Brief notes on this parallel session from E-science all hands meeting on Tuesday morning. Continue reading “AHM2007 Medical E-science session”
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.
Through a PRISM darkly
I don’t really want to add anything more to what has been said in many places (and has been rounded up well by Bora Zivkovic on Blog Around the Clock, see also Peter Suber for the definitive critique, also updates here and here). However there is a public relations issue here for the open science movement in general that I think hasn’t come up yet.
PRISM is an organisation with a specific message designed by PR people which is essentially that ‘Mandating Open Access for government funded science undermines the traditional model of peer review’. We know this is demonstrably false in respect of both Open Access scientific journals and more generally of making papers from other journals available after a certain delay. It is however conceivable, for someone with a particularly twisted mindset, to construe the actions of some members of the ‘Open Science Community’ as being intended to undermine peer review. We think of providing raw data online or using blogs, Wikis, pre-print archives or whatever other means to discuss science as an exciting way to supplement the peer reviewed literature. PRISM, and other like-minded groups, will attempt to link Open Access and Open Science together so as to represent an attempt by ‘those people’ to undermine peer review.
What is important is control of the language. PRISM has focussed on the term ‘Open Access’. We must draw a sharp distinction between Open Access and ‘Open Science’ (or ‘Open Research‘ which may be a better term). The key is that while those of us who believe in Open Research are largely in favour of Open Access literature, publishing in the Open Access literature does not imply any commitment to Open Research. Indeed it doesn’t even imply a commitment to providing the raw data that supports a publication. It is purely and simple a commitment to provide specific peer reviewed research literature in a freely accessible form which can be freely re-used and re-mixed.
We need some simple messages of our own. Here are some suggested ideas;
‘Open Access literature provides public access to publicly funded research’
‘Publically supported research should be reported in publically accessible literature’
‘How many times should a citizen have to pay to see a report on research supported by their tax dollars?’
‘Open Access literature improves the quality of peer review’
Emphasis here is on ‘public’ and ‘literature’ rather than ‘government’ and ‘results’ or ‘science’
I think there is also a need for some definitions that the ‘Open Research Community’ feels able to sign up to. Jean-Claude Bradley and Bertalan Mesko are running a session in Second Life on Nature Island next Tuesday (1600 UTC) which will include a discussion of definitions (see here for details and again the link to Bill Hooker’s good discussion of terminology). I probably won’t be able to attend but would encourage people to participate in whatever form possible so as to take this forward.
Followup on ‘open methods’
I wanted to followup on the post I wrote a few days ago where I quoted a post from Black Knight on the concept of making methodology open. The point I wanted to make was the scientists in general might be even more protective of their methodology than they are of their data. However I realised afterwards that I may have given the impression that I thought BK was being less open than he ‘should’, which was not my intention. Anyway, yesterday I spent several few hours reading through his old posts (thoroughly enjoyable and definitely worth the effort) and discovered quite a few posts where he makes detailed and helpful methodological suggestions.
For example here is a post on good methods for recovery of DNA from gels as well as a rapid response to a methodological query. Here is another valuable hint on getting the best from PCR (though I would add this is more true for analytical PCR than if you just want to make as much DNA as possible). Nor is the helpful information limited just to lab methodology. Here is some excellent advice on how to give a good seminar. So here is a good example of providing just the sort of information I was writing about and indeed of open notebook science in action. I’d be interested to know how many people in the School now use the recipes suggested here.
p.s. his post Word of the week – 38
deuteragonist , n.
In a structural laboratory, one who labels his samples with 2H.
e.g. “Jill says that to be successful at small angle neutron scattering you have to be a good deuteragonist.”
c.f. protagonist
nearly got my computer completely covered in tea. And there is much more where that came from. They are probably more funny if you are an ex-pat Australian working in the UK but hey, that’s life.
Open methods vs open data – might the former be even harder?
Continuing the discussion set off by Black Knight and continued here and by Peter Murray-Rust I was interested in the following comment in Black Knight’s followup post (my emphasis and I have quoted slightly out of context to make my point).
But all that is not really what I wanted to write about now. The OpenWetWare (have you any idea how difficult it is to type that?) project is a laudable effort to promote collaboration within the life sciences. And this is cool, but then I realize that the devil is in the details.
Share my methods? Yeah! Put in some technical detail? Yea–hang on.
A lot of the debate has been about posting results and the risk of someone stealing them or otherwise using them. But in bioscience the competitive advantage that a laboratory has can lie in the methods. Little tricks that don’t necessarily make it into the methods sections of papers, that sometimes researchers aren’t even entirely aware of, but which form part of the culture of the lab.
The case for sharing methods is, at least on the surface, easier to make than sharing data. A community can really benefit from having all those tips and tricks available. You put yours up and I’ll put mine up means everyone benefits. But if there is something that gives you a critical competitive advantage then how easy is that going to be to give up? An old example is the ‘liquid gold’ transformation buffer developed by Doug Hanahan (read the story in Sambrook and Russell, third edition, p1.105 or online here – I think; its not open access). Hanahan ‘freely and generously distributed the buffer to anyone whose experiments needed high efficiencies…’ (Sambrook and Russell) but he was apparently less keen to make the recipe available. And when it was published (Hanahan, 1983) many labs couldn’t achieve the same efficiencies, again because of details like a critical requirement for absolutely clean glassware (how clean is clean?). How many papers these days even include or reference the protocol used for transformation of E. coli? Yet this could, and did, give a real competitive advantage to particular labs in the early 1980s.
So, if we are to make a case for making methodology open we need to tackle this. I think it is clear that making this knowledge available is good for the science community. But it could be a definite negative for specific groups and people. The challenge lies in making sure that altruistic behaviour that benefits the community is rewarded. And this won’t happen unless metrics of success and community stature are widened to include more than just publications.