What’s the issue?

New tools to detect ocean microbes have recently been developed by researchers at the University of Southampton. The tiny microbes, known as phytoplankton, play

Algal bloom off the coast of Denmark.

several critical roles in the functioning of the oceans, both good and bad. However, without accurate tools to detect them, understanding their function and behaviour is challenging. A major negative impact is the formation of harmful algal blooms, which produce toxins dangerous to both humans and sea life. With climate change, the frequency of these blooms is increasing. This effect is most prominent in the North Sea and the Mediterranean. Bloom conditions occur when phytoplankton grow excessively. Certain species of these microbes release harmful toxins which can kill sea birds as well as dolphins, whales and other marine mammals. Toxin-contaminated shellfish have also poisoned humans.

Existing methods of detection offer insufficient detail and in some cases cannot distinguish between harmful and non-harmful blooms. Dr Matthew Mowlem and Professor Hywel Morgan, from Southampton University, have made significant progress towards a hand-held rapid detection system to provide early warning of blooms. By regular monitoring of the toxin releasing species trends in population growth can be picked up to offer advanced warning of a harmful bloom. Early warning increases the options for managing these events.

How do phytoplankton impact on CO2 levels?

A scanning electron micrograph of a single coccolithophore cell.

The new detection system is also useful to study more about the beneficial roles phytoplankton play, for example in climate regulation and carbon capture. Like plants, phytoplankton photosynthesise, using light and carbon dioxide for energy. This removal of carbon dioxide from the atmosphere counteracts the greenhouse effect. Blooms of some species could therefore be very beneficial for the environment, capturing large volumes of carbon dioxide. For example, a phytoplankton species known as coccolithophores are responsible for the majority of the carbon deposited as chalk across Europe, including the white cliffs of Dover.

How does the detection system work?

The new detection technology uses specific RNA sequences to determine the number and species of phytoplankton present in a sample of ocean water. For every test a disposable credit-card sized chip is inserted into a portable detection system. The chip makes multiple copies of RNA samples extracted from the phytoplankton which are then compared to known sequences from particular species.

RNA Molecule

If a match occurs the binding of the phytoplankton RNA to a reporter chemical switches it to a state where light is emitted. As each reporter chemical, known as a molecular beacon, can be designed to emit light of different colours, this approach thus identifies what species are present in a sample.

The major challenge in the project was being able to accurately work out from the detected light signal what the original concentration of the microbe species was. This was achieved by including in every chip a known quantity of an RNA segment to act as a calibration control.

So far the sensitivity of the detection system is at a level where 1,750 cells in a thousandth of a litre can be detected. In algal blooms concentrations of the harmful species can reach over 1 million cells per litre, though damaging levels of toxins are released even when there are 1000 cells per litre, the equivalent of just one cell per thousandth of a litre.

The trick to reaching the required detection limits is to combine the credit-card sized detection chip with a sample concentrating unit. This filtration system processes 2.5 litres of seawater delivering a highly concentrated sample for detection.

Rapid, portable testing systems such as this new device provide the ability to generate large quantities of data about the number and type of phytoplankton present in the ocean, and follow changes over time, increasing our understanding of these tiny ocean microbes and the important roles they play in the functioning of our oceans.

GDE Event in Birmingham

Groundwater Dependent Ecosystems (GDEs) are geologically and physio-graphically complex and are recognised as an important but, nevertheless, poorly understood set of habitats. At a recent event organised by the Hydrogeological Group of The Geological Society, held at the at the Birmingham and Midland Institute, the audience were presented with an excellent overview of current research activities into GDEs covering a variety of topics relating to effective monitoring, conceptual understanding and management of this valuable range of habitats, while providing an opportunity to address issues surrounding current and future research and policy challenges.

What is a GDE?

A groundwater spring

A GDE is one in which the plant and animal community is dependent on the availability of groundwater to maintain its structure and function. Groundwater is, therefore, integral to sustaining the ecological health of these systems and any activity which alters the quantity or quality of groundwater can have negative impacts on the flora and fauna. This immediately brings its own set of challenges, for in order to fully understand these systems it is necessary to bring together a range of expertise and knowledge from a diverse variety of scientific disciplines including hydrology, geology and ecology. A task no less challenging that it will be effective, which was recognised at several stages throughout the day. Case studies were presented which showed where this approach was effective. Only by synthesising data and methods from different fields of science will new insights into the functioning of these ecosystems be obtained.

Why are they important and how can they be protected?

Groundwater dependent ecosystems are fragile and prone to damage through drainage for agriculture, over exploitation of groundwater resources for drinking water, pollution from industrial, domestic and agricultural activity and peat extraction. Yet these ecosystems are important, not only for the services they provide in terms of conservation and biodiversity, but also their economic importance with recreational, aesthetic and cultural value. Furthermore, they can have a role to play in the retention of nutrients from the surrounding catchment, they may act in flood defence and can be important stores of carbon.

Many groundwater dependent ecosystems have been damaged and no longer provide full ecological and hydrological functions or ecosystem services. Loss of these habitats has prompted the European Union to introduce legislation requiring member states to protect GDEs. The Habitats Directive requires long term conservation of protected sites, but additionally the implementation of restoration measures to return restorable areas to favourable conservation status. In addition, the Water Framework Directive (WFD) supports the integrated management of water resources and requires that GDEs be protected from significant damage. The day started with presentations covering the challenges policy makers and water managers face in successfully implementing requirements of the Habitats Directive and WFD, both of  which necessitates a conceptual understanding of the ecohydrogeology of GDEs.

What are the different types of GDE?

A Dune Slack

Groundwater dependent ecosystems cover a range of habitat types (e.g. dune slacks, raised bogs, transition mires, calcareous fens etc.). Some of these habitats are unique or rare outside of certain geographic regions. The turlough is one such example. It is an ephemeral karst lake which results from high rainfall and consequently high groundwater levels. Therefore, these fascinating systems can dramatically go from being relatively dry pasture ground to full lakes during the wetter months of the year, and owing to their characteristic ecology have been designated as a Priority Habitats by the EU Habitats Directive. Only through detailed investigations will it be possible to gain the baseline information necessary to improve the conservation management of this distinctive and irreplaceable habitat.

Carran Turlough, Country Clare, Ireland

Groundwater dependent ecosystems also provide habitat for a unique range of biota. These organisms not only include terrestrial and aquatic plants and animals, but also a group of organism which are found only in the groundwater itself and are known as stygobites. In one of the final talks of the day an overview was given of these unique fauna. Most are small crustaceans, worms and microbes adapted to live underground where they are highly adapted to an environment lacking light and with limited resources. There are only eight species of stygobitic macro-invertebrate species recorded in England and Wales, however, very little is known about their spatial distributions and ecology. The presentation served as a reminder of the importance of this often overlooked groundwater dependent ecosystem and the vulnerability of its biological community to environmental change.

Groundwater dependent ecosystems are important natural environments. However, effective protection and management of these ecosystems may be hindered by inadequate information particularly in relation to the environmental supporting conditions required to maintain GDEs in a favourable state. More work is, therefore, required in order to fully define the environmental requirements of these ecosystems. Increased knowledge will allow for improved management and protection of this important natural resource.

Minamata protestors at the gates of the Chisso factory.

Minamata has become a word synonymous with disease. ‘Minamata disease’ was first identified in 1956, after years of chemical company Chisso discharging methyl mercury into Minamata Bay, Japan. It was a process that continued until 1968, and left over 2,500 people affected by mercury related diseases. Symptoms can range from ataxia, muscle weakness and damage to hearing and speech, to insanity, paralysis and death.

In October, Minamata will be in the news again, when the first international treaty on mercury reduction, already agreed by more than 140 countries in Geneva, will be ratified. The treaty concludes almost a decade of work by the United Nations Environment Programme (UNEP) to limit the amount hazardous mercury in the environment.

Why is mercury hazardous?

Minimata isn’t the only place to have experienced mercury poisoning. In the US, the neurotoxin has caused billions of dollars of expenditure on healthcare, causing up to an estimated 6000 heart attacks and 130,000 asthma attacks annually. It’s particularly acute in communities and cultures where there is a large consumption of fish – mercury bioaccumulates in fish and their predators as they move through the food chain. So close to source areas like Japan, eastern India and Uruguay are particularly at risk.

How does it get into the environment?

According to UNEP, in 2010 alone nearly 3000 tonnes of mercury were released into the atmosphere and water systems. Mercury enters the environment by all sorts of pathways – from chemical effluent, as in the case of Chisso, to its inclusion in household items like thermometers, cosmetics, antiseptics, skin lightening creams….

Artisanal miner panning for gold in Madagascar

But two of the biggest sources are coal fired power plants and artisanal mining, together emitting around 1100 tonnes per year.

Coal itself contains mercury, which is released when the coal is burned. Artisanal gold mining involves using mercury to separate the gold from its ore. This forms a gold-mercury amalgam which is burned off with a torch. It’s simple, requires no training, and is relatively cheap.

Mercury is tasteless and odourless, so when it does get into the environment it’s not easy to spot.

The treaty

The treaty comes after years of concern over the growing amount of mercury build up in fish and the environment. But does it do enough?

For a start, it’s not legally binding. Instead, it encourages governments to set out strategic reduction schemes, on a facility rather than national basis.

With current plans to build more than 1000 coal fire power plants worldwide, and mercury emissions not expected to fall until the 2020s, there are even concerns that the treaty could cause an overall increase in emissions – exposure rates would take several decades to fall, with the sheer volume of mercury in the environment.

On top of this, it makes no provision for the identification or remediation of current contaminated sites or the payment of health damages – despite the thousands of people affected.

Supporters say that a complete ban on mercury wouldn’t work – it would only create a ‘mercury black market’. Instead, the treaty focuses on providing technology and information to those in informal mining, rather than setting unattainable or potentially immeasurable targets.

And, though it’s been ratified, it’s not over yet – binding and voluntary approaches can still be added to the treaty in 2013.

Is it enough?

The main thing is to have a treaty which leads to an actual reduction in global mercury pollution. It needs to focus on cheap, non technical methods to introduce to the widespread small scale mining workers around the globe – the most unregulated and prolific supplier of mercury to the environment. UNEP are already discussing alternative cheap, basic separation processes such as a retort flask, to avoid the continued use of mercury.

The problem of mercury pollution isn’t an isolated one. There are clear links with ongoing climate change and water scarcity – particularly the connection to coal fired power stations, with their high CO2 emissions and the significant amount of water they use for cooling. Many of China’s proposed new coal plants are in areas of significant water stress.
Perhaps the answer is to approach mercury contamination from a broader perspective – combining the case for reducing the use of these power plants and mining techniques with wider issues of energy, water and food security.

References and further reading

‘Mercury poisoning is a growing global menace we have to address’, The Guardian

UN Global Mercury Assessment 2013

US EPA – Reducing Mercury Pollution from Artisanal and Small-Scale Gold Mining

World Resources Institute

Voice of America ‘More than 140 nations approve global treaty to cut mercury’

This was originally posted at the GfGD blog at: http://blogs.egu.eu/gfgd/2013/04/10/gfgd-at-egu2013-day-three/, by Rosalie Tostevin

Mid-week at the EGU conference, and we’ve finally got all three GfGD reps in the same place at the same time for a photo!

Faith Taylor, Joel Gill and Rosalie Tostevin in Vienna

Another busy day, and we’ve picked out a few examples of the latest research being presented at EGU:

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The Link Between Rainfall and Cholera in Haiti

Prior to the devastating earthquake in 2010, cholera had never been reported on the small island of Haiti. The outbreak of the disease in the wake of the earthquake affected nearly 8% of the population and killed over one in a hundred. The disease is now endemic in the country and may never leave. The disease was most likely brought into the country by UN soldiers, who arrived to help the Haitian people after the earthquake – the DNA of the virus has been linked to outbreaks in Nepal.

Outbreaks of cholera during the epidemic correlate closely with rainfall patterns. If we can predict rainfall patterns accurately, then maybe we can anticipate, and prepare for, the spread of disease. Enrico Bertuzzo and Andrea Rinaldo, based at the École Polytechnique Fédérale de Lausanne in Switzerland, have created a model that accounts for rainfall as the driver of disease transmission by washout of open air defection sites or cesspool overflows. Their model allows us to draw longer term predictions for the cholera epidemic in Haiti, and the same model could be adapted to help us understand epidemics of other water borne diseases.

“Geoscientists can do a lot for modern epidemiology”

- Andrea Rinaldo

The red line tracks cholera outbreaks, and the blue bars show the amount of rain that fell during the same time period. There is a significant correlation between the two.

Soils and Human Health

Soils have an important influence on human health. It is soil that enriches our food with essential vitamins and nutrients, but it can also exposure us to harmful chemicals and disease causing organisms.

Soil is closely tied to atmospheric cycles and can be influenced by changes in temperature, precipitation and carbon dioxide levels. Climate change could alter nutrient cycling and the carbon cycle, and in turn affect soils.

After 594 mysterious deaths in the united states, a deadly soil fungus that can lead to meningitis was identified in each of the victims. Infections were traced back to contaminated steroid injections, produced by a New England compound centre. Lynn Burgess, a professor at Dickinson state university, admitted that “we have no idea how a soil fungus ended up in a medical injection.”

Soil scientists and health experts are collaborating to try and forge a new academic field, looking at the link between soils and human health. This kind of cross disciplinary work is difficult because it doesn’t fit into our traditional research funding framework. Health and soil researchers are two groups that don’t normally talk to each other, so we need to encourage cross-disciplinary involvement if we want to increase our resilience to soil related health problems.

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Disaster Risk Management

The toll from natural disasters is increasing as populations rise. At the same time climate change is making the frequency and intensity of climate related events harder to predict. We cannot predict the precise location and timing of most hazards, but we can model risk, to help us understand how people and communities respond to events, and how countries prepare for the financial and human impacts of a disaster.

People in developing countries are more vulnerable to disasters – 95% of the total number of deaths in disasters last year occurred in developing countries. This is a result of the increased exposure and vulnerability of populations in developing countries.

“Natural Hazards are a necessary condition, but you need vulnerability and exposure before you have a disaster”

- Reinhard Mechler

Between 1980 and 2009, a total of 90 billion dollars was spent on disaster related activities. The majority of this money was spent on disaster response and relief, and under 5% was invested in prevention and risk management. The UK government’s Foresight report into Reducing the Risks of Future Disasters championed the idea that in risk management, prevention is better than cure. Investing in risk management and reduction makes financial sense. It is thought that the benefits outweigh the costs by a ratio of at least 4:1 in most cases. This means that for every pound we spend before a hazard occurs, we save four in disaster response operations.

“Even in times of fiscal austerity, disaster risk management should be a priority for government investment”

- Reinhard Mechler

Countries can reduce their exposure to financial risk in disasters by grouping together and pooling the risk. This can significantly reduce the cost of disaster management.

“Grouping countries together and pooling their risk makes financing losses much cheaper”

- Stefan Hochrainer-Stigler

How can we ensure decision makers invest the pot of money available for disaster related activities in the most effective way?

One problem we face is perceived risk from stakeholders. A fear of flying is common, but statistically, crossing the road puts you at a much higher risk – people’s perception of risk may not be proportional to the size of the risk. Disasters that receive the most press coverage tend to receive more funding.

“bias in risk perception can be a barrier for implementation of mitigation measures”

- Nadejda Komendantova

Cyclone shelters have been built and maintained in Tamil Nadu, India, for the last 40 years. These shelters could have been easily adapted to provide protection from tsunamis, but tsunamis were not a hazard that worried stakeholders in the area. The tsunami in 2004 resulted in seventeen thousand deaths. Clearly, the decisions made in this case were not based on sound science but on perceived risk from stakeholders.

Nadejda Komendantova, a researcher in risk policy and vulnerability, thinks it would be good to have more communication between scientists researching natural hazards and policy makers working in disaster risk reduction. Geologists are able to quantify risk through studying the past activity of hazardous geological phenomena, for example, we can calculate the repeat time of earthquakes on a particular stretch of fault. This information is very valuable, and we need to make sure it is understood by decision makers and incorporated into policy.

Investment in disaster related activities needs to be based on facts not opinions. People are starting to recognise the importance of investing in prevention rather than cure, but we still need to put more emphasis on incorporating good geoscience into disaster risk management.

Joel Gill talks about his Multi Hazards Research

What are the chances of an earthquake triggering a landslide, which causes a tsunami and leads to flooding? Joel Gill, GfGD Director, is researching the extent to which an individual hazard increases the probability of other hazards occurring as part of a PhD at Kings College London.

Joel Gill presents a poster on multi-hazards at EGU 2013

A guest post from Holly Ferrie, Geosciences student with the Open University.

If you’ve been keeping track of the science press in the last few months, you may have noticed a dramatic headline popping up in a number of places. ‘Life at threat from supervolcano in 200 million years!’  ‘The supervolcano forming under the Pacific that could wipe out life!’  ‘Extinction level supervolcano!’  This is the result of some fab research into mantle plumes by Professor Michael Thorne et al, an unfortunate press statement issued by the University of Utah, and an epic amount of hyperbole by the news outlets that latched on to it.

The big deal was that Thorne had found evidence of piles of magma interacting at the core-mantle boundary (about 2900km deep) in such a way that might, possibly, produce a megaplume one day. Within days this was blown out of proportion with Strombolian force, and the story became that in 200 million years time, one of two things was going to happen; either a supervolcano would destroy all life on the planet, or a flood basalt would. Doubtless these things will happen again countless times in the Earth’s future, but destroying all life? That’s incredibly unlikely.

As expected, supervolcanoes were the stars of the show, but while I was glad to see the word  ‘Ontong-Java’ in papers like the Daily Mail, flood basalts got just a passing mention. To worsen the blow to a flood basalt geek like me, every paper I read made it seem as though flood basalts were over in just one single eruption, and that the outpourings of lava were without a doubt the most dangerous thing about them. No mention of the fact it’s effusive and more like Hawaii on speed mode, no mention of the real duration (it’s in the order of millions of years), no mention of ash or wider environmental effects (although to its credit the Mail did mention ocean anoxia, or loss of oxygen).

So I’m going to give a quick primer on what would really happen in a flood basalt eruption. First off, if the Pacific has not completely subducted by the time this supposed plume arrives at the surface, it will erupt underwater, creating something called a Large Igneous Province (a LIP). After a delay of up to a million years, ocean anoxia would kick in from all the released chemicals, killing marine life. We would of course notice the rising sea level in coastal areas as lava takes up space in ocean basins, displacing water onto continental shelves!

I sought the advice of Professor Paul Wignall – a well-renowned researcher of the Permian mass extinction – to confirm how much of a danger a continental flood basalt would pose.

Prof. Wignall told me that first we would notice rapid cooling. Fire fountains from these eruptions can reach kilometres high, injecting sulfur dioxide into the stratosphere where it reflects sunlight away and cools the planet. Further down in the atmosphere, sulfur dioxide would cause acid rain. In human terms, this would be like Iceland’s Laki eruption of 1773 all over again, but on a global scale; livestock would die, people would get breathing problems, structures would become corroded – and in the modern age, most flights would be grounded.

The Laki fissure

Now here’s where it becomes a proper song of ice and fire, because once the cooling is over, we would find that the volcano has spewed enough carbon dioxide and water vapour into the air to warm the planet up considerably. Over the millions of years that a flood event lasts, this temperature change could rack up into the tens of degrees – more than enough to pose a serious hazard to species that cannot adapt as easily as humans. We would recover quickly from the first eruption, but subsequent eruptions would wear us down, largely because they wouldn’t give plant biomass enough time to recover – and ultimately everything depends on that.

Finally, Prof. Wignall said it was quite realistic for extinctions to start occurring over a human lifetime should a flood basalt province start forming. So, as it turns out, flood basalts have wider and longer lasting environmental implications than supervolcanoes – they are dangerous things, and infinitely more fascinating. Instead of the hyped-up sexy science of supervolcanoes, perhaps it’s flood basalts that should be demanding more of our attention?

NASA might be having a rain-check on its outreach activities, but that’s not why Curiosity has gone silent the last few days. Every once in a while an event known as the Mars Solar Conjunction places Mars’ orbit directly behind the sun with respect to Earth, and makes communications impossible. Transmissions have ceased until May 1st, when the red planet will pop back into digital sight. Until then, Curiosity is working on the ‘B-side’ (like the cool side of the pillow) of its systems and operating autonomously.

In the mean time, I’ve been fortunate enough to be at the MSL (Mars Science Laboratory) Press Conference here in Vienna, with the latest from the little (1 tonne) science-savvy robot. During the current down time, it’s a chance for the teams to begin to really process the data and get the science out there (see here for where Curiosity has got to so far). This is a snippet of what to expect in forthcoming publications.

Panel at the Press Conference: (from left to right) John Grotzinger, Sylvestre Maurice, Sushil Atreya, Javier Gomez-Elvira, and Igor Mitrofanov (click for larger)

Curiosity is equipped with a lethal plethora of analytical weaponry, from the ChemCam chemical analyser, to the RAD radiation sensors. The ChemCam operates by firing laser bursts at samples of either dust or rock, and analysing the plasma released from the superheated materials (plasma is a partially-ionised gas that gives off a diagnostic spectra pattern depending on the bulk geochemistry of what you’re analysing). To date, Curiosity has been trigger-happy enough to fire off around 40,000 shots at various inanimate targets (no Martians) to sniff their fumes and determine their chemistry. These laser shots actually have a secondary function too, and that’s to blast away the perpetual dust covering the rocks, like some sort of Martian maid shockwave-service.

GCMS, or gas chromatography-mass spectrometry, is a way of identifying the substance chemistry in samples and the relative proportions of those substances. It detects the atomic mass of samples that have been vaporised (there’s a liquid version too called LC-MS) and can measure the relative concentrations. The latest GCMS analysis done by Curiosity on clay samples detected water, perchlorates, carbonates, and both oxidised and reduced sulphur phases, which all point towards the presence at some point of a free-fluid phase. This is important, not because it shows evidence of life, but because it shows that the habitable conditions for certain types of organic life were once present on Mars. The origin of the carbon in these samples is still a bit of a mystery, according to Atreya.

Pew pew! (source)

SAM (Sample Analysis on Mars, which the GCMS is part of along with a quadrupole mass spectrometer and a tunable laser spectrometer) on a different sample aimed to measure the relative isotopic ratios in Martian argon (they have a heavier and a lighter version). The relative depletion of lighter argon isotopes, relative to the primordial level (raw, unmixed gas concentrations, determined from analyses of the sun and Jupiter), indicates that throughout geological time, Mars has actually lost quite a bit of its early atmosphere, as the lighter isotopes have not been constrained by gravity and simply floated off. Sushil Atreya (SAM co-investigator) said “We found arguably the clearest and most robust signature of atmospheric loss on Mars”. Other analyses all told a similar story, as carbon and oxygen isotopes were all enriched in heavier isotopes too. In all, estimates indicate that 85-90% of the original argon are gone. (what?).

The DAN (Dynamic Albedo of Neutrons) analysis, where albedo is sort of like the reflective ability of particles, showed that neutrons of hydrogen atoms (either molecular in water, or as a hydroxyl phase) changed state in a way that allows you tell the dose of radiation from emission. In a dual role, the analysis also allows you to measure the hydrogen content of any subsurface water particles. The DAN analysis from multiple locations seems to indicate a trend of increasing water content with depth (water can be intra-particulate in a structurally bound state, as well as in a free fluid phase or gas).

We got an additional update on the environmental conditions since day 1, as apparently Curiosity is a robotic weather machine too (the REMS, Rover Environmental Monitoring Station, equipment). Since ‘landing’, there was a steady increase in atmospheric pressure, which is now evening out, and at around 120 sol days in, there was a sudden ground temperature change (contraction of about 20 degrees), representing a change in rock type and accompanying heat capacity. This didn’t do much for comfort though, as the temperature still could plumet to as low as -80 degrees. Chilly

The next steps will be to test enrichment levels of methane within the groundrock, which will provide evidence for the evolution and state of organic compounds. Slightly more interesting than the state of hydrogen, but not as cool as finding a Velociraptor there. (although see this article).

Soon.. (source)

More stuff I wrote on Curiosity for the Geological Society of London: http://blog.geolsoc.org.uk/2012/08/30/if-a-rover-breaks-down-on-another-planet-does-anyone-hear-it/

Coverage by Jonathan Amos for the BBC: http://www.bbc.co.uk/news/science-environment-22063337

We have spent the last two days filming on and around Anak Krakatau. The boat ride out from the mainland takes about three hours, and we are accompanied by dolphins and the occasional flying fish. The approach to the islands on water is impressive, rounding the steep sided peak of Rakata – pretty much all that’s left of the pre-1883 Karakatoa. The two other peaks, Danan and Perboewatan, were destroyed in the eruption.

Anak is active at present but not erupting, the last of the lava flows from the recent 2012 summit eruption no longer steaming. However fumarole activity is vigorous and we do not attempt a summit climb.

We set up camp for the night on the nearby island of Verlaten, overlooking Anak. The view from my tent is impressive.

We are up with the sun to start work – mostly a succession of boat shots and frames for the CGI team, who plan to recreate the pre 1883 volcano in the background.

The working title for the show is ‘Top Ten Natural Disasters’, and each event has a ‘guest ‘ slot with a presenter justifying why it deserves an entry. The 1906 San Francisco earthquake, the Great Plague and Hurricane Katrina are  all in the mix.

It is rainy season here, fiercely hot and humid. For the last two days I have, for continuity reasons, not been allowed to change shirt. Said shirt is simultaneously damp with sweat, sticky with suncream lotion and reeking of woodsmoke (if that sequence gets into the final edit you will see why). It could walk home by itself except I have to put it on again for the closing piece.

The Shirt, resting.

Yet despite all this beauty, there is a depressing side. The shores are awash in places with rubbish, medicine bottles, plastics of all kinds (absurdly, individual oranges are sold in convenience stores here with their own fitted plastic bag), and, last but not least, a flip flop graveyard, hundreds of them in all colours and sizes.

The flip flop graveyard.

None of this trash would have been here in 1883, It’s a sobering reminder of the rapid environmental  toll imposed by humans. I blame the Anthroprocene myself. Mind you, if there is a special place where flip flops go to die, then they couldn’t have picked a more stunning location.

Today was a day of mixed blessings. It started well, with filming at the 4th point lighthouse destroyed originally by the 1883 tsunami and rebuilt two years later – such was the importance of the spice trade (and safe navigation of the Sunda Straits) to the Dutch. After the usual technicalities of using a boom to film me walking up to the newer lighthouse, something I am now quite good at after so much practice, we got to working inside.

It is 14 floors to the top, but worth it because the view is spectacular. It is also incredibly humid and echoey inside. The sound man was in his element, demanding quiet and static (that is, not moving) before we explained how the 40 m wave smashed the lighthouse, killing the lighthouse keeper’s wife and daughter, while he miraculously survived.

Remnants of the original 4th Point Lighthouse, destroyed in the August 27 1883 tsunami

The afternoon should have been spent doing the now famous liquid nitrogen and water in a trash bin experiment. A plastic bottle is filled up a bit with liquid nitrogen in a bottle weighed down with a brick. The nitrogen boils, ruptures the bottle and produces an explosive column of water, analogous to a gas pressured volcanic eruption. All we needed here was, of course, liquid nitrogen. This had all been arranged well in advance, so I even brought over a dewer, gloves and googles for the occasion. Needless to say, I shouldn’t have bothered. Apparently Mr Jakarta’s Liquid Nitrogen Emporium was closed today. Shame, because we had reccied a beautiful spot on the beach for a sunset finale. But fret not, there are plenty of videos of the experiment already.

The fallback was to film a lump of coral thrown onto land by the tsunami. If you ever watch it, then it will explain the rather ad hoc piece to camera about the power of water. All true, but not what we had planned for.  It was either that, or resort again to the oldest of volcano cliches, shaking up a fuzzy drink and unscrewing the cap. But then who knows what tomorrow will bring? I’ll keep shaking just in case.

Sunset across Sunda Straits, with Anak Krakatau in distance.

The series is called Top Ten Natural Disasters – Indonesia. It’s being made for National Geographic, which means Americans and those of you with Sky will have exclusive rights to see me grace your screens – unless of course a UK terrestrial buys it post production.

Clouds over the Indian ocean.

On the flight out, in between snatching crafty glances at Liam Neeson in Taken 2  (why do action movies look so comical without sound?) I have the chance to re read what is, in my humble opinion, the best historical account of a volcanic eruption ever written. I refer of course to the most excellent Simkin and Fisk: Krakatau 1883: The Volcanic Eruption and its Effects. It was published by the Smithsonian Institution Press in 1983, the year that marked the centenary of the eponymous eruption.

This text has everything. Maps, bathymetry, petrology, vegetation, atmospheric effects, historical accounts and, most significantly, the first English translation of Dutch geologist Rogier Verbeek’s monograph of 1885, which arguably marks the onset of modern volcanology as a science. The last time I was here was in 2005, when we made ‘Krakatoa revealed’ for BBC2, on the back of the BBC1 drama documentary starring that bloke from Spooks and the woman who played Bruce Willis’ girlfriend in Sixth Sense. And no, I really can’t remember their names.

What still perplexes me about the 1883 eruptions are the tsunamis, which rocked ships as far away as South Africa. They are thought to have been due to pyroclastic flows displacing the sea, but I don’t buy it. During filming ‘Krakatoa revealed’, my then PhD student Mark Thomas did some numerical modelling, showing that internal pressurisation during the eruption could have caused catastrophic flank failure, directing massive slumping to the northwest and pushing up the water into a series of waves. We never published this, but the BBC did use graphics from the model to good effect.

Finally and to clear up any confusion, there are two spellings for the volcano, the Indonesian Krakatau and the more common version Krakatoa in the English speaking world. Yes, they are one and the same, but I was once berated  by a science teacher in a talk to school kids for getting the spelling wrong.

By the way, Mr Neeson apparently studied geology at Queens Belfast before taking up acting. To quote Mr T in another of his recent blockbusters, the crazy fool.  He could be working on cross rail now instead of swanning around Hollywood with his fancy A-lister mates!

Read part two here…

‘I would say that what makes smartphones smart, in large measure, is their sense of location’

Michael T Jones – Google Earth/Maps

Smart phones and geoscience fieldwork ought to be a perfect match. Both are about location. Both are becoming increasingly accessible, as smart phones become cheaper and geoscience data more readily available. So why have the two not met yet?

Geology students at UK universities still seem to find themselves with little choice but to use the traditional tools of the field, with research into new digital field techniques still prefaced with the question ‘does this replace the tools we have relied on for centuries?’

But surely quality research relies on adding to, not replacing tools or skills? As things stand, are students currently using smart phones in the field for anything other than listening to music?

I’m researching these issues as part of my PhD at Leeds, hoping to find the techniques that will lead to the development of an app for use in the field. First, I need to identify the specific problems students encounter when using current field tools and techniques, so I’m looking for more first hand accounts, from students and staff.

Smart apps in the field

There are those who say the Earth sciences are the most visual science of all. Yet, whilst there are heavyweight visualisation software applications (ESRI’s ArcGIS to name one) to aid professional geologists carry out their office tasks, there is little to aid geology students carrying out their field tasks – despite the fact that the same packages are ‘offered’ to students in their laboratories.

Student tasks in the field can be categorised into: capturing data, viewing data and analysing data. For each of these tasks, there’s an app.

• Capturing data: As of 6 February 2013, a search in Google Play app store returns 25 results for ‘strike and dip’. The top two apps are Rocklogger and GeoClino.

• Viewing data: We’ve had applications for this since the age of PDAs (Personal Digital Assistants). Again, if we search Google Play we get over 96 results for the same date when querying ‘geological maps’. The top two are RockLogger and BGS iGeology – ignoring WolphramAlpha, which is not free and not a specialist geology application. It should also be noted that RockLogger’s main purpose is not data viewing.

• Analysing data: This is where my research is focused, and searching for relevant apps is not a simple task! I would be very interested to hear from anyone who has had experience of using apps for analysing field data.

Left: what students might see in the field. Right: what they may have with them, whether digital or printed. The centre image represents what they are expected to do – visualise the 3D model.

To get you involved in my research and share your use of digital field tools and techniques, here are some direct questions:

• What specific problems are you/your students having in the field? Is it reading geological maps? Spatial problems?

• What digital tools (apps or otherwise) are you using to address the above issues?

• Do you have any geological app development projects to share?

In the next part I will be discussing the issues I have identified. I will also give a summary of the results of my initial evaluation of current tablet applications such as Google Earth and BGS iGeology3D.

• Layik Hama is an EPSRC funded PhD student at the University of Leeds, working with the Visualization and Virtual Reality group at the school of computing.