There is something marvellous about returning home at the end of a long trip…

… just as there is something inherently bittersweet about leaving a place that you ended up calling home.

A real Basilisk running from somewhere. Or running towards something. Or maybe both.

Reporting live, from Schiphol airport. (Note: most of this post was drafted in Basel airport, if you want the correct info).
I actually enjoy travelling, I find it calming to be at the airport ages in advance, sitting down with an overpriced coffee and a book. I just purchased Game of Thrones — beware, I will become one of those “I’ve read the book”-snobs. Wait, I already was one of those, just not for GoT.
It’s not the first time I’m leaving a place. I have spent two months in Switzerland, and for the past two weeks people have been asking me if I am happy to be going back to Dundee. And like those other times when I was leaving a home, the answer is: “I don’t know, a bit I guess.” Of course I’m happy be going back. It won’t be 30 degrees in Scotland (seriously, I’m not cut out for warm weather, and I sincerely disliked getting searched at security after carrying my heavy bag around and feeling a bit sweaty). I will be back in my own room, in my own bed, back with my friends.
But then on the other hand, I’ve had a wonderful two months. I’ve made a lot of friends in Basel. And it had started to feel like home.
I have learned a lot, mostly about handling stress and deadlines, about how things work in another lab, how to assertive about what you need and when you need it. I have met the most wonderful people. I have met up with friends that I hadn’t seen for months, or years even. I’ve travelled around, I’ve gotten a tan and seen a lot of sun (I know I live in the “Sunniest city of Scotland” but I think this was the most summer I will see this year). In short it was a superb experience. But suddenly it was already time to go, just when I got the hang of how to conduct my experiments, and just when I started to figure out where all the cool spots in the city were.
Maybe, two months was just too short.

One of the last nights I spent like a local Baslerin. With a beer by the riverside. I didn't swim in the river like everyone else, but I did get my feet wet!
One of the last nights I spent like a local Baslerin. With a beer by the riverside. I didn’t swim in the river like everyone else, but I did get my feet wet!

So I am a bit sad to go. There are things I will miss. But I’m glad to be going back as well, get back to the other aspects of my project, not having to attend meetings over Skype (quite often I just miss half the conversation, if Skype even holds up for the whole time). Have an after work beer in Duke’s. You know, back to the normal things.
Bye Basel. I promise I will be back.

View from the top of the Münster in Basel.
View from the top of the Münster in Basel.
Quasimodo's friends were there too!
Quasimodo’s friends were there too!
Basilisk fountains all over Basel. I will miss these dragon-winged chickens.
Basilisk fountains all over Basel. I will miss these dragon-winged chickens.

*Title slightly adjusted from a Lemony Snicket quote about returning home and tuna fish. The more you know.

On Growth and Form

Before I start, a short comment on personal growth:
After a quite frustrating day yesterday, I decided to get up bright and early, go for a run and then head to work today. It’s actually a national holiday here (Ascension), but as I have to take my holidays explicitly, and “I’m here for work and not for fun (except for weekends)”, that was my plan. So I was up and ready to leave for my jog, when my flatmate just entered the front door, after a night out. Made me think.
I guess I’m a “real grown-up” now…
But now, On Growth and Form.
I have discovered that Dundee has had quite an interesting inhabitant. His name is D’Arcy Wentworth Thompson. I had never heard of him until sometime last year when we went out to dinner in a restaurant called The D’Arcy Thompson. A plaque on the wall informed us he was a biology professor in Dundee (at the time the university was still part of the University of St. Andrews) around 1900.
Sometime later, I went to a talk about penguins, more specifically about the two penguins that Dundonian Arctic explorers had brought back from their trip south. The penguins had gone through quite a bit, one even was the official mascot of a student faculty club, but they are now on display in the D’Arcy Thompson Zoology Museum on the campus of the University of Dundee. We went to go see the museum after the talk, it’s a room stuffed with, well, stuffed animals. Quite an impressive collection, including a giant crab. (Giant means more than a meter across. Imagine running into a wild one!)

A stuffed penguin in a vitrine of a zoology museum
The penguin before it went missing. (ca. 1900)

But it wasn’t until last week that I realised how interesting Mister D’Arcy really was – and I just realised that sounds like a sentence from Pride and Prejudice. A research letter in Nature Physics on the combined mechanics of cells in tissues mentions the following:

In 1917, D’Arcy Thomson published a treatise On Growth and Form in which he suggested that morphogenesis could be explained by forces and motion – in other words by mechanics.

You might recall that my PhD is about the mechanics of gut cancer. And I didn’t know about D’Arcy, shame on me! In the meantime I’ve tried to get my hands on the book, not too difficult because there are some on line pdfs circulating with the whole thing. Unfortunately, I’m the worst at reading from a computer screen, so I haven’t gotten very far*, but it seems that Mister D’Arcy was quite interesting indeed. His 1136-paged book reads a bit a philosophy book (or it does in the first 304 pages). He tells the story – for it’s written like a story – of how the mechanics in biology is quite similar to the mechanics of inanimate bodies, and that growth and morphology can essentially be explained by physics. He gives a whole list of examples, where he makes analogies between biological systems and physical systems. He admits that this will not explain every detail of biology, but that it is possible to explain certain simpler phenomena of organic growth and form using mathematical and physical descriptions. His studies on fractal patterns and linear transformations (rotation, translation, shearing) have been important for image analysis, architecture, mathematics and probably many other fields.

Left: sketch of a fish in a grid. Right: transformation of the fish showing the deformed grid
Mathematical transformations of homologous features in fish.

Then how had I never heard of Mister D’Arcy (I realise it should be Mister Thompson but that just doesn’t have that ring to it)? Luckily I’ve figured my lack of knowledge on time and can rectify that mistake. D’Arcy had innovative ideas, that have been pushed to the sidelines by molecular and genetic research in morphogenesis. Nevertheless, is book is merely descriptive, so there is still much to be learned. Which is where projects like mine come in.
Hurray, I have a purpose!

D'Arcy Thompson holding a skeleton of a parrot
Thank you Mister D’Arcy!

*If anyone knows where I can get my hands on a good hard copy, please let me know! Amazon only cells “bad quality and incomplete” versions, so it’s proving quite difficult.

How to win a Nobel Prize

I’ve mentioned a while ago that I’d write a post focussing on how to win a Nobel Prize. Recently, a 10 simple rules paper (something I mentioned in that same post) was published on that exact subject, reminding me that I should step on it and write already.
So, here we go, inspired by conversations with friends and that paper I just mentioned (1), some guidelines on how to win a Nobel Prize.

  1. Eat chocolate and drink milk.
    It has been suggested a few years ago that the suspicious relation between the number of Nobel Prize winners in Switzerland might be related to chocolate consumption (2). Obviously, as a Belgian (though the chocolate consumption of Belgians seems to be suspiciously low) and chocolate fiend, I found this very interesting. A follow-up study suggested that the consumption of milk (3) might also play a role, something I don’t expect to be a problem either. In the end, both articles were more of an illustration of how correlation and causality can easily get mixed up in (amateur) statistics, rather than encouraging people to stock up on milk and coco. Eating habits aren’t very likely to increase your chances of winning a Nobel Prize, but one can hope that loving chocolate can’t hurt…

    Correlation between Countries' Annual Per Capita Chocolate Consumption and the Number of Nobel Laureates per 10 Million Population
    Correlation between Countries’ Annual Per Capita Chocolate Consumption and the Number of Nobel Laureates per 10 Million Population (2).

    Correlation between countries’ annual per capita milk consumption and the number of Nobel laureates per 10 million population (3).
  2. Choose your contacts wisely 
    Nowadays, most Nobel Prizes are won by a group of 3 people. Additionally, most science is done through collaborations nowadays. Different backgrounds, expertise, points of view and even different disciplines mixed together, provide for good science and innovative discoveries. So collaborate, but not with too many people. If you’re not yet in a position to collaborate (I assume that’s easier once you’re a principal investigator), choose your workplace wisely. Perhaps working in the same institution or even directly in the laboratory of a Nobel Prize laureate and gain from his or her experiences, will provide you with the inspiration to win your own Prize. For example, 9 staff members of the Medical Research Council (MRC) Laboratory in Cambridge have won Nobel Prizes. And if you can’t find such a position, another strategy is to pick your family wisely. Sometimes children of Nobel Prize winners go on to win the prize themselves, as has been shown already seven times. But since choosing what family you’re born into isn’t exactly practical, perhaps consider marrying a prospective Nobel Prize winner, as four married couples have won the prize, as was the case for the Nobel Prize in Physiology and Medicine last year (1).
  3. Serendipity.
    A topic I have brought up before but sheer luck, or a certain degree of serendipity, seem to have an effect on your chances of winning a Nobel Prize. Andre Geim and colleagues were messing around with some scotch tape and that led to a Nobel Prize, and penicillin is a similar example. Sometimes things going wrong are not such a bad thing. Often great discoveries are made “by accident”. If your experiment doesn’t go as expected, perhaps it’s time to re-analyse: is it through faulty protocols or maybe because of wrong assumptions. Challenge everything you do, ask questions, and if something cool and unexpected happens, maybe this is something worth looking in to?
  4. Life sciences are the bomb.
    The article (1) mentions that Biology is the field in if you’re aiming for a noble prize. There’s still so much to be discovered in biology, and it’s forever changing (evolution, my dear Watson). It often needs interdisciplinary approaches, making it easy to do collaborative research (see point 2). And there are two Nobel Prize categories you can aim for, so more chance!
  5. Just have fun.
    But most importantly (and strongly emphasised in (1)), don’t aim for a Nobel Prize. Science shouldn’t be about winning prizes or aiming for fame. Science and research are about curiosity, wanting to know how the world works, finding solutions that can help humans and the earth, and most of all, about having fun. You should be in research because that is what you love. If you feel a great sense of accomplishment when you successfully finish an experiment or make a beautiful and informative microscopy image, if you squeal like a fan girl when you read about novel scientific breakthroughs, if you make plans with your friends to do “Friday afternoon experiments” (yes, that’s doing research just because you want to), then go into research. Perhaps you’ll win a Nobel Prize one day. Probably not. And who cares, you’re doing what you love.

Related to that, Switzerland is great. In the week I’m busy busy busy working, in the weekends I feel like I’m on holiday, riding on boats on Zürichsee and whatnot. In this country where people actually stop to let you cross the road or hold tram doors because they think you’re trying to catch it, I feel quite at home. Maybe it’s because of the wonderful weather and the delicious chocolate, but the first weeks have been great. I think I will enjoy my time here.

A view of the Alpes and the lake of Zürich (taken on the lake)
A view of the Alps and the lake of Zürich (taken on the lake!)

References and Inspirations:
(1) Roberts RJ (2015) Ten Simple Rules to Win a Nobel Prize. PLoS Comput Biol 11(4): e1004084. doi:10.1371/journal.pcbi.1004084
(2) Messerli FH (2012) Chocolate consumption, cognitive function, and Nobel Laureates. N Engl J Med 2012; 367:1562-1564. doi:10.1056/NEJMon1211064
(3) Linthwaite S, Fuller GN (2013) Milk, chocolate and Nobel prizes, Pract Neurol13:63. doi:10.1136/practneurol-2012-000471

Competition, conversation and collaboration

photo of a city (Basel) along a river
Last weekend I moved to Basel for a two month impersonation of “guest researcher” in a nanobiology lab.
Before I even get to the point, I want to say that Basel is awesome. Except for the evening I arrived, the weather has been the perfect example of “Spring is in the air” and Basel’s traditional emblem and guardian creature is a Basilisk. First of all, this city has a guardian creature. Second of all, this creature appears in one of my favourite books (I was going to say in my favourite septology but I’m pretty sure that’s not a word, so I decided to refer to Newt Scamander’s Fantastic Beasts and where to find them instead). A quick look at the various statues scattered around the city – most of them spouting water – as well as the wikipedia page – I’m such a professional -, taught me that unlike my expectations of a giant snake living in sewage under girls bathrooms, a basilisk looks more like a dragon with a bird’s head. It does still have Medusa-like statue making abilities or killing-at-a-glance powers (depending on the source) and a weakness for weasels/Weasleys. Come to think of it, I’m pretty sure the emblem of Dundee involves dragons and that of Scotland in general has a unicorn. I sure know how to pick my magical creatures. (That of my home town is a boring old swan though…)
In any case, moving to a new lab, albeit for only two months, reminds me of one of the things I love about being in science (as far as I can call my current career “being in science”. A friend of mine basically covered this same topic in her blog recently and I’ll probably just plagiarise repeat some of what she said, but one of the things I love is moving around for conferences, lab visits or even just a new job (as I have for my PhD) to not only explore the world but also explore the minds of all the amazing people I encounter. I might be because I’m still quite young (no need to settle down yet), adventurous at heart (always moved around a bit) and get amazing opportunities (an international and interdisciplinary PhD), but I also believe that the future of science lies in international, collaborative and interdisciplinary research. Also, it’s surprisingly refreshing to pack all you basic needs in one suitcase and just step on a plane.
The thing is, I’ve heard disconcerting stories about research groups not willing to present unpublished work at conferences in fear their ideas will be stolen. Or people naming collaborators as reviewers when submitting papers, while steering clear of their competitors. Science seems to exist in an atmosphere of suspicion and nepotism (though I like the Dutch word vriendjespolitiek – literally friends politics – better) where results and ideas are only shared with collaborators but hidden from competitors.
Of course there’s merit in a bit of healthy competition, it drives people to be ambitious and bring out the best in themselves, but as it is becoming increasingly clear that science is no longer a one-man’s-job (though my friend that I mentioned earlier is well on her way of becoming a homo universalis), I am supporter of more collaborative and open science. I for one have had great ideas by conversing with other people, inside and outside my field of research (and so we bring in the aspect of interdisciplinary research as well). Bouncing ideas off each other, seeing different points of view and geeking out during lunch breaks brings out the best of us, or at least of me.
Well, in any case, I am glad to be here in Basel, these first few days have already been amazing and mind opening and I’m sure there are many more inspiring moments to come.
I’ll leave you with this quite funny looking basilisk. It doesn’t have any jet black scales or horcrux-destroying fangs, but I’d still not look in the eye…
Artist rendering if a basilisk: somehow a cross between a dragon and a chicken.

Nerdy is the new cool

Nerds have been making an uprise for quite some time now. Seth Cohen from The OC was maybe the first one, or was it Freaks and Geeks that started it all? But in times of The Big Bang Theory and hipsters copying the big glasses look, it no longer can be denied;

Nerds are cool.

Actually, I would like to rephrase that. Even though nowadays the term “nerd” or “geek” don’t have that much of a negative connotation anymore, and I acknowledge the awesomeness of Dr. Who, Harry Potter or Star Wars franchise, I would like to focus of a specific type of nerds. So lets say this:

Science is cool.

Admittedly, I may be prejudiced. But the popularity of science shows, ranging from sitcoms to panel shows and Facebook science feeds (such as ifls), only back up my claim. The internet is full of science nerds with artsy hobbies, trying to find an outlet for their nerdiness.

There’s someone who knits dissected animals, like this mouse from aKNITomy:a knitted mouse being dissected
There’s someone who makes stuffed organs (iheartguts):
a plush large intestine
And yes, I chose these examples because they’re loosely related to my own research (and I not-so-secretly incorporate them into my presentations), but I just wanted to point out that the gap between the general public and the science community is decreasing. And therefore it becomes more and more important to provide channels for communicating science to the general public in a clear and correct manner.
But talking about hyped science journalism would just make me rant for another 1000 words at least, so I’ll leave that for later…

I spent another day behind a microscope.

2D MDCK layer
Image taken on a Zeiss 710 Confocal microscope at the University of Dundee.
MDCK spheroid and 2D layer
Image taken on a Zeiss 710 Confocal microscope at the University of Dundee.
3D MDCK spheroids
Image taken on a Zeiss 710 Confocal microscope at the University of Dundee.
Glowing edges filter
Image taken on a Zeiss 710 Confocal microscope at the University of Dundee, but then put through a filter.

The last images are put though the very professional “Glowing edges” filter found in Microsoft Office Powerpoint.

Remember why you became a scientist?

A few days ago we passed a poster on a door that said: “Remember why you became a scientist?” It was a poster promoting outreach activities, such as promoting STEM (Science, Technology, Engineering and Mathematics) in primary schools. However, it had a slightly different effect on us. A simultaneous groan was uttered. You must know that this happened in the middle of the week, a quite stressful week for most of us. I also had a hard time remembering. PhD’s tend to go in ups and downs, a fact that is sometimes cleverly used for a whole range of webcomics. And at that moment, even though I’m only 6 months – no wait, 7 months – into my PhD so I can hardly complain, it was a bit of a down. So running into a poster asking if I remember why I wanted to be a scientist caused me to slip into a tiny existential crisis.
Luckily it didn’t take to much remembering.
In the good old days of sending around questionnaires (“How well do you know me?“) by email, a friend filled in the following:

Q: What will I be when I grow up?
A: an inventor

It all fit. When we were kids, that friend and I had made plans to build a “test-car”, where we could interchange the engine to test different alternative fuels, not-so-loosely based on the grasmobile. It never got past the plans, but nevertheless, we had the ambition to better the world and help the environment. We wrote poems about time travel. My personal heroes were not movie stars or superheroes, but the quirky old professors in the comics I read, like Professor Barabas, Professor Gobelijn or even Professor Zonnebloem (Professor Calculus). All bonkers (especially the latter), but amazing geniuses. I played with a microscope, collecting leaves and dirt to look at. I had plans to solve global warming and cure cancer.

I became a bit more realistic when I got older, but still, I got into engineering and research. I still want to discover the world, make an impact and make the world an ever so slightly better place.

 Twitter screenshot: "One step closer to understanding the mechanics of the gut, one step closer to curing cancer! #ShareMyThesis"

 Beside that, I simply like science. I find pleasure talking about it with friends, reading about new new findings, in short, simply geeking out. Science is awesome. We scientists just loose sight of that sometimes.
And if I have a hard time remembering, I have results to remind us. Even if things don’t turn out exactly the way I predicted or hoped, interesting thins happen: A 3D OCT* scan that looks like a galaxy;

A 3D rendering of a sample that looks like floating specs in a dark universe
Image taken on the OCT system at IMSaT (UoD).

or a result just simply asking me to be its valentine…

A 3D rendering of a sample that shows a heart-shaped area
Image taken on the OCT system at IMSaT (UoD).

So there is still hope for me!

* Optical Coherence Tomography (OCT) uses the interference patterns of backscattered light to form an image, or in other words: as light travels through a sample, it is scattered back differentially by different objects in the samples. By looking at the light coming back and comparing it to your initial light beam, you can deduct structural information of your sample. The “stars” in the image, the bright dots, are hopefully spheroids of cells. The brightest spot in the middle is strong reflection from the liquid surface (because it’s not flat). Another way to think about OCT is “Ultrasound with light.”

Sunrises

A Sunrise over the university campus in Dundee
Sunrises (and probably sunsets as well) are particularly beautiful on this part of the world lately. Maybe it has to do with the fact that I live in the “sunniest city in Scotland” (and here I was thinking that was a silly thing to say) or it’s just the time of year…
In any case, I’ve been enjoying my walks to work lately, they seem to be perfectly times with the sun rising over the Tay river.
The wonderful colours during sunrises and sunsets due to the fact that sunlight has to travel much longer through the atmosphere than during midday. As sunlight travels, more blue and violet light is scattered out of the beam that eventually reachers our eye (this is called Rayleigh scattering, i.e. differential scattering depending on the wavelength – or colour – of the light), causing the sky to appear more red for the morning or evening observer.
When clouds are added into all this, sunsets become even more awe-inspiring. Clouds reflect the first rays of light (in the case of sunrises) back to the surface. With their interesting shapes, the result is fantastic.
So why are there so many wonderful sunrise views here? I have a few theories:

  1. Scotland is pretty Northern (at least compared to what I’m used to). That means the sun stays relatively low to the ground this time a year, prolonging the “best light” duration. Sunrises and sunsets do take a while here.
  2. Weather in Scotland can best be described as “temperamental”. Quite often we get all seasons in one day. The day can start out wonderfully, but end up in pouring rain. In any case, the chances of having the combination of sun and quite some clouds is probably quite high compared to some other places I’ve lived.
  3. I’m easily impressed.

Probably, the reality is a combination of all three. In any case, waking up and walking to work in this light often makes my day. It makes the lack of mountains all around – something that made me love my time in Grenoble, in the French Alps – completely bearable.
So before I head home for Christmas, let this be my present to you. The view from my flat followed by the room in my office. If I plan things right, that’s how my day starts (though in the summer I doubt I’ll be getting up at 4AM just for the view).
Sunrise views from the university building towards the river Tay

You know you’ve worked too long in a lab when…

Today I came across this list of signs that you have been working too long in a lab. I would even say it applies to working too long in a certain branch of science, or doing research for too long.
But, slightly plagiarising inspired by that list, here are some things that I have noticed are indications that you are working in a lab, any research lab, but mostly a biology/biochemical lab. Well, let’s just say that they’re indications of me at the moment.
You know you’re doing PhD research in Life Sciences when…

  • … you sometimes have to run from social activities, such as lunch, because you’re busy with a protocol.
  • … you’re no longer scared of rodents.
  • … no one of your family or non-work friends can really explain what you do. And face it, most of your work friends can’t either. Can you, come to think of it?
  • … you can’t watch CSI/The Big Bang Theory/Any SciFi movie/… without cursing at at least one scientific inaccuracy.
  • … you use acronyms for everything and never stop to explain what they mean. Do you even still know?
    (APC… Adenomatous Polysomethingamajingy?)
  • … you sometimes have a headache at the end of the day from looking down a microscope/at a computer screen for too long.
  • … you slightly disappointed that you don’t have to wear your safety equipment all the time. You actually think a lab coat and safety goggles look cool.
  • … while choosing an outfit to where in the morning, you make sure the skirt/dress is long enough so it won’t look like you’re wearing nothing/just tights under your lab coat.
  • … you want dry ice or liquid nitrogen at home to do silly experiments with.
  • … you want parafilm at home because it’s obviously really useful.
  • … you nudging friends to do “Friday afternoon experiments” with you. (Oh, that’s how you win a Noble Prize, by the way.)
  • … you try to make the best out of failed experiments.
  • … you find a way to use LEGO for science, so you can go shopping on Pick a Brick.
  • … you feel slightly exhilarated travelling on public transportation with some samples, even though they in no way can start a epidemic ever.
  • … you’ve been in the lab so long that you’re afraid to ask what people are talking about when they say HET or Min (and eventually realise they’re really obvious things).
  • … you start a blog about it. (Wow, meta…)

Just to illustrate a few of these points:

Sometimes a failed experiment can result in something beautiful.
(It’s just crystallised salts. No biggie.)

Image of crystallized salt after drying a hydrogel
Image taken on a Nikon eclipse TS100 at the University of Dundee.

How Lego had the perfect dimensions for exactly what I wanted to do.

Top left: lego blocks in a petridish. Top right: a bit of agar molded by lego. Bottom: a 6 well plates with molded lego-wells
But I was like this before I started this PhD…

My first confocal image

Originally posted on 17 Nov 2014

It might not be much.
It might not be particularly good.
It might not show anything significant.
But nevertheless… I have run my first confocal image sequence. And I have proof!
I present to you: a Phalloidin/Hoechst stained MDCK cyst!
(both a single slice as a multiple intensity projection of the z-stack)

MDCK cyst (hollow clump of cells) with nuclei in blue and actin in green
Image taken on a Zeiss 710 Confocal microscope at the University of Dundee.
MDCK cyst (hollow clump of cells) with nuclei in blue and actin in green
Image taken on a Zeiss 710 Confocal microscope at the University of Dundee.

More/nicer to come soon!