Geographies of the microbiome: call for papers for a special edition of Geo

GEOGRAPHIES OF THE MICROBIOME

Call for papers for a special edition of Geo: Geography and the Environment

Microbial communities are fundamental components of every ecosystem and every species on the planet. Although recent advances have been made in understanding their interactions with human, animal and environmental well-being, many of the specific geographies and functional roles of microbial life remain uncertain. Answering these questions requires new forms of enquiry which reach across the domains of life, spaces, and disciplinary perspectives.

We are seeking high-quality contributions (original scientific papers, reviews, perspectives and data papers) about the geographies of the microbiome. Papers would bring the different sub-disciplines of geography into dialogue in seeking to make sense of these patterns and processes. We are interested in the range of interdisciplinary and collaborative approaches (e.g. human / physical / biological / citizen science practices) which are helping to further our understanding of the connections between microbial communities and spatial processes at different scales. We encourage submissions which discuss the methodological challenges of mapping microbiomes and managing microbial data, including engaging with the complexities of taxonomies and metagenomics. We also welcome studies which focus on managing microbes, as well as recent perspectives on both antimicrobial resistance (e.g. practices of spread, containment, evolution) and the recognition of microbes with respect to questions around more-than-human geographies. We are interested in contributions that explore the social dimensions and political ecologies of microbiome science and its translation.

Geo: Geography and the Environment has an international and interdisciplinary reach, making it ideally placed to facilitate exchange on emerging work on the microbiome across the spectrum of geographical and environmental research.

This RGS-IBG and Wiley journal publishes open-access articles, funded through Article Processing Charges (APCs). These are normally available through your Higher Education Institution; you can check your eligibility by submitting your institution and funder here. There are also a series of discounts and waivers available from Wiley. Further full-fee waivers will be considered for high-quality submissions for this special issue on a case-to-case basis, where authors are unable to access other institutional funds for APCs. Please contact journals@rgs.org for queries relating to APCs. To ensure that editorial decisions are never influenced by ability to pay, the editors are not involved in correspondence with authors regarding payment of APCs.

The submission deadline for manuscripts is February 2018. We welcome early enquiries to the special edition editors:

Arwyn Edwards: aye@aber.ac.uk
Jamie Lorimer: jamie.lorimer@ouce.ox.ac.uk

 

Remediating the inequalities of geographic knowledge production through ‘chromatographical’ visualizations

There has been significant academic coverage of the inequitable power dynamics of geographic knowledge production (c.f. Simonsen 2004; Ferenčuhová 2016).   By now, we are well-versed in the ways in which some representations and narratives win out over others.  We are attuned to the fact that the production of geographic knowledge is also a story of imperialism replete with racialized and gendered processes.  Emerging from this scholarship is the notion of a lopsided geography (Friedman 2016) characterized by the starkness of divisions between the core and periphery wherein some places are represented strongly and others remain largely absent.  Values and practices continue to be shaped by a Northern research agenda.  Additionally, the rich debates and discussions of strategies to decolonize knowledge tend toward the theoretical with few methodological interventions.

In our paper in Geo (http://onlinelibrary.wiley.com/doi/10.1002/geo2.38/full)  we attempt to redress some of these inequities by developing a new method for visualizing knowledge production which goes beyond formalized indicators. To illustrate, we chose first to focus on the location of selected dominant critical theories in Geography. By conventionally mapping two sites of theory production (critical GIS and critical urbanism), we demonstrate how normative methods reinforce lopsided geographies by relying narrowly on authorship and scholar affiliation. Our choropleth maps of these two theoretical strands in Geography double as a story of which places are being annotated and who participates in this process.  They also illustrate how conventional indicators silence the contexts informing the research.  The data is ‘extracted’ in one place (often in the Global South) and ‘processed’ elsewhere (often in the Global North).

Figure 1 conventionally represents the production of knowledge for critical GIS and critical urbanism (i.e. the number of country publications per every 10 active geography departments).  Critical theory, exemplified through these two schools of thought, mainly tends towards ‘Western-centrism’.   Production is dominated by the US, Canada, the UK, Australia and South Africa (as the exception). This result, generally, is consistent with our argument that the representation of knowledge through these conventional means suggests a ‘global intellectual divide’.

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Figure 1. Conventional representation of the sites of both critical GIS and critical urban theory knowledge production

To get at the heart of the inherent separations embedded in the representation of scholarly research production, we must acknowledge the uneven distribution of value between data production and the generation of theory.  The conventional map is in effect a series of bundled components that must be unpacked in order to bring to light the contexts that have generated both the data and subsequent  conceptual work.  We propose a ‘chromatological’ visualization whereby, just like in Chemistry, we extract the absorbed materials that are not currently visible or acknowledged.  The heuristic device of chromatography subjects the product (research, data and knowledge production) to a process of scrutiny which serves to ‘write in’ the separation. In other words, we separate the building blocks of critical geographic scholarship by articulating the absorbed components methodologically.

Figure 2 seeks to capture the multiple geographies involved across research processes.  Our chromatographical map is based on our review of the publications with more than 50 citations for both critical geography theories.  In it, we separated the conceptual and situated (empirically based) publications. Using the situated publications, we developed a table showing the frequency with which a country is used as a field site (i.e. where the researchers gathered their empirical data from and/or made their empirical observations). This counter mapping now shows countries such as India and China conventionally represented as part of the ‘silent side’ of knowledge production.

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Figure 2. Chromatographical representation of the sites of knowledge production for both critical GIS and critical urban theory

Our choromatological framework enacts a way of relational thinking currently obscured in discussions of geographic knowledge production.  The methodological alternatives described in our work conceptualize actors, field sites, and research products as a multiplicity of inter-scalar interactions.  Sites that were formally ‘off the map’ can now be recognized as new generative sites crucial to critical geographic scholarship.

Margath Walker is an Associate Professor in the Department of Geography and Geosciences at the University of Louisville. Emmanuel Frimpong Boamah is an Assistant Professor in the Department of Urban and Regional Planning at the State University of New York, Buffalo 

References

Ferenčuhová S 2016 Accounts from behind the curtain: history and geography in the critical analysis of urban theory International Journal of Urban and Regional Research 40 113–31

Friedman U 2016 The lopsided geography of Wikipedia The Atlantic 21 June

Simonsen K 2004 Differential spaces of critical geography Geoforum 35 525–8

The place of data papers: Producing data for geography and the geography of data production

Binary Tempest LogoGeo: Geography and Environment recently published two papers on data practices in the geography. It is an accident they were published on the same day, but it presents an occasion for us, as editors, to reflect on two related issues in academic writing and publishing: the growing role of the data paper and the spatial (and often unequal) distribution of value between data production and theory generation.

It is also good opportunity to remind people we have been promoting debate on open science and data in Geo since our 2015 launch, with the opening commentary from Sabina Leonelli et al and blog responses from George Adamson and James Porter. These pieces are all worth returning to now. The issues that emerge as practices around data sharing meet academic incentives, interdisciplinary research and public outreach continue to gather pace, with data papers offering a new venue for exploring them.

The TEMPEST team have produced the first data paper published in Geo on Dealing with the deluge of historical weather data. This paper explores the practices of assembling a digital resource of historic weather data from documentary archives. It positions their work in relation to other online datasets and offers this resource as an opportunity for future research and public engagement. It also demonstrates an exciting alternative to the drive that Adamson suggests follows the “pressure to analyse, interpret and publish before any data is shared”.

We are keen to encourage more data papers in Geo, both before and after analysis. At its simplest, a data paper describes how a dataset is assembled; reflects on its context and value; and invites others to use it by linking to the data. As the TEMPEST paper indicates, these issues are always complex in practice. Data papers are thus increasingly important in enabling connections in data-rich parts of the discipline and filling gaps in data-poor areas. These topologies of data availability are often complex and increasingly political.

Academics, and others, are facing renewed questions over the value of data and access to it. Access to government data may be removed – as in the disappearance of climate change pages and animal welfare data from US websites. Access to data may be restricted by commercial interests – by excluding data points to shape narratives or introducing high costs for data use.

Conversely, for academics, providing access to data is increasingly mandated. We are being asked to invest our time and resources in curating and archiving data produced in projects by funders. We are also asked to justify why we can’t use existing datasets as we search for new funding. Currently these processes are not well linked, meaning time spent curating data and resources spent collecting new data may both be wasted.

The second paper published, by Margath Walker and Emmanuel Frimpong Boamah on Alternative visualisations of geographic knowledge production indicates the political issues in other aspects of data generation and use.  Their work maps the relation between data production and concept work in critical urban studies and critical GIS, prompting some critical geopolitical questions.

These include: who is involved in generating our data, who is included in generating theory, and where are they both located? How are credit and value distributed across these practices, how do these reproduce existing global inequalities in knowledge production, and how might we enact these relations differently?

We are used to thinking about the responsibilities we have to the stories our respondents contribute to research. But, we are perhaps less used to considering our responsibilities to data and related questions around the ownership, interpretation, openness, and access to this data. The value attributed to ‘progressing’ theory over advancing data reinforces the unequal geographies that Walker and Boamah map out.

Data papers can play a part in exploring and addressing both issues. The detailed explanation of data production in a data paper is a way of reflecting on challenges within a project and of facilitating the recontextualization of data required for reuse beyond it. They also provide a further avenue for redistributing the value from data, by acknowledging the multiple geographies and authors that underpin data production, transforming these into a published research output, and opening space for different interpretations.

We are grateful for the questions that Veale et al and Walker and Boamah have prompted about the aggregation of weather data and the geographical distribution of value through theory and data. We hope they will inspire others to explore the challenges of putting data together and the responsibilities we share in authoring data and facilitating access to it.

Gail Davies, co-editor in chief, Geo: Geography and Environment

Joining Up Divided Data: The TEMPEST Database

We were very pleased to launch TEMPEST – our database of historical weather events – at this year’s RGS-IBG Annual Conference. With the support of the Geo team we organised a panel discussion and a small display of original and facsimile archive materials. Both were connected to a recent paper in Geo‘Dealing with the deluge of historical weather data: the example of the TEMPEST database’ – the journal’s first ‘data paper’.

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‘The great frost’:  Frontispiece for The cold yeare 1614: A deepe snow: in which men and cattell have perished…or of strange accidents in this great snow, attributed to Thomas Dekker

Following an introductory post by the journal’s editors, in this contribution we wanted to reflect on our motivations for writing the paper, and creating TEMPEST, particularly in designing it as a freely accessible online resource.

Interest in historical weather is far from a new area of investigation. A number of well-known chronologies of British weather have been published and over the past 20-30 years, attempts have been made to produce searchable databases of historical weather information (instrumental data, proxy data and narrative descriptions of particular phenomena). It is widely recognised that these compilations of data or datasets have utility for the scientific study of climate, as well as satisfying the simple desire that many people have to know more about past meteorological events and their impacts on particular people and in specific places. However, in spite of rapid advances in technology, the growing amount of data (generated by labour intensive means) and the popularity of such resources, and the definite benefit that could come from uniting them, efforts largely remain separate. They are divided because they are technologically incompatible (the relevant data comes in many different formats covering instrumental observations to lengthy descriptive accounts in different languages, and database systems are constantly changing), or because they are funded only for finite periods. They can quickly become forgotten when new projects take priority or face obsolescence and lie in need of maintenance. They may also remain little known or largely indiscoverable, can be difficult to get to grips with or inaccessible to the general user.

As a research team we had some difficult conversations regarding the format, availability and deposit of our research data. It was a significant time investment to input the data into TEMPEST, time that could have been spent writing papers or our currently unfinished project book. However, we persevered and it now contains c. 18,000 event records – and we have already experienced the rewards. TEMPEST makes it possible to quickly see where we have gathered multiple narratives detailing the same event (creating a picture of the geographical extent of impact), and to piece together particular seasons or the weather of particular years or groups of years. Without TEMPEST these tasks would have required another significant time investment, and would have been reliant on the quality of our memory of the research data. Full recollection would have been an impossible challenge given the sheer quantity of data we have collected.

Although the creation of a freely available online resource was detailed in our original funding application to AHRC, as the project progressed and the volume (and quality) of our research data surpassed our expectations, team members were understandably reluctant to have our research data freely available before we had completed writing it up. However, the desire for others to use it, and our belief in its utility and popularity won over. Yet, even with an obligation to the AHRC to make our data available, but no dedicated arts and humanities data repository in the UK, it took some time to explore the various options that existed for depositing our dataset. We have just completed depositing our research data with CEDA (Centre for Environmental Data Analysis) where is it available for registered users to download as .csv files and analyse within Excel or other statistical software. A reference and DOI is provided for the dataset, alongside guidance notes relating to the data format, collection method and quality.

The database is also now ‘live’, though we may still change the url as a result of institutional moves and the conclusion of the funded period of the project.

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Putting our own research data ‘out there’ is not enough. Few people are likely to find it unless we engage in targeted publicity and promotion, and it remains the case that significant time investment is required to properly come to ‘know’ the data, and use it to its potential – it is quite difficult to just ‘dip in’. We hope to use some of the time and finances allocated by a AHRC ‘Follow on Funding’ project to produce some sample ‘database stories’, promote the resource, and to embed and reconnect it with the archival repositories from which we have drawn data. We will also circulate our Geo paper to researchers involved in connected initiatives throughout Europe and further explore how it might be informally ‘joined up’. We also hope that we’ll be able to trace usage of our research data, whether it be by other academics wanting to contextualise their own research, by climate scientists developing computer models, by members of the public interested in the weather history of the place where they live, or by archive professionals interested in linking with other archives through documentary connections. As publications relating to the project are completed, where funds can be secured we are publishing them through the gold Open Access route, and we have definitely received wider readership and more interest in our work as a result – we can now also include reference to our research data and encourage its use.

Lucy Veale is a Research Associate in the Department of History, University of Liverpool, Georgina Endfield is Professor of Environmental History at the University of Liverpool, and Sarah Davies is a Reader in the Department of Geography and Earth Sciences at Aberystwyth University. 

Digital Data: Opening up the Weather Archive – Geo at #RGSIBG17

Join us on Wednesday 30 August at the RGS-IBG Annual International Conference for our Geo sponsored session ‘Digital Data: Opening up the Weather Archive’ (Education Centre, session 3, 14.40-16.20), convened by Georgina Endfield (The University of Liverpool), Lucy Veale (The University of Liverpool), and Sarah Davies (Aberystwyth University).

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This session brings together researchers working on weather and climate history, existing or potential end users of research databases, and custodians of manuscript weather data, to critically evaluate the construction, management, application, and implications of digital weather data. Emphasis will be placed on thinking about the future of these tools and how we can improve connections between them, both technical and geographical.

The session will also include a live demonstration of the TEMPEST database (Tracking Extremes of Meteorological Phenomena in Extent across Space and Time). TEMPEST’s c.20,000 records are drawn from primary research into original documentary sources held in archives around the UK and offer personalised and geo-referenced insights into the relationship between society and extreme weather in the UK spanning a period of over 400 years.

Audience members are encouraged to send in live queries relating to historical extreme weather events via twitter (using the conference hashtag, #RGSIBG17); the discussion will also be of interest to researchers working on databases of other kinds.

Read the associated data paper: Dealing with the Deluge of Historical Weather Data: The example of the TEMPEST (Tracking Extremes of Meteorological Phenomena Experienced in Space and Time) Database.

Veale L., Endfield G., Davies S., Macdonald N., Naylor S., Royer M.-J., Bowen J., Tyler-Jones R., and Jones C. Dealing with the deluge of historical weather data: the example of the TEMPEST database. Geo: Geography and Environment. 2017, 4 (2), e00039

Visit the associated display in the Ambulatory: A Deluge of Documentary Weather Data, curated by Lucy Veale, Georgina Endfield and Sarah Davies.

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This display explores extreme weather events in the UK, drawing on primary archival materials used in the AHRC funded project ‘Spaces and Experience and Horizons of Expectation: The Implications of Extreme Weather, Past, Present and Future’. It also features primary archival materials from the RGS-IBG archives, including resources relating to the meteorological investigations of the Terra Nova expedition 1910-13, led by Captain Robert Falcon Scott.

The database and project have an audience beyond academia. The project-team has worked with the RGS-IBG Schools team to produce a range of resources for teachers and students.

Watch the online lecture: Extreme Weather – The history of human-environmental interactions and our climatic past  Georgina Endfield explores the weather histories of unusual and extreme weather events, weather memories, and human responses linked to these events in an RGS-IBG School Member Lecture. (Free to access for a limited time).

Listen to Georgina Endfield on the RGS-IBG ‘Ask the Expert’ Podcast Series
In this podcast Laura Price (RGS-IBG) spoke to Georgina about the TEMPEST. The podcast explores how and why extreme weather events have been inscribed into our cultural fabric. (Free to access).

Primary teacher guide *coming soon*
The guide aims to promote the use of the Tempest weather archive in schools, and pupil’s understanding of historical weather and climate extremes more broadly.

Animation *coming soon*
The animation, for KS4 students, introduces the historical diversity of weather experiences in the UK. Using examples from the RGS-IBG archives, it explores the environmental and cultural implications of the events.

Interested in finding out more about extreme weather geographies? Take a look at Georgina Endfield and Lucy Veale’s Discovering Britain trail, the Great Dun Fell walk. It explores the Helm wind (Britain’s only named wind), the landscape of the North Pennines, and the work of Gordon Manley, a geographer who pioneered the collection of meteorological data.

Revisiting the effects of climate change on salamander body size: the role of natural history collections

Our recent paper, The relationship between climate and adult body size in redback salamanders (Plethodon cinereus), found that salamanders were larger in warmer parts of their range. We also found that that body size increased significantly in places where the climate had become hotter and drier.

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Image credit: Brian Gratwicke

Small-bodied lungless salamanders breathe through their skin, and tend to come to forage on the surface in cool, damp conditions associated with spring and fall, which is the best time to find them. They have thrived in the cool, temperate climate of the Appalachian Mountains, making this region a global hotspot for salamander diversity. Because of their preference for cool, damp environments, salamander biologists worry that predictions of warmer climates and more intense rainfall events and longer dry spells in between may be bad news for these distinctive creatures.

Several studies using museum specimens found that salamanders in warmer areas have larger bodies, but one recent study suggested that salamanders were actually shrinking in response to climate change. Subsequent papers have dwelled on the challenges of using museum specimens to draw these types of conclusions, but none re-examined the actual phenomenon of the shrinking salamanders. We designed a new study to revisit the question using museum specimens in a way that accounts for some of the previous limitations.

We selected redback salamanders, which are one of the most abundant vertebrates both by number and biomass in forests in the Eastern United States. One classic study by Thomas Burton and Gene Likens at Hubbard Brook Forest in New Hampshire found densities of about 3,000 salamanders per hectare, mostly redbacks.  This wide-ranging, abundant species is also very well represented in museum collections. About 70,000 redback specimens are held in the Smithsonian’s Museum of Natural History, mostly collected between 1950 and 2000.

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A Redback salamander Plethodon cinereus specimen at the Smithsonian Museum of Natural History. Image by Brian Gratwicke

A collection of this size allowed us to pre-emptively select our comparison groups in a way that would eliminate sampling bias, maintain large sample sizes and maximize our power to answer the question.  We corrected our samples for potential sources of sampling bias including seasonal collection bias and potential destructive sampling bias. We found that redback salamander body size actually increased 1.8% in the places that had warmed significantly. Our observations do not really shed any light on whether climate-change is a potential threat to redback salamanders, but there does appear to be a measurable effect on the species.

The nature and culture surrounding natural history collections is changing, and very few redback salamander specimens were lodged after the year 2000, restricting the time period we could analyze. This likely is a product both of the ethics debate surrounding indiscriminate collecting, and the growing popularity of new citizen science tools like iNaturalist which create photographic specimens in publicly accessible databases with critical collection information. We were able to use citizen-science databases like the Maryland Herp Atlas  and iNaturalist to verify that the salamanders are still common in all the counties that have warmed significantly, but body size data were not available. We actively support and participate in these non-destructive efforts, but view them as complimentary to well-curated natural history specimens, rather than a substitute.

Brian Gratwicke is a biologist at the National Zoo’s Smithsonian Conservation Biology Institute in Front Royal, Virginia, USA

Multiple stressors and ecological surprises

The expanding global human population, now about 7.5 billion, is increasing the pressure that we as a species put on the environment.  2016 was the warmest year ever recorded, and temperature records continue to be exceeded. Each year, more natural ecosystems are lost to dam construction, deforestation and urbanisation. Rates of species invasion are increasing, and pollution events continue to pressure native wildlife. Many ecosystems are now threatened simultaneously by these multiple human-caused stressors, yet we still know very little about their combined interactive impacts.

In our paper in Geo (Linking key environmental stressors with the delivery of provisioning ecosystem services in the freshwaters of southern Africa) we review the impacts of multiple stressors on ecosystem services in freshwater ecosystems in southern Africa (e.g. the Okavango Delta; see photo). We chose these systems because freshwaters contribute disproportionately to ecosystem services despite covering less than 1% of the earth’s surface. Freshwater systems are also especially vulnerable to environmental stressors and over exploitation, with water and fish protein growing in importance as commodities, and average species population declines since 1970 estimated at 81% (WWF Living Planet Report, 2016). Communities in southern Africa rely on freshwater ecosystems for critically important provisioning services, such as drinking water and food (e.g. inland fisheries)

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The Okavango Delta

We found evidence that water resources for drinking, agriculture, sanitation and power are declining because of both climate and land use change. In some areas, fish production increased because of dam construction or species invasions, but these stressors can have negative impacts elsewhere. Evidence also suggests that stressors can interact to alter one another’s impacts or promote the proliferation of further stressors.

Multiple stressors often cause impacts which are hard to predict because of both complex interactions between the stressors themselves, and interactions within communities (such as those between species in a food web). These unpredictable impacts have been termed ‘ecological surprises’ and global analyses indicate that they are very common (e.g. http://onlinelibrary.wiley.com/doi/10.1111/gcb.13028). This creates problems for decision makers when prioritising which stressors to manage or control, especially when it comes to the supply of the goods and services which we rely on from natural ecosystems.

We provide a framework to categorise multiple stressor effects on ecosystem services where they can either be additive (i.e. predictable and the sum of their independent effects) or four different types of non-additive ecological surprises.  For instance, nutrient enrichment in Lake Victoria (because of high nutrient inputs from the surrounding catchment) causes low oxygen levels, killing fish (Photo 2). At the same time the nutrients promote growth of invasive aquatic plants (water hyacinth) causing a successive and synergistic multi-stressor interaction whereby the increase in plant biomass triggers further fish kills in the lake. In addition, the introduction of non-native fish (Nile perch) caused a dramatic decline in native fish biodiversity but boosted the overall fishery catch in the lake, benefiting the surrounding populations (see figure below).

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With the growing population, it is becoming difficult to protect biodiversity and rely on our planet’s natural ecosystems for food and water security. Multiple stressors are causing a downward spiral, where our use of ecosystem services threatens the environment and therefore impairs the delivery of these services for future generations.  We need more research into multiple stressors and ecological surprises, and much more needs to be done to reduce the impact that humans have on the environment.

Michelle Jackson is a Researcher at Imperial College London.