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.

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 https://giovanni.sci.gsfc.nasa.gov/giovanni/.

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.

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.

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.

How was it, being on national TV?

In the end I got a lot of praise for my attendance in the SVT Barnkanalen Morgonshowen kids show. Everything from a simple 'well done you!' to a friendly suggestion of a career change (to TV host).
However, funny thing is that it was more or less chance that gave me this opportunity. Because that's exactly what it was, despite "only" being a kids show. An opportunity to communicate science.

Basically an editor at Morgonshowen called a professor at my department in search of microscopes and someone who could show them, and small things in them, in their show. I've no idea why they didn't contact the the Biomolecular department, but that doesn't matter.
The professor they first contacted didn't have access to any microscopes and those research groups who did included mine and a few others. Mine just happened to be the first one to be contacted and since I'm the only swedish speaking researcher in my group that meant that I would be the only one capable of pulling it off.

Before I even knew what the fuss was all about I was reading through a brief manuscript on looking at small, everyday things in a microscope. Apart from that I was free to add my own research and expertise. Knowing that, the decision was a no-brainer and in hindsight I think it turned out even better than I had hoped.
Being a perfectionist I immediately started to put together an instrument/computer setup that would allow me to best visualize what I wanted to show, and of course, writing a simple manuscript of my own with simple facts and metaphors that would come in handy during the actual recording in their studio. During that time I also, in my mind, went through what I would say in response to different questions I would get, since it would mostly be improvisation at the time of recording.

In the end I brought two different microscopes (40x and 400x magnification), a camera that fit both microscopes, my laptop with visualization softwares and a 24 inch monitor. The microscope slides and materials were all prepared in advance and with the helpful assistance and support of my supervisor I had everything ready, including tiny beakers with phytoplankton cultures of different colors (e.g. red, green and pink), within two days. Despite these preparations there were still some improvisation happening with the microscopes on the day of recording.

The setup I used, trying it out in my lab (one microscope less).

When that day finally arrived I was really nervous. I remember that my supervisor and the public relations manager at the department accompanied me to the studio, and the drive there seemed to last forever. I had the feeling that I wanted to get to the studio that very instant and just get this thing started so I could better handle my nervousness.
The security at the SVT main building was rigid and we had to register and wait for quite some time before the editor finally showed up to greet us and let us into the studio.
My setup was already there and ready to go, since I assembled everything the night before. All I needed to do was plug in my computer. But before that happened, I met all the people involved, including of course, the host of the show for this episode, Tobbe 'Trollkarl'. Those of you who aren't swedish will probably not know who he is, but suffice to say that he has been on TV for a relatively long time, even when I was a kid. So I had a surreal moment of meet and greet with him before getting ready. The studio was fairly large and had a double setup depending on the different shows they were recording. It was a ridiculous amount of stuff, both technical and otherwise, lying around waiting to be put to use. And of course, in the middle of it all, a massive mixer table, cameras, lights microphones, you name it.

Apart from double checking my instruments there was not much preparation to be done. No make-up, no briefing, I just put my lab coat on and had a brief rundown with Tobbe about what he was going to say and do. I more or less played along and did my thing. To be honest it was a fairly simple task since Tobbe made life easy for me with his genuine interest and excitement over getting the opportunity to look at all these different things in a microscope. For example, I would guess that a lot of people have no idea that grains of regular salt is actually cube shaped.

Me and Tobbe Trollkarl in the studio

The recording was done in three segments and during the first I was really nervous, and I remember my supervisor happily saying that I should try and smile more. In time for the second segment I was getting warmed up and everything felt more comfortable. I got some pointers from the camera woman which also helped. In the end it felt really good, even though I always get the nagging feeling that there are things I could have done better, which I guess is natural.
By the time we did the third segment I didn't want it to end. I could do this for quite some time more. I had a blast.

There were no re-recordings and the session, which should have taken two hours, was done in only one hour. Everyone seemed really pleased with how it turned out and after watching the show on TV on the 27th of August I can see why, although it's quite weird seeing myself on TV. My kids were thrilled!
The week after the recording in the SVT Barnkanalen studio the editor called me again.

RNA extraction and quality control of your Volvo

I got an e-mail the other day. It was from Agilent who said that my order of two custom microarray slides scheduled to arrive around the 5th of September were already finished and were being shipped from Germany to the analysis facility BEA at Karolinska Institutet (KI) now.

Guys! You're two weeks early! I haven't even gotten my own stuff (samples) together yet. Germans... How often does this happen? By experience - always when you're lagging behind. That's not what I replied though, but it's what I silently told myself.

Now you might think 'hey, you only have to fill one slide, 8 samples, how hard can it be?'. If you just thought exactly that, I'll give it to you. You're right, it's only 8 samples and it would take me 2 hours to extract. However (I hate that word, and I use it all the time), out of the 12 samples that were already extracted only 2 had enough total RNA for analysis, and don't get me started on the quality control of that RNA... ops, I already did that myself... they all failed.

At this point I have nothing. Fortunately for me, we have lots of archived RNA with corresponding DNA samples which have already been processed in the qPCR. Basically, that means that I can see in which RNA sample that I should have the right organisms and enough material. However (here we go again), that doesn't guarantee good enough quality RNA.

There are several reasons why the RNA in my samples might not be of good enough quality, and when I'm talking about quality it's rather specific and doesn't entail the comparisons between e.g. longevity of brands that we're so used to in modern consumption society. No, here, I'm talking about degradation and size of the RNA fragments. Like if you removed a few parts from your Volvo, it would still be a Volvo, but it would probably not function very well, and if the parts removed were body parts, the untrained eye might not even recognise the car as a Volvo anymore.
A similar problem arise when I have low quality (degraded) RNA. The probes in my microarray are all extremely specific (untrained eyes) and when the genes (Volvos) in my samples are missing a few parts due to degradation they will not be recognised.

Image credit: Fabian Oefner

To be short and simple, RNA is the coded message that our DNA relays for our cells to, down the line, translate and produce proteins with various tasks and properties. Naturally, the message doesn't stay intact for very long since, in most cases, when the message has been delivered and translated it has outlived its usefulness and is recycled within the cell.
So, I might just have been unlucky and the RNA in my samples was naturally degraded when the research vessel arrived (too late) on site. I might do a terrible job extracting the RNA, and perhaps, mysteriously introduce RNase (an RNA degrading enzyme) to my samples. The agitation step (shaking the samples really, I mean REALLY, fast together with tiny glass beads to crack the cells open) might shear the RNA to tiny bits and pieces. The latter is the only explanation that I can actually test.

I'm assessing the RNA quality in an instrument called Bioanalyzer 2100 (Agilent), which gives me a value from 1 to 10 (10 being the best - most intact RNA). It has developed into an industry standard since it uses an algorithm to objectively calculate and compare the amount of two different ribosomal RNAs. This way us scientists know that we will get good and reliable results and we secure the possibility of reproducing the experiment (important for e.g. peer-review and validation). Everyone is happy. Me included, if I can get good quality RNA, otherwise no.

Grit and the growth mindset: The recipe for success

I recently watched a TED talk by Angela Lee Duckworth. It was recorded in 2013, so I have no idea how this inspiring talk has eluded me for so long.
Anyway, Lee Duckworth tells her tale of how she left a demanding but successful job in consulting to teach math to 7 graders. That's where her ideas and research started to develop when she observed the struggles of her pupils. After a few years she started studying psychology and pursue the unverified observations she made as a math teacher.

You can see the entire 6 min talk right here.

In her talk she also mentions, at the very end, a concept called the 'growth mindset'. This is also an idea that has been around for quite a few years. It was coined almost 30 years ago by Carol Dweck who studied how students dealt with failure. The opposite of the 'growth mindset' is the 'fixed mindset' and what sets them apart is the belief that talent is either static or developmental. This means that if you believe in the 'growth mindset', talents, abilities and even intelligence is not something that is restricted to life's lottery, but is actually something you can improve and develop.

I first heard about the 'growth mindset' during the workshop I co-hosted in Communication, feedback and presentation techniques, where I had a very interesting discussion with my department's Public relations manager. I didn't think much more of it after that, to be honest, but when I now heard it in the context of Lee Duckworth's TED talk, it made perfect sense. It is also how I would define my own success.

So together with the 'take home word of the talk': grit - the 'growth mindset' is what defines success. As nicely put by Lee Duckworth "grit is living life like it's a marathon, not a sprint". It's about setting up long term goals and sticking to them, not by hours, days or weeks, but years. Perseverance.
It's about not giving up, and use the inevitable failures to grow, work harder/smarter, and eventually succeed. Because the thing about success is that it doesn't always happen right when we want it to happen.

Lee Duckworth wraps up her talk with the task that stands before us all, and that is teaching our kids to be grittier. Because talent and intelligence means nothing if you're not willing to work hard.
When I was a kid I played hockey and I strongly remember a small piece of paper that hung on the whiteboard in the club's meeting room. It said: "The will to win must be stronger than the fear of losing". I didn't quite understand the deeper meaning of it back then, and I'm not sure whoever put it up did either.

In hindsight I wish that someone would have explained it to me. I wish that I had even a fraction of the knowledge I have now, back then, and I'm surely not alone with that wish.
I think Lee Duckworth is right, and when I think more about it, I'm actually subtly teaching my kids grit. Perhaps it's time that we do the same, although more formally, in our schools.
No matter how small the task I always tell my kids to never give up and keep trying until they make it. Often to their utter frustration, when they can't get their seatbelts fastened in the car. However, not a single occasion have they not made it, eventually, and their howling annoyance been instantly replaced by silence. Dad was right.