Friday, 25 November 2016

The International Conference in Paleoceanography 2016... by Sonja Felder and Rowan Dejardin

Hello everyone,

Rowan in discussion at this poster about the Holocene
paleoceanography in South Georgia (Southern Ocean).
It’s us again, Sonja and Rowan, two BGS BUFI PhD students. Recently we took part in the twelfth International Conference in Paleoceanography, aka “ICP”, in Utrecht, Netherlands. Held every three years, ICP is the biggest international paleoceanography conference, so it was unsurprising that some of the biggest names in the field turned up to present their work. This gave those of us new to the field a great opportunity to discuss our work and socialise with them at events like the conference dinner or the traditional “paleomusicology” concert.

The conference was structured so that a series of key-note lectures where given in the morning and the afternoons were taken up with poster sessions. The key-notes are generally given by up and coming researchers in the field, whose work is doing a significant amount to push forward the boundaries on paleoceanography. By convention, researchers will only give one talk at ICP in their entire career and the resulting talks providing a fascinating insight into the cutting edge research currently occurring. The conference also had a strong focus on the poster sessions: there were almost 700 posters from researchers from all stages of their careers, from PhD students, to postdocs and professors, including some of the most well-known names in the field.

Sonja in discussion at her poster about the
Mid-Pleistocene climate transition at
 IODP Site U1427 (Sea of Japan).
An obituary for Harry Elderfield, a giant in the field of paleoceanography who passed away in April this year, was given by Nick McCave of Cambridge University. The obituary ended with a very impressive demonstration of Elderfield’s impact on the field: those in the audience who are the “children” and “grandchildren” of Elderfield, having worked with him directly or being supervised by his former PhD students, were asked to stand, and a significant proportion of the audience did so. Next, all those who worked with the proxies Elderfield developed were asked to stand and virtually all attendees of the conference stood up and gave Elderfield a standing ovation for his life’s work.

On Friday afternoon the conference closed with “the big debate” during which the panel and the audience discussing the idea that the current trend towards more focus on resolving social issues arising from climate change may be a threat to the fundamental research in paleoceanography. To illustrate this the debate started by highlighting the number of times the word “paleoceanography” appears in the most recent IPCC report, and with this the impact our field has on policy makers, which turns out to be zero! What followed was a lively and spirited debate with delegates offering arguments to support the whole spectrum of opinions on this issue. Although we paleoceanographers believe the past is the key to the future and that ocean records are integral to unlocking the past, policy makers mainly use the present alone to try to understand the future. One of the main conclusions from the debate was that the field needs to go further to foster a better understanding, among other scientists, policymakers and the wider public, of the importance of paleoceanography to our ability to predict future climate changes, whether this be through interdisciplinary collaboration, outreach work, or other avenues.

All in all, ICP12 was a really, really good experience full of fascinating insights and we hope to be part of the next ICP, which will take place in 2019 in Sydney, Australia. By then, surely we will be the big shots, giving the talks!


Tuesday, 22 November 2016

The BGS Aurora Camera (AuroraCam) Blogspot...by Ciaran Beggan

Background
In early 2016, the Geomagnetism team decided to install an experimental camera at the Eskdalemuir observatory to see if we could observe the Aurora Borealis during times of heightened geomagnetic activity. The aurora are caused by large electrical currents flowing in the ionosphere around 110km above our heads. These current systems are normally found in an oval around the magnetic pole at high latitudes (such as over Iceland), but during geomagnetic storms the oval expands southwards and can move to lower latitudes.

When it does, the magnetic field recorded at our observatories starts to vary rapidly – first at the station furthest north in Lerwick (Shetland Islands), then in Eskdalemuir (the Scottish Borders) and, if the storm is large enough, in Hartland (Devon).  During these stormy periods, the aurora may become visible – though it’s not always guaranteed. The Geomagnetism team do try to issue alerts if we think the aurora may be visible in the next day or two.
Raspberry Pi with camera in its IP68 box. The lid
with a Perspex dome is to the left.

Hardware
We decided to see if we could capture images of the aurora ourselves, by using a camera automatically triggered from magnetic field variations at an observatory. We’ve been working with Raspberry Pi computers for our School magnetometer project over the past few years so we are familiar with them. As you can now buy a cheap five mega-pixel camera for the Pi, it seemed a good system to experiment with. There is plenty of advice on the Internet about how to build a time-lapse camera like this.

Software
Once the hardware had been built, the next step was to write the software to drive it. As the Raspberry Pi comes with the Python language, it seemed the obvious one to use.

We wrote a small piece of code to (a) check if it is dark and (b) to check if the geomagnetic activity measured at our observatories is high (above some particular threshold). If these conditions are met, the camera is triggered. It takes a six -second exposure. A timestamp is placed onto the image and a note is made into a log file and then the system goes to sleep for five minutes. The camera continues to take images every five minutes until the geomagnetic activity declines or the sun rises.

Installation
The camera was installed in June 2016.  The first task was to lay the cables for power and communications from the ground floor office to the roof. This involved passing a cable through two floors, a window and up to the balcony where we wanted to mount the camera. Once the wire was laid, the camera was mounted on some unused scaffolding.
 
From L-R: Tim Taylor mounting the camera on the roof, the camera is angled to point north and just captures the top of the
horizon in the image to the right; Camera pointing north on a typical (i.e. cloudy) day in Eskdalemuir.
Aurora pictures?
There have only been a few large storms since we set up the camera in June 2016. However, the camera has been triggered by a few periods of higher activity but usually it is raining or cloudy. The best image we have was captured at 4:34am on 28th September 2016. It shows stars and a very faint aurora on the horizon. The photo has been processed to increase the gain and the colours have been auto-corrected using an image processing package.
 
Image captured by the Eskdalemuir AuroraCam on 28/09/16 at 03:34 UT.
Future plans
We plan to add images of the aurora to our alert pages the following day once they have been processed. It will be interesting to see if this relatively cheap setup will survive the cold and stormy winter months in Scotland.

For more information on the Aurora Cam then visit the website here.

By Ciaran Beggan & Tim Taylor, with thanks to Ted Harris and Tony Swan.

Monday, 14 November 2016

Learning the fundamentals of continental scientific drilling with ICDP at GFZ, Potsdam…by Jack Lacey

The International Continental scientific Drilling Program (ICDP) is a global initiative that provides financial and operational support for multinational research teams to drill the Earth’s continental crust, with the principle aim of better understanding our Earth system through cutting-edge transdisciplinary scientific research. ICDP has supported drilling projects across the world to investigate a broad range of science themes, including geological hazards, natural resources, and palaeoclimate (see the extensive list here). The program comprises 24 member countries, and the UK has been an active member since 2012 funded by the British Geological Survey (ICDP-UK).
Key ICDP research themes (source: icdp-online.org)
Each year ICDP hosts a training course that covers the fundamentals of continental scientific drilling, and I was one of 29 scientists, including four other UK-based participants, selected to attend this year’s event hosted at the GFZ in Potsdam, Germany. The course is designed to provide a foundation in the theory and practical aspects of drilling for those involved in current and future ICDP projects, and is delivered through a series of lectures given by leading ICDP scientists. The sessions covered a comprehensive range of topics from drilling technologies, core sampling, and geophysical logging, to the importance of outreach, proposal writing, and data management – all in just under three days! Dr Virginia Toy from the University of Otago also gave us a fascinating look into the history and achievements of the Deep Fault Drilling Project, an on-going ICDP project that drilled into the Alpine Fault in New Zealand to investigate the processes of rock deformation and earthquakes.

Delegates of the 2016 ICDP training course on continental scientific drilling (courtesy of ICDP)

Imaging a core on the line scanning device at the
BGR Core Repository (the core is rotated
during a scan producing an ‘unrolled’ image
 of the whole outer surface)
The course is normally hosted by an active project to enable delegates to experience a drilling campaign first-hand. However, ICDP is celebrating its 20th anniversary in 2016 and so the training was held at the GFZ to coincide with an important workshop being attended by over a hundred invited scientists, funding organisation representatives and the media (see Melanie Leng’s recent blog) – a valuable networking opportunity. To cover some of the practical aspects of drilling projects the training course included a visit to the BGR Core Repository in Spandau, where we were shown how to image and log core sections, scan cores using XRF, and use a multi-sensor core logger.

Whilst in Potsdam I was able to visit the Sanssouci park that contains several palaces, including the Neues Palais built in the 18th century. One room, the Grottensaal (Grotto Hall), is particularly impressive being encrusted with over 24,000 shells, rocks and fossils – an idea for what to do with those rock collections back home perhaps?

A section of marble wall encrusted with geological specimens

Overall, the training course and workshop were extremely useful and provided a great opportunity to meet others involved in continental scientific drilling. If you are, or will be, involved in an ICDP drilling project I thoroughly recommend applying for next year’s course (details will be announced here).

By Jack Lacey (Centre for Environmental Geochemistry and Stable Isotope Facility, British Geological Survey). Jack is involved in the ICDP Scientific Collaboration on Past Speciation Conditions in Lake Ohrid (SCOPSCO) project.

@JackHLacey

Friday, 11 November 2016

JC142 MarineE-tech cruise to Tropic Seamount, north-east tropical Atlantic...by Paul Lusty

Autosub 6000 being launched from the RRS James Cook to undertake a
24 hour multibeam, sidescan sonar and sub-bottom profile survey. 
We are now about two weeks into the RRS James Cook cruise, which departed from Santa Cruz, Tenerife on the 29 October. The current cruise forms part of the ‘Marine ferromanganese deposits - a major resource of E-tech elements (MarineE-tech)’ project. The project is funded by the NERC Security of Supply of Mineral Resources (SoS Minerals) Research Programme, which aims to understand ‘E-tech’ element cycling and concentration in natural systems, and determine how to minimise the environmental impacts of extraction. The ‘E-tech’ elements are those mineral raw materials critical to environmental technologies (e.g. cobalt, tellurium, selenium, gallium, indium and the heavy rare earth elements), and for which concerns about security of supply exist. MarineE-tech (http://prj.noc.ac.uk/marine-e-tech/) aims to improve understanding of E-tech element concentration in seafloor mineral deposits. The project partners involved in this cruise are the British Geological Survey (BGS), National Oceanography Centre (NOC), HR Wallingford, and the University of São Paulo, who are running a parallel research programme on Fe-Mn deposits on the Rio Grande Rise, funded by the São Paulo State Research Foundation (FAPESP).

Some of the E-tech elements are highly concentrated in hydrogenous ferromanganese (Fe-Mn) crusts, which develop on oceanic seamounts. The MarineE-tech study area is located in the north-east tropical Atlantic, about 650 km south of the Canary Islands (about 2 days sailing on the RRS James Cook), and at the south-west end of the Canary Island Seamount Province. The islands and more than 100 seamounts, which extend over a distance of some 1000 km form one of the most significant volcanic provinces in the Atlantic Ocean. Our research focuses on the Tropic Seamount, the southernmost in the archipelago (23.5° N, 20.4° W). Tropic Seamount has an area of about 770 square kilometres, comparable to the Island of Anglesey in North Wales. Previous, limited work has identified Fe-Mn crusts on this and a number of the other seamounts to the south of the Canary Islands.

Clockwise from top left: Typical exposure of Fe-Mn crust broken by pelagic sediment cover on the summit of Tropic
Seamount; ROV Isis collecting a Fe-Mn crust sample to be placed in the basket; A cut sample of Fe-Mn crust showing
distinctive layering that develops from accumulating on the seafloor over millions of years; The first batch of Fe-Mn crust
samples collected by Isis laid out in the laboratory an-board the James Cook. 
During the six week cruise we plan to assess the distribution and thickness of the Fe-Mn deposits, through a combination of high-resolution seafloor imaging and detailed sampling across the range of heterogeneous environments that exist on the seamount. The new samples will be used to characterise the gross geochemical composition of the crust, and the micro-scale mineralogical, textural, geochemical and isotopic composition of individual growth layers. This data will be used to assess the significance of the temporal and spatial environmental factors, and processes (including palaeo and modern oceanographic conditions e.g. seabed morphology, sedimentation rates, upwelling rates and microbiology) that control the compositional, textural and thickness characteristics of seafloor Fe-Mn deposits. We will also be collecting data on the seamount ecosystem, and conducting plume generation and modelling experiments to investigate the potential environmental impacts from exploring for and extracting Fe-Mn deposits. We plan to acquire bulk samples of Fe-Mn crusts, which will be used to assess the potential for the recovery of E-tech elements from these resources using novel, low energy (and low-carbon) extraction technologies such as bio-processing, ionic liquids and hollow fibre membranes. This work is being led by the University of Bath.

New ship-board multibeam swath bathymetry acquired over Tropic Seamount
that will be used to select areas for detailed follow-up mapping and sampling
To date we have been focusing on acquiring new bathymetry data across the seamount to inform subsequent mission planning. We are initially mapping the area using ship-board multibeam swath bathymetry (25 m resolution) and geoacoustic sub-bottom profiler. These data will be used to identify areas of rock outcrop (from acoustic backscatter), and sub-areas will be identified for detailed follow-up surveying using the NOC autonomous underwater vehicle (AUV) Autosub 6000, and the remotely operated vehicle (ROV) Isis. We have already conducted five AUV missions, principally to the test the Autosub 6000 for acquiring higher resolution swath bathymetry (1 m resolution), sidescan sonar (5 cm resolution), sub-bottom profiles (10 cm resolution), colour still images and magnetic data. We have 24 hours of operation on the ship, divided between two science shifts (17 scientists in total), so we are almost continuously acquiring new data.

The primary objective of the first ROV dive was deploy a seafloor lander platform on the summit of the seamount. This has been designed by HR Wallingford, with the objective of collecting time series data on the hydrographic regime and sediment movement in the water column across the seamount. During the cruise we plan to generate sediment plumes (in an attempt to simulate potential disturbance associated with seafloor mining) on the seafloor by sucking up pelagic sediment with the ROV and blowing it into the water column. The movement of the sediment plume will be monitored for several hours by a range of sensors on the lander and compared with results of previous modelling.  Additional hydrographic data will be obtained from three moorings that we have strategically positioned across the seamount. When we recover these at the end of the cruise they will have been deployed for at least 30 days, and provide a time series dataset on currents, temperature and conductivity (which can be corrected with temperature to give salinity) of the water column around the seamount. Additional data on the water column is being collected by numerous CTD deployment (we have undertaken 16 to date), which measure conductivity, temperature and depth (pressure), and can collect water samples for subsequent analysis.

From L-R: Manipulator arm of ROV Isis holding a tube from the sediment pump and generating a plume in the water column
to be detected by the lander; Seafloor lander placed on the seabed ready for monitoring and testing of plume. 
The majority of Fe-Mn crusts samples collected from seamounts globally have been acquired by dredging. This indiscriminate technique provides little or no spatial control on the location or depth from which material is acquired. The high resolution geochemical and isotopic research we are planning at BGS requires the acquisition of a new sample suite with good understanding of the spatial relationship between samples, in terms of their location on the seamount and water depths. In order to accomplish this we plan to collect samples from specific locations using the manipulator arms on the Isis ROV and a new core drill attachment, which NOC have specifically built for this project. The second Isis mission tested the core drill and obtained a 20 cm rock sample. During the ROV missions we are also mapping the distribution of sediments, Fe-Mn crust, other rock types and seafloor fauna using the high resolution cameras on Isis.

Paul Lusty

Co-Chief Scientist JC142

Wednesday, 9 November 2016

The first year of my PhD research: iodine geodynamics… by Olivier Humphrey

The shores of Lake Malawi.
Hi, my name is Olivier and I have just started the second year of my PhD at the Centre for Environmental Geochemistry (University of Nottingham and the BGS). My research revolves around iodine geodynamics and plant availability. In this blog I will provide a brief update of some of the work I have been doing over the past year.

Iodine is an essential micronutrient involved in the production of thyroid hormones. Approximately one-third of the world’s population has inadequate iodine intake, and this causes a spectrum of clinical and social issues, collectively known as Iodine Deficiency Disorders (IDD). Dietary supplementation, by means of iodised salt, is commonly used around the world to reduce the prevalence of IDD. However, iodine biofortification represents an area of active research as a cost effective strategy to address global iodine deficiency without the limitations associated with iodised salt. Despite this a much greater understanding of soil-plant uptake is required.

I’ve had a busy year becoming familiar with the extensive literature surrounding iodine geodynamics and plant uptake/availability, working on a review paper and planning/starting various experiments. One of my current experiments includes investigating the uptake mechanisms of iodine in spinach and tomato plants. These are two crops which have been shown to respond well to iodine treatments and have great potential for biofortification programmes. A series of experiments have been designed to investigate the uptake, translocation (from root to foliage and foliage to root) and storage in the mature plants. These experiments will include the use of stable radioactive iodine (I-129), by using multiple isotopes it will be possible to observe potential changes in chemical speciation (conversations between iodide and iodate) as the plant interacts with the iodine. Over the summer I was able to conduct an experiment to investigate where mature spinach and tomato plants predominately store iodine. I have now harvested and prepared the samples; I will perform the ICP-MS analysis very soon.

Peat bogs of Hautes-Fagnes. 
This summer, I attended my first international conference in Brussels for the Society for Environmental Geochemistry and Health’s (SEGH) annual conference, where I presented a poster summarising my PhD research. This was a great opportunity to meet other scientists from around the world with similar interests. We happened to be in Brussels for the Ommegang of Brussels which is an annual religious procession, naturally this involves people fighting on stilts and a huge wooden horse being paraded around Brussels’ Grand Place! On the final day, we went on a field trip to the peat bogs of Hautes-Fagnes, where we were given a talk about how the peat bogs were being used to look at the effects of industry on pollutant levels in the area.

I also participated in a 2 week Africa-UK doctoral training network capacity strengthening exercise. The network, established between the UK, Zambia, Zimbabwe, and Malawi, held their annual meeting in Lilongwe, Malawi this year. After the official opening meeting, which included multiple presentations from our various guests of honour and a brief appearance on national TV, it was time to get to work. The network is aimed at providing sustainable capacity strengthening in soil geochemistry and associated disciplines (see previous blog by Michael Watts). It was great to see all the Royal Society - Department for International Development (RS-DFID) PhD students, local scientists and lab technicians and catch up with their progress again after they visited the UK in May. The first week was based at the Department for Agricultural Research Services in Chitedze for training in soil chemistry, quality assurance and preparation of reference materials via lectures and participatory demonstrations from Dr. Charles Gowing and Dr. Michael Watts (BGS). I was also fortunate enough to visit Lake Malawi following a lecture in the field from Malawi’s leading pedologist Prof. Max Lowole and try some of the Lakes famous Chambo fish after a hot day in the African sunshine. The second week, based at LUANAR: Lilongwe University of Agriculture & Natural Resources, focused on generic training and included statistical analysis, GIS, ethical awareness and presentation skills, the sessions were run by Dr. Murray Lark (BGS), Prof. Amon Murwira (UoZ), Dr. Kate Millar (UoN) and Prof. Martin Broadley (UoN).

Prof. Max Lowole providing a lecture to the research group on a Malawian vertisol. 
Over the next few months I will continue with my plant experiments to identify uptake pathways and investigate translocation mechanisms when iodine is applied to the plants in the form of a foliar spray. These experiments will be based in the growth rooms at Sutton Bonington (UoN) and analysed at BGS, thereby maximising the resources made available to me through the Centre for Environmental Geochemistry, from which my funding originates. I am also planning an innovative soil experiment involving microdialysis probes that I hope to use to extract soil solution and analyse the chemical speciation over a short-term period using size exclusion chromatography (SEC). The use of SEC, coupled to ICP-MS, will enable me to look at different size fractions of iodine, including organically bound iodine. This will provide a much clearer understanding of how iodine behaves in soils shortly after rainfall or fertilization events when iodine is most available for plant uptake. By understanding the dynamic processes that occur during these events it will be possible to understand the factors that limit plant uptake.

@OlivierHumphrey

The PhD is supervised under the umbrella of the Centre for Environmental Geochemistry:
Dr Scott Young, Dr Liz Bailey and Professor Neil Crout (University of Nottingham) and 
Dr Michael Watts and Dr Louise Ander (BGS)

Monday, 7 November 2016

The 20th year celebration of the International Continental scientific Drilling Program (ICDP)...by Melanie Leng

This October the ICDP celebrated 20 years since its formation in 1996. During this time ICDP has contributed funding to around 50 deep drilling projects including drilling into the San Andreas Fault, taking sediment cores from some of the biggest and oldest lakes in the world, and most recently (this summer) drilling the “ring peak” of the Chicxulub impact crater. Here Melanie Leng talks about the 20th year celebration event of the ICDP...

One hundred ICDP stakeholders from across the world and member countries
met at GFZ in Potsdam to discuss ICDP into the future. 
Over the last 20 years the ICDP program has grown both in member countries (now around 20) and funding. At present the ICDP supports on average 3-5 deep drilling projects a year spending much of the combined $5M annual membership fees on drilling contributions (usually between 20 – 40% of the drilling operations cost). For this 20th year celebration, ICDP held a 2 day event in which key stakeholders were invited to present and discuss the way forward for the program. We were asked to think about and discuss whether the Operations Support Group (who look after everything from supporting project and operations, to on site drilling expertise and oversight, data management and archiving, to training courses, outreach and events) needed to be changed.

Over the 2 days we discussed ways in which the operations could be bettered, for example ICDP staff helping more with the over sight of the drilling operations, ICDP having a greater equipment pool (especially for down hole logging) and attaining greater “reach” rather than outreach. Educating and training of our early career researchers was seen as a priority.

The ICDP now has the task of thinking about the suggestions of the 100 or so stakeholders. I am sure our discussions will help ICDP continue supporting the global geoscience community with great international research that is underpinned by the technically challenging and expensive drilling that ICDP enable.

One surprising outcome of the meeting was the discovery that ICDP did not have a Facebook page! This was soon rectified with the help of some of our social media users (take a look at http://facebook.com/ICDPDrilling/).

The UK is a member of ICDP and as such our geoscientists can propose and participate in world class geoscience research with teams made up from amongst the best in the world. Melanie Leng (@MelJLeng) is the UK lead for ICDP and represents the UK on the ICDP Executive Committee.

For more information have a look at the ICDP-UK website or the main ICDP website.

Tuesday, 1 November 2016

Hacking semantic paths to make BGS resources more accessible... by Rachel Heaven

Rachel Heaven works in geoinformatics, developing spatial databases, applications and standards to share and visualise geoscience information.

BGS ran an internal hackathon a couple of months ago and Team Semantic Search (starring Agelos Deligiannis, Rachel Heaven, Tim McCormick, Gemma Nash, Ike Nkisi-Orji, Marcus Sen) took on the challenge to implement a semantically and spatially intelligent search service.

The aim was to improve access to BGS's resources with an enhanced search tool that can cut through the tangle of complex geoscience terminology, and to improve navigation between information resources.

Why should we do this ?

BGS is custodian of a wealth of textual information, including the important observations and interpretations that accompanied BGS’s traditional core product, the hardcopy 2D geological map. Our digital-era information products make it easy to view interpretations of the spatial extent of geological properties but they are not easy to discover, are difficult for non-experts to understand and they are divorced from the documented evidence they are based on. These provenance links are increasingly important when information is used in decision making.

So how do we make a search "semantically intelligent"?

Well, if you do a regular web search or directory search for content, all you are matching is a sequence of letters. The search engine doesn't know that other terms mean the same thing, or are related to your search intent in some way, or that the term you are using has different meanings in different eras or contexts – all of which happens a lot in the long history of geoscience terminology. All of these problems mean that the user has to filter out "false positives" in the search results and often run repeated searches using the alternative terms that he/she knows about, potentially missing out on valid results, especially if they don’t know the experts’ terms.

But what if the experts who knew all about the terminology and all the relationships between the terms and the things (we call them concepts) had already captured all of that knowledge (we call that an ontology) ? And even better, if that was available in a machine readable form and the search engine could use it with some algorithms that made it behave as if it knew what your search term meant ? That is what we mean here by semantically intelligent.

The "spatially intelligent" bit means we also want the search engine to understand the various ways that locations are mentioned in unstructured text so that a user can find all information relevant to a chosen location no matter how it is represented.

The good news is that this has been a goal of the web community for some time (e.g. Tim Berners-Lee Semantic Web paper in 2001) and there are standards we can use to specify the terminology and tools to use them (e.g. W3C Data Activity that BGS are contributing to).

Furthermore, codifying geoscience terminology has been an activity of BGS for a long time - before any sniff of the semantic web - so we have some really mature vocabulary resources, some of which we published in the appropriate web standard form a few years ago, and we also work on internationally standardised vocabularies with the IUGS-CGI Geoscience Terminology Working Group.

To push things along further BGS have been supporting PhD research (with Robert Gordon University) into these topics, and our student Ike was able to join us at the hackathon and contribute algorithms he has written to use the ontologies.

So what happened during the hackathon ?

Planning
With handy post it notes on a flip chart, we identified 5 separate components to work on in parallel:
  1. document indexing for the search engine
  2. application to run the search service as a simple search
  3. extending the search service to use the ontologies
  4. web interface for search
  5. coordinate to placename converter
  6. links to the search from Groundhog Web virtual cross section and borehole viewer (as an example just because that’s an application that I develop anyway so know the codebase)
Indexing
On task A, Rachel, Marcus and Ike worked together to install elasticSearch (open source search engine software) and used it to create an index of plain text terms in a set of BGS publications – no ontologies involved yet. After a few failed starts this was then left to cook overnight.

On task B, Marcus and Ike implemented Ike’s existing search application as an elasticSearch client to run a simple text search.
Indexing complete
Search service running
Search interface working

On task C, Gemma created a web front end to launch the search, display the results, highlight relevant terms in the pdf documents and to capture user evaluation of the search results – useful for Ike’s PhD. “High five at 11.25” moment on the second day when the search was working properly and the web interface submitted searches, showed results and highlighted the found terms in the pdf documents.

Tim McCormick concentrating
On task E, Tim started adapting (and then found it was quicker to write from scratch – hacking isn’t always the best option for a quick win then !) a few database functions in PL/SQL to create a gazetteer translation and expansion tool. This meant querying a corporate spatial database of OS administrative placenames, map sheet names, some geological feature names to convert a coordinate location to a list of placenames, and expanding a single placename to a list of all co-located placenames. This performs a similar function to Ike’s semantic comparison algorithm but in the geographic space. Marcus created a small web service that would work as an interface to Tim’s function.

Search links added to virtual borehole viewer
On task F, Agelos and I tried (and failed) to get the BGS Groundhog Web code to compile locally (new PC missing some vital configuration that we couldn’t pin down), and in the end I captured an example page from its output and hardcoded new links to Gemma’s search form and Marcus’s interface to Tim’s Gazetteer tool. Going great at 12.08 – even with a bit of cheating!

Existing BGS Lexicon entry for Vale of York Formation
On task C, Ike continued indexing the document collection using concepts in the geological timescale ontology (BGS Chronostratigraphy), and adapting the search engine to use that ontology in his query expansion, semantic comparison and relevance ranking algorithm. Agelos also developed some web scraping scripts to pick up BGS Lexicon terms from structured web pages so that search links could be applied in that way if we wanted.

Going like a dream at 13.17 ! Tasks A,B,D,E,F complete and ready to demonstrate at the final presentation at 2pm. Task C was always going to be the tricky bit so we weren’t too worried that it wasn’t finished yet.

At the close of the hackathon we were able to demonstrate the web front end to the search and show it running to retrieve text-matched results from the indexed document collection.  We also demonstrated a Groundhog virtual cross section from the Vale of York 3D model with new context sensitive “Search publications” links from the legend of model layers that open the search form pre-populated with the placenames and geological time or formation name term relevant to that part of the cross section. Just after the hackathon, and just a little too late to demonstrate, Ike managed to plug in the full semantic comparison algorithm using the Chronostratigraphy ontology, completing Task C.

The hackathon judging panel were impressed at how much we achieved and were excited about the possibilities and the way it could help users discover and navigate through our wealth of resources. We all enjoyed working in a new environment and with a different team of people to usual – despite the extreme heat on those days ! On a personal level this team effort brought together various strands of work that I have been working on – sometimes in the sidelines - for a number of years so it was really satisfying to finally have something to show. Huge thanks to all the great team members.

What happens next ?

We would like to build on the work we did to
  • implement a more robust version on our intranet for staff to assess
  • add further ontologies to the search tool
  • use third party online data sources or APIs for some of the gazetteer translation and expansion service rather than having to maintain our own copies of OS data
  • index documents by location by geoparsing for recognisable coordinates, or proxies for locations such as borehole registration numbers
  • provide a similar application on the BGS external website to search publications, showing snippets of documents and links to the BGS shop if the publication is not open access
  • eventually implementing a single point of entry to search and navigate through all BGS website resources


Wednesday, 26 October 2016

Getting a Read on Radon: measurement of radon activity in groundwater samples from a proposed fracking site - a student project!...by James Dinsley

My name is James Dinsley, an Environmental Science student from the University of Nottingham and I am currently a quarter of the way through a one-year placement with the British Geological Survey, working in the Inorganic Geochemistry Laboratories in Keyworth, Nottingham. Over my year with the BGS, I have been supporting projects with Dr Charles Gowing and Dr Andy Marriott looking at the development and validation of (i) a method for determining the amount of radon in groundwater and its application to environmental baseline monitoring at proposed shale gas exploration sites, and (ii) a method of using a form of radioactive lead (210Pb) to determine the age of lake sediments. I will also be working in the aqueous chemistry laboratories, where I will use different chemical tests to analyse the composition of water samples for clients. As part of my work, I have learned how to conduct key laboratory tests such as determining soil pH and organic matter content, water pH and alkalinity, electrical conductivity and total organic carbon.


What does radon have to do with shale gas and fracking?


Fracking is a controversial topic due to public concern about it’s potential environmental and health risks. The process of fracking creates micro-fractures in the target shale rock to release natural gas (methane) for energy supply. One area of concern with fracking and the shale-gas development more generally is the possible release of naturally occurring radioactive materials (NORMs) contained in the shale, e.g. radon (222Rn), a known carcinogen, either as a gas or dissolved in the produced water that also comes up the shale gas well. Human exposure to radon is known to present a health risk if it is not adequately controlled.

In order to understand the potential additional risks that might arise from shale gas operations, a clearer understanding of the baseline groundwater chemistry is needed in areas around proposed development sites.

What have we found so far?


Libby preparing the samples for analysis to
determine radon concentration. 
Charles, Andy and Libby Gallanaugh, the previous placement student from the University of Surrey, refined a method for looking at the emission of alpha particles (a type of radiation) from the radioactive decay of radium (226Ra) in order to quantify the amount of radon present in groundwater samples. To do this, organic chemicals called ‘scintillators’ are used to convert the energy generated by alpha particle emission into light, which is then measured by a detector. More light pulses will indicate a higher amount of radon in the samples.
Libby’s work has identified the most suitable scintillator type and an appropriate scintillator/sample ratio to use, alongside helping to determine the most efficient analytical run time needed. Her results have helped to enhance both the counting efficiency of the detector and improve the quality of the results. It is hoped that the technique that Charles, Andy and Libby were working on could be used directly in the field to reduce the length of time that radium has to decay before analysis.


What are the next steps?


Alongside my duties in the aqueous lab, I will continue to further this research by investigating both the influence of sample temperature on the detector’s ability to quantify the radon concentration; and the influence that major ions in water (e.g. chloride, bicarbonate, etc.) can have on the detector’s readings, since water collected from different environments and rock types will have different chemical compositions! This work will help to ensure that the quantification of radon from field samples are more accurately represented despite variation in where and when sampling takes place.

During my time with the BGS I will also be working on another project, looking at refining a method for using a radioactive lead isotope (210Pb) to determine the age of Malaysian lake sediments. Ageing these sediments will help to reconstruct past pollution events from possible human activities. 210Pb dating can show us changes in sediment deposition over time, which is key as this can lead to changes in the lake’s physical and chemical characteristics. By using data collected from 210Pb dating, decision makers will then be able to determine the best method to remediate contaminated lakes. This project is being run in collaboration with the University of Nottingham through the joint Centre for Environmental Geochemistry.

I am enjoying my time with the BGS so far, and I am looking forward to getting involved with learning and experiencing as much as possible, alongside having the opportunity to meet many more people!


Monday, 24 October 2016

Examining the chemistry of mushrooms: a valuable tool for archaeology?...by Angela Lamb

The edible oyster mushroom, Pleurotus ostreatus, in Mere
Sands Wood Nature Reserve, Lancashire.
Mushrooms are a common part of modern human diets, yet they are rarely considered from an archaeological perspective. As soft-bodied organisms they readily rot, so are very rarely found on archaeological sites. Search for academic papers on archaeology and fungi and you are most likely to find articles discussing how microscopic fungi eat wall paintings and artefacts, and there are very few examples of mushrooms in relation to diet. The most famous exception is Oetzi ‘the Iceman’ from the Copper Age of Italy who had two species of bracket fungi in his possession. Neither of these are terribly edible but one could have been consumed as a vermifuge (something to kill parasitic worms), and both can be used as tinder to light fires.

A new collaboration between Dr Hannah O’Regan from the Department of Archaeology (University of Nottingham), Dr Angela Lamb (Centre for Environmental Geochemistry/British Geological Survey) and Dr David Wilkinson, (Liverpool John Moores University) set out to consider this lack of mushrooms from another angle -  as they are made of protein, can we see evidence of fungus consumption by looking at the stable isotope composition of people in the past?

An Italian mushroom shop.
Examining their chemistry

Stable isotopes of a range of elements are widely used in archaeology and ecology to estimate the food source used by an organism – for example plants, herbivores and carnivores tend to show different stable isotope chemistries. We found that very few studies have been performed specifically on edible mushrooms, so we collected and analysed fungi from the wild in North West England. We combined our results with published data to see how variable isotopes of carbon and particularly nitrogen can be. It turned out to be that fungi are extremely variable, with nitrogen values ranging from those you might find in legumes up to those you’d see in a polar bear!! Edible mushrooms had a smaller range, but were still very varied. This means that a human – or other animal – feeding on lots of mushrooms could, depending on which species they are eating, have a bone chemistry that could lead people to think they were being carnivorous. But the main thing this work showed was how little we know about fungi and the archaeological record. There is still much to learn!

This work is published online in the Journal of Archaeological Science.

Monday, 17 October 2016

Linking Geology & Biology in Europe’s oldest lake: a 1.3 million-year record of climate change and evolution from Lake Ohrid…by Jack Lacey and Melanie Leng

Lake Ohrid SCOPSCO science team, photo courtesy of F. Wagner-Cremer.
The Lake Ohrid drilling project has featured regularly on Geoblogy over past years, now reaching its final stages Jack Lacey and Melanie Leng from the Centre for Environmental Geochemistry travelled to the Netherlands to attend the 6th project workshop in Utrecht. Here they report on the meeting and provide a much overdue update on this ground-breaking interdisciplinary research…

Lake Ohrid is one of only a handful of lakes worldwide that has continuously existed for millions of years and contains hundreds of unique species found nowhere else. It represents an outstanding natural laboratory allowing us to explore the links between geological processes (climate change, volcanic eruptions, tectonic activity) and biological evolution – i.e. what drives speciation; stable conditions or rapid environmental change. To this end, the lake was drilled in 2013 as part of the International Continental scientific Drilling Program’s (ICDP) Scientific Collaboration On Past Speciation Conditions in Lake Ohrid (SCOPSCO) project (see blog series). The fieldwork campaign recovered over 2000 m of sediment from four sites around the lake, with a master record in the central basin reaching 569 m below lake floor that archives at least 1.3 million years of Earth’s history back to the Early Pleistocene.

Recently, we published our findings from the upper half of the core - covering 650,000 years - as a special issue in the journal Biogeosciences (open access). The team has been working extremely hard to finalise analytical work on the lower half of the record, and we met in Utrecht last week to discuss new developments and future efforts. In short, progress has been exceptional and for many proxies (e.g. isotopes, pollen) the majority of work is complete for the entire lacustrine succession (equivalent to the upper 430 m of sediment). The project has now reached a very exciting stage, proxy data from different research groups are being collated and we can start to understand how the lake has responded to both long- and short-term environmental change, answer fundamental questions about why/how the lake first formed and ultimately determine what drove biological evolution. We also have one of the longest and best land-based archives of tephra (volcanic ash) in the Mediterranean, which will allow us to accurately date our core material and directly compare to other regional and global sequences. However, there is still much work to be done - so keep an eye out for future updates!

Thanks go to Friederike Wagner-Cremer and Timme Donders at the University of Utrecht for organising the workshop, and to the entire SCOPSCO team who exemplify the best of interdisciplinary and collaboratory science.

To find out more about SCOPSCO visit the project website, or for further information please contact jackl@bgs.ac.uk.
By Jack Lacey and Melanie Leng (Centre for Environmental Geochemistry & Stable Isotope Facility, British Geological Survey)



@MelJLeng