Week 5

After my first month as a PhD was so exciting and jam packed with things to do, I hoped this week would slow down, so that I had the time to sort out all those little things that get pushed aside when you have big projects to work on. Some of the topics in this week’s post may get a little scientific, so I will make the words or phrase in bold and leave some links at the bottom of the post for any of you that are interested in reading more.

Spangled Darter (Etheostoma obama) named after Barack Obama.
A common tread of the Darter fish, is they are named after a
USA presidents. 

The week started with the usual meetings with the unit and lab team, I found out that I was accepted onto the genomics workshop in Český Krumlov, Czech Republic and was followed by my very first session of Journal club. Journal club is a very interesting concept, were people present interesting journals that could be very different from their own topic, but still relevant to our departments field. It is something I will definitely take part in when I find a paper I enjoy enough to take the time to present. This week Alexander Jüterbock gave a very good presentation on an extremely interesting, but a not so statistically significant paper. The paper was called “Epigenetic divergence as a potential first step in darter speciation” (Also linked at the bottom of this post).

Epigenetics, for those of you that don’t know it is the study of genetic effects that are not caused by DNA itself and may be a result of environmental factors, that switch genes on and off and change how a cell works. If it is still a little confusing let me give you a quick example, every cell in your body has all the DNA within them that makes you, you. Your skin cell is a skin cell and not a white blood cell for example, because only certain genes are being expressed. In this paper it focused on a particular type of epigenetics known as “DNA methylation”, which is when methyl groups (a chemical compound) are added to DNA, which in turn modifies how it functions. The papers results, simply put, tried to show that epigenetic changes such as DNA methylation, could influence or be the first step in speciation (evolution).

The excited little scientist! 

As I mentioned previously the paper was extremely interesting, but the paper seemed to be lacking in significant statistical evidence. I could write an entire paper on how modern science has become too focused on significant statistics that we are blind to papers like this, but I won’t go into that here! However, one very interesting thing this paper did for me, was that I started thinking about how it could affect my own project and if I could look at this DNA methylation in my own subject genus Fucus. After speaking to my supervisor, it turns out that we don’t even know if Fucus use DNA methylation, something we plan to find out about in the near future. This could open up a lot more questions, which I would be very excited to answer!

Finally, at the end of the work week I worked on fixing a computer with Linux, I finally got around to apply to Research Gate, ARCTOS and applying to be a SSB student representative, but I was mainly working on my CV. This was something I didn’t think I would need to do since I was offered the PhD, but I could not have been more wrong and have already submitted it 4 times since I started in September!

Although this week was not as exciting as my last, I hope you still enjoyed my post! Please feel free to leave me feedback and comment and have a great week and I will see you all in my next post!

Pictures from the grand finale of the Researchers Battle
in Stormen last week. From top lefts, Me, Peter Schulze,
Asan Mohideen and Helene Rønquist Knutsen.    

Article

https://www.researchgate.net/publication/292949637_Epigenetic_divergence_as_a_potential_first_step_in_darter_speciation

Societies

ARCTOS - https://arctos.uit.no/home

SSB - http://www.systbio.org/

Interesting links

Český Krumlov - https://en.wikipedia.org/wiki/%C4%8Cesk%C3%BD_Krumlov

Epigenetics - https://en.wikipedia.org/wiki/Epigenetics

DNA methylation - https://en.wikipedia.org/wiki/DNA_methylation

Fucus -  https://en.wikipedia.org/wiki/Fucus

Research Gate - https://www.researchgate.net/

       

Welcome to the blog and my first month as a PhD student!

Hello and welcome to my PhD blog! 

You might be wondering why I am starting a PhD blog, and why now? The reason I am wanted to start a PhD blog is because during the three years of my PhD, many things are going to happen and this way I can note them down so that I don’t forget (you never know it could be useful one day!). Also I get to talk about what I have learnt and allow my friends, family and anyone else who is interested, know about my progress during my PhD and anyone interested in Fucus research. So you might be wondering why start now, you are already a month into your PhD? Well I had thought with the idea of writing a PhD blog, but the move to Norway and adjusting to my life here got in the way. Now that things have settled down I feel I have some time to sit down and type away. I would also like to point out that this blog will be for fun, so I will not go back and check with a microscope for spelling or grammatical mistakes, I am dyslexic, there are going to be some. 

Although it has just been my first month there has been a lot that has happened and to post everything in to this blog post might be long. I will be making a post dedicated to what I plan to do during my PhD at a later date as the project plan is still a work in progress.

Just before I started my PhD, one of my colleges needed help to collect samples early in the morning. I used this opportunity to get to know one of the loveliest people I have met so far here in Bodø (Chloé Maréchal), snap a few photos and collect a few samples. 

My samples!

Cyanea lamarckii

Chloé Maréchal sampling.

My first week was a mix of getting settled in both the administration side of my PhD and the project side. On the administration side you need to get used to the university, how it works and getting your office and computer up and running. On the project side I was getting to know my research team and reading papers, so that I can get my roots in the topic I will be working on for the next three years. At the end of the first week we had a gathering for all the PhD students as there was around 6/7 new PhDs all starting at the same time. I cannot tell you how lucky I am to be working around such a lovely group of people. They are all intelligent, kind, and likeminded people whose topics range far and wide.    

At the start of my second week I had my first meeting with my supervisor and co-supervisor to discuss the direction of the project. It is a strange thing starting a PhD, especially if it’s in a new field of study. The first port of call is to write a project plan, which requires you to know everything and plan the entire 3 years of you PhD, which includes the timing of all experiments, data analysis, writing, courses and so on. The rest of my week was mainly filled with searching for the courses that I will need to take during my degree. At this point in time, I have applied for a one-week course in Gothenburg, Sweden on “An introduction to bioinformatic tools for metagenetic and population genomic data analysis” and a two, two-week workshop in Cesky Krumlov, Czech Republic on “genomics” and “phylogenomics”. I am very excited and hopeful, as both will be a great kick start to my PhD and will give me the skills I need to do great work. Also during the week, we had a meeting about an upcoming event, in which I put forward a few ideas to make it more exciting for young children. At the end of my second week I went to a local event to support my research team present their work to the local community of Valnesfjord and even ended up in the local newspaper!   

Some of the helpful people at Valnesfjord. 

My son enjoying the marine creatures.

My week three was a little bit of everything, I started with a couple of meetings and followed by some applications to be a member of some scientific communities (ForBio, ARCTOS and Evolution digests). I also found out that I had been accepted onto the Swedish course and so had to organise my trip to Gothenburg. As this was my first time during my PhD I had to learn all the do’s and don’ts when traveling for work. Near the end of the work week I was working on my presentation about hybridisation for the “Research Battle” qualifying round on Monday next week. Finally, at the end of the week I took my family to the university's research stations "open day" and it was great. My son was able to take a look and get his hands on some marine creatures, such as starfish and jellyfish which he enjoyed. In the meeting last week, I suggested hiding some finding nemo/dory toys inside the tanks/mesocosms to encourage the young children to look into them to win a prize and it seemed to go down very well.

The final presentation.

Last week, week 4, was a crazy week! It started on Monday with the qualifying rounds of the “Research Battle”. I presented my PhD topic "Hybridization" to the public at the local student bar for science week. I have never presented to such a large crowed and have never had to make my complicated topic understandable to the public. Only the top 7 presentations got through to the next round, but me and a few of my friends (Helene Knutsen, Asan Sahib and Peter Schulze) managed to get through to the final! On the Wednesday we had a course on how to improve your presentation skill, so that we could put on a good show for Fridays final of the "research battle". We started by jumping around, making weird noises and then some improvisation and although very similar to fatherhood, it was a very different work day than I was used to. The course improved all of the finalist’s presentations exponentially and so it was going to be a tight competition for Fridays final. The finals for the “research battle” were held in the cities library Stormen and the attitude was a lot more serious than the qualifying rounds on Monday. My presentation went very well and I had improved a lot since Monday and managed to get 4^th place, with my amazing friend Helene Knutsen stealing the show and coming in 1st place.

Now that you are all caught up on what has happened so far in my PhD I am sure the future posts will be far smaller and on a weekly basis (I hope). I hope you enjoyed the read and I hope you will join me on this amazing ride that will be my PhD.