Open notebook science

This article has been reposted; it’s a direct copy from my original written for my blog at The Lay Scientist.

I guess people have different opinions about open access journals and things like that. I was at a conference run by the RSC earlier this spring and a guy came on stage for 5 minutes in between people talking about new esoteric new chemicals they’d managed to make. He was trying to promote a new open access journal called ‘chemistry central‘.

All the academics in the room were huffing and puffing at him through the whole of his polite spiel, and he apologised for taking up people’s time at the end of the talk.

I happened to be standing behind the guy when it came to coffee time and remarked that ‘you might have to wait for a few of the professors to die before your journal ever really takes off,’ which he seemed not quite sure how to take. I guess I was a little too forward. I then told him I thoroughly supported the idea of open access journals and that, if I a choice and something to publish, I’d plump for one of them. he asked who I was, and when I said ‘I’m just a PhD student’ he politely excused himself.

Well, we’ve established I’m an idiot. But blimey, about open access stuff; it’s true isn’t it? There’s so much built in hostility in the older generation of scientists to the idea of open access publishing. I would never even dream of suggesting to my supervisor that we publish any of my work in an O.A. journal. He’d shout me out of his office before you could say ‘equal access rights’.

So I was rather amazed to receive an email a few days ago from a senior academic in the department where I work recommending we submit articles to a new open access platform called ChemSpider SyntheticPages.

The idea of this free-to-view database is to collate firsthand experience about doing chemical reactions in one place. In chemistry, it’s a massive pain when you read a procedure in the literature, it seems simple, but when you try it yourself it doesn’t work. It’s usually just because there’s something you’ve neglected to do which the author didn’t put in because it they thought it was too obvious or it wouldn’t sound professional in an academic journal. For example here’s an extract from a procedure I carried out recently:

…saturated aqueous ammonium chloride was added to the mixture dropwise over ten minutes. The slurry formed was filtered and washed with THF (3 x 50ml).

THF, by the way, is a colourless solvent which looks a lot like water. This is part of the prep which I got wrong the first time i tried it. If it had been written more like this, then I might have a had a better chance:

…saturated aqueous ammonium chloride was added to the mixture dropwise over ten minutes. The slurry formed was then shaken vigorously with copious amounts of THF in a sealed container before filtration. You really need to shake this bad boy hard, as the dense filter cake formed sticks to the compound you are trying to isolate and it’s hard to extract.

The synthetic pages are the first example I’ve come across of what is basically a well run and professional looking online lab notebook. Which means writing something akin to the second version of the procedure above would not be an academic faux pas, but rather actually appreciated for its helpfulness to the reader. Well that makes sense.

An extreme minority of chemists already practice so called ‘open notebook science’, such as Jean-Claude Bradley of Drexel University in Philadelphia (see his notebook here) But the problem with forward thinking individuals like him doing this is that unless you’re very, very interested in their specific area of expertise and happen to know they operate in this area, you’re unlikely to ever read the details of their notebooks.

Obviously ChemSpider – if it became widely enough used – would be the solution to this problem as one could go to the database, search it and get honest, realistic accounts of how any chemistry you like works from the people who did it in the laboratory.

Since it’s a free service, the ‘articles’ aren’t peer-reviewed in the traditional sense of the phrase, which could be a worry. However, the site operates like a wiki; there is the opportunity to write comments after articles, share tips and even potentially criticise accounts if you find them wanting. Everyone can see everyone else’s credentials, as each user must have a proper account and user profile.

Clearly, it’ll be a while, if ever, before this kind of community based resource can compete with proper journals. Still, I think it’s got to be a step in the right direction. It shows that among chemists at least, there are some who are taking the first steps towards a more honest and open way of talking about science.

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This entry was posted in Open Access, Science, Science and society, Science communication. Bookmark the permalink.

One Response to Open notebook science

  1. Pingback: Open Laboratory 2010 – submissions now closed – see all the entries | A Blog Around The Clock

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