Open Notebook Science – the Carl Boettiger Interview

notesCarl Boettiger, a pioneer of the Open Notebook Science movement, shares some reflections and gives some advice to those who want to join in.
In the early years of blogging, digital journal keepers became more and more candid and open towards the digital world around them, disclosing even private information about their lives. A similar trend can currently be noted in the area of personal homepages in science.

Accordingly, a global community of scientists have finally taken the last steps towards total openness and become Open Notebook scientists, hence ”making the entire primary record of a research project publicly available online as it is recorded” [Wikipedia].  This means that they are giving the world— both friend and foe—free access to their  lab notes (sometimes even including failed experiments) as well as raw data and unpublished results.

One of the trailblazers in this area is Carl Boettiger, currently a post-doc in Theoretical Ecology and Evolution at University of California, Santa Cruz. In a Nature interview in January 2013, he explained that it started like ”a kind of career experiment” and that he hadn’t yet experienced any scoops. ”I think it is an overrated fear, especially when compared with the risk of being unknown in your field.”, he said.
wadirumCarl has an extraordinarily structured personal homepage, including a thorough description of his Experiments with Open Science.  Scientia Crastina decided to get in touch for some questions.

How did you become a open notebook scientist in the first place?
By accident I suppose.  As a theorist I was never trained to keep a lab notebook — and didn’t, for the first two years of my PhD.  Aware of the practice among wet lab researchers and frustrated by my own inability to reference what I had done months earlier, I started looking around for examples.  Naturally I began with Google and thus hit upon the (open) notebook of UK experimental chemist Cameron Neylon, (La)blog. Despite the differences in our fields I was impressed by the effectiveness with which Cameron leveraged a digital web platform for a lab notebook.  Some of these had nothing to do with being open, others did.  i thought I would give it a try.

Describe your technical platform in brief!
I write plain-text (markdown) files for each entry, which are stored on Github and rendered by Jekyll with Bootstrap CSS into the fast and lightweight static website you see.  I use and write small extensions which add machine-readable semantic markup (rdfa) and pull in additional data from web APIs, such as my current reading, code commits, tweets, and project tasks, as well as timestamps, sha hashes and pageviews.  All essential elements of the platform are free and open source.  (Excepting Google Analytics, which is free but not open source).

I experiment with my technical platform as a way of discovering, testing, and sharing tools that assist my workflow and my research.  I discuss some of the more valuable features I have come across in technical detail in a growing series of posts.

Have you heard about any disagreements between open notebook scientists and their group colleagues?
No.  I try to be upfront with my own collaborators about this, and respectful of their concerns.  At times this means keeping certain content private, at least delaying release until after publication.  Open Notebook badges help me be transparent about this.
Which are your three main suggestions to any early career scientist who wants to start practicing open notebook science?
1) Discuss your plan and your objectives with your collaborators first.
2) Start small – select a particular project or the delayed-release model.
3) Don’t try and build the perfect platform at the start, but learn and add features as you need them.  Value experimentation over perfection.  Above all, the notebook should save you time, not waste it.

Are you still convinced that getting scooped is not a major problem?

Being scooped is part of science whether you keep and open notebook or never talk about your work.  Sharing your work can make it more likely that someone will scoop you; but it may also discourage others from working on a topic they see as “taken”, and thus less likely that someone scoop you.  Such effects are difficult to measure or infer.
Communicating just how you have tackled the complex questions I work on in a way that is clear enough for someone to successfully replicate and publish is really hard.  Despite my best efforts, I suspect members of my own subfield would still find this challenging to do.
Science is full of risks.  Papers and grants get rejected, people scoop you, experiments fail or results are less interesting than we anticipate.  We take these risks because the rewards are worth it — the risky experiment, the investment in learning a new skill, the time it takes to write grants that may go unfunded. The risk that the jobs we want may not be available.  I believe their are risks in sharing my work, but they are not the risks I worry about.  The benefits are clear, diverse, and quick to pay off.  I don’t worry about someone finding answers before me; we’ll all learn something new and move on to more exciting territory.  What I fear is never being able to find that answer.  The more that want to join the journey, the merrier.


3 replies

Trackbacks & Pingbacks

  1. […] Open notebook science […]

Leave a Reply

Want to join the discussion?
Feel free to contribute!

Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.