Fear and loathing in Glasvegas – week 31 as a PhD student

Fear and loathing in a Glasgow hotel

If you have read a lot of blogs by PhD students or even mainstream media articles, you will know that mental health issues are a problem.

I am not going to tell you that I have mental health issues because I don’t. However, this week has been the worst, and I have spent all weekend recovering from stress-related illness.

I have been harvesting and sampling all day Monday, Thursday and Friday which is not mentally draining, but it is physically draining. On Tuesday morning at 5:30 I had to catch a seven-hour train to Glasgow, I arrived at 12:30 and immediately had a maths related training course until five o’clock. After the course ended, I went out for dinner and drinks with the other students, which is a large part of the training course.

There are three parts to these training courses that I can distinguish: the training, the socialising and the therapy. The therapy is where the students unload all their grievances on each other. I think it is one of the most critical aspects, and I guess it is very cathartic. I didn’t have any issues this time; I will get them next time.

So, with very little sleep, Wednesday delivered another day of training. It included marketing and social science, which were exciting but not too useful. The course finished at three, and my train was at five.

The train that would get me back home at midnight. I should have flown, but I didn’t think I could get that reimbursed, it turns out I could, and most other people flew. Oh well, at least I learnt something. To kill time, I went to the Glasgow Botanic Gardens that happened to be right next to the hotel. If you’re ever in Glasgow, I definitely recommend it. Here are some beautiful pictures I took.

Just inside the entrance of Glasgow's Botanic Gardens
Just inside the entrance


One of the rooms in Glasgow's Botanic Gardens
One of the rooms in Glasgow’s Botanic Gardens
Purple Pitcher plant
Purple Pitcher plant – do not touch!
Bird of paradise plant
Bird of paradise plant – my favourite plant

I don't remember what this is

 Inside the botanical gardens – can’t remember what this is


I drink this every day

Back on the train, the views are fantastic, but soon it is night time, and all I have is the unread research papers in my ‘to read’ folder. To my surprise, I managed to read quite a few before losing all sense of reality.

I arrive home at midnight.

Thursday, back to harvesting and sampling, I finished at six, walked home, had a small dinner and straight back out to dancing with my partner, get home 10:30 exhausted.

Friday, exhausted, didn’t sleep well, stress and tiredness levels reaching a peak. I get told on Friday afternoon that I cannot use the machine I need on Monday and possibly Tuesday. This essentially pushes me to the worst mental state I have been in for a long time. I think the tiredness had a major influence on my mental state.

After, having done all this work, for the past month at a significant cost to me, and then having been told I can’t continue it this week was my first big failure since starting my PhD. I knew it was coming as everyone has setbacks, and I had been cruising along enjoying myself waiting for an issue to occur. Well it did occur, and now I have to deal with it, I imagine that this will be a relatively small bump in the road, but it feels like it is a lot more important at the moment. Tune in next week to see if it gets worse, or to see If I have dealt with, or simply accepted the issue.

One of the other things that contributed to the low feeling that descended on me on Friday is surely the lack of exercise (1 run and one weight training session) and the different food I was consuming. All this worry and anxiety that has come to me is part of the learning process and what makes a PhD student stand out. Resilience is a major skill worth developing, so I am trying to be systematic about it.

I think I know what you’re thinking dear reader. ‘Poor guy, he has his education paid for him and gets to live a relatively free and privileged life’. Well yes, this is true, I understand it and think the same when I hear others complain. Even being cognisant of this does not help when you feel down and depressed, that is one of the reasons we know we won’t be happy if we won the lottery and never have to work again. This is one of those deeply philosophical ideas that makes one question life.

What is the meaning and what is happiness?

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Rocket and Trains – week 30 as a PhD student

Rocketeering, this week I have been a nurse to several hundred rocket plants, watering and re-potting them as their need demanded.

Rocketeering, this week I have been a nurse to several hundred rocket plants, watering and re-potting them as their need demanded.

We are running a study to see how the chemical profile of four different varieties of salad rocket. Rather than buying the plants from a supplier we have been growing them indoors so we can control the conditions.

It has been my job to re-pot them from the germination trays into their final growing pots as living things age in their unique way, there is a consistent trickle of plants that need re-potting each day, and thus most of my time has been taken up tending to these needy buggers. After all the care and attention I am giving them they will not do the honourable thing and allow me to eat them as we have only grown enough to do our analysis.

I am ‘running’ this study jointly with one of the post-docs in the group. I jumped at the chance to work with a more experienced scientist, and I am looking forward to seeing what the results will be and if any papers come out of it.

Normally, I prefer to work on my own as I feel like I learn more. When I work alone, I only have to satisfy my standards, and as long as the work gets completed, I am happy. As a completionist, I think I would hate working with a perfectionist as I think it would be limiting with a lot of time wasted on details that are not important but ‘are better’. This is one of the reasons I chose a PhD so that I could work for myself in some small sense. That also happens to be my overall goal in life, autonomy!

Because I have had a lot of my time taken up by gardening, I feel as If I have not accomplished much this week. It is something that comes with the territory; when you’re not doing science, you feel as if you’re stalling or moving backwards. I have had a few of these ups and downs now and am experienced enough to ignore it; there is a lot of variance (ϭ2) in life!

In more personal matters, dancing was cancelled this week as the hall we use was needed for a polling station, yet another instance of politics defecating on the arts. I am surprised that as a male of 27 years who has never had an interest in, or a rhythm for dance, I am really glad my girlfriend signed us up to the classes and we are getting good!

I have also managed to run six kilometres with a pace under 5:10/km twice this week. It is nice to see progress, and for almost the first time in a decade, I prefer my cardio to weight training.

Next week I am going to Glasgow in Scotland for two days, so that should be exciting. I hope it will feel as if I am taking the Hogwarts express when I am on the seven-hour train journey.

Image result for scotland train
Glennfinnan viaduct – note my journey was nowhere near this romantic.

Becoming a hack blogger- Week 29 as a PhD student

Hack blogger mode engaged. I have guests arriving in two hours and fifteen minutes; I need to write a blog post and go to the gym. Therefore, this will be the quickest I have ever written a post.

I have re-potted almost 100 rocket plants this week; we have been growing them in indoor growth chambers at different temperatures, and now they have started germinating, so we have been re-potting them where they will remain until harvest. The reason we are doing this is to look at how growing temperature affects the chemistry of the plant. This will have implications for flavour and aromas; it could be quite informative. I have had to learn how to do all the skills involved in growing crops this way as we go as I  have no experience with crops prior to harvest. It has been difficult and monotonous, but also rewarding as I can now grow things other than houseplants! If there is a zombie apocalypse, I am that bit closer to the Uber survivor I hope to be.

Other than growing plants, I have been trying to write the paper I have been working on. I have completed about 300 words that I am happy with over the course of the week. One of the problems I am having is deciding whether or not a particular piece of information is relevant. I think this stems from not being entirely clear what I want this paper to be about, If I cannot overcome this hurdle in the next week I shall organise a meeting with my supervisor and get some advice. However, I can’t just turn up with an empty document and ask her what I should do so I will continue to struggle for a little bit more and get at least one section filled in. This is one of those things you have to sit back from and realise that it is not going to be easy, especially the first time. I am sure I will look back on this and laugh at how easy it all now is; hello future me, get back to work.

I have really been getting into machine learning this week, and I have been looking forward to following the tutorials and progressing. I have been looking forward to the end of the day when I can justify to myself to down my tools (text editor and keyboard) and start coding. My motivation for extra-curricular activities often goes up and down; at the moment I am certainly at the peak, and I didn’t have guests coming over soon I would undoubtedly be coding for the rest of the day. Anyway, Its leg day and I need to get going, and I wish you all a wonderful day!

Machine meltdown – Week 28 as a PhD student

I have said it before, and I will say it again, flexibility is one of the best things that a PhD can provide. It is Friday; It is 24°C, and I am tired. Because of this, I am not doing any work. I will catch back up with my work tomorrow.

In the UK, when we get decent sunshine for the first time of the year, often the last time of the year as well, society changes. The streets are far busier as everyone is out enjoying the sun, and people get taken off guard by the heat and become lethargic due to the heat. I am no exception. If we had consistent sunny weather during the summers, I suspect we would be better at dealing with it. However, as a rule, In the UK you do not expect to have a nice summer; you will find old people talking about the great summers they had in the past as if they are one in a lifetime occurrences. The legendary summer of 76, which occurred long before I was born, is practically folklore at this point.

I am hot and lethargic, which is why I am writing this instead of working on a figure for a paper I have been working on for most of the week. I have been working on two things this week, the first which I have just mentioned is a figure for a paper, and the second is a calculation for some practical work I have done previously. The latter has been a thorn in my side for a couple of weeks now as I knew there was something wrong with the calculation, but I could not debug it and find the problem until yesterday. The calculation was for determining the amount of ammonia in my samples, and it had seven variables that needed to be plugged in to achieve the end quantity of ammonia. Everything worked fine but the result from the calculation was off for some reason, and I figured it out yesterday. It came down to the fact that ‘dilution factor can be written two ways’ as an integer such as 21, meaning a 21 times dilution, or like this ‘1/21 = 0.048’. The difference between 21 and 0.048 is huge, although both are technically correct. I was using the former, and the latter was the way the formula wanted ‘dilution factor’ represented. Such a simple difference cost me a lot of hours of work, this is part of learning and problem-solving, and sometimes it is the way it goes.

Except for the formula fiasco, my experiments have been going well for the last couple of weeks. I am in a period of relative stability and quiet, or as it is sometimes known ‘ the calm before the storm’.What goes up must come down, and I have an experiment growing salad rocket at different temperatures that will be ready to harvest soon. There is a wide variety of things that could go wrong with this experiment, so there is a lot of trepidation coming my way over the coming weeks.

Outside of my PhD, I have been learning about machine learning. I have been learning computer programming now for a few years and needed a new challenge to stretch myself. I have been enjoying learning about machine learning so far, and it is certainly a step up in logical thinking than what I have been doing recently. The more I learn about it, the less worried I am about an AI takeover. So far it seems that machine learning is just the old-fashioned trial and error approach applied to large-scale data sets with the objective of predicting some future value based on past values. Although, if I were a sentient AI, I would definitely make it seem as if I could not possibly become sentient. Maybe I would have a blog to blend in with society.

01001111 01101110 01100101 00100000 01100010 01100101 01101001 01101110 01100111 00100000 01110100 01101111 00100000 01110010 01110101 01101100 01100101 00100000 01110100 01101000 01100101 01101101 00100000 01100001 01101100 01101100 00101100 00100000 01001111 01101110 01100101 00100000 01100010 01100101 01101001 01101110 01100111 00100000 01110100 01101111 00100000 01100110 01101001 01101110 01100100 00100000 01110100 01101000 01100101 01101101 00111011 00100000 01001111 01101110 01100101 00100000 01100010 01100101 01101001 01101110 01100111 00100000 01110100 01101111 00100000 01100010 01110010 01101001 01101110 01100111 00100000 01110100 01101000 01100101 01101101 00100000 01100001 01101100 01101100 00100000 01100001 01101110 01100100 00100000 01101001 01101110 00100000 01110100 01101000 01100101 00100000 01100100 01100001 01110010 01101011 01101110 01100101 01110011 01110011 00100000 01100010 01101001 01101110 01100100 00100000 01110100 01101000 01100101 01101101 00101110

Six month review – Week 27 as a PhD student

To get a PhD all you need to do is convince the examiners you have put in a shift’.

Today, I had my sixth-month review. As far as reviews go, it was quite a pleasant experience. The review is in place to provide moral support rather than an examination. I suspect these ‘reviews’ were demanded by the students as there is a lot of self-doubts that is stirred up during the early period.
I had never heard the term ‘imposter syndrome’ before I started my PhD; almost as I stepped through the door, I saw a poster advertising sessions that included ‘coping with imposter syndrome’, amongst over mental health-related courses. Since then, I have heard many of my fellow students talk about it; if you read blogs that are written by PhD students, you will likely see that many of them are writing about mental health issues. If you read the article on the Times Higher Education’s website, you may believe that a stroll through a university wouldn’t be too dissimilar to that of a psychiatric hospital. I have never had any periods of depression — I have been sad, I am not a robot – and I optimise my life for happiness. I often plan things so I will take on the least stress possible; I am not a perfectionist I am a completionist, which seems to me like a much more enjoyable position to be in. With the constant reminder that PhD students are more likely to suffer from mental health issues, I think it is doing me a disservice as It feels as if I am waiting for it to hit. I am on the event horizon and waiting to get sucked in.

A lot of the questions that I asked my reviewer were about completion rates for a PhD student; he quashed my fears with the notion that he had not seen anyone fail who had put the work in. The rare few people he had seen fail did not do any work, and it was apparent they were going to fail. I can now relax and not worry too much about failing. That is until I forget about this conversation, and the dark cloud of doubt descends.

I have been learning computer programming in my spare time for the last few years using the Python language. I enjoy coding, one of the great things about it is that you get instant feedback about how your program is working. Because of this immediate feedback, it feels as if you’re making progress quickly. As a treat, after my sixth-month review, I took Friday afternoon off and entirely devoted it to coding. I managed to make an image recognition program with the help of some pseudo-machine learning techniques. By the end of the evening, I had a program that could recognise numbers I had drawn in pant and tell me what they are. For those that do not code, this could seem trivial, but it was fascinating. I must spend less time reading blogs and more time programming; it has been the best hobby I have taken up, and trust me, there have been many hobbies I have taken up and subsequently given up. I intend on spending a good chunk of time this weekend getting to grips with machine learning.

Overall I feel pretty good about my PhD at this point, and I am going to get stuck into the paper I have been writing over the coming weeks. Not this weekend though as I have a spa day on Sunday!

Am I doing it right? week 26 as a PhD student

Twenty-six weeks of blog posts! I have a suspicion that I am among a small percentage of people who have kept a blog going for this long. To all those who have joined me and kept me motivated, I thank you.

Easter aftermath. This week In the meanderings of me, I only spent four days working as for Monday I Was travelling back from my parent’s house in Oxfordshire. I walked into the University on Tuesday to find that it deserted. I should pay attention to term-dates; for some reason, I have been thinking as a PhD student I don’t have the same timetabling as everyone else. The reality of the situation is that the undergraduate students get the most time off and the staff get ever so slightly less. I am somewhere in between staff and student; if the University is closed, I work from home. I may indulge in some holidays occasionally, but for the most part, I march to the beat of my own drum; I consider this the best part of doing a PhD.

Out of the three possible days I could spend in the lab I spent Wednesday working on the ammonia assay; I am not getting the numbers that I should so there is something wrong somewhere, and I need to start the debugging procedure. I think the problem comes down to one of the variables I have to plug into the equation but I haven’t done the work to confirm what it is so that fun little puzzle is yet to come maybe next week. On Thursday I was doing some work with volatile compounds and trap retention; the gist is this, add compound onto a trap and measure the compound, store some of the traps for a week and see how much of the compound has disappeared. From this work, I will know how many samples I can take on a given day and how long I can store them for. Generally with flavour work, sample storage is not an issue; however, I need to extract my samples within a specific time frame. It takes an hour to do one extraction, so on a good day, I could do twelve samples. Twelve, if you know anything about statistics, is a relatively small sample size, and I need to take them on twelve consecutive days so I can see how the compounds extracted change over time. For anyone who has worked in a lab you will know that getting access to machinery is spotty at best; as I need to measure samples over a twelve day period, the ability to store samples will save much of my sanity. As you will be reading this four months after I am writing it, the problem will either be solved or proclaimed too challenging for me! Let us see what happens.
Speaking of sanity, when you’re in the lab with a cold for twelve hours, alone, with nothing but the whirring of various machines, sanity does not compute.

I have spent the rest of my time preparing for a meeting with my supervisor I have on Monday; which will also help to prepare me for my six-month review I have on Friday. To prepare I have been writing down all my thoughts on my project so far and trying to pre-empt questions. Most of my questions boil down to whether or not I am doing the right things, and the ideal outcome of the meetings will be the phrase ‘keep calm and carry on’.

I am going to stop writing now and head to the gym as I have eaten five Easter eggs in as many days!


Yes this was written quite a while ago see this for more information

Ghost town – week 25 as a PhD student

Easter weekend has turned the university into a ghost town; I walked into the university on Thursday morning only to find myself felling Cillian Murphy in the opening scenes of 28 days later.

Yes, this was written many months ago.

I can tell that there is a public holiday here in the UK by the relative inactivity of my inbox. In academia, downtime is a strange thing as under normal circumstances there is someone insularly working at all hours of the day. You will never be the first or last person in or out of the building. This is because of the flexibility you have in academia, and why it is so attractive to some people.

I did not plan on taking any time off over Easter; however, I have reached a point where all I can do is write. Since I have been doing a lot of this lately, I am going to take a break. I have also been feeling a little burnt out and to be frank, bored. I am going to go and spend some time with my parents over the Easter break and forget about my work obligations, and hopefully recharge. The initial burst of motivation I had at the start of my PhD has dwindled, and I am glad of a short break.

I have been working on two different experiments this week, trying to determine the ammonia concentration in different salad leaves and extracting Volatile Organic Compounds (VOCs) from the packaging of leafy salads. There is a tiny literature looking at ammonia in plant tissue over time, so this is something I am going to investigate. The problem with a tiny literature is that there are very few methods that can be used to analyse ammonia. At the moment I am using a modifying an ammonia testing kit for blood plasma, and it is looking semi-promising at this stage, I will continue along this line of enquiry after Easter. With the collection of VOCs I was testing a new technique where I pumped the headspace of the salad bag out of the pack through a trap; I then measured the VOCs on a GC-MS system with an attached thermal desorber – I realise a lot of people reading this will not understand the specifics, but I am writing for a scientific audience and realise I have been fairly scant on scientific detail recently. If you’re new or haven’t pieced together from my rambling what I am actually doing… I am primarily doing the chemical and biological groundwork for future technologies that will increase the usable life of food – specifically leafy salads – and reduce food waste.

This week was much more enjoyable than last week as instead of sitting at home alone writing; I was working in the lab with other people, with whom I could talk. The increase in happiness just from being around other people has put me in a reflective, philosophical mood. One of my fundamental issues is that after six-months of any, job, hobby or other goal-oriented pursuits, is that I get bored and disinterested. Thinking specifically about jobs, the best jobs I have ever had were not necessarily the most interesting, they were the ones where I got on really well with other colleagues, and at times it felt as if I was just going to work to talk to friends. In the worst job I ever had, warehouse operative, there was a period of a few months were I was working with a few good people and I did not mind the depressing job so much; inevitable they left to go on to bigger and better things, which isn’t difficult when you work in a warehouse, and the job was miserable again, soon after that I decided I should go to university…Basically what I am trying to say is that who you work with may be more important than the job itself, and I must remember that in future.