PhD Blog Posts

Broken! – week 44 as a pH D student

Broken! Not physically or mentally, but technologically. This week, two out of two of the machines I was needing to use broke. One of them, a single quad LC-MS broke twice.

I have been extracting like a third world country that has just discovered a rich mineral wealth under its feet, or a hedge fund that had based its headquarters In the UK. But seriously, Seeing as I have a few a big deadline coming up, where a lot of data is required. I have been busy running lots of experiments to collect said data.

The list of things I have extracted from Iceberg lettuce and rocket this week is as follows:

That is quite a lot of data, however, I can only extract these compounds from fewer than half of my samples as the rest are yet to be freeze dried, and are currently sat in a freezer waiting for there turn in the drier. I have just remembered that one of the driers is broken, so that makes three out of three.

When I have weeks like this, I question as to how anything gets delivered on time in science. It is a constant stream of ‘fix, run samples, repeat Because. The machines we use are very sensitive and relatively rare, they often break down in ways only official engineers can fix. Which is costly, both in time and money.

Another speed bump we had to contend with this week, was in the form of refrigeration. Because the storage space is currently at a premium, we had to hire our own freezer trailer. Well, this week, the terms of our lease were up and we had to move all of our samples into a backup freezer, which is not designed for long-term storage. This is one of the aspects of project management, that I dislike. In fact, I do not enjoy project management at all. I wish I had a surplus of everything, and therefore, remove the need for any planning.

One of the positives, and I know I am clutching at the thinnest of straws, at least it wasn’t my fault.

I am going through, the proverbial meat grinder of late as I have a big exam coming up. One hour I am feeling fine and its not even on my mind, the next minute, I am a shuddering wreck prepping for my exit from university life. You buy the ticket, you take the ride.

I am at the stage where I have cut back all non-essential activities, and am focusing all my efforts on my PhD at the moment. It is not a state I like to be in, as I am reading, exercising and learning less; which is ironic.

I cannot wait to get back to the time when leisure was a word I understood. Only a few weeks to go. I realise that with a few tweaks, this post could be the ramblings of someone prepping for Brexit. But, as a remain voter (a metropolitan liberal elite), that is none of my business.

New distractions – Week 43

I have had a new distraction come into my life this week, and it is watching sailing videos on YouTube. To give some context, I have only been sailing once, and that was when I was a child. I have come to accept the fact that I am a fantasist; I often fantasise about living a life of leisure, no alarm, and no responsibility for anyone other than myself, and a life-long adventure.

This is why I have been living vicariously through people on YouTube who travel around the world doing whatever they feel like. The only barrier to entry for this fantastical life is money; either a means to make it whilst on your travels, or a sufficiently stocked investment portfolio that you can live of the dividends indefinitely. Usually, you reach both of the aforementioned states by the time you’re at retirement age; I am making a conscious effort to achieve both of these ASAP.

This month marks the one year anniversary since I started investing. I am well aware we are In one of the biggest bull markets in history, but this year, my portfolio returned me +15%. For those of you that don’t invest my money grew by 15%. By my calculations, based on the amount of money I have been investing, I can retire in 45 years! I was only putting in less than half than I could afford because I was scared. Since finding out how long it is going to take me to retire, I have redoubled my efforts. Anyway, that’s enough rambling for one week, if you want to understand my philosophy towards money, go here, here and here as gained all my knowledge from them, I also read this book.

I have spent a considerable amount of time this week trying to perfect a few graphs using a Python sub-package called matplotlib. It results in similar looking graphs to excel, but it is far more customisable and therefore, far more inconvenient. However, I have resolved to learn how to program, so I shall persevere no matter how perverse. After many lines of code, I achieved what I could have done in Excel in under twenty clicks. However, once the code is there, each following graph only takes seconds to produce, so at some point in the future, there will be a crossover point where this long-winded method of producing graphs will come good: I hope.

As my one-year report is due soon, I have been running around trying to organise equipment I need to collect data, so that I can have a horrible time right before the deadline writing about all of the data I have collected. In between me running around like a headless chicken, I have been writing my report and watching sailing videos.

Because of this looming deadline, I have dropped a lot of my hobbies, so that I can stress about my report for more hours per day. I find it hard to think and do anything else when I have deadlines, which is part of why I want to live a fantastical life of leisure. Why won’t people just let me do what I want and pay me unconditionally is that too much to ask?

I am very much looking forward to getting this report behind me and going back to being content with life; I expect you will see my mood towards my PhD decline at a fast rate for at least the next six weeks. Then it will bounce back up to baseline after that, and hold steady for a few years, then a significant period of depression when I have to hand in the final piece of work.

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.

Expectation

summer_relax_chill_summer

Reality

dtifsuD

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.