Wednesday, 21 September 2016

BGS Hackathon: Tracking change in global volcanic activity... by Katy Mee

The BGS Volcanology team receive regular enquiries from government and media about volcanic activity around the world, particularly if it’s likely to have an impact on UK citizens abroad or there’s potential for humanitarian needs. When we get an enquiry, we normally first consult the appropriate volcano monitoring institution (volcano observatory) for status reports and the regional Volcanic Ash Advisory Centre (VAAC), which produce notifications for aviation about volcanic ash in the atmosphere. Volcanic eruptions may last for weeks or longer and changes in eruption style, intensity and scale can occur over  minutes to hours, so it can be challenging to keep track of what is happening and where new activity is occurring….…this is how our idea for the BGS Hackathon was born……

We pitched a challenge to take the advisories issued by the VAACs and see whether our hackers could use their programming skills to (1) automatically extract the relevant information, (2) populate these data into a database and (3) visualise the data on a map or graph.  Ideally, all of these things would be updated automatically as new ash advisories were released so that we could track changes in activity and look for new volcanoes erupting, in near real-time.

About volcanic ash advisories

There are 9 Volcanic Ash Advisory Centres (VAAC), each with a defined area to monitor, that cover most of the globe. The VAACs use a range of information – from volcano observatories, satellite and ground-based remote sensing, pilot reports and aircraft observations, and weather forecast and dispersion models – to identify and monitor the movement of ash in the atmosphere. They then issue advisories and guidance products for the aviation sector telling them where, how high and in which direction the ash cloud is moving so that pilots can avoid them.

The nine Volcanic Ash Advisory Centres (VAACs) and their areas of responsibility

 The advisories are in a standard format, meaning that they all provide the same categories of information e.g. the volcano name and ID number, summit height, information sources, height of the observed ash cloud, forecasted movement of the ash cloud, date that the next advisory is expected etc. If we could extract information detailing which volcanoes had ash advisories issued for them, when and how often they were being issued, we could produce a graph tracking this change, which could help to:
  • Look for new eruptions at volcanoes
  • Look for the end of an eruptive episode
  • Track the number and frequency of advisories issued in near real-time
  • Look for patterns in eruptive behaviour over the longer term.
Typical structure of a volcanic ash advisory

Team VAAC   

After pitching our challenge at the Hackathon, there was a slightly awkward wait whilst hackers decided which challenge they wanted to accept, but luckily for us, we enticed 5 very enthusiastic hackers with a wide range of skills. Team VAAC consisted of Charlie Kirkwood (environmental geochemist), Ailsa Napier (web developer), James Passmore (GIS and web specialist), Peter Stevenson (geomagnetic data analyst) and Carl Watson (geoinformation business analyst). Between them, they had a wide range of skills that were ideal for our hack challenge: computer programming, databases, geographical information systems (GIS), mapping and visualisation, building websites and…..making pizza – what more could you want?
Head scratching and concentration from Team VAAC

Extracting information from the ash advisories

Task one was to start scraping the relevant data from the ash advisories which are written in HTML code. Three of our hackers – James, Peter and Charlie – started working on this problem, each using the programming language they were most familiar with: ColdFusion, Python and R, respectively. Their task was to write a script that could extract the following information from the advisories and output this in a format that could be easily ingested into a database:
  • Date of the advisory
  • VAAC name
  • Volcano name and ID number (VNUM)
  • Geographic area
  • Date and time of next advisory
ColdFusion was quickly scrapped because we were getting quicker results from the other two methods and so we decided to streamline our resources into those two options. The R script was struggling to process the HTML code, so Charlie decided to work on an archive of advisories in text format from one of the VAACs. This not only gave us a different format to test the R script on, but also give us a back catalogue of data to help us analyse any patterns in activity over a much longer time period. By the end of the day, both Peter and Charlie had successfully written scripts, in Python and R, to extract the data and export these as either .CSV or .XLS files.
 Scraping information from the ash advisories using Python (left) and R (right) programming languages

Data via RSS feeds

As well as checking the VAACs, we regularly check over 30 volcano observatory websites for activity updates on dozens of active volcanoes. Although we receive reports and updates directly from many observatories we’re looking for rapid and global updates. Extracting this information into one database would be programmatically very challenging so Ailsa looked for RSS – or ‘Rich Site Summary’ – feeds, which use a standard web feed format to publish frequently updated information, such as volcanic activity reports. Subscribing to an RSS feed means that web updates are sent directly to you, meaning you don’t have to constantly check the website for updated information. Unfortunately, none of the VAACs use RSS feeds – which would have saved us a lot of time – but several of the observatories do. Ailsa was able to use RSS feeds from the USGS (United States Geological Survey) and KVERT (Kamchatka Volcanic Eruption Response Team) to compile relevant information from both websites onto a single webpage. This shows that for any observatories using RSS feeds, we could quite easily compile their information into one place, saving us lots of time in visiting many different websites.

An RSS feed of current volcanic activity updates issued by USGS (left) can be used to populate our own list of activity updates, saving the need for us to check individual websites

Building the database

Whilst Charlie, James and Peter worked on the scripting, Carl began work on the database. Having already identified what attributes the database table should contain it was fairly straightforward for Carl to set up a new database in Oracle. The ‘NOTE_ID’ was automatically generated whilst all other values were taken directly from the two scrape processes, which were loaded into the database manually. Ideally, we would have wanted these data to be automatically uploaded into the database to save someone from doing it manually, but this would have required writing a separate script to handle this process – something we didn’t have time to address during the hack.


As Day 1 came to an end, the hackers were treated to a healthy concoction of sweets, fizzy drinks, takeaway (and maybe a sneaky beer) before heading off to their programmer pits. And if one round of pizza wasn’t enough, we were treated the following morning to a second dose courtesy of the culinary delights of chez Passmore! Everyone loves cold pizza, right?
Famous takeaway pizza outlet vs Pizzeria Passmore

Web viewer and visualisation tool

The final element of our challenge, after all of the scraping, databasing and stuffing our faces, was to display the results on a web viewer, preferably updated in real-time. So once Carl had set up the database, he and James set to work on adapting an existing web viewer that had been created for the EPOS (European Plate Observing System) project (thanks Simon Burden!), for our needs – the true sense of hacking! The ‘hacked’ web viewer had 4 windows which showed:
  1. A map of all volcanoes, highlighting those with current ash advisories
  2. A list of all volcanoes with current ash advisories issued for them, from which you could select any volcano of interest
  3. The details for the selected volcano that have been extracted from the volcanic ash advisories
  4. A graph showing the number of advisories issued per day for the selected volcano
The windows in the viewer should all be linked so, for example, if you click on a volcano in the map, its details will appear in the other windows, or if you click on a volcano in the latest advice list, it should zoom to the volcano on the map. We did manage to get most of the windows linked apart from the map window, which you could pan around and zoom into independently. This is something that could have been easily linked we just ran out of time!

So all in all, we managed to achieve the majority of our aims in (1) extracting relevant data, (2) building and populating a database and (3) creating a web viewer to display our results – quite an achievement in less than 2 days! We didn’t manage to link all of the elements so these had to be done manually, and we didn’t quite manage the automatic updates so that we could monitor new volcanic activity in real-time.

Web viewer showing 1) map of volcanoes, 2) volcanoes with current ash advisories, 3) details from selected advisory, 4) graph of number and frequency of advisories for the selected volcano


A bit more time was what we wished for……and a bit more time was what we got!! After the shock announcement that Team VAAC were being crowned hack champions (so unexpected that half our team had already left!), we discovered that our reward was more work – 15 days extra to be precise! Oh, and a coaster!

Members of Team VAAC receiving their winners’ coasters.
Note that Carl and Ailsa had little confidence in our chances of winning and had already left :)
(From left: James, Peter, Katy and Charlie).

Since the Hackathon

Peter has continued working on his Python script to extract data from the VAACs and produce an automatically updated map showing number of advisories over time for all volcanoes with current activity. The graph shows data for the past 7 days (from the current date) and plots the cumulative number of ash advisories, for each volcano, over time. When an advisory states “NO FURTHER ADVISORIES” the count returns to 0, signalling that there are no more ash observations. The graph shows which volcanoes have had particularly intense periods of activity, such as Sinabung in Indonesia, which had 6 advisories issued in the space of 18 hrs. We can also see which volcanoes are producing ash clouds over the course of the week, shown by more than one spike e.g. Sinabung and Klyuchevskoy (Russia). If we were to track this sort of activity over weeks, months and years and compare with other information, it’s likely that we’d start to see patterns emerging for certain volcanoes, helping us better understand how good observations of different eruptions are, how volcanoes and ash clouds behave, and thus how to best interpret such information in the future.

Automatically updated graph showing cumulative number of advisories issued per volcano over past 7 days

Sunday, 18 September 2016

Zoo elephants help their wild counterparts in Kruger National Fiona Sach

Fiona feeding lemurs.
Eight zoo elephants from Knowsley Safari Park and Twycross Zoo have been contributing to work that is being carried out to reduce Human-Elephant Conflict surrounding the Kruger National Park. This unique, interdisciplinary project involves environmental geochemistry, plant science, and animal health between a range of partners including BGS and the University of Nottingham (UoN) through the joint Centre for Environmental Geochemistry. Read more about the project in a previous blog here.

The working hypothesis is that the elephants in this study group, originally from the Kruger National Park, are deficient in phosphorus, owing to a deficiency in the soil and forage. This drives the elephants to supplement their phosphorus from the water, soil and forage on land surrounding a phosphate mine in close proximity to the National Park. En route to the phosphorus mine, elephant incursion into nearby human settlements has resulted in human-elephant conflict, causing risk of injury and lost income. The results of the project may help to inform  key locations in the elephants’ home range where mineral-supplemented forage or mineral licks may be placed to reduce the drive to seek additional sources of phosphorus, thereby reducing human-elephant conflict. Samples (hair, toenail, blood and urine) from the UK elephants will be used to validate their possible use as biomarkers of mineral status in the wild: This is a brilliant example of the contribution captive animals can make to directly benefit research on their wild counterparts.

From L-R: Browse sample; water sampling at Knowsley Safari Park.
Five UK zoos have kindly agreed to assist with and contribute samples to this research with each zoo being visited four times throughout the year to collect necessary samples from the elephants and from items which the elephants consume from their environments in the zoos. Biological samples required include toenails, faecal samples, serum and tail hair. Environmental samples include all food items (browse, hay, grass, pellets and fruit and vegetables) consumed and soil and water samples to assess the influence of geochemistry on dietary intake and land use decisions. These will be analysed for “essential mineral” content (e.g. zinc, iron) to estimate dietary intake and possible seasonal changes in browse, grass and hay over the year. These data will be related to mineral measurements in the elephants’ biological samples to validate methodologies for use and comparison to wild elephants.

Elephants at Knowsley Safari Park.
In June, the second set of UK sample collection took place at Knowsley Safari Park, having commenced a first seasonal cycle in April at that facility. It was especially exciting to collect a longitudinal toenail sample from one individual that will be analysed by spatial analysis using techniques such as laser ablation coupled to ICP-MS or ion beam analysis to give an indication of mineral status over time in that elephant. We would like to thank all the elephant team at Knowsley Safari Park for their assistance with procuring samples and enthusiasm for the research and of course the elephants for their ongoing cooperation. We then moved on to Twycross Zoo for the first very successful sample collection at this facility. We would like to thank all of the elephant team at Twycross Zoo, especially Team Leader Andy Durham, and the veterinary team for their assistance.

Thanks to the NERC Envision Doctoral Training Programme, the Hermes Trust and Royal Society International Exchange scheme. The project is based on a Centre for Environmental Geochemistry collaboration between the Inorganic Geochemistry (Dr Michael Watts) and Stable Isotopes teams (Professor Melanie Leng) at BGS and Schools of Veterinary (Dr Lisa Yon) and Biosciences (Professor Martin Broadley & Professor Simon Langley-Evans) at the University of Nottingham. The collaboration is further strengthened by partners in five UK zoos and with partners in South Africa who have been studying elephant populations there for the past two decades, tracking elephant movements using GPS and GMS to better understand their habitat use.  In addition, Dr Ellen Dierenfeld (E.S.Dierenfeld Nutrition Consulting, LLC) is an internationally renowned expert on elephant nutrition and a co-investigator on this project.

Elephants at Twycross Zoo.
I am very excited to be starting my PhD full time this October, having contributed to activities over the summer months in advance. I will be leaving my current employment at the Zoological Society of London (ZSL), where I have been Nutrition and Research Officer at London and Whipsnade Zoos for the past 4 years. My role has included maintaining accurate diet records for all the animals within the collection, reviewing animal diets based on clinical need, working with procurement to source the myriad of food items needed to feed a zoo and working with keepers to implement diet changes. I am also a Research Advisor for the BIAZA Elephant Focus Group and aid the EAZA Elephant TAG Chair with the strategic planning of the TAG giving input into the direction of the group. This experience has put me in touch with the global captive elephant community and given me an understanding as to the work zoos can do to benefit wild counterparts. I look forward to starting this new challenge, collaborating with several UK zoos to directly advance field research and to employ a multi-disciplinary approach to the PhD research question – “Are land-use decisions made by elephants influenced by geochemistry?”

For further information please contact:,  and

More information will follow from the Centre for Environmental Geochemistry and from Knowsley Safari Park.

Keep up to date with the project on the Knowsley Safari Park Twitter (@KnowsleySafari) and Facebook pages.

Tuesday, 13 September 2016

Jumpsquiffling geodiddlyology: the many landscapes of Roald Kirstin Lemon

Today we're celebrating 100 years since the birth of Roald Dahl, one of the world's best known authors and one that fired the imaginations of generations of children. Many of his stories took inspiration from places that he had lived in or visited, often exquisitely described, transporting the reader to far off and distant lands or simply making them feel that they were in the story themselves. We've taken a look at the landscapes that played a part in his life, or appear in Roald Dahl's literary works, many of which have since been on the silver screen.

1. Roald Dahl Place, Cardiff

Roald Dahl was born on 13th September 1916 in Llandaff, Cardiff and wrote about his early years in his book 'Boy: Tales of Childhood' including the story of the mouse in the gobstopper jar. He is commemorated in the newly redeveloped Roald Dahl Plass, a public space in Cardiff that is home to the Welsh Assembly Building. Originally a dock, this was once a thriving coal port exporting millions of tons of coal mined from the Valleys of South Wales. The space was formerly known as the Oval Basin and many of the original building stones can still be seen and have been reused. For example, Pennant Stone, an Upper Carboniferous sandstone found within the Warwickshire Group, also from the South Wales Coalfield, and a common building stone in the South Wales and Bristol areas.

Tenby Harbour, Pembrokeshire

2. Tenby, Pembrokeshire 

A regular holiday destination for the Dahl family, Roald spent many holidays here as a child, exploring the rocky coastline and fuelling his lust for adventure. Part of the Pembrokeshire Coast National Park, the coastline at Tenby is predominately limestone from the Lower Carboniferous period and part of the Pembroke Limestone Group. Once of the many characteristics of limestone is that it is particularly susceptible to chemical weathering, giving it a characteristic craggy appearance and the ideal location for searching in rock pools!

3. Oslofjord, Norway

Roald Dahl's parents were both from Norway and for at least the first few years of this life, the only language spoken in their household was Norwegian. After the death of his father in 1922, this all changed, but the Dahl family continued to spend summer holidays in Norway. These holidays inspired the setting for the first part of 'The Witches' and the landscapes around the Oslofjord were described in the story as where many of the children went missing in mysterious circumstances. Despite the name, Oslofjord is not a fjord in the geological sense, a name reserved for a long, narrow, flooded inlet, carved by glacial erosion. Instead, Oslofjord uses the Norwegian word fjord in its literal sense meaning sea inlet. In actual fact, the Oslofjord is a rift valley formed as crustal extension formed a long linear lowland with higher ground on either side.

Aerial view of Oslofjord

4. Great Missenden, Buckinghamshire

Great Missenden was where Road Dahl lived for the last 36 years of his life and many features of the village and surrounding area featured in his books. Located in the Chilterns, the entire area is underlain by Upper Cretaceous chalk, part of the White Chalk Subgroup. This has led to the formation of a number of landscape features including natural springs, one of which has given its name to Angling Spring Wood, an ancient woodland just outside Great Missenden. It is this forest that was not only the setting for Hazell's Wood in 'Danny the Champion of the World', but one of the trees (known as the Witching Tree) inspired the story of 'Mr Fantastic Fox'.

The Headland Hotel, Newquay

5. Newquay, Cornwall

'The Witches' is perhaps one of Roald Dahl's darkest children's book and in one section the main character of the book stumbles across a Witches convention at a seaside hotel. The Headland Hotel in Newquay in Cornwall was used in the film version and due to its imposing position atop the cliffs overlooking Fistral Bay it is not hard to see why it was chosen. The cliffs themselves are Devonian sandstone, part of the Meadfoot Group and the stark contrast between the grey sky, the red brick building and the grey sandstone has made the location for this grand hotel appear nothing short of sinister.

The Old Man of Hoy 

6. The Old Man of Hoy, Orkney

The most recent addition to the list, the Old Man of Hoy is a 137m sea stack on Orkney and was used in the film adaptation of the BFG this summer quite literally as a 'stepping stone' as the BFG travelled home to Giant Country. The stack is made up of Late Devonian sandstone sitting on top of a plinth of volcanic rocks of a similar age. It is separated from the main cliffs by about 60m, although due to the dynamic coastal nature of its location it is not expected to stay that way for long. In the 1750s paintings show the Old Man of Hoy as a headland, and then in 1820s it was once again painted but this time as an arch and a stack, giving rise to the name of an Old Man as it looked like two legs. Since then one of the legs has been removed by stormy seas so all that is remaining is the other leg!

7. Mount Kirishima, Japan

This one is a bit of a wild card, but Roald Dahl didn't just write children's stories, he also wrote short stories for adults as well as screenplays for many famous movies. One such movie was the 1967 James Bond film 'You Only Live Twice'. Mount Kirishima in Kyushu, Japan was the filming location for the exterior shots of one the most famous bad guy hideouts of all time, the Blofeld volcano lair, complete with a retractable 'crater lake' opening. The real Mount Kirishima is a group of active volcanoes and described as one of Japan's most active volcanoes, with the last notable eruption being in 2011. Despite the physical impossibilities of having an evil lair inside an active volcano, you have to admire Roald Dahl for his choice of location, one that went on to inspire many other movie and TV writers.

Friday, 9 September 2016

Unexpected Iran: caves, cardamom and one or two Kirstin Lemon

Kirstin was travelling with fellow assessor
Mona Holte from Norway
As a member of the UNESCO Global Geopark evaluation team, each year I get sent to evaluate or revalidate an aspiring or existing UNESCO Global Geopark. Finding out where you're being sent is perhaps one of the most exciting parts of the process and something that all of the team very much looks forward to. This year, when I got the call I was asked 'How do you feel about going to Iran?'. To be honest, my initial reaction was one of fear; we've all seen the news footage and watched the dramatisations on TV, so I expect most of you will understand my reticence. But the scientist in me quickly decided that some proper research was required to see if my initial reaction was deserved, after all, I come from Northern Ireland and know how my home country is portrayed to the rest of the world on occasion. After a little digging, involving several blogs, Sky News reports and countless travel websites, I concluded that Iran was actually safer than some parts of Europe this summer, and that as long as I was sensible, then there was no reason to not go.

The preparations began

My initial fear was quickly replaced with excitement as the preparation got underway, with visa applications, vaccinations, insurance, a whole new wardrobe to satisfy the strict cultural requirements, as well as the actual work that I was being sent there to do. As a UNESCO Global Geopark evaluator, I was being asked to visit the Qeshm Island Geopark to see if it met the required standard to become a UNESCO Global Geopark. The application dossier gave me all the information that I needed to know as well as giving me a lot that I still needed to find out, after all that's why the evaluation mission was happening in the first place.

From Tehran to Qeshm Island

The journey to Qeshm Island was a long one as I had to first of all travel to Tehran before making my way south. But Tehran was not without its attractions and I was fortunate to be able to spend half a day exploring the sites with our colleagues from the Geological Survey of Iran who were to accompany us on our entire journey. I also had the chance to at least partially acclimatise to the intense heat that I was due to experience. I arrived in Qeshm Island, late at night and was instantly met with what can only be described as a wave of steam as I got off the plane. With a temperature of around 39oC at 11pm and a humidity of about 90%, it was likened to an outdoor sauna.

Visiting Chahkooh Gorge. 

Internationally important geology

Qeshm Island is located in the Persian Gulf, off the southern coast of Iran. It is part of the Zagros Mountain Range made up of rocks from the Late Precambrian to Cambrian periods. One of the common features within this range are salt domes that form as salt intrudes into overlying sediments causing them to deform and doming to occur. The Namakdan Salt Complex is one such dome in Qeshm Island and is home to the world's longest salt cave at a distance of 6500m. The majority of the other geological features are formed within much younger Oligo-Miocene sedimentary rocks, and are visible as impressive erosional landforms usually as river canyons such as the one at Chahkooh Gorge. I was taken to visit all of these important geosites and was able to assess not only the geological significance but also the visitor access, the interpretation and the conservation objectives for each one. All of which are an important element of a UNESCO Global Geopark. 

More than just geology

One of the many Women's Co-operatives on Qeshm Island. 
As well as assessing the impressive geological heritage of the island, I was also there to see how this was being used as a tool for sustainable development and due to support from the Iranian government they had been able to develop some pretty significant projects. A Geopark Hotel, a Geopark Square in the main city and countless visitor centres, museums and information points were just some of the examples. But perhaps more impressive was how the Geopark had worked with local communities to try and improve their lifestyles especially through the development of women's co-operatives, the aim of which was to provide local women with a viable means of supporting themselves economically.

A cultural eye-opener

Eating dinner on the floor! 
Whilst I was there we got to experience true Iranian culture, in some ways very different to my own, but in others very similar. The dress code for women is strict in that our heads must be covered at all time, and that our entire bodies must also be fully covered (so full length tops and trousers). This might not have been a problem at home, but when the temperature got to 45oC with a wind-chill of 51oC, this was really quite tough going. Most of my meals were eaten on the floor which I discovered required a great deal of skill, that I rather embarrassingly don't think I ever obtained. The type of food was very different to anything that I had ever experienced with lots of cardamom-flavoured dishes and even the local Qeshm coffee was full of cardamom, but it was all very delicious. Of course the landscape was very different, and instead of the usual cows and sheep that I see when I'm driving home, I encountered herds of roaming camels that more than once stopped us on our journey. One of the most memorable parts of the Iranian culture however, was the warm welcome that I received everywhere I went; I lost count of the number of people that invited us to their homes for tea and of the many invitations that were accepted everyone was only too willing to show me their home and treated me like part of the family. 
Camels by the side of the main road. 

Mission complete 

My trip to Iran, albeit very short was a real cultural eye-opener, and was completely unexpected, especially given my initial reaction. It just goes to show how much the media influences your opinion. As for a UNESCO Global Geopark on Qeshm Island, well the evaluation report has been submitted to UNESCO so we'll just have to wait and see! 


Perspectives on sediment supply: views from water, earth and Katie Whitbread

A team from BGS Scotland has been getting thigh-deep in the Eddleston Water, a tributary of the River Tweed, developing a new monitoring programme to investigate sediment supply and the evolution of the stream following the reintroduction of channel meanders.

The Eddleston Water, like many streams across the UK, has been strongly affected by historic river straightening to protect road and rail infrastructure, and by the effects of agricultural land use in the catchment. In efforts to protect the nearby town of Peebles from river flooding and improve the ecological status of the stream, the Tweed Forum has been working with partners in the Scottish Environment Protection Agency and CBEC Eco Engineering to re-meander the stream and develop a natural flood management (NFM) scheme which has been funded by the Scottish Government.

Alongside the management works, a long-term monitoring system has been established to assess the impact of the NFM and meandering on the rivers’ ecology and hydrology, including the groundwater system, with partners in Dundee and Edinburgh universities working alongside the BGS Groundwater team. Now a team of BGS geologists are utilising both state-of-the-art technology and ingenious shed-built solutions to get to grips with the catchment’s sediment supply system.

UAV pilot Jez Everest, usually to be found on an Icelandic glacier, has been out with the BGS drone capturing high-resolution aerial footage of the re-meandered reaches in the first tranche of a series of monthly monitoring flights to assess channel evolution following the most recent re-meandering work. Footage showing the connecting of the new meanders can be seen in Jez’s video “Re-meandering the Eddleston Water” from the first survey. The footage will be used to construct a sequence of digital elevations models of the channel system which will be analysed to assess how the new channel morphology evolves.

Meanwhile, Chris Thomas and Katie Whitbread have been out wading to empty a prototype integrated sediment sampler constructed (to high specification) from a length of sewer pipe and some funnels. Despite its humble origins, the sampler performed impeccably, yielding several hundred grams of sediment (a months’ worth) captured from the flows’ suspended load. Following the success of the first sampler, two more are under construction for deployment along the stream, and geochemical analyses in conjunction with connectivity modelling will be used to trace the sediment sources to learn more about the geological controls on sediment supply in the catchment.

Katie Whitbread – Geology Scotland
Chris Thomas – Geology Scotland
Jez Everest – Marine Geology

 Chris Thomas installing the prototype sediment sampler in the Eddleston Water (K Whitbread/BGS/NERC)
Jez and Chris getting ready to fly the first UAV survey at Lakewood on the Eddleston Water. The sediment bars have formed since this section of the stream was re-meandered two years ago, creating a diverse range of riverine habitats (K Whitbread/BGS/NERC).

Wednesday, 7 September 2016

A new lake for Wales? Gareth Farr

The low lying valley in which the ephemeral lake 'Tir-llyn Nedern' forms, the
gate in the middle is part of a footpath when water levels recede. 
A recent hydrological study sheds light on an unusual wetland in South Wales. During the autumn and winter a shallow lake, up to 2m deep and 1.5km in length can form, only to dry up completely during the spring and summer.  The lake is not marked on any maps, neither does it have a name. Gareth Farr (BGS Wales) and Catrin Grimstead (Natural Resources Wales) explain why this type of wetland is rare and what causes this unusual flooding.

The unnamed lake is partially located within the Nedern Brook Wetland SSSI, located near the picturesque Caldicot Castle in Monmouthshire. The wetland is a popular site for overwintering birds, especially waders and waterfowl including Bewick's swans, redshank and widgeon.

Situated in a broad valley, the wetland is underlain by glaciofluvial sand and gravels and Carboniferous limestone bedrock. A small main river, the Nedern Brook, flows North-South through the wetland. The brook has a long history of alteration (too long to describe in this blog post), being both over-deepened and canalised, resulting in a loss of morphological and ecological status.  It was due to these negative impacts that Natural Resources Wales were required by European Law to consider options for restoration of the water course. Previous studies in the area highlighted a lack of hydrological evidence (in both the book and associated wetland) as the main knowledge gap prohibiting restoration plans. To help fill in the knowledge gaps we undertook a year of groundwater and surface water monitoring, recording the levels and flow to better understand the hydrological regime.

Tir-llyn Ndern in flood (L) and after the flood waters have receded (R). 
 Our study, funded by Natural Resources Wales, suggested that as water levels rise in the Carboniferous limestone aquifer below the site (eventually reaching the surface), springs and seepages result in the formation of a temporary (or ephemeral) freshwater lake. The process by which the temporary lake occurs is not due to ‘fluvial’ flooding caused by the over-topping of river banks but is a result of rising groundwater levels. This process is entirely natural and is dominated by the seasonal changes in groundwater levels coupled with the topographically low setting of the Nedern (it is just 5m or so above sea level).  The lake dries up as groundwater levels in the underlying aquifer recede during the spring and summer.

Flood depth map for Tir-llyn Nedern. The old river meanders can
still be seen (yellow) adjacent to the more linear present day
channel (also in yellow). The map is based on maximum flood
levels (Ordnance Survey Data © Crown Copyright and database
rights 2016). 
Naturally fluctuating wetlands, that form ephemeral open water bodies, are rare in the UK. They are rarer still when groundwater controls the flooding. Currently the only recognised examples of this ‘aquifer fed naturally fluctuating wetlands’ habitat in the UK are the Norfolk Breckland Meres, a single turlough in south Wales and three turloughs in Northern Ireland, covering just 31ha combined. The Nedern Brook Wetlands, when flooded, covers an area of nearly 40ha and could potentially be a significant addition to this rare UK habitat. It is tempting to suggest that the Nedern Brook Wetlands is referred to as a ‘turlough’, but in Wales we need a name to distinguish our fluctuating wetlands. Thus we propose a new name for this ephemeral lake; ‘Tir-llyn Nedern’. (Tir-llyn translating as ‘land lake’ in Welsh).

Acknowledgments: Natural Resources Wales for funding of the study and numerous staff at NRW including Catrin Grimstead, Liz Lawrie-Meddins, Rob Bacon, Alan Price and Julian Woodman.

Reference: Farr, G. 2015. Nedern Brook Wetlands SSSI Phase 1 hydrological monitoring. British Geological Survey Open Report OR/15/038 for Natural Resources Wales.

@NatResWales @BGSWales @garethfarr1 @Caldicot Castle

Monday, 5 September 2016

A study into the chromium content of the dust on Lee Evans

Hi, my name is Lee and I am a sandwich student from the University of Surrey just starting my placement year here at BGS working in the Inorganic Geochemistry team under the supervision of Elliott Hamilton. I will be helping out around the lab, specifically working on the multi-elemental ICP-MS instrument with Elliott and hopefully operating this on my own before Christmas. I will be completing a research project which will lead to a presentation and poster ceremony in October 2017 for Industry Day during the final year of my Chemistry degree to showcase my achievements during my time here.

My work will follow on from my predecessor, Emily Leeder, who has recently completed a report focusing on iron intake from dust deposits on pumpkin leaves, which are a staple part of many African’s diets. This was following up from Michael Watts and Elliott Hamilton’s “The Future is Africa” project; where they visited both Zimbabwe and Zambia in January and November 2014.

Two billion people worldwide suffer from iron-deficiency, often due to consuming various types of iron which cannot be absorbed. In some developing countries, extrinsic iron can contribute to dietary iron from contaminants such as soil or dust. Emily’s project featured different types of applications of dust, as a paste to mimic wet conditions and also when dry and blown onto the leaves. The leaves were ground for 15 minutes and microwave digested before being analysed using the ICP-MS.

She concluded that even after washing thoroughly, a significant proportion of dust remained on the leaf, from which the iron content of the leaves coated in dust increased from the control (no dust applied) which had an iron concentration of 60 mg/kg. However, when a paste was used to replicate a soil splash the iron content rose significantly greater to almost 50 times the control. The underside of the leaves were found to be the most susceptible to absorbing the dust, due to the hook-like stomata present.

Scanning Electron Microscope image showing dust adhered
on the washed leaf surface. 
So far, I have been assisting where I can in the labs; from sample dilutions for the ICP-MS to analysing elephant toenails for an on-going project (link to previous blog). A multitude of different tests are carried out in the lab each day, often leading to new and interesting techniques. I have also begun to familiarise myself with a variety of literature, focusing on identifying the different species of chromium, both Cr(III), an essential nutrient, and Cr(VI) which is toxic and a known carcinogen. I will be conducting a glasshouse study, similar to Emily’s, analysing the different quantities of both chromium ions present after the application of dust to coincide with ongoing field experiments in proximity to mine tailings in the Zambian copperbelt (Elliott Hamilton’s blog).

I’m looking forward to making the most of my time here at BGS, hopefully utilising the facilities and experts to develop both my own scientific ability and also helping the team to the best of my ability.


Friday, 2 September 2016

Glasgow’s got the Hydrocarbon Hump: Urban Pollution Transport Corridors in the River Christopher Vane

Recent research on the surface sediment chemistry of the upper River Clyde, Glasgow reaches and tributaries as well as tidal estuary has shown that Glasgow’s urban tributaries have got the ‘hump’. Organic geochemists call the ‘hump’ a fancy name, the unresolvable complex mixture (UCM), because it’s comprised of thousands of hydrocarbon compounds which are difficult to separate using standard analytical methods such as gas-chromatography (GC).  The largest humps are usually found in soils and sediments which have accumulated weathered crude oils and or refined oil products such as engine and industrial lubricants. These leak into soils and are washed into river sediments via road run-off .

BGS geochemists Drs’ Chris Vane,  Alex Kim and Raquel dos Santos extracted oil from sediments in the Clyde found that nearly all the samples in and around Glasgow had the hump and that the hump disappeared in sediments collected a few kilometres downstream of the city only to return again in and around Greenock and Port Glasgow which are situated toward the outer estuary. 

This suggests that these areas are either receiving modern day fugitive hydrocarbon pollution or that legacy hydrocarbon pollution is being remobilised or both. Other eco-toxicological studies have suggested that the UCM (hump) is toxic and has known negative health effects on sediment dwelling biota.  We also discovered that with a few exceptions, sediments from the more rural upper Clyde didn’t have the hump but were comprised of straight chain hydrocarbons called n-alkanes which show up as nice straight peaks that are easy to separate and mainly sourced from the natural peat and soil in the catchment  suggesting no or very low man-made hydrocarbon input.

Other  new investigations by the Organic Geochemistry team at BGS  focus on understanding the  concentration and possible health effects from persistent organic pollutants in Glasgow’s soils measurement and tracking the distribution of  the toxic metal mercury through the Clyde river-estuarine continuum  as well as assessing  the transport of natural soil carbon from land to out to sea.  The findings have just been submitted to Earth and Environmental Science Transactions of the Royal Society of Edinburgh special issue on the Clyde Basin organised by BGS’s Diarmad Campbell and Fiona Fordyce.  

Taken together the existing and new organic pollution studies (see references below)  show us that the urban tributaries act as conduits, both receiving and occasionally delivering polluted sediment to the main river and then out to sea. Additionally, we show that the impact of the anthropogenic pollution extends down-stream but not upstream due to the flow of water and the presence of tidal barriers which can impede sediment movement.

Published References on Clyde estuary sediments:

Vane, C.H., Chenery, S.R., Harrison, I., Kim, A.W., Moss-Hayes, V., Jones, D.G. 2011. Chemical Signatures of the Anthropocene in the Clyde Estuary, UK: Sediment hosted Pb, 207/206Pb, Polyaromatic Hydrocarbon (PAH) and Polychlorinated Biphenyl (PCB) Pollution Records.  Philosophical Transactions of the Royal Society (A) 369, 1085-1111. DOI: 10.1098/rsta.2010.0298

Vane, C.H. Yun-Juan Ma, She-Jun Chen and Bi-Xian Mai. 2010. Inventory of Polybrominated diphenyl ethers (PBDEs) in sediments of the Clyde Estuary, U.K. Environmental Geochemistry & Health, 32(1), 13-21. DOI: 10.1007/s10653-009-9261-6

Vane, C.H., Harrison, I., Kim, A.W. 2007. Assessment of Polyaromatic Hydrocarbons (PAHs) and Polychlorinated Biphenyls (PCBs) in surface sediments of the Inner Clyde Estuary, U.K. Marine Pollution Bulletin, 54, 8, 1301-1306. DOI: 10.1016/j.marpolbul.2007.04.005

New BGS Research on River Clyde and Glasgow Soils: 

Vane, C.H., Moss-Hayes, V., Kim, A.W., Edgley., J Bearcock.  Mercury (Hg), n-alkane and unresolved complex mixture (UCM) hydrocarbon pollution in surface sediment across rural-urban-estuarine continuum of the Clyde, UK. Earth and Environmental Science Transactions of the Royal Society of Edinburgh (In Review)

Kim, A.W., Vane, C.H., Moss-Hayes, V. Berriro, D.B., Fordyce, F., Everrett, P. Nathanail, P.C. Polycyclic aromatic hydrocarbons (PAH) and polychlorinated biphenyls (PCB) in urban soils of Glasgow, UK. Earth and Environmental Science Transactions of the Royal Society of Edinburgh. (In Review).

Lopes dos Santos and Vane, C.H. Tracking natural organic carbon in the River Clyde using glycerol dialkyl glycerol tetraethers (GDGT). Earth and Environmental Science Transactions of the Royal Society of Edinburgh (In Review)