Land – spare or share?


The debate on what is better for the environment and by extension many ecosystem services, high intensity conventional farming using large amounts of fertiliser and pesticides on mostly homogenous areas or low intensity possibly organic farming in a heterogeneous landscape seems to be a no-brainer. High intensity farms are pressing into natural habitats, pesticides are impacting pollinators and natural pest controls such as beetles or spiders (Hole et al., 2005, Biological Conservation) and the overuse of fertilisers are contaminating ground and surface water leading to eutrophication and even drinking water pollution.

However, on a larger scale this question seems to be more difficult to answer. The problem is that in theory, and most of the recent scientific literature supports the hypothesis that the product yield of organic farming is lower by 5 to 34 % (e.g. De Ponti et al., 2012, Agricultural Systems; Seifert et al., 2012, Nature). In return, to maintain the production levels, more land has to be devoted to agriculture, potentially destroying natural habitat. This leaves the following question: On a landscape scale, what is environmentally better, a large area of organic farming with a decent environmental footprint, or a mosaic of intensive farming and high quality natural habitat?

This debate is still ongoing and far from concluded. In their paper Grau et al. (2013, Current Opinion in Environmental Sustainability) showed that current research is still conflicting, especially since results vary quite a bit when looking at different taxa in different landscapes. On one side sparing supporters point out that in addition to the already mentioned higher land-availability, the higher yield will potentially reduce the per yield impact of farming (e.g. the greenhouse gas emissions per ton grain harvested).

On the other side supporters of sharing point out, that apart from the already mentioned effects of intensive farming on ecosystem services, there should at least be a bold question mark added to the statement that increasing yield will actually lead to land being made available for natural habitat. Land might become available for urban sprawl instead, especially in times of high property prices people might be drawn into a more rural/suburban setting, or the land may not leave agriculture at all but rather be used of agricultural expansion.

So what is the better solution? We don’t know yet. The most likely answer is neither. The best strategy will be dependent on factors on all spatial scales, from disturbance resistance of present taxa, to environmental conditions such as climate and soil type up to socio-economic issues such as land planning. Still the debate has been most beneficial to science. It has sparked multiple excellent large scale research projects that boosted the understanding of landscape scale impacts of farming on ecosystem services, and how regional-scale agricultural management can best benefit ecosystem services and by default ourselves.


Jesko Zimmermann, zimmerjr[at]

Photo credit

wikimedia commons

Badgery Fieldwork

cuddle time

One of the best things about my PhD has got to be the fieldwork. My project involves analysing the GPS data of a population of badgers to find out where they forage, how big their territories are, who lives with whom and how they disperse. This means putting GPS collars on them twice a year. Badgers have a bit of a bad rep, one they really don’t deserve. Contrary to popular opinion they are not vicious beasts that, once clamped on to your foot, won’t let go until they hear the bones crack (people say this to me a lot). They are in fact quite timid and very cute with it!

head tuck

I work with the NPWS and DAFM vets to trap and process the badgers. We set cages baited with yummy peanuts each night close to sett entrances and near regularly used latrines. Very early the next morning we go and check our haul. I love the anticipation of approaching the cage to see if we have a badger and who it might be. Each badger has its own distinct personality. Kenny will invariably be feigning sleep. Muffin huffs, puffs and chuffs a bit. Billy (RIP L) loved his peanuts and could be counted on to be in a trap most mornings, whereas Louis has proved to be a bit of an escape artist. Boru is the most chilled-out dude and saunters rather than runs out of the cage when we release him. We approach quietly because whether a badger is quiet or growling, it is afraid (except maybe Boru), and we want to minimise their stress as much as possible. Invariably even the feistiest badger shuts-down and plays dead, either covering its eyes with its forepaws or tucking its head under its belly. It’s just like kids thinking that if they can see you, you can’t see them. So cute! But every now and then a tremor of fear passes through their bodies. So quietly does it.

good teeth

Teresa, my vet colleague, goes in to anaesthetise the badger so we can fit the collar and do all the other bits and piece we need to do. When first caught a badger gets weighed, has blood samples and pharyngeal swabs to test for TB, is given a BCG vaccine to provide immunity and/or mitigate against TB infection and is given a general health check. We take a tissue sample for genetic analysis. We take photos of the teeth to estimate age. We check general body condition, remove fleas, treat any wounds and give antibiotics if necessary. New individuals get a microchip (and a nickname!) so we can ID it in future and I tattoo the last four digits of this number on its belly – which is a pretty awesome job. I’m a badger tattoo artist! The tattoo allows anyone else who should come across the animals (usually after a road traffic accident) know that the badger is special, and we can hopefully have it tested for TB status post-mortem. Finally the collar is fitted and the badger is placed in a “recovery box” to which allows it to come around in peace and return to the sett in its own time. If it’s a retrap with a good collar, we simply let the badger go. That night the collar begins transmitting the badger’s position, allowing us to build a picture of its movement patterns in fantastic detail. I now have over 50,000 GPS data points available for further analysis (but that’s a whole other blog post/dissertation).

GPS fixes

Fieldwork also involves retrieving lost collars which can be tedious, locating dead badgers which is sad (it is hard not to get attached to your research subjects), checking fields for foraging signs and looking for new setts & latrines which is always enjoyable. I never thought I’d be so excited about faeces…I’ve had to stop sharing photos on Facebook or risk being defriended.

Ballard Latrine

Badgers really are beautiful animals – they have a distinct “badgery” smell, wonderfully powerful forelimbs with massive claws for digging setts and rooting for food. Their distinctive facial mask is thought to have evolved as warning colouration to would-be predators (although there are no natural predators in Ireland, bar man). Their bodies are low-slung but they can move with incredible speed when they want to. Being nocturnal and living in underground setts they do have small eyes, and their large noses demonstrate that scent is their most important sense. In fact, one of our badgers, Fern, is completely blind but continues to do very well for herself, being the heaviest individual we trapped last autumn. Fatty pants!  It is a real delight to be able to work with these animals, seeing them in the kind of detail that most people never do, and to be able to dispel the myth of an aggressive, vicious beast.   Some are even TV stars.  Keep an eye out for the upcoming season of Living The Wildlife on RTE which tells the story of our badgers.


Aoibheann Gaughran, gaughra[at]

Photo credit

Aoibheann Gaughran


Ostrich Knees

Ostrich,_mouth_openDear Dr. Jeal,

Why is it that when a mammal kneels down its legs bend forwards, but when an ostrich bends down its legs bend back?

– Junior Sophs.

The question you ask is quite curious, but I don’t think you’re on the right track,

Saying “knees of a mammal bend forward, while knees of an ostrich bend back.”

But I quite see the cause of your problem, and it’s really quite simple you see,

As the bend in the leg of an ostrich is more like an ankle than knee,

The true knee of an ostrich bends forwards, and it’s quite a remarkable thing,

It’s up at the side of the body, tucked closely under the wing.

The leg is quite similar in all birds, but ostrich proportions are wrong,

As the femur is very foreshortened, while the foot is extraordinarily long.

As the leg is made largely of foot-bones, you’ll ask “What are its feet” I suppose,

I’ve an answer all ready for that one. What you think are its feet are its toes!


Frank Jeal

Photo credit

wikimedia commons

The importance of being Earnest – The case of climate change


In Oscar Wilde’s comedy “The Importance of Being Earnest”, Cecily and Gwendolen want to marry a man named Ernest simply because of the name’s connotations. They are so fixated on the name that they would not consider marrying a man who was not named Ernest. The name, sounding like “earnest”, shows uprightness, inspires “absolute confidence”, implies that its bearer truly is honest and responsible.

A name can truly be very important when it embodies the communication of a message. Surprisingly (or not) it is also important when dealing with international treaties and initiatives. An example is the story of the Ozone Hole and the Montreal Protocol, the most successful governmental agreement on an environmental problem at the global scale. The Montreal Protocol, signed in 1987 by 46 countries (now having nearly 200 signatories), banned the use and production of chlorofluorocarbons (CFCs) worldwide, recognizing that they represented a threat for the stratospheric ozone layer. During the celebrations for the 25th anniversary of the Protocol, Jonathan Shanklin, Head of Meteorology and Ozone Monitoring Unit for the British Antarctic Survey declared that in retrospect, the Ozone Hole was a really good thing to call the ozone depletion problem “because an Ozone Hole must be bad. Almost automatically, it meant that people wanted something doing about it. The hole had to be filled in”.

Much more confusion is involved in naming another problem at the same global scale: global warming, or climate change. The international agreement on it, the Kyoto Protocol, is not being as successful as the Montreal one.

“Global warming” and “Climate change” are two different phenomena, casually related. “Global warming” refers to the observation of a long-term trend of increasing temperatures. “Climate change” refers to different changes in climate phenomena driven by the increasing concentration of greenhouse-gases in the atmosphere. The alternative use of the two “names” probably contributed to the misunderstanding of the problem for the general public, giving alibis to those who are (conveniently) sceptical about climate change. That happens for example whenever a winter is colder than the year before, or more snowy, then “where is the global warming?”.

Surely the fact that the Montreal Protocol was successful and Kyoto Protocol is not, has much more profound and complex reasons than just the “naming”. There is however a trade-off between scientific rigour and effective communication to deal with. Scientific rigour should guide our management plans, effective communication should stimulate actions.

The scientific community and political stakeholders have to be “earnest” in balancing rigour and communication strength.


Luca Coscieme, coscieml[at]

Photo credit


Trip to the tropics: rising water in the Rift Valley lakes


We drive out of the compound just after dawn; a convoy of four vans full of final year science students and staff. We heard lions calling beyond the fence last night, and we haven’t gone 500 meters before we see them: two males strolling off to the left. Within hours, we will have seen herds of buffalo, jackal, giraffe, vervet monkey, baboon and, most impressively, both black and white rhino, among many other birds, reptiles and mammals. The tourist in me is delighted to see so much so quickly, but there is a good reason why the animals are so close to the tracks.  This is Lake Nakuru National Park in Kenya, and Lake Nakuru is rising, forcing the animals living there into a narrowing strip between the water and the boundary of the park.


The water levels in the Eastern Rift Valley lakes have a history of fluctuating wildly. From a peak in 1961, they have fallen and risen in response to drought and heavy rainfall for the last 50 odd years. Current lake levels are the highest they have been since the 60’s, but now, something very interesting is going on.  Weather conditions have not changed to the degree that would predict such an extreme rise in the lake water, and people are searching for other explanations.

Some commentators believe that the changes are driven by human impacts.  They claim that activities such as tree felling, house building, cultivation and increased grazing pressure have caused more water to run off the land into the rivers which feed the lakes.  Because of the very seasonal rainfall, flash floods are common and they carry large sediment loads into the lakes.  This sedimentation has also been blamed for the rise of the lakes, which is a bit confusing as sedimentation was previously blamed for falling water levels.  Tectonic activity has been suggested as a possible explanation: local compression of the African plate governs opening and closing of fractures through which water can seep.  A change in the pattern or amount of local rock fracturing could affect water levels.


While the debate over the cause of the changes continues, there are obvious social and environmental implications.  At Nakuru, the land area of the park has decreased and animals are more concentrated along the margins of the park.  The problem of over grazing has intensified, animals are easier to find for tourists but also for poachers, and the potential for human-wildlife conflict has increased.  The lakeshore hotel at Baringo now stands under several feet of water, no longer providing jobs or bringing valuable revenue into the area from tourists.  At Lake Bogoria, the lake water has become fresher as it has risen.  This has inhibited the growth of the cyanobacteria upon which the lake’s iconic lesser flamingo flocks depend so flamingo numbers have fallen.  But it is an ill wind that blows no-one good – rising water levels are a boon for fishermen.

Looking back over the 20th century, fluctuating water levels appear to be the norm in the Eastern Rift Valley, but they are very difficult to foresee.  Knowing how frequently, how far and how fast the lakes rise and recede would be a huge benefit to local people.  It is a complex problem, and one which would require a wide range of expertise and a lot of money to solve.  In the meantime, the lakes are mercurial, providing and destroying land and livelihoods.




Aoife Delaney

Photo credit

Aoife Delaney

Stress Busting


Inspired by recent reports of rising mental health problems in academia plus an acute increase in stress around the department this summer when many PhD students were writing up, we decided to run a “Dealing with stress” seminar at NERD club (ironically this session was canceled previously due to the PIs being “too stressed” to run it!). It turned out to be a really positive experience, and I’d definitely run something similar again. Here is what we found out!

What is stress and why is it bad?

Stress is an “adverse reaction to excessive pressure”. Short term stress responses can actually be beneficial, either for escaping angry bears or finding that last bit of energy needed to finish a manuscript, thesis or endless admin task. However, longterm chronic stress is really bad for you. Symptoms include headaches, nausea, digestive problems, ulcers, lowered immune responses, changes in appetite, altered sleep patterns, mood swings, lowered self esteem, negative thinking and more. All of these can trigger chronic mental health issues like depression and anxiety.

What causes stress?

Causes of stress are really varied; what stresses one person out has no effect on someone else. Some articles put causes of workplace stress into six categories: (1) too many demands; (2) too little control; (3) poor relationships with coworkers/superiors; (4) too much change; (5) too little support and (6) lack of clarity about your role. Unfortunately, as one PI pointed out, these six things define academic jobs!

We started our stress seminar by independently writing down everything that made us stressed/worried on Post-It notes and then placing these into a bin at the centre of the room (this was for convenience but I guess you could say we were symbolically throwing our troubles away…). We then shared these with the group. Unsurprisingly we’re stressed about similar things. I expect you’ll recognise some of the following:

Lack of structure/direction, pressure to come up with new ideas, balancing fun stuff with work stuff, the two body problem, struggling students, R, GIS, statistics, field work, risk assessments, paywalls, graphs, “the literature”, bad paper reviews/rejections, losing data due to a bug, forgetting deadlines, worry about not finishing PhD on time, feeling out of control, lack of public understanding of science, admin, pressure to produce outputs more regardless of quality, letting people down in and out of work, dealing with conflict/difficult meetings, saying yes too much, grant writing/rejections, public speaking, and, my personal favourite, how much coffee is too much???

We also had several things that everyone was stressed about. These were deadlines (aka having too much too much to do and too little time to do it), career uncertainty (sadly not something we can solve), and a lot of worries that fall under the category of impostor syndrome. The latter included worries about finding errors in data/analyses after submitting/publishing papers, worries about saying stupid things in front of people, feelings of inadequacy in relation to others and to your own potential, fear of failure etc. Generally the terror of being “found out” for being too stupid to do research. I think most of us found it quite reassuring to share these fears, including the PIs!

How can we reduce stress?

There are lots of suggestions online for reducing stress (including dowsing your house for geopathic stress – hmmm yeah…), here are just a few we discussed:

1) Talk about it.
Talk with family, friends, workmates or anyone really. If you’re having problems at work it’s a good idea to talk to your supervisor or line manager, or another staff member if your supervisor is the problem! Many of us also flagged how useful it is to speak to a professional counselor when problems get too big for you to handle alone (most universities offer free services to staff and students). An important point was that you shouldn’t be embarrassed – everyone feels stressed sometimes and it is not a sign of weakness.

2) Look after yourself.
Get plenty of sleep and exercise, don’t drink too much caffeine or alcohol, and try to eat a well-balanced diet (apparently chicken dippers are fine because BBQ sauce counts as a vegetable).

3) Learn to notice when you’re stressed and do something about it. If you don’t realise you’re stressed it’s hard to solve the problem, so learn the warning signs and symptoms and act accordingly when you notice them. It may help to keep a stress diary to work out what triggers your stress, and then avoid those situations and/or people!

4) Increase your productivity.
Many of the issues of having too much to do, or worrying about deadlines, can be helped by increasing your productivity and/or improving your time management skills. Check out the tips here for some ideas. The most important point here was to “work less but achieve more” rather than working ridiculous hours. Which brings us to idea 5…

5) Lower the bar!
If you come into work and have big plans for the week but don’t achieve them (for whatever reason), you tend to feel crap. Instead, set a lower bar. In fact, set a *really* low bar that you can hardly fail to meet. Even though you know your bar was low, you’ll still feel better having finished something! To help with this, try breaking tasks into smaller, more manageable chunks. For example, aim to finish the introduction of a paper rather than the whole paper. Oddly enough I finish things more quickly this way than if I work my ass off trying to achieve my grandiose aims!

6) Have a Plan B.
Although we can’t fix the problems with the academic career pyramid scheme, we did come up with some suggestions to reduce stress about it. Most of the PIs revealed that they had a Plan B (and Plan C) for if academia hadn’t worked out for them. This made them feel less panicked when approaching the end of contracts. Additionally, we decided we would look at our CVs and extract skills that would be useful in non-academic professions. PhDs train you for all kinds of jobs even if we don’t talk about them much. Knowing there are other options out there will hopefully reduce stress.

7) Dealing with impostor syndrome.
We spent a long time discussing this, and no-one really had a solution. Unlike many of the other problems which have external causes, this is an internal perception problem that is hard to fix. Instead focus should be on recognising it and dealing with it rather than eliminating it. Even the Chair of our department feels this way sometimes! Talking to other people should help (especially people you look up to), also trying not to compare yourself to others and realising that everyone has very different skills. A student with a lot of fieldwork shouldn’t expect to produce as many papers as a student working on an existing dataset for example. This is really hard in academia because there will *always* be someone out there who is better than you at something. But my favourite piece of advice on this is that people who never suffer from impostor syndrome are probably faking it, or gigantic assholes.

Hope some of this is helpful! Now go and lead less stressed lives!


Natalie Cooper, ncooper[at], @nhcooper123

Photo credit

wikimedia commons

The more the better?


These days I’m writing up the discussion of my sensitivity analysis paper on missing data using the Total Evidence method (more about it here and here). One evident opening for proposing future improvement on my analysis is the obvious “let’s-do-it-again-with-more-data” one… But a recent Science paper by Jarvis et al made me reconsider that. Is more the always better?

Jarvis and his numerous colleagues just published one of the biggest bird phylogenies that contrasts with the previous reference one (by Jetz et al in Nature). In Jetz’s paper, the authors were interested in the relations among modern birds (read “non-dinosaurs ones”) and tackled the question by trying to sample the whole of bird biodiversity (9,993 species!). However, as in most analyses of this kind, the molecular data can be fairly poor (note that they still managed to collect a maximum of 15 genes for 6663 species). Even though the global picture of avian diversity is clear, some regions are less resolved than others and an obvious way to fix that would be to sample more genes per species. And that is, in a way, exactly what Jarvis and his colleagues tried to achieve.

In this new study, the authors went on sampling not 15, 70 or 150 genes but 8251 genes per species! This led to a really deep and long analysis – over 400 CPU years, and I thought 150 was long! – of the complete genome of birds. By the way, they use the name Total Evidence nucleotide tree (TENT) to design the results of their analysis which is pretty confusing since a total evidence tree means something quite different to me. But that’s just a semantic rant. Using this massive TENT, the authors fixed some previously poorly resolved nodes, redefined the names of ancient divergences among birds (with the Passerea – tits and relatives – and the Columbea – pigeons and relatives), demonstrated an explosive (“big-bang”) radiation after the K-T event and determined the patterns of certain traits evolution (such as raptoriality or vocal learning). In short a thorough work that allowed the authors to say: “The conflict we observe with other data types can no longer be considered to be due to error from smaller amounts of sequence data”. I feel that writing something like that in a paper is a nice achievement!

However – don’t get me wrong, this paper is yet a great example of collaborative work and insight in new methods – the sample size is… 45 species. In other words, Jetz et. al sampled 100% of the species but less than 1% of the data as for Jarvis et al., they sampled 100% of the data for less than 1% of the species. In this case, we have two extreme views of the same question (“how did avian diversity evolve?”) and in both cases, I think the macroevolutionary claims are weakened by the number of species or the amount of data… However, from a practical point of view, I think the method that included more species will be preferred by researchers since their species of interest are more likely to be present in that tree. What’s the best balance? Full genome or full sampling? I’ll leave it to you to decide…


Thomas Guillerme, guillert[at], @Tguillerme

Photo credit

War of the Words – The Conflict between Science and Journalism, Part 1


Science journalists have a vital role to play in modern society, typically acting as gatekeepers of scientific knowledge for the public. According to the sociologist Peter Conrad (1999), “Science journalism is an increasingly important wellspring of public understanding of science.” Science journalists are an interesting subset of journalists in that they depend on press releases of areas of scientific research for their stories. The broadcaster Toby Murcott (2009) says that science journalism has a “rhythm” that tracks the publication of notable science journals like Science and Nature. “As press releases describing research arrive in our inboxes they are scanned for stories, the most newsworthy picked, offered to editors and then reported.” However journalists do not simply abridge a research paper; they typically contact expert sources to add to their stories. In this role science journalists use experts for a number of reasons. An authority can explain a finding and its implications both positive and negative. Moreover, quoting an expert can add credence to a story and give balance (Conrad 1999). According to Anders Hansen (1994) “[b]ecause of the complexity of much science, science journalists are seen as being uniquely dependent on the co-operation of their sources”. He adds that it is essential that there is a “relationship of trust” between the two. But does such a relationship hold? Or are science journalists and their sources in a state of conflict?

Differences of opinion

Clearly, science journalists are journalists first and specialists second whereas scientists are obviously science focused. This difference does not necessitate conflict but it permits it. One can conceive of a number of reasons that could foster disharmony between journalists and their scientific sources.

David Dickson (2005) expounds on these purported problem areas when he bemoans the latest trends in science reporting saying, “Sadly, we are currently witnessing a worrying trend within much of the world’s media, where a traditional commitment to reporting facts is giving way … to a more colourful, but less reliable, tendency to concentrate coverage on interpretations of fact (or ‘spin’).” He contends that the main problem with journalism in this respect is more to do with inaccurate reporting of the facts than bias. Bucchi and Mazzolini (2003) state that “The media are blamed for…allocating inadequate space to scientific topics, their inaccuracy in reporting about the issues, and exaggerating the political or non-scientific significance—indulging in dramatization and sensationalism.”

Another issue is that the conclusions science draws are never final, rather there are different levels of confidence assigned to theories. But uncertainties and probabilities with assigned statistical likelihoods do not make good stories from a journalistic perspective. So-called news values are not always applicable to scientific progress. Take timeliness for instance. Rarely is a scientific discovery an instantaneous thing, instead there is a lengthy progression from initial observations to final conclusions. So journalists are actually reporting on the publication of a journal paper.

In addition to news values Dorothy Nelkin (1996) points out that the different ways journalists and scientists use language can lead to conflict. She argues that “Certain words routinely used by scientists have different meanings for lay readers. Scientists use the work “epidemic” to describe a cluster of health-related incidents greater than expected; to a lay person, an epidemic implies a rampantly spreading disease.” She also points out simplifications that a journalist will draw on. For example they “will refer to the “fat gene” rather than to the “marker that may predispose an individual to obesity”.” The reason for this different use of language is that journalists use words for “graphic appeal” in contrast to frank, specialised scientific writing.

She goes on to contend that one of the most important areas of conflict arises from the different opinions scientists and journalists have about the role of the media. Scientists see the press as means to transmit information about their research to the public in an accessible way. Science journalism, in their view should popularise science and “convey a positive image”. According to Nelkin “they are reluctant to tolerate independent analysis of the limits or flaws of science, or the relative costs or benefits of new technologies.” This, in her view, is in contrast with journalists, “who do not see themselves as trumpets for science, [with] many … beginning to suspect promotional hype.” Nevertheless I do not think that scientists are entirely wrong with their view of science journalism. There is still an element of ‘Gee Whiz’ about science stories in my view. Indeed, I think a case could be made that many reporters do act as “trumpets for science.”

There also seems to be an inherent distrust of journalists by some scientists. Medical Doctor and blogger Ben Goldacre writes of media science coverage, “It is my hypothesis that in their choice of stories, and the way they cover them, the media create a parody of science, for their own means. They then attack this parody as if they were critiquing science.” Goldacre (2005) groups science stories into three categories wacky stories, scare stories and breakthrough stories. These categories nicely align themselves to the news values of unexpectedness, negativity and threshold.

The idea that there are two sides to every story can be a dangerous one when it comes to science writing. There are some instances where the science is well-founded yet journalists will quote a minor yet vociferous opposition. It seems likely to me that the main author of the study will be irked if his research is countered by somebody who has a bone to pick or is just manifestly wrong. This is all too common in the area of climate change. This point is raised by Nelkin (1996) who writes, “The norms of objectivity in journalism call for giving “equal time” to different points of view—for balancing conflicting claims. This is a source of irritation to scientists, because scientific standards of objectivity require not balance or equal time but empirical verification of opposing hypotheses.”

Next time out I’ll discuss some research that shows most scientists are quite happy with how their work is portrayed in the media as well as critiquing the relationship that has developed between journalists and scientists.

Author: Adam Kane, kanead[at]

Photo credit: