How to write a scientific paper

It is often at this time of year, as my postgraduate students are madly trying to finish writing papers, that I’m reminded of this post by Prof. Corey Bradshaw on how to write a paper. The method works. It is worth a read. Follow it to success!

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…

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Climate change and the collapse of fisheries

This is the thiFishing down foodwebsrd article in the series that I’m writing for a Chinese magazine targeting wildlife conservation. As you may guess, they started with Panda conservation, so the magazine is called Giant Panda, but they are running a series on exploitation of natural resources. So far I have covered overfishing, trawling and longline fishing. In this current article we discuss the interaction between fishing and climate change. I say we, because this article was led by Charlee Corra, a postgraduate student of mine. Charlee really deserves the credit for this one!

The first article in this series discussed the effects of overfishing and how it causes degradation to the environment. However, changes to the environment also affect fisheries and their sustainability. In any ecosystem, the survival of a species is dependent on its ability to grow to maturity and reproduce, which is in turn dependent on many factors such as environmental conditions that support healthy physiological functioning. Temperature, salinity, and water quality are all examples of integral abiotic factors that can have the power to support life or pose a serious threat. Global climate change is rapidly altering these environmental conditions, and thus altering marine communities in a way that scientists, fishermen, fisheries managers, and policy makers must understand in order to predict future stocks and improve sustainable practices

How the environment affects plants and animals
Physiology:  Marine organisms differ widely in their tolerance of environmental conditions. Some animals can survive better under stress than others. These differences in biological responses determine where an organism can live. For example, in the intertidal zone temperature sets the upper limits of species distributions such that barnacles, mussels or oysters with a greater heat tolerance live higher on the shore than those with a lower tolerance. While almost every organism has the ability to withstand heat stress to varying degrees, most organisms are also adapted to the temperatures in their particular habitat. Thus, many species, and even populations, have different thermal limits beyond which survival is brought into question. As an extreme example, imagine that you grew up in the polar regions and summer for you only gets as hot as, say, 10°C and you were put in the desert in summer – you would be above your thermal tolerance and likely would die.

The water chemistry of our oceans also heavily affects physiological functions. Calcifying organisms, such as corals, oysters, mussels, and some crustaceans, rely on specific levels of CO2 (usually low) and several other chemical compounds (usually high) in order to induce the chemical reaction that allows them to make their skeletons and shells. Changes to the water’s chemistry can compromise the structural integrity of these essential parts. Of particular concern is that constant and increasing CO2 emissions are causing more CO2 to dissolve into the ocean, causing Ocean Acidification (OA). OA is already making it difficult for shelled organisms to make their shells in some parts of the ocean! You can do a small experiment to demonstrate this effect: put a small seashell or piece of egg shell into a glass of an acidic liquid like Cola or vinegar and watch it slowly dissolve (this can take a day or two).

Climate change and long-term climate shifts: Climate fluctuates and changes naturally across many different time scales from seasonal to multi-decadal and millennial. However, in the last two centuries industrial activity has begun to influence these cycles, mostly because of emissions of greenhouse gases such as CO2 into the atmosphere. Of particular concern is that in addition to causing OA this CO2 also causes the earth’s atmosphere to warm, in turn warming the ocean. Unless something is done to change this trajectory, CO2 levels will continue to rise, negative effects on the environment will become stronger, and the impacts on marine habitats and communities will become more visible.

Shifts in distribution of plants and animals: As environmental conditions change, and especially as oceans warm up, many species are predicted to move poleward to higher latitudes to live in more optimal conditions. These range shifts are not always consistent or predictable among organisms or across regions due to complex ecological interactions with other physical and biological factors such as currents and larval dispersal, competitors and predators. Importantly, as the distributions of different species change, the balance of ecosystems is upset and their function is degraded.

Just as with other species, climate change will invariably impact fish populations and dynamics. For example, fish populations may either get smaller where they currently are or move to a new area. Adjusting fishing practices and quotas to these changes is essential for the future of sustainable fisheries.


Photo courtesy of the NOAA photo library ( Photographer: Robert K. Brigham

Effects of climate change on fisheries
Range shifts represent a huge threat to the productivity and success of fisheries, especially when they occur to economically and socially important species. In addition to losing an important species as its range shifts poleward, fisheries may be further affected by the opening of a gap in the ecosystem that can become occupied by a new species. This ultimately changes the structure and function of the ecosystem, potentially reducing the productivity of not only that single fishery but also the ecosystem overall.

In addition to range shifts, decreases in abundance of fish may also occur simultaneously. For example, warming has already caused decreases in populations of Norwegian Cod, leading to a less sustainable fishery. In such cases, the fishermen must either change to another fishery or risk damage to the fishery, degradation of the ecosystem and going out of business.

Together, the combination of range shifts and declining abundance has the potential to be devastating to fisheries if vulnerable fish stocks are fished at the same intensity.  Particularly sensitive fish stocks could easily collapse under these combined pressures. Considering that over 80% of the world’s fisheries are either already fully fished or over-exploited, collapses will become more likely under future conditions. However, armed with more accurate knowledge of how fished populations will be impacted, fishing regulations could be fine-tuned to protect the viability of fished species and avoid such a bleak future.

Predicting future stocks
Knowing that these issues exist, a lot of research is currently being done to predict the trajectory of future fish stocks and assist in managing fisheries in a more sustainable way. Because we are trying to predict what will happen in the future, one of the common techniques is to use computer-generated models which use complex calculations based on as many environmental and biological variables as possible to predict the effects of climate change on fish populations. These models take into account the physiological effects of climate change (mentioned above) on the targeted species to predict parameters such as growth, survival, and reproductive output to determine the future supply of adults. Then, in combination with experiments to test the outputs of these models, managers and policy makers decide how many and what type of fish can be caught annually to avoid depleting populations but also to maximize profits and food security. Importantly, these models can, if used properly, help managers prepare for the future of fisheries and to hopefully avoid more fisheries collapsing. However, it is extremely important to remember that predictions are not certainties and models, while very powerful tools, are far from perfect. There will always be variability across regions and habitats due to the interaction of many different factors and projections might represent some outcomes but not all.

It is important to remember that we can formulate all the regulations that want, but unless we are also simultaneously making an effort to decrease or mitigate the impacts of a changing climate on the ocean and its ecosystems, fisheries will continue to decline. The ocean is an important source of food for humans. In many countries seafood is a way of life. Many smaller communities rely exclusively on fish and other marine organisms for protein.  Therefore, it is important for everyone to understand how climate change will impact on the ability of marine organisms to survive because our fate is inextricably intertwined with that of the marine environment.

Top predators are essential to ecosystems: wolves revisited

In a recent post I explained how top predators are essential for healthy ecosystem function. Being a marine ecologist I obviously focused on sharks. I did, however, use the example of wolves in Yellowstone National Park in the USA and how their reintroduction lead to the reestablishment of the forest ecosystem.

Last night I discovered a video that tells the wolf story much more eloquently than I can. I have been an ecologist for nearly 20 years, I know this “story”, and I was still left amazed at the extent to which the presence of wolves improved the ecosystem and the landscape. Even more stunning to me was the multitude of pathways that this improvement takes; from direct control of deer populations to behavioural change which means that deer don’t graze in certain areas.

Not only is the video based on good quality ecology but the visuals are stunning. A must watch. Enjoy!

Scariest part of climate change isn’t what we know, but what we don’t

A good colleague of mine at The University of Adelaide, Corey Bradshaw, recently posted a blog on what we don’t know about climate change….. and the answer is scary. It is such a poignant article that I thought I would share it again here.

image-20150731-18728-1ntffbr © Nick Kim

My good friend and tropical conservation rockstar, Bill Laurancejust emailed me and asked if I could repost his recent The Conversationarticle here on

He said:

It’s going completely viral (26,000 reads so far) in just three days. It’s been republished in The Ecologist, I Fucking Love Science, and several other big media outlets.

Several non-scientists have said it really helped them to understand what’s known versus unknown in climate-change research—which was helpful because they feel pummelled by all the research and draconian stuff that gets reported and have problems parsing out what’s likely versus speculative.

With an introduction like that, you’ll just have to read it!

“It’s tough to make predictions, especially about the future”: so goes a Danish proverb attributed variously to baseball coach Yogi Berra and physicist Niels Bohr. Yet some things are so important — such as…

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Top predators are essential to the oceans

Source: Photographer: David Burdick

Gray Reef Shark (Carcharinus amblyrhynchos) Source:
Photographer: David Burdick

The global media was recently full of reports about the interaction that Australian pro-surfer Mick Fanning had with a shark during a competition in South Africa (see the video here). There is no doubt that the experience would have been terrifying and I’m very happy that Mick was not injured. The reactions across media and social media have been broad and varied. Many reports have reasonably pointed out that the rate of shark attacks is less than other more frequent dangers (like being killed by a cow) while some have, unreasonably in my opinion, postulated that we should “clear the ocean of sharks”.

There is no doubt that shark attacks are an emotionally charged event and that they sometimes have tragic outcomes. This has, in some instances, been used as an excuse to have shark culls. Rather than add to the chorus of voices stating how ridiculous this approach is (which it certainly is), I thought I would state something that seems to get forgotten: sharks are essential to the health of marine ecosystems and therefore essential to human life.

Why should we care about marine ecosystems? This seems like an inane question, but many people either don’t care or don’t understand how important healthy oceans are to our lives. Approximately 50% of the oxygen we breathe is produced in the ocean – can you skip every second breath? Over one billion people worldwide rely on seafood as their primary source of protein. Much of our food and pharmaceuticals relies on marine-based products. Basically, we can’t live without healthy marine ecosystems.

Why should I mention that? Because ecosystems rely on balance. When they are out of balance, they are unhealthy and become less productive. One of the services that top predators such as sharks provide to marine ecosystems is this balance. They control the species which would otherwise rapidly expand and dominate systems, lowering species diversity and productivity. A very good example of this in a terrestrial ecosystem is wolves in Yellowstone National Park in the USA. Wolves were hunted to local extinction in the area because they were thought to prey on livestock in the surrounding farmlands. In the absence of the wolves, however, elk populations expanded to the point where massive ecological damage was being done to the forests by grazing elk. Since reintroduction of the wolves, the forests have once again become healthy.

Another of the services that sharks perform is to “clean-up” marine ecosystem. Again, a terrestrial example that most people would be familiar with is lions in Africa catching the sick, diseased or old animals from herds. By removing these weaker individuals the lions are strengthening the herd as well as increasing the per capita resources available to the herd (by reducing its size).

Indeed, there is now a plethora of information on the benefits of top predators to the health and function of different ecosystems. We don’t seem to doubt this information for terrestrial systems, but our fear of sharks makes us irrational when it comes to marine systems. If one person is attacked by a shark the media goes crazy and we hear phrases like “shark cull”. If someone is killed by a cow…….. well, you’d never hear about it.

The reality is that in marine ecosystems the top predators are often sharks and these ecosystems cannot function properly without them. Humans need marine ecosystems to survive. Ergo, without sharks we can’t live as we currently do. While interactions with sharks can be terrifying and even tragic, we need to accept that the oceans are their habitat and we humans need them.

Ocean Acidification science: insightful and essential

Turfs overgrowing coralThe concentration of carbon dioxide in the atmosphere is rapidly increasing as we burn fossil fuels. Nobody doubts this. One of the emerging global consequences of this activity is Ocean Acidification (OA); approximately 30% of the CO2 that we emit into the atmosphere is dissolved into the oceans, forming carbonic acid and reducing the pH of the seawater. This is basic chemistry and can already be measured in many marine waters of the world.

The biological and ecological consequences of OA are, however, more complex to understand. Therefore, over the past two decades there has been a dramatic increase in the number of scientific studies investigating the effects of OA. Last week, a review of over 465 of these studies, written by Christopher Cornwall and Catriona Hurd, was published in the ICES Journal of Marine Science. They assessed a number of different scientific methods for rigour and concluded that overall OA science is well designed and executed, and provides useful insights into a complex problem.

There has been some good coverage of Cornwall and Hurd’s paper (e.g. in the journal Nature). Unfortunately, some media outlets misrepresent the findings of the paper. This is of great concern, as the inaccurate and sloppy journalism threatens an essential branch of marine science. I asked Cornwall to write something for this post:

Recently the Daily Mail reported that climate scientists are doom-mongering because their work is flawed. This report is misleading and only serves to introduce misinformation into the public arena.

The Daily Mail quotes an article in Nature by Cressey (2015) that highlights research by Cornwall and Hurd (2015).  Science is always evolving, and its aim is to improve both methods and theory in any given field, to be better equipped to answer the most complex of questions.   Cornwall and Hurd was merely a call for improvement in only one aspect of research amongst a multitude of methods.  The report in the Daily Mail misrepresents our findings.  There is overwhelming evidence that the effects of ocean acidification will impact our oceans through reductions in the growth and calcification rates of calcified organisms (e.g. shellfish, corals, etc., that make calcium carbonate ‘skeletons’), and an alteration of the behaviour of other marine invertebrates and fish.  This fact is unequivocal.  Rather than being “flawed”, the majority of ocean acidification studies have been carried out carefully, using a multitude of methods, and most provide extremely useful and insightful data on this complex problem.

Certainly, the consequences of OA are complex and modified by interactions with other stressors (e.g. nutrient pollution, global warming) and biotic interactions such as herbivory, competition and habitat complexity. This does not mean that the OA science to date is flawed, it simply means that we have more research to do to understand the future impacts. We need to understand all of the effects of OA, from the physiology of single organisms, through population dynamics and up to ecosystem-level interactions. This pattern of discovery is across all of science. For example, Einstein’s theory of relativity is complex. Physicists are making great discoveries but still have research to do. Ocean Acidification is no different.

Herbivores compensate for nutrient pollution

Photo courtesy of the NOAA photo library ( Photographer: Paige Gill.

Photo courtesy of the NOAA photo library (
Photographer: Paige Gill.

This post is a guest blog by one of my (now ex-) Ph.D. students, Dr Chloe McSkimming. Chloe has been working on what drives decline in seagrass systems and how we may be able to help stop the decline. The work described below is from one of her recent papers in the Journal of Experimental Marine Biology and Ecology.

Human activities continue to challenge the capability of ecosystems to absorb disturbances, yet many systems that face substantial human pressure remain stable, resisting change. Over the past several decades, ecologists have extensively studied resilience – the ability of an ecosystem to bounce-back – but we really don’t understand resistance, or the ability to not change. There is recent evidence that in marine systems this resistance may be in part due to biological compensatory mechanisms – basically processes that can counter disturbances which cause change. Therefore, understanding how these mechanisms allow systems to resist change to a degraded state is essential for improving our current knowledge of habitat stability.

In coastal systems, change in resource availability, particularly the increase in available nutrients via land-based runoff, favours the growth of weedy species which can displace highly productive, slower-growing species. In seagrass systems, nutrient inputs increase the growth of algae that overgrow seagrass, significantly reducing the amount of light available to the seagrass themselves, and ultimately leading to seagrass death. Small herbivores are important consumers which may provide a compensatory mechanism in these systems by eating these fast-growing algae, potentially increasing the survival of seagrass under nutrient pollution (also demonstrated for other benthic systems by myself and one of my colleagues Laura Falkenberg).

In this present study, we increased nutrient concentrations and altered herbivore abundance in a seagrass meadow to test whether this compensation does exist; that is, does nutrient pollution stimulate herbivores to increase feeding to counter the increased growth of algae?

As expected, nutrients increased the growth of algae so that they started to smother the seagrass. However, this effect was only present when herbivore abundance was reduced. When the herbivores were present, however, they reduced the effects of nutrient pollution by reducing the amount of algae on seagrass leaves. Interestingly, the abundance of herbivores did not increase, meaning that the increased consumption of algae was due to an increase in how much individuals were eating.

We still have a long way to go to understand compensatory effects in ecosystems. However, these results suggest that in some situations natural populations of herbivores may help to reduce the effects of nutrient pollution in seagrass systems by consuming the additional growth of weedy species. Herbivores are therefore an important component in the management of nutrient addition in coastal systems. BUT, it is also essential to remember that there is still a global decline of seagrasses driven by nutrient pollution, meaning that such compensatory mechanisms do have limits and ultimately the only way to stop the negative effects of nutrient pollution is to stop nutrient pollution!