Tuesday, July 10, 2007

Giving Open Notebook Science a try

One thing I didn't expect when I started blogging a month ago was to read other people's blogs. But I did, and I've been positively surprised at the quality of the writing in the science part of the of blogosphere. I think the lack of top-down editorial control spurs more novel ideas.

I've seen a number of posts in the blogosphere about different aspects of Open Science. I don't want to explain Open Science, particularly since it's not clear exactly what it is yet. But Bill Hooker at 3 quarks daily wrote a nice three part series (I, II, III) on the subject, which you should read if you're interested in the details. Here I'm only going to discuss Open Notebook Science, which is a term coined by Jean-Claude Bradley. The idea is simply that the heart of every person's research - their lab notebook - should be open to the world.

Since most of our scientific work is funded by tax payers who expect their money to be well-spent, it's interesting that openness isn't required. Science typically builds on the body of available knowledge - the more knowledge available the faster science goes. It's striking when you visit other labs in person; you see all of their unpublished work, and you know that most of their results and data won't be available to the bulk of the scientific community until a year after each particular scientific project is finished. By the time papers are in print, it's old news to the insiders. More striking is when you visit labs whose work you've thought about replicating and expanding on. It's not too uncommon to find that only one person in the entire lab is able to get the technique to work, and even for him the technique only works on Wednesdays. This type of information would be useful to know before you embark on a useless three months trying to adapt their method. But scientific publications are covered in a thick coat of high-gloss finish, making these unacknowledged difficulties hard to detect.

Lab notebooks on the other hand are flat black. As long as people keep them regularly updated, they contain the good, the bad, and the completely nonsensical results.

Today I test the waters of Open Notebook Science.

The latest version of my lab notebook is now automatically posted on J's Lab Notebook Page each night. I've been using an electronic lab notebook for two years now, so there's quite a bit of data in there - good and bad (300+ pages).

What I hope to gain by being Open Notebook:
  1. a nice warm fuzzy feeling that I have nothing to hide
  2. less likely to be accused of scientific fraud (though I really wasn't worried about this in the first place)
  3. potentially helping others by allowing early access to my results and failed experiments
  4. I really hope people will notice stuff I'm doing wrong and LET ME KNOW - would be a very big benefit if it were to occur
Bad things I don't think will happen by being Open Notebook:
  1. people will take little details of the results from my experiments and nitpick about conclusions I've published based on the results - claiming the results in my notebook don't support the results and conclusions in my publications.
    • I don't think this will happen, since I'm pretty careful with what I publish and with doing proper stats and such.
  2. people will take my data and scoop me
    • I think people are busy enough with their own work that they don't need to publish mine.
    • By putting my data on the web as soon as I make it, I have a pretty strong case to say I'm first (as long as other people see my results too; otherwise, you have the problem with the tree falling in the forest that may or may not make a sound)


Bill Hooker said...


Jean-Claude Bradley said...

Your pdf notebook is really very impressive! I'll post comments about what tools you might find useful in your next post.

Do you plan on submitting these results to a specific journal and have you discussed it with your supervisor?