“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!

Curing the GWAS-infestation — Nature Genetics regaining its old form?

Something good must have happenend at Nature Genetics. After a flood of GWASs they seem to be back to publications I am actually interested in. I’m not exactly sure when the change happened, but in the current issue several computational papers stand out:

Mix Tape #2: Best Songs by Scientists — No one in the lab got science like us!

After the success of my collaboration with NotNicolajames here comes a new collection. This time it is Best Songs By Scientists: from frustrated love to educational propaganda and nerd-core!

Procrastination in context

Who doesn’t know procrastination? I know I have done my fair bit of it. You got a thesis to write, but -hey- shouldn’t these windows be cleaned immediately? Or you need to prepare slides for an important talk, but instead decide to read piles of papers – background knowledge is always important.

But a flyer from the Cambridge University Student Counsel I read today finally put it all in context by quoting Thomas de Quincey:

“If once a man indulges himself in murder, very soon he comes to think little of robbing; and from robbing he comes next to drinking and Sabbath-breaking, and from that to incivility and procrastination.”

Florian

“Detecting Novel Associations in Large Data Sets” — let the giants battle it out!

Computational and statistics papers usually don’t make it to glossy high-impact journals. “Your manuscript seems better suited for a more technical journal” is a regular response for submissions focussing on theory not data.

But sometimes these papers make it through, usually to Science, which has a much better track record for theoretical papers than Nature. An encouraging recent example is Detecting Novel Associations in Large Data Sets by Reshef et al in Science:

Here be dragons! Thomas Kuhn, Statistics and System Biology

Thomas Kuhn had physics in mind when he wrote Structure of scientific revolutions but his key ideas also apply to statistics and systems biology and can explain some of the confusion in the field.

Thomas Kuhn’s Structure of scientific revolutions desribes the history of science as phases of normal science separated by revolutions and paradigm shifts. During normal science, research is guided by  a ruling paradigm, which identifies feasible problems and routes to tackle them. Normal science is a period of puzzle solving. The better your paradigm, the clearer the puzzle, the better your chances to solve it and progress.

The Joy of Books

This is amazing! The whole book store comes alive!

It’s not the first stop-motion video about books, but it’s quite a bigger effort than your regular “I got bored over the weekend and reorganized my bookshelf“-video.

Florian

Mix Tape #1: Best Songs About Science

The future of science lies in collaborations! And it is in the spirit of scientific collaboration that the blogging couple – a.k.a NotNicolaJames and her ScienceBoy – have joined forces to bring to you this collection of Best Songs About Science.

“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:

Spare me your method; show me your finding!

Developing statistical and computational methods is fun…

Figuring out the mathematics, making the algorithms more efficient, using every programming trick in the book — it’s like producing a piece of art. The rush of adrenaline, when you discover a bug; the satisfaction, when it all comes together and does what it is supposed to. Faster and more accurate, hopefully, than all competitors. Victory!

I can completely understand why so many people in computational biology are busy developing more and more methods. I even got some of my own. It’s fun and an intellectual challenge – the scientific equivalent of cross-word puzzles.

… but computational biology has too many methods already

But more and more I find myself wondering if I should indulge in this fun exercise. Computational biology has too many methods already. Only a tiny number make an impact. Most are just marginal improvements to existing methods. Not what you would call a game-changer.

What’s up with Scientific B-sides in 2012?

Happy New Year!

Scientific B-sides is less than three months old, but growing quickly. Here are my personal highlights, one for each month:

• October: Feyerabend and the tyranny of science, the post that started it all.
• November: Faster forwards than backwards — scientific de-discovery and forensics.
• December: Obsessive-compulsiveness at its best — Ursus Wehrli’s art of tidying up.

And what are my plans for Scientific B-sides in 2012?

First, and most importantly, I have teamed up with the woman, who is not Nicola James but my wife, to create a collection of Best Songs About Science, which will come out in the next few days or so.

Science

On the science side, I’ll start with a short series on research strategy in computational biology. I will claim that we have too many methods already and discuss a question-driven approach. The first post in this series will be called: Spare me your method! Show me your finding!

Philosophy

On the philosophy side, I plan a series on Feyerabend. Since duty called me to rubbish some articles I had to read on Feyerabend, I think I should have a look behind the polemics and describe the messages I took out from reading The Tyranny Of Science myself.

Skills

And finally, I plan a series on scientific soft skills, based on my collection of resources. I plan to post on leadership, presentation and writing skills.

Stay tuned!

Florian

image source: http://im03.thewallpapers.org/desktop/21486/london-wheel-wallpaper