Gould Mine


The career of Stephen Jay Gould eludes easy definition because of his prolific output in so many areas. Michael Shermer characterises him as a historian of science and scientific historian, popular scientist and scientific populariser.

The popular science writings of Stephen Jay Gould (20 of his 22 books and hundreds of articles) are responsible for making me want to study macroevolution. He said of his popular essays that they were intended “for professionals and lay readers alike”. We have already covered some aspects of science communication, like how to do it and which kind of scientists should engage in it. Gould wrote 479 academic papers during his career, so any thought of public outreach damaging one’s science certainly didn’t apply to him.

Let’s have a closer look at his academic legacy. Gould is well known for his theory of punctuated equilibrium co-written with Niles Eldredge. This fuelled the debate around ideas such as species selection and the mechanisms explaining macroevolutionary patterns.

Despite this being the work for which he is best remembered it represents a tiny fraction of his output. He actually published only 15 papers with this theory as a main topic, which represents only 3% of his academic work! As a comparison, he published more papers (17) on baseball!

His primary field was invertebrate palaeontology (he was the curator of Harvard’s Invertebrate palaeontology collections from 1973 to his death in 2002) but again, even his main focus in this area (on Cerion snails) represents only on one quarter of his work. Shermer describes him as being “no single-minded fossil digger or armchair theorizer.”

Actually, nearly one fifth of his massive scientific output is primarily focused on the history of science. Again, as Shermer says, he was a “Historian of Science and Scientific historian”.

So Gould should not be only remembered for his proposal of punctuated equilibrium. Gould published 169 papers in 23 last years of last century, which gives him an average number of publications in the history of science of 7.34 per year. To put it in the historical context of the field, the only names that have been more productive are Aristotle, Kant, Goethe and Newton.

It’s rare to see a scientist who divided opinion so much, hagiographies have been written about him but he’s also loathed. Look at these for contrasting views:

“In the field of evolutionary biology at large, Gould’s reputation is mud.”

“Steve is extremely bright, inventive. He thoroughly understands paleontology; he thoroughly understands evolutionary biology.”

I’ll leave it to the reader to find out where they stand on Gould for there is a lot of controversy to consume. I prefer to remember him through his essays on Natural History than through his few papers about punctuated equilibrium, better illustrating the “measure of a man” (that’s Shermer’s pun). His life illustrates how interdisciplinary studies exponentially increase scientific productivity: “Gould has used the history of science to reinforce his evolutionary theory (and vice versa)” writes Shermer. And that applies as much to punctuated equilibrium as to baseball!

Authors: Thomas Guillerme (guillert[at]tcd.ie, @TGuillerme) and Adam Kane (kanead[at]tcd.ie,@P1zPalu)

Image Source: Wikicommons

School of Natural Sciences Postgraduate Symposium 2014: Part2/4


On the 20th and 21st of February we had our annual School of Natural Sciences Postgraduate Symposium. Over the course of two days many of our PhD students presented their work to the School. We also had two interesting plenary talks from Dr Sophie Arnaud-Haond (Ifremer) and Dr Lesley Morrell (University of Hull). Unfortunately our third speaker, Dr Fiona Jordan (University of Bristol) had to cancel due to illness.

For those of you who are interested in exactly what we work on here at EcoEvo@TCD, here are the abstracts from the PhD student presentations. Check out the TCD website for more details!

Aoife Delaney: Eco-hydrology of humid dune slacks*

*Highly commended

Dune slacks are hollows in coastal sand dune systems where the groundwater table is close to the surface. Many dune slacks flood in winter to form temporary ponds which can last from a few weeks to several months. Humid dune slacks are an Annex I habitat (2190) and in accordance with Article 17 of the Habitats Directive they have been mapped and assessed in Ireland on the basis of their vegetation. During monitoring in 2013, Humid dune slacks (2190) were assessed as Unfavourable-Inadequate and topics for further research were identified. The extent and effect of water abstraction and wastewater from recreation facilities has not been firmly established in Ireland, and work relating biological communities to water quality or depth and duration of flooding has focussed almost entirely on vegetation up until now.

This project will assess variation in vegetation, mollusc and water beetle communities present in dune slacks in Donegal, Mayo, Kerry and on the east coast. It will also investigate the effects of land management by comparing biological communities of sites which are under different management regimes such as extensive pasture and golf courses. The hydrological functioning of dune slacks will be related to biological communities they support.

Anne Dubearness: Systematics of the genus Embelia Burm.f. (Primulacae — Myrsinoidae)*

*Highly commended

Primulaceae subfamily Myrsinoideae is a species-rich tropical group containing over 2000 species, with several taxonomically difficult genera with poorly defined limits and many novelties needing description. Within the subfamily, Embelia is a genus of climbing shrubs distributed mostly in South and South-East Asia and tropical Africa. The last monograph of this genus (made by Mez in 1902) recognised 8 subgenera and 92 species, but the total number of species is currently estimated at 140. The systematics of this group needs investigation using a modern phylogenetic approach: indeed, Embelia displays extensive morphological variation (especially regarding the position, shape, size and merosity of the inflorescences) and is only distinguished from other Myrsinoideae by a climbing habit and distichous leaves. This project aims to combine molecular and morphological data in order to investigate the systematic of Embelia at 3 levels: first of all the monophyly of the genus must be tested, then the existing subgenera must be assessed and refined in order to produce a taxonomic framework of the genus, and the final focus will be on the subgenus Euembelia Clarke, which contains more than 65 species and could certainly be split into several sections.

Thomas Guillerme: Combining living and fossil taxa into phylogenies: the missing data issue*

*Highly commended

Living species represent less than 1% of all species that have ever lived. Ignoring fossil taxa may lead to misinterpretation of macroevolutionary patterns and processes such as trends in species richness, biogeographical history or paleoecology. This fact has led to an increasing consensus among scientists that fossil taxa must be included in macroevolutionary studies. One approach, known as the otal evidence method, uses molecular data from living taxa and morphological data from both living and fossil taxa to infer phylogenies. Although this approach seems very promising, it requires a lot of data. In particular it requires morphological data from both living and fossil taxa, both of which are scarce. Therefore, this approach is likely to suffer from having lots of missing data which may affect its ability to infer correct phylogenies. Here we assess the effect of missing data on tree topologies inferred from total evidence supermatrices. Using simulations we investigate three major factors that directly affect the completeness of the morphological part of the supermatrix: (1) the proportion of living taxa with no morphological data, (2) the amount of missing data in the fossil taxa and (3) the overall number of morphological characters for all of the taxa.

Florence Hecq: Effects of scale and landscape structure on pollinator diversity and the provision of pollination services in semi natural grasslands

Over recent decades, humans have been changing the environment more rapidly than in any other period of history. Technological advances and new agricultural policies have led to a simplification of landscape structure resulting in the loss and fragmentation of habitats for flower-visiting insects which play an important ecological role as pollinators. Pollinating insects are very mobile and are influenced by the availability of flowers and nest sites over a scale of several kilometres.

In this study, we investigated the effects of the complexity of landscape structure on the diversity of four pollinating taxa and on the provision of pollination services to four plant species. Pollination data were collected in 19 semi-natural grassland sites in north midlands region of Ireland and related to the composition and configuration of surrounding landscape at two spatial scales (500m and 1km radius around sampling sites). Landscape structure was characterised by digitising each landscape feature with aerial photographs and GIS, and then ground-truthed using field-based surveys. Knowledge of these pollination/landscape scale relationships is crucial for a better understanding of pollinator diversity patterns and should be helpful for future conservation management decisions; ensuring essential levels of pollination services to wild plants are maintained.

Lindsay Hislop: Does nutrient enrichment moderate the effect of water level fluctuations on littoral communities?

Freshwater abstraction from lakes in order to support a growing human population is rapidly becoming a major global stress on lacustrine ecosystems. The consequent amplification of water level fluctuations disproportionately impact lake littoral zones, which contain the majority of their biological diversity. However, remarkably little is known about the impacts of amplified water level fluctuations on littoral assemblages and less still is known about how they interact with nutrient enrichment, one of the most pervasive and important of human disturbances on the biosphere. To address this, we established an experiment in large outdoor pond mesocosms where we quantified the effects of water level fluctuations and nutrient enrichment, both separately and together. We found that the impacts of water level fluctuations on both primary producers and benthic consumers varied significantly along the depth gradient. However, we found no interactions between nutrient enrichment and water level fluctuations. Given that the problem of amplified water level fluctuations is likely to be exacerbated considerably by predicted increases in climatic variability and enhanced water demand, our findings have profound implications for the conservation and management of global aquatic biodiversity.

Nuria Valbuena Parralejo: The impact of artificial sub-surface drainage on greenhouse gas emissions, change in soil carbon storage and nutrient losses in a grazing cattle production system in Ireland

In Ireland, over the 33% of milk is produced on a Heavy Soils farms. Heavy Soils are characterised by low permeability and often form in high rainfall areas. The combination of both can lead to waterlogging, promoting soil compaction which significantly affects the grass production. Drainage has been shown as an effective tool for improving the soil permeability. Little data is available to assess the effect of the artificial subsurface drainage of a grassland production system, on greenhouse gas emissions, change in soil carbon storage and nutrient losses. This experiment will be carried out in Teagasc Solohead Research Dairy Farm (latitude 52° 51’ N, 08° 21’ W; altitude 95 m a.s.l.). Different treatments (i) mole drain winter, (ii) mole drain summer, (iii) gravel mole and (iv) control were imposed in one site of the farm in 2011. A new experiment will be set up at a different site on the farm in summer 2014 with (i) control and (ii) gravel mole into collectors. Nitrous oxide (N2O) flux measurements, soil respiration measurements, soil total carbon and total nitrogen analysis, soil nitrogen mineralisation and net nitrification, water analysis, water table measurements and herbage production will all be perform in both sites over two years.

Adam Kane: Ontogenetic dietary partitioning in Tyrannosaurus rex*

*Highly commended

Obligate scavenging in vertebrates is a rare mode of life, one which requires very specialized morphologies and behaviours to allow the scavenger to cover enough area to find sufficient carrion. Yet, a number of studies have suggested that Tyrannosaurus rex occupied this niche with others arguing for its role as an apex predator. In this study we move away from the polarised predator-scavenger debate and argue that T. rex underwent an ontogenetic dietary shift, increasing the proportion of carrion in its diet as it aged due to both the increased availability of carrion through direct intraspecific and interspecific competition and also by exploiting resources unavailable to its smaller competitors, namely bone. We follow an energetics approach in our study to explore the effect of this previously unrealised resource on the ecology of T.rex and look at the impact of the proposed ontogenetic dietary shift.

Image Source: Wikicommons

School of Natural Sciences Postgraduate Symposium 2014: Part1/4

tcd logo

On the 20th and 21st of February we had our annual School of Natural Sciences Postgraduate Symposium. Over the course of two days many of our PhD students presented their work to the School. We also had two interesting plenary talks from Dr Sophie Arnaud-Haond (Ifremer) and Dr Lesley Morrell (University of Hull). Unfortunately our third speaker, Dr Fiona Jordan (University of Bristol) had to cancel due to illness.

For those of you who are interested in exactly what we work on here at EcoEvo@TCD, here are the abstracts from the PhD student presentations. Check out the TCD website for more details!

Sven Batke: High energy weather events – long term responses on forest canopies and epiphytes

High energy weather events are often expected to play a substantial role in biotic and abiotic forest dynamics and large scale diversity patterns but their contribution is hard to prove. In this study we modelled cumulative hurricane impacts at Cusuco National Park, Honduras. The model was validated on the ground and microclimate and epiphyte data were collected along the forest profile and the modelled hurricane impact gradient. During this talk preliminary data will be presented that highlights the importance of including such events in understanding current abiotic and biotic canopy dynamics.

Qiang Yang (Marvin): The multidimensionality of ecological stability: A theoretical study

Understanding the factors that determine the stability of biological communities has been a focal point of ecological research for decades. However, a challenging aspect of stability is its many components, including asymptotic stability, resilience, resistance, robustness, persistence and variability. However, in spite of its multidimensionality, the few studies that measured multiple components of ecological stability simultaneously considered them as independent and therefore analysed them separately and we know remarkably little about the mechanisms underpinning relationships among components of stability and whether there are any general features of these relationships that are common across ecosystems.

Here by simulating the dynamics of distinct food-web structures following a range of perturbations on the species abundance in these food webs in silico we quantify 1) the general relationships among different stability components, 2) the effects of the strength of perturbations (i.e. the extent of biomass loss), the structure of food webs (i.e. trophic levels and connectance) and the individual species (i.e. its trophic position, generalist/specialist, omnivorous/monophagous) on the multivariate relationships among components of ecological stability in a range of food-web structures.

Mirjam Ansorge: Infectious diseases in squirrels and their importance for human health*

*Highly commended

It is well known that emerging infectious diseases like HIV or SARS have their origin in primates, and understanding the drivers for parasite sharing between humans and our closest relatives is an important factor for human health. However, some of the worst pandemics in history came from more distantly related animals. For example, the bubonic plague, which erased almost half of Europe’s human population in the 13th century, and was transmitted by fleas living on rats. This suggests that we should also investigate diseases in species that are not closely related to humans but that do come into contact with humans regularly. Squirrels are ubiquitous and share our parks and forests. Because they are considered non-threatening and often used to human presence, they are likely to have contact with humans and therefore to transmit parasites and vectors, such as fleas. These contacts can result in serious diseases in humans such as plague. I reviewed the recorded distribution of disease carrying squirrels in the USA from 1978 to 2002 and analysed the geographic range of parasites and parasite species richness in squirrel species. I will also discuss the importance of squirrels for human health.

Sai Krishna Arojju: Association mapping of agriculturally important traits in perennial ryegrass (Lolium perenne L.)

Linking genotypes to phenotypes and explain the natural phenotypic variation in terms of simple changes in DNA sequences is a major objective in plant breeding. Association mapping is a method which can be employed to search for genotype-phenotype correlations in individuals without population structure to identify co-segregation of genetic markers and phenotypes. This project aims to conduct an association mapping study in 1800 genotypes of Lolium perenne under three experimental regimes (1) simulated grazing management, (2) silage management and (3) persistency grazing management with 2 clonal replicates in a randomised block design. Each replicates consists of 40 blocks with 50 plants. 30 populations with different background have been selected for this study (10 released varieties, 8 half-sib breeding families, 8 full-sib breeding families and 4 Irish ecotypes). Genotyping will be performed by developing genotyping by sequencing (GBS) libraries for Illumina HiSeq2000 sequencing and we will also combine this with phenotyping on a range of forage quality traits including biomass accumulation, lignocellulose determination, flowering time, tillering capacity and digestibility on Lolium accessions. Variations in candidate genes of forage quality traits will also be examined.

William Burchill: Closing the farm nitrogen balance at Solohead Research Farm

Nitrogen use efficiency on Irish dairy systems tends to be low and leads to high farm-gate N surpluses (N imports minus N exports passing though the farm gate). The objective of this study was to quantify all N flows on a white clover based system of dairy production at Solohead Research farm from January 2011 to December 2012 and to account for surplus N. The system was rotationally grazed at a stocking density of 2.35 cows ha-1 received annual fertiliser N input of 112 kg ha-1 (BNF) was quantified using two 15N isotope techniques. A 15N gas flux and  static chamber method were used to quantify N2 and N2O emissions, respectively. Inputs (fertiliser N, BNF, feed and rainfall deposition) and outputs (milk and livestock sales) of N (kg ha-1) from the system were 274 and 80 respectively, with a farm-gate surplus of 194 kg ha-1 in 2011. Total measured N losses (kg ha-1) were 210 including 19, 43, 25, and 123 as N leaching, NH3, N2O and N2, respectively. The results of the present study indicate that a large proportion of Irish dairy systems N surpluses are returned to the atmosphere as environmentally benign N2 gas.

Donna Hawthorne: Fire, human and climate interactions throughout the Holocene

Significant changes in global and regional climate as well as changes in vegetation, land use, agriculture and policy, have promoted an increase in fires in the Irish landscape. To understand these changes the interrelationship between fire, climate and people will be explored. Past climatic oscillations have been studied at 8 sites throughout Ireland in an attempt to understand the current climatic changes which may mirror future patterns in climate. The landscape character and fire regime of each of these sites will be reconstructed and will seek to develop a model of risk assessment and management for future fire in the Irish landscape. The data span from the early Holocene to the present day, drawing on charcoal and pollen data, radiocarbon dating, and mineral and chemical data from lacustrine sediments. This work presents the first chronological comparison of regional fire activity across various locations throughout Ireland, and provides a base line level of data which can be drawn on in future scenarios when fire frequency is expected to increase. This work is in its third year of a four year PhD programme and preliminary discussions and results will be presented.

Louise Esmonde: Toxicity assessment of the agricultural pesticide Roundup Pro Biactive using Myriophyllum aquaticum and other test organisms.

Pesticide use in Ireland has increases over the last number of years yet its impact on the environment and in particular freshwater ecosystems is still not fully known. This study examines the toxicity of agricultural pesticides on non-target organisms with special reference to submerged macrophytes. In this study the toxicity of the herbicide Roundup Pro Biactive (active ingredient glyphosate) was examined using the plant species Myriophyllum aquaticum. Plant shoots were exposed to Roundup Pro Biactive concentrations of 0.01%, 0.1%, 1%, 5% and 10% for a period of 14 days. After the test period the response of the plant to the herbicide was measured in terms of wet weight, dry weight, shoot length, root length and root number with Relative Growth Rates (RGR) and EC50 values being calculated at each concentration. Preliminary results show a clear difference between the relative growth rates of control and test specimens. At concentration above 1% significant reductions in relative growth rates were recorded and physical deterioration of shoots was observed at concentration above 0.1%. Further studies will focus on the toxicity of five other agricultural pesticides on these same test species.

Killing in the Name of Science – Dying for Conservation

Conservation. Noun. From the Latin verb conservare, to protect from harm or destruction.

Dallas safari club auctions off permit to hunt rare rhino.

Giraffe unsuitable for breeding killed at Copenhagen zoo .

Six Lions at Longleat safari park destroyed due to excessive population increases.

What on earth is going on?

These stories have gone around the world and caused almost unanimous outrage. This is not surprising. The disparity between the ideals of conservation and the sometimes tricky real-world dilemmas that occur can cause consternation and indignation to many. Given my previous posts you won’t be surprised to learn that it might be a bit more complicated that the headlines have led us to believe. So let’s delve a bit deeper and see whether these animals were justifiably killed or whether there’s something else going on. As always, I’m going to try and leave the ethical considerations to one side as much as possible and focus on analysing the scientific justifications given. So, on with the show . . .

The Rhino


In early January a permit to shoot an elderly rhino was auctioned off to raise money for rhino conservation. There are arguments on both sides as to whether this was a good idea. The rhino was, according to reports, an old, non-breeding male rhino who had the potential to injure or even kill younger males. Removing him as a threat seems to be a good idea. Culling occurs in many managed populations and is used to maintain healthy, sustainable populations. Removing this animal from the population is, based on our understanding of male rhino dynamics, the best course of action scientifically.

Whether the auction was the best way of achieving this is outside my remit. Culls can, and do, occur with less publicity and spectacle. Given the outrage expressed, it would be interesting to know how many of the people complaining had ever donated to rhino conservation organisations. If the organisations were not so desperate for money would they have ever considered such a headline-grabbing action?

The Giraffe


Copenhagen zoo killed a giraffe that was considered useless for breeding . They then publicly dissected it and fed it to their lions. This story is the most interesting as it has two separate components: the killing and the treatment of the animals after death. Here I am extremely split. Captive giraffes are, to some extent, victims of their own success. Breeding programmes across Europe have been very successful and zoos are pretty much at ‘carrying capacity’ with few able to take excess giraffes and genetic inbreeding is becoming a problem. One of the zoos that offered to take the giraffe already has his older brother which was the argument used against the transfer.

The obvious solution would be to prevent the giraffes from breeding in the first place but this isn’t always easy in giraffes. From the BBC article,

“Contraception and castration have been raised as possibilities, but both would require sedation. This is a relatively high-risk procedure in the case of giraffes, as they are liable to break their necks when they fall while sedated.”

There are contraceptives available now that can be used with little risk so the number of ‘excess’ giraffes should reduce in the future. However, Copenhagen Zoo has a policy of allowing their animals to breed naturally, even though this is clearly causing a surfeit of animals.

As to the treatment of the body, I’m in no doubt they did the right thing. One of my favourite TV programmes in recent years was Inside Nature’s Giants where large animals were dissected and their anatomy and evolution was described and shown in all it’s ‘gory’ detail. I am all for increasing the public understanding of how animals work and the crowds that gathered to watch are proof that this interest exists. It is important to demystify biology and this is a great way of doing so. As for feeding the giraffe to the lions, well, what else were they going to do with it? Bury it? Burn it? Either way a waste of meat.

While I’d intended to ignore everything but the science, it’s proving incredibly hard! So my editorial for this story is that I’m not sure that killing the giraffe was the best idea. There were zoos that were offering to take the giraffe and, while it may not be the ideal option in terms of the breeding program, it is up to the zoo taking the giraffe to determine this. If they think the benefits of having another giraffe (and the public goodwill they will receive for offering sanctuary) outweigh the costs then I think this is their decision, not Copenhagen Zoo’s. The zoo needs to consider contraception as another instance like this will not go down well with the public and zoos are reliant on public support for their continued existence. I’ve seen several people say they will never visit the zoo and if they hold true to their word and their example is followed, Copenhagen Zoo is looking at tough times ahead.

Their decision to use the killing as an educational exercise was the best thing they could do, though I do find it strange that a lot of the outrage seems to be directed at the public nature of everything rather than the killing in the first place. The outrage is precisely why this should be done in public, though I do think the attitude of the zoo has been a bit too confrontational and almost designed to cause outrage.



Finally, the lions. Lions have been synonymous with Longleat for decades so to hear that they have killed six is almost unbelievable. As with all these stories there is public outrage, with people unable to understand how an organisation that has looked after lions for over 50 years can end up with killing an entire litter. As with all these stories, digging a little deeper reveals a more complex story. A statement from Longleat was given to HuffPo where they explained why they felt the litter needed to be destroyed. The cubs had genetic problems due to inbreeding which was could result in brain tumours and was already causing behavioural problems. From their statement,

“. . . all [cubs] individually exhibited adverse neurological signs such as ataxia, incoordination and odd aggressive behaviour that were not considered normal . .  One of the cubs had to be put down because he was attacked by his brother and by Louisa [his mother]. The further lions referred to were put down due to associated and severe health risks.”

From this statement it seems that euthanasia was an inevitable and unfortunate consequence of inbreeding in their mother (breeding that did not occur at Longleat). It highlights why breeding programs must be carefully monitored and controlled and why animals like the giraffe should not enter the breeding population.


This has turned into more of an opinion piece than I’d intended which was, I suppose, inevitable considering the contentious nature of the stories. I hope I have shown that there are more to the stories than the headlines and they are more justifiable than they may first appear.

Zoos play an important role in conservation and education. They have to make difficult, unpopular decisions at times and when they do it is vital that they explain clearly their scientific rationale. The public are quick to react without getting all the facts and if you don’t explain your case carefully you risk a backlash that can have significant negative consequences. The science may be sound but the ‘politics’ surrounding the stories is more controversial and must treated with as much care as the scientific decisions that instigated them.

Author: Sarah Hearne, hearnes[at]tcd.ie, @SarahVHearne

Image credits: Wikimedia commons

Systematic Reviews


Before I came to TCD, I spent my last six months at Lancaster University working with Dr Georgina Key on a systematic review of methods to make agricultural soils more resilient to threats like climate change, and erosion. What is a systematic review I hear you cry? Allow me to elaborate, and share some of our experiences from doing something slightly different.

A systematic review draws together and summarises the available scientific literature surrounding a particular topic or method. The Cochrane Collaboration, which produces systematic reviews in medicine and healthcare, defines such reviews as “a systematic, up-to-date summary of reliable evidence”. The aim of a systematic review is to provide the public, policy-makers and practitioners with a clear, unbiased picture of the latest, most reliable science on a certain practice, so that they can make informed decisions on how suitable that method is likely to be for them.

The goal of our systematic review was to produce a list of actions that could be used to improve the resilience of agricultural soils under pressure from a variety of threats. The first steps we took involved coming up with a list of key issues that would be important to manage agricultural soils in order to maintain sustainable food production in the future. We then took to the peer-reviewed literature, searching for experimentally tested solutions to the issues we’d identified, using a combination of journal trawls and keyword searches.

Journal trawls involved identifying relevant journals, like Soil Use and Management and Geoderma, then systematically searching all volumes of each journal for articles involving the issues we’d identified. Our keyword searches took a more targeted approach, using combinations of keywords to whittle down a selection of relevant articles. These approaches produced a large number of articles – far too many to summarise effectively in the time available – so we shortlisted them based on a number of criteria, foremost of which was ‘Has the action (e.g. non-inversion tillage) been tested using a robust, experimental design?’ We also filtered our keyword searches, carried out in ISI Web of Science, to the top 100 results, sorted by relevance.

Having eventually come up with a list of articles that tested the actions we’d identified, we set about summarising them. This was done according to a set template, using a specific style. This was initially restrictive, and difficult to adapt to – each article had to be summarised using specific vocabulary, within 200 words – but it ensured that the summaries would be understandable by people without a science background, and that the key message of the article wouldn’t be obscured by our own prejudices regarding the research.

Writing the summaries was the most time-consuming, but also one of the most rewarding, aspects of the project. By writing lots of summaries, we started to develop more of an understanding of how to write about science in a way that completely avoided jargon. This isn’t as easy as it sounds! But it is a vital skill for scientists to learn, in order to communicate their work to the public, and the people who will eventually turn it into policy. Having read lots of abstracts, those that stood out were the ones that communicated the message of the paper succinctly, in language that a non-expert could understand.

The article summaries and key messages from our short synopsis are now online– you can select an ‘action’, and read through the key messages, definitions, and all the evidence that we found and summarised for the use of that action, and its effects, in agriculture. I think there’s real value of having all this information collated together in one place, and communicated in an understandable way. Our soils synopsis is one of a number of synopses that you can browse through on the NERC Sustainable Food Knowledge Exchange Programme website.

Although it was only a short project, putting the synopsis together was a rewarding experience for both of us, particularly in terms of communication skills developed and networks joined. The synopsis that we produced is by no means the final product, and will need to be updated in the future to keep up with the amount of continual research in this area. The next step is to assess the synopsis, and its implicit recommendations, by asking experts and practitioners in the field how effective they think the research we covered would be, if it was implemented. This step should provide valuable feedback, helping to highlight any gaps in our synopsis, as well as improving future synopses.

Authors: Mike Whitfield and Georgina Key

About the authors

Mike Whitfield has a PhD in peatland carbon cycling from Lancaster University. Last year he helped to design and implement a long-term grassland biodiversity experiment in the Yorkshire Dales and worked with Georgina Key on the soil sustainability synopsis for six months, before moving to Dublin. Mike’s current postdoc at TCD focuses on modelling greenhouse gas emissions from agricultural land, with the aim of producing a map of estimated greenhouse gas emissions from soil for the whole of Ireland.


Twitter: @mgwhitfield

Georgina Key has a PhD in ecosystem service provision, specifically conservation pest control. Having completed her first postdoc at Manchester reviewing literature on maintaining soil fertility, she is currently doing an assessment of the literature in collaboration with Cambridge University and Waitrose. In the future she hopes to work with tea and coffee companies, implementing sustainable growing practices and improving rural livelihoods.


Twitter: @KeyGeorgina


Image credit: Treehouse1977 on Flickr


A review of the ecology of the common zombie



In recent years fear of the zombie apocalypse has been an increasingly important subject in public media. Cinema, television, novels, both graphic and written, as well as computer games cover this subject more and more frequently. Public awareness of zombies has reached an historic height. However, within the scientific community this topic has rarely been investigated at all. The aim of this review is to summarise present day knowledge on zombies and assess its suitability in a possible encounter.

Generally, there is not much consensus regarding the nature of the common zombie, however a few traits seem to be found throughout the literature. Most sources agree that the zombie is a degenerate form of humans, lacking any form of higher intelligence. Some sources even describe them as devoid of any form of bodily function, defining them as the living dead. This would indicate that zombies have developed a unique way to transport carbohydrates, oxygen and carbon dioxide transport. One hypothesis is, that zombies are capable of consuming their own body for energy production. This is supported by the fact, that most sources describe them as slowly degenerating. Their main diet seems to be human flesh with a special preference for brain tissue. Most sources agree that the common zombie is indeed monophagous, refusing any other food source. Having effectively no brain function the zombie’s hunting strategy is limited to cursorial hunting. However, unlike more elaborate hunters such as wolves, zombies do not seem to display any cooperative strategies, even though the presence of human prey seems to trigger clustering of zombies. Even though most sources are agree that zombies have no natural enemy they have developed a remarkable defence mechanism. They can suffer significant amounts of injury, including destruction of the heart or complete blood loss, and still be fully functional. The only commonly accepted weakness of the zombie seems to be the brain, as severe brain damage is generally described to be lethal.

Generally it is accepted that zombies reproduce via infection, mostly through bites or when zombie blood gets in touch with an open wound. All sources agree that the human epidermis cannot be penetrated by zombie blood or saliva. Zombies are always described as r-strategists, showing rapid reproduction rates and no ability to adapt to changing environments, though some sources report the ability of zombies to hibernate for months or longer if no food is available.

We conclude that the zombie is a dangerous hunter which compensates limited rational abilities with an extreme endurance and low vulnerability. Their high reproduction rates makes them an extreme danger for any human society. However, due to their limited food range and lack of adaption to changing environments it might be possible to starve them out as any kind of muscle movement requires energy in the form of carbohydrates. Given their limited cerebral capacity it should be possible to effectively avoid zombies and therefore remove their only food source. Due to their high reproduction rate the population should collapse quickly even if single human individuals cannot avoid predation.

Author: Jesko Zimmerman, zimmerjr[at]tcd.ie

Image Source: Wikimedia commons

Seminar Series: Nathalie Pettorelli, Institute of Zoology, London

space monitoring

Part of our series of posts by final-year undergraduate students for their Research Comprehension module. Students write blogs inspired by guest lecturers in our Evolutionary Biology and Ecology seminar series in the School of Natural Sciences.

This week, views from Sharon Matthews and Sinead Barrett on Nathalie Pettorelli’s seminar, “Monitoring biodiversity from space: a wealth of opportunities”.

Space, the final frontier for ecology?

Okay, you got me.  I am a trekkie who is fanatical about anything space related. So when I saw that this week’s seminar was to do with conservation biology from space, I was hooked!  Dr. Nathalie Pettorelli from the Institute of Zoology, London spoke with passion and enthusiasm about a new wave of ecology; monitoring species and ecosystems from space.

We were treated to information about remote sensing and how data from satellites can be used to help ecologists in the tasks of assessing population size and habitat condition. Earth observation (EO) data is free and is ripe for the picking.  Satellites are able to “boldy go where no one has gone before” or very few people have (sorry, I will stop with the star trek quotes now!).  They can get information on places that are often inaccessible and inhospitable for the lowly researcher like Antarctica and the Sahara desert.

One of the major tasks ecologists face is estimating the size of a population.  Dr. Pettorelli talked about an ingenious research project that used information from satellites to gain an estimate of the population of emperor penguins (Aptenodytes fosteri) in Antarctica.  Emperor penguin populations may be affected by climate change in the next few decades due to changes in sea-ice distribution and therefore it is important to get an estimate of the extant population.

Frettwell et al. (2012) examined quick-looks from three different very high-resolution satellites.  These have a resolution of ~ 10m and are able to show great detail.  The researchers looked for staining on images and classified it as snow, penguin, shadow or guano.  When areas with penguins were identified, they analysed the penguin pixel area through regression equations.  The statistics gathered from this were used to convert the area of penguins to population numbers.

In this study, the identification of a penguin from a pixel area was done by human interpretation and this led to some error especially in areas of high guano staining.  This could be resolved with future development of higher resolution satellites.  However, there were other issues that arose from using this technology.  Researchers identifying penguins from pixels made an assumption that a pixel constituted one individual when it may in fact have been an individual with a chick close to it.  This can affect the estimated population size.  The kind of error association with using satellites makes me think that this satellite approach should be backed up with other methods such as field study where possible.

Remote sensing can allow research to be undertaken over a broad spatial and temporal scale.  One of Dr. Pettorelli’s projects involved using EO data to assess a game reserve in central Chad for its ability to sustain a reintroduction of the Scimitar-horned Oryx (Oryx dammah).  A vegetation index (an indication of ‘greeness’) and annual mean precipitation, were assessed over a 27-year period for this game reserve. The results showed that precipitation was a main driver of vegetation dynamics and there was an intense greening in the south of the region.  Dr. Pettorelli also found that there was a contraction of the transition zone from north to south. This was an area that was identified as most suitable for the oryx.  This study showed how remote sensing can help inform ecologists about variation in a region over time.  It can greatly enhance the success of reintroducing a species into a suitable area.

There is no doubt in my mind that data from remote sensing can help ecologists in their work but I don’t think it should be used in isolation. Ecosystems involve a complex mix of interactions of many variables. Therefore, this approach could be used alongside other tried and tested (down to earth) methods of studying ecosystems and biodiversity.

Author: Sharon Matthews


Evidence of Global Change is Sky High

As we all know, climate change is affecting the world in which we live. One aim of scientists is to find out the extent of this change. At a seminar given recently in Trinity College Dublin, Dr. Nathalie Pettorelli from the Zoological Society of London informed us about a new method of doing this. With benefits including the cost, its sustainability, reproductivity and standardised information, satellite usage as a way to monitor biodiversity seems like an excellent option.

Dr. Pettorelli mentioned the vast array of options of satellites available for monitoring depending on what you want to find out in the study. For example, very high resolution imagery has been used in order to count penguins in colonies, Landsat has been used to study the gorilla habitat in Virunga and LiDAR satellites which give a 3-D image have been used in the Bavarian forest. But what interested me most was when Dr. Pettorelli mentioned the ability to monitor vegetation indices and how this technique was used in the reintroduction process of the Scimitar-horned Oryx in Ouadi Rimé-Ouadi Achim Game Reserve in central Chad.

The Scimitar-horned Oryx was last found in the wild in the 1970’s. However it has been kept in captivity and there were plans of reintroducing it back into this area in central Chad. In order to do so, a habitat assessment was undertaken to establish whether the area would still be suitable for the species to live in. The primary productivity over the past number of years was viewed using remote sensing (satellite) techniques. It was seen that the vegetation in the north had significantly dried while the area to the south showed intense greening. Because the Oryx lives preferably in sub desert regions, suitable habitat here was declining and it was not advised to reintroduce this animal to the area.

To me, this shows just how important this method of monitoring is. Due to the increased changes that come about as a result of climate change, species are no longer suited to their natural habitat. Although it wasn’t mentioned in detail in the seminar, it struck me that one use of this satellite method of monitoring would be to use it in assisted migration. This is a method of conservation that involves humans undertaking a translocation of an animal or plant species. This is used when a species can no longer survive in their habitat and so must be moved to a more suitable area. This method of conservation is debatable as there are many associated risks involved including the impact on original species in the new habitat. However, with scientists doing research on this to study possible effects, it may save a species from dying out. Suitable habitat needs to be found for assisted migration to work. The methods that Dr. Pettorelli uses in her habitat assessment in central Chad could be the ideal way to find these habitats needed. This highlights the need for this new method of data collection. Because it is done at such a big scale, it seems like an excellent way of finding large habitats suitable for a new species, whether it’s a tree or a large carnivore.

Changes are occurring globally as a result of anthropogenic actions, and species worldwide are dying out as a result of this. It is clear from the numerous examples mentioned at the seminar that there are many uses of satellite imagery in monitoring biodiversity worldwide. After hearing Dr. Pettorelli talk about this subject, I left realising just how important technology such as satellites are in a time when global change is sky high.

Author: Sinead Barrett


Please consider this a polite spanking


The recent hilarious #SixWordPeerReview hashtag on Twitter got me thinking about the first ever review I got for my first ever paper (thanks @Phalaropus for the reminder!). I thought I’d share it here (and if you want to see if you agree with the reviewer, the paper was eventually published in Global Ecology and Biogeography: Cooper et al 2008).

As a bit of background, I collected lots of data during my Masters project on life history traits of amphibians and then looked at macroecological correlates of clutch size, body size and geographical range size, and also at how these variables correlated with IUCN Red List status. My dataset contained over 600 species of amphibian – pretty much all the species I could get hold of data for at that time. Here are the “best” comments from the reviewer (the whole review was two pages long so I’m not reproducing the whole thing). My favourite comment was at the end.

“the study was done on less than 10% of the appropriate species […] Such academic laziness is inexcusable and scandalous”

“there are many instances where the authors appear to pull the wool over the reader’s eyes”

“It is a strong reflection of the workers to submit such a poorly conceived and obvious “quick and dirty” first stab at something that needs to be taken much more seriously”

“the clear misinformation in the abstract […] is obviously the kind of positive spin more associated with politics than science.”

“Who would be fooled by such tricks as claiming that data on <10% of amphibians is “large”. Certainly not this reviewer.”

“Without even a cursory explanation for such an egregiously low sampled diversity, it is hard to glean any merit at all from this study.”

“How can sane scientists think that <10% of the diversity would be sufficient to advocate involved analyses and draw conclusions?”

“This is another example of embarrassingly obvious laziness.”

“That goes beyond even forgivable bending of the truth”

“If any of the authors were thinking, they would have realized that ALL of the reasons to do a phylogenetically corrected analysis are not met by their data. In fact, if there was ever a gross and more ill-conceived reason to NOT do a phylogenetically corrected analysis, this would be the dataset to do so on.”

“Errors in basic addition are another serious embarrassment” [FYI the maths was fine, the reviewer made the error not us!]

“I could go on, but I think that it is not worth my time at this point to find more problems (there are still many other issues the authors should go back to first principles on)”

[And finally the crowning glory of all the comments I’ve ever received in a review]:

“Please consider this a polite spanking.”

As a first year PhD student this obviously upset me. But after a quick cry, a slice of Battenberg [cake], and a couple of pints of cider I was able to see the funny side! I still keep a print out in my office as a reminder that even when I get a bad review, it can never be as terrible as my first review! I’ve never worked out who the reviewer was, but as the editor said they were clearly having a bad day! I hope things got better for them! This review also reminds me to always write constructive comments, especially for PhD students, and if I don’t have anything nice to say I write a short review rather than airing all my grievances in print!

Author: Natalie Cooper, ncooper[at]tcd.ie, @nhcooper123