I’d like to bring to wider attention an article series, The Roots of Bioinformatics.

The roots of prairie plants (Source: Wikimedia Commons.)

The roots of prairie plants (Source: Wikimedia Commons.)

Hold up.

Before experimental biologists run away, you’re some of the people I’d like this to reach!

At a recent bioinformatics meeting I attended, a senior experimental biologist from overseas commented to the effect that it was hard for bioinformatics researchers to build their own careers, to publish their own papers. My take on his comment was that he was referring to the tendency of experimental research to treat the bioinformatics as a service, seconding the work or linking to service centres, rather than treating bioinformatics researchers as collaborators, stand-alone groups in their own right.

I’m not about to argue the ins and outs of that here, but to draw attention to understanding the origins of bioinformatics, and hence it’s deeper alliance with biology.

One senior scientist at that meeting showered praise on Lincoln Stein for ’his pioneering work in bioinformatics’ (I’m paraphrasing here). I gritted my teeth and bit my tongue. Stein certainly contributed in a fine way to the human genome project, but he was no pioneer of bioinformatics.*

I thought it very telling that a senior biologist would think that.

It made me think that some (still) think of bioinformatics as a young field that emerged as a consequence of the service needs of the genome projects. I worry that an overly service-oriented view of bioinformatics prevails because of this.**

It’s a topic I touched on in The mythology of bioinformatics. My article doesn’t attempt to give a history of the field, as this series in PloS Computational Biology I am introducing here does, but briefly points to early work whose that could clearly be recognised today as being bioinformatics, and highlights other issues that I felt at that time were leading to misunderstanding.

By contrast, the new series in PloS Computational Biology is squarely aimed at giving an anecdotal narrative history of the field; another approach to better understanding bioinformatics today and what it has to offer to biology.

David Searl’s editorial introduces the Roots of Bioinformatics series, starting with a little light philosophy on the dual roles of tools and knowledge, bioinformatics combining the two.

The  second paper in the series, Russell Doolittle’s The Roots of Bioinformatics in Protein Evolution is now available. I like the approach he takes, working from the biological issues of the day, looking at how issues from the pre-electronic approach to protein biology lead to protein bioinformatics.

I would like to like to see this series more widely read, beyond preaching to the choir, as it is being published within a specialist journal.

My only worry is that the series will prove too patch-meal or specialist for those outside of the field. Hagen’s article might be useful to some (free PDF copy).

It will be interesting to see what the rest of the series brings, and I welcome that attention is being paid to the deeper origins of the field.


* All I am saying is that the field has older origins than his excellent contributions.

** I’m not saying that services don’t have a role, they certainly do, but that there is more to the field than just services.


Searls, D. (2010). The Roots of Bioinformatics PLoS Computational Biology, 6 (6) DOI: 10.1371/journal.pcbi.1000809 (open access)

Doolittle, R. (2010). The Roots of Bioinformatics in Protein Evolution PLoS Computational Biology, 6 (7) DOI: 10.1371/journal.pcbi.1000875 (open access)

Hagen JB (2000). The origins of bioinformatics. Nature reviews. Genetics, 1 (3), 231-6 PMID: 11252753 (subscription, but free PDF copy available on-line)

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