Wednesday, 30 October 2013

What's 'appening' with DE:FT

By @deftfood

Progress so far 
Now that we are six months into the project we thought it was time we let you all know how things are progressing. We have prototypes of three apps - FoodCloud, ShopStamp and Gradeback - which are on our website as power point slides.  For those who left comments on the forum page of the website, many thanks!  Any further comments would be most welcome too! We have also designed a questionnaire survey, which is looking at shopping habits and technology.  Again please feel free to complete it.  There is also the chance of winning some Amazon vouchers for those who do.

Following on from some of the feedback we have received we have slightly modified the FoodCloud prototype, removing the quiz and simplifying some of the links that we had built into it.  Just to recap, the idea behind FoodCloud was to develop an app which would show people how they were ‘surrounded by food’ so, for example, what was growing in the fields, how food was moving all around them, the routes it was taking and the outlets available to them.
Progress to date 
David Grey from Computer Science at the University of Hull is one of the co-investigators on the project and he has been busy turning our paper prototype of FoodCloud into a working app.  The app has, of all things, a ‘back end’, which can be found at so please have a look at it and tell us what you think. The link will take you straight to the log in page and once logged in it is then possible to input descriptions of what the fields are used for using the fields tab.  David has built in a link to ‘MyFarm’ so that anyone who logs in as a farmer can locate their farm using the map which will be displayed, zoom into their fields and label them accordingly as well as providing a brief description of their farm and any farm gate sales they offer.  It’s amazing what a campus can be used for as in order to test how well the ‘back end’ works we have turned the Hull site into a virtual arable farm. The Cohen building was a field of wheat which has been harvested and will be made into biscuits.
Opening up the app 
This information is stored in the ‘back end’ of the app and when the app is opened up it uses GPS to locate any fields that have been added to the ‘back end’ data base.  
Image of smartphone screen and field ‘flags’
Once the fields are located a small ‘flag’ appears on the phone screen (see image above),and by touching the ‘flag’ labelled, wheat, for example, an image of a wheat plant will appear together with the information that was loaded onto the ‘back end’.  We now have a working prototype which is exciting which we can take out ‘into the wild’ and demonstrate to people something we have just started to do and if anyone else would like to see the app working please get in touch at  Any feedback is invaluable and will help us in making the app more responsive to the needs of user groups.
Next steps.
At present we are in the process of trying to develop extra ‘layers’ to ‘FoodCloud’ so that it can be used to make the link between food and sites of historical interest. We have also been thinking about a broader ‘FoodCrowd’ concept which would involve children, for instance collecting and inputting data on their local area thus learning about their localities and how they are surrounded by food.

Wednesday, 23 October 2013

The Hot Potato: Starch, Thermal Adaptation and Enzymes

By Karen Scott (@DrKarenScott)

When the word geography is mentioned, microbiology is not always the first thought, however this was probably the main focus throughout my PhD studies. Being able to understand the microbiology of the environment can greatly assist in putting together the bigger picture, especially where sustainable organic waste management practises are concerned, as they rely ultimately on understanding the mechanisms that control organic matter decay.

This study builds upon my earlier findings on gully pot waste degradation and enzyme activity (see my previous blog) assessing the effect of starch on degradation rate and enzyme activity (α- and β-glucosidase) under mesophilic (moderate temperature typically between 20 and 45 °C) and thermophilic (relatively high temperature between 45 and 122 °C) conditions. A key focus was to assess how the enzymes potentially adapt to different temperature regimes to assist in understanding whether the effect observed was an acclimatisation effect, or it is in fact a true temperature effect that is a result of the composting process. This reciprocal design measured the differences between increased or decreased assay temperatures compared to the temperatures the waste was composted at. The enzyme activity was measured to assess the degradation dynamicsThe experiment took place over a 6 week period where mesocosms (a mix of water and sieved gully waste) were incubated under mesophilic (30ºC) and thermophilic (50ºC) conditions, a starch additive was added to half of these mesocosms.

The messy job - mixing the slurry ready for the experiment
This study confirmed previous findings showing that the waste was able to decompose under both sets of temperature conditions. Interestingly though, the losses observed were similar throughout, indicating the losses were temperature independent, which appears to contradict the general literature, where temperature has been shown to be a main controlling factor during composting. However, many other studies have indicated that temperature is not necessarily the driving force in every situation.

The results for the enzyme activity did not follow the same suit, showing greater activity in those that had the starch addition, confirming that a starch addition significantly increases the activity of both α- and β-glucosidase, albeit weakly for the β-glucosidase. Whilst β-glucosidase activity is on average higher with the higher assay temperatures, this was not statistically significant in this instance, indicating neither in situ temperature or assay temperature are significant explanatory variables. However, the effect of increased activity of β-glucosidase with increasing temperature is consistent with previous results. Interestingly, the interactive effect of assay and in situ temperature on α-glucosidase activity is weakly significant which would be indicative of an adaptive effect of temperature on the enzymes responsible for this activity. 

The mean activity for b- and a-glucosidase over the sampling period. the labels for each bar shows the in situ temperature followed by the assay temperature.
Similar results were obtained when α-glucosidase activity was investigated with the starch amended samples only. Therefore, the data for α-glucosidase assay provides evidence for thermal adaptation in this environmental system. The results presented here would be consistent with α-glucosidase being under selection (in an evolutionary context). Whilst α-glucosidase activity is on average twice as high when assayed at 50ºC than 30ºC for the 50ºC starch amended samples, it is only 20% higher when assayed at 30ºC as compared with 50ºC for the 30ºC starch amended samples. Therefore it appears that as enzymes become adaptive to increasingly high temperatures, they become increasingly less adaptive at lower temperatures.

This study demonstrates a positive association between enzyme activity and its putative substrate (starch) and also the effect of temperature appears to have an adaptive selective influence on enzyme activity. Examining these temperature variables provided a better understanding of the processes occurring and displaying the wastes ability to decompose, to a degree, under conditions similar to those that it would be subjected to if using ex situ management system. Whilst complete agreement between enzyme activity and in situ degradation was not observed, it does leave scope for more investigation into enzyme parameters which could potentially shed more light on these issues.

The paper which this blog was based on can be found here

Adams, J. D. W. and Scott, K. M. (2013). Enzymatic analyses demonstrate thermal adaptation of α-glucosidase activity in starch amended gully waste. Bioresource Technology 127(0): 231-235.

Wednesday, 16 October 2013

Conferences from the inside

by: Drs M. Jane Bunting and Michelle Farrell

Between August 5th and 9th, we were the hosts and organisers for a small conference with associated workshops (small = 35 people on the busiest day).  Organising a conference makes the experience of being at the event quite different - for a start, some days you don't even get close enough to the coffee table at break to grab a biscuit!

The meeting was supported by the Crackles Bequest Project, which pays Michelle's salary at the moment.  The goals of the conference are described here.  We'll write more about the research later as we get final results and work on the papers; this blog post is about the experience of organising a small conference.

The process began in January when we sent out emails checking the availability of our project partners (a wonderful group of people who provided all sorts of support for fieldwork in different parts of Europe, arranging permits, translating, bringing their students and colleagues along to help our team with the actual work, and being enthusiastic about what we are trying to do, which really helps when you're half-way up a mountain in the driving rain or crawling around in a haymeadow in thirty degree heat trying to identify a lot of very small green leaves, which does tend to start you wondering why this ever seemed like a good idea). We then set the dates so that as many of these people as possible could come, and began to plan in earnest.

The 'who can come when' spreadsheet was just the first of many.  We had to work out how much to charge for registration at the meeting, to cover printing abstract volumes and lecture handouts, provide copies of software and pens, and of course the all-important regular infusions of caffeine (and biscuits) to keep everyone alert.  We got quotes for a conference dinner and developed teaching plans for the workshops.  We booked rooms on campus, contacted the local conference bureau to get their help with negotiating some cheap rates with local hotels, and put together an advertisement to send out to the pollen-counting community via various mailing lists.  We even had lists of the lists we needed to make!

Although it felt like we did a lot of planning in advance, and the deadlines for booking to attend the conference and to get the hotel rates were relatively early on the 31st of May (over two months before), the week before the event ended up being manic.  I really should be used to that by now, but it always takes me by surprise.

Michelle demonstrates field methods in a field
We had fun stuff to do, for example sitting down with the menus from the campus catering service and choosing the options for the lunches (why yes, there WAS a chocolate option on the sweet platter every day, and twice it was brownies).  Michelle had a never-ending stream of emails - the pricing policies of the UK's railway system are baffling at the best of times, but trying to help someone travelling from abroad to find the best value ticket makes you question the sanity of the person who came up with it (or maybe they were just feeling particularly misanthropic that day?), and advising people who come from locations with very predictable weather on the possible conditions during the field day ("honestly, it could be pretty much anything, although snow is unlikely") reminds us that our normal is not anyone elses.  Friday afternoon found us settled in the committee room in our building with piles and piles of paper all over the big tables, assembling the handouts for the workshops - I got a bruise on the palm of one hand from banging the hole-puncher (yes, I should have done smaller wodges of paper, but then I'd not have got home before midnight) and Michelle stuck name labels on folders, assembled badges, and cut out individual slips of paper showing the menu choices for the conference dinner (we decided that would be easier than taking the spreadsheet to the venue or hoping people would remember what they'd chosen).  We moved furniture and put up signs pointing to the various rooms being used, and finally got to go home.

Attendees in the quad
I remember how hot the computer room got during afternoon practicals, an Indian attendee huddled in a coat after the dinner while the rest of us enjoyed the cool of the evening (it was about 18oC by my car's temperature gauge - pretty cold if you come from the tropics I guess), some fabulous pictures of landscapes in a presentation about new work beginning in South Africa and some lovely data from more advanced projects, talking about science until my throat ached (and if you know me that's a LOT of talking) and a lot of laughing.  So here are a few pictures:

Before a session starts (in the earth science lab)

A summer's evening in the Hull docks area

As usual for conferences, people began to travel home at different points on Thursday, and by Friday afternoon only those who'd both stayed for the last workshop and had further to travel were still around.  We decided to meet up at a pub in Hull's docklands, where people could have fish and chips for supper if they wanted - obviously pub fish and chips are not as good as those purchased from a van (or shop in obscure location, depending on your particular favourite) and eaten out of paper, but they do come with beer.  Sitting around a table talking, teasing and gossiping like a group of old friends even though we'd mostly been strangers at the start of the week really brought home one of the benefits of this job to me - meeting other people who share the same strange interests and curiosity about how the physical world works, and having them become friends as well as colleagues.

Organising this meeting was a huge amount of work - I think we've finally dealt with the last of the expenses claims and bits of paperwork, and can sign off on the last spreadsheet, now it's October.  However, it is also very rewarding - all the intellectual stimulation of a conference PLUS you still get to sleep in your own bed, and don't have to put your pets in kennels.  But maybe we can all go to India or South Africa next time?

Wednesday, 9 October 2013

Iceland: a geographer’s paradise

I recently co-led a 7-day undergraduate field trip to south-western Iceland.  This was my first visit to the country so I was really excited to see the land of fire and ice that I had heard so much about!  One of my motivations for becoming a geographer is my love of the outdoors, thirst for exploration and knowledge of new places and environments, so the field trip element of physical geography has therefore always held a huge appeal for me.  And to date my career has taken me to some amazing places - both within the UK and further afield.  So not surprisingly when I was approached to take part in the student field trip to Iceland, I jumped at the opportunity!

Iceland is a fascinating country - it lies between two continental plates, the Eurasian and the North American, that are constantly pulling away from each other.  The rift valley that this is creating is one of only two places in the world that you can see this happening on the Earth’s surface, the other being the Great Rift Valley of Eastern Africa. You can literally walk between, and next to,  the edge of actual continental plates and on some of the ‘youngest’ crustal surface on the planet.  This geographical rarity alone is reason to visit Iceland but this incredible place has much more has to offer!

Þingvellir: the rift valley in Iceland where the Eurasian and North American continental plates are pulling apart. The photos are showing the edge of the North American plate, with the lower photo looking out over the rift valley towards the Eurasian plate.

Iceland is also located over a hotspot (see the previous blog post by @volcanologist  for more information on hotspots), which is thought to have originally formed the island. This and the rift valley mean that Iceland is tectonically active, as you drive around, the horizon is littered with spectacular volcanoes and relict lava flows are dotted across the landscape.

The volcanic scenery in Iceland: the snow-capped summit of the volcano Hekla, the basalt cliffs at Vik formed from 3 distinct lava flows lying on top of one another, and the lava field from the 1783 Laki eruption (from left to right).

Not only do the volcanoes and related features provide a stunning backdrop, they are of interest to geologists to better understand how and why they erupt and what this means in relation to the inner workings of the Earth.  The rich history of Icelandic volcanic eruptions also provides a fantastic resource for geographers trying to understand the surface processes.  Each eruption deposits a layer of tephra across the ground in affected areas, these are then reburied by subsequent layers of soil through time. The composition, thickness and biota in these layers can tell us a lot about the environmental conditions occurring at the time of deposition (for example we can use the pollen as explained by @DrM_Farrell in one of her earlier blog posts).  The date of  these volcanic eruptions is well documented and, as each eruption has a unique signature, we can identify the date of the tephra layers and as such you can constrain the time periods of the other soil layers using a technique called stratigraphy.  This method has been used to better understand the influence that humans have had on the landscape since settlement in the 9th century, the impact of deforestation and the effect of changing climate on soil formation and erosion.

A soil profile showing the distinctive black tephra layer at the top of the photo.

My main research area is the fluvial environment, so I was really excited to see the amazing braided rivers and waterfalls that Iceland had to offer, and I wasn’t disappointed! The scale of these are far greater than any in the UK and it was amazing to see them.  Below are some photos giving examples of some of the fluvial features we visited. The top row gives some examples from the many impressive waterfalls there are along the southern coast of Iceland. From left to right, these are Gullfoss (translated as Golden Falls), Hjálparfoss (Help Falls) and Skógafoss (Forest Falls). On the bottom row are images of some of the rivers, at either end are examples of braided river systems from the Þórsmörk valley into which the Eyjafjallajökull glacier (sitting on the slopes of the volcano that created havoc to European air space in 2010) drains. The high sediment load in the area creates these fantastic braided channels in the river systems. The middle picture on the bottom row shows the River Skeidará , the different colours represent the merging of water from two different sources, glacially fed water that has a heavy sediment load and fluvial (clearer) water.

As well as flowing water, as you can imagine Iceland also has plenty of frozen water and there are numerous glaciers and ice caps. The northerly location of Iceland -65° latitude mean that winters are cold and dark.   These cold conditions promote glacier formation.  On the field trip we investigated the geomorphological evidence for the retreat of the Skaftafell glacier which included a hike on the glacier ice of the Sólheimajökull glacier to measure the impact of debris cover on the glacier surface.  It was a great thrill for the students to get up close and personal with a real glacier.

Looking up the Skaftafell glacier from its terminus (left image), the glacier walk on the Sólheimajökull glacier (2 right hand images).

Field trips typically consist of long days in the field followed by long nights analysing the data with the students, so although the trip was hard work it certainly didn’t in any way detract from the awe of the place.  Iceland presents a fantastic opportunity to investigate a variety of geological and geographical processes and landforms, and experience incredible scenery.  As an added bonus I was also treated to my first ever viewing of the Northern Lights, as well an Arctic fox up close!

Arctic Fox

So overall I found my field trip to Iceland both exhilarating and exhausting, and I would wholeheartedly recommend Iceland as well worth a visit for anyone.  I’m certainly planning to go back for my own research so watch this space for updates…