The floodgates have opened – week 42 as a PhD student

Note: this was written three months ago

The rains have come after three weeks, and it genuinely feels novel. Yes, rain feels novel in England; this is the first time in my almost twenty-eight years in residence that rain has felt like a gift. It is not a closely guarded secret that England is not a garden-of-Eden-esque summer paradise; although that is the image we give out in all of our media.





The rains have come, and it feels like a metaphor for my PhD. The threshold has been exceeded, and now it is a constant grinding run all the way to the end. Long gone are the days where I can wake up and do the bits of work I like, and now I have to dig in and do the work I have put off.

It has put off for a few reasons that main being that I don’t enjoy it, the second being that I am not good at it which affects my enjoyment of it. It is writing a scientific report. The practical reality is that I have to sum up all of the things I have been doing over the year in a format that I find hard to write for people that will never read it.

They will skim read it and use their judgement as to whether or not it is of the standard someone in my position should produce. By the time you read this, I will have undertaken the exam I need to take to progress. If I fail, you will know by the sudden drop off of PhD related posts, and if I pass you will see a few upbeat posts that slowly degrade back the mean over time. Plus, I will probably tell you as it would be one of the highlights.

The pressure of having to produce this report has focused my mind slightly; I have realised that I do too many things. I Wonder if you’re anything like me dear reader. I do a lot of different hobbies, and every few months one gets added, and one falls off the list.

The problem with this is that I have lost of things that I need to do each day so that I can please myself and feel as if I am moving forward. For example, I dance, I run, I lift weights, I blog, I read, I code, I play video games, I do yoga, and I have a girlfriend.

All of these things require varying amounts of dedicated time. I have realised that I need to go deeper into my hobbies rather than wider! I should get good at a few of them rather than keeping a bunch of different hobbies that is forever growing. I think if I had thought about this at the start of the year I would have never started a blog, as it takes a lot of time.

This week I have spent a lot of time in the lab doing mundane, boring, tedious activities that would have been interesting if I weren’t the one doing the work. A few years ago, seven actually, I was working in a warehouse hating my life wishing I was doing something I thought was meaningful.

Skip forward seven years, and now I am in a lab doing research that has not been done before and contributes to mankind’s greater knowledge, and I feel the same as I did seven years ago. It is all part of figuring out how to deal with life I suppose. For any of my older readers, do you feel as if you have life figured out? And at what age did you figure it out?

As the rains have come, it is time for me to get back to my first-world-middle-class-centre-left-metropilitan-elite problems.

An average week – Week 41 as a PhD student

What witty opening line can I come up with this week? I’m drawing a blank; perhaps you could suggest one.

Words are merely tools and if you use the right ones you can actually put even your life in order. Hunter S Thompson

I guess the first thing of note that I have done this week is sign up for a half marathon next year. The furthest distance I have run before is eight miles, although I regularly run five kilometres twice a week. Why did I do this? I needed a new physical challenge, and I have never had a running goal, plus it was a spur of the moment thing where I saw an advert and decided it we be a good thing to do.

I am looking forward to it, and hopefully, it will be a stepping stone to the full marathon someday. I am not a natural endurance runner, I am very quick, and was always the fastest sprinter during my youth, but as is normally the case, the talent for sprinting I was gifted was taken from me in endurance.

That was Thursday, so what did I do for the rest of the week? I set up the freeze driers for someone who was on holiday. We tend to freeze dry everything because plant material has a limited shelf-life, and it is difficult to measure everything you need to measure in that period; therefore, we need to preserve it. We remove all the water from the plant and then grind it up, so we have a homogeneous sample that does not degrade. Water is essential to life, and almost all biological reactions stop once you remove water, therefore once we dry our samples they are frozen in time, and we can study them in our own time.

It is quite an interesting process, and setting up the machines is relatively simple, but I keep forgetting exactly how to set them up as I use them so infrequently. Whenever I do these things for other people I feel as if I am getting in positive favour balance; being in positive favour balance is something I always try to achieve. I am sure I will need all the favours I can get very soon.

I will need the favours as I had my summons for my one year transfer viva; this is very important as it is essentially the only exam other than the final thesis that you have to do during a PhD. I have to submit a dissertation and sit a viva; it is very much like the end of a Masters degree from what I understand. If I pass, I continue as normal; If I fail, I change to a Masters program. It seems like a win-win situation, but that kind of thinking is a trap.

I came for the W and will not accept an M.

I got to spend a lot of time programming this week, which is my favourite thing to do these days, if I were starting my career again I would certainly study computer science. There is something that I find really satisfying about automating mundane tasks. I am actually considering trying to push my career in a direction to where I get to combine my agricultural skills with technology; this is something I will have to figure out how to do before I finish my PhD.

In summary: it was an average week.


40-week writing streak – week 40 as a PhD student

Ladies, Gentleman, Machines and Others, you are about to bear witness to an act of discipline as I have never been less motivated to write. It is Sunday, and all I want to do is relax and watch videos on YouTube, with the possibility of chocolate. However, all I have is a coffee and a 40-week writing streak that I am not going to break.

I spent two days this week photographing sliced lettuce in a glasshouse. I know what you’re thinking, and yes, it is the bleeding edge of science. I am in the glass house because that is where the lighting chamber happens to be; probably because they had run out of other places to dump it.

I am looking at how the colour of the lettuce changes over time, and for that, you need everything to be perfectly constant. If the lighting changes slightly, and I am not vigilant, I could interpret this as a change in colour of the lettuce and therefore find a type 1 error, which, for the non-statistical, is where you see a significant result where there isn’t one – a false positive.

To account for this potential drama, I have included reference standards for each image; form this standard I can adjust the image and normalise if there is a problem. For the first 30 samples, I collected there is a problem. There is a hole in the top of the lighting chamber, and I didn’t realise it for quite some time. The effect of this hole, is the images taken when it was not covered are five percent lighter.

This could have a significant impact on the results so I will have to adjust the lighting levels in post for these images. In fact, I will normalise all the images, but these will need the most adjusting, lucky for me I have learnt to program and the one-thousand-plus images I have taken will all be adjusted and analysed automatically, what a time to be alive!

I spent another two gloriously dull days milling dried rocket samples (the plant, a.k.a Arugula in the USA) so that they can be analysed. The essence of this procedure is putting the plant into the top of the grinder, which is kind of like a desktop wood chipper and collecting the resulting homogenised plant matter.

Repeat the grinding procedure for well over 200 samples, and you have yourself one mindless, monotonous task to be completed by any anonymous flesh. I still have a couple of hours worth to do with these samples, and then there are the samples of lettuce that I have just collected which will need to go through the same process: beautiful!

I’ll be honest with you dear reader; I cannot remember what I did with the other day this week. If I were not so lethargic, I might be more distressed by this issue. Anyway, it is time for me to get on with some work (boooo), so I shall leave it here this week, I hope you all have a pleasant week!

Glasshouse challenge – week 39 as a PhD student.

Note: this was written three months ago, as were all my posts.

As I sit here writing this, it is one of the hottest summers I can remember, and England are about to play Sweden in the world cup; there is a lot of potential for this to be one of those talked about summers for years to come.

I have managed to complete two days of what I am going to call the glasshouse challenge. What is this challenge? Well, for my project I am monitoring how the colour of plants change over time. To monitor the plants I need to take pictures of them, which means I need a lightbox. The lightbox resides in the glasshouses at the university – I haven’t had any time to move it.

I have spent about six hours on each of the two days that I was photographing the plants in 38°C heat. For an Englishman, this is the approximate temperature of hell. Because I was using my phone as a remote trigger for the camera – the lightbox has to be hermetically sealed, so no outside light interferes with the image – I needed a complicated charging/cooling system.

Towards the end of the shoot, my phone would run out of battery, so I needed to charge it. The problem with this is that it overheated! To remedy this, I wrapped some Ice in some tissue paper and laid my phone on top of that; it was a highly sophisticated solution, perhaps It will get published in Nature?

One positive from my time in hell is that I am now able to withstand this relatively mild 30°C heat with ease, whilst my girlfriend won’t even let me near her as I am ‘too hot’. She has been severely crippled by the heat and spends most of her time sleeping on the sofa.

I have spent a lot of time trying to find out what chemicals I need for my experiments and how much they are going to cost me. Provisioning for myself is something I did not expect to have to do at the start of my PhD, partially because of the undergraduate experience, my expectation was that I would turn up to some room and say I need x and they would hand it over.

It turns out; this is not the case, you have to buy absolutely everything yourself as if you are a member of the general public buying research chemicals for personal use. Maybe this is different at different universities, but here it is every man/women (mostly women) for themselves.

For the first time in roughly 15 years, I am excited to watch a game of football. I have not seen this level of shared excitement throughout the nation before, not even during the 2012 Olympics in London.

It really goes to show how popular football is here in the UK and Europe. I realise that most of the readers of this blog are American, and when I say football, In American that would be soccer. American sport is fascinating in many ways. Americans have many unique sports that are almost exclusive to America, American football, basketball, baseball etc. Of course, they are not exclusive to America, but they might as well be as I don’t know any other nation that takes those sports seriously.

Imagine if America competed in sports that the rest of the world did! Due to the size of the population, I imagine they would win most competitions, making the country even more popular. I may write about this subject at some point as it is fascinating.

Re-inventing the wheel – Week 38 as a PhD student

It has been between 25 and 30 Celsius all week, with a high pollen count. For an Englishman, this weather is nice to look at, but uncomfortable to work in.

As I was drinking my morning coffee and skimming through BBC news, I spotted an interesting article that was highly relevant to me.

It is relevant as on Monday I am going to be collecting 90 bags of lettuce, which is 27 kilograms worth. I am in half a mind to delay my trial and sell them for a profit!

I have spent the last month trying to organise delivery of these samples, and the week where they finally get delivered is the week where the supply of lettuce to the UK population is likely to fall short. I think it is best to carry out experiments on the lettuce rather than satiating the nation’s appetite. It is not as if they are missing out too much, after all, lettuce is essentially a bag of water.

It has been a much more balanced week; I have managed to balance writing with more practical pursuits, in turn, this has made for a much more enjoyable time. I spent a lot of time trying to track down people who could help me find a suitable place to image my samples; when I was about to settle on a system, someone recommended the exact thing I was looking for – which was a large box with purpose-built lighting inside, and painted walls of consistent off-white colour: perfect.

This is one of the inherent problems with academia. PhD students carry out most of the research and create most of the specialist equipment, but because they are only around for 3-4 years after they leave the equipment they have made or purchased gets lost. Because of this inherent inefficiency, I assume, the wheel gets reinvented quite a lot: I almost re-invented last week.

It is not like I am taking an inventory of all the physical stuff I acquire/create, so I am sure someone will re-invent this stuff long after I am gone, and the cycle will continue. I am sure this kind of thing never happens in business or government.

We had a lab meeting with a twist this week. We had it at out supervisors house, with a BBQ and lots of beverages – red wine for me.

It was a great bonding experience, and it went almost flawlessly. I say almost as there was one person – who is quite absent-minded socially – who proceeded to whine about their project towards the end of the night.

One of my unwritten rules when it comes to social engagements with collogues is that you do not talk about work as down that road there be monsters. Fortunately, it seems that most other people share this view; however, one person did not, and now she is even further in negative favour with our supervisor.

She is older, than I am and really really book smart, but has no ‘common sense’, I am not sure how to help, or if I should. I am sure everyone knows a person like this, how do you deal with them? I’m guessing you don’t.

You reap what you sow – week 37 as a PhD student

The sweet, gentle, torture of having a week off of lab work; where instead, I try and write my literature review.

Writing is still my weakness. I am perfectly adept at filling a page with words that are vaguely related to the subject I am trying to write about. I still feel as if the thing I am trying to say is entirely lost from the piece; also, the section doesn’t flow well. I am confident I can fix the flow of it, but I am not sure I can figure out what I am trying to say.

One of the underlying issues is that with scientific, academic writing you need to have evidence for all the points you make for obvious reasons. However, I struggle with integrating the points I am trying to make into a coherent argument where all the points work together to make a piece. What I have just described is the source of my frustration this week; well, most of it anyway.

The other source of frustration is that it is proving a lot slower to get samples delivered than I thought it would be; I was expecting to make one phone call, and the samples would be on their way as this is what happened the previous time. Alas, this is not the case, this supplier is not so fast as the bureaucratic processes that were in place with the previous supplier are not developed. Therefore, I have to play the waiting game, and this creates some anxiety as I fell as if nothing happens soon my supervisor will be on my case.

Now that the happy stuff is out the way…

It was quite a nice week; on Tuesday we harvested all the rocket plants we planted two-weeks prior. It was backbreaking work again and the rest of the day was a write off once we got home. Although it was a nice change of pace, I will not be too worried if it doesn’t happen again.

For the rest of the week I was sat at home writing, and although I found it frustrating working from home has its charms. It is quiet, and I can manage my time how I want. This was the main draw of a PhD to me: the autonomy. It is nice to make lunch in my kitchen and nip out for a quick run whenever I reach a sticking point. It felt a lot like the earlier months of my PhD, And I hope that I have many more weeks like it. I expect next week will be the same.

Because I had been doing an awful lot of lab work in the previous month my reading has fallen behind, and next week I intend to finish A brief history of time by Stephen Hawking; I started it over a month ago, and it is a relatively short book. I was enjoying it, and as it was my second time of reading I was understanding the concepts a bit better than the first time.

One concept that fascinates me and I still don’t fully understand it time — I even wrote a post about it. For those of you who have never read any physics books you might think time is an easy concept, but in the eyes of relativity and the physical universe, it is very strange.

If anyone has any book recommendation, I would be glad to receive them as I need to get back on my reading train! Preferably non-fiction.


A song of procrastination and ire – week 36 as a PhD student

Game of Thrones clips are filling my procrastination periods this week; I do not know why. The interesting thing about procrastination is that it, for me at least, is spontaneous. If I could predict when and why I would procrastinate, it would be easier to avoid.

Image result for Game of thrones procrastination

This week has been a relatively good week as it was more balanced than usual. By balanced, I mean that the writing to lab work ratio was much more favourable. I have previously discovered that the best week for me involves writing and practical work; if I do too much of one or the other, I get bored and disinterested quite quickly. Two days of writing with three days of practical work seem to be the sweet spot at the moment.

I have noticed that my writing has improved; mostly it has improved in the fundamentals, grammar, punctuation etcetera. What I am finding hard, is the scientific storytelling aspect, linking ideas and guiding the reader through my thought process.

I think there are three main reasons as to why this is. Firstly, a lack of experience, I imagine once I have published my first paper it will get much easier. Secondly, I do not have a model of how I should write, this is related to experience, but also it is related to understanding your subject intimately and converting your thoughts into prose. The final thing is something I just mentioned, knowing what you want to write in the first place, I certainly do not know exactly what I want to write; I have a rough idea.

I have spent a lot of this week doing admin related activities, I am trying to organise some samples to be delivered, and it just so happens that all the people that can make this happen are away, so I am on a bit of a wild goose chase. Oh well, you can only do what you can do; I’m not too bothered about it, there is always next week.

I have a weekend of work ahead of me, there are a few hundred samples I need to analyse, and I need to learn how to use my camera! Furthermore, I would like to get some writing done; I need to keep pushing with my reports before the anxiety of not having completed it catches up with me.

I also ‘need’ to go to the gym and watch the rugby! Next week, I am going to harvest the 9000 plants we planted two weeks ago. I am much less enthusiastic about it this time around as I have already experienced it once. I did it last year in Rome, in the 40°C heat. The lunchtime meal in Rome was perfect, but it was not worth a second day of harvest.

In England, the food is much more standard, and we are much less pretentious about it. It is fuel. This may sound strange, but I would much rather be in the English countryside where the weather is mild than the outskirts of Rome, where it is far too hot to work! We shall see if I still have this opinion after the harvest.