From PhD to JSA

Good day! It's been a while! I suppose I haven't been feeling very sciency for a long time now. Take a seat, get comfortable and I shall tell you why...

In October 2010 I began my PhD course. From the very beginning my primary supervisor and I didn't get along. Let's call it a personality clash. My supervisor thought that the best way to motivate their students was to scare and bully them and threaten them with expulsion from the course whilst I (a new graduate, fresh from the uni bubble) thought that I would be gently handled, trained and encouraged. (In fact, with hindsight, I think the best way of handling a PhD student like me is a nice balance between the two. A little chivvying along coupled with lots of encouragement and help. A PhD is supposed to be a learning process after all.)

Gradually my enthusiasm for work waned and, after about a year of feeling belittled and bullied, I went to speak to the admin department to find out whether my supervisor could - as threatened - remove me from my course. It turned out that, as one cannot simply walk into Mordor, one supervisor cannot simply sack a PhD student. They just don't have the power.

After realising this I was very relieved, but a year of stress and worry had taken its toll on the progress of my project - and on my confidence and motivation - and I was rather behind with my work. During year two I tried hard to catch up on work and re-motivate myself. My supervisor improved a bit after a talking-to from the higher-ups and I began to think that perhaps there might be a PhD at the end of this tunnel.

Unfortunately by this time I had gradually but completely lost my interest in the subject at hand and (I didn't realise this until a little later) I was becoming very depressed and anxious. I was completely and irrationally terrified of my supervisor and would actually hide from them when I heard their footsteps in the hallway. I would avoid going onto campus as much as possible and would put off everything until it was impossible to put it off any more. Then I'd have to work around the clock to try to generate some results, making myself more unwell in the process. Thinking logically I knew that procrastination wouldn't help, and I knew that the best way of carrying on would be to put in proper regular hours, but the illogical and anxious part of my brain won every time and I repeatedly found myself holed away in my room watching box sets of Gilmore Girls, House M.D. and Naruto Shippuden and eating box sets of Mr Kipling's Bramley Apple Pies.

One day I found myself sobbing uncontrollably in the shower and began composing a letter to The Samaritans for some help (once fully dry - please do not use a laptop in the shower). I felt like I had no future. Like I was incompetent and completely unable to function in society as a regular human being. Whilst I was in the middle of my email (which never got sent) my mum called and heard from my voice the state I was in. We decided that I should go and see my doctor. After my diagnosis of depression and anxiety by my truly excellent doctor I was given medicine and referred to my university counselling service. This treatment process helped me to face some of my problems and begin to get me back to feeling a bit more able to take on the world. However the improvements weren't instant and during the months I was trying to get better, months ticked away towards my deadline and my work got more and more delayed.

During my second year review with my internal assessor I discussed my feeling that I couldn't generate the work required for a PhD thesis and enquired about changing course to an MPhil. While this seemed sensible to me it turns out this is quite an unusual request and there was no information available online or within university circles to help me make my decision. After talking with my supervisors (I had four in total) it was decided that it could be done and I just needed to complete my current experiments, analyse and conclude, and write a thesis to get that postgraduate degree. Order me my cap and gown! Job practically already done!

Errr... It wasn't quite that simple. The continuing depression, anxiety and my overall lack of motivation still persisted and even the small hillock of work required for an MPhil seemed to be the size of Everest.

Some time later I went home for a week-long visit to rest and to try to inspire myself. And indeed when I got back to my university town I was feeling inspired, but I was actually inspired to admit that I had well and truly had enough and to try to change my life for the better. I went to the student services department and met with the disability support lady (who was excellent) and spoke of my desire to leave. After taking a day or two to think it over I went back and signed a withdrawal form, cleared my desk and ran from campus as fast as I could and I haven't regretted it since.

Don't get me wrong, there were things which made me so happy and kept me going while I was going through such a hard time. I really miss my wonderful friends. I miss the wages. I miss my city - and it will be my city forever. But I do not miss how I felt about work for those two and a half long years.

Today I am claiming Jobseekers Allowance and searching the internet for minimum wage jobs which are nowhere near my field of expertise - and you might think that would be depressing in itself, but I'm so grateful to be worlds away from where I was a year ago. I'm anti-depressant free and I'm looking forward to some kind of future where I can contribute to the world instead of contributing solely to Cadbury's shareholders and UK baked goods profit margins.

Here's some advice for you. If you hate your life, if it's making you sick and you are sacrificing your mental health to try to conform to what you think you are 'supposed' to do, just stop. Stop doing what makes you ill and try to find an alternative. It might not be so easy for you to leave your job as it was for me, but start looking for something else. Update your CV and get out there. You never know how things might have changed in a year's time.

Here's some more advice. If you manage people, get some training. Not everyone is the same. One person might respond well to constant kicks up the metaphorical. However another might actually become very distressed by this method. Figure out your employees and you will get good results every time.

Now if anyone hears of any jobs going, let me know ok?

What is a Fungus?

Here's a lovely video detailing what Fungi are, with the use of some pretty drawings!

GM in the News

Just over a month ago I saw some tweets from Rothamsted Research and read a blog post on Nelly's Greenhouse which made me aware of intended action of Take The Flour Back to destroy a research field trial. In the last month the topic has gained a lot of publicity and now everyone seems to be talking about genetic modification (GM), which is pretty cool! I think it's really important to talk about science. Of course we must remember to do it in a way that uses unbiased facts and avoids scaremongering, but all the publicity is raising awareness of the potential of GM technology.

Before I go any further I should explain that I am pro-GM, as long as it is highly regulated and tested so we can know more about what we are dealing with. I can't see the use in discarding what could be a fantastic tool for crop improvement because people are telling lies and are threatening vandalism. I also believe that people should have a choice about what they want to put in their bodies and that this new technology should not be forced on anyone who doesn't want it. I wouldn't like it if you made me eat boiled cabbage, for example, so I wouldn't make you eat GM food if you didn't want to.

I admit cabbage can be pretty! Image from here

In case you somehow missed it, here's what all the fuss is about: Rothamsted are running a small outdoor trial to test the ability of wheat, with an added man-made gene, to repel aphids. Aphids love wheat and unfortunately cause damage and spread disease. Currently the only way to get rid of aphids is to spray crops with pesticides. Adding this synthetic gene into the wheat DNA by genetic modification techniques makes the wheat emit a plant chemical (produced in peppermint, amongst other species) which smells really grim to aphids and has the added bonus of attracting their natural predators, such as ladybirds. The hope is that if the plant can repel insects by itself we will not need to apply pesticides to our crops and we can reduce damage to our environment.

(I'm kinda hoping in the next 100 years they figure out how to do this with humans. Maybe we could start giving off a chemical which repels mosquitoes! Sign me up, I hate mosquitoes! (Or maybe we could repel those annoying salesmen who hang around town centres trying to make you buy car insurance..).

Image from this blog which is anti-GM.

But seriously, it's understandable that people worry about GM. All new technology can be scary because the consequences are unknown. In the case of GM, it is important to view the process as a tool and not to immediately associate the term with so called "Frankenstein foods". GM is actually just a technique, which can be good or bad depending on who is using it and what their reasons are. Trying to get rid of GM without investigating it further is a bit silly really because it could be a great way of improving our crop productivity and it could help feed the world. Then again it might not, but we don't know until we try!

In the case of Rothamsted's aphid trial, this is probably one of the most sensible approaches to testing GM I've seen. It has been approved by The Food and Environment Research Agency. They have not involved any companies who may want to sell the wheat for profit. This trial is purely for research purposes. They have safeguards in place to stop any transgenic material (that's material with an added gene) from escaping into the wheat population. Anyone who works with wheat will know that wheat pollen doesn't travel very far (although it still manages to get up my nose and give me hay fever), and even if the pollen does manage to reach another wheat flower it is unlikely they would be compatible. Wheat self-pollinates you see.

My field trial :)

The Take The Flour Back website puts a large emphasis on the synthetic gene in this GM trial being a cow-gene. One feature of their video campaign shows a bread-cow. The gene is not from a cow. This is a lie! The gene is man-made and just happens to be most similar to a cow gene. I work with fungi and when I enter the DNA into a website I can find hundreds of different organisms from plants to animals to humans with matching sequences. This does not mean my gene is from a hippo! Things like this drive me barmy. It's like that tabloid headline which said "Victoria Beckham rejected by Simon Cowell". Everyone was thinking that it was all sexy and gossipy but actually the truth was that he didn't sign the Spice Girls to his record label. My point is that you should take everything you read with a pinch of salt. Even what I'm writing here! This is just my opinion. I made my opinion by reading about the subject. If you haven't read up on it, don't view the activist propaganda and get scared because someone is telling you that your bread will soon be made from cow. Try reading more about the subject first. If you are one of these people considering destroying this research, not understanding something is not a good reason to go and ruin someone's work.

Take The Flour Back are planning to "clean-up" the trial site on the 27th May. In other words they are going to trample through centuries old field trials at Rothamsted to access the GM trial and then tear up all the plants. In any other career this planned "decontamination" would be seen as madness. It makes me sad just to think of it.

How about a hypothetical situation: I'm going to break in to my local dentist next Tuesday and start smashing things up because I don't think that they should be allowed to extract teeth. I'm scared by the thought of extracting teeth and have heard that you can die if they put you to sleep when they do it. I haven't bothered to understand why it is necessary to remove bad teeth and I haven't asked for more information on the safety measures in place. I just believe I'm right and that I'm helping everyone out by stopping this process.

Stupid? Sensible? Ridiculous example? Let me know your thoughts.

I have too many thoughts surrounding this issue to be able to write them all here so I will leave you with two videos. One from Take The Flour Back and one from Rothamsted Research. Watch and tell me what you think.

On Ho-li-day!

From today all will be quiet on the blogging front for two weeks. I'm off on holiday! Yay! I'll bring you back a gift ok?

Stem Base Assessments

Lately I've been looking at a lot of wheat stem bases to find eyespot disease, using a method designed by Goulds & Polley. I felt like playing around with MS Powerpoint and making a flow chart from their assessment key to make it easier to digest. I'm no maestro when it comes to design but here's what I came up with:

What Do You Even Do Anyway?

I get asked a lot by friends and family who aren't necessarily familiar with the academic system what the heck I actually do. I decided that I would respond to these FAQs and try to write about my PhD project in a way that doesn't make non-scientists start weeping and clawing at their eyes out of sheer boredom.

Science.

Ok, so, what is a PhD?

PhD means "Doctor of Philosophy" or "a person who thinks a lot about stuff". These three letters are awarded to people who have written a mighty long thesis (I'm talking a monstrous report, at least two inches thick and hard-bound y'all) and gone through a gruelling interview after spending 3-4 long years devoting their lives to a very specific topic which nobody but them gives a hoot about.

PhD projects often begin when someone at a university (who usually becomes the project supervisor) comes up with an idea that they think is interesting and posts it on findaphd.com (other PhD finding sites are available). This idea could be about desiging a fancy new machine, analysing a poet's works, interviewing the public, proving or disproving a theory, and so on.

The would-be-supervisor convinces someone with money (a charity, an independent body, a company, the government) that your idea really is worth forking out for and if you're lucky they get people on board who can pay for things like laboratory costs (commonly £1000 per year for one student to have lab space), a wage or "stipend" for the student (around £13,000 pa at my university) and consumables; like printing, chemicals, blue plastic gloves and other things you might desperately need. In return for you providing them with some most excellent data and results of course.

Trust me, it's an achievement.
This image came from this blog which you should read if considering a PhD yourself.

Wage..? Hang on, you get paid for being a tax-dodging student bum?!

Yes, it's such an intense few years that it's unlikely most PhD students would be able to do a "real" job as well as study and we all need to pay the bills! (Well we don't pay council tax but, you know, all the other bills). From the funder's point of view, paying a stipend to a student means they shell out less than they perhaps would employing a career-researcher, plus they get to make useful business connections with universities.

In my case, alongside my university, the HGCA (Home Grown Cereals Authority) provide most of my funding. They take a levy from sales of a farmer's cereal crop, such as wheat, which they use to fund PhD studentships, resarch and development, crop market info and marketing for the cereal farming world. At first I was surprised when I found out that money was being taken from farmers to fund my work (it did add a bit of pressure to get some decent results), but I figured that if someone didn't pay for research into new methods then we wouldn't progress to bigger and better farming practises. It should all save farmers money in the long term so hopefully they aren't too cross!

I am also funded by FERA (The Food and Environment Research Agency) which is an offshoot of the governmental body DEFRA (Department for Environment, Food and Rural Affairs). As well as financial support, they provide me with opportunities to work in their labs and to hob-nob with professionals in the plant biology business. The experience of working in a business environment compared to a university one is something I have really enjoyed. University life can be like living in a bubble and getting out there into the workplace is eye-opening.

 

What's your work about?

My working thesis title is: Development of novel methods of detecting and quantifying viable inoculum of Oculimacula yallundae and Oculimacula acuformis.

That's a bit of a mouthful so, first things first, Oculimacula yallundae and O. acuformis are the names for the two species of fungus which causes eyespot disease of cereal crops. "Oculimacula" comes from the latin "oculos" meaning "eye" and "macula" meaning "spot". Logical. It looks like this:

Eyespot on wheat. Image borrowed without permission from Dr Paul Dyer.I hope he doesn't mind!

It might not look like much but when the fungus grows through the stem it interrupts the flow of water up the stem and can weaken the stem so much that the plant collapses.

The aim of my work is to design a new method in the lab which people can use to test samples of plants to see: how much fungus is there, which of the two species is present and whether it is alive and able to cause disease. I can't tell you much about this fancy test because it's TOP SECRET (and this has nothing to do with the fact that I haven't actually finished the work yet... *cough*). In theory this will help people decide early in the wheat's growth whether they have the disease and whether they need to spray on some fungicides to kill it off before it does too much damage.

 

And instead of getting on with it, you spend all your time writing blogs instead of doing anything productive?

Admittedly I do spend a bit of time writing blogs but I think it is productive because it helps me practice my writing. If I'm behind with my jobs I'll work into the evening to finish things off. My building usually has PhD students in it during evenings and weekends, outside of 9-5 is often the best time to get things done. It's quiet and you don't have to fight for machines in the lab. On the flip-side they don't put the heating on at the weekends so it can get really very cold.

Aside from my office work (writing reports, making posters, sending emails) I have lab work to do developing that TOP SECRET method I mentioned and I also have field and polytunnel (i.e. a big long tent) trials on the go.

This means I spend time not only in my white coat and gloves but also in my wheat field in wellies and waterproofs squealing because there are creepy-crawlies, or in the tunnel tending to my potted wheat, counting its leaves and so forth. I need to grow the crop I'm studying so I can prove that my work in the lab actually can be useful in the field to help crops grow better. There have been some cases where things that work like clockwork in the lab completely fail when you take them into a real-world situation, so I'm trying to make sure I've got all my bases covered.

For those city types who don't know what a field looks like.

 

What's the plan today then super scientist?

Yeah this one wasn't an FAQ, I made that one up myself, nobody, not even my mother has ever called me a super scientist *sigh*. In case you were wondering, today's job list is here:

• Get hold of some compost and sterilise it.
• Pick up some little pots from the potting shed.
• Get a poster printed.
• Run a PCR (that's a method for increasing the amount of DNA you have in a tube by making lots of copies).
• Go to the field and get some diseased plants for testing.
• Make up a DNA extraction chemical mixture (one of my favourite jobs because it's just like following a cooking recipe).
• Count number of dead leaves on plants in the polytunnel.

Whoever said science isn't glamourous was probably working with anaerobic digestate (that's sewage folks!).

That's it about it then huh?

Yeah! Thanks for reading! I hope that helped you understand what I do, if you were bothered in the first place. I'm sorry to disappoint if you thought this might be a blog on snail populations in Madagascar. Let me know if you find any science that you would like translating into normal-person-speak and I'll do my very best to help!