101 questions with a bioinformatician #11: Ewan Birney

This post is part of a series that interviews some notable bioinformaticians to get their views on various aspects of bioinformatics research. Hopefully these answers will prove useful to others in the field, especially to those who are just starting their bioinformatics careers.

This is a special 'If we need that extra push over the cliff' edition of '101 questions with a bioinformatician'.

This week's interviewee is the Associate Director of the European Bioinformatics Institute and also the head of CTTV (the Centre for Therapeutic Target Validation). Furthermore, he is a winner of the prestigious Benjamin Franklin Award, a winner of the Overton Prize, and he was recently elected as a Fellow of the Royal Society. He helped found Ensembl, was an early supporter/developer of BioPerl, and has contributed to an improbably large number of genomics and bioinformatics projects.

And yet, these are not the accomplishments of Ewan Birney that I am most impressed by. Rather, I am in awe that he helped define life to Douglas Adams (a very special kind of DNA). And most impressively, his entry on Wikipedia lists one of his roles/accomplishments as follows: 

[Ewan] acted as a bookmaker to the genomics community, taking bets on different estimates of the total number of genes in the human genome.

Ewan Birney, a man who will help satisfy your genomic gambling needs! You can find out more about Ewan by following him on twitter (@ewanbirney), or reading his blog (Bioinformatician at large), or attending any bioinformatics conference (he asks all the questions at all the conferences…it's in his contract).

And now, on to the 101 questions...



001. What's something that you enjoy about current bioinformatics research?

Learning new stuff. My research is heading towards leveraging outbred genetics to understand basic biological processes in a variety of metazoans (fly, medaka, human). I’m learning about statistical genetics (population structure, other stuff…), fly development, medaka anatomy and human physiology along with my students. It’s great.


010. What's something that you *don't* enjoy about current  bioinformatics research?

Broadening this out to life sciences, not just bioinformatics, it’s about a chronic set-point problem in our collective investment into information infrastructure. Fundamentally, biology is an information science; we need to understand how things work and we need to pass data, information and knowledge both on in the future and between people now. Writing papers is part of this, but other parts — just as important (perhaps more?) — are both raw and derived sets of information. To do this we need robust information infrastructuresCollectively we are happy that multiple billions are spent on data generation/experiments/analysis and yet we often agonise on the millions spent on aggregating (over space) and propagating (over time) this information. This is a fundamental mindset that we need to change.


011. If you could go back in time and visit yourself as an 18 year old, what single piece of advice would you give yourself to help your future bioinformatics career?

  1. Get your head around statistics — frequentists, bayesian, etc. You will really need this.
  2. Be open (the few times I’ve not been, I’ve regretted it).


100. What's your all-time favorite piece of bioinformatics software, and why?

 Hmmm. Tough one.

 Perl? (though the cool kids do Python now)

 R? (though the insanity of the function conventions drive me mad…)


101. IUPAC describes a set of 18 single-character nucleotide codes that can represent a DNA base: which one best reflects your personality?

I’ve always had a soft spot for Y. Perhaps thats because I first got into bioinformatics through splicing and the 3’ splice sites have the polypyrimindine tract beforehand. Or that T and C seem like the underdogs in the nucleotide world…