Wednesday 14 December 2016

Week 14: A quick Summary!

My bike After the snow this Sunday!
Hello once again everyone and welcome to the blog, with Christmas getting closer there is not much going on around at the university, however I am busy trying to finish off as much as I can before I leave for England.

I started the week with the usual group meeting, here I spoke to my supervisor about my conversation with Roger Butlin the week before and he suggested that I invite him to be a part of my project. After the meeting, I shot off an email to Roger and not too long later I received an email from him confirming he would be able to be a bit more involved in my project. This was amazing news, his advice on my project will be invaluable and with his reputation and knowledge on the topic it should help my project do very well.  

My amazing Christmas advent calander! 
During the week I had multiple PhD student representative responsibilities, the majority of which was administrative issues such as, poster placements router, records of our previous meeting and passing along the votes of the PhD students on the structure of our “chain of command” to the administration. Also during the week I fixed my trip to Český Krumlov in the Czech Republic along with my hotel and the workshop itself. I will be away for a month in January taking part in a very intensive course, so I hope to learn a lot and have a lot to talk about in my blogs.

The two images are  the type of food
 we ate at the works Christmas party
By the end of the week I had finished writing my second digest but soon had it sent back for some major revisions. Also, the first has now been edited and is soon ready to be published. After this second digest, I will not be doing any more, although the experience I have gained doing them and the publications themselves are amazing for my portfolio, I believe I have reached the maximum of what I can get out of them. At the very end of the week I had a day course on academic writing. The course provided some very useful information, on the entire concept of writing and publications and how to do it. I can already see myself using some of the advice I was given and I feel much more prepared for my first piece of work/publication. If I have some more time next blog post I will go into detail on the things I learnt as they were extremely useful and think that anybody who is involved in writing publications should know. Finally at the very very end of the week we had the departments Christmas party. It was such a lovely evening with fun games and the Norwegian Christmas dinner is truly amazing! 
Playing in the snow instead of writing my blog! 

Although this blog is very short and I would have loved to go into more detail about a few topics I brought up this week, I do not have the time as you can tell it is already 3 days late (I was out in the snow when I should have been writing my blog post :D )! Next week I hope to have more time to put into my blog, however I will be traveling to England that day so it may be late again. I hope you enjoyed the quick summary of my week and I hope to see you again in the next one.  

Monday 5 December 2016

Week 13: A bumpy week

Hello again everyone, I hope everyone enjoyed my big catch up blog last week and now I will try to get back to a normal upload. However, last week did not start off so smoothly as I was ill on Monday, but I was back to work on Tuesday.

Renaissance Tuscany Il Ciocco Lucca (Barga) in Italy
This week I have found out that I was given a place at the Gordon Research Conference (GRC) and Gordon Research Seminar (GRS) which were recommended to me by Roger Butlin, a leading expert in speciation. The conference and seminars topic is speciation which is very important for my research and should provide me some useful contacts for the near future. It will be held at Renaissance Tuscany Il Ciocco Lucca (Barga) in Italy.

Český Krumlov in the Czech Republic
After finding out this good news I was hit with the unfortunate news that I could not receive a credit card through work due to me not having a “permanent” personal identification number here in Norway. I also cannot get this number until I have passed my trial period on my contract which is set at 6 months. So, I was having problems paying for the workshops, travel, and courses however thanks to a work around I have managed to get this sorted and I am very excited for my trip to Český Krumlov in the Czech Republic.

I was also lucky enough to have a skype call with Roger Butlin, where we discussed my project a little and my upcoming ethics work. Roger, described speciation in a way that I had never thought about before and had really redirected my energy on a more constructive path.  The point he made about speciation was that the time it takes to complete the process for example in birds is around 10 million years. The length of time of speciation is also similar to the average interval between species events (7 million years for birds based on phylogeny) on a lineage and so most lineages are in the process of speciation most of the time.

A nice example of  Fucus distichus
I was also in contact with James Coyer an expert on Fucus who I have had previous contact with and asked some more about species and speciation in the Fucus genus (The Fucus distichus complex). He explained that the Fucus distichus complex is comprised of several morphs, each of which has been described as a separate species or subspecies. The morphs seem to be stable from generation to generation and in common garden studies, yet hybridization is common. On the basis of a mtDNA ITS spacer, his research had determined that there was no difference among the morphs and suggested that they all be considered F. distichus. This was verified by another study using 13 nuclear markers. Using this information and what I have learnt from Roger Butlin I will attempt to write a nice little paper on the species concept and tie it nicely into my research and the genus I love so much Fucus!

This was the last bit of sunlight we will see in Bodø this winter. 
I understand that this blog has been rather short as it was quite a lot of random administrative work this week. However, I have used some quite in-depth scientific terms in this blog post which I will leave some links explain them in the bottom of this post(found in bold) if you are confused and want to learn more and some other interesting links! I hope you all have a great week and I will see you all in the next blog post!  




Interesting links:

Highlighted words:
Phylogeny/Phylogenetic treehttps://en.wikipedia.org/wiki/Phylogenetic_tree


Monday 28 November 2016

Week 8-12: Mega catch up post!

Hello once again everyone, I am sorry for not uploading in the last month but it has been one hell of a busy month! While my partner returned home to Sweden I had to take a single parent role which has truly left me exhausted. However, now that we have been back home for a week I finally have a few minutes to myself and I have some time to write a BIG catch up blog.

For all the people who do not want to read the entire blog post I have made a quick summary of some of the key events that occurred in the last month. I will go into greater detail below:

·         Issues with payment finally resolved
·         I participated in an algae workshop, which was a lot of fun although 75% was in Norwegian.
·         Prepared for course, packed for my trip to Sweden and a variety of travel stories and travel issues.
·         Participated in a bioinformatic pipelines course.
·         A week in Umeå meeting friends.
·         Participated in an ethics course
·         My evolutionary digest will be published soon.
·         I have taken over journal club.
·         I am now the PhD student representative for the Faculty of Biosciences and Aquaculture at Nord University. 

So, I will start of by saying that I have final resolved all the issues that I have been having with payment in Norway! At the end of October I was worried that I would not be able to pay for food for me and my son, due to an error made by some of the administration department. When I had asked them what was wrong, I was told “oops I pushed the wrong button”. There was not even an apology and I think these people just live in their little bubble and do not understand that their mistakes can have major impacts! However, I do not want to complain now, everything was resolved and I do not have to worry about this any longer. With that I can now buy winter tires for my bike which I so desperately needed with winter setting in, ow and I could buy the new Pokémon! ;). 

During the same week, I had also been invited to participate in the first ever algae workshop at Nord university the very next week. I was hesitant at first due to most of the workshop being held in Norwegian, but I was convinced by my supervisor that it could still be useful. It turns out that my knowledge in Swedish really helped and I can honestly say I understood around 60/70% of all the Norwegian. I was introduced to many people in the industry of macroalgae(seaweed) production and sales and I got to see the beginnings of an industry that could become very important in the future in Europe. It’s funny to think that in Asia eating seaweed is such a normal thing and that there is a major industry around it. However, in Europe very few cultures use seaweed for anything, but I believe that in the near future this could change and the research I am doing on Fucus could become quite important to this developing industry.

So much snow! 
Later in the week, after preparing my computer for the course, I had to take time to prepare the house and my luggage for traveling to Sweden. The trip me and my son would take took over 20 hours and was the longest but most relaxing trips I have ever taken and that is something when considering I was traveling with a child. I got to see some of the most beautiful sights in Norway as I travelled 5 hours north to take the train from Narvik. The bus even took a trip on the ferry as the road meets a fjord. Once we were on the train me and my son had our own carriage for the majority of the ride to Umeå, Sweden. The seat we started on turned into three very covenant and quite comfortable beds. The trip confirmed my love for trains, but the length of the journey really took it out of both me and my son. Once I had arrived I had one day to enjoy the enormous amount of snow that fell in Umeå and then the next day I was off again to Gothenburg by plane. This time it was not relaxing and due to delayed by the snow in Stockholm I arrived a lot later than expected and missing parts of my travel due to the delays.

The accommodation at Tjarno research station.
I arrived at midnight in the pitch black to this big beautiful white house full of rooms which would be my home for the next week. The next day I woke up for breakfast to one of the most beautiful research stations ever set into a very picturesque bay. The course was full of fantastic information and fantastic people, I was new to bioinformatics in command line and the course was a perfect introduction into it. I will now continue the work myself along with the workshops in the Czech Republic I will be attending in January and the people I met on the course were a group of very intelligent, strong minded and fun people, many of whom I hope to have future connections with. During the course, I had the chance to meet Ricardo Pereyra, who is also researching Fucus seaweed. We discussed some factors in regards to my project, he offered some advice and pointed me in a direct which I am very interested in following.

Tjarno research station.
After the course my trip back to Umeå was much smoother and a little less lonely as I travelled with a few of the people from the course about 50% of the way home. Once I got back to Umeå there was not a single day where I did not meet somebody who I missed after my move. I was surprised how many people wanted to spend their time meeting up with silly old me, but it was very nice to see everyone again. After speaking with Ricardo Pereyra during the course in Gothenburg he suggested messaging Roger Butlin, a leading research in the field of speciation.  I was surprised that Roger Butlin quickly replied to my messages and we have plans to have a Skype meeting and further communication.

After an extremely busy week In Umeå, Sweden we headed home back to Norway the same way we came, only this time it would take 22 hours. The first week back home in Norway I had started an ethics course, when I first started the course I was not looking forward to it as I am not a big fan of philosophy which is a large part of the course. However, the course was amazing and really pushed some boundaries in how I look at things. One of the key topics of the course was the species concept, something we has discussed the course in Sweden in great detail, something I will speak to with Roger Butlin and also something I am personally very interested in. The course has now ended and we must write a paper on our research and two points of view, (eccentric and anthropocentric) I could not think of a way to do this so I have discussed with the teacher that I will focus on the species concept and my work.

Yay for me! 
During this week, I also found out that the Evolution Digest that I wrote will be published soon, here is the link to the publication: http://onlinelibrary.wiley.com/doi/10.1111/evo.13135/full here it is so you can give it a quick read. I have also taken over the journal club, I have spoken about it on this blog previously. Journal club is when someone feels a paper is particularly interesting they can present to the club as a whole, then we can ask questions and discuss it. The last Journal club was a very interesting topic which discussed great white shark size and what is the biggest (https://www.ncbi.nlm.nih.gov/pubmed/17746627). The final bit of news I have for all of you is that I was “elected” the PhD student representative for the Faculty of Biosciences and Aquaculture at Nord University. Which means I now have the responsibility of communication between the PhD’s and the rest of the department and organizing social events.

So now that’s the end of another blog post, I have had to rush this post a little and was not able to go into great detail on a lot of the topics due to the large amount of information I have had to convey to you. If you have made it this far I really appreciate you taking the time to read everything I have had to write and I hope you have enjoyed this post. If you have any questions about anything I spoke about in this blog post, please do not hesitate to ask. I also hope to make this blog a weekly thing once again where I can go into much greater detail about what it really means to be a PhD student.
   







Sunday 23 October 2016

Week 7: Mimics and maniacs!

I want to start off by saying that everyone should now be able to make a comment with or without an account. I have also put a survey on the website and some ratings on each post, please feel free to comment with questions and rate so that I can improve my posts, I wont bite!  
Really, I wont bite!

Linux penguin, Tux
This week started off with some great new that I had officially been accepted onto the PhD program. Now I bet a lot of you are asking, having you already been working for around 2 months and you were not officially accepted? Nope, not until this Monday where I found out that the project plan that I told you all about last week had been accepted. So now not only am I an employee for Nord university I am also a student (yes I know that sounds strange)!

During this week of work my energy was very low, this is because I am temporarily a single parent for the next few weeks, however I have been getting work done as best as I can. Most of the week consisted of reading and I have nearly covered most of the literature on my specific topic. I was also preparing my computer for the course I will be going on in two weeks time near Gothenburg. I had to install several bioinformatic programs along with installing a virtual computer so that I could run Linux on my Windows PC.

larval fish(mimics) mimicking jellyfish/gelatinous larvae
 (models) (Greer et al. 2016) .
This week was also time for another journal club, with this week’s presentation being done by Amalia Mailli on the paper “Larval fishes utilize Batesian mimicry as a survival strategy in the plankton” (Greer et al. 2016).  Batesian mimicry is a form of mimicry where a harmless species has evolved to imitate the warning signs of a harmful species for protection from predation. In this paper, they looked at larval fish(mimics) mimicking jellyfish/gelatinous larvae (models) for protection (See image). The jellyfish larvae are poisonous to predator fish and will be avoided, so the mimics are protected from predation. There are many crazy different examples and is almost as interesting as hybridization. There is so much more I could talk about on this topic but due to my low energy levels I believe it is best to keep it short, instead I will link some interesting sites at the bottom of this post.

One of the many  interesting examples of  Batesian mimicry,
one which I have always thought about as a child, the hover fly
and the wasps! 1- German Wasp, 2 - Hoverfly, 3 - Hoverfly,
4 - Wasp Beetle, 5 - Sawfly, 6 - Hoverfly.
http://alexhyde.photoshelter.com/image/I0000fkOVUVljQXg
Finally, in my free time I have been working to improve my scientific writing and my portfolio. It is a piece of side work that I am hoping to submit for an Evolutionary Digest and once my work has been submitted I will go into more details. Once again, thank you so much for everyone who is reading my posts, please comment and leave feedback, I would very much like to hear what you think, but until next week, I hope you all have a great one!    







Interesting sites:

Sunday 16 October 2016

Week 6: My project and why it is interesting!

The 5 PhD students that started along side me. From top left,
Arseny Dubin, Kyle Rogers, Maeve Mcgovern, Peter Schulze,
Solveig Sorensen and me!.  
Greetings once again from my PhD journey, this week was not very exciting and consisted of a lot of reading and learning how to use the command-line on my computer. So in this week’s blog post will be dedicated to letting you all know what exactly the idea is behind my PhD. I will also decorate the post with pictures from my week and I will try to keep it clear and understandable for everyone. So please sit back, relax and enjoy the presentation!

We have always wanted to know the mechanisms behind speciation (the formation of species), but there are so many different factors that leads one species to become two species. It is also becoming more complex and the reason for this is that we have started look at speciation as a continuum (something that goes through a gradual change). One thing that we do know for sure and that is the process of local adaptations where populations evolve to better fit local conditions. When a species evolves there are changes in its DNA, but they usually accumulate in specific parts of the DNA sequence.

The northern lights dancing around the moon this week.
In my research, I will be looking at reproductive barriers, reproductive barriers stop species reproducing and when this happens is key to establishing when a species becomes a species. Reproductive barriers can be a result of many different factors and can be either before an embryo is form or after.  One other key aspect of my research is hybrid zones and the formation of hybrids thought he process of hybridization. When reproductive barriers form between hybridizing species it is very interesting and complex due to the nature of hybridization. Hybridization allows genetic information to be move and shared between the two species, known as “intergression”. Due to intergression, this makes hybrid zones the perfect natural experiment to study the forces that select specific genes which lead to reproductive isolation and ultimately speciation.
Autumn is here and someone is happy about it!

The species I will study, if you had not guessed it already, is the macroalgal (sea weed) Fucus, in particular, Fucus serratus and Fucus distichus. These species provide me the ideal system in which to study the mechanisms of speciation. It has been shown that these two species can produce hybrids in the wild, the sperm from F. serratus can fertilise the eggs of F. disichus. The next important factor about these species is that there are a few hybrid zones, some that have existed for 100 years and one that has existed for around 10,000 years. The reason that this is important is because the older hybrid zone does not produce hybrids whereas the younger hybrid zones do. The reason for this is that hybrids have been shown to be less efficient than either parental species and so natural selection has over time selected individuals that do not produce hybrids or produces less and this process is known as reinforcement. The genes behind this effect are unknown and this is where my research comes in.
My first fish here in Norway!


The central aim of my project is to understand how reproductive isolation mechanisms evolve in the Fucus speciation continuum, from a local adaptation to complete reproductive isolation. And that ladies and gentlemen is the idea behind my PhD.  I hope that you all were able to follow the post to this point and if you had any questions please feel free to ask, I would be very happy to answer them.  But until next time, have a great week everyone!


Sunday 9 October 2016

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

Societies

Interesting links



       

Tuesday 4 October 2016

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 4th 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.