PhD Blog Posts

Alcohol and blogging – week 21 as a PhD student

This is my first time writing early on a Saturday morning after an evening which involved more drinks than I am used to. I feel as if my mind is only 60% in attendance so this might be an interesting one. One of the key questions that one who is financially sensitive has to ask themselves is: ‘ Does the feeling I have this morning, and the £-41 from my bank, balance with the enjoyment I had last night?’. My answer is maybe. We were out on the town as it was the last night that our friend would be staying with us before moving out. The real question is whether or not we could have achieved the same experience for less money. My guess is that, yes, yes we could have had the same experience for less money. However, that would require thinking and effort, which as a human, does not always come easy. Preamble over.

Time is flying at the moment; my six-month review is due at the end of the month. Six months! It feels as if I still have ten months of work left to do in my first year. I need to get ahead on my writing; I am starting to feel as if I need to increase my working hours, or maybe micromanage my schedule better and make sure I do a lot of writing. Actually, I need to do more coding, data analysis, reading, and writing. The workload is starting to pile up; I can barely see over it.

So, what did I do this week? Well, Tuesday and Wednesday, were the long-awaited Waitrose Science days. It was mostly two days of presentations and networking with high-level management and PhD students; this is one of the rare opportunities you get by virtue of being a PhD student. My networking skills leave something to be desired, but fortunately for me, these science days occur yearly, so I will have at least three more opportunities to improve. I had to present a poster for the first time. The first thing I noticed was that you could tell who the supervisor of the student was based on the poster. A colleague and I both have the same supervisor, and you could tell this by the fact that our posters had more than double the words anyone else did. The 2nd thing I noticed was that there are two kinds of response from people looking at your poster. The first of these and the best are the ones who ask you about it and try to understand what your thoughts on the subject are. The second type of person, will listen to what you have to say, ignore it, and then proceed to tell you there opinion on the matter. Often the latter tend to take up the more of your time. Still, in spite of this, I still had nothing but positive feedback. One of the most significant revelations about the world of academia is that 99% of people are very good human beings; I can see why many people choose to stay in this world.

If you were on the fence about choosing academia over the industry, I would urge you to at least try academia.

You should judge a book by its cover

You shouldn’t Judge a book by its cover.

This is a phrase to which I take exception, and I do not know why this phrase has become so renowned as it seems so false to me. I am not talking about this phrase in its literal sense with regard to books; however, I still think it is false when talking about literal books. I have a degree in nutrition and food science, and there are thousands of books that I can judge by the cover and know they are trash and not worth my time. Time is a resource I do not wish to waste, so I will judge some books by their cover to save it.

Onto the more philosophical application of the phrase. The cover is all the information you have about someone whom you’ve never seen before. If you have already seen someone or something, you have already judged them/it at least once. One extreme example I have to evaluate this involves children or vulnerable people. Should you allow a child to interact with any random person as you should not judge them by their cover, or should you judge them and base your decision on all the visual cues you have?

As an adult I judge people, rightly or wrongly – here I am arguing that it is rightly– by their cover. If I am walking down the street and see some drunk men quarrelling, you can safely assume that cover will be judged harder than an autobiography by a reality TV star.

Why I think this phrase still has some credibility is that invariably whenever you meet someone, they are a good person. Should you judge a person as good before you’ve gotten to know someone? And is It even possible to not judge someone? I doubt it.

In fact, I would go further than saying you should judge a book by its cover; you continually judge by the cover. As you gain information, you should continually re-adjust your judgement as people can and do change.

There are a number of reasons as to why I do not understand this phrase and therefore, do not take it seriously. I imagine this could be a contentious issue and my opinion may be somewhat naive, so please educate me.

Apparently the phrase was first published in the mid 18th century, and frankly, that’s where it should have stayed.


Week 20 as a PhD student

We have reached a tiny milestone this week, this is my twentieth consecutive week of writing, and the fifth month of my PhD. I have just come to the end of a hectic period; as the light of the tunnel came within a few metres, I received more tunnel. The first piece is in the form of an exam, and I need to do an online course culminating in an exam, to be able to attend a course allowing me to use liquid nitrogen. Of course, this is something I want to do and will help me with many experiments, but the notion that I have to sit an exam still sends shivers down my spine. I have a few weeks to complete the course, so it is not an immediate priority. The second piece of the tunnel is the first of my bi-yearly reports. I have to fill out a form and produce a thousand word document on the work I have done thus far. This gets assessed by my primary supervisor and an external assessor: I have one month to complete this.

I am starting to worry that this recent trend of deadline-after-deadline will continue until I am finished my PhD. The pressure will keep building with each week that goes by, and there is no time for thinking. I am seriously considering blocking out part of my diary for thinking, My project is quite broad, and has some philosophical elements to it. For example, what does ‘fresh’ mean? My conclusion is that ‘fresh’ is a simile for ‘recently’. Shelf life and how to define it is a much more challenging proposition, and for me, requires a lot of thinking.

This week I received more details about my Knowledge Transfer Network course that I have to attend as part of my studentship on a yearly basis. It is a two-day course, which will be held Glasgow’s Hilton hotel, where I have got to attend different workshops. These include things like: maths for biologists, advanced data analysis, managing social media and so on. Again this comes back to the strangeness of higher education, where for an undergraduate degree you have to sell your soul, at PhD level you get paid to do the most fantastic things. For that reason alone I would recommend doing a PhD, especially is your primary joy in life is learning.

This week I have been extracting data from the previous weeks experiments, which were the extraction and quantification of glucosinolates and isothiocyanates from rocket leaves. I am looking at these compounds for potential markers of shelf life; in an ideal world, they would change in a predictable linear fashion over time so that I can use them as makers of shelf life. So far, it looks as if Isothiocyanates do reduce over time; however, I have only used small sample sizes so far, and need a more significant experiment to confirm this. I have not been able to analyse the glucosinolates yet as the damn undergrads are hogging the computer that has the software on it. I will install the software on my laptop next week! Agilent Chemstation for those who are wondering. I may or may not have taken the databases from the lab’s computers so I can use them on my laptop. I have also continued work on my review paper, and this is an arduous task at the moment as I don’t know what I am trying to say. Progress is slow, but it will get easier; I need to keep setting time aside to write, as I have been demoting it to a secondary activity, with experiments being the primary.

I feel like I am at a peak at the moment, as I am looking forward to a lot of things, and the dips (deadlines) are while away. I shall enjoy this time, for I know it is only temporary.


Note –  this was written approximately three months ago.

Where the word ‘Blog’ comes from.

On my, about me page, I have mentioned that I don’t like the word ‘blog’. This Is mostly due to the connotations associated with the word.

Let us see if you have the same image as me. Approximately, it is a young person, mid-twenties perhaps, with a profile picture standing on top of a cliff or [insert scenic cliché], and the filter used makes it very envious. It’s mainly a picture that says look how great and exciting I am, come and learn how you can be more like me. If you want to experience this post in 4d, I recommend putting on in the background ‘That positive feeling’ by Alumno or ‘make it shine’ by Sophonic or better yet ‘Carefree’ by Kevin Mcleod. Does this put in mind blogging to you?

Since I have said that I do not like the word I thought I should find out where it came from. A quick google search and I am on Wikipedia. Not the best source for academic enquiry, but seeing as this is quite frothy it will do.

According to Wikipedia, the word blog is a truncation of the ‘word’ weblog, as in web-log. This seems to make sense to me; people have kept logs for the ages, and I mostly associate the word with nautical . If you’re keeping a log on the web, it makes sense to call it a web-log. Would web-diary, or webdi have been a better alternative, we will never know. I am sure you can have fun with potential alternatives.

To read the blog of the person who coined the word blog look here!

According to the same Wikipedia page, there are over 156 million blogs in existence. That means that the chance that you’re reading this particular blog is less likely than winning the lottery? It also puts into perspective how much competition there is to be a successful blogger. Based on these numbers it should surely be one of the biggest industries in the world. To put it another way, 0.00064% of bloggers have followed this blog.

My opinion of the average blogger has changed a lot in the three months I have been weblogging. The picture I have of a blogger now is an artisan that produces interesting niche content in many forms for seemingly no other reason than catharsis. Maybe there is a hint of, ‘I know I am better than 95% of people, so surely I will become successful as a blogger’. Superiority illusion is surely a key driver for a lot of things, and weblogging would be no exception.

Physically shaking – week 19 as a PhD student

Once again, a skill that I thought was overhyped in its importance has had a significant impact on me this week. I am talking about networking; as an introvert, this is a not a skill I enjoy nurturing. I mentioned last week that I had to give a presentation this week, it went okay. It was a three-minute thesis competition that I did not have a choice about my participation. I felt okay giving the speech as I had practised it around 50 times in the mirror; however, my legs were physically shaking behind the lectern. I did my talk, got off the stage and that was that, or so it thought. At the lunch break, to my shock, I had many people coming up to me and saying that they found my talk interesting. I accepted the compliments and just assumed they were being nice, and perhaps they were. The next day I ran into someone whom I had never met, and again, to my surprise, they said they liked my talk. I started talking back to this person, and asking her about her work; we had a good conversation about measuring sugars! The most exciting impact from my talk was yet to come; I received an email from someone in the audience who worked for the British Nutrition Foundation (BNF), and she said that she enjoyed my talk and wanted me to write a guest post for their website(1). Of course, I will jump at the opportunity, and post a link to it on here once it is live; the only issue is that it will remove my anonymity, maybe it is time to own my work. So, what did I learn from this experience? Giving talks, no matter how terrifying and seemingly irrelevant looks as if it is an excellent way of increasing your opportunities.

The conference that I had to give my talk at occupied most of my time this week. However, I did manage to run two different experiments; making this week one of the busiest so far. I measured the volatile compounds given off from rocket leaves, and the microorganisms that reside on them. I also got close to finding out what compounds I have seen that are not in the standard library’s.  I also extracted glucosinolates from rocket leaves and will review those next week. This weekend, I have spent almost all of it trying to make a poster for a conference I have next week; I am looking forward to the conference but do not relish making this poster. February has consisted of two presentations and a poster presentation; I hope I do not have any more for a long while as I need to get my head down and write.

I did not win any of the prizes on offer for the three-minute-thesis competition; normally, I would probably just ignore this. I have kept the book of abstracts, and intend on going through it and looking at the writing to try and figure out where I can improve. The younger me would not do this, I believe in learning from your mistakes and intend to get around to reading the abstract booklet later today! Maybe I will do a teardown of what I wrote and how I could improve it, and compare it to some of the other entries.

On a more personal note, we – my partner and I – have had a friend staying with us, as she split with her partner and needed somewhere to stay while she finds a new property. She is occupying the room where I keep my gaming PC, and as a result, I have not been playing games all week. This might be the solution I needed to the time suck, that is video games. It has been quite refreshing to have a flatmate; I have not shared accommodation with anyone other than my partner before – except holidays – so this should be an exciting experience, and might stop us becoming too comfortable and predictable with our lifestyle.

The most significant lesson I learnt, or re-learnt this week is how important networking is. I shall ensure that I keep it at the forefront of my mind when considering what I should be doing with my time. I hope you all had a great week, please let me know what you’re up to, maybe link your blog?

(1) – I ended up going through with that guest blog post which you can see here

How digital cameras work

Some of my PhD work involves the use of cameras, and pre-empting a talk I will inevitably have to give at some point, I should learn how they work.

The first thing you need to know is that cameras detect electromagnetic radiation. For us humans, we can only detect this radiation between the wavelength of 390-700 nm. Because of this, most digital cameras are set to capture this specific band of radiation. Cameras can be built to detect wavelengths of almost any size, from X-ray’s which are very small to radio telescopes which are extremely large. Here is an excellent graphical representation of this.

Source –
The word camera, according to Wikipedia, ‘comes from camera obscura, which means “dark chamber” and is the Latin name of the original device for projecting an image of external reality onto a flat surface.’ I prefer to think of cameras as electromagnetic (EM) radiation detectors.

Cameras detect the EM radiation that is not absorbed and therefore, reflected from whatever they are pointed at. The sensor is mostly a trap for the EM radiation. Then EM is trapped, and the camera’s computer converts the signals it has in its ‘trap’ into colour In the form of digital values.

In most cameras that you will encounter, a Bayer filter is used. This filter filters light into three colours: red, green and blue (RGB). The filter is positioned in front of the ‘trap’ and using this filter, and you can quantify how much R, G or B is landing on your ‘trap’. The other two primary colours are estimated using good old maths. Here is a good image showing this.
Image result for bayer filter

Source –


After the relevant processing steps, a giant array of pixels is created. Pixels are the smallest elements in the image. The atoms of the image world. An image can be thought of as a three-dimensional array with width, height and depth. Where depth, in this case, is a different colour channel. So, you will have three two-dimensional arrays stacked on top of each other in an RGB image. With a value in each channel. For example, see the picture below.

rgb array
rgb array

In this case the cell in position (o,o,o) – [255,255,255] would be rendered as white, black would be [0,0,0]

The meeting – Week 18 as a PhD student

I will start this week with a quick update on my experience of publishing these posts. I posted two posts on the first day of making my site; It has become clear to me how important a headline is. One of my posts is titled ‘An unexpected PhD student’, the other is titled ‘ Week 1 – mediocre expectations’. I will let you be the judge of which one got 100% of the views that day. I don’t know why I expected the fact that being a PhD student would be more interesting than the run-of-the-mill fitness or lifestyle blogs. Oh, how I was wrong. This adds another dimension to this experience; previously, I thought people would click on my posts and give me feedback on my writing. My current belief is that I will have to become a lot more savvy with self-promotion and become the corporate-waster I despise. Although, It will probably look good on a CV…

This week1 I had my first supervisor meeting, I had to give a presentation about all the work I have been doing, and mostly justify my funding to my industrial sponsors. At my university, this occurs every 3-4 months, with larger formal reviews at the 6six month and one year mark. I am glad to say it went well, and that my supervisor’s – all four of them – are very supportive. I had been looking forward to this meeting as I have not had any feedback as to how I am doing; this is worrying as you feel as if you could potentially be wasting your time – and their money. I saw this meeting as more of an opportunity than an interrogation, as I needed the feedback. I am glad I do not have to prepare for it anymore though as I am bored of preparing presentations for the meantime. On that note, I have been asked to present a poster at the end of the month; another couple of weeks not working on my actual work is upon me. I should reframe my thinking, and see it as an opportunity to improve my communication skills; at the moment I see it as a chore.

If you have read some, or all, of my previous posts. Firstly, Thank you! Secondly, you will see that I have been complaining about not knowing what to do, and wondering if I am doing enough work. Well, ladies and gentleman, I now have too much to do; it took 18 weeks for this to occur, what a joyous 18 weeks. If experience is anything to go by, the time will start to pass a lot quicker! I have been preparing for another presentation that I have coming up next week, so my week has been quite boring. However, I did manage to do something other than prep presentations; I have started work on my first academic paper, mostly just the research but I did manage to write my first line, which as we know, is a start. A lot of the research involved looking for journals I could publish in; it looks as if anyone can start a journal as many journals had websites I would describe as home-brewed. There were not many that I will consider for publishing; I think that sticking to the big players – those owned by Elsevier etc. – is the best strategy for me at this point. Writing this paper will be a massive undertaking, and I expect it will take a year.

I have finally finished Infinite Jest by David Foster Wallace, to be honest, I don’t recommend it. Unless you want an endurance challenge, I don’t think it was interesting enough for me to recommend it over other books. I will be running back to non-fiction for a while; I am unconvinced that reading fiction is a good use of my time. I have mentioned in the past that I have been writing code as part of my PhD; I have come across a few barriers recently regarding the installation of python packages. I have had a little bit of luck, but I am still stuck, however, I will continue to work on the problem as it is deep-rooted now, and I want the satisfaction of solving the problem. A less mature version of myself would have given up, and gone with another, a lesser method of achieving the same goal – measuring the colour of leaves objectively. I think this resilient mindset is something that is worth cultivating. It may be a cliché, but I believe that the work is much more important than the result. It is just important to take time to appreciate what you’re doing and enjoy the ride, as the happiness from the result is very short acting.

1. I need to find some more opening phrases.


As with all these posts, they are roughly 4 months behind the present. Interesting how all the problems I had at this point are the least of my problems 4 months down the line.