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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Write English well? Help get published someone who doesn’t

The following post is from Prof. Corey Bradshaw, who writes for his blog, Conservation Bytes. Corey’s experience with international collaborators, in particular in China, so mirrored mine that I thought I should share. Over the last year, I have discovered the joy of working with some of the excellent scientists in China; they truly are brilliant at what they do and I would encourage anyone to work with them. Spending time in China and writing papers with Prof. Yunwei Dong, Prof. Kunshan Gao, and their research groups has (and continues to be) an amazing experience.

imagesI’ve written before about how sometimes I can feel a little exasperated by what seems to be a constant barrage of bad English from some of my co-authors. No, I’m not focussing solely on students, or even native English speakers for that matter. In fact, one of the best (English) science writers with whom I’ve had the pleasure of working is a Spaniard (he also happens to write particularly well in Castellano). He was also fairly high up on the command-of-English ladder when he started out as my PhD student. So. There.

In other words, just because you grew up speaking the Queen’s doesn’t automatically guarantee that you’ll bust a phrase as easily as Shakespeare, Tolkien, Gould or Flannery; in fact, it might put you at a decided disadvantage compared to your English-as-a-second- (-third-, -fourth-, -fifth- …) language peers because they avoided learning all those terrible habits you picked…

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Recovery of seagrass from overgrazing depends on species morphology.

Above: A meadow of seagrass (Amphibolis antarctica) that has been heavily grazed by sea-urchins to the point where only dead shoots and detritus remain. Below: A moderately dense meadow of Posidonia sp. with aggregations of sea-urchins (Amblypneustes pallidus). This genus of seagrass appears to have a much greater capacity to recover from grazing than Amphibolis antarctica. Photo credits: Andrew Irving (Above), Owen Burnell (Below)

Above: A meadow of seagrass (Amphibolis antarctica) that has been heavily grazed by sea-urchins to the point where only dead shoots and detritus remain. Below: A moderately dense meadow of Posidonia sp. with aggregations of sea-urchins (Amblypneustes pallidus). This genus of seagrass appears to have a much greater capacity to recover from grazing than Amphibolis antarctica. Photo credits: Andrew Irving (Above), Owen Burnell (Below)

Following on from my last post on how sea-urchins alter how much they eat in response to nutrients and CO2, here Owen Burnell describes his latest paper (in as many months!) that shows why Amphibolis antarctica and other morphologically similar species of seagrass may be so susceptible to grazing.

Sea urchins are important marine invertebrates, which in many parts of the world can shape sub-tidal habitats via their grazing. In South Australian seagrass meadows the short-spined sea urchin Amblypneustes pallidus generally occurs in low densities, however, population increases of the species have recently been documented by researchers at The University of Adelaide.

It was observed that the grazing activity of these urchins was impacting seagrass meadows, in particular the species Amphibolis antarctica, when compared with adjacent Posidonia spp.  By manipulating urchin density to measure seagrass loss and then simulating urchin grazing to study seagrass recovery, we found that while urchins grazed equally upon both seagrass species, Posidonia sinuosa recovered much faster from simulated grazing than Amphibolis antarctica. It appears the different morphology of these two seagrass species, in particular the meristem location (or centre of growth) of Amphibolis spp., which is elevated within the canopy and thus exposed to grazers, is likely to be the cause of these asymmetric grazing impacts. In essence, if the urchins eat the meristem that seagrasses grow from they don’t recover as quickly!

While sea-urchins are by no means a rampant force destroying local seagrass meadows, population expansions such as these are important to document, particularly if they have deep seated connections with changing trophic interactions or urchin fecundity. In many marine systems worldwide population expansion of macro-grazers such as urchins can be linked to over-exploitation of their predators (e.g. fish or crustaceans, or before their protection, sea otters!) or changes to temperature that affect their reproduction and metabolism.

For more information, check out the abstract (below), journal website (subscription required), or link to the full manuscript

The persistence of seagrass meadows reflects variation in factors that influence their productivity and consumption. Sea urchins (Amblypneustes pallidus) can over-graze seagrass (Amphibolis antarctica) to create sparse meadows in South Australia, but this effect is not observed in adjacent Posidonia sinuosa meadows despite greater densities of inhabiting urchins. To test the effect of urchin grazing on seagrass biomass, we elevated the density of urchins in meadows of A. antarctica and P. sinuosa and quantified seagrass decline. Urchins removed similar amounts of biomass from both seagrass species, but the loss of leaf meristems was 11-times greater in A. antarctica than P. sinuosa. In a second experiment to assess the recovery of seagrass, we simulated urchin grazing by clipping seagrass to mimic impacts measured in the first experiment, as well as completely removing all above ground biomass in one treatment. Following simulated grazing, P. sinuosa showed a rapid trajectory toward recovery, while A. antarctica meadows continued to decline relative to control treatments. While both A. antarctica and P. sinuosa were susceptible to heavy grazing loss, consumption of the exposed meristems of A. antarctica appears to reduce its capacity to recover, which may increase its vulnerability to long-term habitat phase-shifts and associated cascading ecosystem changes.

Atmospheric CO2 reaches 400 ppm

In May 2013 the National Oceanic and Atmospheric Administration in the USA reported that the atmospheric concentration of CO2 at one of their recording stations topped 400 ppm for the first time. The media surrounding this event seems to have been very much based around the event itself with little comment on what it may mean. I find this moderately disappointing because we can be moderately confident of one thing  – increased CO2 in the atmosphere means that more will dissolve into the ocean, which means an increase in ocean acidification (this is classical chemistry!).

Despite the recent efforts of some of the worlds best scientists, both here in Australia and overseas, we still have an incomplete picture of the likely biological and ecological effects of this ocean acidification. However, we can be fairly certain of two things:

1. Ocean acidification will have negative impacts on organisms which form calcareous structures like the shells of molluscs (see pictures below) and the skeletons of corals; and

2. We are becoming increasingly aware that the increase in CO2 as a resource will cause changes to systems that are dominated by primary producers like seagrass and algae (e.g. kelp), mostly for the worse (for a starting point you could look at my webpage, but contact me for more information if you want!).

Unfortunately, as we enter a time of uncertainty for science funding in Australia, we may not develop a complete understanding of the system-wide effects of ocean acidification until it’s too late.

The growing edge of a juvenile abalone under high atmospheric CO2 (ultra-high magnification). Photo: Owen Burnell

The growing edge of a juvenile abalone under high atmospheric CO2 (ultra-high magnification). Photo: Owen Burnell

The growing edge of a juvenile abalone under normal atmospheric CO2 (ultra-high magnification)

The growing edge of a juvenile abalone under normal atmospheric CO2 (ultra-high magnification)

The sins of the parents…..

Are not necessarily visited on the children, at least not with ocean acidification.Clownfish

There has been a lot of discussion over the last few years about the ability of plants and animals to adapt to ocean acidification. Some researchers are adamant that the rate of change is so fast that no animals will be able to adapt. A recent study by Miller et al. suggests that this may not be the case. In fact, they show that nature may just be a little more resilient than we give her credit for (or at least some species will be).

Professor Phil Munday and his team from James Cook University has been working on this concept for a while. The difficulty is that it is hard to raise multiple species of long-lived animals (or plants) in the lab to conduct these experiments. Miller et al. show that it’s worth trying. They exposed breeding pairs of cinnamon anemonefish to different levels of ocean acidification (OA) for two months before the breeding season. The astonishing thing is that their offspring weren’t negatively affected by this OA, whereas other juvenile fish coming from “normal” seawater were. What does this mean? That there was some sort of non-genetic adaptation within one generation!

We don’t know the underlying physiological mechanisms for this adaptation, or what other long-term trade-offs it may have (e.g. reduced reproductive output in the offspring?), but it is a promising outcome. Now all we need are more long-term, multi-generational research and we may begin to put a picture together on how our oceans will (or won’t) adapt to ocean acidification!

Common synergies


Algal turfs (brown fuzzy stuff) are overgrowing the hard corals at high CO2 concentrations near volcanic vents – a good “natural” experiment. Note also that the seagrass (green, long leaves) are also doing well – a subject for another post.

We frequently hear about “climate change” in the media these days. How could you avoid it? If you do a search of the scientific literature there are thousands of publications a year on the topic. When thinking about the worlds oceans, the most common things that we hear about are ocean warming or ocean acidification (aka. the “evil twin” of warming). Do you notice somthing about this statement? We hear about warming OR acidification. But is this a realistic scenario?

We as scientists commonly break things down into their components and try to understand them one at a time. This is understandable, because the best way to comprehend the functioning of amazingly complex systems is to break them down their component parts and then put them back together again. In this case, however, we are just starting to understand that by breaking things down to individual conditions, either temperature or acidification, we may be missing the most important part of the study. My research group started to realise this in 2009 when we discovered that, when increased in combination, carbon dioxide and nutrients had a massive effect on the growth of “weedy” species of algae which can help to maintain the loss of kelp forests (download the paper here). In hindsight, this result should not be so surprising – both carbon and nitrogen are resources which the algae use to grow. Isn’t hindsight a wonderful thing?

What was surprising is that when carbon dioxide was elevated in the absence of nutrients these algae didn’t respond by grow faster. In fact, they didn’t respond at all to the increased availability of carbon. This means that CO2 and nutrients cause a synergistic response in these algae – where the response to the combined conditions is greater than the sum of responses to the individual conditions (see here for a good review on the topic).

What now worries us is that increasing availability of carbon in the oceans will happen with ocean warming – these are not either/or conditions. Indeed, the first warning shots were fired when we discovered that these same “weedy” turf algae showed the same synergistic growth in response to combined CO2 and warming (see our results published here). We can do something about nutrient pollution (something I will post on in the near future), but CO2 and warming are inherently linked. I think it is time to not talk about warming or acidification but rather to discuss them in tandem.

Active Oceans Blog

Welcome to Active Oceans, a blog about just that!

I have set up this blog as a discussion forum for global activities concerning the world’s oceans. Why? Becuase the ocean forms the basis for all life on earth, yet we as humans seem determined to ruin it. So, in coming posts I will talk about my research about the ways in which we are damaging the ocean and how we can change the things we do to help keep our oceans active.

In the mean time, check out my home page for mor information about my research and publications!