Why are so many biologists scared of programming?

By Jane Charlesworth, University of Oxford.

I am a biologist. I also love computers. Sadly, I have many colleages who find programming scary, and I used to be one of those people. Here is how I learned to stop worrying and embrace programming as a tool for my research.

All the tech skills are self-taught, or picked up from eavesdropping on computer scientist friends in the pub. Most of my colleagues are either in the same boat or reluctant to spend their research time learning to write reproducible code. Even those of us who are eager to learn don't know where to begin. I think this represents a crisis in biology education.

I did a degree at a top UK university about ten years ago. A good 95% of my degree consisted of training for working in a wet-lab, doing molecular biology. I have never worked in a wet-lab. Granted, when I did my degree, the first human genome was still unpublished, but I find it impossible to believe that our course organisers could not have foreseen that sequencing was a rapidly maturing technology and the students they were training would need to be equipped with the skills to deal with the resulting deluge of data.

I recently looked up the course content of my degree, ten years on, expecting things to have improved. The course descriptions were virtually identical, despite the fact that computational biology and bioinformatics are some of the fastest growing areas of biological research. At university, our sole bioinformatics practical session consisted of doing a single search of an online database (BLAST). It didn't take much imagination to ask "is there a way of automating this task, if you want to do it for a whole bunch of genes?" The answer was: get a student to do it.

The idea that I might want to learn to program was never mentioned until I graduated and started a PhD, where I was expected to arrive proficient in skills that hadn't been part of my undergraduate training. This expectation knocked my confidence and turned programming into a big, scary thing in my mind. After spending more time than I'd like to admit panicking, I dived into a pile of books, Googling at least every other word.

I still spend the bare minimum part of my work day on writing a functioning script, and spend time generalising and refining it during the evenings (I've grown to learn that programming can be satisfying and frustrating in equal measures). Learning tech skills on top of full-time work as a research scientist is daunting, and it's hardly surprising that people find it difficult to find the time to develop their skills beyond the most rudimentary scripting.

Nevertheless, investing the time to learn some tech skills is invaluable as a biologist. Every single thing I've learned about software engineering has made my research massively easier, usually by forcing me to organise myself. Tools like version control can be very useful even for lab scientists, allowing people to collaborate on papers or protocols in a systematic way. What researcher would say no to half a day's training if that half-day meant saying goodbye to folders of files with cryptic suffixes like newest or latest?

I can't think of a good reason why these tools aren't being taught and I hear the same complaint from colleagues, over and over again. Organisers of undergraduate biology courses need to stop believing that biology students are scared of tech and maths and start encouraging their students to embrace these subjects if their aim is to train the next generation of researchers.