fredag 4 maj 2018

Just a taste

The first day in Barbados was relatively uneventful.
I continued working on my computer, to write a really detailed and easy to follow daily sampling routine for the work at sea. I would like the base sampling to be as smooth as possible as to enable me to, if opportunities arise, think more freely on spontaneous sampling or experiments in case we encounter bloom densities of the DDAs.

Apart from work I met up with the two German scientists joining the cruise and we ended up going for food, drinks and swimming at the Boatyard (Brownes Beach), which was really nice. I also got to try the famous Rum Punch made on local rum.
The Boatyard is basically a beach bar with some water activities tied to it. I'm sure that it would have been a lot more lively if it wasn't for the fact that it's currently off-season. By 19.00 we were the only ones there...

Brownes Beach at the Boatyard.

So my limited experience of Barbados so far is that it's an amazingly friendly place. The people are in general very nice, polite, social and laid back, even to strangers, which is not something I'm used to being a Swede.
This behaviour even applies to traffic!
Walking down the street, people would greet you. Ordering food or drinks, the bartender would introduce himself/herself and engage in conversation. Their language is very polite, and honking your horn in traffic means 'thank you' or 'hello'. And they honk a lot!

Today I moved over to the research ship docked at the Bridgetown Cruise Pier and got settled in in my cabin, got all my stuff stashed away and had a short look around the ship.
After trying to WiFi with a phone call home (which worked ok, but had a few seconds delay) I went to the Boatyard again together with some of the ship crew. Most of the science party was already there, drinking local beer (very very light) and socializing, so it was nice to finally meet everybody.

The research vessel.

Tomorrow I will set up my equipment and practically prepare for departure on Sunday. Hopefully I'll get a good spot in the lab.

torsdag 3 maj 2018

Safely arrived in Barbados

Leaving a cold, 7 degrees C, Sweden behind. Below you can the see Gothenburg archipelago and in the distance the city of Gothenburg.

I arrived in Bridgetown, Barbados, yesterday afternoon local time.
It took a while to get through customs and immigration, mainly because they ran out of forms for us to fill out beforehand on the airplane.
The immigration officer had a few questions about my stay, but nothing major and after getting my two checked bags I went through customs who wanted to take a peek inside my metal box (filled with research supplies). It was fairly brief really, and I was soon on my way to the hotel via a shuttle bus that I booked before leaving Sweden.

Panorama of the beach outside my hotel, which is the yellow building to the right. Panorama is nice, but my camera doesn't really do this scenery justice (poor exposure)

After arriving I sat down to go through my emails and final preparations before the cruise. The plan was for me to head out and get some supplies and something to eat, but when I was finally done with my computer work I was way too tired to even leave the room. Getting up at 5 o'clock in the morning with only 4 hours of sleep and then with a subsequent day of travels (extended by 6 hours due to flying west over multiple time zones) certainly takes its toll.
My plan was to not sleep anything on the airplane as not to be too jet-lagged once I arrived in Barbados (it certainly made that commitment a lot easier having a long list of new cinema releases at my hands on the airplane entertainment system).
In the end it worked fairly well, even though I was tired and still didn't sleep as heavy and long as I usually do (woke up at 5.30 local time).

One part of the Gap at 6.30 in the morning, so very empty and quiet in difference to the evenings and nights.

This morning I had a little stroll down the Gap (to a nearby supermarket), which is the street I'm staying on. It's basically a beach front street peppered with bars, restaurants and nightclubs. After that I had breakfast at my beach front hotel, all alone. It seems that it's off-season.
Anyway, so far it looks like an amazing place and I'm planning to at least have a walk along the western beaches when I'm done with my work today. They look really nice, with fine, white sand. There's some sea going on at the moment so the waters aren't as blue-turquoise as when I flew in, but the breeze is refreshing since humidity is fairly high and the temperature is around 30 degrees C in the shade.

I just have to make sure I put on proper sunblock, since I've already done that mistake one time too many in my days.

torsdag 26 april 2018

Caribbean research cruises

The day for me to share this is here.
My close friends and family have already known for a good while, even though the details have changed on a monthly basis since the very beginning of 2018.
To make a long story short: last year my lab (supervisor) was invited to two back-to-back research cruises in the tropical and subtropical Atlantic, by two different research groups based in the US. A region well known for high abundances and blooms of the particular diatom-cyanobacteria symbiosis that I'm interested in.

My PhD student colleague, our lab's post-doc and one master student got the opportunity to go on the first cruise, going from Cape Verde to Puerto Rico aboard the legendary R/V Atlantis (the mother ship of the submersible Alvin). This cruise was completed late March after almost 6 weeks at sea, crossing the equator twice.

Map of the Caribbean and Central America. Barbados is located north of Guyana and Puerto Rico is located north of Venezuela. The Amazon River is located at the edge of the bottom right corner of the map (south of French Guiana).

Now, the second cruise is due the 6th of May until the 1st of June, and I've been scrambling these last few weeks to get organized and prepared for departure. I'm leaving, as the lone representative out of my lab (and Stockholm University), to participate in my third research cruise, which will go from Barbados, down to the Amazon River and back up to Puerto Rico, aboard the R/V Endeavor.
It is an extremely unique and exciting opportunity, but it is also important to remember that I will most likely work non-stop and collect crucial samples for my current and last project for my doctorate. Next year I'm supposed to defend my PhD thesis.

The R/V Endeavor sampling at open sea.

So as I'm writing this, I've packed the last of the equipment I need from the lab together with our lab group technician, I've fixed all the required paperwork, I've managed my visa's, I've taken my vaccines, I've put together a robust sampling plan together with my supervisor and now I'm sitting on a train back home to my family. I'm looking forward to a few days off before I fly out of Gothenburg next week.
This blog will once again be one of my channels of communication while I'm out at sea and I will try to update it regularly.
Stay tuned!

tisdag 24 oktober 2017

Workshop expansion - Presentation techniques

Last week, the Research Education Committee (responsible for all questions concerning the education of PhD students) at my department decided to (financially) support me and my good friend and colleague, Tom Staveley, with our workshop in Communication, Feedback and Presentation Techniques, that we successfully hosted last semester.

To be honest, it was never certain we would host the workshop again, due to both of us having more than enough on our hands with our own projects, so we basically agreed that we wouldn't host it again unless someone specifically asked (read begged) us to.
Based on participant evaluations we already knew where we could improve and also had a clear picture in what direction we wanted to steer any future development, so that part of any future organisation plan was already set.
So one day the Director of Studies called out for suggestions to new PhD courses and workshops to be hosted, either internal or external (if a subject is of broader scientific interest it could possibly be hosted by the BioResearch School instead). Almost immediately I got an e-mail from the Public Relations Manager stating that me and Tom's workshop should definitely be up for discussion. That was the cue we needed and after some discussion and phone calls it landed on the agenda of the Research Education Committee.

The main differences from last time is that we will now have more allocated time for the entire workshop spread over two weeks, there will be more emphasis on presentation techniques and we will get departmental funding to invite external speakers where my own and Tom's expertise is lacking. Of course it will also mean that there will be some more time to dig deeper into communication and feedback, which I would argue is equally, if not even more, important in research than presentation techniques.
Practically, we are aiming to move the student presentations within the workshop to our large lecture halls, for everyone to have a chance at proper practice with feedback before the day of dissertation (where most PhD candidates tend to use our grand lecture hall).

The workshop is currently scheduled for spring, 2018, and if you're a PhD student or master student currently enrolled in a project at the Dept. of Ecology, Environment and Plant Sciences, Stockholm University, feel free to contact me if you have any questions.

Myself (right), on one of the obstacle courses used for team-building purposes at Dalslands Aktiviteter, more than five years ago. A lot has happened since. Photo credit: Robert Karlsson.

I celebrated this decision in the most fitting way, by taking on the role of team-building instructor (together with two other instructors) for a mid-size private company, at my previous full-time employer, Dalslands Aktiviteter, again. I was thrilled to be back in those shoes, and I spent half the weekend putting the participants through difficult group exercises followed up by debriefings, often concerning (but definitely not limited to) resource management, synergy, communication, feedback, project planning, honesty and work relations. I'm happy to say that it went really well and I'm looking forward to more of those commissions.

torsdag 19 oktober 2017

Taking the leap

The last month or so has been relatively uneventful. I've been struggling with our Bioanalyzer for more hours than I care to count and in the end, it is no longer in my hands. I usually have no problem troubleshooting instruments or computers, especially not when I have expert help from a qualified and helpful technical support, however, even though I would refer to myself as fairly tech-savvy, it felt like I was wasting time and my project was getting nowhere.

My solution to this was not just dumping the issue on someone else's table (because in the long run, that would solve nothing), so I did what I could for the poor instrument in terms of replacing parts, cleaning of electrodes (with a toothbrush - I felt particularly scientific doing that) and modifying system settings. Meanwhile, with some invaluable help from fellow researchers, I was able to move my RNA work to our neighbouring department, which also had a Bioanalyzer instrument (functional). This way, my project slowly progressed and I was able to finally identify the first 8 samples for the first microarray slide.

The slow progress also enabled me to dedicate some time on a side-project though, but I now realise that it has grown into something larger than that. My supervisor opted for me to have a private meeting with one of the cruise chief scientists from where I got the cool dataset I've been working on for this side-project. Basically I've expanded on my initial piecewise SEM modelling by increasing my model size from 9 mixed effect models (one response variable per model) to 24, effectively more than doubling the size. In the beginning I wasn't even sure I could incorporate that many variables and successfully get any useful information out of it, but as I progressed through my optimization routine everything slowly fell into place. Now it's just a matter of interpreting it and put it into an ecosystem and oceanographic context. The cool thing about this dataset is that I had access to, in addition to the classic abiotic factors and nutrients like temperature and nitrogen, both abundance measurements of all major diazotrophic cyanobacteria and a range of different pigments, which can be linked to different kinds of phytoplankton in the water column. For most people, I'm guessing, that doesn't sound too exciting, but even though the marine diazotrophs I'm mostly interested in were first discovered more than a century ago, we know precious little about most of them. One being the nature of their different symbioses with eukaryotic phytoplankton. Therefore, I was hoping that the SEM could shed some light, by use of the pigments, on which type of phytoplankton the cyanobacterial diazotrophs seem to be hanging out with (in addition to all other interesting hypotheses)..
Map with integrated surface particulate organic carbon in the region of sampling for the dataset I used for my side-project. Southern Vietnam and the South China Sea. Satellite image generated from

Anyway, today I took the leap and delivered my samples to the microarray analysis facility, and I'm hoping that it will give me some good results soon enough. I packed them neatly in a styrofoam box together with lots of ice and ice packs. Ideally, you want to transport RNA samples on dry-ice, but since the trip to the analysis facility is only 35 minutes, I'm fine with regular ice.
The thing about this project though, is that I've no idea of knowing if anything actually work until I get the results back of this analysis. In that regard I kind of see it almost as a leap of faith, since I always have this "worst-case scenario"-thought in the back of my head.
I've been rewarded with a lot of freedom (based on previous success) regarding this project, which I thoroughly enjoy, since it makes the science even more exciting, but that also means that success and shortcomings alike will fall squarely on my shoulders.
I had a similar conversation with my supervisor today and her only response was: "if that turns out to be the case, then at least you've learned a lot".
I know she's right. I tell myself the same thing from time to time, but for obvious reasons it felt better coming from her (she pays for both my time and material after all).
I'm really excited about the possible results and I'm hoping that the wait won't be too long.

fredag 22 september 2017

Like a kid on Christmas Eve

First off I just want to clarify the title. If anyone was wondering, Christmas Eve is the major event in Swedish Christmas celebrations, and not Christmas Day. That was today's bit of cultural knowledge for you. So now on to what I actually intended to say with this blog post.

A bit more than a week ago I was doing some major lab work, which unfortunately didn't work very well. In the end I narrowed down the issue to an expired kit of reagents.
I proceeded to talk with my supervisor about this (who is in possession of the big bag of money), and she supported my decision to buy a new kit.

However, just ordering the damn stuff was not as simple as your everyday internet shopping for clothes, the latest blockbuster on blu-ray or any other odd item from a dark corner of the internet (because I'm sure even that would have been easier).
After finally finding the product I wanted, in the less than straightforward online store - I mean where have you even bought anything online where a simple search function in the store has given you nothing, but a bloody google search did? - I, as a first time customer, had to register for an account.

I've been using other online services of the same company before and was convinced that I already had an account. Oh boy was I wrong. Sure enough, I found my login credentials, but apparently the web store had a separate login system. However, instead of telling me something along the lines of  'wrong password and/or username' or 'there is no such e-mail address in our system' when I tried to retrieve the password I thought I had changed and forgotten about, their webpage simply said that the webpage I'm trying to access could not be retrieved.

Stupid me didn't realise that making another registration was even an option until two days later, when the mysterious internet access failure was still there.
After registering and adding "new" delivery and billing addresses everything had to pass through manual confirmation by the company before they would send me anything, naturally.

I thought the day I would be back in the lab would never come, in my wait I even had time to realise that I need a plan B for my current method in case everything goes south, and proceeded to order another kit (for a different but related purpose), which for the record (and thankfully), was much easier and faster to order.

So yesterday three packages with my name on them finally arrived and with all these cool new kits and reagents I felt like a kid on Christmas Eve! They were all neatly packed with two styrofoam boxes and one cardboard (there was a styrofoam box inside the middle cardboard box). The styrofoam boxes had the reagents which had to be shipped cooled or frozen, so naturally they had ice packs and dry ice in addition to my stuff.

For those that don't know anything about dry ice, it's basically frozen carbon dioxide (yes, the gas!) which has an approximate temperature of -80 degrees C.
Apart from being a convenient cooling agent it can also be used for some silly things in the lab with a little help from sample tubes, a regular sink and a little imagination.
Put a pellet of dry ice in a 2 mL tube, shake it briefly and throw it to the ground and you have your very own "fire cracker" (minus the fire). The thawing pellet will evaporate into carbon dioxide gas, build up the pressure and then pop the lid on the tube.
However, chances are that you will grow bored of cleaning up your messy floors long before you run out of dry ice pellets, so before putting away the box you could pour some of it into the sink and pour some regular tap water on it. This will quickly turn your sink into a "bubbling witch's cauldron".
There certainly are potential for some good pranks here, but if anyone asks, I never said (or did) any of these things.

tisdag 12 september 2017

Due to popular demand

In general, most of my lab oriented work has come to a grinding halt. Which is more than a little frustrating considering that my microarray slides are waiting in storage at the KI analysis facility (BEA). I'v narrowed down the issue to expired reagents as the source of my problems in quality controlling my RNA. For that reason I will not extract any more RNA, or do any other RNA work until I've received and tested the new RNA analysis kit I just ordered. Anything else would be a waste of my precious time and samples. Apart from that, I've gotten some kind assistance from my colleagues in trying out different RNA extraction kits and methods to see if I can optimize my protocol for a higher yield of good quality RNA.

On a more positive note, me and my good friend and colleague Tom got invited the the departmental plant ecology meeting to hold a condensed seminar on the first session of the workshop we hosted in communication, feedback and presentation techniques. The emphasis will be on promoting a better 'feedback-culture', since most of us agree that the scientific community could do good with a lecture on how to communicate properly.

I feel honored to have been given this opportunity and I'm hoping for a large, enthusiastic and diverse audience so we can spark some interesting discussions.
I also feel that this is a testimony to the success of the workshop, and depending on the outcome of the seminar we could be looking at another workshop next year. Likely the same format, but with some fine tuning and improvements based on previous participant evaluations. However, it will only happen if we're asked (read begged), since both me and Tom are in no need of extra credits (HP) and are only doing it because we like the subject.
Stay tuned.