Peer Review and Science2.0: blogs, wikis and social

networking sites

Jean-Claude Bradley

March 15, 2010

Guest Lecture for “Peer Review Culture in Scholarly Publication and Grantmaking” course at

Drexel University

Associate Professor of ChemistryDrexel University

What Peer Review Does

1. Provides authors with a publication format that counts in academia.

2. Assists editors to determine if the findings of an article are consistent with the data provided and commonly accepted scientific models.

3. Assists editors in attempting to provide a consistent style and focus for a particular journal. (not fundamental – see PLoS ONE)

What Peer Review does not do

Verify the analysis of all the raw data supporting an article.

Even if peer-reviewing tried to take on the responsibility of verifying all the raw data, there are not enough

resources to cope.

TRUST

PROOF

A solution that scales: Open Notebook Science

How bad is our current system? Try to find the solubility EGCG?

=2.3 g/L

WTF?!

The End of the Chain of Provenance

The Tragedy of the Trusted Source Cascade

The NaH oxidation controversy

Information spreads quickly through the blogosphere

15% NMR yield

Khalid Mirza and Marshall Moritz

Top results on a Google search

The Scandal of Bell’s Lab Notebook

Motivation: Faster Science, Better Science

Open Notebook Science Logos (Andy Lang, Shirley Wu)

Sharing: how much and when

There are NO FACTS, only measurements embedded

within assumptions

Open Notebook Science maintains the integrity of data

provenance by making assumptions explicit

The solubility of 4-chlorobenzaldehyde

The Log makes Assumptions Explicit

The Rationale of Findings Explicit

Raw Data Made Public

Splatter?

Some liquid

YouTube for demonstrating experimental YouTube for demonstrating experimental set-upset-up

Calculations Made Public on Google Spreadsheets

Revision History on Google Spreadsheets

Wiki Page History

Comparing Wiki Page Versions

Proof of Purity with interactive NMR spectrum using JSpecView and

JCAMP-DX

Linking to Molecules in Chemistry Databases

Experimental Spectra and User-Deposited Data on ChemSpider

(Andy Lang, Tony Williams)

Open Data JCAMP spectra for education

(Andy Lang, Tony Williams, Robert Lancashire)

Database Curation via Game Playing

Over 100,000 spectrum views so far - worldwide

Link Spectral Game to Open Educational Content

The Ugi reaction: can we predict precipitation?

Can we predict solubility in organic solvents?

Crowdsourcing Solubility Data

ONS Submeta Award Winners

ONS Challenge Judges

Teaching Lab: Brent Friesen (Dominican University)

Solubility Experiment List

Solubilities collected in a Google Spreadsheet

Rajarshi Guha’s Live Web Query using Google Viz API

WE ARE HEREWE ARE HERE

How can the scientific process become more automated?

Semi-Automated Semi-Automated Measurement of solubility via Measurement of solubility via

web service analysis of web service analysis of JCAMP-DX files JCAMP-DX files

(Andy Lang)(Andy Lang)

Solubility Measurement Requests: DoSol sheet

•Outlier Bot: flags measurements with high standard deviation to mean ratios•Google Analytics queries – new solvent/solute searches•Solubility request form – researcher in Israel requesting pyrene in acetonitrile solubility for environmental soil contamination study•Application based models – high priority Ugi reactants

Solubility Prediction (Andy Lang’s Model)

Understanding in addition to empirical modeling

Missed in a prior publication on

solubility for this compound

Data provenance: From Wikipedia to…

…the lab notebook and raw data

Including links to the literature

•Concentration (0.4, 0.2, 0.07 M)•Solvent (methanol, ethanol, acetonitrile, THF)•Excess of some reagents (1.2 eq.)

How does Open Notebook Science fit with traditional publication?

Paper written on Wiki

References to papers, blog posts, lab notebook pages, raw

data

Paper on Journal of Visualized Experiments (JoVE)

Pre-print on Nature Precedings

ChemSpider Automated Mark-up of Chemical Names

BUT…

Open Access: the Choice that Keeps Giving.. and Giving…

Beware of your addiction to metrics: redundancy will reduce

them

Cameron Neylon’s NotebooksCameron Neylon’s Notebooks

Other Open NotebooksOther Open Notebooks

Anthony Salvagno’s Notebook Anthony Salvagno’s Notebook (Steve Koch group)(Steve Koch group)

Archiving Open Notebook Science Projects

What is the role of the librarians, researchers and other parties?

What are options for citing?

Librarians and Science 2.0"The Internet Archive is a 501(c)(3) non-profit that was founded to build an Internet library, with the purpose of offering permanent access for researchers, historians, and scholars to historical collections that exist in digital format."

The internet Archive is not practical for practitioners of 

Open Notebook Science or 

Science 2.0 

Good concept but.....

Most pages look like this....

Where We Began: The ONS backup spreadsheet and ONSPreserver

Publishing Google Spreadsheets as XLS

Where We Are Now

ONSArchive: Semi-Automated Snapshot of the Entire Scientific Record

Snapshot is Self-Contained and Live on the Internet

Lulu.com Data Disks

DSpace – Handle (hdl)

Lulu.com - ISBN

Google Spreadsheet

s

Google Documents

Web Services

ChemSpider & Indiana

Real Time Linear Regression, Unit

Conversions, Style Sheet, etc

Data Book

Bradley, Jean-Claude; Lang Andrew. Solubilities Summary Sheet. Open Notebook Science Challenge. 2009-12-11. URL:http://spreadsheets.google.com/pub?key=plwwufp30hfq0udnEmRD1aQ&output=xls. Accessed: 2009-12-11. (Archived by WebCite® at http://www.webcitation.org/5lx5ry3BV)

Book Editions on Nature Precedings

More about the ONSarchive project:

1) Accept that reporting science in real time is not always pretty. Do your best to avoid and correct mistakes as soon as possible but mistakes and ambiguous results will happen on the way to completing any scientific project. Just be honest about your level of certainty when discussing preliminary results.

2) Provide as much raw data as is reasonable and frame it in such a way that other researchers can understand what you have done and follow your conclusions based on your data without having to ask you questions.

3) Don't wait for the perfect technological solutions before starting to share. General purpose wikis can serve as an excellent starting point for an Open Lab Notebook.

4) Don't wait for the perfect data structuring scheme before starting to share. First share for human readability - you can always restructure the data later for machine readability.

Open Notebook Science Tips - I

5) Periodically write summaries of your research progress in the form of milestones or significant challenges in a format that non-specialists can understand. A blog is a good platform for this. If you link to specific lab notebook pages from your summaries, experts can always click through to dig deeper.

6) Create snapshot archives of your notebooks and supporting raw data files. You can use these as backups and as a convenient way to cite a particular version of your entire research project.

7) Cite specific lab notebook pages and archives when publishing in peer-reviewed journals.

Open Notebook Science Tips - II