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.

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.

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!

Why I don’t think I will be a successful scientist

I have been comparing myself to established scientists within my field, and without exception, the result of my comparison leaves me thinking that I do not want to be like any of those people. I suspect this is mostly my naivety clouding my opinion, but there is a vital component to being a scientist which I currently do not care for. The essential component is producing papers and hustling to get noticed by the relative popularity of these papers. A lot of what you read in a paper is not crucial and usually is only there because publishers want a specific style to differentiate their journal from the others – classic business behaviour. I have extremely low motivation to try and get good at producing papers, and this is why I do not think I will be a good scientist. I have been pondering this for a while, and when I was re-reading Thinking Fast and Slow, I spotted these few sentences which, of course, resonated.

I have yet to meet a successful scientist who lacks the ability to exaggerate the importance of what he or she is doing, and I believe that someone who lacks a delusional sense of significance will wilt in the face of repeated experiences of multiple small failures are rare successes, the fate of most researchers”.

Daniel Kahneman – Thinking Fast and Slow, page 264.

Ninety-percent of the time when I talk to my colleagues, they will be the one talking about their project. It is not that I do not enjoy my project, because I do, it is because I rarely feel the need to tell people what I am doing. I would rather talk to them about non-work related stuff; I found this lack of wanting to show-off about my project even more pronounced when I went on a residential course with lots of other students. I was a shoulder to cry/climb on for people to moan and brag about their projects. I preferred to talk about them and get to know them. I love the problem-solving part of my project, the rest of it I could easily delegate to someone else if the option was available. I suspect if I had a big ego, or I had been damaged in some way so that I had this burning desire to prove the demons in my head wrong; I would be on a mad crusade to reach the top. Luckily for me, or maybe unluckily I do not have the ego or desire.

Reflecting on what I have said so far, I assume my thoughts will be a lot different in five years. I think this as my goals have changed drastically over the years, and I have no inclination that this trend won’t continue. I also realise that you could probably apply my particular dilemma to a lot of different disciplines, so I hope it has not been too narrow!


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.

Blogging overload – Week 24 as a PhD student

Repetitive, monotonous, tedious, is how a feel about writing blog posts at the moment. I have been writing blog posts all weekend, and my motivation for writing this one is undoubtedly lower than average. My guest post for the British Nutrition Foundation has been sent back to me with some suggestions and corrections. At first glance, this seems like a bad thing, however, they told me that they definitely want it, after the changes have been made to make it more relevant to their audience. I have never seen so many comments on a word document before It is all a valuable learning experience especially as they phoned me up and went through it with me! I did not expect this to happen, I was waiting for it to be accepted or rejected. Instead, I am getting a mentor on how to write blog posts. A few of the many things I have learnt are:

  1. Be inclusive of everyone. I was using words and sentence that would be specific to people similar to me. An example would be that not everyone understands what the word heuristics means, so I changed it to rules-of-thumb.

  2. Don’t use the same keyword two sentences in a row. For example, Consumers have different levels of sensory perception. Varying levels of perception among individuals lead to different results. Doesn’t read as good as: Consumers have different levels of sensory perception. Individuals sense things to different levels which leads to varying results. This may be a poor example, but hey, what do you want from a noob like me!

I will do a detailed blog of the development of my guest post at some point in the future.

I have got back in the lab this week, which has lifted my spirits a bit; I have been trying to use an ammonia assay kit to determine the quantity of ammonia in plant tissue. Day one of testing with this kit was mixed; I need to find a sample of plant tissue with ammonia in it to confirm if my method is okay. I have also had confirmation that I can go and use the GC-MS equipment next week, so I can do more practical stuff and get out of this writing rut that I am in. I have discovered that I like practical problem solving much more than writing. Don’t get me wrong I don’t hate writing, I have just become a bit tired of it with the amount of it I have been doing lately: I need to find balance in my work.

I have also sent off my 6-month report, which was a document that talked about everything that I have done in the past six months and everything I will do in the next six months. One piece of doubt that is starting to creep into my mind is that I am good at the practical elements and am sure I can meet the end goal of the PhD. However, I am not so confident I can do the writing aspect of the PhD, it is something I am going to have to talk to my supervisors about. I have been thinking about it for a while without acting on it. I shall add it to my diary to make sure I do it!

I spent about £200 of my research budget this week on the ammonia assay kit and a NoIR camera to play with. I am going to try and assess plant health with it. I had a bit of retail therapy, with the house’s money!