The secret to scientific success….

PublishingThis post tackles one of the big issues in science – how to be successful. It turns out that the basic principle is simple, publish. But, there’s some detail that needs to be considered. Most of all, it seems that the earlier you start publishing the better for your career (yes Ph.D. candidates, that means you!). To explain the detail much better than I ever could, I have reproduced a post from a colleague of mine, Prof. Corey Bradshaw (see his blog, Conservation Bytes). He can be controversial, but it gets the point across and it’s fun. His post and blog are definitely worth a read if you want to be successful in science…….

Early to press is best for success

by CJA Bradshaw

This 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?

There are a few possibilities here, with some well-known mechanisms, and others that are only suspected. Using the CVs of 1400 biologists in various disciplines (excluding medical) from four different continents, we measured the number of publications they had written by the time they had completed their PhD and ten years later. We also collected information on the scientists’ gender, whether English was their first language, and the international ranking of the university where they obtained their PhD.

Combining the data into a series of linear models, we asked the following questions:

  1. Given that our sample included people that stayed in science for at least ten years (i.e., we didn’t include people that gave up their scientific careers in the interim), do males publish more than females?
  2. If you went to a highly ranked university for your PhD (e.g., Cambridge, Oxford, Harvard, etc.), were you  likely to publish more than someone who had received theirs from a lower-ranked institution?
  3. Most scientific results are published in English these days, so if English is your first language, do you have an advantage and therefore publish more than someone for whom English is a second (or third, fourth, etc.) language?
  4. If you start publishing early in your career, does that set the pace for the rest of it?

The results? Drumroll, please.

Most will be happy to read that the most important determinant of your ‘long’-term (10-year) publication success is how many papers you’ve written by the time you’ve completed your PhD. This effect increases markedly if we take the number of papers you’ve published three years after PhD completion as a predictor. To make the point again that publication output is a reasonable metric of ‘success’, we also found that it was highly correlated with the ten-year h-index of the scientists for which we had data.

But there were other effects, albeit of lesser importance. Yes, even after removing the well-known ‘attrition’ effect of female scientists (i.e., leaving their careers earlier than males), men tended to publish a little more than women. There are many potential reasons for this, including still largely male-dominated academic and publishing systems, misogyny and the extra constraints of child rearing. We still have a long way to go here.

English as a first language also gave scientists a publication advantage as hypothesised, although the effect was weak.

Possibly one of the most interesting results was that PhD-university ranking had absolutely no discernible effect on publication output, regardless of which ranking metric one uses.

There a few take-home messages in all of this. First, if you are a PhD student and/or early-career researcher, make sure you put the effort into getting those first papers out. Second, if you’re considering people to hire for a new position and you’re taking a gamble on their potential to publish, you should perhaps place a strong importance on their publication output to date (all other considerations being equal).

However, employers should NOT choose men over women, nor should they blindly hire people with English as a first language. Case in point is that most of my lab’s best and brightest are early-career women from non-English-speaking countries. The gender and language effects were weak at best, and nearly disappeared once we considered the data three-years after PhD completion.

Finally, if an employer is considering choosing one of two recently completed PhD students for a postdoctoral position, and the one from the higher-ranking university has fewer publications than the other from the lower-ranked institution, my advice would be to choose the latter (all other things considered being equal, of course). Maybe students (and their parents) should also put less emphasis on university ranking and more on the people with whom they will be working when considering where to do their postgraduate studies.

CJA Bradshaw

Mediation of global change by local biotic and abiotic interactions

Dr Laura FalkenbergThis post is basically a short synopsis of the work done by one of my (now ex-) Ph.D. students, Dr Laura Falkenberg. Laura’s work has turned much of what we thought we knew about the effect of increased CO2 and nutrients on its head; we found synergies where we didn’t expect them (reviewed in a book chapter) and system resilience and resistance to change beyond what we hoped (via strong competitive interaction and trophic links; published in Oecologia, PLoS One and Marine Ecology Progress Series). Laura has certainly helped us look at things in new ways and given us hope that in marine systems where synergies between stressors exist that management of local conditions could potentially buy us some time in mitigating climate change (e.g. reducing nutrient flows into the marine environment, in Journal of Applied Ecology).

Ph.D. thesis: Mediation of global change by local biotic and abiotic interactions
by Dr Laura Falkenberg.

Throughout my Ph.D., I assessed the conceptual model that while cross-scale abiotic stressors can combine to synergistically favour shifts in marine habitats from kelp forests to mats of turfing algae, management of local conditions can counter this change. My experimental manipulations found broad support for the hypotheses that; 1) cross-scale factors (i.e. local and global) can have interactive effects which increase the probability of expansion of turfs but not kelp and, 2) management of local conditions (e.g. maintaining intact forests, limiting nutrient enrichment) can dampen the effects of global change (e.g. forecasted carbon dioxide). I published the results from my thesis in four papers. In the first, I showed that experimental enrichment of CO2 and nutrients influence the biomass accumulation of turf and kelp differently, with turf responding positively to enrichment of both resources while kelp responded to enrichment of nutrients but not CO2. Given that such direct responses could be mediated by interactions with other taxa, in the second paper I considered a key competitive interaction and revealed that the presence of kelp can inhibit the synergistic positive effect of resource enrichment (i.e. CO2 and nutrients) on their turf competitors. Similarly, in the third paper I highlighted the importance of herbivory by showing that under enriched CO2 conditions rates of this process were increased to counter the expansion of turfs. Finally, in the fourth paper, I considered a scenario in which these biotic controls were absent and identified that where multiple resources had been enriched and prompted a synergistic response (i.e. the expansion of turf where CO2 and nutrients are modified), subsequent reduction of the locally-determined factor alone (i.e. nutrients) substantially slowed further expansion of turf algae, but that the legacy of nutrient enrichment was not entirely eradicated. Together, these results represent progress in ecological tests of hypotheses regarding global climate change as they incorporate comprehensive sets of abiotic and biotic community drivers.

You can access all of Laura’s publications from the University of Adelaide’s digital library, or email her for a copy.

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.

Eutrophication offsets sea urchin grazing on seagrass caused by warming and OA

Amblypneustes pallidus in a Posodonia seagrass meadow. Photo: Owen Burnell

Amblypneustes pallidus in a Posodonia seagrass meadow.
Photo: Owen Burnell

The title to this blog seems a bit counterintuitive, almost like eutrophication is a good thing. Don’t believe that for a second! In a recently published paper, Owen Burnell of the University of Adelaide presents some interesting data on the interactions between eutrophication (an all too common local stressor), ocean acidification and warming (both increasingly alarming stressors of global origin). As I keep discovering, interactions between these stressors never seem to turn out the way we expect:

The accumulation of atmospheric [CO2] continues to warm and acidify oceans concomitant with local disturbances, such as eutrophication. These changes can modify plant– herbivore grazing interactions by affecting the physiology of grazers and by altering the nutritional value of plants. However, such environmental changes are often studied in isolation, providing little understanding of their combined effects. We tested how ocean warming and acidification affect the per capita grazing by the sea urchin Amblypneustes pallidus on the seagrass Amphibolis antarctica and how such effects may differ between ambient and eutrophic nutrient conditions. Consistent with metabolic theory, grazing increased with warming, but in contrast to our expectations, acidification also increased grazing. While nutrient enrichment reduced grazing, it did not fully counterbalance the increase associated with warming and acidification. Collectively, these results suggest that ocean warming and acidification may combine to strengthen top-down pressure by herbivores. Localised nutrient enrichment could ameliorate some of the increased per capita grazing effect caused by warming and acidification, provided other common negative effects of eutrophication on seagrass, including overgrowth by epiphytes and herbivore aggregation, are not overwhelming. There is value in assessing how global and local environmental change will combine, often in non-intuitive ways, to modify biological interactions that shape habitats.

Digital library

How to track the environment with fish

Clockwise from right – Juvenile Murray cod after calcein marking; Juvenile silver perch during the experiment; An adult golden perch. Credit: Zoe Doubleday

Clockwise from right – Juvenile Murray cod after calcein marking; Juvenile silver perch during the experiment; An adult golden perch. Credit: Zoe Doubleday

Following up on an earlier post about how hard body parts can be used to reconstruct environmental signatures, Dr Zoe Doubleday and her team have identified the relative contribution of water (that the fish are swimming in) and diet to otolith (fish ear bones) chemistry in freshwater fish. Now I know that this isn’t strictly a study about oceans, but the techniques and findings of this paper are extremely useful if you want to do this in the ocean as well! See her report below.

Otolith chemistry is used extensively around the world to address key questions relating to fish ecology and fisheries management, particularly in marine systems. Nevertheless, there is limited research on the relative contribution of water and food to elements within otoliths.
Using a controlled lab experiment, researchers at the University of Adelaide sought to address this gap by explicitly testing the relative contribution of water and food in three iconic Australian freshwater fish species — silver perch, golden perch and Murray cod.  Water was found to be the key, but not sole, contributor to otolith chemistry in all fish species. This research will improve interpretation of otolith chemistry data in freshwater fish and will help to build a more accurate picture of their movements and the environments they inhabit.
Read journal article here: http://bit.ly/12pHsLr

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)

Aquatic body parts reveal all

This post is written by guest blogger Dr Zoë Doubleday, who is a Post-doctoral Fellow in the Marine Biology Program at The University of Adelaide. She has a particular interest in the utilisation of hard calcified tissues found in aquatic organisms as tools for answering critical questions in aquatic ecology. What interests me about Zoe’s work is how you can apply the techniques below to understanding past environmental conditions in the ocean and what that can tell us about the future…..

Zoe

When you look at a tree stump what do you see? That’s right, rings, rings radiating out from the center to the edge; rings that represent the growth history of the tree.  Aquatic species also have rings laid down like this, year after year, decade after decade, in all kinds of body parts.  Fish and squid ear bones, shark vertebrae, coral skeletons, marine mammal teeth, bivalve and gastropod shells, cuttlefish bones. . .and the list goes on.  The beauty of hard calcified tissues is that many form growth rings with a precise periodicity (e.g. daily or annual), providing a time-calibrated archive of biological and environmental information.  To extract information from these natural chronometers we can analyse their chemical composition (such as trace elements and isotopes) and examine their growth ring

The otolith (ear bone) of a Murray Cod showing annual growth rings. Photo: Zoe Doubleday

The otolith (ear bone) of a Murray Cod showing annual growth rings. Photo: Zoe Doubleday

patterns (such as number and width) in relation to the temporal context of ring formation.  From here we can examine both the biological history (e.g. age, growth, diet, and movement) and environmental history (e.g. temperature and salinity) of an individual from birth to death.  This type of data can additionally tell us two important things: how the environment is changing and what biological impact that environmental change is having.

Another valuable attribute of calcified tissues is that they can hang around long after the organism has died.  This allows us to compare information derived from modern-day samples with information derived from historical (e.g. 19th and 20th Century), archeological and even paleontological samples.  Such comparisons are very powerful and can provide a rare and crucial insight into past biological baselines and what aquatic environments may have been like, say, prior to industrial-scale fishing or European colonization. This in turn can help us make a more realistic assessment of how much humans have impacted, and are impacting, the environment and about what environmental changes might happen in the future.

In the Marine Biology Program, we have a number of biochronologists working away on a range

Red Gurnard Perch (deep-water marine fish) ear bone with growth ring measurements. Photo: Gretchen Grammer

Red Gurnard Perch (deep-water marine fish) ear bone with growth ring measurements. Photo: Gretchen Grammer

of calcified tissues collected from freshwater to oceanic environments.  From here we are linking chemical and growth pattern data to various climatic and oceanographic variables, tracking movement patterns of individuals over large spatial and temporal scales, and seeing how biological indices, such as growth rate, age, and diet are changing.  However, there is still much to discover and uncover in calcified tissues and, in my opinion, is a mu ch underutilized resource of historical data, particularly in Australia.  As we continue to dig up long forgotten sample archives, find novel body parts with chronological properties, and work with constantly evolving analytical technology, who knows what we will find next…

Vertebra of Port Jackson Shark. Photo: Chris Izzo

Vertebra of Port Jackson Shark. Photo: Chris Izzo

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!

Disrupting synergies – making things not so bad.

Healthy forest of the kelp Ecklonia radiataI’ve posted on synergies between environmental stressors (what most people think of as pollution) before. Basically, a synergy is when the impact of the two stressors, say increased CO2 nd nutrients, is greater than the sum of their individual impacts. Once you recognise that synergies can occur, and are often much worse than we predict, the next question is can we do anything to stop them? The short answer is in most cases yes.

The way that synergies work means that, theoretically, if you remove one of the stressors then the “extra” impact should also be removed. In essence, if a synergy is 1 + 1 = 5, then removing 1 means that 1 + 0 = 1. When you’re talking about impacts to ecosystems that are essential to our GDP and way of life (not to mention that they have intrinsic value anyway) that is a really big consideration.

One of my Ph.D. students has just published a rather elegant study demonstrating it is possible to disrupt a synergy between CO2 and nutrients that has the potential to cause the loss of our kelp forest ecosystems. Basically, where CO2 and nutrients cause the synergistic growth of “weedy” species of algae you can remove the nutrients and remove the synergy. There is, however, a caveat. If you wait to remove the nutrients from the system then a large part of the impact will remain – things won’t go back to normal.

The thing that I like most about this outcome is that it provides useful information to the people who manage our coastal waters. If you are concerned that increasing concentrations of CO2 will have a negative impact in areas around major population centres then recycling and redirecting treated waste water away from the ocean, such as into industry or agriculture, can increase the resilience of marine systems. But, timing matters. Sooner is better.

Coral reef structures resistant to Ocean Acidification

Coral reefs are structurally complex and "cemented" together by Crustose Coralline Algae.

Coral reefs are structurally complex and “cemented” together by Crustose Coralline Algae.

Unlike some of the media coverage, I’m not saying that coral reefs will be resistant to ocean acidification, and I’m certainly not saying that corals will be. There is some good news for the gloom of ocean acidification. Yet, the devil is in the detail!

Unknown to most people, Crustose Coralline Algae (known in the field as CCA to stop us tripping over the long name) are the pink algae which cement together the matrix of coral reefs the world over, effectively solidifying the structure that we know as “coral” reefs. These CCAs also form a dense, concrete like ridge on the exposed side of most reefs, protecting the more fragile corals from destructive wave energy. So, from a reef perspective they are very important.

Until now, most of the research into the future of CCAs under ocean acidification has demonstrated that they are likely to dissolve (e.g. Tropical species and temperate species). However, some colleagues and I have recently discovered two important things about these CCAs, (1) that they contain dolomite, a rather robust mineral that most people associate with mountains in Italy; and (2) that dolomite is quite resistant to pH which we are expecting in the world’s oceans in the next 100 years (link to the paper here).

What does this mean? Unfortunately it doesn’t mean that the world’s coral reefs are going to be saved from ocean acidification by dolomite-rich CCA. By all accounts the corals are still in trouble (though I still have my hopes for more adaptive capacity than we give them credit for!). However, there is some hope, because these CCA are likely to maintain their structure and thus continue to protect reefs from damage by waves.