Books, Creativity

Who else likes a Goblin? The daughter and I do.

As the offspring of two bona fide bibliomaniacs, my toddler daughter continuously demands to have books read to her.

Some of the books she likes I find boring (but as a dutiful father soldier on reading them to her) and some of them I quite enjoy (like everything Donaldson and Scheffler cook up).

But now for the first time we seem to have found an age-appropriate book that Daddy might even be more enthusiastic about than the daughter: Nobody Likes a Goblin by Ben Hatke.

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Books, Science

New Book! SYSTEMS GENETICS by Markowetz and Boutros at Cambridge University Press

The book on Systems Genetics I have edited with Michael Boutros just came out! Wohoo!

You can get a look at the first copies at ISMB this year and I will shamelessly promote it in my talk at the Networks SIG on July 10th.

You can download the first introductory chapter written by Michael and me here.

Here is the promo text for your pleasure and enjoyment:

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Books, Science

Steven Weinberg and the smugness of hindsight

One of the more helpful pieces of advice I recommend to new starters in my team are Steven Weinberg’s “Four golden lessons“. Weinberg is a physics Nobel laureate and “considered by many to be the preeminent theoretical physicist alive in the world today” (says Wikipedia). I guess this means he knows his physics … and his four golden lessons certainly are helpful:

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Books, Science

The Emperor of All Maladies — now on Television

Science announces:

Based on the 2010 book by Siddhartha Mukherjee (Science, 22 April 2011, p. 423), this three-part documentary weaves together a sweeping history of cancer with intimate stories of contemporary patients. Told largely through interviews with researchers and oncologists, the series highlights Sidney Farber’s efforts to galvanize a national “war on cancer” in the 1940s, delves into the development of targeted drug compounds in the late 20th century, and explores the promise of personalized immunotherapies.


Mr Penumbra’s 24-hour bookstore by Robin Sloan – Dan Brown meets Dungeons&Dragons


I read Robin Sloan’s Mr Penumbra’s 24-hour bookstore within 48 hours. It’s not a huge book, but more important: it’s page turning stuff!

The book is a colorful cocktail of ideas that will look great in a movie:


  • A bookstore full of unreadable books in shelves that span several floors and can only be reached by tall ladders;
  • A 500 year old secret society of code breakers;
  • A miniature city in the kitchen;
  • A secret underground library;
  • A self-organizing warehouse where the items find you;
  • Google Books, optical character recognition, and spidery book scanners;
  • the history of book printing and typography;
  • and finally: a fantasy epos that contains the key to the solution.
  • And all of the above combined in a quest for a party of adventurers: a rogue (an ex-web developer, now bookstore clerk and main character), a wizard (a Google programmer) and warrior (an entrepeneur, bodybuilder, and best friend of the main character from teenage role-playing times).

It’s like Dan Brown meeting Dungeons&Dragons. And I always knew these crazy books with covers of maidens in chain-mail bikinis were full of wisdom!

But it’s a bit of a pity that some ideas are not worked out well, I thought. The main theme of the book is the contrast between Old (printed books, secret society) and New (Google, computers, algorithms, data visualization). Sloan constructs a scenario where Google focusses all its computational power on decoding a book. No one on the planet can read their emails, because Google is trying sooo hard – and still fails. There must be neater ways to show that the Old contains secrets that even the power of the New can’t crack.

And then there is this global museum inventory system, where a nice lady calls you up if you try to register an item they have already stocked. And exactly because you don’t have security clearance you get invited inside the gigantic warehouse to pick up your stuff yourself. Again … shouldn’t there be neater, easier and more logical ways to make a point and drive a story forward?

Anyhow … I don’t want to be nit-picking. I really enjoyed the book and read it in one go. It’s so full of ideas – you need to see yourself.


Books, Science

Life out of sequence – Hallam Stevens’ data-driven history of bioinformatics


How do people like you ever get last-author papers?” The person who asked me this question in 2008 during the interview for my current job was (and still is) a well-known stem cell biologist with decades of experience in science. But she still didn’t really know what to think of ‘people like me‘: bioinformaticians and computational biologists. Aren’t bioinformaticians just service providers? Handy to have, but without any real scientific vision and contribution? She clearly worried about my ability to do independent research.

And she wasn’t alone. A couple of years later I interviewed for an EMBO fellowship, which I didn’t get because the panel –mostly cell biologists, no one computational or from genomics or medicine– thought my group was a “mathematical service unit” and my research was “overly driven by my collaborators”. I’m still not sure what a ‘mathematical service unit’ could be (proofing theorems on demand maybe?) but their comments showed me how far removed their research practice was from my own.

Even though bioinformatics is by now an established field these personal experiences show that ‘old school’ biologists, who form the scientific establishment and direct mainstream research, are still very uncomfortable with ‘people like me’ who were trained in other disciplines, pursue biological questions different from their own, and use approaches not covered in classical biological training.

Life Out Of Sequence Cover

Hallam Steven’s book Life Out Of Sequence, A Data-Driven History of Bioinformatics starts with the tension between old and new biology that ‘people like me’ experience every day and describes the way biology has been and is being changed by computational methods.

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Freaks versus clerks — Jedediah Berry’s The Manual of Detection


“I am an enemy to messiness in all its forms,” says a detective while polishing the handle of his office door. In Jedediah Berry’s novel The Manual of Detection two forces are pitted against each other: the dark, austere Agency with its strict hierarchy of uniformed detectives, clerks, messengers and watchers that all follow clear rules versus the messy, colorful Carnival full of limping, asymmetric and over-sized inhabitants that defy this order.

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Books, Science

Books on cancer — science and history

Interested in cancer research? Here are the books to read:

Siddhartha Mukherjee:
The Emperor of All Maladies (2011)

I have written several times already about this Pulitzer- prize winning book – it’s really great and everybody interested in cancer research should have read it.

Ok, that was an easy pick! After all Mukherjee was all over the news in the last year. But there is more:

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A philosophical suicide — Julian Barnes’ The Sense of an Ending

“I don’t envy Adrian his death, but I envy him the clarity of his life,” says Tony Webster about his friend, who committed suicide when they were at university. Julian Barnes’ award-winning novel The Sense of an Ending explores the themes of history, memory and responsibility while bringing some clarity into Adrian’s death.

Tony, a man in his 60′s, looks back at his life: Four friends at school; a one-year relationship with Veronica at university; a humiliating visit to Veronica’s parents; a split-up; Veronica coming together with his best friend, Adrian; Adrian’s suicide in a bathtub — that’s the first half of The Sense of an Ending, Julian Barnes’ award-winning novel.

The story Tony tells about his life gets challenged in the second part, when it turns out that Adrian had kept a diary, which surprisingly was in the possession of Veronica’s mother until her death. In her will she passed it on to Tony, but Veronica is reluctant to hand it over. Tony’s efforts to get the diary from Veronica start the second part of the book and end in a complete reassessment of the initial story.

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Books, Creativity, Science

Revitalizing labs with “artscience” — David Edwards: The Lab

In science, meticulousness and diligence trump creativity and imagination. At least that is how it’s often perceived: Scientific logic and order lead to Truth; imaginative creative chaos leads to something looking nice at best.

This dichomtomy is all wrong and obstructs innovation, argues The Lab by David Edwards, a Harvard professor with a vision of disciplinary cross-over:

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Books, Science

“The fame she so richly deserves” — Rebecca Skloot: The immortal life of Henrietta Lacks

HeLa cells are everywhere: every biomedical research lab has samples and they are in the middle of current disucssions about how “the new cell biology” will look like.

Of course I had heard of them before, but before reading Rebecca Skloot’s book The Immortal Life Of Henrietta Lacks I had never wondered where they came from. For example, I was suprised to learn that they were named after Henrietta Lacks, the woman they originated from:

Henrietta was a black woman born of slavery and share-cropping who fled north for prosperity, only to have her cells used as tools by white scientists without her consent. (…) It was also the story of cells from an uncredited black women becoming one of the most important tools in medicine. (p225)

And what a great story this is!

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“She ate Oscar!” – Nelson: a life in 54 graphic episodes


Imagine asking James Joyce, JRR Tolkien, Ernest Hemingway and 51 others to write about one day in a person’s life and then compile the results in a book. Stream-of-consciousness next to lean, economic prose next to elves – chances are high that the combined text would be an unreadable chimera.

But the same idea works brilliantly in a graphic novel, as Nelson from Blank Slate Books demonstrates:

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Kent Haruf’s Plainsong

Kent Haruf’s Plainsong is an aptly named novel: a plain story in plain writing style. My copy contains a dedication by a previous owner: “Enjoy – the words of this novel ring true; always have told the children: ‘Life is what happens to you while you are making other plans!'” – which seems like a fitting description: Plainsong tells of the day-to-day struggle of everymen and -women living in Holt, Colorado, a ficticious town. There is no big conflict and no happy end – just plain life. The name and place and time don’t matter – Holt is a cipher for every Small Town, USA.

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