Hello and welcome to my blog! My name is Caroline and I am a PhD student at the University of Sheffield. My research project focuses on Striga - a genus of parasitic plants that devastates harvests by infecting food crops. I am exploring the defence reactions that can make host plants more resistant against Striga. Due to my ongoing battles with anorexia, I haven't made as much progress as I would have liked but I am determined to finish the course.

This blog charts the ups and downs of life in the lab, plus my dreams to become a science communicator and forays into public engagement and science policy....all while trying to keep my mental and physical health intact. Along the way, I'll also be sharing new plant science stories, and profiles of some of the researchers who inspire me on this journey. So whether you have a fascination for plants, are curious about what science research involves, or just wonder what exactly I do all day, read on - I hope you find it entertaining!

Thursday 22 October 2015

Meeting a marvellous woman in science....Professor Sunetra Gupta on thetrials of physics, translating poems, the politics of science and more!

Sunetra Gupta, Professor of Theoretical Epidemiology at Oxford University, is renowned for her research studying the evolution of infectious diseases, such as influenza and HIV. In 2009, the Royal Society recognised her as a pioneering woman of science by granting her the prestigious Rosalind Franklin Award. Besides forging this stellar career in science however, Sunetra is also an accomplished novelist with her works attracting various accolades including being longlisted for the Orange Prize. To top it all, she is a passionate scientific communicator and frequently appears on the media to discuss the links between science and the arts. This week, the University of Sheffield was honoured to host her as a visiting speaker for the Departmental Series and a Q & A to discuss everything from her own career, the politics of science/literature and how science is taught in schools. 

What inspired you to take up a career in science?
When I was trying to choose what to do with my life, I didn’t really know because I found everything so interesting. I was fascinated by biology but also loved physics and I originally enrolled at Princeton University as a Physics major. But then I realised three things: Number One, that it was extremely hard.  Number Two, I would be spending most Fridays tackling problems that often had no solutions and we were rewarded for how far we got! Number Three, I had started to find advanced physics less exciting. What I really enjoyed was using mathematics to solve problems. A key moment was when I took a course on Animal Behaviour and I realised that we could use mathematics to study biological systems. Since then, I have never looked back. 

Professor Sunetra Gupta (Photo credit: Charlie Lee Potter)

Science and mathematics have a very technical language, yet you are also a novelist. Do you find that these occupations help each other in any way?

I like to think that both are manifestations of a creative urge and a desire to understand some form of reality – whether that is a physical reality or an internal reality. And in both cases, understanding comes through playing and experimenting. When building scientific models, playing comes by applying precise algorithms, like playing a game with very strict rules. Novels, on the other hand, try to push the boundaries of language but there are other rules that they have to abide by, such as narrative. I get great satisfaction when I feel I have understood something. In science, this is more concrete and, in my field, it essentially takes the form of generating a testable hypothesis. It is more difficult to tell in literature when you have understood something, but I feel happy when I create something with an internal consistency. 

You have also translated poetry. Does this consideration of language help you when writing novels and generating scientific hypotheses?
Translation – whether poetry or not – makes you aware of the gap between what is actually there and what you are doing. Mathematical modelling is based on a similar principle. You often can’t replicate the situation exactly, but you want to have an insight to understand it. When I translate poetry, there is sometimes such a gulf between the original words and what I write that I feel overwhelmed. In these cases, rather than directly translating the text, I feel that I have interpreted the poem, made a new poem in some senses. It makes me aware that science is not about replicating something exactly through experiments but finding a new, valuable insight into what is there. 

As a woman, do you find that you get different receptions as a novelist and a scientist?
In neither case have I felt discriminated against for being a woman but I have felt that both areas are very male dominated. What is really beleaguering the sciences and arts in general is their “clubbiness” – little groups that help and support each other but exclude others.  Also, it seems very important now for both scientists and authors to have a public presence and remain visible and this can really militate against women who often have other things on in their life. It is a complex combination of being visible, being networked and gender bias that has created this situation. 

You are a passionate advocate of science communication. Do you think that there should be more creativity in how science is taught in schools?
I think written exams are really very 19th century. Perhaps they were quite good for identifying who would do well in the Indian Civil Service, but they don’t make sense to me now. I enjoy outputs where you can be creative, enjoy the process and have a really enriching experience. Exams just cause so much stress. On top of this, at Oxford, the undergraduates actually have to dress in a very uncomfortable formal outfit to take exams…

If it was up to me, I would give the students a bunch of papers and a set of questions then see if they can read them in three hours and write something interesting,. This would be more challenging and it does still require that you know something, but at a more conceptual level. Another thing wrong with the current educational system is that it is not “strategic” to take courses in areas that you are not so good at. Yes, part of society is about badging people and finding out what they can do well, but education should also be about understanding things that you find difficult. 

With the money she was awarded as part of the Rosalind Franklin Award, Sunetra has been working on an exciting new website that creatively tells the stories of a fascinating collection of women scientists from history who deserve to be more widely known. The website has just gone live – do take a visit and meet these “Shooting Stars” from the past!

Saturday 17 October 2015

Getting ready for a big night...

Do you remember way back in April, I visited Westfield School as part of a Departmental outreach initiative called the Krebs Fest? This event, taking place across the whole of November, celebrates the life and work of Sir Hans Krebs, a researcher at the University of Sheffield who received the Noble Prize in Physiology and Medicine in 1953. This was awarded for his discovery of the citric acid cycle ( now named the 'Kreb's Cycle' after him), one of the key, fundamental processes that liberates energy from food in every cell. The University has really gone to town with the celebrations including public lectures from Noble Prize winning scientists, interactive exhibits and art installations ( including giant inflatable microbes in the Winter Gardens in the city centre - see below!). One of the showcase events will be a film-festival where local schools will present homemade mini-videos on a scientific topic based on the theme 'hidden worlds'. 
A giant E.coli, 28 m long and 5 million times larger than life.....if a scale model of a person stood next to it, they would be 9,000 km tall!

Which is where I come in. To inspire the schools in their search for a suitable theme, the Unviersity linked each school to PhD students who would go in and describe their own research. I paired up with Carly who researches nematode worms which infect Asian elephants, so we decided to do a joint 'Parasite' theme. Last April, we went in with chief animator Steve Poole to talk to the year 8/9 STEM club ( Science, Technology, Engineering and Maths) and we had great fun showing them some of my infected plants and Carly's box of elephant poo ( although we didn't get it out due to health and safety...).
At the entrance to Westfield School

Anyway, the long summer break now over, it was time to see what they had come up with. Not surprisingly, kids find elephants more interesting than plants and the pupils had decided to base their film on Carly's research. I don't take it personally though - I'm used to plants being left out of the limelight! Nevertheless, they had put together an impressive animation showing the lifecycle of the parasites and how they make elephants ill. Especially good seeing that it was produced during lunch breaks!

 It was brilliant to see how the students had really got to grips with the project and were taking the science seriously. At one point, Steve suggested that they could animate a parasitic worm so it flew up the elephant's bottom. One of the pupils immediately pointed out that it wouldn't be scientifically accurate - the elephants ingest the parasite from contaminated plant material, so it goes in through the other end! The students were also keen to run through the introduction they would give on the night, explaining why they chose the theme of parasites, how they made the video and what they learned from the  project.  
Steve the animator at work

I'm looking forward to the Celebration Night when the presentation will be projected on a colosall scale on the walls of Firth Court, along with the other entries. Keep your fingers crossed that we win the prize for most imaginative presentation! 

Tuesday 6 October 2015

Counting Stars, not parasites for once!

Photo courtesy of GlaxyZoo.

There are times in my PhD when  I feel overwhelmed by the amount of data I have to process on my own....although compared to some scientific disciplines, I have got off reasonably lightly! At the Gatsby Annual Network Meeting, Chris Lintott, Professor of Astrophysics at Oxford University, Introduced us to one solution - take to the web and recruit an army of virtual helpers!

"The problem of having too much data is now present across all the sciences but astronomy got there slightly earlier" Chris began. Most famous for presenting the BBC series The Sky at Night, Chris has spent his research career investigating whether there is an underlying structure to the universe. "In some parts of the universe, there is a lot of stuff and in others, not so much" he said. "It may seem random but there does seem to be some sort of honeycomb-like structure to it all..." One way to test this is to look at the shape ( or 'morphology' if you want a more technical term!) of galaxies as "the shape of a galaxy can show us the interactions that formed it - like an integrated history of 30 billion years".

In the early days, when the most modern telescopes could only photograph so many galaxies at a time, the Professors themselves would study these images. In the 1980s, technology improved so that thousands of galaxies could be captured at once, so the job was passed onto PhD students, the traditional 'willing workhorse' of the lab. But now up to millions of galaxies can be imaged and the field has hit a data processing wall.  You might ask, surely the minds that built these telescopes and satellites could work out a way to automate the process? Unfortunately not. "The job involves recognising fuzzy patterns and you just cannot teach this to a machine with 99% accuracy" said Chris. But PhD students can only do so much (and I should know!). Chris cited the example of Kevin who managed 50,000 galaxies in a week before "telling us where to stuff it". After  bribing Kevin with beer and begging the Vice-Chancellor for more PhD students both failed Chris knew he needed a radically new solution. 
Professor Christ Lintott in action! (Photo - Chris Lintott)

And so in 2007, GalaxyZoo was born. The idea was that interested members of the public who wanted to do their bit for science could sign up, classify a few galaxies in their lunch break and so help Chris and his colleagues work their way through the mountain of images. Although their expectations were low, within a day of launching the website had rocketed its way to the top of the BBC NEWS story board ( just pipped to the first post by 'Man flies to wedding a year early...'). Chris and his colleagues could hardly believe it - people actually wanted to get involved and help! "We were soon doing a Kevin-weeks' worth of classifications in an hour!" he said. The researchers realised that they had created a "distributed supercomputer" - albeit one with opinions and which volunteered it's time in unpredictable ways. In addition, they realised that this collective approach significantly improved accuracy; after all, if 7 out of 10 people think a galaxy has a sprial shape, the estimate of confidence is greater than a single person's verdict. 

Another advantage of using people rather than machines soon became apparent. Whilst computers can only look for what you tell them to, "people can become distracted by the unusual". Perhaps the most famous example of this is Hanny's Voorwerp, a rare astronomical phenomenon spotted by Dutch school teacher Hanny van Arkel. After noticing a strange green 'blob' on one of the GalaxyZoo photographs, she mentioned it on the website's discussion forum, where it caught Chris's attention. "Everyone was referring to it as a 'Voorwerp', which we thought was a very technical term, so we used it too" said Chris. "But it turns out it actually just means 'thingy' in Dutch". It also turned out that the blob in question was a 'quasar ionisation echo', where a powerful emission of light triggers star formation. In short, the astronomical world was delighted, Hanny became famous and GalaxyZoo participants rushed to be the next to put their name to a new Voorwerp.
Very pretty data.... (Photo courtesy of Galaxy Zoo)

This might be helping the researchers to solve the riddles of the universe but now there was a new mystery: why exactly did ordinary people feel compelled to spend time sorting through photographs of galaxies? Surprisingly, when GalaxyZoo participants were surveyed, only 12.4% gave an interest in astronomy as a reason. By far, the most powerful incentive was a genuine desire to contribute to science. "There is clearly nothing magical about galaxy morphology itself" said David. "Rather, this was something that anyone could do in their lunch break to feel useful". 

This suggested that similar online projects on different topics could also be a success. And so, in December 2009, Chris helped to launch Zooniverse, a general platform for 'poor sod' projects ( as in ' Which poor sod is going to have to sort through all this data on their own?'). Since then, this repository has only grown and grown - now you can count penguins, spot wildlife in the Serengeti, identify rare orchids and help sort through the archives of the Natural History Museum to name but a few. These online interfaces are also being put to uses beyond curiosity-led research : during the disaster relief efforts following the Nepal earthquake, online volunteers helped to spot affected villages on aerial photographs that were missing from official maps. Meanwhile, biodiversity surveys are already demonstrating the impacts of climate change, including documenting plants that are now flowering up to 10 days earlier. 
But what SHAPE is it?! (Photo courtesy of Galaxy Zoo)

But won't people eventually get fed up with looking at galaxy photographs? ( even the hardcore devotees that have clocked up a million galaxies so far?) And surely the growing choice of projects will mean that fewer people will participate in each of them?  Possibly, but Chris is already using the data generated from GalaxyZoo to preempt loss of interest. "These projects are themselves fascinating studies of human behaviour" Chris said. "We can now model with 70% accuracy a person's drop out rate within the next five galaxies". Hence, at the critical moment, the participant is automatically sent a grateful email, reminding them of their valuable contribution and to encourage them to keep going! Some projects try a 'gamification' approach, including the protein-folding game, FoldIt. Here, participants manipulate a protein structure to find the most energetically favourable structure ( and thus,the most probable structure to occur in nature). By solving these 3D puzzles, participants can access higher levels and harder challenges. 

But as satellite technology advances ever onwards, and the data mountains grow ever higher, oerhaos one day even online volunteer networks will not be enough. So now researchers are investigating whether it is possible to use the wealth of results generated so far to educate a machine to do the job automatically. "After all, the face-recognition system on FaceBook uses a similar principle" said David. "Every time we tag someone, we are training a machine to do it automatically next time". 
The Zooniverse Portal

 It can only be a good thing to make scientific research more accessible to the public who, after all, fund many of these projects through their taxes. Furthermore, online platforms demonstrate that you don't need a degree to help investigate the unexplained. Now...I wonder if I can convince anyone to help me count the number of parasites in my photographs?

What could you do in five minutes each day? Go to http://www.galaxyzoo.org or https://www.zooniverse.org to find out more!

Friday 2 October 2015

Finally getting the hang of it!

For those of you who have been following my frustrated attempts to grow enough parasitic Striga gesnerioides to harvest seed for my depleted stocks.... I may have finally turned the corner!

My previous attempts to do this essentially involved mixing large quantities of my remaining Striga seeds with sand, putting this into pots and transplanting young, susceptible tobacco hosts into these. The first attempt failed completely, and whilst I had more success with the second ( see blog post for 3 rd August), less than fifty shoots emerged for the thousands of seed that went in. Not nearly enough seed to even fill the base of a glass vial, never mind filling it to the brim!

The problem is,this was all done very unprecisely. It essentially trusted to luck that by the time the Striga seed had preconditioned for long enough to break their state of dormancy, the young tobacco would have grown enough roots so that there would be one in the proximity of each seed to infect. Many of the seeds may well have germinated underground, but, finding nothing to attach to, withered and died. Striga seeds are so minute - like dust - that they do not have enough reserves of their own to grow without a host. And given that all of this happens underground, it was impossible for me to tell what was going on!

So I tried an experiment. When I infect my Arabidopsis plants with Striga for the main experiments of my PhD, the host plants are grown in square petri dishes ( rhizotrons ) with the roots pressed against the lid. This means I can take the lid off and apply the parasite seed directly onto the roots using a paintbrush, so the seed will germinate and infect the host straight away. So I decided to try this with the tobacco. After squashing some young seedlings into rhizotrons and leaving them a week or so to adjust, I then liberally painted the roots with preconditioned Striga seed. I let another week or so pass to give the seed time to properly attach, then transplanted the  seedlings into pots. Then I wished them a fond farewell and left for my holiday! Which was, incidentally, absolutely WONDERFUL - a complete break from work,with the nearest I got to plants being the picnic lunches I enjoyed in the Giardini by St Mark's square....

Meanwhile, my good colleague Emily was looking after the infected tobacco. The most I was hoping for was 20 shoots on each plant. But when I returned, I was in for a surprise!

It was a Striga EXPLOSION - a forest of shoots thrusting up around each host, packed so closely together it was impossible to count. There must be at least sixty shoots on each plant with more coming up every day! So many that they have left the tobacco hosts in a sorry state - shrunken, wrinkled and yellow a due to all the nutrients and water they are siphoning off. But it looks like I can finally stop worrying about my seed!

So all I have to do now is leave them to it and let the shoots flower, form seed capsules and then dry out so I can harvest them.  I'm beginning to see why there is so much fuss about 'Precision Agriculture' - sometimes it really does pay not to leave things to chance!
A very poorly tobacco...