As an environmental microbiologist with a biological
background I didn't think I would end up working in a geography department. In
fact thinking back to my childhood I never thought I would end up in academia,
or geography come to that - to be honest my only memories of geography from my
school days involved writing a news article on the Exxon Valdez oil spill and
drawing a cross section of the Earth! Having always been fascinated by animals,
I grew up wanting to work with them in some way or another (once my dad had
burst my bubble about a career in bricklaying not being like an episode of ‘Auf
Wiedersehen, Pet’!).
I got a place on a BSc Animal Behaviour and Science course
at Bishop Burton College in the East Riding of Yorkshire, which I thoroughly enjoyed. However, I found studying
animals less engaging than I expected and instead was drawn towards modules
assessing the impact of the environment on them. Developing my skills in this
environmental sector made me re-evaluate the direction of my career.
Anaerobic workout in the lab
Once I’d completed my degree I got a job working in a
microbiology laboratory testing a wide variety of samples ranging from fresh
food to environmental water samples. It was a demanding job with long
hours but it had its perks, such as free turkeys for the family at Christmas! After
a year of working there I’d managed to save up enough money to cover the fees
for a Masters degree. I joined the University of Hull Biological Sciences Department and spent a year assessing the effect of contaminated water on shore crab behaviour.
Thoroughly enjoying my year researching and writing I
decided the research route was for me, and that’s when I started looking for
PhDs. I picked up another microbiology role, similar to the previous one, while
I hunted for a PhD and after a few months of looking I found one back at Hull
based in Geography. The project investigated the ability of organic matter to
decompose within the drainage system in the City of Hull, in particular studying
the microbial community, and assessing if it could be increased in some way (outlined in my earlier blog post). Although
the project was out of my area, it was cross disciplinary with biology so with
a bit of extra background reading before starting, I was able to hit the ground
running.
Nice day for fieldwork at Winscar
After I completed my PhD, I commenced a six month research
position in the department where I was split between two environmental projects.
I'm now based in the School of Geography at the University of Leeds for the
next 13 months working in moorland management and hydrology. The project
enables me to expand my skill set within the environmental area, while allowing
me the opportunity to get my teeth into some research within the department,
which remains a great passion of mine. While I'm not sure if after this project’s
completion I will take my career into industry or remain within the academic
sector, I am excited by the opportunities for both that come my way.
This week is kind of quiet around the Department - the second years are away on their overseas field study weeks, along with just over half the academics, the first years have mostly gone home for a break (hopefully with plenty of reading to catch up on, since it is technically reading week for them) and the third years are working away on their dissertations. Watching the different teams get their equipment together and listening to students (and colleagues) swapping the usual "my trip will be more work/more fun/sunnier than your trip" banter reminded me again of just how varied our subject is. We study... well, pretty much anything that comes our way. Geographers don't just study the world, we poke our noses into every corner of the world of study. However, the field trips also point up things we have in common. The students are going overseas to experience places on their own terms, to try to observe objectively what happens, to compare it with what happens in other places, and then to understand something of why and how it happens, whether "it" is a piece of public art, a type of agriculture or a distinctive rock formation. Observation, then trying to understand what we see, then trying to explain that understanding to other people, lies at the heart of the business of being a geographer.
Stationery lust objects. I WANT THEM ALL.
Asked to write a post at short notice, I decided to write about some of the tools I use as a GEESologist, then realised that just the list would take up most of the post! So perhaps we can have a series, along with the "my story" series... we all have our favourite pieces of kit. I get that "ooooooo, Jane waaannnnttttt" reaction some women get at the sight of Jimmy Choos to a really well-made collapsible quadrat, to almost anything
in the latest Nikon microscopy catalogue or Van Walt field soil sampler
catalogue... and to a really decent notebook. Last week one of our colleagues arrived at the Departmental Meeting with a brand new Moleskine notebook - a rich red, A5 one. At least half a dozen people watched with varying degrees of envy as he removed the plastic, snapped back the elastic, and smoothed open that first all-important page. One of the nice things about working as a GEES-ologist is being around other people who share some quirks with me! As a youngster, I had a bit of an obsession with stationery, and would
regularly spend my pocket money on notebooks, pens, stickers and so on.
I especially liked notebooks, and often made my own by cutting scrap
paper to size, sewing a binding, making and decorating the cover...
Actually that should be in the present tense: I like notebooks. There
are about twenty empty notebooks of various kinds stashed in a drawer in
my house and another 30 or so around the office at work. Notebooks are
neat, and I like to know I'm not in danger of running out any
time soon. I'm clearly not alone: in searching for images for this
post, I came across a blog devoted to notebooks - oh dear, another procrastination location for me!
One essential supply item for the undergrad field trips is the issuing of the Field Notebook, a.k.a. Field Diary. This emphasised to me that, like all scientists, our most basic toolkit consists of our ability to observe what is actually there in the world, and to record our immediate observations for later consideration. I find myself frequently telling students that they need to have "something to write ON and something to write WITH" for classes, field trips, meetings etc. and the same is definitely true of the professional GEESologist, even if some are beginning to transfer these functions to a virtual electronic notebook.
A page from Lyell's 1840 field notes
a page from Darwin's field notebook
The notebook tradition is quite well established - the picture on the right is a page from Darwin's notebooks kept during the Voyage of the Beagle, and on the left a page from Lyell's 1840 notebook. Clearly the tradition of quick sketches and crossings out has a decent history! Darwin wrote:
'Let the collector's motto be, "Trust nothing to the memory;" for the
memory becomes a fickle guardian when one interesting object is
succeeded by another still more interesting.'
Technology, I'm pleased to say, HAS moved on a little - the mechanical pencil (removing the need for carrying a pencil sharpener in the field), the gel or cartridge pen (ink without the bottle!) and best of all the waterproof notebook all make it easier to take notes under field conditions - but observation, and the recording of observation, is still and always will be at the heart of the GEES-ologist's toolkit.
Whenever fieldwork is mentioned the first thing that comes
to my mind is long summer days walking in t-shirts by lakes or across fields (or
Hull council estates as most of my PhD sampling days were spent), maybe even in
an exotic location or an overseas field trip. However, it’s no secret this is
not always the case, especially in this field where outdoor working is a
necessity whatever the weather (much to my parents surprise who thought as soon
as the temperature dropped below t-shirt weather, it became slightly chilly or
the forecast suggests a bit of drizzle, it would be home time).
In fact I sit writing this having spent 6 hours trudging
across the Yorkshire Moors in freezing rain that came at you sideways (no
matter what direction you faced) and eating my soggy sarnies sheltering in a
gully trying not to fall into a patch of boggy bare peat. And it’s with the recent weather hitting the news, I thought I’d blog about the effects of weather on fieldwork, or
more so, how its put up with (I will try to avoid moaning where possible!).
These pictures were taken within 24 hours of each other
Starting my new job in September (working on a project assessing moorland management on water quality at the University of Leeds, meaning 3-4 field days a week) I was greeted with relatively
warm long days with beautiful views across the moors - which I wasn’t shy in
sharing, after all it beats the office wall! But this soon changed as winter reared its head. The
thing I found most interesting during field work as winter started to set in
was how everything changed so quickly and how I had to change how things were
done. The lack of daylight was the main issue - having to set off early to
squeeze as much daylight into your working day as possible, which is something you don't normally have to think about when you are heading into the office every day. Relatively dry
areas of land turned into huge boggy patches that would swallow your wellies
before you had a chance to work out which piece of heather you could reach to
drag yourself out. You never really find out what kind of land you are safe to
walk on / avoid until you’re shin deep in it – I find frosty/snowy days the
worst, as there will always be that one bog that has thawed a bit more than the
others you have walked across! A lot of the vegetation dies off, which in
theory isn’t a bad thing when walking along the flat, but when steep banks
become involved that’s when it is time to
be cautious as they become quite slippery. I generally approach these with a
foot slide or a bum slide, because let’s face it, I’m probably not going to be
spending much time on my feet!
Bleak view for four hours
Chilly day in the field wearing approximately 12 layers!
Due to the change in weather my bag seems to have doubled in weight. This is mainly due to extra batteries for the equipment (they aren't as keen on the weather either), extra clothes (in case I fall in a stream and need a spare pair or it gets too cold and I have to bulk up), a flask containing luke warm tea, extra food (obviously for the cold, and not to
cheer me up on bleak days) and extra water samples (with the weather being
wetter the streams run more, so I need to collect more to carry home). Gauging the weather forecast in remote areas is
always a difficult one. Finding the nearest town to your site seems like a good
idea at first, and can be quite uplifting when you are driving to your site, it might looks a bit misty and chilly but generally a decent field day. Until you got up
to the tops, turn that corner, and are greeted with snow / blizzards / hail / bears
(got to be prepared!). And to finish on my favourite: the waterproofs... They never
seem to be 100% dry and after going over a few stone walls they always seem to
leak in the worst place.
As much as bad weather can put a damper on fieldwork (no pun
intended) I still enjoy the variety it gives my job and the sunny days always outweigh the wet and the cold ones. Plus there are always others ways
to brighten up the wet and windy days where it’s impossible to stand upright
and even your waterproofs have given up, such as cake.
This week, we have a guest blog written by Jessica Keeble and Richard Caley who joined us this summer to gain some experience in what its like to do academic research and the highs and lows of lab work.
As two Geology with Geophysics students in between our
second and third years at the University of Leicester, we found ourselves with
a rather long summer break which needed to be filled. After spending 4 weeks in the field carrying out coursework we came to the Department of Geography, Environment and Earth Sciences at the
University of Hull to try and be helpful and learn one or two things! We were
very lucky to spend 5 weeks in the department and although there were times
where we could have cried (lab equipment can really try your patience
sometimes!), we had an absolutely fantastic time with lots of great photo
opportunities so we thought we would share our experiences (and funny pictures)
with you.
Rich
feeling very smart in his lab coat whilst filtering water samples
In the first two weeks of our work experience we learnt two
things: 1) there is a LOT of paperwork and introductions to be made before you
can even start being helpful; 2) sometimes being helpful means filtering a lot
of water… Yes, in the first couple of weeks we did filter a lot of water. This
was for Dr Karen Scott who is helping out on a project associated with The Deep (@TotEnvSimulator), which is looking at the effects of sediment concentrations on
sedimentation and erosion in fluvial environments. Filtering the samples
received from The Deep was quite a lengthy process, however, we did feel pretty
cool getting to wear lab coats and doing actual work (not just making cups of
tea/carrying out a lot of photocopying!). Filtering the water produced small
disks of sediment trapped on filter paper, which when collected together looked
more akin to a Dulux colour chart than a scientific experiment. Nonetheless, it
wasn’t just sample preparation we were involved with. No, we were then
introduced to the delights of the QICPIC machine.The QICPIC measures the size and sphericity
of the sediment grains and when it works, is a really neat piece of kit.
However, working with the QICPIC machine was one of those times were we could
have cried – it was very temperamental and there was a lot of stopping/starting
and cleaning equipment involved (we really sympathise with anyone who has to
use one of these machines for labwork/project work!).
"All hope is lost" - Jess contesting with the
latest tantrum the QICPIC is throwing
In between filtering water samples and testing our patience
with the QICPIC, we catalogued the extensive geological map collection the
department owns (and when we say extensive, we are talking about >2000
maps), and organised a section of the sample collection which had been locked away for
twenty-odd years. Admittedly, cataloguing the maps wasn’t the most exciting job
in the world but we did subject the department to some interesting music (along
with Jess’s rather out-of-tune renditions) so luckily the job didn’t take too
long! On the other hand, organising the sample collection was really enjoyable
and we unearthed some absolutely brilliant samples which gave rise to the
unfortunate picture of Jess below.
"Maybe Palaeo isn't so boring after all!" - Jess with one of her favourite samples from the collection
The main project we were involved in during our time in the
department was testing out a handheld-XRF machine to determine its suitability
for use in the field.This involved
getting up at an ungodly hour to collect the equipment and receive an induction at the Scarborough campus first, followed by many days of testing
samples. Firstly we tested manufacturer's standards to determine the accuracy of
the equipment, followed by testing our own standards and then some of Dr Williams and Dr Rogerson’s rock samples. Experiments included: rough vs.
smooth surfaces to determine whether the XRF could be used on weathered rocks
in the field; carrying out multiple tests on the same sample point to determine
accuracy and reliability of the XRF; and carrying out tests on multiple sites
on the same sample to determine how well the XRF deals with heterogeneity. Once
we had completed the experimental work, we then began the rather extensive task
of writing up our results (and to this day we are continuing to finish up the
report we started to create – don’t worry Becky, we’ll have it with you very
soon!)
The Handheld XRF kit - yes it does look just like a
supermarket scanner, but it can't check the prices of your groceries for you
We were incredibly lucky to have such an active role in the
work the department carries out and feel really privileged that, despite being
only Second years, we were trusted to carry out experimental work and our
opinions are truly taken into consideration! Despite the, at times hilarious,
low points (running a whole test cycle on the XRF when we had forgotten to even
add a rock sample; the QICPIC failing us for what felt like the hundredth time,
and dealing with rush hour traffic on a bus) we had an absolutely brilliant
time in the Department and gained a real insight to the life of an academic.
I'd like to add a huge thank you to Jess and Rich for their invaluable help in a number of research projects this summer.
Work experience in an academic department is an excellent way to add to a CV, gain skills outside of your degree programme and to trial what research is like if you're thinking of doing a PhD. If you would like some research work experience, get in touch!
Measuring
Rainfall by Chris Skinner (@cloudskinner)
Before I embarked upon my PhD research I had not paid
much attention to how we recorded rainfall. My previous experience, probably like
many people, came from my Primary School that had a small weather station in
the grounds, that consisted of a weather vane for measuring wind direction, and
a raingauge for recording the rainfall. It was nothing more than a small
bucket, which collected the rainfall and you recorded the level from the side
each day. If it was up to 4mm, you would record it as 4mm of rain having fallen
in the last day.
That was it, as far as my knowledge went, and as far as I
assumed it went in regards to recording rainfall for the weather forecasts. I
wasn’t wrong, the Met Office here in the UK do still make extensive use of raingauges
to observe rainfall. I will let Ralph James explain them to you –
However, as I soon learnt, raingauges only measure
rainfall at one stationary point. The little bucket I used at my Primary School
could tell me how much rain fell at the school, but it could not tell me how
much rain fell at my house, or how extensive that rainfall was. To fill in the
gaps, meteorologists use weather radars. Over to Biz Kyte –
Brilliant! There we have it then, measuring rainfall,
easy peasy. You just need a network of thousands of raingauges, enough radar
stations to cover your country and enough highly qualified engineers and
scientists to operate and maintain it all.
You won’t be surprised to hear that these conditions do
not extend to many areas of the world. Sub-Saharan Africa for example has not
had the resources and/or the political will to establish the infrastructure
required for timely, accurate rainfall observations, and this has implications
when trying to forecast floods, crop yields, droughts or water resources.
Obviously, being able to observe rainfall in realtime in this region would be
greatly beneficial, but the installation and maintenance of raingauge and radar
networks is just not currently feasible.
One way is to turn to satellite observations. Satellite
platforms carrying Passive Microwave (PM) sensors are the most accurate for
this role, with the instruments measuring the amount of microwave backscatter
from the Earth’s surface. As droplets of water scatter the microwave signal in
a distinctive way it is possible to directly observe where it is raining and
its relative intensity. But (there’s always a but), PM sensors have to be
placed in Low Earth Orbits (LEO) to operate, and therefore travel over the
planet’s surface, recording snap shots of the rainfall as it goes. To add to
problem, sandy ground scatters microwaves in a similar way to water, making
observations by PM satellites more difficult in arid regions, such as much of
sub-Saharan Africa.
Another way, such as that adopted by the TAMSAT team at the University of
Reading, is to use Thermal InfraRed (TIR) instruments mounted on geostationary
platforms. These satellites orbit at a distance that allows them to orbit at
the same speed as the Earth’s rotation, meaning they always observe the same
area of the planet’s surface - this is known as a geo-stationary orbit. TAMSAT
use a relationship called Cold Cloud Duration (CCD), where it is assumed that
if a cloud is cold enough, it will be raining, and the amount of time a cloud
is below that temperature will let the team calculate the rate of rainfall. It
is an indirect relationship, so it does not directly record the rainfall, but
it does provide an estimate that is accurate enough, and timely enough, to be
useful in forecasting seasonal crop yields or droughts.
Again, there is a but. TAMSAT produces ten-day
observations, useful for the above applications, but not very useful for flood
forecasting, for example, that requires realtime observations at atleast a
daily timestep. It is possible to use the CCD method for this, but the
observations are highly uncertain so require some complex statistics to be
properly used. This has led meteorologists to get creative.
Telecommunications are taking off in sub-Saharan Africa,
with mobile phones spreading fast. Professor Hagit Messer, of the University of Tel Aviv, suggested that
interference of signals sent between antennas by rainfall could be used to
measure the rainfall rate between the antennas. Over a whole network of
telecommunication antennae the spatial spread of rainfall and its intensity
could be built up, evolving over time. This form of rainfall observation could
be used to dramatically improve the spatial and temporal coverage over
sub-Saharan Africa, with little need for additional investment.
And again, there is a but. Whether it is observation by
radar, satellite or telecommunication networks, the instruments can only record
where it is raining, when it is raining, and the relative intensity of the
rainfall. That relative intensity needs calibrating, bringing scientists full
circle back to the humble raingauge. There are raingauges in sub-Saharan
Africa, but not a lot of them. The study area I researched had one gauge per
7,000km^2, enough to cover the whole of the UK with just 27 raingauges, and of
course these weren’t evenly spread, concentrated along rivers and in towns,
leaving large areas relatively uncovered.
They can also be poorly maintained and not all raingauges record all of
the time.
There are some good stories about raingauges in Africa. A
couple I have heard from the TAMSAT team are of one gauge that recorded no
rainfall at night, even during the wet season. When investigated it was found
the locals looking after the gauge were storing inside so it wouldn’t be
stolen. Another gauge was consistently recording a light drizzle – this was
caused by people hanging wet clothes on it to dry. We have similar issues in
the UK, with one organisation who should know better placing a gauge on their
roof next to an air conditioning vent that blew rainfall away from it.
One project that I am excited about is TAHMO. The project team
have the highly ambitious objective of dramatically increasing the raingauge
coverage (as well as coverage of other meteorological instruments), for
sub-Saharan Africa by mass producing a cheap, self-contained weather station
and distributing them to schools. One of the most significant outputs to date was
the creation of a low cost acoustic disdrometer, that uses the vibrations of falling
raindrops to measure rainfall rates and reports the readings automatically
using mobile phone technology. For me, this is the great hope of rainfall
observation for poorly gauged regions and really hope they can pull it off. For
now, I’ll leave you with Rolf Hut discussing TAHMO, acoustic disdrometers and tinkering.
The formal presentation of research in academia is pretty
traditional. I doubt it has changed much in the last 500 years, if not longer,
and for a progressive sector of society it really does not look set to change.
Basically, you get your results, write it up as a paper, some experts look it
over and request more details or changes, you do them, they pass it, you get
published.
The published article then goes into a journal. Most of
these are still printed but are available, usually as a PDF file,
electronically. This is where the embrace with the modern world ends. I mainly
read articles either on my computer or my tablet – most articles are formatted
into two columns on a page which makes it very awkward to read off a screen. So
optimisation for electronic presentation is not high on publishers’ agendas it
would seem.
But are we missing out? A magazine I have been reading
since I picked up my first copy in October 1993 has changed many times in the
last two decades. It isn’t a science publication but is related to a hobby of
mine, and last year they started publishing a version of the magazine optimised
for the iPad. They could have just bunged out a PDF of the paper copy, but they
knew that the new technology provided them with a platform to support more
content. In place of a photo there is an interactive 360ยบ image, instead of a
price list for new products there are hotlinks direct to their entry on the
online store, plus there’s additional videos, interviews and zoom panels. If
the magazine contains typos or erroneous details, it is automatically updated.
The company have started rolling out this idea to their other printed
materials.
What if these ideas were used in academia? What sort of
content could we include? The most immediate thing that springs to my mind is
animations. I produce tonnes of them, and conference presentations aside, they
rarely get seen outside of my research group. Why do I make them? Because they
are useful for very clearly showing how systems work, if your model is
operating how it should or demonstrating patterns in data - (*Thanks to @volcanologist for pointing out that animations can sometimes be submitted, and hosted on a publisher's website).
Take for example some work I have been doing on historic
bathymetry data from the Humber estuary. Bathymetry data are readings of water depth at the same tide level, and I use the data to create maps that show the shape and elevation (heights) of the bottom of the estuary. To find out more about what estuaries are, take a look at Sally's previous blog. Provided by ABPMer, the data spans a
period between 1851 and 2003 – I processed the data, calculated rates of
elevation change between each sampling period, and from this produced yearly
elevation maps. By putting these together as an animation I could see the
evolution of the data (it is important here to stress the difference between
‘data’ and reality - not all areas of the estuary were sampled by each survey, and the number and locations of reading varied. Much of the change seen in the video is because of this and not because the Humber has actually, physically, changed in that way).
What immediately struck me was the contrast between the
middle and the inner estuary. The middle estuary is the part between the Humber
Bridge and the sea, where the estuary’s course deviates southwards – it is
remarkably stable over the 150 or so years. The inner estuary, from the Bridge
towards Goole, sees lots of internal changes – driven by interactions between
the river inputs and the tides – but overall very little change. The Mouth of
the Humber, the part closest to the sea, looks to see little overall change,
but most of the variations seen in the animation are due to differences in
sampling point in the data, and not actual changes. Similarly, changes around
the banks of the estuary observed in the animation are most likely caused by
sampling difference in the surveys, rather than actual elevation changes.
I have recently been continuing work on adapting a
landscape evolution model, Caesar-Lisflood, to model the Humber estuary, and a
big step towards this is to accurately model the tides as they are observed by
tidal stations recording water depths. Numerically we can do this, but it is important to check that
the model is representing the tides in a realistic way - this is a very important step in making a model as it has to be able to accurately simulate observed behaviours before you can experiment with them. Again, animations are a
really useful tool for doing this.
The video above shows the variations of water depth
throughout several tidal cycles, as modelled, with light blues as shallow and
dark purple as deep water. The model changes the depth of the water at the right hand edge in line with water depth data recorded from the Spurn Point tidal station near there. The water then 'flows' from there, down the length of the estuary as the depth increases, and vice versa - this simulates the tides going in and out. From this I can tell that the model is operating
well, as the tide is advancing (coming in/going up/getting deeper) and receding (going out/down/shallower) as expected, throughout the whole
region and not just at the points where the tidal stations are located. You'll notice that the early part of the animation shows the estuary filling up with water - this is part of something called 'spin-up', where you let the model run for a period of time to get the conditions right before you start the modelling. In this case it is a 'day' as the water levels gradually builds, filling the estuary.
Another check would be the velocity of the flow as the
tide floods and ebbs - this is the speed with which the water is moving (both in or out). The velocity should increase as the tide advances or recedes,
but slack water (where the water is hardly moving at all) should be observed at high and low
waters. If the model is working as expected, the area of slack water should
progress from the sea and up the estuary towards Goole. From the video below,
this is seen to be the case. Light blue shows low flow speeds, and darker
purples higher flow speeds. The video shows the same modelling procedure as the previous video.
This type of content is really useful to me as a
modeller. It is also really useful for presentations as I can show a group of
people something that takes a few seconds, yet would probably take a lot of
slides and quite a bit of explaining. If academic publications were to begin to
include enhanced content in peer-reviewed publications, I believe this could
advance the communication of research, not only to other researchers but also
to the wider public. For now, Blogs, like the GEES-ology one here, are the best
outlet. I hope you enjoyed the animations!
