Team Shrub goes to the Google Earth Engine Users Summit

It’s hard to imagine that only four months ago we were starting our introductory training in using the Google Earth Engine. Ever since February, we have been dreaming of how we can address our research questions with the Google Earth Engine. The Google Earth Engine allow us to expand our horizons from scaling from plots to landscapes to the entire tundra biome and to quantifying the drivers of biodiversity change around the planet. GEE gives people an easy and efficient access to many global and regional remote-sensing datasets, with the additional possibility to upload your own data. The GEE training we did in London definitely motivated us to advance our JavaScript skills and we were thrilled to travel to Dublin for the Google Earth Engine Users Summit!

We were both intimidated and excited to attend. The thing that struck us most as we walked into the Google Campus in Dublin was seeing our names on the illuminated stairs, which made us feel like we belong in this global community of remote-sensing scientists, conservationists, government researchers, small business and start up communities.

We are ecologists so we don’t always think of ourselves as programmers… how that changed, perception of quantitative skills. We always have our research questions at the forefront of our minds, but it was amazing to explore using a new tool to address. We learned new skills and pushed ourselves farther than we’ve gone before in terms of our quantitative skills.

Our favourite new skills

  • Breakpoint algorithms and LandTrendr

LandTrendr is set of spectral-temporal segmentation algorithms that allow us to detect changes in satellite imagery through time. Applications include monitoring changes in forest cover due to logging and fires, as well as changes in land cover types in general.

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Estimating time of land abandonment near Tyurkmen in Bulgaria using LandTrendr – the lighter the areas, the earlier they were abandoned (starting in 1986).
  • Using the Python API to access the GEE 

We think of ourselves as primarily R users, so it can be daunting to step outside of our comfort zone, but we did it!

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Imagery of Qikiqtaruk-Herschel Island from the Sentinel satellite, as seen through the Python API!
  • Machine-learning and TensorFlow

Outcome-ish: Flowers and stuff about Karol’s dissertation

• Science communication and engagement

We were especially excited about the preview of the user interface app feature for the Earth Engine! We had lots of fun building our first interactive apps and are looking forward to using web apps to share the findings of our research!

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  • Maps and embedding google maps into websites.

Outcome: embedded map of Qikiqtaruk

  • Websites and search engine optimisation

We also learned about using Lighthouse to audit website performance. Lighthouse is a great free tool to see how users experience your website, and the suggestions for improvements are quite useful. We changes a few quick things on the Team Shrub website and our performance score sure went up! Though we still have lots of photos that are bound to slow down the website, we quite like sharing photos, so a few seconds of a loading delay is worth it for us!

Hackathon: Drones and the Earth Engine

How can we integrate very high resolution RGB and multispectral drone data into multi-scale analyses?

The drone hackathon was a chance to explore working with drone data in the Earth Engine and a meet up for people to discuss and test the power of the Earth Engine to answer key research questions with drone datasets.

Hackathon: Detecting land abandonment using LandTrendr

Gergana participated in the LandTrendr hackathon, which linked nicely with her research of the effects of land-use intensification and land abandonment on population and biodiversity change through time. During our hackathon, we explored how we can use LandTrendr to detect the timing, magnitude and duration of land abandonment.

We are super inspired by the new skills we have and we can’t wait to get coding! Though of course it’s always great to expand your skill set, the most inspirational part for us was meeting an amazing group of people. From high school students, first year undergraduates to Rebecca Moore, the Director of the Earth Engine and Earth Outreach Programmes, we were thrilled to meet so many motivated and determined people.

Here’s to the Earth Engine and all the important research questions it can help us answer!

By Gergana and Isla

The field season is coming!

Time flies when you’re preparing for fieldwork in the Arctic! From months to weeks to now days of preparation left before we head north to the Arctic there is always much to do! Styrofoam parts have step-by-step turned into drones, permit applications and risk assessments have been submitted and approved, protocol files have been written and refined and our boxes and bags have been piling up and making their way across the ocean ready to head North! Read on to find out more about what is in store for Team Shrub during the 2018 field season!

Our goals for the 2018 field season

Warming of tundra ecosystems is causing rapid rates of ecological change in the Arctic from vegetation change to dramatic permafrost thaw. Recent advances in drone technology allow us to quantify these climate change responses.  This summer, funded by the Royal Geographical Society‘s Walters Kundert Fellowship, we will be testing the correspondence of tundra greenness, productivity, phenology and permafrost disturbance across spatial and temporal scales on Qikiqtaruk – Herschel Island, Yukon. How quickly is vegetation changing and permafrost thawing and can we predict where in the landscape the most rapid changes might occur? This research will allow us to answer this question and to identify the optimum scale of observation for tundra change.

Drones also allow us to quantify the landscape context of ecological change in ways that were not possible with on-the-ground data collection or satellite observations from space. Funded by a UK-Canada collaboration bursary from the NERC Arctic Office, we will use our drones to capture the representativeness of long-term ecological monitoring at focal research sites including Qikiqtaruk – Herschel Island in the Yukon, Alexandra Fjord on Ellesmere Island in Nunavut in collaboration with Greg Henry’s lab at the University of British Columbia and on Svalbard with collaborators from the Norwegian Polar Institute. We will use drones to collect spectral and structural data of tundra vegetation across scales of observation following common protocols established by the High Latitude Drone Ecology Network and will combine these data collection with ongoing ecological monitoring. Are our long-term records of vegetation change really representative of the change going on across the tundra biome? This summer’s research will help us figure out the answer to this key question.

This year for the first time, members of team shrub are off in three directions this summer from West to East and of course North to the Arctic! To find out more about members of the team this year and the specific projects they will be leading – read on!

The 2018 field crew:

How is Arctic plant diversity changing through time? by Gergana

We’ve been monitoring vegetation change on Qikiqtaruk-Herschel Island for around 10 years now, and we are looking forward to another round of some of the classic tundra protocols – such as pointframing! It’ll be our seventh year of collecting data on the changing plant communities in 12 1x1m plots. Last year we found 32 species in both the Herschel and Komakuk plots, will we spot any new species in the plots this year? An added bonus will be the second run of the ITEX species pool protocol – we will start from the center of our plots and walk around in concentric circles (trying not to get too dizzy), recording all new plant species along the way. We will get the precise locations of the first individuals of each new species, so that then we can link the rate at which we find new species with the characteristic of the landscape, derived from drone imagery! Understanding tundra biodiversity changes at this and the other sites in the International Tundra Experiment Network requires looking beyond the 1x1m plots – a key goal of this summer’s research.

Species Pool Protocol

At what rate are shrubs expanding in the Arctic? by Mariana

Another Qikiqtaruk classic field activity is continuing the repeat time series photographs of Ice Creek (see below). Each year the team captures photos in the same location looking out at the very same view as a photo that was first taken in 1987. In this series of photographs you can clearly see the vegetation change that has been occurring on the island over time. This year’s first aim is, of course, to continue the time series! But we will also take a new approach to quantify shrub growth over time with image analysis software by combining these repeat photographs with plot surveys and drone imagery. This will allow us to precisely quantify the shrub change that has occurred in this flood plain landscape and also enable us to better forecast future responses of shrub expansion across sites in the tundra. Are we seeing this dramatic change because the climate is warming, the growing seasons are getting longer or because this permafrost landscape is thawing releasing more nutrients into this Arctic watershed? Only with more data, will we know the answer.

First Test Flights in North America by Noah

I’m new this year and looking forward to making my way North to the Arctic for the first time to fly drones for Team Shrub. A few newly purchased or built drones were sent to me in Washington, D.C. so I could practice flying before reaching the island. However, DC is the largest ‘No Drone Zone’ in the United States! Once reviewing flight procedures and assembling the drone fleet, Jeff and I drove an hour out of town, outside of the Federal Aviation Administration’s no fly zone, in search of an area suitable for operations. After a few failed attempts, we convinced a farmer to let us use his open field that was mostly used for polo matches on the weekends. This made for ideal conditions to launch and land the fixed-winged platforms. We successfully completed flights with the DJI Mavic Pro and Parrot Disco Pro Ag using the Pix4D capture app for mission planning. Finally, we completed multiple flight missions with the newly built FX-61 fixed wing: Malruk (the number two in Inuvialuktun the language). After two days spent testing drones with minor technical issues, no damaged equipment, and some brutally hot and humid weather, we packed everything in the car and rushed to the airport for Jeff to catch his flight out of town! With drone training complete, I am excited to join up with the field crew and to head up north to go collect some drone data!

Headed to the High Arctic – by Isla

I’ve been working in the Arctic for over a decade now. Seems like a long time ago that I first made my way across the Arctic circle in 2002 to check out the Toolik Lake research station – when I first discovered my love for tundra shrubs. Since then I have been to many tundra locations around the North, but there is one place I have never been – the Canadian High Arctic and Ellesmere Island. For as long as I have been working in Arctic ecosystems, I have been hoping to make it up to the iconic Alexandra Fjord research site. This is one of the longest running tundra ecological monitoring programmes out there led by Greg Henry from the University of British Columbia.  Since 1992, Greg’s Lab have been monitoring the plant communities. Our very own Anne Bjorkman conducted her PhD research at this site. In fact, Team Shrub has been working with data from “Alex” for over five years now, but this summer for the very first time I will actually get to go myself and with the help of Team Shrub collaborator Jeff Kerby add some new drone data collection into the mix. With the data we hope to collect this summer, we hope to contextualize the long-term records from this site. This work will allow researchers to return in future to the precise locations where data collection has occurred for the past three decades. The drone data from this summer will also help us to figure out if long-term ecological monitoring records here, on Qikiqtaruk in the Yukon, and elsewhere in the Arctic are really representative of the responses to global change across the tundra biome.

So, here’s to a productive field season for Team Shrub!  In our final days of field preparation we will be working hard, so that we are as prepared as we can be for the field adventures to come.

By Isla, Gergana, Mariana, Noah

Keeping up with biomes

As we prepare for the upcoming field season, the end of my first PhD year looms closely on the horizon. It then seems like a good moment to recap what has been happening during this intense year and to test whether my elevator pitches have improved since I was first overwhelmed to describe my thesis!

My PhD project has turned out to be a bit unconventional, to say the least. I have always been a fan of the big picture and global issues, so when I decided to do a PhD, it was clear that I would be fully embracing macroecology and biogeography topics. The preliminary title of my thesis (because this is perpetually changing) is ‘Quantifying vegetation shifts under climate change in extreme biomes’. What this means is that I am carrying out a comparison of plant responses in two extreme biomes: the tundra and the savannah, both extensively distributed biomes across the planet. You are probably shaking your head and thinking “but… why?”, which is a perfectly normal first reaction and a question that I have been asked lots over the past year.

Let me explain a bit. As you know, the tundra is found at very cold temperatures with low precipitation, while the savannah is found at high temperatures but with a wider range of rainfall conditions. However, both biomes are characterised by a strong seasonality (i.e. summer is the growing season in the tundra, while the savannah is characterised by a dry and a rainy season). Something else that these two have in common is the fact that they are structurally very similar. Both are characterised by an open landscape dominated by mainly grasses and shrubs, with trees too in the case of the savannah. Their ecological structure and functional groups are very similar, with some authors even referring to the tundra the ‘cold savannah’. If you look at the photos below, can you identify which biome is which?

Hint – no trees is usually a good sign that you are in the tundra and not in the savannah. Elephants could potentially be a helpful indicator too though.

These similarities mean that the tundra and the savannah have been undergoing similar changes under current climatic conditions. The most conspicuous process so far is woody expansion or encroachment (a.k.a. shrubification), where trees and shrubs expand into open areas. Shrubification has been reported widely over the last decades in grasslands across the globe. However, the fact that the tundra and the savannah are found in extreme climatic conditions, which are bound to continue shifting under climate change, means that they could be particularly at risk.

While this is good news for shrubs, which are happily conquering new lands, this comes at the cost of other species, such as lichens and mosses, which end up being outcompeted. Wide scale ecosystem changes like this can also affect the carbon cycle and nutrient exchange, and ultimately, the persistence of these biomes at local scales. The tundra can lose ground to in favour of the boreal forest following warming temperatures, while parts of the savannah can be converted to tropical forest or agricultural lands due to herbivory influence and shifts in wildfire regimes.

The tundra and the savannah are pivotal in supporting biodiversity and providing ecosystem services. For this reason, we need to understand if they are responding in a similar manner to climate change or if their behaviours are highly specific – this will enable us to better predict and act in the face of global change. These rates of change rates are yet to be quantified, so here is where I come in! This is what I have been working on for the past year and hope to have some outcomes soon. Stay tuned for some (hopefully interesting) results in the near future!

By Mariana

Arctic Above – A Team Shrub Photography Exhibition

Our scientific research expeditions to the Arctic often reveal dramatic landscapes, exciting wildlife encounters and lots of natural beauty. We are always keen to widely share those experiences, and one way to bring the Arctic closer to people is through photography. This year, we are continuing our science & art outreach work (you can read more about our outreach events at the Edinburgh Science Festival last year here) by organising a second photography exhibition. This time, in addition to the physical exhibition, we also have an online exhibition, so that anyone with internet access can get a glimpse of Arctic environments, wildlife and ecosystem changes.

We present photographs of Arctic tundra landscapes and the plants and wildlife that inhabit them, captured as a part of scientific research expeditions to the rapidly warming Arctic. Images are captured from above using drones, helicopters or planes and on the ground as we hike out to our research sites. Some of these images are part of scientific datasets used to model the 3D structure of the tundra environment.

This work represents the interface between science and art, where the process of data collection has produced imagery that communicates the reality of global change and captures the patterns and beauty of remote Arctic ecosystems.

Arctic Above – online photography exhibition

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You can explore our photography exhibition online here!

Arctic Above – Exhibition in the Main Library, University of Edinburgh

If you are based in Edinburgh or visiting the city to experience Scottish spring, you can also check out our photos in the Main Library of the University of Edinburgh, first floor on the right. It’s always exciting to see our photos printed in large! It is also cool how even though we all have distinct photographic styles, our photos complement one another so well! We hope those who visit our online exhibit as they make their way into the Library to study for their exams or out to enjoy a bit of spring sunshine get a glimpse of what it is like to study the changing ecosystems of the Arctic.

Sandra and Gergana set up the exhibition in the Main Library – feel free to stop by to check out the photos and tell us what you think on Twitter – @teamshrub #ArcticAbove!

By Gergana

The Plants of Qikiqtaruk. Part 1: The Shrubs

On a cold and distant island the stars of our science are sleepingBuried under a thick winter blanket, Qikiqtaruk in winter is exactly what many people imagine when I say I work in the Arctic: awash with snowdrifts, locked in sea ice, home for polar bears and not a huge amount else.

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Qiqiktaruk in winter

Yet here on Team Shrub we study plants. Come the summer sun, green tendrils of life emerge from the snow and the hardy, beautiful and fascinating plant life of the tundra begins to grow. Diverse in the manner of tropical rainforests it may not be, but these cold lands are nonetheless brimming with more life than you might think, featuring old favourites that adorn the hills of Scotland to wacky monstrosities that seem to spring out of some primeval past.

In this series we will be exploring some of our favourite species from our most northern field site, starting with our namesake: the shrubs.

The Shrubs

What makes a shrub? Such has been the dinnertime conversation at many a Scottish Feast. In short: short. Woody. Multi-stemmed. Sometimes evergreen, sometimes deciduous, always beautiful.

The willows

Qikiqtaruk is home to a grand total of nine willow species. Not bad for an isolated Arctic island. The Salix genus dominates much of the upper shin-high canopy, though you can find yourself wading through some of the bigger fellows. Bjorn even reaches chest height. Deciduous, green-leaved, the willows add a certain magic to the tundra as their fluffy seed spirals in the air on a breezy day, while bright red catkins dot the tundra floor underfoot.

Salix pulchra

Possibly our favourite shrub on the island. This beautiful willow surely lives up to its name: long ruby stems and startling emerald-bright diamond leaves, giving Salix pulchra its common name, diamond-leaf willow. On Qikiqtaruk Salix pulchra grows mostly along the ground in large, clonal mats that creep between tussocks of cottongrass and shelter small white Stellaria flowers. It’s one to watch though, as further south this willow can reach well over head height. Here, where the weather is sheltered and nutrients seep from the permafrost, Salix pulchra grows faster, bigger, redder, standing out from its neighbours atop the palsas, while on the hilltops we have already seen a tripling in its canopy height since we first started recording in 1999.

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Salix pulchra leaves catching the sunlight. The beautiful willow is a Western Arctic specialist found across tussock tundra and mountain landscapes of the Yukon and Alaska.

Salix richardsonii

One of the giants of Qikiqtaruk, Salix richardsonii, or Richardson’s willow, is the most common tall shrub on the island. It grows mostly in wetter, sheltered areas such as river floodplains, where nutrients flow freely and life is as easy as it gets in this bastion of land in the Arctic ocean. Forming a dense, shrubby canopy of bright green leaves, Salix richardsonii nonetheless has a rather grizzled visage, giving it our nickname ‘Old Man Willow’. Twisted branches and flaking orange-brown bark, flecked with white specks of age or hardship. Fat, hairy stipules easily mark it apart from other willows. A canopy bully, Salix richardsonii is now dominating areas where it can grow, rapidly expanding in many parts of the island as the climate warms.

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Encroaching Salix richardsoni is taking over the Ice Creek watershed on Qikiqtaruk. This is one of the tallest willows on the island and elsewhere in the Arctic where in can dominate tundra landscapes with dense, metres tall and sometimes impenetrable thickets of willows.

Salix arctica

This small willow is a remarkable example of the success and resilience of plants in these cold lands. Salix arctica, the Arctic willow, has the most northernmost geographic range of any woody plant, reaching all the way to the north coast of Greenland at 83 degrees north. A ground-hugging, prostrate woody shrub, it spreads woody limbs akimbo, stretching out in all directions along the top of the permafrost. Thin stems become roots, become stems again and it advances clonally, covering much of the surface until it is impossible to tell where one plant begins and another ends. Even if the main “trunk” is destroyed or decays, the plant will not die: an attempt at immortality. Unlike many of the other dwarf willows, Salix arctica eschews the small leaves and catkins of its fellow family members, and sticks to the strategy of the taller shrubs that bigger is better. Big, fat leaves emerge from the brittle stems, which giant fluffy catkins can strike up from the ground surface several times taller than the rest of the plant. Unusually, on Qikiqtaruk even the leaves and stems of Salix arctica strike upwards for the sky, possibly a hybridisation of one kind or another, and can stretch up even as much as 20cm from the soil.

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Salix arctica the Arctic willow with flowers blooming in spring. This is one of the most widely distributed plants across the tundra biome found from the Rocky Mountains of Colorado to the very tip of Greenland.

Salix reticulata

Just like Salix arctica, this dwarf willow hugs the floor with brittle stems and clonal creeping growth in all directions. The thick, leathery leaves of this plant give it its common name: net-leaved willow, which are criss-crossed and pocked with deep grooves. Once fallen in winter, these hardy leaves last, resisting decomposition and creating a crunching carpet underfoot.

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The waxy leaves of the net-leaved willow, Salix reticulata. Like with Salix arctica, this is a very widely distributed willow found in much of the Arctic, the Alps and even in Scotland!

Salix polaris and Salix phlebophylla

The smallest of Qikiqtaruk’s willows, these two species take you down onto hands and knees to appreciate their tiny round leaves and stalk-like stems. Hugging the ground in dense mats, often on the drier sections of hillsides or edges of tussocks, I often have trouble telling these apart from leaves alone. Yet catch them right in the season, and the red catkins of the polar willow (Salix polaris) stand out as one of the brightest flashes of red on the tundra, flecks of delicate colour, blood-rich, that in a matter of days dissolve into white and wind.

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The bright red catkins, fluffy white seeds and verdant green leaves of Salix polaris often remind Isla of the colours of Christmas!
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The tiny 2 – 4 mm long leaves of Salix phlebophylla covering the ground in a mat. Named for the skeleton leaves it ‘leaves’ behind year after year, this is one of the smallest willows in the world!

Salix glauca and Salix niphoclada

Two of the rarer tall shrubs on Qikiqtaruk, grey willow (Salix glauca) and snow willow (Salix niphoclada) can be a challenge to find, but occasionally stand out on the hillside where some seed has found its way to establishing. The grey-tinged haze of glauca willows sets them apart from the rest, while the sometimes rose-tinged stems and somewhat brighter leaves of niphoclada can cause us headaches when we search for Salix pulchra to sample. These two willows with green leaves covered in fine grey hairs and stems with a blue-green and waxy look to them can be indistinguishable when they have no visible catkins, which is much of the time, so they are often clumped together in our analyses.

Salix glauca
Less majestic than Salix glauca in other parts of the Arctic, here on Qikiqtaruk this willow can only eek out an existence in the warmest microclimates of south-facing slopes.

Salix alaxensis

Finally, the Goliath of Arctic willows. Salix alaxensis grows tall and often somewhat spindly up on Qikiqtaruk, almost buddleia-like, as if it wants to reach the sun and doesn’t care how it gets there. The leaves are grey-green, but a bright, fluffy white underneath – lannate, densely villous or tomentose if you will. Did you know there are over 20 botanical terms for being hairy! Certainly easy to identify. We have only recently discovered Salix alaxensis, the Alaskan willow, on Qikiqtaruk, though since individuals are already well established, thus it must have been evading detection for many decades.

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Isla with a particularly tall Salix alaxensis found on Qikiqtaruk in the summer of 2016 on a particularly buggy walk back from the retrogressive thaw slumps along the coast.

The birches

Betula nana and Betula glandulosa

If you spend much of your time tramping about the high hilltops of Scotland you may already be familiar with dwarf birch. Small, thickety and brittle, the dense brown stems of Betula nana or Betula glandulosa have snagged many a bootlace and tripped many a toe. Still, I love the Betulas for their leaves alone, some of the most perfect forms on the tundra. On Qikiqtaruk, Betula nana holds sway on flatter patches of hilltop; a low growing shrub that announces its presence as a darker green blur on the landscape, or from the waft of crushed Labrador tea underfoot, which tends to grow alongside birch. Unlike many other tundra sites, where Betula has run rampant as the climate warms, it so far seems to be losing out to the willows here, though in some places the dense, spotted branches form an impenetrable tangle across whole swathes of tundra. As for the difference between nana and glandulosa, the latter is taller, larger leaved, greater noduled. Or not, as the case may be – perhaps they are one species after all, marked apart not by genetics but simply variation.

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A very dwarf birch, Betula nana/glandulosa – is it one species or two? – nestled amongst compatriots including Rhododendron tomentosum and Vaccinium vitis-idea (see below).

Tundra tea

Rhododendron tomentosum

A hero of the Arctic smellscape, Rhododendron tomentosum is another favourite of ours. The shrub itself is part beautiful: white flowering baubles full of rich scent, rusted felt underside of leaves, and part ugly: the ash-black branches spindly, frail and commonly dead, dark leaves often matted and speckled, a formless shape creeping amongst better rivals. But altogether outstanding are the leaves themselves. Rhododendron tomentosum, marsh Labrador tea, may not quite have the glamour of its more grandiose and much less marshy southern cousin, but its leaves still bear the scent of a thousand tundra days; that unmistakable and uncapturable spice of terpene and midnight chlorophyll. This is a shrub that makes trait work bearable, and often one that prompts a pocket full of leaves for the walk home.

 

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We are crazy about the fragrant smell of Labrador tea (Rhododendron tomentosum), Ledum (its old name), I got to get some!

The berry bearers

Arctostaphylos rubra (Arctous rubra)

One for the photo albums. A. rubra, or bearberry, is certainly one of the more iconic tundra shrubs due to its bright, Rudolph-red leaves that can stain the bare tundra at certain times of year. Another prostrate-growing shrub, the ovate, vein-y leaves can bear a resemblance to the leather coins of Salix reticulata when green, though are stretched and less waxy. It is when the winter begins to draw in that Arctostaphylos rubra sets itself apart as the leaves turn, and formerly invisible patches of bearberry shine out. Red too, the berries that hide in amongst the leaves: a food source for humans and wildlife alike, though their diuretic properties also lend themselves to herbal medicines and may explain the preponderance of stained bear poo littering the tundra in autumn. A closely related species, Arctous alpina, looks almost identical except for the red berries that turn black when ripe.

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The bright red leaves of Arctostaphylos rubra in the autumn intermixed with some Vaccinium uliginosum.
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Arctous alpina the black berries of alpine or ‘black’ bearberry.

Vaccinium vitis-idea and Vaccinium uliginosum

Another set of plants that will be well known to hillwalkers, the Vaccinium genus is the main fruit bearer for local people and hungry researchers. The smallest, Vaccinium vitis-idea (Ligonberry, cranberry, cowberry – you name it!), carpets the surface with tiny, glossy leaves and even glossier red berries where cover is sparse and soils fairly dry. In places the leaves can turn to a deep, merlot red, or still drip with pink-white cowbell flowers. Harder to find on Qikiqtaruk, Vaccinium uliginosum (blueberry, bilberry etc.) rise higher from the undergrowth where soils are wetter, their berries blue, stems tough brown-green and leaves thinner and more leathery.

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Vaccinium vitis-idaea (and Empetrum nigrum). These Arctic cranberries make a delicious pie and jam if you have the patience to pick enough!

Rubus chamaemorus

Cloudberry, baked apple, or knotberry in England and averin in Scotland is best known on Qikiqtaruk as aqpik. This is one of the most prized of berries in this part of the world and when perfectly ripe is a delicious topping to pancakes, makes an excellent jam or is the perfect snack when stopping across the tundra. Quick to turn from unripe to rotten, finding your patch of cloudberries in season on Qikiqtaruk can be a challenge.  It is rare out there, preferring the wetter habitats on the edges of ponds or in ice-wedge terrain.

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The delicate salmon pink berries of ripe aqpik or cloudberry.

Empetrum nigrum

A heathery-looking dwarf shrub that is equally at home in the Scottish Highlands, on mountaintops around the northern hemisphere, under conifer canopies of the boreal forest, and in vast swathes of tundra. Also a clonal shrub, Empetrum nigrum can form dense mats stretching uninterruptedly for meters, or even tens of meters. Its super-power is allelopathy: the leaves contain toxic chemicals which, when leached into the ground after the rain, hinder germination or growth of other plant species. Fun fact: the wood smells delicious when boiled in water (don’t ask, and probably don’t drink).

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The bright leaves and black berries of Empetrum nigrum

The dwarf evergreens

Dryas integrifolia

The spear shaped leaves of the mountain avens is to me another iconic shape of the tundra. Whether forming into a sharp coniferous tip, or padded out into the more billowy, deciduous-tree form of Dryas octopetala, these OS map symbols of leaves are unrecognisable wherever they grow. But for many, Dryas integrifolia is best known for its flowers – the perfect white circles that polka-dot the tundra floor – and for the twisted filaments that are the phoenix seedhead, catching the sunrays and diffracting light and themselves across the tundra air.

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The bright white flowers of Dryas integrifolia.
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Twisting filaments of Dryas integrifolia as the flowers set seed at the end of the summer.

Cassiope tetragona

Growing amongst the rocks and along the dry hillsides, the weeping white bells of Arctic bell heather are another distinctive site at the height of a tundra summer. A relative of the glorious purple heather of the Scottish hills, Cassiope tetragona is similarly small and woody, minute spear-shaped leaves wrapped tight into the stem, forming scaly round limbs. As the season turns, these stems gradually shift from green to orange-brown, giving the tundra an almost burnt look, flowers rusting away to leave the brittle seed heads proud to the wind.

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Cassiope tetragona with four flower heads as per it’s name is one of the longest lived of tundra shrubs, with individuals being found that can be dated back to over 200 years.

Bonus: The uncategorised

Silene acaulis

If you’ve reached this far, well done for getting to the end. As a special bonus, I’ve included Silene acaulis, better known as moss campion. There is some confusion here as to whether Silene acaulis is best classed as a shrub or a forb. Silene as a genus refers to the campions, delicate flowers of field and rocks, all pink and white and herbaceous green leaves. Yet the harsher climates to which Silene acaulis has adapted produces a hardy, cushion-like shrub, past leaves compressed into woody stems. For myself, I class this bright plant as a forb, yet since I have seen it classed otherwise so under some schemes, it is worth a brief mention here.

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The resilient and secretive Silene acaulis

Beyond confusion of classification, Silene acaulis is by no means one to be relegated to the bottom of any list. It grows where often nothing else will, building a bivouac out of its own sharp leaves against the elements. Within this thick shell, the plant can grow to engulf surrounding rocks occasionally supporting other tiny plants as they grow through chinks in its armour. Most spectacular are the pink-purple flowers, which at the height of the summer dot these minuscule mountains like dewdrops, or like pins in a pin-cushion. Silene acaulis is rare on Qikiqtaruk – the soft, undulating landscape means there are few surfaces too harsh for competitors. But I have seen one once, in passing, making a mental note to come back to sample it later. I have never found one since.

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A rare find for Qikiqtaruk, a bit of Silene acaulis, spotted by Isla in the summer of 2017.

By Haydn, Sandra and Isla

Our Google Earth Engine adventure

We love big bold questions. Synthesising data over large spatial and temporal scales and bringing together information from different sources to support our findings. Along the way, we have our trusty SuperShrub (our mini-supercomputer), but there are some things even SuperShrub can’t handle, or can’t do in the most efficient way. So how can one extract NDVI, land cover, climate data and more over thousands and thousands of kilometers and across many, many days, months and years? Why with the Google Earth Engine!

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Hanging out at the Google Academy in London – where life is a beach!

Last week, Isla, Jakob, Sam and Gergana headed to London to attend a training workshop led by Noel Gorelick and Nick Clinton. A rainy morning in London with travel delays for some and generally long train rides for all wasn’t a particularly promising start, but it turns out we were off to the beach. We escaped the cold and rain at the Google Academy, where there was a strong beach theme, with colourful beach balls, giant beach chairs and even sand and faux sea grass in the corners of the room. With dreams of working with MODIS, Landsat, Hansen data and more, we were ready to tackle JavaScript and see how we can use the Earth Engine to expand our research horizons. And what did we learn??? Read on to find out.

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They even have inflatable unicorns at the Google Academy!

The Earth Engine is fast. Very fast!

Gergana: Being able to quickly access and extract land use information for thousands of locations around the world is a key part of my PhD research on the drivers of biodiversity change. I had heard the Earth Engine is fast, and I knew that one of the datasets I am working with, the Hansen et al. Forest Cover Database, is accessible through the engine, but I am also stubborn and I love R! So many a day were spent trying to push R and SuperShrub to their limits… and well, the code never finished running, as I stopped it after a week of waiting! That is why I was pretty excited to see the Hansen database mentioned in the presentation prior to the workshop, and I couldn’t wait to try extracting information. I adapted some of the code we learned in the workshop and a bit of code I found online, and what do you know, 42 seconds (only 42 seconds!) later, I had a csv with thousands of rows specifying the forest loss and gain in 2001-2014 for the areas I was interested in. Amazing!

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A zoomed in view of forest cover change based on the Hansen et al. database. Red is loss, purple is loss and gain and blue is gain.

The Earth Engine is flexible!

Isla: In a one-day workshop, we covered a lot of ground – from pixel classification, spectral unmixing to phenology analyses. We had a chance to explore the greening of our focal field site Qikiqtaruk – Herschel Island all the way up to the greening of the Arctic! We knew that the Earth Engine was a powerful platform, as some of us had dabbled before, but it is great to finally get a better understanding of what the possibilities are. The Earth Engine could be a game changer for earth observation. Below you can see MODIS NDVI trends for our focal research site all the way up to the Western Arctic at 1 km resolution, all calculated in under 10 minutes.  You can see pixels with active coastal erosion and permafrost thaw slumping getting browner and the less disturbed tundra vegetation getting greener at the local scale and the patterns of greening and browning in the Western Arctic region.

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The greening of the Arctic from Qikiqtaruk to the entire Western Arctic calculated using the Google Earth Engine. Green pixels are sites where the normalized difference vegetation index (NDVI) is increasing (robust regression), brown pixels are where the NDVI is decreasing. You can see browning pixels in areas influenced by active coastal erosion and permafrost thaw slumping at the local scale plot and greening pixels where we have evidence of tundra vegetation change. And at the larger scale you can see the strong greening pattern in the Western Arctic near our field site.

Taking time out of our usual routine to learn new things is important.

Team Shrub recently met to discuss our New Year’s resolutions, and one of our general life goals – “to keep learning new things” – was pretty high up on that list. It’s not always easy to make time for new things in our busy lives, but sometimes it is just something that you have to make happen. Even if it involves taking many trains and feeling motion sick on every single one! As much as we love coordinating Coding Club and teaching students quantitative skills at the University of Edinburgh, it’s also nice to be the one being trained and getting to attend a coding workshop from time to time!

So, for Team Shrub, harnessing the power of the Earth Engine might allow us to expand our horizons from scaling from plots to landscapes to the entire tundra biome and to quantifying the drivers of biodiversity change around the planet.  And now that the training is over, we can’t wait do dig in deeper and explore our earth observation research questions in a whole new way.

By Gergana and Isla

5 (More) Steps to Becoming an Awesome Field Assistant

Being a field assistant for the first time isn’t always easy. Following on from Izzy’s recent post, here are five more great tips from Cameron on how to be an awesome field assistant (and to have an awesome time).

1. Apply for funding

Being a field assistant costs money. In many cases you might be employed by an organisation, research group or researcher to carry out the role, in which case they will be covering your costs. However, you may be required to (or want to) provide funds yourself. But don’t fret! There are plenty of funding opportunities hidden out there for the proactive field assistant to find. Most funding requires you to submit a proposal outlining what you will be working on and how much you think it will cost. Once you have drawn up a proposal for one funding application it is easy to tailor it for others. Keep an eye on the submission deadlines and apply to as many funds as possible. In my experience, funds for undergraduates aren’t very competitive, so make use of them!

Information for funds available for University of Edinburgh Students can be found here. 

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Cameron fishing for funds

2. Take good equipment

When you are setting up experiments in a snowstorm, or climbing mountains before breakfast, you quickly learn to appreciate the value of good equipment. However, if you haven’t been in the field before it can be hard to figure out what sort of stuff to bring with you. For me, the most important bits of kit are good waterproofs, a decent backpack, and an excellent pair of walking boots (we had a pair fall apart this summer). If you are going to spend a lot of time in the field you should treat yourself to some nice gear. It’s totally worth the investment and good quality stuff can really improve your comfort and safety. Why not add the cost of a beautiful jacket and boots into your funding application (for health and safety reasons, of course)?


3. Ask lots of questions

“Why are we digging up old tea bags from the ground and what’s the deal with all of these dead leaves?”

Take the opportunity to learn as much as you can from the people you are working with. Asking questions and figuring out why you are doing a task can really help you get more out of your time in the field and cement knowledge learned in the classroom. You will also likely be working with people further on in their career than you. If you are thinking about a career in academia, take this chance to pick their brains about all aspects of academic life.

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Haydn showing us the ways of the shrub


4. Take the bad with the good

 Hopefully you will experience many great things during your time as a field assistant but you might also experience some pretty bad lows. The work can be gruelling and the days long. A healthy mentality is key to enduring the bad moments and enjoying the good. Make sure to talk to your team if you are having difficulties, and look after yourself. It really is worth it at the end.

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Conquer your mind and you can conquer the tundra


5. Let yourself be enchanted…

Fieldwork can take you to some truly special locations. We get to explore hidden valleys, shadowy forests, and secret little places far from any path. Please take some time, in-between sampling and recording data, to fully appreciate the wonderful environment and people around you. Not only does this add to your overall experience, it can also turn you into a passionate advocate for these incredible areas. Tell the stories of these places anyway you can, be it on Facebook, in prose, or down the pub. The more people know about your field site, the less likely it will fade into obscurity and be lost.

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Soaking up the view

By Cameron

Team Shrub – 2017 in Review

It was a big year for Team Shrub in 2017.

Like an Arctic willow in the tundra sunshine, we soaked up the beautiful rays of knowledge and delved further into the active layer of understanding. We grew taller and bushier as new members joined the team, and branched out into new areas of research. We bore fluffy research paper catkins, for our ideas and findings to be spread on the breeze of scientific discovery, and we put down new roots, to support, work with and learn from others in the future. And, of course, we had a thoroughly enjoyable time doing it all.

So as we look forward to all that 2018 brings, we are taking some time to revisit the year gone by, our favourite blog posts, and just how far we came in 2017.

Looking ahead: After a politically turbulent 2016, who could know what 2017 would hold? We spent the start of the year looking ahead with some trepidation, some anticipation and a good dose of excitement.

Decomposition in the cold. We kicked of a busy year as Haydn and Isla headed on a tour of Denmark and Sweden to attend the Oikos symposium on Decomposition in Cold Biomes (https://globalsoilbiodiversity.org/content/oikos-satellite-symposium). It was appropriate as the temperatures had dropped that week and it was quite snowy and chilly in beautiful Lund, Sweden as we chatted about cold-weather decomposition while cosy inside.

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Taking a tea break in Umeä

To Aberdeen. In March, it was our first Team Shrub trip to Aberdeen. We had a beach coding holiday and attended the Scottish Ecology, Environment and Conservation conference with Gergana, Haydn and Sandra presenting. We teamed up with Francesca Mancini from the Aberdeen Study Group to lead a coding workshop on efficiently analysing and visualising big-ish data in ecology.

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Jumping for joy at the thought of more coding!

Glimpses of our future? By April, we had a wee glimpse into what 2017 might have in store for us through a traditional Bulgarian pastry dish with our fortunes inside!

Tundra Greening and Browning. Also in April, After a lab trip to Durham, Haydn’s home town, to talk permafrost for a day at Durham University. Andy and Isla went to the home of the Crucible, the land of snooker, the (real) region of Robin Hood, and the heartland of the only English football team named after a day of the week. (Also the home of the Arctic Monkeys – who incidentally haven’t spent much time in the Arctic). If you haven’t guessed yet, we went to the town of Sheffield for the ‘Arctic Browning Workshop’. The Arctic is warming and satellites have shown a fair bit of greening, but recent evidence suggests a decrease in the rates of increasing greenness at high latitudes and some browning events. The theme of the workshop was exploring that Arctic browning and what might be causing it.

A trip to the Highlands. Also in April and before the field season, Team Shrub headed to the highlands to show our visiting scholar Jeff Kerby and our summer drone pilot Will Palmer the beautiful countryside in our own backyard.

Traits. In June, Haydn, Anne and Isla headed the deep South of the UK to almost tropical temperatures at the University of Exeter. We were at the New Phytologist 39th Symposium on Trait covariation. Whether in the symposium sessions or out on Dartmoor, we had a great time pondering plant traits from the tropics to the tundra.

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Team Shrub strike out across the Highlands.

The Field Season. Suddenly it was the field season. Team Shrub divided into two teams: Team Drone and Team Kluane to concurrently conduct our data collection on either end of the Yukon. From drones, tea bags, phenology, stories, sounds, smells, feasts, birding, to reunions many adventures were had and a ton of data was collected. We managed to capture over 100,000 images or more than two TB of data with our drones, to dig out over 300 tea bags from the ground, and to fill several field books or iPad spreadsheets with numbers and notes. It was a productive period and we are still working away on processing the data.

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Team Shrub together at last!

New beginnings. This September marked the start of Mariana’s and Gergana’s PhD research. Mariana is modelling how plant species distributions will shift under climate change at two extreme biomes – the tundra and the savannah. Gergana is quantifying the effects of land use change on global and local patterns of species richness, abundance and composition. Sam, Claudia and Matt have joined Team Shrub for their honours dissertations. The data presents will soon be rolling as new student projects come together and our first three Team Shrub PhD students finalise their dissertations over the coming months.

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First day of being a PhD student for Mariana and Gergana!

Coding. Coding Club celebrated its first birthday! Coding is a big part of our work on Team Shrub, we use coding in our research, teaching, our lives in general… where would we be without it. Perhaps a bit less constantly frustrated, but also without those moments of glory when everything runs error free! We even made up a fictional journal for the Conservation Science course that Isla organises and Gergana and Mariana are tutors on. You can find out more about AQMCS (Advanced quantitative methods in conservation science) here – Same data – different results? ConSci 2017 introduces AQMCS!

Conservation in the Cairngorms. In early October, members of Team Shrub took our annual pilgrimage up to the highlands of Scotland for the weekend fieldtrip on the Conservation Science course. With all sorts of weather, mountains, drones, delicious cake and an epic music jam, fun was had by all!

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Learning about conservation in a majestic landscape

Biodiversity, the New North and the science/policy interface. Also in the month of October, along with keen undergraduates from the Conservation Science course, we went along to the Spotlight on Scotland’s Biodiversity conference. For the undergraduates involved, it was their first ever conference. It was pretty inspiring to see the next generation of conservation scientists getting the opportunity to talk with the Scottish experts in the field. A few weeks later in November, we headed to the “Scotland and the New North” policy forum, where Isla got to hold the door for Nicola Sturgeon! A new focus looking Northward for Scotland could mean new things for Team Shrub research in future.

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What will Scotland’s new focus northward mean for Team Shrub?

Also in November, Mariana attended two  policy-related events: the EEB Changing Landscapes conference in Edinburgh and the BES “Understanding science policy in Scotland“ workshop in Stirling. The first was a high-level event where major conservation organisations discussed the future of nature in Europe; while the second zoomed into Scotland to understand how science can feed into the policy-making process.

Writing. In November, Team Shrub had our first official writing retreat. We have been talking about having a writing retreat for years and finally things came together with a chance to focus on our writing goals, away from distractions. We were so inspired that we are planning on having a residential writing retreat sometime in the Spring of 2018 – where we can go from one day of super high productivity to hopefully a long weekend.

Dual Conferences. In December, Team Shrub headed to two big conferences happening at the same time! You can read about our parallel conferences experiences here. At Ecology Across Borders in Ghent, Belgium, Anne, Mariana and Gergana joined over 1500 ecologists to take in lots of exciting science, go to workshops, meet new people or catch up with old friends. Gergana and Anne gave talks, in sessions happening at the same time!

At Ecology Across Borders, we also led a Coding Club workshop, titled “Transferring quantitative skills among ecologists”. We shared our approach to teaching coding to keen participants from the conference. All of our workshop materials are online: Transferring quantitative skills among scientistsYou can also check out the Coding Club website to find all of our tutorials as well as information on how you can join our team and organise workshops at your home institution.

The other half of Team Shrub, Isla, Sandra, Haydn, Jakob, Andy and Jeff went to Quebec in Canada for the penultimate ArcticNet meeting – Arctic Change 2017. You can check out the daily round-up blog posts about the conference here – day 1day 2, day 3 and days 4 and 5. A pinnacle moment for Team Shrub was Haydn and Jakob winning the top two prizes from the conference elevator pitch contest!

Rejections. When we drafted our goals for 2017, we also set out our rejection goals. The idea behind rejection goals is that if we never get rejected, then maybe we aren’t aiming high enough. We decided to collectively aim for 50 rejections. So how did we do? We counted 23 rejections out of our goal of 50. Now perhaps we didn’t manage to count every single rejection this year, some of them we would rather just forget, but can we count the fact that we didn’t achieve our rejections as one additional fail?  Then technically we are at 24 out of 50?

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Team Drone on Qikiqtaruk – Herschel Island in the Northern Yukon.
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Team Kluane at Outpost Station in the Southern Yukon.

Outreach. At Our Dynamic Earth, we shared the excitement of using drones for science. At the Edinburgh Science Festival, we explored art as a way to communicate science. We put together the photography exhibit “Arctic from Above” and developed collaborations with Simon SloanArchie Crofton to explore how art and data interface and ASCUS looking at tundra shrubs as time machines. Then at Curiosity forest, part of Explorathon 2017, we used drone simulators and cool dendrochronology samples to learn about how to study Arctic change.

There were also many jolly meals and trips to the pub. Many heated debates as we discussed science in lab meeting or over lunch. There were many moments of coding frustration followed by a sense of achievement as we worked through our scientific goals.

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One of many lab meetings!

So those were some of the Adventures for Team Shrub in 2017.

What will 2018 hold? We already have some exciting things to share with you over the coming months, and many more in the pipeline. Hopefully we will also have some fantastically fluffy catkins this year: keep your eye on the breeze.

So from all on Team Shrub, a very happy new year and we look forward to sharing with you, working with you, and learning from you in the year to come.

By Gergana, Isla and Haydn

One day, 12 795 words: The Team Shrub Writing Retreat

12 795 words in one day! That is a dissertation right there pretty much. And members of Team Shrub wrote those words over a mere four hours of structured writing time. How did we do it? To find out more read on…

We have long loved the idea of a writing retreat – setting aside time to just write. No distractions, no emails, even no coding, just pure writing. It always feels hard to focus just on writing – little urgent tasks creep in and next thing you know, the day is over and that Word document is still blank. Writing retreats are a fun combination of peer pressure and peer support. Nothing like the sound of many people writing to make you realise that you really should be writing, too! We all have things we could be writing right now – a manuscript, an assignment, a thesis chapter, a blog post (a great distraction from what I really should be writing right now, but hey, this is still writing…). It’s great when we have a special occasion when all those things do get written – the Team Shrub writing retreat!

In November, Isla organised a writing retreat, right here in Edinburgh, so a convenient location for all of us. It was quite the fancy setting, with a particularly inspirational ceiling in our writing room!

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The fancy setting of our writing retreat!

We started off the morning by laying out what we would like to achieve during the day and in the specific one hour writing sessions ahead of us. We shared our writing goals, Isla told us a bit about how writing retreats work, and with an alarm set off to ring in an hour’s time, we began writing! The break between the writing sessions gave us the chance to refuel with tea and coffee and chat about how our writing is going. And then another one hour of solid writing followed.

Next, we moved onto a delicious lunch in a nearby cafe, followed by a casual work session with even more delicious lattes, flat whites, mochas and such! Our cafe visit gave us the chance to chat about our writing projects, how they are progressing, and ponder over any questions we might have. We liked the combination of the more strict writing sessions in the writing room with the casual cafe session – the best of both worlds!

We also pondered what kind of writers we are and what our strategies for success at the writing retreat were. Do you edit as you write? Do you write everything that comes to mind and edit later? These questions, and many more, are covered in Stephen Heard’s great book “The Scientists’s Guide to Writing”. I particularly like the chapter on writing behaviour. I over-analyse to a fault, so if I give in to the temptation to really discuss or write about writing behaviour and writing strategies, I’d never write anything else! I may or may not be wondering whether there is a test online about writing personalities, but alas, I shall be strong and focus on this.

We wrapped our writing retreat feeling very accomplished. So how did we do it? Here are a few of the elements that came together to bring our writing successes, though of course, everyone is different and everyone writes in a different way.

  1. Make the time. Most of us could have been doing different things that Friday, some of which important, but with writing, often one really has to make the time to make it happen, which sometimes involves some tough decisions and prioritising writing over all the other tasks on our to do lists.
  2. Set specific goals. It’s hard to asses progress if you are not quite sure what you are aiming for, so being specific always helps. How many words would you like to write, or are there particular sections of your writing project that you would like to finish before the day wraps up?
  3. Share your goals. Here comes the peer pressure and support again. Sharing your goals makes them more real, which can motivate you to really achieve them, and knowing that someone else is watching and knows what you are meant to achieve, can provide a dose of healthy pressure to write.
  4. Track progress and adjust your goals as you go. At our writing retreat, we had one hour writing sessions, followed by a break where we could reflect on how we are progressing with our goals. Things don’t always go to plan, some things are easier, others harder than anticipated, and that doesn’t mean you’ve failed. On the contrary, being able to accurately asses your progress and adjust your goals is a great skill to hone.
  5. Just write. We had a few rules for our writing retreat, which I think helped us all focus more on just writing. We had to do our reading and note taking in advance, so that during the writing retreat, we focused on just writing.
  6. No internet, no phones. Sometimes writing retreats are purposefully in places with no internet, so that you don’t get stuck answering emails and constantly having to restart your writing process. In our case, we were right in Edinburgh, so the internet was there, so it was up to us to decide whether or not we turn it off. But the peer pressure was there to not check one’s phones during the writing blocks.
  7. Save, back up. Make sure you save often and that your work is backed up – it would be a shame for all that writing to go to waste! Isla had a complete computer melt down in one writing session with her reference software, but she managed to get things back on track and rewrite that paragraph that got deleted!
  8. Reward yourself. Writing retreats are intense and it’s always nice to have a little reward at the end. The satisfaction of having done something you’ve been postponing for ages, a nice hot drink, a delicious meal with the jolly company of your lab mates.
  9. Follow up on your writing projects. Especially if you are the kind of writer that leaves a lot highlighted text saying things like “insert reference, add link, double-check this is true”. Setting aside a full day or more to pure writing is great and it can be really efficient, but it’s also important to remember your writing projects and to try making the time to work on them in between all our other daily tasks.

We all thought the writing retreat was great, we wrote a lot, and we’ve said we should have writing retreats more often, so here’s to a happy and productive 2018 and more writing!

By Gergana