I’m a biologist Jim, not a programmer

A interview with the head of a bioinformatics software company got Tiago thinking about how much time biologists should devote to computing. Deepak also has a few ideas on the topic. This one is always a favourite in the “biologists versus bioinformaticians” debate and here’s my $0.02.

First, I can’t answer the question “how much programming should a biologist know?” It depends on the individual and the nature of their work. What I will say is that since we live in an age where the ability to acquire, process and interpret large amounts of data is an important research skill, I’d assume that any biologist with any common sense is thinking about improving their computer skills.

Second, my own experience as a biologist moving to bioinformatics has been entirely positive. I’ve learned new skills, been able to work on a wide variety of problems and improved my job prospects (if not in academic research, than elsewhere). I’ve also found that thinking about problems computationally has vastly improved my decision making, problem solving and data analysis skills. My generation of biologists were taught that biology was different to other sciences; it was fuzzy, messy, illogical, a collection of facts with no common threads. That attitude was rubbish then, it most certainly is now and we can thank bioinformatics for helping to change it.

Third, I cannot understand the attitude of some biologists that learning computational skills “gets in the way” of their research. “I’m a biologist Jim, not a programmer”, as Bones McCoy might have said. These same people think nothing of expending time and effort to learn a new laboratory technique, because they know that it will benefit their research. Yet they see learning a computational technique as tangential, or a potential waste of time, or something that they shouldn’t have to think about because it’s just a tool, a means to an end. I just cannot see the difference between learning how to write a Perl script and learning how to purify a protein, or sequence a plasmid insert. If you need it and it benefits you, you do it.

Incidentally, my personal suspicion is that many PIs discourage their young researchers from getting into computing because they know that they will find it far more enjoyable and satisfying than lab work and stop doing experiments ;)

My fourth point is very dear to me – I just cannot stand to see my biologist colleagues performing a computational task badly. It almost causes me pain. I look at it like this: why are you spending 6 hours on a manual task (copying and pasting between a web page, Word and Excel, for instance) when you know that a Perl script of a few lines would do the same job more or less instantaneously? “Because I don’t have time to learn Perl.” Well, if it’s a task that you perform regularly on similar datasets, those hours soon add up. Essentially, you’re wasting 6 hours of your life every time you do that task inefficiently. Do it five times, you’ve wasted 30 hours. And you know, most intelligent people can learn a lot of basic scripting in 30 hours.
Time saved now is time saved later.

So I’m in full agreement with Tiago when he objects to the sentence “when biologists start asking about where they can learn to program a computer, just so they can do their job you know something is wrong”. I’d say it’s a sign that something is very much right.