Friday, 19 January 2018

Back to geoscience research after a career Andrea Snelling

Working in research is brilliant but at times it can be tough. Post-doctoral work often means working on short-term contracts ranging from a couple of months to several years, with the constant shadow of where or when the next position will be. Trying to get a foot in in the first place can be extremely hard and finding a permanent position can feel like an impossible goal. There is always so much competition and it often feels as if you are on the back foot and of course there is the perpetual voice of doubt of “when will I be found out?”

Taking a career break as an early career researcher could perhaps be viewed as less than smart but sometimes life just works out that way and anyway when is a good time to take a career break? The bigger issue perhaps is how do you get back in again? If you want to return to research following some time out, especially if you haven’t got a job to go back to can be a big challenge. So many doors seem to have closed, techniques have moved on and your publication record has likely gone into dormancy. From personal experience I felt like I’d blown my chances of working in research, I’d made a decision to take some time out, and getting back in was proving difficult. It’s hard not to take job rejection personally, especially when vacancy after vacancy gets filled with others who have more recent relevant experience. Job applications are draining, interviews are nerve wracking and rejections are demoralising, but somehow you keep going, just one more.

I’d got to the “just one more attempt” before facing up to the “I’m going to need to make a career change” place when I found out about the Daphne Jackson Trust Fellowship scheme. They offer a fellowship for people who have had to take a career break of more than 2 years and, along with a host institution provide funding and support, including retraining for a part-time, two year research position in a STEM subject. It seemed to be the perfect opportunity to return to research and there was a sponsored position available at the University of Nottingham. I allowed myself a small sideways look at hope.

I knew I wanted to get back into palaeoclimate research using diatoms (photosynthesising algae) for silicon and oxygen stable isotope analysis. I had the basis of an idea of what I wanted to do and so I approached a contact in the School of Geography that were happy to support me. The application process is rigorous and there are several selection stages to go through before you are invited to put together a proposal of the research idea, which is then peer reviewed. It felt empowering to write the proposal for a project that I hoped I would get the opportunity to complete and the support from both the trust and university was exceptional. 

Being offered the fellowship was amazing and renewed my faith in myself that this was something I could do and that other people believed I could do it too, a feeling which had been lacking since I’d decided to return to work.

I’m now three months into my fellowship: Assessing the role of biogeochemical cycling in the North Pacific and the Bering Sea through the Mid Pleistocene Transition. I’m up to my eyes in sample preparation and I’m looking forward to learning new techniques in silicon isotope analysis with the Stable Isotope Facility within the Centre for Environmental Geochemistry at the BGS. I’m really happy to be back in the depths of research and the potential of what is yet to come.

Andrea has started her Fellowship working with George Swann at the University of Nottingham and Melanie Leng at the BGS.

Wednesday, 17 January 2018

Why do we need to know what's under our cities? And what's it got to do with Icebergs?! ... by Catherine Pennington

Drill auger sections and debris on the London
Underground track (photograph courtesy of Network Rail)
Do you remember when a London Underground tunnel was accidentally drilled into by a piling rig from a construction site above it?  It happened near Old Street Station in March 2013 and, thanks to the driver of an out-of-service passenger train reporting it immediately, no one was hurt. 
"This was a serious incident that could have ended very differently had it not been for the vigilance and prompt reporting and actions of our drivers. We carry two million people a year on the Northern City Line"   First Capital Connect managing director Neal Lawson, as reported by the BBC.
The construction site was 13 metres above the tunnel and because the location of the tunnel wasn't shown on any map available to the site developer or the local planning authority, Network Rail was not consulted during the planning application stage.  As a result, no one knew the tunnel and the drills were going to collide.

It also turns out that when the Rail Accident Investigation Branch examined the incident, over half the piles intended for the site would have crashed their way through the tunnel, had they been constructed. 

You can read more about it in the RAIB Rail Accident Report.

This kind of scenario, where an asset (e.g. railway tunnel) is damaged or affected by something else (e.g. a drill), is known as a strike.

How on earth can a 'strike' happen with today's advanced detailed mapping technology?

This situation could have been avoided entirely had the data about the ground beneath the construction site been coordinated and available to the right people at the right time.  Sadly, this incident is just one of many.

At the moment, subsurface information is quite tricky to get at unless you know what you are doing.  Data quality can be variable - entirely absent or poor.  Meanwhile political and organisational boundaries make it difficult to get a wider picture of the subsurface conditions.  Ultimately, there is no central digital map showing what is present, exactly where it is and what issues you need to be aware of.

An incomplete view of subsurface data can have costly and far-reaching outcomes.   As well as damage to the underground assets themselves, other consequences include environmental costs and economic costs associated with the millions of hours of road disruption, huge repair and replacement costs, project re-designs and overruns. The Department of Transport estimates that street works account for an estimated cost of £4.3bn annually. Meanwhile the Treasury estimated in 2013 that greater cross-infrastructure collaboration can save the economy an estimated £3bn.

Introducing Project Iceberg

Project Iceberg aims to address the serious issue of the lack of information about the ground beneath our cities and the un-coordinated way in which the subsurface space is managed. This is an exploratory project undertaken by the British Geological Survey, Future Cities Catapult and the Ordnance Survey

The long-term goal is to help make future urban land development a safer investment through better management of the information that is held about the subsurface.  It will also improve the way data are managed and coordinated.  The full potential of subsurface data – when integrated with other city data - needs to be countered against the separate delivery of data and services which are often incentivised on efficiency over better (long term) outcomes.

With national subsurface data integrated with surface data from our cities, new technologies can be developed and approaches to urban planning can be streamlined and improved. Would we see augmented reality being used to view the accurate location of pipes before they dig? Sustainable drainage schemes being modelled to help manage surface water and reduce the pressure on the water pipe network? Quicker and more accurate estimates of the costs of remediating land for housing? A speedier conveyancing process for homebuyers? Project Iceberg aims to explore these opportunities and potential benefits to support integrated urban planning.

Stephanie Bricker, British Geological Survey
Stephanie Bricker is leading the project and says:
"Our study aims to enable a means to discover and access relevant data about the ground’s physical condition and assets housed within it.  This needs to be in a way that is suitable for modern, data driven decision making processes and in a way that is meaningful for city practitioners".

What are we likely to find in the ground beneath a city?

The short answer is ... a lot.  It's a complex, highly variable environment that has been through multiple phases of development.  Not only are the natural ground conditions varied and often highly disturbed, but the ground contains a large number of built structures and utilities.  There are gas mains, sewers, water supply pipes, drains, oil pipelines, old mine workings, tunnels, power cables, telecom cables, boreholes, landfills, basements... and the list goes on.  These are owned or managed by different entities, making the job of uniting data quite an undertaking.  As well as assets, there's geological information that needs to be taken into account for the design of foundations, slopes, retaining walls, tunnels, roads, rail and more.

Take a look at this:

©Future Cities Catapult

And what's it got to do with Icebergs?

It's well known that a large proportion of an Iceberg lies below the surface (Isostasy).  The same is true of our cities.  We rely on the ground for a wide range of applications: for example provision of natural resources and housing of critical infrastructure and utilities.  When it comes to planning, we often focus on the visible parts of our towns and cities and forget the complex and valuable ground beneath our feet – the name Project Iceberg is a reminder not to forget what you can’t see!


For more information, you can contact Stephanie Bricker at BGS or see Project Iceberg

Friday, 12 January 2018

Sharing AGS data via HoleBASE Rachel Dearden

After two years of work, our BIM for the subsurface project, funded by Innovate UK is starting to yield the first of its exciting deliverables. The project was funded by the Digitising the Construction Sector and that is exactly what we have set out to do; to enable the geotechnical industry to access and share digital data. This blog describes the first of our project outcomes that have been achieved working collaboratively with Keynetix and Atkins.

So the problem…

BGS have a huge archive of scanned borehole records. These provide unique insights to the 3D make-up of the geology beneath our feet and provide the geotechnical industry with an unrivalled source of subsurface data. We know that UK industry find this resource incredibly valuable, but it is analogue and we know that many hours are spent transcribing our borehole records into digital format for onward use.

The solution moving forwards… 

The geotechnical industry has for some time adopted the Association of Geotechnical and geoenvironmental specialists (AGS) digital format for borehole data. Transferring borehole data in this format allows the industry to share data more easily, load it into a range of software types, create bespoke graphical logs and also re-use the data for creating 2D cross sections and 3D geological models. The AGS format has been specifically designed for the sharing of geotechnical data and thus our project aimed to make this a reality from the BGS archive; we wanted the ensure that the National Geoscience Data Centre not only archived and shared analogue borehole data, but also digital AGS data.

Sharing is key here

Our aim was to make it as easy as possible for the geotechnical industry to upload AGS data to the archive and also to download the data that we hold. Where is there a better place to locate this interface than in one of the UK’s leading borehole data management software packages? Working with Keynetix, we developed two webservices accessible from within HoleBASE SI.

Our first development is an AGS download function that allows users to explore the AGS data we hold via a mapping interface, select relevant AGS boreholes and then download these files directly to HoleBASE SI. These files can then be incorporated into projects in the same way as any other AGS data but each of the locations is marked as historical in HoleBASE SI so it is easy for the data user to see the origin of each borehole they are using.

The usefulness of such a service is dependent on the volume and quality of the data uploaded to the archive, so the second function we developed was an AGS upload function that allows HoleBASE SI users to select their own data and upload this to the BGS AGS archive directly. This service validates the data and ensures that the donator provides sufficient metadata such that the data is good quality and can be shared and re-used. If you want more information about what constitutes good AGS data, take a look here.

So now the proof will be in the pudding…

The service is live. Please donate your data to the archive and in return take advantage of the growing archive of AGS borehole data that will ultimately improve our knowledge of the UK’s subsurface.

Now, if you aren’t a HoleBASE SI user, don’t despair. You can upload data (AGS, site investigation reports or a whole range of other geological data) to our new ingestion portal and you can search data that has been donated to us via the donated data search portal . We’re working on a mapping interface for AGS data, but you’ll have to wait a little longer for that.


I’m worried that my AGS files contain sample analysis data that is confidential.
  • Uploads from HoleBASE SI exclude all contaminant data. You can choose to upload just the data you want to
I have data but it’s not mine, can I upload it?
  • We do need you to get permission from the data owner to upload your data. This allows us to openly share it onwards.
How many AGS files can I download at any one time?
  • Just 10 at the moment, but once we understand how robust our system is to large downloads we intend to increase this.
Are you going to transcribe your analogue borehole records?
  • We’d love to, but we don’t have the resource to do this. If you transcribe our analogue records, feel free to upload it.
Is the AGS data you receive uploaded to the borehole scans map interface?
  • Yes, we compile a log from the AGS data and upload it to the analogue borehole scans map.
Is this service free?
  • Yes!
What versions of AGS file do you accept?
  • Version 3 or version 4
What versions of AGS file can I download? What AGS groups can be downloaded?
  • We’re providing AGS 4.0 downloads as standard. We share all the mandatory groups and the GEOL and LOCA groups at present, but plan to expand this. The original uploaded AGS file ismade available through our donated data search portal
Can I access the originally deposited AGS file?
  • Yes, there is a link on the metadata file that comes with the AGS data when you download it, or you can get the original file from the donated data search portal
If I state that the data is confidential what happens?
  • We don’t release the data openly until the confidentiality period that you state has passed. We don’t want to encourage the deposit of data that is confidential forever – that’s not very useful to us.

Wednesday, 10 January 2018

An Update from the Elephants…by Fiona Sach

Elephants within the Kruger National Park
The last year has been an absolute whirlwind of activity involving fieldwork at five UK Zoos, in the Kruger National Park and at a nearby mine in South Africa. There has been seemingly endless sample preparation, sample analysis and now, just recently, I have started to analyse the data generated. It is tremendously exciting to see these data from the UK zoo elephants, their diets and their environments and to use this information to identify the best matrix for reflecting mineral levels in free-living counter-parts. 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, South African National Parks Authority (SANParks), South African Environmental Observation Network (SAEON) and Elephants Alive (EA). Read more about the project in a previous blog here.

The working hypothesis for this project is that African elephants (Loxodonta Africana) are being drawn towards a mining area just outside the Kruger National Park in South Africa, due to the unique geochemistry of the area. Previous studies have suggested that the soil in areas surrounding the mine, and associated plant and elephant faecal samples may be low in minerals such as phosphorus, causing a deficiency in the plants, and driving the elephants to seek these minerals elsewhere. It is therefore thought that the elephants may be attracted to the mining area due to the mineral provision in the plants, soil and water. Unfortunately, elephant incursion into the mine and nearby human settlements has resulted in human-elephant conflict, causing risk of injury and loss of income. It is hoped that 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 minerals, thereby reducing human-elephant conflict.

African elephants on land next to direct mine site
Last summer I spent a fantastic month in South Africa on fieldwork sampling soil, water, elephant faeces and plants (from the 6 key browse species consumed by elephants) in the Kruger National Park, Associated Private Nature Reserves and directly on and around the mine. In addition, dust samples from the plants in the mining area were collected. These samples have been processed and analysed using Inductively Coupled Plasma Mass Spectrometry (ICP-MS) to give a suite of 55 elements (to account for any nutrient interactions).

The project is very fortunate to have access to banked blood and tail hair samples from the Kruger National Park BioBank, collected opportunistically from elephants within the Kruger National Park, banked tail hair, toenail and blood samples from collared elephants monitored by Elephants Alive (EA), as well as tracking data from seven animals collared by EA on the mine site. These data greatly inform elephant movement and thus the sampling strategy for environmental sampling in the area, as well as providing a baseline level for minerals in African Elephants (Loxodonta Africana). I am very much looking forward to processing and analysing these samples in the coming months and pairing the data with the appropriate environmental samples.

I would like to thank the fantastic field team and especially our game guard Desmond who gave great reassurance during long bush walks – his knowledge and experience was phenomenal. I would also like to thank all of the staff at SAEON who gave up vast amounts of time to assist with fieldwork, scientific services and Peter Buss & the veterinary department at SANParks (KNP) and collaborator Michelle Henley from Elephants Alive.

I would like to take this opportunity to extend my thanks to all five of the UK zoos which have assisted with this project to date; Colchester Zoo, Knowsley Safari, Twycross Zoo, Noahs Ark Zoo Farm and ZSL Whipsnade Zoo, to all the elephant keepers for collecting the samples and acting as an endless bank of knowledge for the animals they care for, the vet and research teams for assisting with logistics, and of course the elephants themselves. I am enormously excited to visit each zoo in the coming year and explain the results obtained, to provide a profile of the mineral status of each animal and hopefully give the zoos valuable data, to aid them in continuing to advance the captive care of these phenomenal animals.

Friday, 5 January 2018

New research to investigate human impact on the Yangtze Linghan Zeng

One of our collaborators from China (at the
back) and me collecting sediment core
Hello, I am Linghan, a PhD student within the School of Geography at University of Nottingham which is a part of the Centre for Environmental Geochemistry at BGS. I have recently started by PhD on using lake sediments to investigate how lakes in the middle Yangtze floodplain respond to multiple stressors created by human impact.

The Yangtze River which has a length of ca. 6400 km is the third longest river in the world. The various societal, economic and biological benefits that the Yangtze floodplain provided make it appealing and productive for human to inhabit. In 2011, more than 300 million live in the middle and lower Yangtze floodplain and it generates more than 20% of the nation’s agricultural production. Over the last several decades, large amounts of pollutants have been generated with the rapid expansion in population and agricultural and industrial activities. As a result, lakes in this area are severely polluted and some of them are faced with the problem of algae bloom. In addition, more than 50 thousand dams (e.g. the Three Gorges Dam) have been established in this flooding area for benefits such as flood control and hydropower, which may influence the floodplain lakes by changing the hydrological condition. The plan is to use palaeolimnological proxies (including chlorophyll and carotenoid pigments, chironomids, C/N ratios and stable carbon and nitrogen isotopes) to examine the combined effects of hydrological modification and increasing pollutants on the ecohydrological evolution of lakes in the middle Yangtze floodplain.  

The plan is to combine the geochemical data with historical archives which will help to quantify the relationships among eutrophication, aquatic plant coverage, hydrological connectivity and organic matter cycling. As well as improving our understanding of floodplain lake ecology and ecosystem dynamics, we will be able to provide a regional overview of the consequences of these changes for shallow freshwater lakes in the middle reaches of the Yangtze floodplain.

Fuchi dam constructed at the confluence of the Yangtze River and Honghu Lake in 1971

In the first instance this study is based on sediment cores from six shallow freshwater lakes spanning the middle section of the Yangtze River. Two of them are freely connected with the Yangtze River and the others have experienced hydrological modification caused by the dam construction. Sediment cores from the six lakes have been collected and dated, and in June samples from surface sediments, catchment soils, seston, submerged and emergent aquatic macrophytes were collected to facilitate interpretation of downcore changes.

At the moment the analysis of the carbon and nitrogen isotopes is underway at the BGS and it is hoped that these will help to track the source of organic matter in ecosystem state change and provide information about the productivity of these shallow freshwater ecosystems.

Linghan Zeng is a PhD student in the School of Geography, University of Nottingham working within the Centre for Environmental Geochemistry.