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 31 December 2015

2015: How was it for you?

Another year draws to a close and it is natural to ponder on the successes and achievements of this year - for ourselves, our families and nation. But was 2015 a 'good' year for science? How have we pushed the boundaries of our knowledge and can this be usefull in benefitting mankind?

One way of assessing the impacts of academia outside our ( very often) closeted institutions is to see which papers captured the public's attention the most. The Altmetric Top 100 list does just that ( http://www.altmetric.com/top100/2015/ ), providing an intriguing summary of which research caught the most interest on public media streams,blogs, social media, Wikipedia, etc, besides within their academic circles. Nevertheless, it is a sobering reminder that, out of the thousands of research projects being conducted by diligent scientists across the globe, so very little 'makes it' onto the wider stage. It just shows how you have to be in this game for love, not fame!

Not surprisingly, medical and health science stories took  the lion's share of the list, but the environmental sciences were bolstered by a strong interest in climate change (likely to increase given the recent floods?) . Meanwhile, some of the papers were less to do with research than the issues which surround it, including a study which used hiring experiments to show that certain science faculties show a 2:1 preference for female candidates ( Number 14). In keeping with the Western world's preoccupation with diet, various nutrition experiments also made the list, including a study which concluded that drinking Diet Soda contributes to obesity ( Number 56). Modern technology, and its impacts on quality of life was also a strong presence with featured studies investigating whether smartphone dongles could help diagnose infectious diseases (Number 61)  or whether using light emitting eReaders in the evening disrupts sleep (Number 15). And a special Royal mention should go to Number 53: Identification of the remains of Richard III !

It's certainly worth having a look, if only to marvel at the range of things people study these days ( who knew that there are scientists investigating whether the oral microbiota can be changed through 'intimate kissing'?)! And it is nice to see that the age- long fascination with dinosaurs and outer space endures! 

To see the list for yourself visit http://www.altmetric.com/top100/2015/

Happy reading and a very Happy New Year to you too!

Saturday 12 December 2015

SIP hit Westminster!

Sorry it's late in coming, but finally here is my write up of the Science in Policy's trip to Westminster last month!

Although the London traffic tried to thwart us, we just made it through security in time to meet our Blue Badge guide in St Stephens hall. This is the oldest part of Westminster Hall and originally a residence for the king: one could feel their presence lingering still in the stark medieval grandeur complete with the original oak hammerbeam ceiling - the oldest of its type in Europe. These days, it forms a spectacular setting for official banquets and speeches from visiting dignitaries, including President Obama and the Pope. But we didn't have time to linger  and were immediately whisked up to the main lobby to catch a glimpse of the procession bearing the speaker's mace into the House of Commons Chamber. As the main junction between the Houses of Commons and Lords, this area seemed like the central nervous system of the building with media teams hovering about, MPs and ministers hurrying to and fro and groups of tourists  milling about. Despite being the heart of our modern democracy, however, the room was sumptuously decorated in the Victorian ornate style - think carved stonework, gilded mosaics and beautiful floor tiles. To continue this theme, we proceeded through the State rooms, following the route that the Queen herself takes when she visits Parliament. My favourite was the 'dressing room' where the Queen pauses to swap her tiara for her official crown, brought specially from the Tower of London. A commanding throne took centre stage whilst the surrounding walls seemed to groan under the weight of the monumental artworks, depicting tales from the Arthurian legends. When I asked if they ever used the room during the rest of the year, I was assured "Oh yes, it's a popular venue for parties!"
Because the Lords weren't sitting that morning, we were able to enter the Chamber itself and tiptoe between the benches ( red for the Lords, green for the Commons) where so many decisions of national importance have been made. I was surprised - it was a lot smaller than I had imagined - but apparently many of the Lords aren't particularly active in their political duties, so it is rare that they are all in attendance at one time - just as well! 
The Houses of Parliament, complete with festive decoration. ( I'm afraid we weren't allowed to take any photos inside!)

After a speedy lunch in the Jubilee Cafe, we moved from the ancient sphere of tradition to the modern machinery of Parliament. Paul Blomfield, MP for Sheffield Central met us and escorted us along the underground tunnel to Portcullis House on the other side of the road. This had a much more cosmopolitan atmosphere -  lots of glass and silver fittings, white marble tiles and even an indoor garden of fig trees - and in each direction, very important- looking people were ploughing through stacks of papers, crouched over their phone or huddled together in discussion. In one of the meeting rooms, Paul patiently fielded our questions for an hour and gave us an insight into how difficult it can be to effect changes through Parliament. "I hate the Punch and Judy show in the Chamber" he said. "Politicians are very good at saying things which aren't true but with  confidence". Nevertheless, he assured us that, behind the scenes, it can be possible to make a difference. "Some of the big changes that you make will never reach the headlines". He believes that engaging with the public through select committee is a more effective strategy and encouraged us all to get involved. "MPs are keen to reach out. When they are elected, they are expected to know everything about everything and they can only meet that challenge by drawing on expertise".

Appropriately, we then sat in on a select committee discussion - most people opted for the 'anti-terror strategies' session but I decided to stick with a science theme and joined the group in 'the challenges of big data'. I was surprised by how friendly the atmosphere was and the positive flow of dialogue between the Science and Technology Committee and the invited panel of experts. It was a far cry from Lord Sugar's boardroom in the Apprentice! One of the Committee members even joked " I organise a local book club and often have to buy a lot of cheese and wine in one go - what conclusions will Tesco make of my health from the data they collect from the checkout?!"
It was a long day but utterly worth it!

We then headed back through the tunnel to Westminster Hall - nearly getting trampled by a stampede of MPs who were being summoned by a bell to rush to the Chamber to vote. We decided to follow them and headed to the public gallery in the House of Commons. Unfortunately, by the time we had queued for our tickets, there wasn't much action going on - just a very calm discussion about transport networks ( apart from one gentleman becoming very excited about ferry boats). But it was worth the experience to be look out over such an iconic setting and it put me in mind of the Suffragettes, who sat here so many times in hope as each new bill for a Woman 's Vote was discussed ( although the giant bullet-proof glass screen wasn't there then).

A final call in the gift shop to stock up on House of Commons wine, then it was time to reach our coach and struggle back through the trials of London in rush hour and Storm Barney. It was an epic (if exhausting!) day and a big thank you to the Science in Policy Committee for organising it!

Thursday 3 December 2015

Big Ideas in Biology...

We've been spoilt rotten in Sheffield during the Krebs Fest -including departmental open nights, the schools film festival and lectures from Nobel-Prize winning scientists. It's sad that this is coming to an end, but we're going out with a bang with guest speaker Sir Paul Nurse, whose insights on the cell cycle have fuelled tremendous advances in cancer cell research. A Nobel Laureate and President of the Royal Society "for three more days only", he gave us his views on what are the five "Big Ideas that have shaped Biology".

"Biologists don't tend to talk about 'grand theories' or 'big ideas', unlike physicists who love them" Professor Nurse said. "They tend to prefer specific details, such as the number of hairs on a beetle's leg, the sequence of a gene and so on". Nevertheless, he feels that certain themes have helped to open up vast new areas of research by changing the way we approach the living world. 

1. The Cell
It's hard to imagine how difficult it would be to study living organisms without understanding the smallest unit which you are working with. Yet the idea of the cell only originated in the 17 th century, when Robert Hooke looked down at a cork tissue using his fascinating new invention - the microscope - and observed that they looked rather like the 'cells' of monks' quarters. According to Professor Nurse, this demonstrates two principles: "technology begetting discovery" and "how once one person sees something, everyone spots it and the idea spreads like a virus". As microscopes become more and more sophisticated, we are able to see with increasing detail the tiny,microscopic processes inside cells which,  combined together, sustain life in the whole organism. Understanding life at the cellular scale is crucial, for instance, in determining at what point things go wrong in disease - such as uncontrolled cell divisions leading to cancer. But it also offers us the opportunity to use that knowledge to put things right; as Professor Nurse observed, we now see headlines featuring stem cells almost daily. 
Noble Prize Winner and scientist extraordinaire, Sir Paul Nurse ( photo courtesy of BBC )

2. The Gene
Although ideas about hereditary have been postulated since the time of the ancient Greeks, it took the rigorously mathematical approach of a quite extraordinary character to define the concept of a discrete unit of inheritance. Gregor Mendel, the famous Austrian monk, was in fact a 'failed physisict' who turned to biological research after he didn't pass the exams to teach at the Univeristy of Vienna. It might seem an odd career move, but Mendel's training meant he worked in a way that was unknown to contemporary naturalists, who typically investigated the world through observation. Instead, Mendel generated a theory and tested it quantitatively by patiently crossing thousands of peas to determine the ratios by which certain characteristics were inherited in the offspring. Curiously, others (including Charles Darwin) had noted these 3:1 inheritance ratios, but they "just noted it down and moved on"; what set Mendel apart was that he tried to explain it.  Unfortunately, no one took any notice at the time, but since then "much of the science of the 20th century has been about giving a molecular understanding to Mendel's ideas". Indeed, as we learn more and more about the structure of DNA and how it shapes our lives, we encounter searching questions about our identity. For instance, as Professor Nurse said, "What does it mean for crime and punishment if our identity is genetically determined?"

3. Evolution
"If you go into a bookshop, you could be forgiven for thinking that there are only two topics in science: Evolution and String theory" said Professor Nurse. And you could be forgiven for thinking that Charles Darwin was the only one who came up with the idea. However, others had also pondered the idea of 'evolution by natural selection', including naturalist Alfred Wallace, whose letter to Darwin on the topic prompted the latter to publish On the Origin of Species. However, even earlier than this, the notion that living organisms could adapt to their environment over time was postulated by tree grower Paul Matthews in 1831. Surprisingly, these figures - whose names have almost dropped out of history - "didn't seem to mind not getting the credit" according to Professor Nurse ( compare this to the bitter feuds that arise nowadays between scientists over who gets to be named first author on a paper!) But why was this? Quite simply - Data. Darwin had amassed a vast collection of evidence to support his case, including his observations on the voyage of the Beagle, fossil specimens and his own experiments. It was only on the strength of this that the theory, controversial as it was, could begin to even be considered. Now evolution shapes our understanding not just of where we come from and where we are going, but also how we interact with the environment. For instance, can wild species adapt in time to cope with the changes we have imposed on the climate? And can we keep up with the 'evolutionary arms race' between superbugs and antibiotics? 
The new portrait,of Hans Krebs commissioned for Firth Hall to celebrate the Krebs Fest (artist : Keith Robinson) 

4. Life as chemistry.
Whilst we like to think of ourselves in terms higher than the Periodic Table, the truth is, we are just a big bundle of atoms. But it was quite a leap for early scientists to start thinking of life in terms of chemistry, leading to the birth of biochemical research. French aristocrat Antoine Lavosier was one of the first to suggest that living organisms were based on mechanistic processes, rather than a vague force of 'vitalism', and likened a guinea pig respiring to a pile of burning charcoal. Unfortunately, his brilliant career was cut short by the French Revolution, leaving others, such as Louis Pasteur, to pick up the baton. Slowly we came to understand that "within our cells, just microns across, hundreds and thousands of reactions are going on". As Professor Nurse said, rather than thinking of the cell as a homogenous sphere, it is more accurate to view it as "a myriad of different environments, separate but connected", all engaged in different chemical processes. Being able to understand life in terms of its supporting chemical reactions is especially central to medicine, allowing us to use pharmaceuticals and other interventions to restore imbalances in metabolism.

5. Life as information
"All the big ideas and complex processes in life - such as homeostasis, reproduction and communication - can be reduced to a flow of information". According to Professor Nurse, an informatics approach is key to translating mere descriptions into true understanding how systems work. "For instance, DNA is a digital information storage device" he said. "We could describe it in terms of its structure - the atoms and the angles of the bonds - but true biological comprehension comes from understanding that these molecules store information and that the sequence of the bases is central to heredity". Similarly, the physical interactions between proteins and enzymes are only meaningful is we understand how these tightly regulate key chemical reactions. "We should think of cells like electrical circuits" Professor Nurse said "except these are 'wetware' not hardware - they can retire themselves to connect different components".

It's clear that some of biology's greatest advances have come from visionaries who, defying conventional approaches, took their ideas beyond what they could see and 'dreamed big'. Indeed, one audience member cheekily asked if it would be better to do away with biologists and fill the labs with "physicists, chemists and five-year olds". Professor Nurse agreed that interdisciplinary collaboration would be vital in the years to come as biology is only likely to become more and more mind-bending....

"In physics, the smaller you go, the more bizarre it becomes" he concluded. " I wonder if biology is on the edge of such a transition into complexity..."

Tuesday 24 November 2015

Straight from a Nobel-Prize winner's mouth....

It's not every day a Noble Prize-winning scientist visits town...but as part of  the KREB FEST (a science-extravaganza celebrating the life of pioneering biochemist Sir Hans Krebs), the University of Sheffield has been inviting distinguished researchers to explore 'Big Ideas in Science' in a series of public lectures. I went along to hear Professor Sir Jules Hoffman discuss 'The Innate Immune Response - From Insects to Humans'.

As human beings, we often like it think of ourselves as somewhat more 'sophisticated' than other organisms. The truth, however, is that many of the most fundamental processes that keep us alive are common across the whole Kingdom of Life, making us not so very different from plants, fruit flies, bacteria ...etc. And the immune system, as Professor Hoffman explained, is no exception to this.  

Humans display two types of immunity - innate and adaptive immunity. The innate system is a generalised set of responses to infection - including the production of antimicrobials compounds - that takes place rapidly, within hours. This is activated by common features shared across pathogenic organisms. Adaptive immunity, on the other hand, is a more specific response and involves the production of an army of specialised immune cells ( such as T and B lymphocytes) that destroy the invader. Although this response takes longer to initiate, some of these activated immune cells remain as an 'immune memory' against that particular pathogen. Adaptive immunity is generally thought of as a more complex, 'higher' response as it is only present in vertebrates, whereas innate immunity is found throughout the animal kingdom. Yet for a long time the innate response remained a mystery - we knew the OUTCOMES ( e.g. Antimicrobials production) but not HOW exactly it is activated. 
Eagerly awaiting the start of the lecture

When Professor Hoffman started his career, insects were the model of choice for investigating this: they show strong innate immunity responses, making them highly resistant to infections. For instance, just pricking a fruit fly with a needle that had been dipped in a microbial solution is enough to prompt the production of a wide range of antimicrobials, belonging  to seven different families. To find out what triggers this, the gene of one antimicrobial, called Diptericin, was cloned and found to contain distinct elements in the promoter,later called NF-KB elements. When these are mutated, Drosophila fruit flies are unable to mount such a strong innate immune response, and become vulnerable to infection. It turned out that many antimicrobial genes are recognised by a transcription factor called NF-KB which recognises and binds to NF-KB elements to activate the gene. Normally, NF-KB is held inactive in the cytoplasm by an inhibitor protein ( IF-KB) ; during infections, this inhibition is lifted and NF-KB can move to the nucleus to activate antimicrobial genes. But what was detecting pathogenic attacks in the first place and controlling IF-KB?

It took years of painstaking research, by groups across the globe, to identify these receptors - a problem complicated by the fact that different receptors seemed to activated different antimicrobial compounds. To cut a long story short, Toll receptors were found to be the main agents in activating the production of antifungal and antibacterial compounds in Drosophila ( actually, Toll Receptors do not sense pathogens directly but are activated by cleavage of another protein called Spaetzle....but that's another story!)
A giant model of Green Fluorescent Protein (GFP), commissioned for the Krebs Fest ( see my previous post for the giant E.coli!) 

You might be thinking - 'years of work - just to work out the immune system of a fly?' However, Toll receptors were found to have their counterparts in mammals, controlling similar pathways of innate immunity. However, it has recently emerged that Toll- Like Receptors (TLRs) have an importance that goes far beyond anything previously envisaged. "The initial notion that TLRs were sentinels against microbes turned out to be too restricted" Professor Hoffman said. Now it appears that TLRs play a whole variety of crucial roles, including allergies, neuro-regeneration in the central nervous system and kidney function. It just shows how years of incremental research, putting a puzzle together piece by piece, can open up whole new vistas in areas you would never have guessed at first.

This has promoted a paradigm shift that has seen the innate immune system garner much more respect, rather than being simply a 'primitive' relic. In fact, this response is so effective, that out of millions of bacterial and fungi species, only a handful can evade innate immunity and must be dealt with by the adaptive immune system - the pathogens that we regard as key problems. Evolutionarily speaking, adaptive immunity is a relatively 'late player', only appearing 450 million years ago in the ancestor of vertebrates, compared with innate immunity which has been present for approximately 1 billion years. "Essentially, we survive microbial infections through innate immunity" said Professor Hoffman. Without this "brilliantly successful" system, we would all be dead by lunchtime - each person produces roughly 10 g of antimicrobials a day, to fight off invaders they will never be aware of. Perhaps you may feel it is demeaning to compare a human with a fly....but in this case, I'm grateful that our immunity shares so many similarities!

Next week, Sir Paul Nurse will be coming to speak about his groundbreaking work elucidating how the cell cycle in controlled in mammals - and how this goes wrong in cancer. I'll be there! 

Tuesday 10 November 2015

How can scientists engage with the new Parliament?

Presenting a brief round up of our last Science in Policy Session - 'Engaging with the New Parliament'. Our guest speakers Lynn Hobson (Parliamentary Outreach), Dr Grahame Danby (Science Clerk from the House of Commons Sci and Tech Committee) and Dr Cat Ball (Science and Technology Policy Analyst) gave us a masterclass in how scientists can engage with policy makers and submit evidence to influence key government inquiries. 

First Lynne Hobson from Parliamentary Outreach gave us an introduction to the structure of Parliament, and in particular, how the work of the House of Lords complements the House of Commons. Although the House of Lords can have an elitist image, Lynne argued that it is actually more representative of British society than the Commons, representing a wider range of ethnicities, professions and industries. She also disagreed with the view that having the two houses is an idiosyncratic system that slows down the process of law-making. "The Lords aren't there to cause trouble - it is about creating a debate to get the best laws possible, ones that are robust and fit for purpose" she said. 

Both the Lords and Commons have select committees, who commission inquiries into specific topics. Some of these committees are permanent, such as the Committee for Human Rights, whereas others are reactive, formed in response to major events, such as the banking crisis. The only committee which has the same name for both houses is the Science and Technology Committee, and we were very lucky to hear from Dr Cat Ball, Policy Analyst for the Science and Technology Committee of the House of Lords. 

After introducing us to the committee members (an eclectic bunch including a former head of MI5!), Cat described how their work reflects the most topical issues of the moment. "We are currently taking oral evidence for the potential uses of GM insects and our next big inquiry will investigate the relationship between EU membership and science". During these inquiries, members of the public are invited to submit evidence - this can be from world- leading experts, people who simply have an interest or even PhD students! Even though thousands of people may submit evidence, the administrative staff "read and consider everything and unless it's completely balmy, we will put it forward to the committee". But do these enquiries actually make any difference? Cat gave us some compelling examples that they do, including a 2011 enquiry into nuclear research which the Government used to develop its nuclear strategy up to 2050. Nevertheless, Cat stressed that the committees are strictly limited to an advisory role. "We have much more of a scrutinising function than one of law-making" she said.

For all these inquiries and for informing parliamentary debates, it is vital that MPs and select committees have all the information they need right at their fingertips. Not surprisingly, Parliament is supported by a huge army of administrative staff who play a critical role in 'keeping everything working'. Dr Grahame Danby, Clerk to the Commons Science and Technology Committee, gave us an insight into this behind the scenes work. Part of his role involves signposting MPs and ministers to the correct department that can answer their questions and to retrieve key information from the vast repositories stored in the Government libraries. In one famous example, an MP once asked which department he should go to for information about asteroids. The reply: "Well, the DTI (Department of Trade and Industry) deal with space but if it comes closer to earth, it might become an issue for the Ministry of Defence". 

Grahame stressed how the pace is in a completely different league to the sometimes ponderous world of academia. "An MP might literally only have a few minutes before they have to be in the Chamber" he said. "I don't have time to commission a PhD for every question I'm asked". The libraries get a lot of use, with the clerks receiving enquiries on every topic under the sun. "MPs get approached with all sorts of problems, especially from their constituents" Grahame said. "If one of David Cameron's constituents complained to him about the height of their neighbour's hedge, he would almost certainly refer to the library for guidance". MPs also 'like to know what they are talking about' for media appearances and public debates. Hence, Grahame found himself writing briefing notes on the Higgs Boson the day before its discovery was announced! More recent examples of issues that have drawn heavily on published scientific research include plain packaging for tobacco, ash dieback and how neonicinotoid insecticides affect bees.

It was a fascinating overview of a little- known and often unappreciated range of careers which cross the boundary between being a scientist and being a policy maker.

Meanwhile, keep watching, we're off to Westminster on 17 th Novemebr!

Highlights from the questions:

Do select committees like receiving evidence from academics during an enquiry?

Grahame: "I personally like getting information from Academics as you can tend to trust them to be impartial and their research is put to a rigorous peer review process"

Can even PhD students submit evidence?

Grahame: "The select committees tend to go for heads of departments and Professors but there is no reason why a PhD student could not submit evidence"
Cat: "We welcome input from early-career researchers. In many cases, they will be the ones most affected by new legislation". 

What happens if someone submits untruthful evidence?

Grahame; "You used to be locked up in Big Ben....that doesn't happen now but 'contempt of Parliament' doesn't look good on your CV!"

Do you have any advice on how to contact MPs with scientific issues?

Lynne: "Be BRIEF - ask yourself, 'Could my MP read this on the train?' Tell them who you are, why you are contacting them, what the issue is and why it is relevant to them now. And certainly don't use any academic lingo!"

What is the main limitation of the select committees?

Cat: "The main limitation is that, despite putting a lot of time, detail and trouble into our recommendations, we can't force the Government to do anything. All we can do is hope things move along".
Grahame: "Yes, but it does take forward the public debate. E only way things happen in a democracy is through public debate". 

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...

Wednesday 16 September 2015

Time for a HOLIDAY!!!!

I won't be posting over the next week as - fisnlly - I am going on a PROPER holiday ( the Prague conference certainly didn't fall into the category of 'relaxation'...). With no internet or phone, there isn't the remotest chance of doing any work....unless I print off a few scientific papers? Somehow I think I will be too busy reading up on the unique history of La Serenissima and just gazing at that magical marriage of light, water and bobbing Gondolas.....see you soon!

Tobacco Uodate: tobacco are still going strong, one is even starting to flower again! ( perhaps I should rename them 'Resurrection Plants'...) The Striga shoots are beginning to dry out so hopefully I can start harvesting the seed soon. 

Monday 14 September 2015

Gatsby Annual Network Meeting Day Two - From ancient history to cutting edge science

Nine 'o clock on Friday and we were back in the auditorium for day two of the meeting. Judging by the empty seats, some of the delegates were still recovering from a tour if Oxford's pubs last night...

We started with a topic which, unfortunately, preoccupies many researchers - the money. Or, more accurately, where can we go to get funding? Bizarrely, only 4% of the UK public spend on scientific research goes to Plant Sciences - a proportion which hasn't changed since the 1970s. This despite  the question of how we will feed everyone in a world undergoing climate change, environmental degradation, water scarcity - and so on and so on! 

Of course, the competition is fierce - every scienctist believes their project is fabulous, game-changing and ultimately worthy of a pot of money! So what is the solution for UK-based plant scientists? Cast your net wider and look for international opportunities, particularly those from philanthropic organisations. Perhaps the best known of these is the Bill and Melinda Gates foundation which - with an endowment of $44 billion - also happens to be the wealthiest. "Plant science used to be the poor relation in international development" said Gatsby Mentor Nick Talbot, but that is starting to change. Now plant science is being promoted alongside high profile campaigns, such as providing mosquito nets to combat malaria. Even the biomedical giants, such as the Wellcome Trust, are beginning to take note. "After all, it doesn't matter how much you vaccinate people - if they don't have enough to eat, they will never be well" as Ottoline Leyser, another of the Gatsby Mentors, put it. Such organisations are particularly keen to support programmes that facilitate the exchange of scientists - and hence knowledge - between different countries. This includes both UK institutes inviting foreign scientists to their labs, and UK scientists spending time in overseas labs. Given the size of the problems mankind faces, it makes sense to disseminate ideas on as global a scale as possible. 
Another beautiful morning at Queens

But even when the money IS there, UK scientists - particularly early career researchers - can be afraid to go for it. "There is a tendency for early career researchers or newly established lecturers to be nervous and only apply for small grants" said Nick. "But really, you should be going for a large grant as soon as your CV makes you competitive". To make this less daunting, there are a number of grants specifically aimed at researchers just starting to climb the academic ladder. These include the European Research Council (ERC) 's Starting Grants, open to those who have 2-7 years of research experience after their PhD, besides the BBSRC* Future Leaders Programme and Marie Curie Fellowships. But even these are highly fought for, hence the Gatsby Mentors had some tips. "It is much better to have a consistent record of good solid research than one or two 'blockbuster' publications" said Liam Dolan. "And try to have a really exciting research plan that could potentially change the field". But Ottoline warned against overdoing the hyperbole. "One research proposal I read was going to shift four paradigms - I just got fed up! You don't need to keep spelling it out - it should be obvious that the research will make a difference". Having some preliminary data can also make an application stand out,although this isn't always necessary. I wonder if I ever be in a position to go for a pot of money myself, and put my own ideas on the table?

We then had an update from Ginny Page, from Science And Plants for Schools (SAPS), about the new IntoBiology website. This aims to firmly debunk the notion that 'plants are boring' and there is a wealth of inspiring lectures and resources available to all. It's not just for kids - if this blog has made you at all curious to learn more about plant science, do check it out! In particular, have a look at the 'film advert' to see what a media team can come up with when challenged to make plant science careers look exciting! See http://intobiology.org.uk

During the talks from the third year PhD students, Patrick Diaz described his progress using temperature insensitive  mutants in Arabidopsis to determine genes involved in temperature sensing. I was particularly interested in this, as I helped to identify some of the first of his mutants during an undergraduate summer placement at the John Innes Centre four years ago. His results suggest that the components of the temperature sensing pathway are linked to photosynthesis, a reaction that is itself temperature dependent. The rate limiting step of photosynthesis is the conversion of reduced plastoquinone. As the temperature increases, reduced plastoquinone accumulates and this forms a feedback loop with temperature sensing proteins. It seems an ingenious solution to me, to use a process that already varies with temperature to work out how hot it is!

Whilst we broke for coffee and the undergraduate poster display, I caught up with naturalist John Midgley to talk blogging. His blog (Dr M goes wild) is in a completely different league to this one however with over 1,000 hits on some days! I will be writing a separate post on his blog and further outreach work soon so stay tuned. 
The tree in the courtyard of the Fellows Garden

A couple more talks then a final 'treat' - two scientists from the Cambridge Sainsbury Laboratory described the fascinating research they are doing at this state-of-the-art facility. ( I had a tour once and it's true! They even have whole walls you can write ideas on). Amazing how quickly this lab - completed in December 2010 - has filled itself with pioneering research leaders. Dr Siobhan Braybrook, for instance, is investigating how plants, with their rigid cell walls, can perform delicate 3D movements such as the circling motions of young shoot tips ( known as circumnutation). Professor Yrjö Helariutta, meanwhile, is researching how undifferentiated root stem cells become  highly specialised sieve plate elements. These form part of the phloem vascular system which transports nutrients and carbon sugars around the plant. Seive plate elements are unique - unlike the xylem elements that transport water, they are living cells which form continuous channels connected by seive- like plates ( hence the name).  To do this, the nucleus and organelles completely degrade and the walls undergo thickening. To understand how this takes place, Yrjö is using the latest 3D root imaging systems to compile serial sections into exquisite images that document how the cells change over time. I wish I could borrow it to study how Striga gesnerioides infects my Arabidopsis plants. It would make for some pretty pictures for my thesis!

A priceless relic of British history .... The exquisite Alfred Jewel  © Ashmolean Museum, University of Oxford.

And then quite suddenly it was all over for another year. Farewell lunch, pick up bags, disperse to trains, cars and coaches.I just had time to pop into the Ashmolean Museum to seek out the Alfred Jewel. It was amazing how many people walked past it, despite it being one of the most significant finds of Medieval Britain, commissioned during the reign of King Alfred (871-899). The exquisite  jewel-work depicts a figure - said to be Christ or the personification of Sight - surrounded by the words "AELFRED MEC HEHT GEWYCAN" - "Alfred ordered me to be made". It is all the more alluring in that no one is exactly sure what it was used for - part of a crown? A rod for coiling manuscripts around? A pointer to follow the lines of scripture? Either way, it marks the transition from pagan societies to a culture based on Christianity and learning.

And now it really is time to depart...until next year Gatsby and thanks for the memories!

* The UK Biological and Biotechnological Sciences Research Council