When is open notebook science not?
Well when it’s not open obviously.
There are many ways to provide all the information imagineable while still keeping things hidden. Or at least difficult to figure out or to find. The slogan ‘No insider information’ is useful because it provides a good benchmark to work towards. It is perhaps an ideal to attain rather than a practical target but thinking about what we know but is not clear from the blog notebook has a number of useful results. Clearly it helps us to see how open we are being but also it is helpful in identifying what it is that the notebook is not successfully capturing.
I have put up a series of posts recently in the ‘Sortase Cloning‘ blog notebook. The experiments I did on 29th August worked reasonably well. However this is not clear from the blog. Indeed I suspect our hypothetical ‘outsider’ would have a hard time figuring out what the point of the experiment is. Certainly the what is reasonably obvious, although it may be hidden in the detail, but the why is not. So the question is how to capture this effectively. We need a way of noting that an experiment works and that the results are interesting. In this case we have used Sortase to do two things that I don’t believe have yet been reported, fluorescently label a protein, and ligate a protein to a piece of DNA. This therefore represents the first report of this type of ligation using Sortase.
Perhaps more importantly, how do we then provide the keys that let interested people find the notebook? UsefulChem does this by providing InChi and smiles codes that identify specific molecules. Searching on the code by Google will usually bring UsefulChem up in the top few searches if the compound has been used. Searching on ‘Sortase’ the enzyme we are doing our conjugation with brings up our blog at number 14 or so. So not bad but not near the top and on the second page not the first. For other proteins with a wider community actively interested the blog would probably be much further down. Good tags and visibility on appropriate search engines (whatever they may turn out to be) is fairly critical to making this work.