d like to share a little of that perfect science recipe with you now.

I’ve said it before, but it can stand being repeated: done right, workshops can be some of the most efficient structures for doing big science.

First, let me define ‘workshop’ for those of you who might have only a vague notion of what it entails. To me, a workshop is a small group of like-minded scientists – all of whom possess different skills and specialities – who are brought together to achieve one goal. That goal is writing the superlative manuscript for publication.

So I don’t mean just a bog-standard chin-wag infected with motherhoods and diatribes. Workshops are not mini-conferences; neither are they soap boxes. It is my personal view that nothing can waste a scientist’s precious time more than an ill-planned and aimless workshop.

But with a little planning and some key ingredients that I’ll list shortly, you can turn a moderately good idea into something that can potentially shake the foundations of an entire discipline. So what are these secret ingredients? Read the rest of this entry »

Making science matter

14 10 2013


I’ve been home from my last overseas trip now for nearly two weeks, but despite not feeling caught up, it’s high time I report what I was up to.

Some of you who follow my Twitter feed or who saw a CB post about cartoonist Seppo Leinonen know that I was visiting the University of Helsinki to participate in a three-day short course for PhD students entitled ‘Making Science Matter‘. I was so impressed with how well Mar Cabeza and Tomas Roslin put together the course, that I thought I’d share the format with CB readers (just in case any of you out there can be convinced to design a similar course at your university).

I think it’s important first to discuss the philosophy of the course and what it hoped to provide those early-career researchers.

Most science PhD students will tell you once they’ve completed their degree that they feel completely unprepared to launch themselves into the extra-curricular world of communicating their science beyond the ‘traditional’ (peer-reviewed journals) outlets. Swamped with learning how to write concisely and clearly, getting up to speed with the entire body of theory on which their projects are based, mastering advanced modelling and statistical approaches and learning how to apply efficient computer code, it’s no wonder that many students find precious little time for anything else (including families, good food and proper hygiene).

Once they do land that precious post-doctoral fellowship though, they are immediately expected to interact professionally with the media, embrace social media and give fantastic public lectures to engage the uninformed. Right. Read the rest of this entry »

Early to press is best for success

19 09 2013

publishingThis paper is bound to piss off a few people. So be it. This is what we found, regardless of what you want to believe.

Led by the extremely prolific Bill Laurance, we have just published a paper (online early) that looks at the correlates of publication success for biologists.

I have to preface the main message with a little philosophical discussion of that loaded word – ‘success’. What do we mean by scientific ‘success’? There are several bucket loads of studies that have attempted to get at this question, and several more that have lamented the current system that emphasises publication, publication, publication. Some have even argued that the obsession of ever-more-frequent publication has harmed scientific advancement because of our preoccupation with superficial metrics at the expense of in-depth scientific enquiry.

Well, one can argue these points of view, and empirically support the position that publication frequency is a poor metric. I tend to agree. At the same time, I am not aware of a single scientist known for her or his important scientific contributions that doesn’t have a prolific publication output. No, publishing shitloads of papers won’t win you the Nobel Prize, but if you don’t publish, you won’t win either.

So, publication frequency is certainly correlated with success, even if it’s not the perfect indicator. But my post today isn’t really about that issue. If you accept that writing papers is part of a scientist’s job, then read on. If you don’t, well …

So today I report the result of our study published online in BioScience, Predicting publication success for biologists. We asked the question: what makes someone publish more than someone else? Read the rest of this entry »

Fast-lane mesopredators

29 07 2013

Another post from Alejandro Frid (a modified excerpt from a chapter of his forthcoming book).

I fall in love easy. Must be my Latino upbringing. Whatever it is, I have no choice on the matter. So for five years and counting, I have been passionate about lingcod (Ophiodon elongatus) and rockfish (Sebastes spp.), upper- and mid-level predatory fishes on rocky reefs of the Northeast Pacific.

Lingcod are beautiful and fierce. Rockfish are cosmic. Both taste mighty good and—surprise, surprise—have been overfished to smithereens throughout much of their range. Howe Sound, my field site near Vancouver, British Columbia, is no exception, although new protective legislation might be starting to give them some slack.

Our dive surveys1 and earlier studies, in combination, have pieced together a story of ecosystem change. In the Howe Sound of today, lingcod rarely exceed body lengths of 80 cm. But up to 30 years ago, when overfishing had yet to inflict the full extent of its current damage, lingcod with lengths of 90 to 100 cm had been common in the area. There is nothing unique about this; most fisheries target the biggest individuals, ultimately reducing maximum body size within each species of predatory fish.

As predators shrink, the vibrant tension of predation risk slips away. The mechanism of change has a lot to do with mouth size. Predatory fishes swallow prey whole, usually head or tail first, so it is impossible for them to eat prey bigger than the width and height of their open jaws. And bigger fishes have bigger jaws, which makes them capable not only of consuming larger prey, but also of scaring bigger prey into using antipredator behaviours, such as hiding in rocky crevices. As predators shrink, big prey enter a size refuge and only small prey remain at risk, which can alter trophic cascades and other indirect species interactions. Read the rest of this entry »

Ecology: the most important science of our times

12 07 2013

rocket-scienceThe title of this post is deliberately intended to be provocative, but stay with me – I do have an important point to make.

I’m sure most every scientist in almost any discipline feels that her or his particular knowledge quest is “the most important”. Admittedly, there are some branches of science that are more applied than others – I have yet to be convinced, for example, that string theory has an immediate human application, whereas medical science certainly does provide answers to useful questions regarding human health. But the passion for one’s own particular science discipline likely engenders a sort of tunnel vision about its intrinsic importance.

So it comes down to how one defines ‘important’. I’m not advocating in any way that application or practicality should be the only yardstick to ascertain importance. I think superficially impractical, ‘blue-skies’ theoretical endeavours are essential precursors to all so-called applied sciences. I’ll even go so far as to say that there is fundamentally no such thing as a completely unapplied science discipline or question. As I’ve said many times before, ‘science’ is a brick wall of evidence, where individual studies increase the strength of the wall to a point where we can call it a ‘theory’. Occasionally a study comes along and smashes the wall (paradigm shift), at which point we begin to build a new one. Read the rest of this entry »

Learning how to fail

6 06 2013

On the way to work yesterday I was listening to ABC Radio National‘s Life Matters program hosted by Natasha Mitchell about how school children are now apparently being given so much positive praise and encouragement that they can no longer handle failure. Poor, wee dears. Maybe that’s why we have such a high attrition rate once they get up to postgraduate level, because that’s when they REALLY experience failure.

Jokes and whinges aside, there is a hard truth in that message that applies to all scientists, and especially the early-career ones. I’m talking about having your paper rejected from a journal.

Even the terms we use to describe the peer-review gauntlet appear designed to instil fear and inadequacy: reject or accept. I don’t know how many times I’ve seen a PhD student’s face figuratively melt off the skull as they shuffle into my office to show me the journal’s rejection letter (now just usually forwarded in an email accompanied by implied stooped shoulders – is there an emoticon for that?). As I’ve mentioned before, we scientists can be real bastards to each other, and it comes out in spades during peer review.

While neophytes tend to take these hits the hardest, I want to impart a little wisdom from some of my very well-established and successful colleagues. Rejection should be viewed as an asset, not a mark of failure. Let me explain. Read the rest of this entry »

Help us restore a forest

12 04 2013

plantingI’m not usually one to promote conservation volunteer opportunities, but this is a little different. First, I’m involved in this one, and second, it’s very near to my home. As you might know, the Mount Lofty Ranges area has had about 90 % of its forests destroyed since European settlement, with a corresponding loss of ecosystem services. We need smart restoration on massive scale, and Monarto is one place where we can develop the best practices to achieve this goal. We really do need some help here, so I encourage anyone in the Adelaide area with an interest in evidence-based forest restoration to lend us a hand.

The Monarto Restoration Project will provide an internationally recognised opportunity to experience and engage with wild Australia as it was.

Our aim is restore and expand habitats at Monarto to represent what used to exist in the region before clearing for agriculture and the introduction of pest species. Monarto used to be teeming with wildlife. The remnant vegetation at Monarto is unique as it is located at the cross-over of two vegetation communities (the Mt Lofty Ranges and Murray Mallee). This means it provides important habitat for a range of threatened bird and plant species. However, there are still a number of species in danger of being lost from the area, so we need to focus on restoring habitat to support them too.

We provide an opportunity to see the bush in a way that is no longer possible in most parts of Australia. We hope to help you see what we have lost and encourage you to participate in conservation. It gives us the opportunity to include everyone in on-ground conservation work and pass on skills that can be applied beyond a day or this project. With your help we can reduce the impacts of pest species on the property and re-introduce some of the native species that are now locally extinct. Read the rest of this entry »

Software tools for conservation biologists

8 04 2013

computer-programmingGiven the popularity of certain prescriptive posts on, I thought it prudent to compile a list of software that my lab and I have found particularly useful over the years. This list is not meant to be comprehensive, but it will give you a taste for what’s out there. I don’t list the plethora of conservation genetics software that is available (generally given my lack of experience with it), but if this is your chosen area, I’d suggest starting with Dick Frankham‘s excellent book, An Introduction to Conservation Genetics.

1. R: If you haven’t yet loaded the open-source R programming language on your machine, do it now. It is the single-most-useful bit of statistical and programming software available to anyone anywhere in the sciences. Don’t worry if you’re not a fully fledged programmer – there are now enough people using and developing sophisticated ‘libraries’ (packages of functions) that there’s pretty much an application for everything these days. We tend to use R to the exclusion of almost any other statistical software because it makes you learn the technique rather than just blindly pressing the ‘go’ button. You could also stop right here – with R, you can do pretty much everything else that the software listed below does; however, you have to be an exceedingly clever programmer and have a lot of spare time. R can also sometimes get bogged down with too much filled RAM, in which case other, compiled languages such as PYTHON and C# are useful.

2. VORTEX/OUTBREAK/META-MODEL MANAGER, etc.: This suite of individual-based projection software was designed by Bob Lacy & Phil Miller initially to determine the viability of small (usually captive) populations. The original VORTEX has grown into a multi-purpose, powerful and sophisticated population viability analysis package that now links to its cousin applications like OUTBREAK (the only off-the-shelf epidemiological software in existence) via the ‘command centre’ META-MODEL MANAGER (see an examples here and here from our lab). There are other add-ons that make almost any population projection and hindcasting application possible. And it’s all free! (warning: currently unavailable for Mac, although I’ve been pestering Bob to do a Mac version).

3. RAMAS: RAMAS is the go-to application for spatial population modelling. Developed by the extremely clever Resit Akçakaya, this is one of the only tools that incorporates spatial meta-population aspects with formal, cohort-based demographic models. It’s also very useful in a climate-change context when you have projections of changing habitat suitability as the base layer onto which meta-population dynamics can be modelled. It’s not free, but it’s worth purchasing. Read the rest of this entry »

Rocking the scientific boat

14 12 2012
© C. Simpson

© C. Simpson

One thing that has simultaneously amused, disheartened, angered and outraged me over the past decade or so is how anyone in their right mind could even suggest that scientists band together into some sort of conspiracy to dupe the masses. While this tired accusation is most commonly made about climate scientists, it applies across nearly every facet of the environmental sciences whenever someone doesn’t like what one of us says.

First, it is essential to recognise that we’re just not that organised. While I have yet to forget to wear my trousers to work (I’m inclined to think that it will happen eventually), I’m still far, far away from anything that could be described as ‘efficient’ and ‘organised’. I can barely keep it together as it is. Such is the life of the academic.

More importantly, the idea that a conspiracy could form among scientists ignores one of the most fundamental components of scientific progress – dissension. And hell, can we dissent!

Yes, the scientific approach is one where successive lines of evidence testing hypotheses are eventually amassed into a concept, then perhaps a rule of thumb. If the rule of thumb stands against the scrutiny of countless studies (i.e., ‘challenges’ in the form of poison-tipped, flaming literary arrows), then it might eventually become a ‘theory’. Some theories even make it to become the hallowed ‘law’, but that is very rare indeed. In the environmental sciences (I’m including ecology here), one could argue that there is no such thing as a ‘law’.

Well-informed non-scientists might understand, or at least, appreciate that process. But few people outside the sciences have even the remotest clue about what a real pack of bastards we can be to each other. Use any cliché or descriptor you want – it applies: dog-eat-dog, survival of the fittest, jugular-slicing ninjas, or brain-eating zombies in lab coats.

Read the rest of this entry »

Individuals a population to conserve make

28 11 2012
Unique in its genus, the saiga antelope inhabits the steppes and semi-desert environments in two sub-species split between Kazakhstan (Saiga tatarica tatarica, ~ 80% of the individuals) and Mongolia (Saiga tatarica mongolica). Locals hunt them for their meat and the (attributed) medicinal properties of male horns. Like many ungulates, the population is sensitive to winter severity and summer drought (which signal seasonal migrations of herds up to 1000 individuals). But illegal poaching has reduced the species from > 1 million in the 1970s to ~ 50000 currently (see RT video). The species has gone extinct in China and Ukraine, and has been IUCN “Critically Endangered” from 2002. The photo shows a male in The Centre for Wild Animals, Kalmykia, Russia (courtesy of Pavel Sorokin).

In a planet approaching 7 billion people, individual identity for most of us goes largely unnoticed by the rest. However, individuals are important because each can promote changes at different scales of social organisation, from families through to associations, suburbs and countries. This is not only true for the human species, but for any species (1).

It is less than two decades since many ecologists started pondering the ways of applying the understanding of how individuals behave to the conservation of species (2-9), which some now refer to as ‘conservation behaviour’ (10, 11). The nexus seems straightforward. The decisions a bear or a shrimp make daily to feed, mate, move or shelter (i.e., their behaviour) affect their fitness (survival + fertility). Therefore, the sum of those decisions across all individuals in a population or species matters to the core themes handled by conservation biology for ensuring long-term population viability (12), i.e., counteracting anthropogenic impacts, and (with the distinction introduced by Cawley, 13) reversing population decline and avoiding population extinction.

To use behaviour in conservation implies that we can modify the behaviour of individuals to their own benefit (and mostly, to the species’ benefit) or define behavioural metrics that can be used as indicators of population threats. A main research area dealing with behavioural modification is that of anti-predator training of captive individuals prior to re-introduction. Laden with nuances, those training programs have yielded contrasting results across species, and have only tested a few instances of ‘success’ after release into the wild (14). For example, captive black-tailed prairie dogs (Cynomys ludovicianus) exposed to stuffed hawks, caged ferrets and rattlesnakes had higher post-release survival than untrained individuals in the grasslands of the North American Great Plains (15). A clear example of a threat metric is aberrant behaviour triggered by hunting. Eleanor Milner-Gulland et al. (16) have reported a 46 % reduction in fertility rates in the saiga antelope (Saiga tatarica) in Russia from 1993-2002. This species forms harems consisting of one alpha male and 12 to 30 females. Local communities have long hunted this species, but illegal poaching for horned males from the early 1990s (17) ultimately led to harems with a female surplus (with an average sex ratio up to 100 females per male!). In them, only a few dominant females seem to reproduce because they engage in aggressive displays that dissuade other females from accessing the males. Read the rest of this entry »

How to write a scientific paper

22 10 2012

Several years ago, my long-time mate, colleague and co-director, Barry Brook, and I were lamenting how most of our neophyte PhD students were having a hard time putting together their first paper drafts. It’s a common problem, and most supervisors probably get their collective paper-writing wisdom across in dribs and drabs over the course of their students’ torment… errhm, PhD. And I know that every supervisor has a different style, emphasis, short-cut (or two) and focus when writing a paper, and students invariably pick at least some of these up.

But the fact that this knowledge isn’t innate, nor is it in any way taught in probably most undergraduate programmes (I include Honours in that list), means that most supervisors must bleed heavily on those first drafts presented to them by their students. Bleeding is painful for both the supervisor and student who has to clean up the mess – there has to be a better way.

Yes, there are books on the issue (see, for example, Day & Castel 2011, Hofmann 2009, Schimel 2011), but how many starting PhDs sit down and read such books cover to cover? Hell, I can barely get them to read the basic statistics texts.

So as is classic for Barry, he came up with his own approach that I like to call ‘La Méthode Brookoise’ (a tribute to another clever jeu de mots). This short-cut guide to setting up a scientific paper is simple, effective and intuitive. Sure, it was designed with ecology in mind, but it should apply to most scientific disciplines. It appeals to most of our students, and we have both been asked for copies by other supervisors over the years. Our original intention was to write a paper about writing papers to flesh out the full Méthode, but that has yet to happen.

Therefore, for the benefit of the up-and-comings (and perhaps to a few of those longer in tooth), behold La Méthode Brookoise for writing papers: Read the rest of this entry »

Hades, fossilised fat-parrot shit and threatened bats

4 10 2012

WTF? © P. Bendle

Sounds like a Monty Python sketch, doesn’t it? But no, it’s about the wonderful complexity of ecology.

An interesting, and very weird paper just came out in Conservation Biology co-authored by my friend and colleague, Prof. Alan Cooper at the Australian Centre for Ancient DNA (ACAD).

Here’s what they have to say about it.

Ancient dung from a cave in the South Island of New Zealand has revealed a previously unsuspected relationship between two of the country’s most unusual threatened species.

Fossilised dung (coprolites) of a now rare parrot, the nocturnal flightless kakapo, contained large amounts of pollen of a rare parasitic plant, Dactylanthus, which lives underground and has no roots or leaves itself. The pollen suggests the kakapo was formerly an important pollinator for the threatened species, known as the Hades flower or wood rose. Researchers from the Australian Centre for Ancient DNA at The University of Adelaide, and Landcare Research and the Department of Conservation in New Zealand report the discovery in the journal Conservation Biology.

Read the rest of this entry »

Ecology is a Tower of Babel

17 09 2012

The term ‘ecology’ in 16 different languages overlaid on the oil on board ‘The Tower of Babel’ by Flemish Renaissance painter Pieter Bruegel the Elder (1563).

In his song ‘Balada de Babel’, the Spanish artist Luis Eduardo Aute sings several lyrics in unison with the same melody. The effect is a wonderful mess. This is what the scientific literature sounds like when authors generate synonymies (equivalent meaning) and polysemies (multiple meanings), or coin terms to show a point of view. In our recent paper published in Oecologia, we illustrate this problem with regard to ‘density dependence’: a key ecological concept. While the biblical reference is somewhat galling to our atheist dispositions, the analogy is certainly appropriate.

A giant shoal of herring zigzagging in response to a predator; a swarm of social bees tending the multitudinous offspring of their queen; a dense pine forest depriving its own seedlings from light; an over-harvested population of lobsters where individuals can hardly find reproductive mates; pioneering strands of a seaweed colonising a foreign sea after a transoceanic trip attached to the hulk of boat; respiratory parasites spreading in a herd of caribou; or malaria protozoans making their way between mosquitoes and humans – these are all examples of population processes that operate under a density check. The number of individuals within those groups of organisms determines their chances for reproduction, survival or dispersal, which we (ecologists) measure as ‘demographic rates’ (e.g., number of births per mother, number of deaths between consecutive years, or number of immigrants per hectare).

In ecology, the causal relationship between the size of a population and a demographic rate is known as ‘density dependence’ (DD hereafter). This relationship captures the pace at which a demographic rate changes as population size varies in time and/or space. We use DD measurements to infer the operation of social and trophic interactions (cannibalism, competition, cooperation, disease, herbivory, mutualism, parasitism, parasitoidism, predation, reproductive behaviour and the like) between individuals within a population1,2, because the intensity of these interactions varies with population size. Thus, as a population of caribou expands, respiratory parasites will have an easier job to disperse from one animal to another. As the booming parasites breed, increased infestations will kill the weakest caribou or reduce the fertility of females investing too much energy to counteract the infection (yes, immunity is energetically costly, which is why you get sick when you are run down). In turn, as the caribou population decreases, so does the population of parasites3. In cybernetics, such a toing-and-froing is known as ‘feedback’ (a system that controls itself, like a thermostat controls the temperature of a room) – a ‘density feedback’ (Figure 1) is the kind we are highlighting here. Read the rest of this entry »


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