DEADinburgh

Last weekend, I took part in the most immersive example of science communication I can imagine. DEADinburgh was a piece of experimental (in every sense of the word) theatre in which the public play a central role deciding the fate of the city...

Modelling the spread of the Lazarus Pathogen

Before the show, a frightening background scenario was laid out; reports of violence throughout the city started to increase, by the time we realised what was going on it was too late to stop it. The "Lazarus Pathogen" has killed thousands, and turned thousands more into flesh-eating zomb- sorry, PALPs (People Affected by the Lazarus Pathogen). Now the city is quarantined and NATO warships lie off the coast with us in their sights. We have been given an ultimatum: if we do not assure them we can find a cure or institute an effective cull of the PALPs, they will destroy the city in order to halt the epidemic.

Since the scientific committee are deadlocked, the civilians will vote on the outcome. Throughout the evening each team of scientists explained their research and the impact this will have on their final decision. Our team from the Roslin Institute and the Wellcome Trust Centre for Cell Biology believe the Lazarus Pathogen to be a virus, we have developed a stain which allows us to tell the difference between healthy cells and those of the infected. As the civilians tested themselves, we made a terrifying - but exciting - discovery: individuals with no symptoms were testing positive, they were carrying the virus and probably spreading it to others. 

In our initial presentation we described how viruses work - they have keys to gates on the surface of the cells, once they get inside they can take over and copy themselves. Our suspicion is that the carriers are genetically resistant to the virus, maybe the gates on their cell surface have a different shape which stops the virus from getting inside (because their keys no longer fit). We used this theory to suggest a cure - gene therapy might allow us to give everyone these protective gates - to make everyone immune! The potential cures from other teams included harvesting protective antibodies from the PALPs themselves, rebuilding the damaged tissues with stem cells and 3D printing or behavioural therapy to get the PALPs off living flesh and onto vegetables (no, really).

The longer a cure takes, the greater the chance of a boundary breach

Despite all these exciting avenues for research, we had to admit they would take months or years to complete and in that time the Lazarus Pathogen might escape the city; the mathematical modelling by a Manchester Met University team suggested this would be the case (I've put a few simplified models into this post, courtesy of Matt Crossley). Maybe a well planned cull would be the wisest approach, when we started the assumption was that this would involve soldiers methodically moving through the city killing PALPs but as the show went on we realised there were ways the science could improve a cull. The PALPs are sensitive to light so maybe we could herd them into the centre of the city where they would be easier to manage.

An attempt to cull...

It was as we discussed the idea of keeping the PALPs occupied in the city centre using air-dropped meat that I had a brainwave. Rabies is an incredibly dangerous virus which is able to infect most mammals, it drives infected animals to bite others and then gets into the new animals in saliva; governments can stop infected animals getting into the country by air-dropping vaccines wrapped up in meat or fish-meal along the border. When wild animals eat these baits they become immune and the country can remain rabies-free; the baits feature a warning label for the public since dog walkers will occasionally find one. So the brainwave was to replace that vaccine with a potent toxin such as botulinum (that's botox) or tetanus, the PALPs should scoff down our toxic baits and any uninfected civilians will read the warning sign and keep away.

Unfortunately, from studies on PALP feeding habits performed by psychiatrist Dr Crow, we learnt that the PALPs will only feed on living flesh, avoiding dead meat unless trained otherwise. Whilst the idea of parachuting in hamsters armed with toxic capsules and "Warning Hazardous Material" tattoos still seems like a good idea to me, several of my colleagues disagreed and advocated the only other solution: sacrifice the city, and ourselves, to stop the disease escape.

A small bomb might not contain the pathogen...

But a big bomb means a lot of collateral damage

It was here my team raised a worrying possibility, namely that the Lazarus Pathogen did not originate within the city, instead it was bought in from abroad. International air travel allows pathogens to spread rapidly, infected individuals can get to the other side of the world and come into contact with hundreds of others before they even notice symptoms. This happened during the 2002/2003 SARS outbreak; a pretty local outbreak escalated into a pandemic and it was only decisive quarantine stopped over 8000 infections turning into hundreds of thousands.

At the end of the show there was a lot of discussion and we could have probably spent the night debating but in the end, the participants involved voted for cure on 3 nights, and sacrifice on the other 2; I guess we'll never know if a hamster-mediated cull would have succeeded...

An "artist's" impression

There are a few lovely reviews floating around (such as this one, this one and this one) where you can find out more, or you can wait for a Little Atoms podcast on the event. The scientific briefing and exercise we performed was created by the marvellous Sarah Keer-Keer and Nicola Stock. Huge thanks have to go to LAS theatre, Director Barra, Creative Producer Andy, along with all the cast, crew, staff at Summerhall and the public that allowed this awesome event to happen.

Snow Animals, Thesis Committees and Sci-Masochism

This is my first blog post for about two months because I'm a terrible blogger, sorry about that. It's been a busy couple of months (I'm starting to think every post will start this way) and I've got a whole bunch of exciting stories to share about PRRSV, related viruses, places where politics/virology intersect as well as general updates on my PhD project. In order to do that, I'm going to post more frequently, with shorter posts.
But before I do any of that, let's talk about the most exciting thing of all - the weather! Scotland is a cold, wet and windy place; in Edinburgh the tall buildings give some protection but out at the Roslin Institute we face the full force of nature and - since the building is made from a prolific amount of glass - we get a hell of a show. To celebrate the Winter Wonderland that our campus became, me and a lab-mate synthesised (which is science-speak for "made") a snow pig. Our beautiful swine was quickly joined by what I think was some kind of chicken....

About 10 weeks into a PhD project, each student is required to hand in a report (several pages summarising the work they've done so far and what they plan to do over the next few months) and give a short presentation to a few experts for them to scrutinise.
My Thesis Committee meeting was a couple of weeks ago now and whilst it was quite nerve-wracking planning it all out, everything seemed to go quite well. Despite reminding myself that it's the job of the committee to find problems with the project at this stage, it was still frustrating to have these identified. Needless to say, I've spent the past couple of weeks looking for solutions and coming to understand how a simple-sounding idea can turn into years of work.
I can't remember who it was, but someone once said that scientists have to learn to be masochists - enjoying their ideas being picked apart and actively seeking out this criticism in order to improve their plans; I can certainly relate to that.

Edinburgh Culture and Cell Culture

This has been an exciting month, I feel like I've finally found my feet in Scotland and in Roslin. I wrote a small piece for the Institute's newsletter - the Roslin Reporter - and a guest post on the most amazing food blog on the internet (okay, I'm a little biased since it belongs to my girlfriend); still, if you fancy a great veggie chilli recipe or a range of other delicious veggie meals then find it here (I recommend the ginger brownies or her coronation tofu).
I I've done a hell of a lot in the past month including attending a pro-choice rally and several other great events by the Feminist Society; learning to make sushi thanks to the Hearty Squirrel food coop and their raw food workshop; seeing Dolly in the National Museum of Scotland (possibly the best museum I've ever been to!); visiting a gorgeous (and utterly freezing) Edinburgh beach; finally seeing The Big Lebowski (and followed it up with a white Russian at Lebowski's Bar); and speaking to about 40 potential PhD students for the first time without peeing myself (Hi, if you found me through that event!).
In other news, I turned 22. My mum and sister visited and took me and the previously mentioned girlfriend to the finest vegetarian restaurant in the city, David Bann. Go there. Eat. Read the rest of the post later, go eat now! In other birthday news, another student in our lab made an awesome cake (which looks rather like a virus particle with Maltesers for entry receptors) for me:

Because cake.

Moving out of my life and into the lab, I finally got to work on cell culture which is one of my favourite things in the world - seeing cells down a microscope as they float in and out of view helps me grasp how very big, and very small, we all are. To explain what this involves I need to make it clear that the cells in our body are pretty puny, take them away from their comfy little homes inside our skulls or lining our blood vessels and they will usually shrivel up and die. Scientists spent many years failing to get cells growing until the cancerous cells from the cervix of a Black American woman named Henrietta Lacks just kept on growing (that's the big problem with cancer, it just doesn't stop growing). I strongly recommend everyone read the story of "HeLa cells" in this book (also available at your local, tax-paying book shop), it's simply written and manages to explore the science as well as the social context (highlighting the appalling lack of respect doctors had for their patients 60 years ago, particularly if those patients weren't White).
But back to the point, we often use irregular cells like these - grown on the side of a flask containing a solution with all the nutrients the cells need - to test how different conditions (a lack of food, for example) will affect them, from their growth to the signals they give out to how they look. This is very useful for studying viruses as they need to control their host cells in dozens - if not hundreds - of different ways. So by infecting cells with with virus, we can explore how the virus fights or escapes the cellular defence mechanisms, how it manages to control the cell's machinery to copy itself, how it gets in and out of cells, where it goes when it's inside and all manner of other questions.
Still it's important to remember this is just a model, as one of my undergraduate lecturers once said "We are not, in reality, cancerous cells stuck to a plastic dish". Wise words indeed.

For the past two years I've grown a stupid looking 'tache each November to raise money for Movember and as anyone who has seen me in the past month will have guessed, I am cultivating another one this year. However, I recently learnt that Movember promote screening practices that may do more harm than good so I've decided to raise money for another charity instead. I am all in favour of more money going towards research and since the central point of Movember is combating cancer, I decided this years charity should be Cancer Research UK.
I think it's worth covering what Movember are doing in a little more detail (though if you want a pro's voice on the matter, this link will help). They are advising men to get excessive screening for prostate cancer as well as several other conditions. This may not seem immediately dangerous but that's because we tend to think of screening as an entirely harmless exercise, in truth screening can have a range of side-effects resulting exposure to toxic chemicals or radiation (for example, in tests that use X-rays). Beyond that kind of indirect harm, there is the danger of false positives - screening tests aren't perfect, they may miss a problem (false negative) or they may suggest a problem where there is none (false positive); in the latter situation, the result can be a patient needlessly going through procedures that severely reduce their quality of life (removal of the prostate can make sex, and trips to the toilet, considerably more difficult).
This isn't to suggest no-one should get screening for fear of a false positive, there is a point at which the benefits will outweigh the harms and that should be decided between patients, their doctors and the evidence.
To their credit, Movember changed some of the advice on their UK site after the issue was pointed out to them however they kept many of the questionable points so if you'd like to make a donation in honour of my face-caterpillar, go here; and for the NHS advice on prostate cancer screening, go here.
Finally, it should be added that Movember has done a lot of good, using a quirky meme to raise millions and highlighting issues that can be easily overlooked because people think prostates are icky. In the words of Doctor Ben Goldacre (and for the sake of a clumsy segway) "Movember is a great, great thing, but I wish they'd stop promoting harmful screening". 

A moustache slightly hidden by sushi

Now go buy Ben's book, Bad Pharma, it's the most important book you'll read this year. He manages to explain the scandalous situation in the pharmaceutical industry with enough detail to give understanding, but keeping things simple enough for people who struggle with stats and controlled experiments (i.e. everyone) to understand. Buy it for your friends this Christmas. Buy a copy and send it to your MP. You can find it on Amazon, and at all good, tax-paying book shops.

That's all I can fit into this post, if it had been a quieter month, I'd talk about the fantastic Science Grrl campaign which raises the profile of women in science where naive bureaucrats/sexist salespeople fail (Oh how they fail). I would have also talked about how whales can get flu, which I only learnt this month and think is very bizarre!

The Disease

Now that I'm a few weeks into my time here, I've been kitted out with a desk, lab book and Roslin coffee cup.There have been a lot of induction talks on science, safety and security. I've been allowed to get my hands dirty by helping out in lab. I've met loads of people and even remembered a few names. A group of students at the Institute run a social committee who arranged a tour of the vaults below Edinburgh followed by a meal at the Elephant House (where JK Rowling wrote several of the Harry Potter books - the toilets are well worth a visit to see the extensive graffiti of a dedicated Fandom) and a trip to the union bar (which ended with me staggering home from a club in the wee hours of the morning), needless to say they are a lovely bunch.

In my last post, I said I'd talk about Blue-Ear Pig Disease and maybe even start on my PhD project however there's quite a lot of info to cover so I'm going to break this up into several posts. In this post I'll cover the disease including its effects, its history and the many names it has received; in the second post I'm going to cover the virus itself, looking at how it's put together, the way it copies itself and some of its relatives.

The disease was first noticed in the late 80s, during the early 90s when papers were first documenting the disease and identifying the virus it was given many names including mystery swine disease (MSD), Porcine Epidemic Abortion and Respiratory Synrdome (PEARS), Lelystad Virus (for the European type, more on that later), Pig High Fever Disease, Blue-Ear Pig Disease, Porcine Reproductive & Respiratory Syndrome Virus (PRRSV) and even pig AIDS (because of its tendency to wreck the pigs immune system). Whilst Blue-Ear Pig Disease gives a pretty good blog title, I'm going to call it PRRSV from now on since that's standard name nowadays; this name has the bonus of being sounding like it was chosen by a happy cat ("purrs virus"), which is always a cute concept.
Moving swiftly away from cute concepts, I want to look at the effects of the virus on pigs, and the results for herds. The symptoms of a pig which is infected with PRRSV can be vary greatly depending on the strain of the virus and the immune system of the pig, some animals will remain seemingly healthy whilst passing the virus on to their neighbors whilst others will suffer from reproductive disorders (pregnant sows may abort fetuses, or give birth to weak piglets), stunted growth, pneumonia or a weakened immune system (that allows other diseases to do damage) which can result in death. With this range in severity, it is practically impossible to distinguish sick animals from others so outbreaks often require the destruction of entire herds. All in all, the result of the virus is a lot of suffering for animals and a loss of livelihoods for farmers.

The virus seemed to appear for the first time in Europe and North America simultaneously however it was quickly noticed that these outbreaks were actually caused by two different types of the same virus which were only about 60% genetically identical. The European strain is called Type 1, whilst the American strain is named Type 2.
Mistakes by their copying machinery cause viruses to mutate over time, these changes occur randomly however they can be guided by their environment. A change that leads to a slower copying virus will probably die out, whilst a change that helps the virus avoid the host immune system is likely to spread as would a change that lets the virus infect a new type of animal. Some changes don't make much difference either way so they will build up over the generations at a pretty steady rate.
Lucky for us, viral generations can be as short as hours allowing us to grow virus in a lab for many generations and figure out what this rate of mutation is. We can then use this rate to figure out how long ago two strains of a virus were the same, or when their last common ancestor was. By we I mean geneticists with a knack for computing, I don't personally know how to do it.
This analysis has been done for PRRSV and it seems likely that the two types branched off around 1880 (give or take 15 years), the current theory is that a disease of mice got into wild European boars around this time, when boars were shipped to America throughout the first half of the 20th century some took the virus with them and managed to spread it to escaped domestic pigs. Over the following years during which the different types were separate, they picked up mutations independently of each other resulting in the two types that appeared in the 90s.

Since that time, the virus has spread (or been noticed for the first time) across the whole of Europe, North America and China as well as parts of East Asia, Africa and South America. The disease costs around $600 million annually to the United States alone and despite several vaccines, it remains hard to control.
There are many questions still to be answered in PRRSV research, why both types popped up at the same time in different places, why vaccines seem so ineffective and - importantly - how we stop the virus from doing even more damage.

A General Introduction to Me, Edinburgh and Societies

Hello, I'm Alex, and this is my blog. 

I am a student ambassador for the College of Medicine and Veterinary Medicine (CMVM) at the University of Edinburgh, one thing I do in this role is update this blog (at least) once every month with posts about my research and life as a student here.

I start my project on 1st October so this post is largely going to be about me and Edinburgh as I know it so far.

I was born in Nottingham where I spent the first 18 years of my education, after cruising through secondary school and college, I applied to do - and was rejected for - medicine; it turns out this was one of the best things that could have happened to me since it was whilst I studied BSc Microbiology at the University of Leeds (2009-2012) that I got really passionate about science.
My excitement about the science I was doing and the people I was meeting meant that I missed out on engaging with the wide array of groups and societies that universities have to offer. Fortunately, studying Edinburgh will give me the chance to get involved with societies and continue doing the science I enjoy.

I am a humanist, feminist vegetarian who enjoys science, comedy, cooking, running, politics, philosophy and computer games. I couldn't really be in a better city for all these things.
After receiving my offer to study here, I checked out the societies available from Edinburgh University Students Association (EUSA), made a list of those that seemed interesting and checked out a few their events during Freshers week.

The Humanist Society arrange events relating to faith, science and reason and have a weekly meet-up at the Pleasance Bar. I met up a few members during the last week of the Fringe Festival who were lovely enough to welcome a total stranger (who claimed he would be starting a PhD soon) into the fold for drinks and discussion.

The Feminist Society run campaigns and have discussions relating to gender equality. Whilst their introductory tea & coffee session was a little awkward (get a bunch of freshers in a cramped space see what happens...), everyone was very friendly and I expect things will pick up as their first campaign begins, FemSoc vs Banter aims to challenge those "harmless" instances of sexism we are exposed to day-to-day.
Beyond FemSoc, Edinburgh has a vibrant feminist community as I discovered on the weekend following Freshers week at an event called "Pussy Whipped - a wee queer-feminist festival" which, over 2 nights, hosted a range of punk rock, alternative and electro bands who were mostly LGBTQ or female.

Furthering the interesting feminist talk, The Debates Union hosted a debate entitled "This house would ban page 3 girls". It was fun to see two experienced debaters from the university thrashing a Member of the Scottish Parliament and a woman who campaigned on the topic, though it was a shame they didn't really believe in their side of the argument (as we learned later).

The Vegetarian Society arranged a picnic in the Meadows and once we found them (how do you spot a group of vegetarians in very large field?), we had a lovely time eating humous and meeting a wide variety of people.
On the subject on delicious foody people, I saw the Hearty Squirrel Food Cooperative in the fresher's fair but didn't get a chance to chat. This group of (what I assume are) lovely people volunteer to provide cheaper, tastier and more ethically-sourced food for students to buy. I have high expectations after using the excellent food co-op at Leeds Uni.

EUSci do a magazine, website and podcast about science, I couldn't find them at freshers fair but the articles on their website and the chat on their podcast were of great quality and I'm excited to get involved with them. They only publish their magazine a few times a year but at least that gives me time to find a topic for an article.
A more regular student publication is The Student, which has a wider focus (being a newspaper, not a science mag). Writing for student newspaper would be exciting enough but on top of that it turns out they were also founded by Robert Louis Stevenson!

So that's the societies I'm really curious about, but there's a load more on offer. I have one last topic before I publish this post and that is the twitter feed to the right of this post, I'm not sure what I'll be doing with it or even whether I plan to keep it. On the plus side, minute by minute updates may give an interesting perspective especially at times like conferences; additionally twitter allows for interesting communication with many groups and individuals (such as EUSci). On the minus side, there are serious issues around confidentiality and safety (since I may be talking about work with animals). It's likely that there wont be many posts there until I've had a chance to talk it over with my supervisor.

For the next post in a couple of weeks, I'll be talking about Blue-Ear Pig Disease and maybe getting into the aims of my PhD project.