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.

Continue reading

Tagged , , ,

The hedgehog and the Quants


Nate Silver bashing everywhere I look. For example in the New York Times. Paul Krugman does it. And someone called Timothy Egan. `Creativity vs. Quants‘ is the title of his OpEd – how silly! Does he really thing we quantitative folks are mechanical calculation machines devoid of any creative thought? If you think quantitative work is not creative, you just haven’t done it yet.

Intimidation by quantification

Much more interesting, I thought, was Leon Wieseltier’s take in the the New Republic. I really like Wieseltier’s phrase ‘intimidation by quantification’ – this is how my biological collaboration partners must feel when I bombard them with p-values.

Wieseltier discusses the old idea of the hedgehog and the fox (dating back to ancient Greece) that Silver had used to explain the Fox logo of FiveThirtyEight: “The fox knows many things, but the hedgehog knows one big thing.”

Continue reading

Tagged , ,

Replication of results in statistics and biology

Do differences between biology and statistics explain some of our diverging attitudes regarding criticism and replication of scientific claims?asks Andrew Gelman on his blog.

I was not very impressed with the post or the comments it received. Here is what I posted as a response:
Continue reading

In science ignorance beats knowledge of facts

New York Biologist Stuart Firestein talks about ‘The pursuit of ignorance’ in science. “Science, we generally are told, is a very well-ordered mechanism for understanding the world, for gaining facts, for gaining data. I’d like to tell you that’s not the case.”

His talk is meandering and has too many quotes from famous people – but I enjoyed it, in particular because I have made ignorance my comfort zone already some time ago.

You can read also about Firestein’s talk on the TED blog ‘In praise of ignorance‘, and if you’d rather read a scientific paper, why not try Martin Schwartz’s “The importance of stupidity in scientific research” in the Journal of Cell Science?



The Morality of Open Access vs Increasing Diversity

Florian Markowetz:

Scientific B-sides is in TEAM DIVERSITY which is also TEAM CAREER. Every time you see one of my papers in a PLoS journal it just means one of the Natures didn’t take it. Simple as that.

Originally posted on :

Earlier today I got some news that I had not been rejected from the glammiest of glamour. However, the editor did request that I make some big changes to the manuscript and I, in typical Isis fashion, had a little pout fest and healthy bout of “I don’t know what to do…..(whine).”

As soon as I hardened the fuck up, I called a mentor and very senior person in my field and asked him whether it would be better for me to submit the paper as I had written it to a field specific journal or comply with the editor’s request and go glam. In no uncertain and pragmatic terms, he told me to go with the latter telling me, “Something like this puts your career on an entirely different level.”

I took my question to the Twitterz and PLoS founder Michael Eisen asked me:

OA Tweet

Nope.  Not Open Access at…

View original 250 more words

Tagged ,



Just got an empty email with the subject line:


As if I didn’t know that!

We got six papers in the pipeline – at different stages of rejection.

How does this guy know about my misery?

Why does he poke his finger into my wounds?


A terribly sad Florian


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.

Continue reading

Tagged , ,

The cancer of Henrietta Lacks: more telomerase, less angels please!


With all the clamor over sequencing the HeLa genome, Rebecca Skloot and her book ‘The immortal life of Henrietta Lacks‘ are making headlines again. I had been very impressed when I read it first (as you can see from my review in early 2012), but I am less enthusiastic now that I had some time to think about it.

The reason is the way Skloot fails to distance herself (and thus the reader) from the Lackses magical world-view.

Continue reading

Tagged , , , , ,

Ah … look at that cell body!

‘I’m a Stem Cell and I Know It’ from the Frye lab at the Cambridge Stem Cell Institute.


Is the publication of the HeLa genome an invasion of the privacy of Lacks’ living relatives?


Mike Eisen has joined the discussion about the HeLa genome:

Skloot’s piece glides from the issue of how to retroactively get Henrietta’s permission to experiment with and publish about her cells to the seemingly related  issue of whether publication of the HeLa cell genome is an invasion of the privacy of Lacks’ living relatives. (…)

I find the way Skloot’s NYT piece moves back and forth between the historical transgressions against Henrietta Lacks and the contemporary threat to her relatives’ privacy incredibly misleading.

I doubt this was intentional – rather I think it reflects muddled thinking on her part about these issues. *

I think this is a very good point.

And when discussing how much threat the HeLa genome is to the privacy of her living (and future) relatives, it would actually be important to know if Skloot is right that a few minutes of analysis of the HeLa genome provide “a report full of personal information about Henrietta Lacks, and her family.”

I still doubt it.

But it’s a testable hypothesis. We just need to sequence other members of the Lacks family and see if their genomes are significantly closer to the HeLa genome than yours or mine or Skloot’s.

Now there’s an experiment waiting to be done.

I’ll start talking to the folks at the EMBL.


Tagged , , ,

How to ask for a recommendation letter – 10 tips

Arthropod Ecology wrote a great post on  Ten tips when asking for a letter of recommendation.

What I would add: Be prepared to write a draft yourself!

All advisors are busy and for them it’s a lot of help if you draft your own letter. This is harder than it sounds. Most of us instinctively undersell their own performance. But if gives you the opportunity to define which particular feature of your CV or work the letter should focus on.

And if you draft the letters for more than one of your advisors, you can actually stress different bits in different letters to make sure they don’t all sound the same and cover your general awesomeness comprehensively.

Update 4/5/13: Make sure that the letters still look unique, even if you drafted them or supplied a list of bullet points. It looks a bit weird if all your letters contain the same sentences. And don’t trust your letter writers to reformulate what you sent them. Like all of us they will be busy (and/or lazy) and most likely just copy/paste what you sent them. So it’s up to you to feed them bits that sound different from each other.


Tagged ,

The Immortal Life of Henrietta Lacks, the Sequel


On March 11th scientists at EMBL announced that sequencing of HeLa cells revealed havoc in biology’s most-used human cell line. Their sequence analysis reveals how the HeLa genome is different to the Human Genome Project reference. Their results are published in G3: Genes, Genomes, Genetics.

Since HeLa cells are indeed one of biology’s most-used human cell lines, this is a great resource for cancer research.

But what about Henrietta?

But wait, … ‘HeLa’ stands for ‘Henrietta Lacks’. It’s not an anonymous cell line. There is a real person (plus still living family) behind it. What does the Lacks family say to having their family’s genome exposed?

Continue reading

Tagged , , , , ,

Maximal Information Coefficient – just a messed-up estimate of mutual information?


Theory papers almost never make it into top journals and this is why I have blogged about the paper ‘Detecting Novel Associations in Large Data Sets’ in Science by Reshef et al before (here and here). The reception in the statistics community was mixed and while Terry Speed seemed to love it, Rob Tibshirani started to point out weaknesses. And now other people have joined the discussion.

Continue reading

Tagged , ,

Pound for pound she is the best philosopher in the department

Jonathan Wolff takes a look at academic references in the Guardian. Some examples are really funny:

“Pound for pound she is the best philosopher in the department.” What can that mean? She’s not very good, but on the other hand she is really small?

He concludes:

[T]he value we get from academic references is minuscule compared to the effort involved on all sides.

That’s what I have always been thinking …



Don’t wear your new shoes (yet)

I have blogged about the ISMB workshop “From Postdoc to PI” before (here and here) and now the organizers published a paper about it in PLoS Comp Bio: “Don’t Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator” Nice!


Tagged ,