Learning the hard way – 71

I have done it again; these words are coming from the mind of an un-caffeinated coffee addict. Once again I have failed to inform my partner, who handles our online shopping delivery, that we are low.

I feel quite absent-minded and uber susceptible to distraction, but I will get through this post even if I have to run to the closest coffee shop.

This week, I had a meeting with one of my funders which is the head of the agronomy section of a major premium retailer here in the UK. As with all things we consider with high importance, they are usually far less of a moment than we had imagined, and this meeting was no exception.

We had lunch in the senior common room, and then I gave a presentation about all of the work I had done over the past year. Contrary to the persona my subconscious had given to this person; they were not a corporate dragon whose sole purpose was to ridicule and take away my funding. They were an ordinary functioning member of society who was a nice, encouraging person like many of us.

So, another week has passed, and it was relatively drama free. It has just occurred to me that I should have hyped up the details of this week’s events for storytelling purposes. But that just wouldn’t be me, I am trying to give a more honest and accurate account of what is happening, plus it is easier to write like this.

I did have one legitimate drama this week. For one part of my experiments, I measure colour changes in crops over time. I do this as it can be useful in assessing disorders with the crop. I do this by taking images and then analysing them with software.

For the first time in my life, I had a drive fail on me. When I went to load my images onto the computer, the images were not on the SD card. This is a disaster as I cant just re-take the images as time is essential with this experiment, so the conditions have changed since imaging. Re-taking the images is not an option.

When I put the card into the computer, I can see that the amount of space available is consistent with the amount of space that there would be given my images were still on there. So I know that they are still on there I just have no way on accessing them.

I ended up on google trying to find a solution. After a few hours, I found a program called photorec, and my mind has been blown. Not only did I recover 80% of the files, but I have also learned a valuable lesson as to how computer memory works.

When you delete something, it is not actually removed…

What actually happens is that it becomes un-allocated and therefore it can be written over by new information, but until this happens all the information is still there. This allows us to recover some files if they are deleted by accident, but if the drive got into the hands of someone with malicious intent, the things we though we had deleted might well be accessible.

I have since learned that to be really secure when you’re getting rid of a data drive you should run a program that writes junk data over the entire drive to ensure the deleted data is no longer accessible. There are many programs that will do this for you with the most recommended being called ‘boot and nuke’ which I quite like the name of.
That was my drama. A potentially catastrophic event, with respect to my experiment, was avoided and I learnt a valuable lesson. I am always wondering why I have to learn things the hard way, but I will be slightly less harsh on myself this time as I am not sure how I could have prevented an SD card failing.

All the best,

See you next week.

Mental resilience through increased stress – week 70

My to-do list is peaking at the moment. I have come to the beginning of what is potentially going to be a couple of unusually busy weeks.

But first, I need to tell you something about my state of being. I had my first ‘proper’ boxing class yesterday afternoon, and I am still feeling the effects of it I think. I am very lethargic today and quite spaced out mentally.

We were partnered up and were practicing the blocking of very light shots to the head; after a hundred or so punches, even with light punches, you still feel a little dizzy. It was very good fun though, so I shall be continuing with it; however, I do not wish for the level to rise more than light punches as I need my brain cells!

I am off to play a round of crazy golf in Oxford shortly; I hope the boxing won’t affect my game!

The primary reason as to my upsurge in busyness is that I have to start a new trial on Monday, which involves me driving to pick up the samples. When I moved to the city in which I currently reside, I got rid of my car as it was an unnecessary expense. So when I do need to travel, I have to organise a hire car, and as organisation is my enemy, it can get quite stressful.

It is not stressful in itself, but when you combine it with having to speak to suppliers etcetera to arrange delivery, the stress adds up. Another added factor is that I don’t know exactly what time my samples will be ready for collection – this adds extra tension as I have a time limit in which I have to return the car. This whole process hinges on several people that are not me which causes more stress than I would like.

I do feel that the more times I have done this, the more relaxed I am becoming about the situation, so there is a kind of progress I suppose.

On Tuesday, I have an even more stressful day as I need to take measurements from the samples all day. At lunchtime, I have my Industrial sponsors coming for a meeting, where we have to discuss the project. It is going okay in my opinion, but it is always nerve-racking having to present to someone that is giving you money! Even though it is an excellent learning opportunity, it is always to difficult to see it like that. What it actually feels like is an interrogation.

So, if I can through the first few days of this week without any dramas I will be much more relaxed! So far, nothing has gone catastrophically wrong with the project. I am aware of the gambler’s fallacy, but I still have that sense that a catastrophic event is due.

In the end, I expect it to be quite a normal week; I expect it will more enjoyable than normal, but all the possibilities of how events could deviate toward the negative are hard to control!

See you on the other side!

How do I do this? – 67

Sixty-seven weeks in a row and I still feel as if I don’t know how to do this. What the hell should I write here?

The problem that is incumbent on the blogger is that the format is for relatively small bits of writing to be churned out in relatively short order. Most of us, I imagine, are doing this as a side project and therefore, cannot commit the time required to produce high-quality writing.

Furthermore, if you’re anything like me, you have far too many hobbies and interests that compete for your time. For me, blogging is but one hobby of many; I would say that blogging is approximately 5th on my priorities.

My current method of writing is to sit down in the after-lunch, pre-gym slot and write from the top of my head. I occasionally make notes throughout the week if I have anything I want to include, but that hasn’t happened in a while. I am waiting for that breakthrough where I finally figure out how to write these posts.

Today is the 2nd of February in my timeline, and you will see this in a few months. My plan for the rest of the day is to do a 15k run and then watch the most important rugby match before the world cup. England vs Ireland in the six nations. Come on England!

I have just realised that this is supposed to be a blog about my PhD and I have just been rambling on like a generic lifestyle blogger.

So, at the start of this week, I spent two-days extracting sugars from lyophilised (dried) Rocket. This has become somewhat of a routine measurement, but it does not tell you that much about the quality status of the plant. Generally, after the plant is harvested, metabolism in the plant continues, and sugars are used up for fuel.

By-products from sugar metabolism are used to form various other compounds, such as those involved in defence. As plants cannot defend themselves physically, they often expend a lot of energy doing it chemically – mainly by producing compounds that don’t taste nice to deter predators.

But as I mentioned previously, it is almost useless when assessing the quality of a crop. What it does allow is for comparisons between crops grown during different seasons. Crops that are grown during the summer, generally have more sugar content and are usually of higher quality.

After I had extracted the sugars, I spent the rest of the week dong data-analysis and planning. Unusually, I have found myself in a position where I don’t have any short-term plans. By short-term, I mean to say that I didn’t know what to do with the rest of my week. This is highly unusual for me.

I ended up writing a list of all the events I had coming up, and this included two conferences at the end of the month. Now I have things to focus on and can fill my time. One of the skills I have not yet mastered is the ability to plan for the long term. I have got through life so far, by being what I can only describe as ‘micro-ambitious’. I decide what I want to happen in the next couple of years and try my hardest to achieve that. Most of the time I don’t plan any further than that.

For example, I had no plans as to what I was going to do after my bachelor’s degree. I got offered a job and PhD, neither of which I sought out. I chose the option I liked the idea of the most, and here I am.

Dr NOir – 66

The light is fading fast, and this coffee is getting cold if only I had spent more time planning I wouldn’t be in this mess.

Hunched over the mechanical keyboard, trying to put words on the screen with the intention of contributing to an ever-expanding stream of content that provides no inherent value. Not only is the premise long forgotten, but the mundane nature of discipline bleeds out all of the interesting.

The coffee-shop smell of this room still isn’t strong enough to build a narrative on, and she, the only thing that matters is too distant to see. Ever since I could remember, she is the only thing that mattered. She is the only thing on my mind, the only thing I write about and the only thing that holds my attention any more.

Its Wednesday, I had spent all of Monday weighing out samples and then adding the highly aggressive organic solvent to extract the chlorophyll from my plants. I switch on the machine only to discover it has given up. Perhaps I should have secured several different machines for every experiment I do; given the notorious temperamental behaviour of scientific equipment, I should have known.

Another week, another chance squandered. I am now in the throngs of a back and forth with the owner of a new one of these machines, hopefully by Tuesday I will have access. Now I am stuck at home and out of action, with nothing left to do but analyse the data that I collected well over six months ago.

I have a conference to attend tomorrow, which requires waking up at 5 am, I didn’t try and get a decent education so that I could wake up at 5 am! Either way, someone from the lab group has to go, and the conference is closest to my area of study – not close enough to warrant the couple hundred pounds I am going to have to spend to get there. With these delays and distractions, she seems further away than ever..



Its late at night at kings cross station, and as expected the conference was not worth my time. However, I did see what the people look like who have always known what they want to do with there life and then spent 20 years pursuing it. Needless to say, they make us normal people pale in comparison.

Time to catch this train, and get some sleep, after all, I have a presentation to give tomorrow.

I had fun with this one! Someone in the comments suggested I try and do one of my normal posts in a noir style. I thought that my writing was getting stale and I needed a challenge; this is why this post exists.

The new and the old – week 65

I am sitting here waiting on one of those recent phenomena; I am waiting for a new keyboard and mouse to be delivered by Amazon’s prime service. Once this delivery has arrived I can engage in one of the oldest and greatest phenomena that humanity has ever created; I can return my library books.

I find myself ordering my day around the delivery of packages more often than I would like to admit, and I would not be surprised if there was a term for the phenomenon. But, I should stop complaining as it was in my lifetime that you had to go somewhere to acquire goods. In my case, growing up in a small village, it involved begging my parents to take me to town, or waiting until I could drive and then do it myself. It indeed wasn’t a simpler time.

But enough rambling and pre-amble, it is time to try and twist and contort my thoughts of what I did this week into something more interesting than it actually is.

It has been a slow week in PhDs-Ville, I am waiting on some consumables, mainly filters so that I can continue analysing samples. I am still not that proficient at time-tabling; if I were better I would be a bit more efficient, but also, a lot more fatigued as I would have less downtime. So, I have just justified my lack of organisation as a device for rest and recovery – winging it is one of the best skills one can learn.

The first two days of the week were as boring as you can get, I weighed out hundreds of samples at 0.01 gram per go, which is quite tricky sometimes. From my PhD, I would say that roughly 40% of the time I am doing something utterly mundane that requires no thought whatsoever, it’s not all chalkboards and equations. The beakers don’t wash themselves!

The remainder of the week was spent doing data analysis and writing abstracts for a couple of conferences I would like to go to this year. Oh, and I had a couple of meetings.

Hopefully, if all goes well, I shall be going to Berlin and Prague this year on-the-house. I will have to give a presentation, but that is but a minor act in the academic conference – so I have been told. Mostly it’s for networking a.k.a. drinking, dining and talking – as well as getting a free holiday. Who am I to not engage in such activities.

Having mentioned that, I hate almost all the aspects of conferences; I detest writing the abstract and then presenting it, and I am not a big fan of networking either. I am mostly going because it feels like one of those things you ‘have’ to do. Talking to other people I am still none the wiser as to why people go to them; I think it has lots of un-apparent benefits that are hard to quantify. Anyway, I shall give it a go this year and try my best to seem interested.

It will be nice to get out of the house!

Starting at the peak – week 62

It is the first week of 2019 as I am writing this; staying at my parent’s house for the conclusion of 2018 had me gain two kilograms in weight. I am training for a half-marathon at the moment and consider it extra fuel for training. I will soon be back to baseline.

I have started the year on a peak, as far as my weight is concerned.

As this will be posted long after the Christmas/New year break, it doesn’t make sense to ask if you had a good time. Personally, it was great for me, it was my only break of the year, and it was well timed. I was starting to get bored by the end of the break, and for me, that suggests it was around the correct length of time to have off.

However, it seems my colleagues have taken advantage of the fact that New Year’s day fell on a Tuesday and have taken the rest of the week off as well. The usually busy lab building was deserted except for a few people that had things to be getting on with. I was one of those few people.

I spent all of Wednesday extracting nitrites and nitrates from lettuce samples, then spent the following two days analysing the samples. The reason I was doing this is: partially because I can, but also because these compounds are quite contentious as far as health is concerned. They have been implicated with some adverse effects, mostly in infants when there are a particularly large dose and some health benefits regarding the cardiovascular system.

http://www.bbc.com/future/story/20190311-what-are-nitrates-in-food-side-effects


What remains to be seen is how these dietary components change as they degrade. The positive or negative health aspect may exist when the crop is harvested, but are they still in similar quantities when the consumer actually eats them? This is what I am looking at.

I have got all the data from this particular experiment, and all is left to do is the data analysis, which happens to be my favourite part. I shall make some time to do that next week. I have a lot of monotonous lab-based stuff to do next week so it will be nice to do something where I actually have to engage my brain. Unfortunately, doing a PhD isn’t only mentally stimulating work, there is still a lot of the mindless grinding in there.

I have mostly fallen back into the routing I had before the Christmas break; however, I have been watching slightly more television than I did before and this has taken up some of the time I used to use for self-improvement. The time in the evenings from about 8pm onwards needs to come back under my control. I need to get back to using this time to practice coding.

I haven’t set any new goals for this year, resolutions are not something I usually do; I am one of those people who will set new goals on the spur of the moment rather than waiting for a certain date. I feel as if I am in the middle of a four-year grind and I am living a kind of hermetically sealed life. After I have completed my PhD, I suspect there will be a large void that I will have to fill with lots of smaller goals.

But until then, the grind continues.

blogging on auto-pilot – week 61

It’s now December*, and I have just realised I have been writing these posts for almost a year and three months with only one week missed.

It has been long enough now that I have forgotten where I got the motivation to start a blog from. I know why I am doing it, but I cannot remember where the initial spark of motivation came from. I was probably reading someone else’s blog and thought I should do it.

Anyway, here we are 62 weeks later, and the compulsion to write a blog post is equivalent to my desire to go to the gym. Desire is not the right word, It is more routine than that, and I often write or go to the gym when I have no desire to.

It is a discipline that I can’t see my self breaking free from; this is good news as far as consistency goes, but it certainly enriches my day as much as it used to.

I wonder how many of you out there are also in this state, drifting through the blogging process on auto-pilot?

Perhaps, much like my day job, I need a break so that I can come back more motivated – hopefully.

Taking a break from something you do as a ‘hobby’ seems like a strange concept to me, and I haven’t really thought about it before. I think taking a break from the normal life is the important part. If I have a break where I stay at home for a week, I think I will not get the reset that is required to reset.

Getting away and doing something completely different seems like the correct way to have a holiday for me. Going skiing for example, where I am busy all day doing something else, and I can’t do any work! The only problem I can see if that is wherever I go on holiday, I will always be there.

I think I have just completed my final week of 2018; things have been winding now for a while, and absolutely everyone is on their last legs. Most people in the lab are rushing to finish things so that they can have some time off over the Christmas period and I am no exception. I endeavor to stop doing any work after the 21st of December.

I am going to write a post in January about my year in review. I have lots of different places I can draw data, from such as my health, my finances and blogging statistics. I am looking forward to producing this data-driven blog post. I think it will be as good as my most popular post about my three-month blogging experience.

So look forward to that if you want!

*Yes this was written a few months ago.