A long time coming

I know this blog post has been a long time coming, but I still intend to keep it short.
There has been no revolutionary happenings but I've been occupied with a lot of different things both professionally and privately.

The year is nearing its end but the holidays doesn't mean much for my workload. I still have to be productive even though I will of course treat myself with a proper Christmas celebration with my family.

I'm wrapping up the last samples and data points for my first publication this week and already starting on my next project, and suffice to say that both are looking really exciting.
Looking back on the data that I've accumulated, I've now run the qPCR instrument through 10 different microbial targets adding up to ca 1350 samples! Including the environmental metadata it will be a huge dataset.
I will get back to you on my new project soon and hold off with my exciting results until I've gotten it published in a scientific journal.

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.

Back to work

Vacation is officially over for this summer, if you can even call it a summer after experiencing the coldest month of July since I can't even remember. At least it was nice to be home with my family.

Now it's time for me to get organized in the new building, my new office and my new lab after the move (or merge) of the institution into a newly built, but not yet finished, building on Stockholm University campus.

I have loads to do, specially in the lab, and most people are still on vacation, which is crappy cause I need some assistance of the techs. I don't even have a key to my office yet! My new computer is breaking down on me too! Great timing. I guess I'm calling the tech support NOW!

Living with type 1 diabetes!

I've been thinking about this blog post for a while now, but never really been sure as to if I should really write it and where (if I did) I should post it. Secondly there's also the decision whether to write it in English or in Swedish.

Stay active, stay strong, stay alive.

What I will tell you about ultimately concerns more than just me. More than just my son and family. More than just Sweden. Therefore I will write it in English and I will post it on my blog where I intended to write posts related to my science and experiences in the field. However, I would be lying if I said that none of this affects me both on a personal and professional level.

It is important that you know that my purpose with this post is purely to enlighten and give my views on the everyday life, the challenges, the outlook and the science of one of the the biggest, the quickest emerging and sadly also most underrated diseases in the western world. This is a tiny window into the life of my family and my son (and most likely other families battling type 1 diabetes), diagnosed with type 1 diabetes (Diabetes mellitus Type 1 - or just DM1). There are many details on diabetes that I will deliberately leave out, so please, for further reading internet is your best friend. Finally, I would very much appreciate if you, as a reader of this blog, would help me spread the word for the benefit of all the current and future children and adolescents in the world with the same diagnose.

What is type 1 diabetes?

First of all I would like to make a clear statement on the difference between type 1 diabetes and type 2 diabetes. Unfortunately media often refers to the disease as only diabetes, as if type 1 and type 2 were basically the same disease afflicting different age-groups. This couldn't possibly be further from the truth and it is a major driver of much prejudice against type 1 diabetes (most commonly afflicting children). The only thing the two have in common apart from the the name is that the body of the afflicted person can't produce enough of the hormone insulin, responsible for feeding our cells with sugar transported with our blood (thus keeping blood sugar on a healthy level), or lacks production altogether.
Type 1 diabetes is fundamentally different in the fact that it is (as of now) an irreversible autoimmune disease which current research propose is both genetically inherited (many genes involved which can be both dominant and recessive) and triggered by an environmental factor (possibly a common viral infection). In difference to type 2 diabetes there's therefore no way to prevent or mitigate the onset of type 1 diabetes by way of i.e healthier living. Developing type 1 diabetes basically means that you're the wrong genetical composition at the wrong place and time. Unlucky, right?
Autoimmune means that the own immune system somehow has been triggered to unrelentingly attack the insulin producing beta-cells in the pancreas, ultimately fully deactivating their ability to produce the essential insulin, which is the only hormone of its kind with the function of decreasing blood sugar (i.e both cortisol and adrenalin are hormones that increase blood sugar by stimulating the liver to release glucose).
Because of this lack of insulin, the afflicted person's only option is dependency on an outside source of insulin by injections, most commonly by use of needles or the rising technological tool, the insulin pump.

Portable "real-time" blood sugar monitoring with a six meter range.

In spite of advanced technological tools and rapid advances in scientific understanding, type 1 diabetes is a widespread and deadly disease which also (at least) doubles the risk of a "premature" death no matter how well it is treated. It is a constant battle of balance of blood sugar, something that the insulin pump has helped a lot to manage but still is nowhere near as effective as the own body. High blood sugar may lead to cell starvation (if insulin is lacking) and ketoacidosis (acidifying the blood and body) and further down the road a range of complications with function of bodily organs, especially kidneys and heart. On the other hand, low blood sugar may lead to insulin induced coma and death.

Current status and living with DM1

Type 1 Diabetes has an estimated 80.000 new cases worldwide each year, while the total number of people with the diagnose is unknown. It has also been observed to increase in magnitude by about 3 % per year in recent years. Looking at diabetes as a whole (both type 1 and 2) an estimated number of 387 million people worldwide has one of the two diseases (8 % of the world's population) and up to 4.9 million people die each year as a direct result of diabetes.
External insulin dependence (type 1) is a constant management of one's blood sugar which then of course, independent of treatment tools, requires plenty of medical consumables, to an estimated cost of $875 per month per diabetic (in the USA). You do the rest of the math.

Insulin pump consumables which are replaced every third day.

With that said, type 1 diabetes is a taxing disease to treat, with a never-ending learning curve which sometimes feel steep and at other times leave parents and medical personnel alike baffled. Either way, it is a constant home treatment which demand regular (mostly not medically trained) parents to take full responsibility for a deadly disease, where death as a result of unintentional mistreatment is a very real possibility. It is a very intimidating thought. At the same time the ultimate goal for all parents is to, with time, foster independent children. How much more difficult is that scenario for both parents and children when the fledgling leaves the nest for the first time carrying with him/her the responsibility of a deadly disease.
Parents have to first learn and then teach how to monitor blood sugar, using needles and a small computer. Continuous  monitoring with less need for needles is also possible if the treatment is by insulin pump but it still needs to be calibrated at least two times a day. Secondly, the correct insulin need at any given time (mostly for meals, if treatment is by pump) needs to be calculated and administered (by needles or pump). Thirdly, unexpectedly and/or unexplained high or low levels of blood sugar has to be dealt with. Every case of diabetes is as unique as the afflicted individual and is a highly personal story. Parents will often refer to it as an additional child to care for. That gives an estimate of the level of attention it requires. 24 hours a day, every day, for the rest of their lives.
The harsh reality is that, as of today, there's no cure for type 1 diabetes.

Research on DM1

In my molecular lab.

So what does science say? There is plenty of research being conducted around the world with different focus. Some research teams are focused on the demography of type 1 diabetes for a better understanding of the disease and possible prevention methods. There are hopes of developing a kind of vaccine for type 1 diabetes which would decrease or even mitigate the T-cells of the immune system's sensitivity to the insulin producing beta-cells in the pancreas. Secondly, as stated previously, this is also a billion dollar industry where companies make huge profits on providing new technology for rather hefty (in my opinion) prices. This is certainly a quickly developing industry where the aim is to make life easier for diabetics. The current "flagship-to-be" in this industry is the "virtual pancreas" which is very much like the current insulin pump but more compact, with a more advanced algorithm for automatically dispensing insulin as a reaction to increasing blood sugar (the current insulin pumps need to be configured and much of the insulin dispensing is by manual input) and being directly attached to the bodily systems by means of surgery.
However, as you can see, this is by no means a cure to the disease.
This is where the third field of type 1 diabetes research comes in, one which has been pioneered by Swedish researchers in Uppsala and Lund.
This research focuses on curing type 1 diabetes and the last few year's initial medical trials on human patients have shown great promise. Personally, I wouldn't go as far as calling it a major breakthrough, but the researchers are well on their way to countering one of the major issues of any treatment of the cause of the disease as well as restoring beta-cell activity and function. The T-cells of the immune system. They propose to use special cells from the own bone marrow to ward off the aggressive T-cells. There's also a possibility of shielding the beta-cells with reactive oxygen. The use of bone marrow proved successful in at least one medical trial where new type 1 diabetes patients showed full recovery of beta-cell function, thus external insulin independence, within a year after the study's conclusion. However, there are some drawbacks to consider.
This is only one case and it has not been replicated since.
Proper evaluation will take years and it is not known if the renewed beta-cell function is time limited. As an initial substitute for a cure I would argue that a major treatment session every 5 years (or whatever it might be in a worst case scenario) is better than the technological alternative.
It was only conducted on newly discovered diabetes, therefore we don't know if the same treatment will work after years with the disease. There is some hope in this reasoning though, since another team of researchers has shown that the T-cells don't, as previously thought, destroy the insulin producing beta-cells, but rather deactivate or suppress them. A course of events that can be reversed.

The disease, the onset and the society for a young diabetic

Tools for measuring blood sugar.

My personal opinions on type 1 diabetes in general and my life in specific living with the disease, are many and colorful even after just 7 months after the initial shock of my son being diagnosed with it. I think most people having to face the reality of type 1 diabetes go through a phase of denial before the ultimate acceptance. Same was true for me, but to be honest, as a parent and a scientist I think that I, at that point, at least owed it to my son to thoroughly investigate type 1 diabetes, its causes, method of diagnosis and possible explanations. The most unlucky coincidence was that he at the time had inhalation spray for child asthma which is known to increase blood sugar. We hoped for dear life that he would get better within a few weeks, but of course that never happened.
So this was where our journey, with my son, living as a healthy diabetic started, all the while looking to science for answers and hopes of a better life in the future. That, however, is no excuse to not live life to the fullest here and now, which I think is very important both for him and for us. Diabetes shouldn't govern our lives, then we aren't doing a good enough parental job, but rather that we plan and buffer for it. The difficulty in this rhetoric and way of living with type 1 diabetes is the constant ignorance and prejudice of the society (most of it anyway). Many times children with type 1 diabetes are excluded or denied participating in activities solely because of ignorance or fear derived of ignorance on involved adults part. All I ask is for children to be able to be children no matter their conditions, but to break that barrier in case of type 1 diabetes society in general, and people working with children in particular, need to be enlightened on what it is and how it is handled in daily life.
Personally I haven't had this argument yet, but I know that it will come soon enough, and I know it will be an essential one no matter the outcome. Equality is not for everyone when it requires a bit of extra time and effort, because nothing today is free. Though I am thankful that we, in Sweden at least, doesn't have to pay for the life-long treatment of type 1 diabetes.
On the other hand I'm concerned that the billion dollar industry that this constant treatment is, will hamper the progress of the true goal in this story, which is a cure. We have probably all heard the rumors about oil companies that buy and shut down projects for developing alternative fuels.
Further, the ignorance of type 1 diabetes is leading to insufficient funding in terms of charity foundations for research. As a scientist I know that every little penny counts but the neglect of type 1 diabetes is no petty sum. I don't want to discredit child cancer, which also is a terrible disease that still not every child recovers from, but purely for comparison, in Sweden, the foundation of child cancer receives about 208 million SEK yearly, while the child diabetes foundation only receives 8 million SEK yearly. I can't speak for the medical research field but for me as a marine biologist 10 million SEK will fund a rather extensive research project for a small team of scientists for several years. 200 million SEK is a lot of money in this context.

Role models and the future

On clear and calm waters.

There are many examples of public figures in Sweden that have learned to master their type 1 diabetes and still be successful (and a role model), but many chose not to tell their story and many yet are never confirmed cases. Why this is I will probably never know, but I guess that type 1 diabetes, being a disease, is frowned upon. It is a brand that people will get and it is a brand that of course never will further a career. It would be a purely altruistic act, an important one that I wished that more public figures would do to inspire our young and enlighten our ignorant.
I will keep supporting my son in his decisions, in life, and spur him on where needed. Because if there is something that I will teach him, then it is definitely that living as a healthy diabetic should never be a limitation of ones dreams and goals, but if anything, merely a speed bump in the road.
So speaking about myself, I'm now pondering where this road will take us. I'm sure it will be a good place in the end, but what will that end look like.
I'm a scientist and I'm passionate about my field, but it has crossed my mind on more than one occasion if my future instead lies in diabetes research rather than marine biology. It is not as easy as that though, since I've learned how our oceanic systems work, not our bodily systems. There's a fundamental difference although it is biology, and there will probably be plenty of pitfalls for a marine biologist. But how would you start to explain to your growing son why daddy didn't use his research to at least attempt to find a cure?

References:

Out of convenience I pulled most of the above numbers and facts from https://en.wikipedia.org/wiki/Diabetes_mellitus and linked pages.
Also, check out the first successful medical trial on curing type 1 diabetes in this paper:
PO. Carlsson, E. Schwarcz, O. Korsgren, and K. Le Blanc. Preserved b-Cell Function in
Type 1 Diabetes by Mesenchymal Stromal Cells Diabetes Volume 64, February 2015.
If you can't access it, contact me and I'm happy to share it with you.

Comment, share and donate to bring hope of a better future, hopefully without type 1 diabetes!

Future endeavours

Before my flight on the very last day I had a few hours to spare. I chose to spend those hours at Pearl Harbour, which was a very interesting and humbling experience and I'm happy I went. So many details about the horrible WWII happenings at Pearl Harbour that I didn't know about.

After a terrible few flights (including a 17 hours involuntary stop in Salt Lake City due to an engine malfunction) I finally arrived back home with my family. Almost a full day late.
My plan was to be back at the lab in Stockholm before my supervisor leaves on summer vacation, which for obvious reasons didn't happen.
In this case it's great that my work is so flexible and I could show up later to get acquainted with the new lab and my new (empty) office. The new building which the department is moving into (kind of a physical merge) should have been mostly done by now, but no. This place is still a barren and somewhat messy construction site, and I have to step over construction workers on my way to the lab on the fourth floor. At least the lab is neatly set up already thanks to the rest of my group.

Officially I now have my first ever paid vacation. I never realised that I had all these perks doing my PhD in Sweden, but now I'm very grateful for it. Still I have tasks with deadlines approaching, but at least I can now spend some well earned time with my family after being gone for three months already this year. There is always more work to do, but for now it can wait.

So Sweden treated me with the best week of the summer so far when I got home, and now it's raining again. It was a nice feeling to be back, enjoying a beer in the sun, going for a swim, having a family barbecue and taking the kids outside. Hopefully July will be good (my vacation).

In August it is back to the lab again with lots of practical lab work (DNA-extraction and qPCR) to accumulate much needed data, analyse that data and put together an "award-winning" poster for the SAME conference in Uppsala, 23rd of August. So if you're going to that conference I'll see you there, specially during the poster presentations.
In addition to the conference I have plenty of future endeavours during the coming autumn. I will finally attend the introductory course on research studies in biology, which also is the first course in pedagogics which will make me eligible to teach on undergraduate courses. That is also exactly what I will do right after. One or two weeks (depending on the number of applicants) of assisting on a basic course at the Stockholm University field station Tovetorp.
Finally I also have another deadline on a writing assignment, but for now I'm fully committed to my vacation.
Thanks, have a nice summer and stay tuned in late summer!

Farewell gala at Waikiki Aquarium

At this very moment I'm well on my way back home to Sweden, but still have a long way to go with a total flight time of 20 hours. I'm getting back to reality soon enough, well that's kind of how it feels after these five amazing weeks at C-MORE, Honolulu. Thankfully I will only have a few days back at work in Stockholm before I go on summer vacation for four weeks, making up for lost time with my family these past 6 months. It will be good.

So citing fellow course participant Michael Henson's Facebook post, "it feels surreal" that the course is over and a very awkward feeling saying goodbye to all these great people that I basically have spent every single day with for the past five weeks. Needless to say, it was a great bunch of people, students and faculty alike. I'm sure I will see most of them again sometime and there might even be opportunities for collaboration. To cite David Karl (the C-MORE director); "science is greater than any one individual", the new generation of scientists (including me) goes down a path of sharing knowledge to further our research to the benefit of all. That's exactly what Dave recognises and perhaps this is one of the contributing factors to why humanity has never seen a greater rate of progress in all fields and aspects. 30 years ago most methodologies and technologies (perhaps even including theories to some extent) never saw much change. Today, in 2015, and with the increasing development of the newly implemented metagenomic tools, we are looking at ever improving methods and new discoveries almost on a yearly basis. It is a staggering development which we all should be proud of and which I'm privileged to be part of.
Now I'm starting to sound like Dave, haha!

Anyway, the final day at C-MORE entailed a two hour long presentation which we students at the course had frantically put together the night before by fusing our individual stories from the data analyses to tell a coherent story of station ALOHA for all people interested (the presentation was open to the public). The lecture hall was almost filled up to the last seat which was really cool, and what was even cooler was that we even had the university dean and a US national science board member among the audience (in addition to all the renowned faculty of C-MORE, David Karl included).
I contributed with a small, but oh so important, story (which I of course told the audience) of nitrogen fixation at station ALOHA. Using metagenomics I wanted to address a few different questions on the subject; What organisms fix nitrogen at station ALOHA? At what depth do they do that? And finally, in what size fraction is most of the nitrogen fixation occurring? After successfully answering my questions I also used chemical and physical data profiles, plotted for comparison, to attempt to answer why I got these results.
In short (which was my conclusion slide during my part of the presentation) I found that the unicellular cyanobacteria and obligate symbiont, UCYN-A, was dominating nitrogen fixation at this time of year at station ALOHA. I also found that the relative abundance of genes for nitrogen fixation (nif-H, which I assumed to be a proxy for actual nitrogen fixation) was highest at the surface and decreased with depth.

The evening was spent at Waikiki Aquarium by the beach which was a farewell gala for us summer course students. All of C-MORE (and more) were invited and I had a great evening mingling with all the faculty a final time as well as hanging out with the rest of the students. Thanks Dave for the talk, the introductions to the rest of the renowned people attending and all the praise (weather it is actually true or not, you're a true inspiration).
I must say that it was a rather emotional evening which Mike set the bar for when he showed a self-made video compilation summing up the course (awesome job, Mike).
So at the end of our time at the Aquarium there were plenty of speeches of praise (specially by Dave), hugging and also a bit of crying. I wish the evening hadn't passed so quickly, but at least I had great concluding talks with everyone involved in the course.
Fittingly enough it just so happened that this very day was a regular day of fireworks at Waikiki. It really felt like it was just for us.
I'll see you soon again all the awesome people of C-MORE summer course 2015!

Now I'm going home with my head held high.

Short on time for final presentation

Just a quick update really. That's all I have time and energy for.
It has been an exhausting week of frantically analyzing and pursuing specific research questions on the samples, and ultimately data, that we pulled out from the cruise at station ALOHA.
I decided to investigate nitrogen fixation using metagenomics, since I'm an absolute beginner at metagenomics.
Tomorrow morning is the final (group)-presentation and there have been a few late nights. I'm probably looking at another one now.
That will be the end of the course, so when I'm done with that I can share my metagenomics work and findings in a bit more detail. Now I need to focus on getting everything right for tomorrow.
It will  be a big day tomorrow (presentation is open to the public). With that said, I leave you with a picture of an example of one step in the metagenomics workflow, for now.

Final week at C-MORE

I just started on my last week of work at the C-MORE summer course. What remains is an intense week of data analysis of the data we all generated from the lab work back at C-MORE hale. It includes many biochemical parameters as well as metagenomics. In the end we are supposed to take all these datasets and, as a group, try to make sense of them and tell a story to a general audience about what we found out at station ALOHA this past week. It will all be presented as a two-hour seminar on the last day.

I've already been part of a lot of work, including both practical lab analyses and data handling. My midsummer was spent calculating low level nitrogen (LLN), bacterial production (radiolabeled Leu) and primary production (14C). Despite a 15 hour workday, my group is not quite done yet. It was a valiant effort that took most of the evening, but in the end we couldn't finalize our datasheets due to insufficient structure in some of the cruise work group's raw data. Annoying, but a wall of numbers without labels is hard to make any sense of.

Anyway, these last calculations will be finished today since most of it by now is just a matter of putting in the data (in the correct order) into the template spreadsheets that we prepared yesterday. This is why I sometimes love Excel. The initial calculations take some time but as soon as the first calculation spreadsheet is set up it is just a matter of entering the raw data into one column and Excel will take care of the rest to automatically give me the calculated numbers at the (far away) end of it. Beautiful.

The lab method I had the privilege to run was, as mentioned, LLN, which is a chemical and gas chromatography (GC) based method where we apply analytical chemistry to measure nitrogen concentrations in the upper surface waters that are too low (less than 1 µM) to be detected by conventional auto-detectors. It is therefore fully manual where we add a few chemicals to our sample together with a carrier gas which will transport the sample through the system and into the GC where the nitrogen concentration will be recorded as a peak on a histogram on a computer. This will ultimately give us concentrations down to the nano-scale. This fact of course makes the method extremely sensitive to contaminations.
Another upside is that due to all the bubbling chemicals, which changed colour when added, you felt a tiny bit like a mad scientist. Muahaha!

The final day of lecture is soon about to start. It will be a day full of omics, Galaxy and also some microbial culturing signed Scott Gifford, former student at this very course. I'm sure it's gonna be an interesting day!

Back at C-MORE hale

The last two days out at sea were stressful, confusing and filled with different kinds of tasks. All of the labs on board needed to be prepared for disembarking and ultimately sample processing while my group (amply named "Triple Threat" by the way, or "Muscles and the Bears" if you ask Grieg Steward) needed to run our productivity samples from last night in the scintillation instrument. This clever instrument registers radioactive decay in our samples (which we spike with 14C to measure primary production) by measuring fluorescence (light) emitted from an added chemical when it's hit by the radioactive particles of the decaying 14C.
But hey, lets start from the beginning, shall we.

It was a sunny morning, like every other morning at station ALOHA (just kidding, but it is actually a whole lot of sunshine out there).
My group did the last day of science on the primary productivity sampling which meant that we had an early morning preparing all our bottles and vials for the 03.00 CTD, spiking the water filled bottles and vials with either radiolabeled leucine (an amino acid) or radiocarbon, 14C, depending on if it was for measuring primary productivity (phytoplankton - photosynthesis) or bacterial production (heterotrophic plankton - eat stuff). This is a somewhat difficult distinguishment to make in some cases since some of the photosynthesising plankton are known to be mixotrophic (they both eat stuff and photosynthesise). An example of this is interestingly enough the most abundant microbe we have in our oceans, Proclorococcus.
Since the ocean is such a vast and diluted place, it kind of makes sense in terms of evolution and competitiveness to do both, whenever either of the strategies is the most efficient. I'm not sure if we have that many terrestrial examples, but I instantly think of plants that catch and digest flies.
It's an amusing thing to picture on land though; how a plant happily would live off the sun's rays until all of a sudden, an aggregate of whatever biochemical compound potentially favoring the plant, flies by and the plant would take a bite at it. It's like a scene out of Super Mario Bros. (for all you nerds out there). Anyway, that's reality for Proclorococcus, and that, ladies and gentlemen, is one of the many things that makes the ocean so intriguing.

After spiking our bottles and vials, they were fastened to arrays that ultimately went down at different depths along a line to be incubated, floating freely, for the most part of the day. In the evening we recovered them, or more specifically the deck group did, or as a matter of fact, they tried to.

Unfortunately the first mate steering the thrusters on the port side took the ship too close to the buoy marking the arrays and the floats attached to the buoy accidentally got caught in one of the back propellers. Needless to say, we were now sitting in a tight spot. Luckily someone had a GoPro with them and could lower it down to actually see how the line was entangled in the propeller, and it turned out it wasn't too bad. The crew got the zodiac in the water and pulled the whole array away from the ship, which solved all our problems, but of course, at this time we were almost two hours late and consequently me and my group had a late evening filtering our samples.

The next morning was early since I had already volunteered to help out recovering the sediment traps (which I was part of preparing and deploying on the first day). I was tasked with the grappling hook to catch and reel in the buoy and floats of the sediment traps. Suffice to say that it all went well.
The rest of the day was just a spectacle of preparing all our accumulated samples for disembarking and processing at C-MORE and then packing and cleaning the labs. The morning and noon was scheduled for different groups to have different tasks, but after that it was just a frenzy of people trying to find something to make use of themselves. After a couple of hours doing the same, I gave up (after at least cleaning and carrying around some stuff).

Since the sediment traps had drifted so far south-west during our week out at station ALOHA, the captain seized the opportunity to make a (by now) tiny detour west, along the eastern shores of one of the other Hawaiian islands, Kaua'i. Incredible scenery is all I can say. The cliffs seen in the picture are actually of mountain size, and by judging from some of the helicopters we saw flying along the cliff faces, I estimated the height to be approximately 1000-1500 m above the sea! To top that off we even had a group of dolphins putting up a show for us at the front of the ship. Amazing!

Next thing I knew, the last night at sea was gone, a great cruise was at its end and we were back in port, Honolulu, unloading the ship (where I fortified my new flattering nickname "Muscles") and heading back to C-MORE hale to plan for the upcoming intense lab days.

Deep cast and flow cytometry

Pipetting during DNA extraction.

Preparing a perfectly even gel for electrophoresis at sea.

The buoy marking the center of station ALOHA.

Subtropical open ocean sunrise at 06.00.

The final size of the cups after being lowered down to 4790 m.

Happy upcoming birthday, my son. This one is for you!

A selfie with the flow cytometer.

Be mindful of your surroundings when working in the rad-van.

I hope the pictures mostly speak for themselves. I was thinking that that should be it for this post but I just feel like I have to write a few lines about the deep cast and the flow cytometer. I was too excited about it, not to.
I can just mention that we did have a "biodiversity-day" (first two pictures) with Grieg Steward and Craig Nelson, who by the way were awesome to work with. This day comprised of DNA-extraction, PCR (polymerase chain reaction) and gel electrophoresis. This is what I do, so naturally it was my moment to shine!

Next up was the flow cytometer with Ken Dogget. This was an instrument/method I was most excited about on the entire cruise. It truly is an ingenious and complex instrument but the application still is fairly simple and unless you're a flow cytometer technician, most of the complicated work included is interpreting the data plots that the instrument gives.
So what the instrument actually does is counting and sorting cells in a water sample. Thats right individuals cells! Im far from an expert on this instrument after only working with it for a day but to simplify how it works, it uses laminar flow to dispense the sample into a so called interrogation zone (where the sample is read by the instrument). Here it shoots a laser beam at the sample which will scatter and fluoress when it hit cells. The angle and light is dependent on cell size and incorporated pigments (you can also dye your sample). This light signal is then picked up by detectors (they do have a fancy name which I can't remember now) which will eventually give a "pixel" in a scatter plot on a computer. Now it is a matter of interpretation and hopefully (and most often in these waters) you can see distinct clusters of cells (one pixel being one cell) and can then make out size ranges and/or pigment intensities of species or populations of microbes in the water, by visualizing them in different light (e.g. chlorophyll in red light).
So that was counting cells, but you can also sort cells, meaning that you can make the instrument put all cells (within a range) of your choosing in a tube, separating up to four species or populations at the same time, from the same sample water. This is achieved by use of electricity and polarization. So the tiny flow of your sample water going through the interrogation zone is made to vibrate, by adding a low voltage to the nozzle. This causes the water to make tiny waves which eventually break off into droplets. The trick here is to calculate and instruct the instrument as to how long it takes for a "laser-read" cell to end up in the first droplet formed down the flow. This droplet will then be charged and easily sorted. The calibration of this operation is mainly done using tiny cameras inside the instrument.
It might sound like this is a process which would take a while, and to be frank, yes it does, BUT the only reason for that is that we have such large quantities of microbes in our waters. The instrument is capable of counting and sorting at a staggering rate of 20 000 cells/sec!

Finally, I unfortunately lost one cup during the deep cast. I had made three, one for each of my kids back home. Apparently there's another deep cast going down later (2000 m) which should be enough to shrink the cups. So I made another cup. Here it is. Hopefully I won't lose it.