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.

Continue reading “A protein in a box”

Less mindless drift, more flavor

True elegance is often found in deducing striking and sound conclusions from very simple observations – observations that are accessible to all. Michael J Sandel’s “What Money Can’t Buy – The moral limits of markets” seems to me a case in point. Sandel starts off with a couple of simple premisses and takes it from there, going roughly along the following lines: 1) The pre-2008 era of market triumphalism has come to an end. The financial crisis did more than cast doubt on the ability of markets to allocate risks efficiently, it also prompted a widespread sense that markets have become detached from morals – and that something needs to be done. 2) While some argue that (an increase in) greed is the cause, the most fateful change that unfolded during the past three decades was not an increase in greed, but the expansion of markets and market values into spheres of life where they do not belong. 3) Inveighing against greed would therefore be a symptomatic treatment at best, we need to rethink the role that markets should play in our society. We need to think through the moral limits of markets, to ask whether there are things that money should not buy, because 4) the more money can buy, the more affluence or the lack thereof matters. 5) This can be expressed in terms of inequality, as experienced by lower and middle class families over the past decades, but also in terms of corruption. Markets are not inert as economists often assume, markets leave their mark. They can crowd out nonmarket values worth caring about. 6) Some of the good things in life can and have been corrupted or degraded into commodities. 7) The discussion of where the market belongs and where it does not has not taken place during the era of market triumphalism, as a result we have drifted from having a market economy to a being market society without realising it or deciding to do so.

until here and no further

Consider the proliferation of for profit schools, hospitals, and prisons; the outsourcing of war and security to private military contractors and private security firms, respectively. Consider pharma’s aggressive marketing and prescription of drugs to consumers in first world countries. Continue reading “Less mindless drift, more flavor”

Q&A: the difference between elitism & anti-intellectualism – and the ethics of switching off your mother

A conversational Q&A session between Sam Harris and Richard Dawkins made for an entertaining listen, yet in my opinion had less information value than a one-on-one discussion between these two gentlemen would have had. Richard Dawkins was clearly in entertainment mode: his focus was more on funny anecdotes and making tongue-in-cheek comments towards the audience than conveying information. I applaud Sam for his devotion to serious conversation. Still many topics contained food for thought, what follows now is my pick of quotes, a lot of paraphrasing and some of my own opinion.

the two horsemen

On science and religion:

Richard (RD): “This is a unidirectional conquest of territory. You never see a point about which science was once the authority, but now the best answer is religious. But you always see the reverse of that.”

BB: This does not justify extrapolation ad infinitum though, so one would have to come up with a different line of arguments if the goal was to convince someone that a theistic world view is not the most probable explanation of our universe.


Q: Does mere scaling of intelligence and information processing get you consciousness?
Why do we need to be conscious?

SH: The conscious part of you is generally the last to find out about what your mind just did. Continue reading “Q&A: the difference between elitism & anti-intellectualism – and the ethics of switching off your mother”

Tempus fugit

A bit of random thought, but it just occurred to me that both – wildly different – songs, of which the most crucial lines are stated below, strike exactly the same emotional chord with me. I find this – one’s realization of having lost the opportunities of youth permanently – one of the saddest personal modern human tragedies that exist. Perhaps because I feel that at some point in my life this could have happened to me as well, even though now it might seem quaint.
Ticking away the moments that make up a dull day
Fritter and waste the hours in an offhand way.
Kicking around on a piece of ground in your home town
Waiting for someone or something to show you the way.
Tired of lying in the sunshine staying home to watch the rain.
You are young and life is long and there is time to kill today.
And then one day you find ten years have got behind you.
No one told you when to run, you missed the starting gun.
When she was 22 the future looked bright
But she’s nearly 30 now and she’s out every night
I see that look in her face, she’s got that look in her eye
She’s thinking how did I get here and wondering why
It’s sad but it’s true how society says her life is already over
There’s nothing to do and there’s nothing to say

You probably had no problem recognizing at least one, but here you go.

An ode to the podcast

The main perk of having a fairly long daily bike commute – though true in The Netherlands, especially more so in the California sun – is the fact that I can spend around 100 minutes of each day listening to people who have something interesting to say. Whether it is hearing spectacular accounts of historical events (e.g. Dan Carlin’s Hardcore History), versatile, insightful documentaries on people from all walks of life (e.g. This American Life), or in depth conversations with interesting people (e.g. the Tim Ferriss show): podcasts make it possible to do this all at times when you would otherwise be forced to stare into the distance.*

In addition to the above-mentioned element of personal knowledge gain, a group of my closest friends and I have experienced how being active listeners sparks all kinds of interesting discussions. Like sharing the latest books one has read, we are continuously sharing anecdotes, insights, or things that podcasts made us ponder about. To my experience, the podcast as a medium can provide a sensible, stable source of knowledge at paces much higher than books can give me. Not that this prompts me to give up on this hardcopy medium directly (though some friends have switched to audio books and podcasts entirely), but I find it difficult to find or make the time to sit down and read non-academic literature these days.

So there you have it: podcasts have changed my life (Thank you Olja!), and so might they change yours. Forget feeding a senseless addiction to anxiety-spreading factual or non-factual daily news. Gone are the commercial breaks** and time limits of the ordinary TV or radio shows. The times to jump in have never been better: though a listener for several years***, I have the impression that podcast quantity and quality has increased as this medium reached maturity. To further share my enthusiasm and help anyone getting started, this site will contain a new page dedicated to podcasts: links to – and short descriptions of – the ones I thought worthy of my time. And most importantly: if anyone feels like I should listen to anything in particular: please drop me a message, I have commute-time on my hands as you now know. Personally, I would recommend to try out several, as liking one’s voice or manner of speech is a very personal matter. Continue reading “An ode to the podcast”

Shark-infested waters

Upon finishing Tony Hseih’s book that had ‘feel good’ written all over it (perhaps even a bit too much sometimes), I started reading Luyendijk’s immersion into the world of London City bankers; ’Swimming with Sharks’. Boy, the contrast with Tony’s book could not have been starker. But like with Luyendijk’s former books on journalism in the Middle East, this book was an absolute page turner. And like he did for the making of his former books, Luyendijk submerses himself into the world of his subjects and manages to paint a picture that is human, balanced, and – perhaps what gives the account a lasting impression – very non-judgemental.

He describes his initial struggle to find bankers willing to share their version of City life, shows that ‘the banker’ does not exist and that – unsurprisingly – how the world of finance entails a vast collection and wide variety of jobs. The people occupying these professions come in as wide a variety of character traits as any other profession, and though the classic stereotype ‘Master of the Universe’ loudmouth alpha does indeed exist, Luyendijk also identifies ’teeth grinders’, ‘blinkers’, and a bunch of other types of character traits that constitute this world. In short, Luyendijk shows that the people in this profession are as human as any one of us.

This leads the reader to a conclusion that is much darker and more worrisome than the picture of ‘a handful of rotten apples that ruin it for all’ would have painted though. Luyendijk points out how the whole incentive structure in banking is set up to favour short-term gains over sustainable growth and prosperity, how incentives push one to ‘eat or be eaten’, and urge every entity – the banks, the employees, the politicians, etc. – to care for nothing else but the self. In many ways the world of (investment) banking is a world of ‘grab all you can grab, because tomorrow the party might be over’. Continue reading “Shark-infested waters”

In pursuit of happiness

When recommended to me a couple of weeks ago, I had never heard of Tony Hseih. However, while I had hardly heard of Zappos, I had on many more accounts heard of and read about some company who offered new employees the choice to quit with a $2k bonus anytime during their 4 week introduction period. I had heard of some online retail store with an incredible customer service that did much more than was asked for. Tony turns out to be the man behind this all, and he tells his personal story in a real, open, down to earth and humorous way.

ding dong

His story starts how he as a young boy wants to become rich by growing a worm farm, and takes you through his youth, college, founding LinkExchange and selling it off, and his almost religious experience at a rave. Eventually a turn of events leads him to take all of his experiences, acquired wealth, and efforts to bet it all on growing a small online shoe store in the way he thought it should be done. That is, growing it such that not only revenues or profitability would grow as fast as possible, but grow the shoe store such that everyone connected to the business in one way or another – employees, vendors, customers, investors, partners, local communities – could grow and prosper – prosper in the broadest sense of the word – with this company known as Zappos.

In 2016 this mindset has not become the standard of business just yet, but in 1999 this was a truly revolutionary way of thinking. In fact, I think many of the companies that are very pleasant to deal with these days (from my own experience I can think of Groupon (NL) with their tongue-in-cheek product descriptions and (NL) with their amazingly fast deliveries, the game it offers you to play as soon as you have placed your order (to kill the time until your package arrives…), or just the very human way KLM customer service talks with you for instance) have borrowed their ‘fun’ in doing business strategy from this pioneering company.

While the second part of the book is dedicated to explaining what exactly the core values of Zappos are and mean, and stresses how they should not become a ‘meaningless plaque on the wall of the corporate lobby’, Tony’s own personal story is what truly appeals to me. He signs off with an attempt to quantify happiness, with thoughts along the line of understanding the principle components, you will become better at pursuing. Most convincing there I found the three types of happiness found in time-happiness space, where pleasure, passion, and higher purpose together form a positive slope.

oh brother, where arth thou

Allow me to explain: first, with the lowest amount of gained happiness for the shortest amount of time comes pleasure: the thing we are all after when seeking thrills doing sports, going out, going travelling, etc. This can be seen as seeking the next high. Then, what leading to more happiness that lasts longer is something felt when totally engaged and in a ‘flow’ doing something, like anything from matters at work or during hobbies can give you. Finally, the largest chunk of happiness to be gained, which could be enough to last a lifetime, is the happiness – or satisfaction perhaps – felt when serving a purpose that extends beyond yourself: this, as I see it, is your raison d’être: it can be anything from having kids and building a happy family to building that company you believe in, pursuing scientific discoveries, helping people in your job, or doing charity work.

Personally, I read this at a moment when my raison d’être had ceased to be: my contribution to humanity’s scientific endeavours – though humble of course, yet personally fulfilling in a lasting way – had come to a pause as I had defended my dissertation months earlier. Upon reading this particular view on happiness, I caught myself at being unnerved by the sudden (apparent) disappearance of a life goal: I caught myself at pursuing the other, less sustainable types of happiness instead: mostly the thrill-seeking kind. The graph made me realise what we all already know one way or another: that while being in search of the next rush in sports, the next party, big dinner with family or friends is for most a necessary addition to a happy life, one should see this as it is: an addition. For if this is the only happiness one seeks, thorough unhappiness is never far away.

All this, and much more eloquent descriptions concerning this topic can be found on, go see for yourself.