Merry Christmas! – week 49

Week forty-nine that is the longest Un-interrupted spree of anything I can remember. This post will most likely be a pivotal point as I hand in my one year report on Monday.

As you may be aware, because I have been whining about it for what feels like six months, I have to hand in a report that is the deciding factor as to whether I can carry on studying for three further years or leave with a simple masters degree.

One of my issues, among many, is that I get bored of reading my work quite quickly and have pretty much lost all interest by this point. There are still a few days of editing and last minute additions to go. Here is a graph of my attitude towards my work when a deadline approaches.

As you can see from the figure, there is an increase in effort up to roughly one month before the deadline. Then I lose enthusiasm as the deadline approaches. Well, folks, I am at the last point where my enthusiasm is very low, I am sick of reading my work and can’t wait to hand it in. They say a thesis is never finished; it is just abandoned. That is how I feel with all work, to be honest.

It will be great to have the life back where I can, spend my weekends relaxing and exploring rather than sitting at my computer finding things to distract me from my work.

In the week of a PhD student, there has not been much to talk about this week. I did do one thing that was slightly interesting. I may be pushing the boundaries of the acceptability for the use of the word interesting, but I did some microbiology!

I had done some micro before, during my undergraduate studies, and thoroughly hated it. The reason I am doing it now is that my supervisor said I should, and I agreed. It may give us some useful data. I had forgotten how much was involved in cultivating microorganisms. I had remembered that something’s had to be sterilised but hadn’t realised that absolutely everything needed to be sterilised and that a special maximum recovery diluent needed to be sterilised and used. So most of the effort of the experiment was spent on sterilising everything. I quickly remembered why I am not too fond of micro work.

The experiment went okay, albeit a few days later than I expected due to the need for sterilising everything. I am going to repeat it in a few weeks to see how much worse the samples have become and hopefully capture the entire range I would expect to find in real-world situations. I will think about that when it comes to it.

Wish me luck people, next time I talk to you I will have handed in my report and had my viva. Although as this was written three months ago, I probably won’t remember what it was like.

Caffeine dreams – week 47

I have now become familiar with a new type of hangover, I am sure I have had it several times in the past, but it has now become frequent enough for me to notice it as a distinct phenomenon.

When I want to work late into the evening, I usually have to be caffeinated. Often I get my timings correct and my caffeine high peters out just in time for bed. Inevitably, however, I get my concentrations or timings wrong, and I am lying in bed until the early hours of the morning waiting for my adenosine receptors to get unblocked.

After I do get to sleep, I inevitably lay in longer, to bring some balance to my life. However, it feels as if there is some universal force that doesn’t want me to sleep past 8 am as whenever I do I have this strange hangover. In theory, I should feel the same after equal periods of sleep; If I get 8 hours of sleep, I should feel as if I got 8 hours of sleep no matter of when those 8 hours are taken. This does not seem to be the case.

An interesting thought came to me while I was in this sleepy caffeinated state, and It is slightly political so feel free to skip this. I was born a European, who also happens to be British and English. And now seeing as Britain(primarily England as far as voting goes) has decided to leave, I will no longer be a European through no choice of my own.

Until now I had never thought of my identity as fluid as it is, but I guess nationality is much more frivolous than I had suspected, which makes nationalism even more of a joke.

This post had meandered away from its intended content, so let’s talk about being a PhD student.

I have found a delicate balance this week between writing and practical stuff. I spent my mornings (9-1) writing and spent my afternoons (1- boredom) analysing data. This is my preferred approach as I can do the thing that requires the most amount of creative input and brain power in the mornings, when I have the most energy, and relegate the monotonous, repetitive tasks to the afternoon. I hope I can maintain a schedule like this indefinitely(unlikely).

I have realised all too well, that collecting data seems to take many months longer than I suspected it would. This means that I will need to run many different trials simultaneously If I want to stay on track. This is another skill I am going to have to get used to. At the moment I am very anxious about it, but I guess I will have to accept this lower standard of well-being as the new normal for the foreseeable future.

I will keep calm and carry on; I hope to strike a good balance between work and play next year as I certainly have not achieved it this year.

Festival season – week 46

Well, I can’t think of anything better to do with my Saturday morning, so I shall write my weekly weblog.

As I write this, it is day two of the Reading festival – I am aware that what I am about to tell you will expose my location, but I shall throw anonymity to the wind – and I live very close to the festival site, so for the last few days I have had a constant stream of taxis going past my house1. Reading festival, as far as I can tell, is a sixth-form convention.

I have been to the festival a few times, but as I live so close, I have never camped. I think you have to be 18and comfortable with no sleep for three days, to even consider camping at a festival. I enjoy live music less and less as time goes by, the whole shared experience thing is not for me. I am not even slightly jealous of anyone attending the festival.

I have heard a lot of people complaining the festival is less ‘rock-centric than it used to be. You hear this kind of thing all the time in music, it is very tribal, and people often attach their identities to the music they listen to.

My point is this, the demographics of the festival is clearly 18-year-old people having fun with their school friends before they leave for University. Clearly, It makes sense to aim the music at the people that are likely to be attending, and as there are fewer rock acts in the public eye, it makes sense that current 18-year-olds will prefer different music. Festivals go in and out of business like empires, well done to Reading for catering to there audience and therefore surviving. Okay, enough about a music festival, you have never heard of.

As has been the theme of me for the last few weeks I have spent a couple of days writing, I shall say no more on the subject it is not the time nor the place. The most interesting – I admit I am playing with the boundaries of the word ‘interesting’ here – the activity I did this week was to spend an entire day analysing the output from one of my experiments.

A quick recap.

We grew Rocket plants at different temperatures 20, 30 and 40°C to see how it affected the chemistry of the plants. You will have to take it from me, that the plants showed a wide variety of phenotypes across the different temperatures which is interesting in itself.

Now I am looking at the results from the chemical analysis. This required me to learn new software and techniques for analysing compounds. I have well over 200 different outputs each with 10 or so things inside I need to look at.

A lesser man would see this as a dull, repetitive task that adds no value to the development of me. I, however, see it as a great learning opportunity. Well, the first ten are a great learning opportunity, the rest is a rinse and repeat process that makes the Marvel universe look innovative2. I learnt how to confirm what an unknown compound I was looking at is. By searching for the output from the UV spectrum and matching that with the extracted ions, I could confirm what compounds I had In my sample.

In short, you look at the mass of the molecular ion and then compare that to the known retention of the compound, if they align you can be mostly sure the compound is correct3.

In summary, it was quite a repetitive week, but I did learn something new, and overall I would say it was a good week. I have had worse.

1. Rented apartment, thanks baby-boomers.

2. A character in the marvel universe is almost exclusively 2-d. They have a super power and hidden secret e.g. murdered parents.

3. Exclusions apply.

Making time to write – Week 45

It is Sunday morning here in England, and I am writing this blog piece early so that I can work on my report. This is not what I imagined when I started blogging. I thought It would be difficult to be consistent, but not writing early morning on a Sunday difficult.

This week has been relatively routine, on Monday I loaded up the freeze drier, a procedure I can now do on my own. It is a large green box, that looks as if it was built in the 50’s. There is very little to it. There is a refrigeration component and a vacuum component. Mostly, you put your samples in, turn on the vacuum pump, and then wait.

Because the all the water in the plants is frozen and there is a vacuum, the ice sublimates to vapour and condenses on the condenser plate in the back of the machine. Five days later, you have a bunch of crispy leaves with no water in them. From this point, you have leaves that will not degrade in a hurry, leaving you to sample at will.

On Tuesday, I had a meeting with my supervisors which is always nerve-racking, but usually a pleasant experience. This one was no exception, I am on track at the moment and need to keep calm and carry on. They talk a lot and try to give good advice, and I try and pick out the best bits as it is tough to remember everything they tell you.

On Wednesday I was doing general busy work, loading samples onto various machines and doing extractions in the lab. On Thursday I had a writing day, where I stayed at home, these are nice to have at least once a week. Friday was a repetition of Wednesday.

As I have entered a period of relative busyness, few of my extra-curricular activities have slipped. I have not had any time to read any of the books I wanted for the last few weeks, and I have not played any video games, which means I haven’t spoken to many friends in a while.

Another activity that has slipped is my blogging; I have not managed to write my mid-week posts. This is because the time that I would normally set aside to do this has been taken over by writing for my PhD. I can handle the disruption for my routine for about a month at a time. I do not think that this disruption is worth it in the long run, and I would not want to put up with it for the entire four-stretch (my PhD is funded for 4 years).

I have had some good ideas – my opinion – with respect to blog posts. I think I am ready to start diving into nutrition and leverage my degree in nutrition in a thinly veiled guise for the creation of easy content. Also, I would like to do some crow sourced science, mostly by the collection of data from surveys as that would be feasible. Please let me know if you know of any decent sites for large scale surveys and data collection!

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.





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.