On systematic reviews

This isn’t really a post – sorry about that – more of a note to say ‘look at this post me and Dr Georgina Key contributed to the excellent EcoEvo@TCD blog over here: http://www.ecoevoblog.com/2014/02/19/systematic-reviews/‘.

It’s all about what my time contributing to a systematic review of sustainable practices for working with soil in agriculture. I’d head on over there and have a read if I were you.

Academia and the infinite horizon

Last week I took part in a very interesting NERD Club (run by @EcoEvoTCD‘s @nhcooper123 – check out their marvellous blog for loads of useful information and perspectives on all things ecology and evolution) session on alternatives to academic careers. In a competitive field, making the choice between a traditional academic career and something that, well, isn’t that, is increasingly becoming a talking point among PhD students and early career researchers. The perceived process of getting a foothold in an academic career is frequently accompanied with expectations of long hours, continual transit between short-term contracts, and much heaping of responsibility – whether these perceptions are correct or not, the result is an increase in conversation about the alternatives.

As I fall into the ‘early career researcher’ box, I can’t really contribute much in the way of hindsight or perspective. However, there were two guests at NERD Club who could – they had both done PhDs and post-docs, and now had non-academic (but, crucially, not non-scientific or non-research) jobs outside of the university circuit. This first fact was interesting in itself, suggesting that, without actually trying a post-doc, it’s difficult to know if you’ll like it or not. If you’ve made the effort to get a PhD, it seems worth the further effort to try the academic route, to decide whether or not it’s for you, unless you’re completely certain that it isn’t for you. My own experience of a post-doc has been quite different to that of my PhD, in ways that I didn’t think it would be.

I got the impression that choosing a non-academic career involved a compromise between the ‘flexibility’ and ‘infinite horizons’ theoretically offered by academic posts, and something with more security, but less autonomy. This post isn’t intended to express a certain position on the issue – rather, I’d prefer it to prompt some discussion. Please do comment below if you’d like to. There were several other useful hints and pointers to come out of the meeting, which I’ll list below.

  • A ‘non-academic’ career doesn’t necessarily preclude ‘doing science’ – it could just mean that the pressure to publish is reduced. However, it might also mean that you have less freedom over the things that you do.
  • Consider approaching an organisation that isn’t a university. Kew Gardens, or the National Biodiversity Network, for example.
  • Do think about career alternatives – decide what you’d be trying to do if you weren’t considering an academic job, and start acquiring the skills that you’d need if you were to apply for a role in that field.
  • One particularly focused way of obtaining the skills you might need is to volunteer. Personally, I’m interested in science communication – I’ve managed to develop some of the relevant skills through maintaining this blog, along with others, maintaining social media profiles for the organisations that I’ve worked with, and maintaining websites. You may be able to pick up some of the skills you need in a way that enhances your current role.
  • The ScienceCareers Individual Development Plan site might be work a try.
  • There are some useful materials on Versatile PhD.
  • Dynamic Ecology has some interesting perspectives on the matter:

* It stands for ‘Networks in Ecology/Evolution Research Dynamic
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The Paper Parade: my Top Ten

The British Ecological Society recently published a list of 100 influential papers, written over the last 100 years, as part of its centenary celebrations. I like zeitgeisty things like this, and enjoyed perusing the papers, each reference accompanied by a write-up by a scientist-in-the-know. It prompted me to think: which papers would be in my personal top ten? They could be papers that inspired me to take a certain approach, to consider my research in a different way, or papers that I just enjoyed reading because I thought they (or the authors) were cool.

What do you think? Do you have any papers that grabbed you by the proverbial lapels and never let go? Post your suggestions in the comments below!

Here’s my top ten (controversially, in no particular order):

Franklin, J. (1995) Predictive vegetation mapping: geographic modelling of biospatial patterns in relation to environmental gradients. Progress in Physical Geography, 19, 474–499.

I first came across this paper during my undergraduate degree studies at the University of Southampton. It inspired me to develop my interest in (plant) species distribution modelling, the topic I ended up focusing on for my dissertation. In her review, Janet Franklin defined predictive vegetation mapping, outlined major contributions to the topic, provided a conceptual framework, and discussed approaches and methods (such as deriving variables from digital elevation models) in detail. The field of (plant) species distribution has advanced a long way since 1995, in tandem with the availability and sophistication of high-resolution spatial data, computing power and statistical methods. However, Janet Franklin’s review has stood the test of time, as far as providing an accessible introduction to the area of species distribution modelling is concerned.

Beilman, D.W., Vitt, D.H., Bhatti, J.S. & Forest, S. (2008) Peat carbon stocks in the southern Mackenzie River Basin: uncertainties revealed in a high-resolution case study. Global Change Biology, 14, 1221–1232.

My PhD supervisor, Nick Ostle, introduced me to this paper early in the first year of my PhD. David Beilman and colleagues used the Mackenzie River Basin in Canada as a case study for getting better estimates of the amount of carbon stored in peatlands, using a combination of landcover data, digital terrain data and peat carbon and depth data collected from other studies to produce a map of carbon stored per unit area of peatland. The study emphasised the importance of generating accurate peatland carbon inventories, and the approach adopted by David informed my own sampling strategy and later spatial analyses as I worked to produce a similar map of carbon storage for my PhD study site.

Couwenberg, J., Thiele, A., Tanneberger, F., Augustin, J., Bärisch, S., Dubovik, D., Liashchynskaya, N., Michaelis, D., Minke, M., Skuratovich, A. & Joosten, H. (2011) Assessing greenhouse gas emissions from peatlands using vegetation as a proxy. Hydrobiologia, 674, 67–89.

John Couwenberg and colleagues applied the very neat and convenient concept of using vegetation composition as a proxy for measured greenhouse gas emissions, testing the concept at two Belarusian peatlands. The idea that vegetation is a suitable proxy for greenhouse gas emissions has its origins in the fact that, in peatlands, water table level is an important driver of greenhouse gas emissions. The authors assert that vegetation is a good indicator of water table level and other factors that determine the amount of greenhouse gases emitted from peatlands. Vegetation patches are easy to map, and represent the combination of multiple years of conditions contributing to greenhouse gas emissions. Associating peatland greenhouse gas emissions to vegetation in this way allows us to test scenarios of vegetation change in an intuitive manner – an idea that I was keen to embrace in my own PhD project using a coarser landform approach, which I think will be useful for estimating greenhouse gas fluxes from peatlands using aerial photographs.

McNamara, N.P., Plant, T., Oakley, S., Ward, S.E., Wood, C. & Ostle, N. (2008) Gully hotspot contribution to landscape methane (CH4) and carbon dioxide (CO2) fluxes in a northern peatland. Science of The Total Environment, 404, 354–360.

This paper from Niall McNamara and colleagues at the Centre for Ecology and Hydrology is another example of a paper that I read early on in my PhD, which shaped my approach from the beginning. In this study, Niall and colleagues measured methane emissions from gullies and surrounding open moorland at what was to become my PhD study site, a blanket peatland in the north Pennines, England. They found that the gullies had much higher methane emissions than the surrounding bog and, despite covering just 9.3% of the land area, accounted for 95.8% of the methane emissions from the entire blanket peatland. The study confirmed that status of wet, Sphagnum– and sedge-filled gullies as hotspots for methane emissions. For me, this emphasised the importance of finding reliable estimates of greenhouse gas emissions from these landforms at the landscape scale – and why not apply the same idea to eroding areas as well? In my PhD, I found that these patches of bare peat played a similar role to gullies, in accounting for a disproportionately large amount of greenhouse gas emissions at the landscape scale, given their relatively small area.

Mitchell, R., Hester, A., Campbell, C., Chapman, S., Cameron, C., Hewison, R. & Potts, J. (2010) Is vegetation composition or soil chemistry the best predictor of the soil microbial community? Plant and Soil, 333, 417–430.

This paper by Ruth Mitchell and colleagues at the James Hutton Institute is one of my favourites, because it features a clever statistical method called Co-Correspondence Analysis, which can be used to determine how useful one community (the plant community, for instance) is for predicting another community (how about the soil microbial community immediately beneath those plants). This is another paper on the theme of using what we can easily see and survey (the plant cover) to predict what we can’t see as easily (the soil microbes, or the greenhouse gas emissions). Ruth found that the plant community predicted the soil microbial community just as well as the soil chemistry. I was keen to see if the same could be said of the plant communities present at my PhD study site, so tried it myself (unfortunately, with less convincing results!).

Treseder, K.K., Balser, T.C., Bradford, M. a., Brodie, E.L., Dubinsky, E. a., Eviner, V.T., Hofmockel, K.S., Lennon, J.T., Levine, U.Y., MacGregor, B.J., Pett-Ridge, J. & Waldrop, M.P. (2012) Integrating microbial ecology into ecosystem models: challenges and priorities. Biogeochemistry, 109, 7–18.

I’ve chosen this paper as one of my favourites because it introduced an idea that I think is particularly important to consider when we’re thinking about modelling the responses of ecosystems to global change pressures, like nitrogen deposition, or a warming climate. Kathleen Treseder and co-authors make the point that integrating some knowledge of soil microbial communities in our models will probably improve the performance of those models. As far as my own research is concerned, this paper helped me to justify the choices I made when selecting the scales at which to measure the soil microbial communities at my own PhD study site – I wanted to characterise them in a way that would perhaps be useful for future use in models of peatland carbon and nitrogen cycling.

Van der Heijden, M.G.A., Bardgett, R.D. & van Straalen, N.M. (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecology Letters, 11, 296–310.

This review paper by Marcel Van Der Heijden and co-authors caught my attention in the first year of my PhD thanks to that titular concept: soil microbes are the unseen majority, like the stage crew working behind the scenes at a West End show that makes the ‘magic’ happen. Well, sort of. The idea of soil microbes as drivers of the patterns we see in aboveground plant communities is one of several theoretical jumping-off points I adopted when drafting my literature review and rationale for my PhD studies. That image of the ‘unseen majority’ captured my imagination.

Wardle, D.A., Bardgett, R.D., Klironomos, J.N., Setälä, H., Putten, W.H. van der & Wall, D.H. (2004) Ecological linkages between aboveground and belowground biota. Science, 304, 1629–1633.

I consider this work by David Wardle and co-authors to be one of the definitive above-belowground interactions papers. The review sets out the concept of linkages between aboveground and belowground communities, and goes on to describe how these linkages can affect the functioning of ecosystems, before suggesting some research priorities. It also emphasises that these interactions are likely to be dependent on spatial and temporal context, and that this should be taken into account when designing studies that focus on this area. While I haven’t focused explicitly on this area in my own research, it’s certainly provided me with plenty of interesting background reading that’s helped to inform my ideas about the interactions between plants and microbes at different scales.

Bardgett, R.D., Freeman, C. & Ostle, N.J. (2008) Microbial contributions to climate change through carbon-cycle feedbacks. The ISME Journal, 2, 805–814.

This mini-review from Bardgett, Freeman and Ostle represents another early-PhD blockbuster, which provided me with a concise picture of the conceptual framework through which microbes mediate the carbon cycle and associated feedbacks with the climate. Figure 1 has appeared – sometimes in different guises – many times in various talks and presentations I’ve attended throughout my PhD and afterwards, which demonstrates the paper’s continuing relevance.

Lindo, Z. & Gonzalez, A. (2010) The Bryosphere: An integral and influential component of the Earth’s biosphere. Ecosystems, 13, 612–627.

And finally, last but by no means least, Zoe Lindo and Andrew Gonzalez present the wittily-named Bryosphere in a mini-review, in which they discussed the value of globally ubiquitous mosses as components in carbon and nitrogen cycling, and The Bryosphere as an ecosystem in itself, often under-valued. I’ll admit to being hooked by the title before the content, but it’s good, isn’t it. Rather than summarise it here, I’ll suggest that you read the article for yourself, and then go outside and appreciate The Bryosphere, in all of its glory.

Wellcome Image Awards 2009

While my primary interests lie in and around biogeography, I also have a soft spot for interesting images derived from photography, or alternative imaging techniques. This year’s Wellcome Image Awards showcase an excellent variety of images from science and medicine, some of which have been taken using traditional methods, while others have been generated using techniques such as scanning electron micrography. Visit the gallery here.

Capillary network