Open Notebook Science

I just listened to Cameron Neylon’s fascinating talk given at Drexel a short time ago, it’s available as a podcast/mp3 via the UsefulChem Blogspot. Neylon has turned to modified blog software to help his team capture their ongoing science and is now opening his laboratory notebooks to the world.

Several things struck me from his talk. First, he points out that grad students are generally reluctant to get involved if it means more work, especially if they are not so hot on keeping a neat paper labbook, but also because their work is suddenly on show to the world. In Neylon’s field there is also the problem of tagging the materials with which his group works – short DNA sequences and proteins. Chemists, of course, have Smiles strings and InChI keys, but there is no single, simple way of tagging a protein like this, that would make it readily searchable across the blogosphere, web or database. This is especially problematic given that many research groups will be working with their own unique sequences.

However, it is the potential power of open notebook science that came across most strongly in Neylon’s talk and it is exemplified by a little anecdote he told in response to a question from the audience at the end of the lecture.

Apparently, one of his students had been struggling with a DNA experiment, finding the heatshock process difficult and not getting the results she expected. Nothing was awry in her procedures until she ran out of sample tubes and Neylon pointed out that the shelves needed restocking. It was at this point that the he and the student realised she had been using a different brand in her experiments to that used in the previously successful runs carried out by other team members.

Of course, the tube brand was not mentioned in anyone’s lab book, it was assumed they were generic components and so brand was irrelevant. Not so. At the scale they are working at, and with highly temperature sensitive materials, a minute difference in tube thickness and precise composition makes all the difference in heat distribution. The students experiments with the other brand failed because this was not taken into account. Industrial chemical engineers would have recognised the problem immediately, I’d assume. Anyway, switching back to the original brand have her almost instantaneous success and results are now being written up.

The point being, that in an open electronic notebook, such problems could be flagged so that group members and supervisor would be alerted. A meta tag in the experiment’s blog post SUCCESS=0,1,NULL could easily be included. Moreover, fields could be added in the equipment section to specify brands so that a failed experiment in which the wrong brand was used might be spotted and a different brand of tube, for instance, used next time. Such information would be archived and available to future generations so that similar mistakes would be circumvented.

Meanwhile, you can listen to the complete talk from Neylon here.

Author: bob投注平台

Freelance science journalist, author of Deceived Wisdom. Sharp-shooting photographer and wannabe rock god.