A protein in a box

Exactly one year ago today I defended my doctoral thesis in Delft. Fast-forward one year, and I find myself writing these words in the California sun. How different life has become! Having embarked on an exciting new project, I am now challenged to think about a whole new universe of fascinating problems. Yet I do enjoy looking back every now and then to remember the good times of grad school. The good times of a protein in a box.


What is life? At the very least it is a concept that we humans find surprisingly difficult to define. Though generally wet and dynamic1, arguments about what defines life inevitably involve terms like ‘reproduction’, ‘growth’, and ‘adaptation’ – matters very common to cells and viruses alike, yet whether the latter belong to the category of living things is a matter of ongoing debate. For the purpose of this thesis (as well as for my own understanding), I adopt a less materialistic and more conceptual definition of life:

Life is a process brought forward by the self-organization of molecules, a process that seemingly violates the second law of thermodynamics2 as it increasingly acquires and maintains information over timescales that vastly exceed the lifetime of the molecules holding this information.

In this manner the distinction between a virus and a cell becomes rather meaningless: viruses are just as much part of the process that we know as ‘life’ as a homo sapiens like you or me is.3 In addition, it allows me to conveniently classify my thesis work as “an effort to gain better understanding of the molecular processes and building blocks of life”. Though this classification is rather broad – as myriads of doctoral theses written over the past century or so belong to this category – my thesis belongs to a relatively small and novel subcategory of the ‘gaining insight into the building blocks of life’ class by making use of two concepts: single-molecule and bottom-up approach.

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As the sun sets over South Holland

A Great New Adventure Out West starts. More on that later, but for now a small visual tribute to two places very dear to me: a place that taught me how to be a scientist, and a place that stole my heart.

rotown from Fenix

The view from a place I loved to watch the sun go down, perhaps a place known for its touch of champagne socialism, but boy what a fantastic spot. And what about this one, though perhaps not Oxford’s ‘Bridge of Sighs‘ this was taken from, the view is a more majestic one if you ask me:

Euromastjestic

There I so many things that I could, maybe should, or probably wish I had written about the city of Rotterdam, the city which I had come to call my home during the final stretch of my PhD (and, what turned out to be my final time in The Netherlands, that is). I wanted to have written how I truly love the fact that in many ways this place was the proud antipode to Amsterdam, an unpolished diamond, a harbor city and a place with rough edges, yet culturally rich and beautiful at its core not unlike the beloved city of my teenage years, Antwerp; how this place cuts strait through a lot of the BS so adorned in the capital, a place of doing instead of talking about doing; how it is the only city in the country that has a true metropolitan feel; how, unlike other Dutch cities, this place did not give me the sense of being a mere spectator in my own country, and so on and so forth. In short, how by a historic and gruesome twist of fate this city had become the non-conformist rebel of the Low Countries, and how this place finally made me feel truly at home in my country of birth for the first time in my life. But as with so many things floating around in one’s head, only minute fractions end up in writing. Perhaps for the better, as I was probably too busy enjoying life. Anyway, enough rambling, let’s let the pics do some of the talking: Continue reading “As the sun sets over South Holland”

Conference(, no skiing this) time

Ox, is that you?!

Just before my Indonesian adventure took off, I got to present my Tus work to an audience of DNA replication specialists. The thought of going to Egham did not particularly excite me – as google maps quickly taught me the town was situated practically on top of Heathrow’s runways. However, England would not be England were it not that even these kerosene fume filled outskirts of London somehow still have the air of being a Harry Potter movie set. Egham turned out to be home to the Royal Holloway University of London. Never heard of the place, even though it seemed to want to compete with Oxbridge in appearance. Besides this, Windsor Castle turned out to be around the corner and, more importantly: Great Windsor park.

The gang.

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Tus fuss (1)

 

The main actors.

My Tus paper in the news, those interested can start reading up. Again, more to follow

 

Today’s headlines

Is it a bird? Is it a plane? No: It’s my project on the cover of Nature Chemical Biology!

Tussle stories.

More will follow soon, for the time being I’ll quote the Journal:

“A single-molecule approach using magnetic tweezers shows that DNA strand separation alone can trigger a lock at Tus–Ter sites where oppositely moving replisomes on circular bacterial chromosomes must avoid crashing. The results support a ‘mousetrap’ model in which replication-related proteins are not necessary and strand separation is followed by an interaction between Tus and C6 of the Ter site that sets up a hierarchy of interactions to allow the Tus–Ter complex to progressively strengthen. Cover art by Erin Dewalt, based on an image provided by TU Delft/Tremani.”

Supporting conversations

During a recent conversation with a technician, let’s call him ‘Cherry Maker’ (CM, not to be confused with cherry picker), I wanted to know what being support staff meant to him. “Assimilation.” he answered, and after seeing my puzzled face, he added: “It’s becoming what you always dreaded as a researcher.” “Well”, I said, “isn’t that a bit dramatic?” CM: “No! I find it quite funny. When I was a young grad student a long time ago, I found the sight of a technician going home at 5, irrespective of the status of the experiment, horrifying. Same when a technician’s interest in a paper did not go beyond his/her own contribution.”

The distorted views of academia. This image is really spot on (@biomatushik – http://sotak.info/sci.jpg)

“Now” he said with an ironic smile, “I can just feel those looks from grad students as soon as I leave for home at around 5! Look Bojk,” CM said in his usual tongue-in-cheek manner, “you PhDs like to think it’s all about you and your research, but as a technician you have come to realize that hierarchy and continuity come first, then comes a whole lot of nothing and other stuff, and then come the PhDs…” Me: “So where’s the assimilation part in this and why is this funny?” CM: “Because I realize now that every researcher-turned-support unavoidably assimilates towards this other way of thinking, irrespective of the initial world view. It’s nurture pur sang!”

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Scientific lubricant

Remember me writing about how stressful life as a last-year grad student was? How many of us walk around sleep deprived, nervous and pale in the face? Forget about all that, life as a final year grad student rocks!

Climbing peaks in Aspen: single-molecule biophysicists in the Rockies. (Steve Block’s Single-Molecule Biophysics meeting, Aspen, CO)

Let me tell you why. For the better part of 3 years you have spent an innumerable amount of time trying to figure out why you are the right (wo)man for the job, messing up, experimenting with flexible working hours, procrastinating, doing useful and less useful experiments, isolating yourself from family/friends/daylight, feeling insecure about your future and ignoring important e-mails from department secretaries. You may even have contemplated quitting, or at least pondered what life would be like as a diving instructor, mountaineering guide or Buddhist monk. But now all of a sudden the mist that clouded you so hopelessly has cleared up as if being burnt away by the morning sun: now you have a story to tell. This means it’s conference time!

And some more in the Alps (Kavli institute Delft retreat, Courchevel, France). 

Those outside academia might now be wondering whether the clearing of the above-mentioned mist also took away my last bit of sanity, but those in science know better. For scientists may not earn six-figure salaries, they will not find themselves surrounded by groupies on a regular basis, and they may have to spend days on end measuring in a basement, but I have to say: they sure know how to treat themselves to a proper intellectual retreat.

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Collective lab exits

The Nynke Dekker lab at CERN.

Just for a mid-week then. Roughly once every two years a couple of us get together to organize an outing for the Nynke Dekker Lab. 2012 took us to the EPFL in Lausanne and CERN in Geneva, in 2014 we spent a couple of very active days in the Belgian ardennes. No idea where our next trip will take us, let alone if I will still join as a lab member(!), but you’ll be able to find us here.

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Back to reality

And yet another academic year kicks off again. What year is this? 2014, check. Which year did I start? 2011, check. Whoa! Wait a minute – three years have gone by?! How did that happen? Why didn’t anybody tell me?! So my last year has started?? Oh boy [picture me becoming pale in the face], in a year’s time I’m expected to have written a book, drawn some very profound and groundbreaking conclusions and am expected to head off to the next step in my career? Oh boy!

“Ah”, I hear post-docs thinking, “the final year grad student – been there, done that. Feel so sorry for those guys (NOT!)…” Well, I guess last-year grads are easy to recognize: walking hastily through the corridor, a bit pale faced, sleep deprived, maybe a nervous twitch or two. You’ve got it, that’s us. To be honest, I actually don’t feel all of this (yet), but the what’s next? question has definitely been popping up in my mind more often these days. Three years ago, doing a Ph.D. to me was a form of safe and comfortable intellectual escapism, curiosity-driven but also having that delightful feeling of being allowed to not think about what next? for the following three years. But here I am again: what’s next?

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