One year anniversary as a PhD student

Today was officially my one year anniversary as a PhD student. Time has just flown by, although I've gotten a lot done and at the same time had great fun.
Doing my PhD has only during my first year proven to be no easy thing, however, I didn't really expect anything else but hard work. A true test of commitment, resilience and adaptability.
So in spite of that fact and state of mind, the first year has been filled with ups and downs and in the end I had to deal with a lack of communication ending in a shocking revelation that what I did was, timewise, not enough.
To be fair, I didn't know what was required, but I quickly had to realise my shortcomings and reorganise my work time to make it more efficient. I also had to demonstrate more outward commitment and passion regarding my project.
Honestly I didn't find it too hard to manage my time at work, however, it was not without its tradeoffs, including gymtime and family.
Outwardly showing my passion for my project was a somewhat more difficult story though, since I guess I'm just not that kind of person. I think I solved it in an agreeable manner though, by constantly sending updates, questions and suggestions to my supervisor whenever something new came up, sometimes several times a day.
As a complement to my first literature review I have to write down my thoughts, plans and hopes for my project. This is where I'm supposed to find my niche and dig down into something that really excites me. I've always been a generalist in my interest of marine biology, and prior to starting my PhD I thought of myself as a marine ecologist. Pursuing questions at the ecosystem level. I still have that interest, often linked to global environments. That is the major strength of my current project where I study tiny microorganisms with a clear link to biomes and global environmental impacts. I'm not a modeller though, so most of these links are interpretations of data and conclusions drawn from previous and complimentary research to form hypotheses and theories. Nonetheless, it's still plausible and damn interesting. There are no experiments that could ever cover a global scale, with acceptable resolution, anyway.
I'm still fascinated by the prospect of "seeing the future" though. My proposed ocean acidification experiment was shut down largely due to technical difficulties and more experienced researchers reluctance to collaborate on the subject.
I'm tempted to try my luck down the road of global warming instead, which is the other major issue of global environmental change. That research question recently showed a lot more promise when we finally got one of our studied microbes in culture.

Back to "real life". What little spare time I have in Stockholm is filled up by the gym so that's fine, but there is a delicate balance between work and family that every healthy relationship needs to accomplish. Our solution was parental leave on Fridays.
Because of this I'm extra thankful for doing my PhD in Sweden where I, as a student, have the perks of both studying and being employed by the state.
It's still somewhat tedious to commute on a weekly basis. I've done it for so many years previously so I've kind of gotten used to it by now, but never this far. However the distance is not the main issue most of the time. Down-time on the train are usually perfect opportunities for reading, writing and napping. No, the worst are those sudden moments of stabbing longingness for my crazy kids and lovely wife. I don't think that is something that will ever change, but I would argue that this, in the bigger picture, is something positive. I just have to deal with it.
In that regard the gym is my sanctuary. It always has been, and always will be. In there it's just me and the iron. It doesn't matter how passionate I might feel about my work. The gym is always... different.

First manuscript soon to come

Sometimes I just want to scream out the results and significance of my research. These things are too cool not to be communicated. I'm finding and observing trends in my data that both excite and begs for further questions and investigations. This is the beauty if science where you're never truly done, and as a scientist you're driving factor is an ever burning curiosity that can't be put out.

My first manuscript for a publication is drawing near. I'm soon finished with my lab work for this initial project. Then, hopefully, I can scream out to all that want to listen (and a few more) that what I found was actually really cool and that it has some implications for what we currently know about open oceans, as well as raising further questions worth pursuing.
Oh, how I love straight-forward graphs with clear patterns. It makes data analysis so easy when the graphs tell you where in your dataset the statistically relevant trends are.
Or perhaps peer-review (or my supervisor) for my first paper will in no uncertain fashion tell me that I need to calm down.

Motivation - Perspective is everything

The following are a few quotes that I found in motivational gym videos on YouTube.
In my opinion they can be applied on any activity or life event, be it work, a difficult assignment, exercise or just reaching one's individual goals and dreams.
If you're into bodybuilding (even remotely), then I recommend you to check out JerichoDMZ's motivational videos on YouTube.

"Work on your focus, perspective is everything.

The problem with most of you is that you see difficult as something negative.

I want you to see difficult differently. Do you hear me? I need you to see difficult differently!

That weight-lifter when he’s looking at those weights, he got that iron. That iron is heavy, but he isn’t looking at that iron like “look at how heavy that iron is”.

He knows what it’s going to do. It’s going to tear his muscles to pieces. He gets it! What he understands is that if it tears them down they will rebuild themselves. They will rebuild themselves that much stronger!

The more you go through, the more difficult it is, the more challenging it is, the harder it is. Are you hearing me? Don’t quit!

I suggest to you, if you want to become diamond, write down five reasons why it is worth it for you to become a diamond.

To experience that level of achievement, what is it that will give you the drive?

What is it that will ignite the courage in you to get up and come back again and again and again?

If it was easy, everybody would be good at it. If you want something you never had before, you have to be willing to do something you’ve never done before.

This is kind of hard to understand but, sometimes you can try so hard at something. Sometimes you can be so prepared, and still fail.

And every time you fail it’s painful. It causes sadness.

I’ve often said that a man’s character is not judged after his celebrates of victories, but what he does when his back is against the wall.

So no matter how great the setback. How severe the failure. You never give up.

You never give up. You pick yourself up. You brush yourself off. You push forward. You move on. You adapt. You overcome. That is what I believe!"

Go out there and show yourself, and everyone else, what you're made of. Today is your day!

What is this thing called science?

As an introduction to science in this introductory course in research studies in biology we were all asked to read the introduction and first chapter of A.F. Chalmers' book "What is this thing called Science?". Obviously it is a deep philosophical question, as I mentioned previously, especially since Chalmers wrote a full book on it which also have been re-released in several editions.

It is initially stated that there is a fundamental issue in the understanding and interpretation of science and what we actually derive from it, and all of that comes down to observation.
Science are based on objective, unprejudiced observations that are used to determine facts of the world around us. At this very point Chalmers dig in and highlight the flaws of science. Be it modern or otherwise, it still has the same roots. The same underlying assumptions and issues.

The main issue here is with observations. That observations is based on more than just what our brain registers by use of our senses of the surrounding environment. It is also based on experience and our current state of knowledge. Chalmers has an example of a 3D image of a staircase which can be seen from either above or below. This image immediately reminded me of an old optical illusion of a spinning dancer which, depending on the observer, is spinning either clockwise or counterclockwise. You tell me.

This might seem like a poor example for the principles of modern science, but when it comes the practices of observation in for example microscopy, I have a direct experience of observer dependent "facts". In this case it was related to experience and previous knowledge, which is another vital part of statements and facts according to Chalmers. Being inexperienced with microscopy and the organisms of my new project, I looked at a slide of sample prepared by my supervisor. What I saw was more or less equivalent to a starry sky at night and the occasional cell that I actually recognised. My supervisor on the other hand could tell a story of the planktonic community by looking at the same slide.

The same story arose out at sea when me and my colleague were looking for the same cells but in a much more difficult setting, with a lot more other microbes on the slide. We observed very few of our target microbes and that was our fact of observation. However, when I later ran the same water on an instrument designed to quantify our target organisms, back at the lab, it gave us a very different result. Our initial observation based on previous experience was not even close to reality. At least we learned something from that. We somewhat gained more knowledge in our field and from that knowledge we can derive statements and hypotheses which can be tested to reach a fact.

Science is based on facts and from facts we can formulate theories. If the objectivity of observations in science is aided or not by technical development, I can't say for certain, but I would argue that it is aided. Because refining a technical innovation and method of observation follows the same principles as for science itself, and basically it is science. Knowledge about an observed phenomenon lead to a statement that could be tested, and as the quote I posted previously said, "many observations can prove me right, but it takes only one to prove me wrong".

Science is not a feeling or a belief. It is observable facts derived from previous knowledge. In my opinion it is both one of its greatest strengths but also its greatest weakness. Falsify one fact and the theory is flawed. By that said, not just anyone can do ground-breaking science, but everyone can appreciate good science with its theories formulated from facts. Unless it's steaming fresh data up for interpretation. I hate that word.

A scientist's life is not always science

These past few weeks since the SAME14 conference I've tried to develop a new work schedule and adapt to that since me and my supervisor agreed that I need to get more laborative work done. This is the downside to weekly commuting to work. The upside is that when I'm actually at work I can fully focus on work and work alone and very often I work quite late. Sometimes because I have to but also because I find it so damn interesting that I must have those final few data points to eagerly start analyzing a, hopefully, coherent picture of my observations. The latter is usually not that simple, but you get my drift.

With that said I want to emphasize the point of this post, as the headline says, that even though I'm hired to learn and do professional science it is not the only thing I fill my workdays with. Far from it. There are many issues or matters that require my attention, not all of them related to science, but those that are might not actually be related to my project or even my subject.

This somewhat covers the never-ending story of the scientist with numerous "professional hats". The hat being a metaphor for a role, profession or title that I put on and take of when needed in my daily work with science. Because that is the reality of many professions I guess but I can only speak for scientists. It is a stressful prospect and not at all simple to deal with. Mainly it requires careful management of your time and work, but it also requires extensive knowledge and skills in areas where you were not necessarily previously trained or only have limited experience of.

Photo credit: Actuation Consulting

The list of requirements is long but the list of highly recommended skills is usually even longer. As a marine microbiologist working in the tropical open oceans, I'm naturally expected to be somewhat of an expert in my subject, quite knowledgeable in marine biology and a generalist in biology as a whole. However, knowled
ge wise it doesn't end there and the reason for that is that any one system that you might study is not limited to biology. There are numerous other factors that sustain, limit and shape biological life other than biology in itself. So to really begin to understand open ocean ecosystems I also need to be an oceanographer. I need to understand the role of currents, eddies and internal waves. I need to be a marine chemist. I need to understand the chemical composition of the waters that I study and be able to follow cycles of elements as well as realising the broader context of elements relevant to the phenomenon I observe. I need to be an ecologist. I need to understand the broader context of the observed phenomenon in the ecosystem as to identify and account for top-down and bottom-up effects.
The list can go on and this is just within the actual science that I'm studying. I also need to be a statistician. I need to analyse, prove and interpret the data from my observations using biostatistics.
I need to be an engineer and build my own experimental setups. I need to be a good writer and speaker to communicate my science and receive funding. I need to be an administrator that keeps track and logs my work for yearly revisions...etc...etc...

Finally I have to have a thirst for knowledge, which isn't a concern really, but to stay abreast with a rapidly improving and developing field I mainly need to read, read and read.

This week, and next, I'm attending an introductory course on research studies in biology. It partially covers the philosophy of science. What is science? Well for me, science in practice is obviously a broad concept, but that is also a deep philosophical question which people make careers on.
I will try and delve deeper into just that in my next blog post.

SAME14 conference Uppsala

Second conference on Aquatic Microbial Ecology, was held last in Uppsala this week.
It was my first opportunity to present my science so far and reap the fruits of my hard lab work these past three weeks.

Most of the presented work during the conference was in the form of oral presentations in front of all participants. Most of it was very interesting, but since the conference wasn't exclusively marine, then some freshwater work was a bit hard to relate to.
As a whole, the conference was heavy on metagenomics and genome sequence approaches, which is super cool, but also difficult to follow sometimes. I will most likely do some genomics of my own further down the road, so I tried to stay focused during all talks. One of the most interesting talks on the topic however, was actually one with hard criticism against how the massive data derived from metagenomics is handled and the lack of consistency between studies. Most often what is presented and compared in a metagenomics study are the different OTU's (Operational Taxonomic Unit) acquired from the data. Part of the criticism against the use of OTU's was that they are difficult to define and usually pre-determined by the researchers of each individual study, meaning that the term OTU can have a wide variety of meanings. They are therefore impossible to compare in a larger context between studies. It is also difficult to assess what the massive dataset from metagenomics actually tell us, where OTU's hardly help.

As of now, I have no idea how to approach this issue, but I'm sure things will be more clear down the road. There was also a metagenomics study presented during the conference where they actually didn't use OUT's.

The other big part of the work presented at the conference was in the form of four poster sessions. It was here that I presented my work. It is a very limited format, much more so than oral presentations even though they had to be no more than 12 min long.
Imagine squeezing in your research on 140x100 cm, knowing that most people won't read a single line of what you've written. This calls for some serious presentation skills where the pictures, graphics and plotted statistics have to tell most, if not all, of your story all by themselves.
In addition to the poster I also had two shots at a speed talk (30 sec) in front of a limited crowd. This was probably among the hardest kind of oral presentation I've ever done. 30 seconds is an extremely short time when you have so much to say. Even though I wrote and practiced my talk, nervousness got the better of me the first time around, but I quickly got to redo the talk and redeem myself.
All in all I was very satisfied with my poster presentation and I really loved to communicate my research and answer a lot of questions from other curious scientists.

I also attended a workshop on communication and outreach during our "day off", which turned out to be a lot more informative and interesting than I thought.
The whole point was to further our skills in reaching out with our research to the broader public. Try to make science a topic of discussion and an interest, not just among scientists of respective fields. Some fields like astronomy have already come a long way with their outreach, but biology has a long way to go.
I was mostly interested in deepening my knowledge on online outreach as to reach as much people as possible. Internet is a powerful tool if you know how to use it, and the take home message I got is that it is mostly about finding and using several channels (of the right topic) to convey my message down the line.
By that said I have now done something I told myself I would never do: I got myself a Twitter account. #MStenegren #MarineBiology.

A student's guide to increased lab work efficiency

Laboratory work has started in earnest and it can sometimes be intimidating business, especially if previous experience is rather insufficient. It can also be horribly messy if taken too lightly. However, it should also be fun and rewarding, considering that you do it for most of the workday. Below follow some of my thoughts and guidelines on the subject in my new molecular lab.

1. Use your PPE

Photo credit: UCSF

This should be the first thing on your mind before starting your work in a lab, regardless of what kind of methodology you will use. What personal protection equipment do you need? Gloves, labcoat, safety glasses? What material should they be? If you reach the conclusion that no PPE is needed for your protection then consider if your samples need protection from you, which is another function of PPE. Finally, if you don't have your own PPE, go and get it. Now. As in right now!

2. Keep it tidy

No one likes working in a chaotic environment where things are randomly lying around everywhere, obstructing workplaces and posing a risk, not only to the quality of your science, but to your safety. This is your responsibility. Everything should have its place. Put it back and take out the garbage. And for the love of science, don't fill the place up with stuff you don't really need at this time.

3. Plan ahead

Image credit: Frits Ahlefeldt-Laurvig

What are you going to do, how will you do it and what do you need? I find following a protocol the best way of staying organized in the lab. Unless you're awesome at remembering details or you have plenty of experience with a certain method, then going
through a protocol on the method of the day will save you a lot of unwanted surprises, tediously running back and forth and most importantly, time. Assemble your lab bench with what you need before you start. The smoother your work goes the better for both your schedule, your samples and your sanity.

4. Change gloves

Just because you're wearing gloves it doesn't mean that you're sterile or even clean. If you work with sensitive samples or methods, change your gloves regularly. In general, have you left your lab with gloves on (for some good reason), change when you get back. Did you have to rummage around in a dark corner of your lab to help a colleague find a certain something, change your gloves. It could also help to actually write "Change gloves" as a strategic bullet point in a lab protocol, i.e. when working with standards.
If you work with hazardous chemicals or materials then just switching your workplace within your own lab is call enough for a change of gloves. Wiping down a lab contaminated with radioactivity because someone forgot to change gloves when switching benches is no fun. No fun at all.
Be mindful. In the end it is your health on the line. Also, it is rather embarrassing to explain why you got gut bacteria in your cultures, because then you're obviously not washing your hands either.

5. No food, drinks or mobile phones

This might seem obvious to most people, but I've actually run across more than one coffee machine happily sitting on a random bench in a lab. In the end I guess it's up to each and every researcher responsible for the lab in particular, whether or not their science or health will be affected by preparing and consuming hot beverages in the lab. In my opinion you do science in the lab and drink coffee in the lunch room. Period.
When it comes to mobile phones, unless you're expecting an important call, leave it in your office. One slide of thought and you'll find yourself grasping your frantically vibrating mobile phone with your gloved hand, possibly contaminating your gloves and/or your mobile phone. Hopefully, this will never be the case, but then you will likely either interrupt your work or be distracted wondering who called, for the rest of the day.

6. Use alcohol

It's a great chemical to keep things clean and decrease the risk of contaminants. Wipe down not just your benches but also your instruments and other equipment that you can't put in an autoclave. On a side note; please refrain from drinking molecular grade alcohol during work hours, it gets you drunk to boot and you'll make a fool out of yourself. It's not really for drinking, but you know, scientists all have their stories.

7. Relax

When stepping into your lab you should feel at ease. Don't stress out. It will affect your performance and ultimately your science negatively. We all make mistakes, but mistakes tend to be more frequent when you're stressed. Plan ahead, ask for help, put on some music, do whatever you need to make your lab work a somewhat relaxing endeavour.

8. Be a mad scientist

Image credit: CKEC

Most people enjoy field work the most and that is usually what a personal scientific story is about. There's not much fun or interesting in describing your late "pipetting-nights" in the lab for neither colleagues or friends outside of academia.
However, lab work is a major part of what most science is, and considering that you will spend most of your work hours in the lab, it should be fun. Spice it up a little and you'll even have a decent story to tell. As long as you're doing good science and staying safe, make things smoke, pop, bubble, change color or glow. It's more fun than it sounds and usually the chemistry/science behind it is really interesting.

9. Take a break

Too much of the good stuff will make even the most passionate of researchers tired. Just like reading a book for too long, your brain will ultimately switch to autopilot. The problem in the lab though is that it's not as easy as flipping the previous page if you missed to register the last few lines. If you lose your focus you could also lose the last hour of work, or worse, precious samples.
When you start feeling tired, have a coffee break and some fresh air, go for a walk or just switch your current task for a while. If you can't just leave your work like that, then plan ahead. I usually hit the gym halfway through the day.

10. Take notes

It doesn't matter how good a memory you have, you will never remember every little detail that comes up while you are working on your different methods. It might just be numbers for your samples or deviations in your protocol which at the time might feel trivial. However, further down the road when you want to look up what you actually did or there are some funny oddities in your results that you need to interpret, your lab notes will be gold. Keep a laboratory journal. One of the best investments you'll ever make.

11. Know your field of action

Fundamentally it's not much practical work in this point. It is more about reading literature and science papers until your eyes roll out of their sockets and your brain melts. Which won't happen anytime soon so keep reading. So when you've plowed
through a decent amount of text, directly or indirectly related to your subject, you will have an easier time navigating and understanding any methodology that comes your way. Because it is important that you know what you're doing, but it is equally important to know why you're doing it. So if you find yourself not knowing enough, ask questions and look it up. Once you're the expert on what you're doing you can perhaps start tweaking and improving your work and approach a problem or hypothesis in a whole new way.

12. Practice makes perfect

There's no such thing as perfect science. There will always be known and unknown biases constraining your research. The only thing you can do is try to mitigate them as best you can with the various tools available to you. Either way, you can still become a jedi master of pipetting and thereby rule out one possible source of bias. The more you practice those nimble hands the better, and that goes for all your work in the lab, regardless of what it is. Embrace your passion but be aware of the dark side of bias.

13. Sort and recycle your waste

After a long day in the lab this is for no other reason than to lighten your bad conscious over the mountain of plastic waste you just accumulated for no other reason than extracting a tiny amount of DNA. This is certainly a conflict of interest for environmental scientists and biologists where furthering the research of understanding and better protecting our environment you produce so much waste, not just plastics. Hazardous chemicals for example, need to be properly disposed of as not to leak out in the environment. Pat yourself on the back, our planet would too if it could.

14. Put on some epic music

Everything you do in the lab will feel soo much cooler with some epic music filling the room. There's a possible major scientific discovery every day when listening to epic music, and it feels good. Get inspired and progress with style. Even pipetting feels epic when listening to a pompous orchestral piece.