Licentiate thesis

The long awaited day of my licentiate thesis defence is closing in (31st of May). Next week I will present my work to this point, at a 30 min seminar followed by a scientific discussion with my opponent, Bethany D. Jenkins from University of Rhode Island, USA.

The content of my thesis (which I also got in print today) is basically a 'kappa', which is an introductory summary of sorts, followed by my first and second paper (the first in review and the second published). The papers were obviously already written prior to the licentiate thesis, so I spent quite some time writing the 'kappa'.
There are certain guidelines for this summary, and is my opportunity to show that I meet the requirements for my examination according to the Swedish Ordinance of Higher Education. As usual, getting started with the writing felt like an uphill run in mid July. It was a struggle in more than one way, but as soon as I reached the summit, and got a better view of where I wanted to go, things started to quickly fall into place as I rushed downhill. With good input from my supervisor I could quickly wrap it up (in difference to my first one year manuscript...).
All in all, it introduces readers to my field of research, including the methods, touch upon the motivation behind the studies, followed by a synthesis of the main findings, and lastly, discussing how to move forward with my research (project no.3, which I will get to in my next blogpost).

The first paper can be found here:

http://www.biogeosciences-discuss.net/bg-2017-63/

This is the results of my first scientific cruise, and it's a lot of science. It covers cyanobacterial nitrogen fixers which are either free-living or lives in symbiosis with another phytoplankton in the Western Tropical South Pacific. In short, we found that there was a clear separation of nitrogen fixers based on a depth-temperature gradient, but not in the way we would have thought. That same gradient has been observed elsewhere. We also found interesting differences between one of the cyanobacteria and its proposed host, which contradicts much of the recent literature.

The second paper can be found here:

http://journal.frontiersin.org/article/10.3389/fmicb.2017.00810/full

I'm really proud of my contribution to this paper, especially since it includes a sophisticated statistical model, something I never thought I would do.
The results of the model were a central part of the paper and an important addition to the research in my field and in particular on the diatom diazotroph associations (DDA) that this paper cover.
The data was generated from two cruises which my supervisor went on outside of the Amazon River in the Atlantic Ocean in 2010-11. We wanted to explain and predict, by use of the piecewise Structural Equation Model (SEM) the Amazon river plume's impact on the DDAs in this region.
In summary, we found turbidity to be the most prominent environmental parameter, but the SEM also allowed us to explain the DDA distributions in relation to the river plume. Lastly, we were able to distinguish between the environmental preferences of two strains of the DDAs, which has never been done before. The results of the model indicated that one is more coastal and the other is more oceanic.

So, there it is. All my hard work of the last two years is now nicely compiled in this thesis. I'm super happy and proud of my achievement so far. During my last year of undergraduate studies I would never have even dreamt of working with either statistics (modelling) or microbiology (because I was terrible at it). Look where life took me. So whoever you are, whatever you're doing, know that with the right mindset, no challenge is ever too great!

A brief summary on 2016

It's about time I update the blog with something of interest, and if nothing else, then a brief summary on the turbulent year of 2016.

When last I wrote in my blog I was just starting to write the manuscript of my first paper. It was not as easy as I would have hoped and in the end it turned out to be year long struggle which felt like it would never end. Subsequently, I lost all my motivation to write anything else during that time.

While struggling to finish the first manuscript I also started working on something totally different in the form of a multivariate statistical model, called Piecewise Structural Equation Model (piecewise SEM) which was developed and applied by Lefcheck in 2016.
The model was something I'd thought about for a while after getting comments on my, comparably simple, statistics done in the first manuscript (which then of course was expanded to include multivariate redundancy analysis (RDA)). It was far outside of my comfort zone, but with the help of Carlo Berg at Science for Life Laboratory in Solna, we put together an R script and code to apply the model on a dataset generated in a previous project (in the Atlantic in 2010-11) which my supervisor participated in.
At first it felt like a longshot and the timeframe was more than a little optimistic since there was a hard deadline for a specific special issue in the scientific journal Frontiers in Microbiology.
However, as our work progressed the optimized model returned more and more satisfactory results and it was decided to be the major part of my second manuscript.

So, while I was struggling with both novel statistics, two manuscripts and a quickly approaching half-time point (where I still had nothing to show), there were internal conflicts that had to be dealt with.
Suffice to say that we're all humans (even researchers) and there are bound to be frictions in a tight, high-achieving workgroup. Still, it was not an easy time, although, I believe we all came out stronger in the end.

By the end of 2016 I started to see the light in the end of the tunnel, and it was thankfully not a train. I was the train, and things were moving fast!
After 36 updated and corrected versions of the first manuscript it was submitted at the same time as the second manuscript on the piecewise SEM, which was written and completed in less than a month.

In hindsight, I've learned A LOT, both about my research and myself as a human being and researcher, during 2016. Workwise I will likely not remember the year of 2016 fondly, but I would not have been where I am now without it.

Stay tuned for an update (in the near future) on the manuscripts and my current, third project.