Per Contra

Summer 2007


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The Pursuit of Automation: Open Notebook Science.  The Per Contra Interview with Jean-Claude Bradley


by Bill Turner

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What do you get when you combine transparency and raw data?  Jean-Claude Bradley says you should get automation of the scientific process, and his Useful Chemistry project is acting as a laboratory for his hypothesis.  For instance, when he attempted to expose a particular product missing a methyl group to fifty percent TFA/CDCl3, it should have caused the furfuryl group to cleave.  It didn’t.


You probably have no idea what that means.  Neither do I.  But the result is published for the world to see (SEE THE NOTES HERE) in the Useful Chemistry blog, available for other scientists to scrutinize and to help them avoid the same dead end.  “We are attempting to do science in as transparent a manner as possible,” Bradley says.  And that means publishing results— failures and all—online as the research unfolds.


“In science, of course, the basic information piece is the laboratory notebook,” Bradley says.  He believes that scientists, using blogs and wikis to post information from their notebooks, will speed research and create a resource that will allow researchers and students to better calculate potential for success in chemical reactions.  “What makes UsefulChem a little bit different than other open source science projects is that we actually keep our official laboratory notebooks on a public wiki.”


You Can See The Project by Clicking This Link


The difference between Bradley’s idea and traditional open source projects is the clutter, i.e., all of the data collected from research.  In a journal article, what the reader receives is a set of findings, published after peer review, along with the conclusions and basic data used to reach them.  Bradley’s project allows the reader to see the process unfold, from hypothesis to conclusion, with all data, experiments and notes that are collected along the way.  This inclusiveness  allows other researchers to better assess their own ideas, because not only do they have the conclusion and data used to support it, but also they have access to every failed or incomplete subset of data to use in their equations.


Useful Chemistry lets the reader look directly into the scientist’s notebook and see precisely what went right and what went wrong.  It’s the what-went-wrong part that makes it different and useful.  The project began using blogs, but Bradley learned that blogs were limited by their format as comments added to a post became cumbersome.  They switched to a hosted wiki, so that people could edit within the research, with a date and time stamp provided by a third party.  The wiki service they uses, Wikispaces, also provides a creative commons license, which provides the stability of attribution.  “We can prove who knew what, and when,” he adds.


But, as many writers can attest, intellectual property theft is a big problem on the internet.  “Right now, social software is your best bet,” Bradley says.  He explains that the date and time stamp actually records a researcher’s thoughts as he goes.  The benefit is that any theft of an idea is open for the public to see, because the idea is traced with clear markers on the software available to all.  Instead of clamping down the notebook and attempting to hide the idea, the researcher protects his idea by allowing everyone to see it and know that it was his idea on a specific date and at a specific time.  It seems odd at first, but like many aspects of Useful Chemistry, it works well and does so in unorthodox ways.


"It can be pretty polarizing sometimes," he says, when asked if traditional researchers, who work in competitive environments, react well to the idea of open notebooks.  “There are a group of people, most of them younger, who are about to enter the research sphere; those people tend to be very enthusiastic about this.  And there is another response from people who may be more established,” he pauses.  “It’s a different way of doing things.  I’m not forcing anyone to do it.”


“It doesn’t stop me either, from writing standard articles and submitting them to journals,” he says.  Right now, they’re trying to find out which publisher will take a paper that has had its research made public on a wiki.


The issues that come to mind as problematic are complex, but Bradley has also thought them through.  First, there are some projects with serious financial considerations.  Some research is aimed at creating products to make profits.  Bradley’s project works on Malaria.  “The people who are sick with malaria don’t usually come from wealthy nations, so it’s not as big of a target as some other drugs would be.”


When asked if the idea were used on other processes, like building the perfect dynamite, he said that the project was specific to malaria and other diseases.  So while somewhere, some person may get the idea to use his process in other ways, his project is focused in a specific field on a specific problem.  And where is it heading next?


“The larger purpose in all of this is to fully automate the scientific process,” he says.  “To really do that, you have to work in an open environment.”  A computer should have free access to data to crunch numbers and report results to the researcher in Bradley’s scenario.  “That’s really the next step, where we’re going to be screening the compounds before we make them.”


And how does he prepare for that?


“To some extent, I can’t control where it’s going to go.  It is like riding the wave, but I feel like it’s something I have to do at this point and it seems to make sense.”


When a scientist coins the phrase “Open Notebook Science” and proceeds to change fundamental ideas about research, control isn’t really an option.  But if Bradley succeeds in revolutionizing the scientific process, the “wave” could take him to exciting and critical discoveries in a variety of subjects.  Or, it could only eradicate malaria on Earth.


Not bad options, if only – if only. 



Jean-Claude Bradley is an Associate Professor of Chemistry and E-Learning Coordinator for the College of Arts and Sciences at Drexel University. He leads the UsefulChem project, an initiative started in the summer of 2005 to make the scientific process as transparent as possible by publishing all research work in real time to a collection of public blogs, wikis and other web pages. Bradley coined the term Open Notebook Science to distinguish this approach from other more restricted forms of Open Science. The main chemistry objective of the UsefulChem project is currently the synthesis and testing of novel anti-malarial agents. The cheminformatics component aims to interface as much of the research work as possible with autonomous agents to automate the scientific process in novel ways. Bradley teaches undergraduate organic chemistry courses with most content freely available on public blogs, wikis, games and audio and video podcasts. Openness in research meshes well with openness in teaching. Real data from the laboratory can be used in assignments to practice concepts learned in class. Bradley has a Ph.D. in organic chemistry and has published articles and obtained patents in the areas of synthetic and mechanistic chemistry, gene therapy, nanotechnology and scientific knowledge management.