MarcoMarco Tompitak

Marco is a theoretical (bio)physicist, currently engaged in unraveling the sequence-dependent dynamics of DNA molecules to earn his PhD at Leiden University. Other passions include literature and history.

All articles by Marco

 

A Simple Sales Model – Kaggle Rossmann Competition

I like Kaggle.com, not for the competitive element, but for the datasets you find there to play with and learn from. I took the data from last autumn’s Rossmann competition and I wanted to show you how far you can get with some old-fashioned modeling. Machine learning is all the rage right now, and for
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Image Analysis: Dynamic Color Binning Applied

Continuing my little project for analyzing surface areas using maps, (see my post on the territorial evolution of Poland and the previous post on Dynamic Color Binning) I decided to automate the process for a whole time series of maps. (Just here for code? Find it on GitHub.) We developed a method for analyzing the
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Image Analysis: Dynamic Color Binning

A while back, I wrote about a little project where I extracted the historic surface area of Poland from Wikipedia maps using color information. The main procedure was to use ImageMagick to extract the most dominant colors, so that I could find the one that corresponded to the area of interest (i.e. Poland.) This color,
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Image Analysis: Territorial Evolution of Poland

The history of Poland has, through the centuries, come with ups and downs. Through numerous wars with its neighbours and invasion by foreign powers, the territory of Poland has fluctuated greatly. So much, in fact, that it is not necessarily straightforward to write down a continuous history of Poland as an entity. If you feel
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A Crackpot’s Justification – Gabor at it again!

Gabor Fekete is at it again. I can tell, because whenever he starts one of his e-mail campaigns of crackpottery, people Google his name and I get a spike in traffic on this here blog. Over the last few weeks, Gabor has taken the awarding of the Nobel Prizes as a new opportunity to spread
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Episode II: Revenge of the Crackpot

A while ago, I wrote about our dear Gabor Fekete, the resolute crackpot who has been spamming physicists’ in-boxes with his theories for a while now. His English borders on the incomprehensible at times, and whatever logic there may be in his theories is impenetrable (despite his claim that his writings “are very simple and
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Cervantes and the Censors

Miguel de Cervantes Saavedra (1547-1616) is generally credited with writing the first modern novel, his famous Don Quixote. The story of the addle-brained old gentleman who decides to become a knight and recruits his gullible neighbour as his squire has appealed to the imaginations of generations of readers ever since it was published over 400
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Doubt-Mongering and the Misrepresentation of Science

Earlier this year, James Powell produced a new version of his telling pie-chart about global warming consensus. For the first version he reviewed the body of peer-reviewed literature from 1991 through 2012 about global warming, to see whether there was any consensus among the scientific community on the matter. He was driven to this experiment
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First Organism Produced with Expanded Genetic Alphabet

All of life, since its beginnings, has used DNA to encode genetic information. This code provides a blueprint for proteins, molecules that perform an enormous range of functions in an organism’s cells, and is passed on to the organism’s offspring when it reproduces. DNA can be recombined and mutated to allow for evolution of the
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Found in Books – Another Weather Forecast

Today a friend of mine – a bibliophile like myself – was rummaging through my old books. I was trying to find the books that contain those old weather forecasts I wrote about some time ago, to show them off. I couldn’t find one of the books, which I seemed to have misplaced. (Don’t worry;
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Translating The Name of the Rose

I recently read The Name of the Rose by Umberto Eco. It’s a delightful murder mystery, revolving around books and set in a beautifully rendered medieval world. I love a good historical novel and this one certainly pushed quite a few buttons. The fourteenth century is not a period I’m overly familiar with, and Eco’s
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On Crackpots; The Bane of Science

Part 2? Yes, Sir. Now that I’m what’s considered a professional scientist, I’m apparently also a target for crackpots. Last month I received an e-mail from one Gabor Fekete, an Hungarian gentleman who has doubts about the veracity of the discovery of the Higgs boson at the Large Hadron Collider. He began as follows: While
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Science after the Zombie Apocalypse

It is generally assumed that, once the zombie apocalypse hits, our societies will crumble into anarchy; and that those who survive the initial panic will be reduced to fighting for their bare necessities. We will be scavenging for food and supplies, and fending off the undead hordes and the darkest excesses of human nature, which
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Pope Formosus and the Dead Man’s Trial

Ah, Pope Formosus. This must be, by far, the most ridiculous episode in the history of the Catholic Church. However, before we get to the juicy bits, let’s have a bit of background. Nine Centuries of Catholic Church Formosus was Pope from 891 to 896, square in the middle of a most turbulent time in
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The Irony in the Rye

Just as a heads up, this post will probably not make a great deal of sense if you don’t know the book at all; it also may contain minor plot spoilers. Still here? Let’s dive in! J. D. Salinger’s The Catcher in the Rye has left generations of readers divided. On one hand, it has
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Found in Books: The War Map

Today a find that was, at least to me, completely unexpected. It was well hidden and I only happened to notice it because I was wondering, for some reason I don’t recall, what my book looked like underneath its dust jacket. Here’s the book in question: a fairly worn copy of Bertrand Russell’s A History
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A Real Life Game of Thrones: Empress Irene (Part 2)

Last time we saw how Constantine finally took power for himself as Emperor of the Byzantine Empire, breaking away from the influence of his mother, Irene. However, his rule so far hasn’t been very impressive, and now Irene is back on the scene. This game is far from over. Irene’s Machinations Irene and Staurakios convinced
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A Real Life Game of Thrones: Empress Irene (Part 1)

The early Middle Ages are generally regarded as a savage period of history, and not without reason. Following the fall of the Roman Empire, politics became more local and more turbulent. A larger number of would-be rulers competed for a larger number of crowns. What remained of the Roman Empire was only the eastern part,
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Found in Books: The Weather Forecasts

Today, another find I think is really cool. I own a small collection of old (Dutch) school books, mostly about physics. In a previous post I showed you a scrap of notepaper I found in one of them. This time a set of finds in two different books, 13 years apart. In the photo below
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One Man’s Bankruptcy is Another’s 250-Year-Old Treasure

The other day I had to make good on my promise to take my girlfriend shopping for her birthday. Luckily, she is not so high-maintenance that this post’s title refers to my own bankruptcy. Even better, she granted me permission to pop into a bookstore when I noticed a sign outside that said, `All Books,
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The World’s First Website

A while ago, in my post about Spam, I noted offhandedly that the World Wide Web celebrated its twentieth birthday last year. I don’t think many noticed, but this was actually celebrated, just a little bit, through a little gathering at CERN, the scientific institute where the Internet was born. The Birth of the Web
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Found in Books: Evil Plans?

Welcome to the second installment of Found in Books! Today we have an intriguing scrap of paper I found in an old schoolbook. The book is a secondary level physics book from about 1945. It’s hard to say when the drawings on the scrap were made, but the paper is strongly discoloured by age (it
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Machiavelli’s Misunderstood Brilliance

History has not been particularly kind to Niccolò Machiavelli (1469-1527), author, diplomat and statesman of the Italian Renaissance, most famous for his book Il Principe (The Prince). He was looked upon with contempt by later generations and his name has become synonymous with unscrupulous, deceptive tactics. Machiavelli Vilified Did he really deserve to be treated
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Found in Books: Second-hand Bookmarks

I tend to buy a lot of my books used, because it saves a buck or because I just run into them, but I don’t usually consider them to be a step down from new books. In fact, there’s just something about a second-hand book that intrigues me. Who owned it before I did? How
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Insight: The Aha-Experience

We’ve all had the experience: you’re staring at a problem or puzzle and suddenly it ‘clicks.’ Almost magically, the answer pops into your head, seemingly without any effort or any relation to what you were thinking of before. How does that happen? Insight It turns out it happens all the time, not always accompanied by
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Peculiar Rulers: Frederick and his Tall Blokes

Prussia, from its inception, was a military state. Its original nucleus around Berlin (which was actually Brandenburg and not Prussia) was a poor, sparsely populated stretch of country, not very fertile and lacking resources. It also had few natural borders, blending featurelessly into other German states in the west and into Poland in the east,
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Coffee: Health Effects and Addictive Properties

It’s Monday and you know what that means. Whether you like it pure and strong or with milk, sugar and your favourite flavours added, drinking coffee is an indispensable ritual for many of us. Scientists, like myself, are no exception. In fact, a few years ago, the infographic in Fig. 1, based on a survey
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Navier-Stokes Millennium Prize Problem Solved?

Back in 2000, the Clay Mathematics Institute put bounties on seven of the world’s most difficult mathematical problems. Some of these problems have been around for over a century, with many a brilliant mathematician racking their brains over them. If you manage to solve one of them, there’s a 1 million dollar prize waiting for
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SixWordPeerReview

Since yesterday, a fun sciencey #hashtag has been trending on Twitter: #SixWordPeerReview. It’s all about people in academia venting their frustrations with the peer review process. A lot of them are just funny, some a bit poignant with a truthful core. Here are some of my favourites:

 

Spam on the Web 2.0

The internet has been with us for a while now: last year the World Wide Web celebrated its twentieth birthday. I found my way onto it roughly halfway down that road, and ever since I registered my first e-mail address (a Hotmail account, its name inspired no doubt by something I thought was really deep
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Welcome to Rapid Diffusion!

As Professor Farnsworth would say: good news, everyone! I’m finally going forward with a project that has long been in the making. It must be three quarters of a year since I first conceived this website. Along the way, it has been shifting its shape, it has been on hold because other things got in
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