Friday, 19 August 2016

Applied photonics in the Southern Ocean

Dr Tom Brown,
School of Physics & Astronomy
So why did I, a physicist who is most at home in the darkened, well-controlled confines of a laser laboratory, find myself dressed in high-viz clothing climbing aboard a big orange ship in Tasmania in January 2016 about to set off for a three-month trip to one of the most isolated areas of the planet?

The story starts with a technique known as Optical Coherence Tomography (OCT), an imaging technique developed in the early 1990s that has had real impact – many optometrists now rely on these systems to provide 3 dimensional images of the retina and its underlying structure and it provides a unique method of diagnosing many important visual impairments. The technique has also found application in many other fields including imaging plaques within arteries and mapping the boundaries of cancer tumours. We have used the system we developed at St Andrews in many medical areas however we have also sought to develop its application in other fields, most recently in providing high resolution structural imaging of Antarctic Krill (Euphasia Superba), one of the most important animals within the food chain of the Antarctic that stretches all the way from microscopic algae to the Blue Whale the planet’s largest animal.

Antarctic Krill (Euphasia Superba)
OCT provides imaging of structure by relying on accurate depth measurement of light which is reflected from the boundaries between different tissue types within a sample. The depth can be measured to a thousands of a mm accuracy by relying on the phenomenon of interference, the effects produced when two waves interact with one another either causing cancellation of a large growth in the signal. A typical OCT system can give resolution of a few thousandths of a mm or better in three dimensions to depths of a few mm within living tissue.

Our studies on Krill started from important biological questions on the effects of ocean acidification on the structural development of the animals. We began by examining preserved lab specimens before shipping the system the Australian Antarctic Division aquarium in Tasmania, Australia to produce the first three-dimensional imaging of living animals.

In the last year we have also taken our technology to the Antarctic itself by taking part in the Australian Government’s K-Axis marine science voyage based on the icebreaker Aurora Australis, which brought together around 50 scientists from a range of disciplines including Physics, Biology, Oceanography, Ecology and Chemistry, to study an area of unusual productivity in Eastern Antarctic between the Kerguelen Islands and the Antarctic itself. We showed that our OCT system, which is normally used within a specifically built optics lab, can be deployed and generated high quality data within the marine science environment with measurements taken even as the ship was rolling by more than 12 degrees in each direction. We have also shown that a wide range of interesting species can be imaged using these techniques and look forward to starting a host of new collaborations with partners from a very broad group of interests contributing new knowledge to globally important effects of climate change and ocean acidification.

The work described in this post has been supported from several sources with EU funding enabling the original development of the system, EPSRC providing ongoing support through a Platform Grant and the Australian Antarctic Division, providing major in kind contributions for voyage costs and hosting experiments.

Throughout the marine science programme our photonics technology performed exceptionally and provided an important compliment to the other photonics-systems on board that provided both imaging and advanced experiments on plankton development. The fact that the ship then ran aground and we had to be rescued by a major international mission – well that might be a story for another post!

Dr Tom Brown, School of Physics and Astronomy

M.J. Cox, S. Kawaguchi, R. King, K.Dholakia and C.T.A. Brown, “Internal physiology of live krill revealed using new aquaria techniques and mixed optical microscopy and optical coherence tomography (OCT) imaging techniques”, Marine and Freshwater Behaviour and Physiology, 48, p. 455 (2015)

N. Bellini, M.J. Cox, D.J. Harper, S.R. Stott, P.C. Ashok, K. Dholakia, S. Kawaguchi, R. King, T. Horton and C.T.A. Brown, “The Application of Optical Coherence Tomography to Image Subsurface Tissue Structure of Antarctic Krill Euphausia superba”, PLOS ONE, 9, Art. No. e110367 (2014)

Monday, 8 August 2016

World politics podcasts: State of the Theory

Dr Anindya Raychaudhuri from the School of English and Dr Hannah Fitzpatrick from the University of Aberdeen run a weekly podcast called “State of the Theory”. Each week, this series tackles a new topic from the world of politics, news or popular culture and try to analyse it using the tools of philosophy and critical theory. The latest episode focuses on the ramifications of Brexit and what we might learn from the EU referendum results. We have previously looked at the Oscars, the UK budget, Islamophobia, and the London mayoral elections.

You can find the episodes on Soundcloud ( or on iTunes ( Please give it a listen, and join in the conversation. We are on Twitter as @DrAnindyaR and @DrHFitz – you can also get in touch through the podcast Twitter account - @TheoryDoctors

The podcast website is 

Monday, 25 July 2016

History of Psychiatry podcast series launched

This is the first of two series of weekly podcasts beginning in July 2016. The podcaster is Professor Rab Houston of the School of History, a social historian of Britain who has published extensively on the history of mental disorders and their cultural, political, legal, and economic context, especially during the period 1500-1850.

The first series of 44 podcasts covers England, Scotland, Wales, and Ireland during the last 500 years, looking at continuities and changes in how mental illness was understood and treated, and at the radical shifts in systems of caring for those who were either mad or mentally handicapped during the last two centuries. The analysis aims to be balanced and fair.

The coverage is broad, ranging from how mental problems were identified and described in the past through changing ideas about their causes and developing therapeutic practices to important themes such as the reasons behind the emergence of psychiatry as a profession and the rise and fall of asylums as a location of care.

The series explores:
  • the history of suicide, 
  • madness in the media, 
  • psychiatry and the law, 
  • relations between medical practitioners and patients, 
and it assesses evidence that the incidence of mental illness has changed over time. It begins and ends with discussion of the value of history and the vital lessons that can be learned by studying the past, not only for psychiatrists, but for all healthcare professionals, welfare policy makers, and indeed anyone with an interest in mental health.

Go to:
For research relating to the podcasts, please visit

Twitter: @HistPsychiatry

Tuesday, 12 July 2016

Multiple projects funded for Mars exploration research

Dr Claire Cousins from the Department of Earth and Environmental Sciences (DEES) was recently awarded four research projects, totalling a value of £422K, funded by the UK Space Agency as part of their ongoing ‘Aurora’ programme and The Leverhulme Trust. All these projects relate to the exploration of Mars, spanning both fundamental research and technology development.

The 3.5 year UK Space Agency PhD Studentship “Chemolithotrophs on Mars: metabolic pathways and biosignatures” will explore the metabolisms and stable isotope fractionation patterns produced by microbial communities in Mars analogue environments, and will be co-supervised by Dr Aubrey Zerkle. This will help us understand what kind of evidence we might expect to be left by any microbial life that existed billions of years ago when Mars was a less hostile planet.

Complementing this studentship is a 3-year postdoctoral project that will explore the habitability of hydrothermal fluids on Mars, Europa and Enceladus (“Frozen but not forgotten: microbial habitability and preservation in planetary fluids”; The Leverhulme Trust). This project will combine natural mineral springs in the Canadian High Arctic and Iceland with experimental studies to investigate how microbial communities survive and are preserved in simulated planetary environments. Dr Gordon Osinksi from the University of Western Ontario who visited DEES during his sabbatical in April 2016 is a Co-Investigator on this project, along with Dr Mark Claire (DEES) and Prof Charles Cockell (University of Edinburgh).

Testing the ExoMars PanCam in Iceland in 2013 

Finally, a 2-year proof-of-concept UK Space Agency project, led by Dr Matthew Gunn at Aberystwyth University, will develop a prototype instrument to conduct “Luminescence age dating for in situ environments” on Mars. Luminescence age dating is widely used in environmental sciences, but has yet to be used in the robotic exploration of Mars. Creating new instrument prototypes means they can be developed into more advanced instruments for missions to the Martian surface in the future. 

Links to related research:

Selecting the geology filter wavelengths for the ExoMars Panoramic Camera Instrument, Cousins, C. R., et al., 2012, In: Planetary and Space Science.

Mars surface context cameras past, present, and future, Cousins, C. R., et al., 27 April 2016, In: Earth and Space Science.

Glaciovolcanic hydrothermal environments in Iceland and implications for their detection on Mars, Cousins, C. R., et al., Cousins, C. R., et al., 15 Apr 2013, In: Journal of Volcanology and Geothermal Research. 256, p. 61-77.

Volcano-Ice Interaction as a Microbial Habitat on Earth and Mars, Claire R. Cousins and Ian A. Crawford. Astrobiology. September 2011, 11(7): 695-710.

Related media stories:

New Scientist: ExoMars rover's Martian-hunting camera takes test run in Iceland
Imperative Space: Aurora and ExoMars Films for UK Space Agency
The Leverhulme Trust:  Looking for life in the UV: fluorescence as a tool for planetary exploration

Monday, 27 June 2016

'New Generation Thinker 2016' winners! Dr Victoria Donovan and Anindya Raychaudhuri

Congratulations to Dr Anindya Raychaudhuri, School of English, and Dr Victoria Donovan, School of Modern Languages two early career researchers from St Andrews (out of 10 total!) who have been chosen as New Generation Thinkers 2016!

BBC Radio 3 and the Arts and Humanities Research Council (AHRC) have unveiled the 10 academics who will be turning their research into television and radio programmes on the BBC. The New Generation Thinkers scheme 2016 is a nationwide search for the brightest minds who have the potential to share their cutting edge academic ideas through broadcasting. After a four-month selection process involving a series of day-long workshops at the BBC in Salford and London, the final 10 were chosen by a panel of BBC Radio 3 and BBC Arts producers, and the Arts and Humanities Research Council. The scheme has been a successful first step for many academics, with previous thinkers going on to appear across television and radio.

Dr Anindya Raychaudhuri is working on the way nostalgia is used by diasporic communities to create imaginary and real homes. He has written about the Spanish Civil War and the India/Pakistan partition and the cultural legacies of these wars. He co-hosts a podcast show, State of the Theory, and explores the issues raised by his research in stand-up comedy.
Dr Victoria Donovan is a cultural historian of Russia whose research explores local identities, heritage politics, and the cultural memory of the Soviet past in twenty-first century Russia. Her new project explores patriotic identity in Putin’s Russia. She is also working on a project that looks at the connections between mining communities in South Wales and Eastern Ukraine.

Tuesday, 21 June 2016

Neil Gaiman brings Beowulf back to St Andrews

Neil Gaiman
(photo credit: Kimberly Butler)
When prize-winning author Neil Gaiman first encountered the Old English epic Beowulf, he did so via the Penguin Classics translation of the poem, made by Michael Alexander, former Berry Professor of English at St Andrews.
This week Gaiman comes to St Andrews to receive an honorary degree and to talk about (among other subjects) his part as writer on the Hollywood film adaptation of Beowulf. Dr Chris Jones of the School of English specializes in the uses that contemporary artists make of Old English literature. You can read his blog about Gaiman’s Beowulf here: School of English blog, or if you have a Reading Group, download discussions questions about Beowulf and the film here: Beowulf Discussion Questions.

Read about the research:   Chris Jones, ‘From Heorot to Hollywood: reading Beowulf in its third millennium’, in David Clark and Nicholas Perkins, eds., Anglo-Saxon and the Modern Imagination (Cambridge: Brewer, 2010), pp. 13-29. Published in Anglo-Saxon Culture and the Modern Imagination, Edited by David Clark &Nicholas Perkins.

Thursday, 10 March 2016

INTRIGUED: INvestigating The Role of the North Pacific In Glacial and Deglacial CO2 and Climate

The geological record offers an invaluable window into the different ways earth's climate can operate. The most recent major changes in earth's climate, prior to modern climate change, were the Pleistocene ice ages. These feature growth and collapse of massive ice sheets, rapid shifts in rain belts, and abrupt changes in ocean circulation. Changes in atmospheric CO2 are intimately linked with these ice age climate changes, but despite decades of effort, we still don't fully understand their driving mechanisms.

The aim of the newly NERC-funded research by Dr James Rae of the Department of Earth and Environmental Sciences is to transform our understanding of ice age CO2 and climate change, by investigating how the deep Pacific stored CO2 during ice ages, and released it back to the atmosphere during deglaciation. Although all leading hypotheses for ice age CO2 change involve CO2 storage in the deep ocean, the role of the Pacific remains unknown. As the Pacific contains half of global ocean volume, and ~30 times more CO2 than the atmosphells, whichere, its behaviour will have global impact. Our work will involve making geochemical measurements on fossil shells taken from sediment cores from the deep Pacific Ocean. These shells - called foraminifera - record the chemistry of the surrounding water at the time they grow, so by making measurements on them down the length of a sediment core, we can read back through the history of ocean circulation and CO2. A particular focus of our grant is the boron isotope composition of these sh reflects ocean pH and CO2. The new St Andrews Isotope Geochemistry labs at the University of St Andrews are among the first in the world to have be built fully boron-free, allowing us to be at the forefront of this cutting-edge technique.

The research is based at St Andrews, but features a team of leading scientists from around the world, including the Universities of Bristol, Kiel, Oregon, McGill, and ETH Zurich, the Woods Hole Oceanographic Institute and Scripps Institute of Oceanography USA, the Alfred Wegner Institute for Polar Research Germany, and radiocarbon facilities in Glasgow and California.

The project will ultimately improve understanding of CO2 exchange between the ocean and the atmosphere, which is an important factor for predicting the path of future climate change.