Bárðarbunga – three weeks of tweets

It’s been over 3 weeks since unrest began at Bárðarbunga, and nearly a fortnight since the fissure eruption began at the Holuhraun.  It’s come at a busy time, so I haven’t managed to blog as much as I would have liked to.  I have been trying to provide context and interesting information via the @volcan01010 Twitter account instead.  This post is a compilation of tweets from the past few weeks.

I’m leaving for Iceland this afternoon to join the team of geologists from the Institute of Earth Sciences at the University of Iceland who are monitoring the lava flow.  I’ll be away for a week and hope to keep you updated from the field.

Enjoy.

Sources of good information

Bárdarbunga monitoring and context

Holuhraun / Bárðarbunga videos and pictures

Iceland geology

Links to my blog posts

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Bárðarbunga – turning Dettifoss into Niagara Falls

While international concern about an eruption at Bárðarbunga is focussed on flight disruption, a jökulhlaup (meltwater flood) is the most destructive potential outcome of a subglacial eruption. It would travel north from the glacier along the Jökulsá á Fjöllum river, and for this reason roads have been closed in the area. Edwin Baynes is a PhD student at Edinburgh University who studies past jökulhlaups in this area. In this guest post, he puts such a potential flood in context.


Turning Dettifoss into Niagara Falls

An Icelandic geophysicist, Magnús Tumi Guðmundsson, has predicted that if a subglacial eruption were to occur at Bárðarbunga, the meltwaters could increase the discharge in the Jökulsá á Fjöllum river by 10 or 20 times (to 2,000 – 4,000 m3 s-1). He describes such a flood as ‘not catastrophic‘ because it is smaller than the jökulhlaups caused by the 1996 Gjálp eruption (45,000 m3 s-1), which washed away the Skeiðarásandur bridge in South Iceland, or the estimated discharge for the Katla 1918 flood (300,000 m3 s-1). It is still very serious, however, and has potential to inundate the landscape and destroy important infrastructure such as bridges and farms. The map below shows the areas most likely to be affected.

Area most likely to be affected by jökulhlaup following subglacial eruption at Bárðarbunga. Published by Morgunblaðið – click image to see original article.

Jökulsá a Fjöllum contains some pretty impressive waterfalls, the most notable of which is Dettifoss. With a vertical drop of around 50 m and a peak summer discharge of 300-400 m3s-1, it is reputed to be ‘Europe’s most powerful waterfall’. Sci-fi fans may recognise it from the start of Prometheus, much of which was filmed in Iceland.

For comparison, the average discharge of the Niagara river is ~2,400 m3s-1 at Niagara Falls. Although Niagara Falls and Dettifoss have similar vertical drops (~50 m), Dettifoss is much narrower (~100 m wide vs ~700 m). A 20 times increase in discharge would mean a significant rise in water level within the channel, increased erosion and a possibly even an upstream retreat of Dettifoss waterfall by a short distance.

    A jökulhlaup down the Jökulsá á Fjöllum river following a subglacial eruption at Bárðarbunga increase the discharge over Dettifoss to levels similar to Niagara Falls.

A jökulhlaup down the Jökulsá á Fjöllum river following a subglacial eruption at Bárðarbunga could increase the discharge over Dettifoss to levels similar to Niagara Falls.

Evidence for past jökulhlaups

Although rare on a human timescale, the Jökulsá á Fjöllum is no stranger to jökulhlaups. There are historic reports of powerful floods in the 17th and 18th centuries that destroyed farmland further downstream from Dettifoss.  There have also been numerous prehistoric jökulhlaups of varying magnitude over the last 10,000 years, since most of the ice retreated from Iceland.  Alho et al. (2005) used computer models to estimate the discharge that would be necessary to produce the water levels indicated by the highest boulder deposits and the highest fluvially-washed surfaces along the channel. Their result was 900,000 m3s-1. This is more than triple the flow of the Amazon and close to rivalling some of the biggest ‘megafloods’ that have ever occurred on Earth.

As expected, such large discharges had a significant impact on the landscape.  The evidence for this erosion by the Jökulsá á Fjöllum river is preserved in the rocks of the Jökulsárgljúfur and Ásbyrgi canyons.

Looking downstream from Dettifoss into the ~500 m wide, 100m deep, Jökulsárgljúfur canyon, carved out by jökulhlaups since the last Ice Age. Photo: E. Baynes, June 2012

Looking downstream from Dettifoss into the ~500 m wide, 100m deep, Jökulsárgljúfur canyon, carved out by jökulhlaups since the last Ice Age. Photo: E. Baynes, June 2012

The canyon is significantly wider than the modern river channel (~100 m wide), indicating that the flow was much greater when the canyon was formed. Within the canyon are strath terraces (white dashed lines) that indicate historical positions of the river bed. The upper terrace is at the same elevation as Dettifoss and has been abandoned due to the retreat of Dettifoss during the largest jökulhlaups. Also shown in the photo is a volcanic fissure that erupted 8500 years ago. The canyon has eroded through one of the volcanic craters, exposing the conduit that brings lava to the surface in the canyon walls. The canyon is therefore younger than the fissure (i.e. <8,500 years).

The product of a catastrophic jökulhlaup

AsbyrgiView

Caption: Looking North into Ásbyrgi canyon. Horseshoe shaped, 3 km long, 1 km wide, up to 100 m deep was carved out during a jökulhlaup that flowed away from where the photo is taken from. The floor of Ásbyrgi is littered with large boulders (some greater than 3 m in diameter) which shows that once there was a high magnitude flow within Ásbyrgi capable of transporting such large blocks. Photo: M. Attal, August 2012

Twenty-five kilometres north of Dettifoss is Ásbyrgi, a vast horseshoe-shaped canyon 3 km long, 1 km wide and up to 100 m deep. According to Norse mythology, Ásbyrgi was formed when Odin’s 8-legged horse, Sleipnir, stumbled and put a hoof down on Earth. However, evidence in the landscape suggests that a more likely hypothesis is that Ásbyrgi was carved during a jökulhlaup along the course of the Jökulsá á Fjöllum.

AsbyrgiRim

The large plunge pool at the base of the headwall at Ásbyrgi. Upstream, the landscape has been heavily scoured and sculpted by the action of water. Photo: M. Attal, August 2012

Large plunge pools are present at the base of the canyon headwall, there is a water-sculpted surface immediately upstream of the canyon and the amphitheatre-shaped canyon head is very similar to features elsewhere such as Box Canyon in Idaho and Dry Falls Lake in Washington. Both of these formed during floods following catastrophic drainage of ice-dammed lakes Bonneville and Missoula, respectively.  Each of these features indicate a jökulhlaup origin for Ásbyrgi and show the potential for catastrophic erosion during jökulhlaups along the Jökulsá á Fjöllum following volcanic eruptions beneath the Vatnajökull ice cap.


Edwin’s PhD project is titled: Constraining bedrock erosion during extreme flood events in Iceland. He researches jökulhlaups in the Jökulsárgljúfur and Ásbyrgi canyons using topographic analysis and surface exposure dating with cosmogenic nuclides. You can find more information on his website at http://www.geos.ed.ac.uk/homes/s1141604/. You can also follow Edwin on Twitter: @EdwinBaynes.

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Bárðarbunga – waiting and watching

The word on the street in Reykjavík

I’m in the Reykjavík this week on fieldwork. People here have been following developments at Bárðarbunga since the earthquakes began on Saturday. The word on the street is wait and see.

The story is on the radio and in the papers, but it remains the same: lots of earthquakes, some quite large, but no sign of them moving towards the surface.

The Civil Protection Agency have evacuated the highland areas to the north of Bárðarbunga. If an eruption happens beneath the glacier, then it is likely that a flood will travel in this direction and could destroy the roads. In technology-loving Iceland, you can still get mobile phone signal in this remote region, so they identified all the phones in the area and sent them SMS messages to let them know that the region was closed.

This afternoon (Wednesday), the Coastguard plane is flying over the region to map the glacier. This will be a reference to make it easier to see changes. It is using the same radar that brought you the famous ‘Scream’ image of Eyjafjallajökull. If an eruption begins beneath ice, a depression will form on the surface of the glacier as it melts at the base. I expect that they will release results form this later.

What’s going to happen?

The best answer to this is no-one knows.

There is a reasonable chance that the answer will be nothing. The earthquakes continue, and their source seems to be extending towards the NE at a depth of 5-12 km. This is rifting; North America and Europe continuing their continental drift apart. GPS data show that magma is filling the gap. Many rifting events do not produce an eruption and the earthquakes simply settle down.

If the earthquakes move to the surface then the most likely outcome is an eruption of basalt. If the cracks reach the surface under ice, then this can be explosive, if it reaches the surface outside the glacier then we can expect lava. Dave McGarvie has a more detailed discussion of scenarios here. Some news reports focus on some much larger eruptions in Bárðarbunga’s history where rifting extended far in the opposite direction (to the SW) through the Veiðivötn region, but these are worst-case scenarios and are much less likely.

Information sources

There is a lot of information available from official sources in Iceland. The three main ones are below:

  1. Icelandic Met Office
  2. Icelandic Civil Defence
  3. Icelandic National News – English volcano page

There is also many blogs covering the unrest and lots of interesting discussion on Twitter. In particular, the Bardarbunga list list compiled by @gislio has many key contacts and links to interesting articles.

Some background reading

I’ve written lots of posts about Iceland volcanoes and ash clouds. The earthquake swarm could continue for some time. Here are a selection that you can read while we wait and become an instant Iceland expert.

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(Almost) 3D view of Háifoss waterfall, Iceland

Haífoss, Iceland.  Click image for larger version.

Haífoss, Iceland. Animated gif file may not animate in some browsers / mobile devices.  Click image for larger version.

Háifoss is Iceland’s second highest waterfall, with a drop of 122 metres.  It’s name means ‘Milky elfin vomit spout’ in Icelandic.  Not really; it’s ‘High waterfall’.  People seem to enjoy the myth that Icelanders believe in elves.  It is located inThjorsadalur, about an hour northeast of Selfoss. Hjálparfoss and Gjáin are in the same area. Note: If you are a tourist photographing a waterfall in Iceland, please don’t complain about the rain.

I took this (almost) 3D image of Háifoss by accident. Flicking between two photographs taken at slightly different places along the path gives an impression of depth. According to Wikipedia, this is due to the motion parallax effect.  Objects in the foreground move further than those in the distance.

The animation was created with the ImageMagick software. This is a command line based tool for rotating, cropping and resizing images, and much more. It is Free/Open Source software, so you can download and install it on as many machines as you like.  I previously wrote a post explaining how to annotate and join images e.g. to make multipart figures for scientific papers. The command used to make the Háifoss animation is:

convert -loop 0 -delay 60 Háifoss_1.jpg Háifoss_2.jpg Háifoss3D.gif

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Volcanic life – the first microbes to colonise the Fímmvörðuháls lava

This is a guest post by Dr Laura Kelly, a Lecturer in Microbiology at Manchester Metropolitan University, UK. It describes her study into the first microbial life to colonise the Fímmvörðuháls lava flow, Eyjafjallajökull, Iceland. Prof Charles Cockell of the UK Centre for Astrobiology in Edinburgh was also involved, and I helped out with a map and some volcanological context.


When the average person thinks of volcanoes, microbiology may be the last thing that springs to mind. However, for the relatively small community of scientists interested in microbes in extreme environments, the connection is obvious.

Microbes such as bacteria and archaea (together termed prokaryotes because their DNA floats freely within the cell instead of in a membrane-bound nucleus), and fungi may not only survive but thrive in environments that appear quite inhospitable. In fact, the earliest forms of life on Earth were prokaryotes adapted to extreme environments approximately 3.5 billion years ago.

Conditions on newly deposited volcanic material are, by comparison, less harsh than early Earth environments. While some present day microorganisms are capable of flourishing in high-temperature environments such as deep-sea hydrothermal vents, temperatures of molten lava are greater than the upper limits permitting microbial survival. Nevertheless, upon cooling lava is rapidly colonised by bacteria and fungi, as recent research by our team of microbiologists has shown.

The Fímmvörðuháls lava is a small basaltic flow that was erupted on the  eastern flank of Eyjafjallajökull volcano from 20 March to 12 April 2014.  Two days after this eruption ended, activity switched to the ice-covered crater at the volcano's summit and began producing the notorious ash cloud.

The Fímmvörðuháls lava is a small basaltic flow that was erupted on the eastern flank of Eyjafjallajökull volcano from 20 March to 12 April 2014. Two days after this eruption ended, activity switched to the ice-covered crater at the volcano’s summit and began producing the notorious ash cloud.

Following the eruption of the Eyjafjallajökull volcano in April 2010, we analysed samples of the resulting freshly formed basaltic Fimmvörðuháls lava flows, collected in July and August 2010, to determine which microbes colonized the lava first. Taking care to avoid contamination, the samples were brought to the UK and crushed to powder to allow the DNA to be extracted.  DNA profiling, using a method known for its ability to discriminate among closely related species (16S ribosomal RNA gene sequencing), generated community profiles for each lava sample. Each profile involved taking all the 16S ribosomal RNA genes from the DNA extracted from the lava sample and determining the sequence of DNA building blocks (called nucleotides) of a random subset of these genes. Comparing these sequences with each other, and with sequences within online databases such as the Ribosomal Database Project, allowed us not only to generate ‘family trees’ for the microbial communities, but also to determine how closely related the Fimmvörðuháls communities were to bacteria found elsewhere.

Ours was the first study of its kind, providing detailed analyses of pioneer volcanic microbial communities. Previous studies of early volcanic communities focused only on microbes which could be cultured in the lab, which is problematic given that most microbes cannot be cultured. Therefore the majority of the inhabitants remained undetected in these previous studies.

The Fimmvörðuháls study revealed some very interesting findings. As fresh volcanic material is nutrient poor, containing little organic carbon and nitrogen, the expectation was that the inhabitants would be largely dependent on community members that could use sunlight for energy and inorganic carbon such as CO2 or CO, much in the same manner as plants. What was in fact discovered was that these communities did not rely on organisms that used sunlight, and that many of the inhabitants were organisms that required organic carbon for growth, although some inhabitants were related to those that could use inorganic sources. The communities were dominated by Betaproteobacteria, which is a diverse class that includes organisms found in glaciers, soils, sediments, water and many other natural environments.  DNA profiles indicated that some of the Fimmvörðuháls colonists are able to use sulphur and/or iron present in the lava flows as energy sources for growth (chemolithotrophs) and others are able to capture nitrogen from the atmosphere (diazotrophs).

Less surprising, however, was that Fimmvörðuháls communities were not as diverse as other communities that we have investigated in older basaltic Icelandic rocks, and that they contained very different bacteria. As lava weathers/erodes over time, the physical and chemical environment changes drastically from a microbial perspective. For example, increased surface area and pore spaces provide refuges and aid water retention, while weathering can also release useful elements from the substrate. This impacts the microbial community as a result. Hopefully, future studies will continue to monitor the progression of microbial colonization of volcanic substrata such as Fimmvörðuháls over extended periods of time to reveal the dynamic nature of volcanic microbial communities.


If you are interested in microbes in volcanic or other geological
environments, please visit Laura’s blog, Geomicrobiology and Microbial Ecology, which has further details about the Fimmvörðuháls project, with additional photos and videos.

* Reference:
Kelly LC, Cockell CS, Thorsteinsson T, Marteinsson V, Stevenson J (2014) Pioneer Microbial Communities of the Fimmvörðuháls Lava Flow, Eyjafjallajökull, Iceland. Microbial Ecology 1-15. doi:
10.1007/s00248-014-0432-3

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Fieldwork guide for robots (and humans)

In the future, all our fieldwork will be done by robots while we play around on our hover-boards. In anticipation of this, I have written a program for the robots to follow.  Until that day arrives, it is also a handy checklist for human beings.  It assumes that future robot programming languages will look a lot like English, and pays special attention to notebook layout and how to geotag photos.


def fieldworkPlan():

  • Before you go:
    • makeSureYouHaveTheRightKit()
    • prepareYourKit()
  • For each day in the field:
    • Write the date and the day’s aims in your notebook
    • For each locality visited:
      • dataCollectingRoutine()
    • endOfDayRoutine()
  • postTripRoutine()

def makeSureYouHaveTheRightKit():

  • Notebook
    # I like the Rite in the Rain with Metric Grid.
    # They’re not cheap, but they are really tough and, with a pencil, you can literally write through rain drops.
    # The metric grid pattern is handy for lining up logs, but easily ignored for sketches.
  • Fieldwork gear:
    • Sample bags
    • Marker pen
    • Hand lens
    • Ruler / tape measure
    • Hammer (+ glasses) / spade / trowel
  • Camera
    # I like to have a waterproof/dustproof compact that I don’t need to worry about getting wet or dirty.
    # I decided that built-in GPS was an unnecessary expense.
    # The Panasonic DMC-FT25 is a pretty good example, and not too expensive these days.
    # It lets you take pictures like this in geothermal pools…waterproof_camera
  • GPS (with cable)
    # The most basic Garmin eTrex is ideal, as I only want the GPS for two purposes.
    # (1) To record waypoints at each location I make observations.
    # (2) To record time-stamped track of where I go.
    # I then correlate this with the timestamp of my photos, which lets me geotag (embed the photo’s location into the file).
    # The most important thing is that you can easily get the data onto a computer.
    # You can also use smartphones with software such as MyTracks (on Android) or Strava that can exports tracks as .gpx files.
    # I find this uses the phone’s battery very quickly.
  • Software:
    • gpsbabel
      # This is open source software that reads data from your GPS and can convert it between various formats
    • GpsPrune
      # This is open source software for editing GPS data.
      # We will use it to geotag our photos.
      # To do this, gpsbabel and exiftools also need to be installed.
      # It also lets you view geotagged photos by location.
    • Photo cataloguing software
      # e.g. Shotwell, Picasa, iPhoto.
      # These are very useful because you can browse photos across folders based on their dates.
      # You can also tag photos e.g. ‘notebook’, ‘logged section’.
      # Some allow you to view geotagged photos on a map.
  • Suitable field clothing
    # See my Volcano suit / What to wear in Iceland post.

def prepareYourKit():

  • Notebook
    # Write contact details in the front in case you lose it.
    # Write useful notes for reference in the back, such as grain size definitions for logging or a key for different symbols in logs.
  • Camera
    # Synchronise the clock with your GPS
  • GPS
    # Set the coordinate system to whatever system your maps use.
    # It doesn’t matter if this is something quite rare, because they are all stored as Lat/Lon within the GPS anyway.
  • Software
    # Practice geotagging photos using GPS track timestamps.

def dataCollectingRoutine():

  • Mark GPS waypoint; leave GPS running to record track.
    # I usually take the automatically suggested waypoint number, rather than fiddling with renaming it each time.
  • Prepare outcrop for logging/sampling
  • Take photographs of:
    • General outcrop context
    • Logged/sampled section
    • Features of interest
  • Note the last three digits of each photo’s file name and, if necessary, make a note of what it shows.
  • Record data
    # The following is an example of how I like to lay out my notebook.
    # Make observations before interpretations.

    notebook_example600

    Example notebook layout. Click to enlarge.

  • Collect samples
    # Write the sample number at least 3 times on the bag
  • Clean up the site
  • Switch off GPS

def endOfDayRoutine():

  • Make a note of any thoughts or wider interpretations that you had
  • Photograph the pages of your notebook that you wrote today
  • If you have a laptop in the field:
  • Pack your samples safely
  • Type up spreadsheet(s) with all your localities, samples and measurements.

Other tips

  • Use GpsPrune to geotag the photographs of the logs from your notebooks. Then you can find them quickly by location.
  • You can Easily change coordinate projection systems in Python with pyproj.
  • On Unix-type systems (e.g. Linux, Mac) you can download your photos and GPS data very quickly and without the fuss of a mouse and GUI with two simple terminal commands
    $ cp -urn /media/camera/ ~/Pictures/Iceland2014/
    $ gpsbabel -tw -i garmin -f /dev/ttyUSB0 -o gpx -F ~/Iceland2014/GPS_data/2014-06-05_gpsdata.gpx
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Do Iceland’s volcanoes pose a threat to the UK?

I recently gave a talk about the threat to the UK from Iceland’s volcanoes at the UK’s largest meeting of geography teachers, the GA Annual Conference.  The talk was kindly sponsored by WJEC, who filmed it and have posted the videos on YouTube.  The full talk is around 45 minutes long and is split over 4 videos.  This post brings them all to one place and provides links so that you can skip to topics of interest if you don’t have time to watch the whole thing.

Part 1 – Eyjafjallajökull 2010 and Grímsvötn 2011

Part 2 – Impacts of ash in the UK and on aviation

Part 3 – Perception and reality

Part 4 – Potential impacts of the largest eruptions

Further reading

Much of the material in the talk has been covered in blog posts on this site.  You can see a full list of them on the Every Post Ever page.  Please bookmark the RSS feed if you want to keep up to date with the latest posts.  You can also follow me on Twitter.

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Sources of reliable information about large Icelandic fissure eruptions

Don’t you hate it when you see the film of a book that you enjoyed and they have missed out lots of the best bits?  Or even worse, the director has made changes to the original story for ‘artistic’ reasons?  Well, that’s how I feel about the news coverage today about a report into the threat to the UK from big lava eruptions in Iceland.

laki_newsWhat’s the story?

Claire Witham of the Met Office, is giving a presentation at the European Geosciences Union conference in Vienna this week about impact on the UK of such an eruption.  It’s serious stuff.  Last October, the British Geological Survey released a report (compiled by Sue Loughlin, Head of Volcanology) that describes what we know about such eruptions:

  • The 1783-84 Laki event erupted over 14 km3 of basalt lava, releasing millions of tonnes of sulphur dioxide gas that polluted the atmosphere across northwest Europe for months with sulphuric acid fog.
  • It’s estimated that it killed over 20,000 people in Europe at the time, and new studies suggest that if it happened again today that figure could be 140,000.  Furthermore, the acid damages crops and can poison waterways.
  • We’ve had two Laki-sized eruptions in the past 1,000 years (Laki 1783, Eldgjá 934), and eleven smaller ones (but only two of these erupted >1 km3 magma), so another such eruption is possible in our lifetimes.

Nevertheless, the reality wasn’t exciting enough for the mainstream media, who have reported this as some kind of imminent apocalypse.  In lots of science communication, there is a problem with dumbing-down of information.  In volcanology, the problem is sexing up.

Media changes to the story for ‘artistic reasons’

  1. A number of reports introduced a new character, the supervolcano.  The term doesn’t appear anywhere in the original report.  In fact, as Erik Klemetti described, it doesn’t appear very often in any real scientific papers.  And when it does, it’s mainly to do with explosive eruptions of over 1000 km3 of pumice and ash.  Laki produced 14 km3 of lava, so wouldn’t even come close!
  2. Another favourite baddie, climate change, also gets a role in the media story.  The summer of 1783 was unusually hot in Europe, and the winter of 1783-84 was very cold across the whole northern hemisphere.  Scientists at the time suggested that there might be a connection, but more recent work shows that (surprise, surprise) things are a bit more complicated than that.  The BGS report itself says that it is not possible to prove that the extreme weather was linked to the eruption.
  3. No self-respecting blockbuster is complete without a massive body count.  So even though the report states that the eruption killed 60% of Icelandic livestock, the International Business Times inflates that figure to 80%.  Even better, the Daily Star posted their report under the headline: TOXIC SMOG FROM ICELANDIC VOLCANO COULD KILL MILLIONS.
  4. Finally, no story about a hypothetical future risk gets as many clicks as one with immediate danger.  Hence the the Daily Star opening with the words “Ministers are on red alert…”  This is the same reason that the Mail Online recently converted an Icelandic volcanologist’s gentle reminder that Hekla is still an active volcano (and you should think twice about climbing it) into “major eruption could happen within days and hit air travel”.  That was on the 19 March, and still nothing has happened.  The BGS report says that, on average, we can expect a fissure eruption of >1 km3 lava once every 270 years or so.

Sources of good information about large-magnitude fissure eruptions in Iceland.

  • The best information comes straight from the horse’s mouth.  You can read the full report into large magnitude fissure eruptions on the British Geological Survey website here, including an executive summary that you can download here.  It contains all the great stuff that was left out of the news reports, such as descriptions of the impacts at the time and of Icelandic fissure eruptions in general.
  • The Cabinet Office National Risk Register of Civil Emergencies, which now contains a Laki-type event, is here.
  • A great blog post by Anja Schmidt, who calculated the 140,000 figure, compares a Laki-type event to the recent air pollution experienced in the UK.
  • For a popular science overview of the Laki eruption in the context of other Icelandic and worldwide eruptions, check out Island on Fire by Alex Witze and Jeff Kanipe.  A review by David Pyle, Professor of Volcanology, is here.
  • Update 1 May: Jonathan Amos on the BBC News has posted the first sensible article covering this, including interviews with Claire Witham, Alex Witze and Jeff Kanipe.

If you’ve still not had your fill of volcanoes for the day, you can also try yourself against my game, Soup or Volcano, or read my last media-based rant, Ash cloud travel insurance / why scientists should blog.

Update: 22:55hrs
This afternoon I gave an interview on BBC Radio Scotland, who wanted some comments on the report.  I’ve uploaded it onto YouTube so you can hear it below.  Can you spot the typo on the slide?

Update: 30 April 2013
The original version of this post incorrectly stated that Sue Loughlin from the BGS presented their report in Vienna, as was reported by the International Business Times.  Claire Witham from the Met Office is leading the study into the impact on the UK and presented the results in Vienna.

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Fitting probability distributions from binned / quantile data in Python

I’ve made an iPython Notebook that explains how to fit probability distributions to data when only binned values, or quantiles, or perhaps a cumulative distribution are available.  It uses a least squares fit approach.  View it by clicking the picture below:

fitting_distributions

The page includes a button to download the notebook so that you can play around with it yourself.

Python is a free and open source programming language that is becoming increasingly popular with scientists as a replacement for Matlab or IDL.  I hope that the notebook will be helpful to anyone who works with grainsize data e.g. volcanologists, sedimentologists, atmospheric scientists.

iPython notebooks are amazing; if you use Python for science and haven’t tried them yet, then I urge you to have a look.  They let you run Python code in little chunks, displaying the results immediately and interspersed with comments and LaTeX-rendered equations.  You can also render publicly-available notebooks using the iPython Notebook Viewer website, as I have done here.  I think that they are The Future.

iPython notebooks come nicely packaged for Windows and Mac in the Anaconda Python distribution (and probably others such as Enthought, too).  You can install the ipython-notebook package on Ubuntu-like Linux distributions with a single command (sudo apt-get install ipython-notebook), but to get the most up-to-date versions it is better to use pip:

# Depending on what is already installed, 
# you may also need to add some dependencies.
sudo apt-get install pandoc python-zmq python-tornado

# Install pip, then use pip to install ipython
sudo apt-get install python-pip
sudo pip install ipython
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The most important journals in volcanology

The Journal Impact Factor (JIF; average number of citations to a paper in a journal in the first two years since it was published) is such a poor predictor of an individual paper’s citation count that quoting it is a sign of statistical illiteracy, yet cursory judgements about the quality of scientific papers are routinely based upon of the JIF of the journal in which they are published.  At one end of the spectrum, this means that a paper in Nature or Science is automatically assumed to be so important that a single one on a CV can be a passport to job interviews, speaking invitations, jobs and promotions.  At the other, papers in discipline-specific journals can be passed over, assumed to be unimportant, despite being more useful to the group of people that actually read them.

Volcanology journals are an example of the latter; it’s a small field and, with just a few volcanologists to cite each other’s work, the JIFs of the specialist journals are quite low.  Nevertheless, they are clearly very important to the world of volcanology.  I wanted to find out what the most important journals in volcanology are, and if there was any correlation with the JIF.

To do this, I looked at the reference list of a recent review article, How volcanoes work: A 25 year perspective, written by Kathy Cashman and Steve Sparks.  Both authors have distinguished careers and extremely wide-ranging interests so can be trusted to give a reliable overview of the subject.  In the paper, they “focus particularly on the physical processes that modulate magma  accumulation in the upper crust, transport magma to the surface, and control eruptive activity“, which is actually a huge scope.  Volcanologists working with data from the depths of the mantle and lower crust or from orbit on satellites may feel a bit neglected, but most of physical volcanology is represented.

The paper cites a whopping 364 references.  I extracted the journal or book title from each, and with a few lines of Python code, got counts of which were cited most.  The number of counts is a proxy for the importance of the journal in the field of volcanology.

The most important journals in volcanology

top20_barchart The most cited journals by Cashman and Sparks are the Journal of Volcanology and Geothermal Research and Bulletin of Volcanology.  Both are respected journals, well-read by volcanologists, so it is no surprise that they are the most important journals in the field.  JGR and EPSL are next.  Between them, these top four journals represent just under half (175/364) of all papers cited in the review.

Nature and Geology feature in 5th and 6th, showing that some important volcanology papers are published there, but they certainly do not dominate in the way that their JIFs would suggest.

Comparison between JIF and citations in Cashman and Sparks (2013)

citations_vs_jifComparing the number of citations in Cashman and Sparks (CCS) with the JIF (2 year citation data from SCImago; top 20 journals only) shows an overall lack of correlation.  The data can be divided into three groups:

  • Journals with JIF > 5:  These ‘big hitters’ show a positive correlation between JIF and CCS, but, with the possible exception of Nature, they are not the most important journals to volcanologists.
  • Journals with CCS > 10:  The four journals shown to be the most influential in volcanology all have a modest JIF that does not reflect their significance within the subject.  With Nature as an exception once more, the most important journals in volcanology actually show a slightly inverse correlation with JIF.
  • Journals with JIF < 5 and CCS < 10:  These show no correlation between JIF and CCS.

Conclusion

The data show that the most important journals in the field of volcanology, based on citations in a comprehensive review of the advances of the past 25 years, are Journal of Volcanology and Geothermal Research and Bulletin of Volcanology.  These are discipline-specific journals with low JIFs.  Consequently, the JIF of these journals is of especially little value in assessing the quality of the work in their articles or the importance of their contribution to the field.

EDIT 2014-03-12 21:30.  Of course the CCS is just another journal-based metric, so it still can’t tell you anything about an individual article or scientist.

If you don’t believe that journal-based metrics, such as Journal Impact Factors, should be used as a surrogate measure of the quality of individual research articles, or to assess an individual scientist’s contributions, or in hiring, promotion or funding decisions, then you can join over 10,000 others in signing the San Francisco Declaration on Research Assessment.

Reference:

Cashman KV, Sparks RSJ (2013) How volcanoes work: A 25 year perspective. Geological Society of America Bulletin. doi: 10.1130/B30720.1

Results in Full:

Journal of Volcanology and Geothermal Research,57
Bulletin of Volcanology,47
Journal of Geophysical Research,40
Earth and Planetary Science Letters,31
Nature,18
Geology,17
Journal of Petrology,12
Geochemistry Geophysics Geosystems,11
Geological Society of America Bulletin,10
U.S. Geological Survey Professional Paper,10
Geophysical Research Letters,9
Science,8
Geological Society of London Memoir,7
Contributions to Mineralogy and Petrology,6
Reviews in Mineralogy and Geochemistry,6
Nature Geoscience,5
Philosophical Transactions of the Royal Society of London,4
Geophysical Monograph,4
Journal of Human Evolution,3
Earth-Science Reviews,2
Geological Society of London Special Publication,2
The Journal of Geology,2
Journal of the Geological Society of London,2
Mathematical,2
International Journal of Remote Sensing,2
Physics and Chemistry of Minerals,2
Annual Review of Fluid Mechanics,2
Geological Society of America Special Paper,2
Journal of the Geological Society,1
Fire and Mud—Eruptions and Lahars of Mount Pinatubo,1
Oceanography,1
Geological Magazine,1
Geophysical Journal of the Royal Astronomical Society,1
Tectonophysics,1
Geological Society of London,1
Religion,1
The Geochemical Society,1
Journal of Colloid and Interface Science,1
Marine Geology,1
Krakatau 1883: The Volcanic Eruption and its Effects,1
Geophysical Journal International,1
GeoJournal,1
Pure and Applied Geophysics,1
Lava Flows and Domes,1
Disaster Resilience: An Integrated Approach,1
Volcano Hazard and Exposure in Track II Countries and Risk Mitigation Measures—GFDRR Volcano Risk Study,1
Assessment of Risk and Uncertainty for Natural Hazards,1
Encyclopedia of Complexity and Systems Science,1
Precambrian Research,1
Eos (Transactions, American Geophysical Union),1
Chemie der Erde–Geochemistry,1
IEEE Transactions,1
Journal of Fluid Mechanics,1
American Journal of Physics,1
Chemical Geology,1
Computers & Geosciences,1
Living Under the Shadow: Cultural Impacts of Volcanic Eruptions,1
Paricutín: The Volcano Born in a Mexican Cornfield,1
Journal of Geology,1
Physics of the Earth and Planetary Interiors,1
Encyclopedia of Volcanoes,1
Volcanic Plumes,1
Progress in Physical Geography,1
Washington,1
Archives of Environmental Health: An International Journal,1
Timescales of Magmatic Processes,1
Scientific Drilling,1
Reviews of Geophysics,1
Applications of Percolation Theory,1

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