Monday, 25 September 2017

Data Science Techniques.... by Simon Flower

Simon Flower is interested in the application of data science techniques to the range of data in BGS. He is also a senior specialist in IT in geophysics, chair of the INTERMAGNET Operations Committee and a Chartered Engineer. He has managed the growth of information technology across the Geomagnetism programme for the past 25 years.

We recently held a hands-on data science workshop for BGS scientists, an opportunity to spend time learning a little about new ways to work with our data. Many of us are becoming aware of the revolution that is going on in data science and of the power of what household names like Google are doing. Sometimes seemingly ‘magic’ things surprise us. Have you received a flight booking by email only to have Google remind you a few hours before you’re due to depart for the airport? Or stopped at a café to find that Google knows you’ve been there and is asking you for a review. The uncanny accuracy with which Facebook seems able to recommend people that you know is the result of some serious data mining activity in the background.

BGS is rich in data, past and present, and is on the verge of a vast increase in what’s available to us through projects like UK Geoenergy Observatories and the European Plate Observing System. At times we’ve possibly thought of this as a problem, having all this data to look after. But it represents a huge opportunity if we can start to master data science techniques. What would it be like if we could do a semantic search(1) of the entire BGS data holdings, past and present – be able to track down things that are relevant to our work from across the whole range of BGS data. Or continuously trawl the web for things that people are saying that are relevant to us – about earthquakes, landslides or the reputation in which the public hold us? Are we really thought of as an independent body, as we hope we are? Data Science techniques can answer this question. As we develop the ability to use these techniques, we will realise that there are new scientific questions that we can answer.

Looking round BGS I can see that there are a number of areas where we are doing some of this data processing manually and already feeling swamped (a case of data being a ‘problem’). Through necessity I suspect that these areas will develop expertise in data science, turning problems into opportunities. At the workshop we had examples of this, some of us using Apache Spark(2) to investigate processing large volumes of groundwater data. It was good to see scientists in BGS  exploring the benefit from these techniques to their work. I hope that we can build on this and create some exemplar systems that not only solve a particular problem, but also provide the catalyst for others in BGS to take the first step. Watch this space as there’s definitely more to come!

Note 1: A semantic search allows you to search for the meaning of words rather than simply matching the way the letters in a word are ordered. For example, semantic searching would understand that, in the context in which I work, aurora refers to the Northern or Southern lights, not to a Norwegian singer or a type of trainer.

Note 2: Apache Spark is a software system that allows data to be manipulated by clusters of computers, enabling large data sets or complex operations to be completed in a short time. A feature of Apache Spark is that users do not need to concern themselves with how the work is split across the multiple computers comprising the cluster.

Wednesday, 20 September 2017

Work Experience at the BGS Stable Isotope James Setchfield

Hi, I’m James and for the past week I have been gaining experience working in the stable isotope facility at The British Geological Survey in Keyworth. I have a burning passion for Geography and the processes that help to shape and change the physical world around us. I am currently in sixth form doing my A-levels but have every intention of pursuing this subject to a degree and career level. The work experience scheme I was placed on helped me to gain an understanding of the career pathways Geography leads to. My week at BGS has allowed me to use and understand scientific equipment that I have only ever seen in diagrammatic form.

To start off the week we conducted an experiment with Chris Kendrick where we took samples of calcium carbonate (CaCO3) with unknown oxygen and carbon isotopic values and reacted them under a vacuum, with Phosphoric Acid (H3PO4). The carbon dioxide (CO2) we produced was transferred into a collection vessel, using liquid nitrogen to freeze the CO2, and any unwanted gases were removed using a vacuum pump.

This process took us 2 days so on Wednesday we had a sample that was ready to be put through the mass spectrometer. We learnt how to set up the mass spectrometer manually, which was very useful in enabling me to understand how the machine runs and produces data from the samples. Our samples needed to be left running overnight, so by Friday we had our data which showed us that the loch we were investigating changed from fresh water to marine water, which coincided with the glacial retreat at the end of the last glacial period. This showed us that as the glaciers retreat and the sea level rises, marine water floods the loch and changes the water composition and we were able to trace this using the different isotopic values for carbon and oxygen in our samples.

During our time at BGS we also conducted an International standard Mass Spectrometer Calibration which calibrates the mass spectrometer with all the others in different stable isotope labs around the world, this is to make sure the results  are to the same degree of accuracy and to make sure the data can be cross checked by different labs.

We also had a chance to speak to Dr Angela Lamb who carried out an investigation on the skeleton of Richard III. She was able to see what he had been eating throughout his life by looking at the carbon and nitrogen isotopes in his teeth (age 3-14) femur (17-32) and rib bones (30-32, when he was king). This was all very fascinating and made me want to find out more about how exactly they discovered what he ate and where he lived all through his life by looking at his skeleton.
On the whole I have had a very informative week working at BGS, it has really given me an opportunity to see what working in a laboratory is like and the type of investigations that go on, who knows maybe I’ll end up working for The British Geological Survey in a couple of years, all I can say is that I look forward to it.

Thursday, 14 September 2017

My work experience week at the British Geological Laura Wainman

Hi, my name is Laura Wainman and I am a sixth form student from Rushcliffe School. I have just completed my work experience week in the Stable Isotope Facility at the British Geological Survey. BGS is a world renowned geoscience centre with its headquarters here in Keyworth, Nottingham. A great variety of research is conducted at BGS, from monitoring and forecasting volcanic eruptions and earthquakes to studying local and global environments.  Along with another student James, I have spent my week learning how, from measuring the isotopes of oxygen and carbon, the climate and environmental conditions from thousands of years ago can be deduced.

On Day 1 (after the health and safety induction) we began our week long experiment to extract Carbon Dioxide (CO2) gas from Calcium Carbonate (CaCO3) samples which could then be analysed in a mass spectrometer. The first stage in this experiment was to weigh out our carbonate samples into small test tubes, drop these into larger glass vials containing phosphoric acid and then attach these to the vacuum pump (see above photo) so that overnight all the air could be removed. We then allowed the phosphoric acid and sample to mix by shaking the larger vessel and leaving it in a 25.2oC water bath overnight so that the reaction could be fully completed and all at the same temperature. The next day we then had to extract the CO2 gas which had been formed by the reaction. To do this we reattached the vessel to the vacuum pump and then used liquid nitrogen (which was at -196oC) to sublime the CO2 whilst we removed any other remaining gases.  The gas was also passed through an acetone water trap to remove any water which would have later damaged the mass spectrometer.

Once all of our samples had been extracted we then attached them to the mass spectrometer and left them to be analysed. It was especially interesting to learn in detail how the mass spectrometers work and see all of the components up close. I had not previously known about the use of a reference gas or the requirements of different machines to analyse different isotopes – the ones we were using looked specifically at Carbon-13 and Oxygen-18. On our final day we were able to collect and analyse our results, from the graphs we plotted we were able to see that the loch from which the samples were collected had gradually changed from a freshwater environment to a marine one. This was due to the increase in sea levels at the end of the last glacial period 12,000 years ago.

Whilst we were waiting for our main experiment to progress we were also introduced to many other areas of the lab. This included using microbalances, tweezers and mini spatulas to weigh out very very small amounts (70-150mg) of one of the BGS internal standards of freeze dried broccoli! Whilst frustrating at times, this has certainly given me a much greater appreciation of the meticulous and painstaking preparation of samples required to conduct good research.

We also helped prepare rock sediment samples from Vietnam and Tanzania for analysis, this involved daily emptying and refilling of (many) beakers in order to wash the samples of debris and dirt. Once the samples had dried out we then scraped them out of the beakers and used a mortar and pestle to grind them into a fine powder before depositing them into small vials ready to be analysed.

Monday, 11 September 2017

Rain, hazards and thin sections: A geological adventure in Sierra Lorraine Field

I have just had the opportunity to spend a week and a half in a very wet, rainy Sierra Leone, working with Kathryn Goodenough as part of a two-year partnership project, funded by the Department for International Development (DFID), that is focusing on building a lasting legacy around capacity in the extractives sector. Sierra Leone has been left reeling in recent decades with a brutal ten-year long civil war that finally ended in 2002, the recent Ebola Crisis, and now a catastrophic landslide in the capital, Freetown. My role in country was to run an introductory petrology course to some of the geologists in the National Mining Agency (NMA). Recently refurbished, the Agency has purchased two microscopes to enable them to study rocks in thin section. This is something we at BGS take for granted, but for the NMA, this will be a tremendous step forward. My first challenge was getting four boxes of thin sections that will form the core of a teaching collection at the NMA into country. According to UK customs, thin sections are an offensive weapon, and I very nearly had them confiscated! The flight was spent in nervous anticipation of arriving in Sierra Leone with four boxes of fragmented glass, but fortunately, the boxes survived the baggage handling intact!

A view of the microscope lab

We arrived in country following weeks of exceptionally heavy rain – one estimate we heard was that the rain in August had been 3 times greater than the norm – and believe me, when it rains here, it RAINS! It’s the first time I’ve had to give lectures and battle with the noise of the rain in order to be heard!

Heavy rain at about 10am at the NMA
Unfortunately, this proved to be a contributing factor in a catastrophic landslide in early August causing ~1000 deaths, and extensive destruction to property. BGS colleagues have been working with Arup and local consultancy Integems on a World Bank-funded hazard mapping project for Sierra Leone, and so Kathryn was invited to represent BGS at a World Bank meeting on arrival in country. This meeting brought together key players, to look at issues such as damage to infrastructure (e.g. roads and bridges), stabilising the landslide, hydrology, and obviously, the factors contributing to the cause of the landslide in the first instance. It was a fantastic experience for me to observe the processes and work involved with major organisations such as the World Bank and UN following such a disaster.

Over the weekend, we visited the landslide site with personnel from the international organisations, but also local staff from the NMA (which includes the Geological Survey of Sierra Leone) and members of the Sierra Leone Institute of Geoscientists (SLIG). The BGS project in Sierra Leone takes every opportunity to provide field training and experience to the younger geologists within the local organisations, by taking them into the field with more experienced geologists.  This was a very humbling experience – the news bulletins really did not portray the enormous size of the landslide, nor the reality of the damage caused. We were able to take a detailed look at the geology from the side of the landslide itself and provide our observations to the World Bank and associated organisations. I was grateful to have the opportunity to really see how our branch of science can play a fundamental role in a disaster situation, helping to understand the causes, and then working towards understanding future hazards and risks. We also collected some eyewitness accounts which provided invaluable insights into the timing of key events, and which really brought the reality of the disaster home to us. Freetown is a relatively small capital city of just over 2 million people, so in such a small community everyone knew someone who had lost their life in this disaster.

A view of the landslip from near the source with some of our colleagues from the NMA and SLIG
The petrology course at the NMA started on Monday, with an intense week of lectures and microscope practical sessions. A colleague from the University also joined us in order to refresh and re-stimulate his knowledge. The delegates were eager to learn and proved to be A* students. We worked through an incredible amount of material, from basic microscope operation to covering identification of minerals and textures in sedimentary, igneous and metamorphic rocks in thin section. It was an absolute delight to be able to teach delegates who were so enthusiastic. I hope by the end of the week that I had been able to achieve the aim of providing a foundation that the NMA staff can build on and develop through experience, and then pass on this knowledge by training more staff themselves. I hope soon they will be able to characterise the thin sections that are currently sent out of country for characterisation by the mining companies, thereby growing a commercial service in country at the NMA. As well as working hard, we had an enormous amount of fun during the week: the people of Sierra Leone have a wonderful, fun loving disposition, and one of my most endearing memories of this country will be that of mischievous laughter! If anyone is interested in becoming involved in the BGS work in Sierra Leone, please contact Kathryn Goodenough.

Friday, 1 September 2017

My first field season: rocks, bubbles and low-cost technologies... by Jo Miles

Hi, my name is Jo and I began my PhD at the British Geological Survey and School of Earth Sciences, University of Bristol in September 2016. My research aims to further our understanding of preservation potential of mineralising systems located in the shallow submarine environment (<100 m). In this blog, I will share with you an aspect of my field season on the Greek island of Milos from this summer.

Dynamic submarine processes can help or hinder preservation, potentially resulting in either a bonanza or a failed ore deposit. Therefore, it is important to understand the dynamic processes and the preservation potential, to determine whether the shallow submarine environment is prospective for future mineral exploration and exploitation. The island of Milos, located in the Cyclades, Greece, provides an ideal on-land laboratory having emerged 1.4 million years ago. The island’s topography reflects the paleo-seafloor, and allows us to directly study and sample mineralised and hydrothermally altered paleosurfaces that formed in the shallow submarine environment.

I have recently returned from my field season where we drove approx. 2000 km (a similar distance from Nottingham to Rome) around winding roads of a 13 by 23 km island over a period of five weeks. The first challenge of the trip included learning to adapt to a Jimny Jeep that was not happy to be in first gear or reverse.

I was joined in the field by my main supervisor, Jon Naden, for a handful of days prior to the rest of the party. This was a great opportunity to visit mineralised and altered outcrops, which I had only read about in literature. This was vital in helping my understanding of hydrothermal systems and begin to visualise how my PhD project will pan out. More students from the University of Bristol and Ottawa shortly joined us for a week, alongside researchers from the University of Athens - the island was certainly busy.  

One aspect I am keen to research involves how mineralisation differs from the western ancient hydrothermal system in comparison to the active system located in the east. In order to observe the active submarine environment and witness the potential ore-forming environment, we collaborated with PhD students Jonathan Teague and Dean Connor from the School of Physics, University of Bristol, whom have experience building and deploying low-cost remotely operated underwater vehicles (ROVs) and unmanned aerial vehicles (i.e. drones; UAVs). With knowledge from the University of Athens, we deployed a BlueROV2, equipped with a GoPro Hero 5 off the southern coastline of Milos Island. This was entirely controlled via a laptop and Xbox 360 controller onshore, which allowed the ROV to move a maximum distance of 100 m offshore.

1. Setting up the office for venting exploration.

2. The ROV in action.

The aim of this pilot study allowed us to decipher the location of active venting fields – were they randomly dispersed or was there a structural or permeability control? Knowing the NW-SE horst-graben structural control on the island, we inferred this lineament out to the southern coastline. Alongside rotten-egg smelling fumaroles located in the cliff faces, we were able to decipher two likely venting locations to deploy the ROV. The rotten-egg odour is indicative of sulfur in the form of H2S: a gas coming directly from an underlying magma chamber.

Three days were spent identifying and undertaking reconnaissance mapping within an area of 1 km2 where we successfully found venting sites. The team from the School of Physics, University of Bristol undertook a Structure-from-Motion (SfM) photogrammetry program, to produce high-resolution 3D topographic reconstructions of the seafloor. Thousands of images taken with the GoPro Hero 5 contribute to a handful of bathometry models. Despite the huge volume of data, this is a much cheaper option.

3. Locating bubbles with the ROV via laptop control.

Since the vents are relatively shallow (<7 m), we returned to the area during the evening to snorkel which was the perfect treat to end an incredibly hot day hiking to outcrops. Luckily, the sun was still shining, which meant the visibility conditions underwater were perfect. Often, you could use your sense of smell to locate the venting fields. Patches where bubbles were rising often resembled the temperature of a hot bath (approx. 60oC). We avoided swimming directly over these areas due to the corrosive nature of the escaping gases.

Unlike the ROV, we had to be patient with the weather in order to fly the drone. Rain and strong winds often set us behind schedule. For safety purposes, a team of four was needed: two would secure the location to prevent the public from being close to the flight area, whilst the pilot and computer-operator would liaise to ensure the drone was following the pre-planned flight lines. We chose terrain-challenging locations to create photogrammetry models, which would enable remote fieldwork with a 10 cm resolution.  When discussing my research and its implications back home, it will now be much easier for the audience to follow my thinking if I display the landscape and rocks to them, as if they were on fieldwork with me.

4. UAV Pilot undertaking a test survey.
This was a great opportunity to be part of a student-led research project with a diverse range of skillsets, with the full backing of our supervisors. We are currently writing our first paper and eager to develop the project further and revisit the venting site next spring.

My supervisory team consists of Jon Naden (BGS), Frances Cooper and Brian Tattitch (University of Bristol), Stephen Grebby (University of Nottingham), Dan Smith (University of Leicester) and Graham Ferrier (University of Hull).

Jo can be found on Twitter using the handle @geologyjomiles

Photography credit:  Jonathan Teague,