Peer Review and Science2.0


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Jean-Claude Bradley presents on "Peer Review and Science2.0: blogs, wikis and social networking sites" as a guest lecturer for the “Peer Review Culture in Scholarly Publication and Grantmaking” course at Drexel University. The main thrust of the presentation is that peer review alone is not capable of coping with the increasing flood of scientific information being generated and shared. Arguments are made to show that providing sufficient proof for scientific findings does scale and weakens the tragedy of the trusted source cascade.

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Peer Review and Science2.0

  1. 1. 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 Chemistry Drexel University
  2. 2. What Peer Review Does <ul><li>Provides authors with a publication format that counts in academia. </li></ul><ul><li>Assists editors to determine if the findings of an article are consistent with the data provided and commonly accepted scientific models. </li></ul><ul><li>Assists editors in attempting to provide a consistent style and focus for a particular journal. (not fundamental – see PLoS ONE) </li></ul>
  3. 3. What Peer Review does not do Verify the analysis of all the raw data supporting an article.
  4. 4. Even if peer-reviewing tried to take on the responsibility of verifying all the raw data, there are not enough resources to cope.
  5. 5. TRUST PROOF A solution that scales: Open Notebook Science
  6. 6. How bad is our current system? Try to find the solubility EGCG?
  7. 7. =2.3 g/L WTF?!
  8. 8. The End of the Chain of Provenance
  9. 9. The Tragedy of the Trusted Source Cascade
  10. 10. The NaH oxidation controversy
  11. 11. Information spreads quickly through the blogosphere
  12. 12. 15% NMR yield
  13. 14. Khalid Mirza and Marshall Moritz
  14. 16. Top results on a Google search
  15. 17. The Scandal of Bell’s Lab Notebook
  16. 18. Motivation: Faster Science, Better Science
  17. 19. Open Notebook Science Logos (Andy Lang, Shirley Wu) Sharing: how much and when
  18. 20. There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
  19. 21. The solubility of 4-chlorobenzaldehyde
  20. 22. The Log makes Assumptions Explicit
  21. 23. The Rationale of Findings Explicit
  22. 24. Raw Data Made Public Splatter? Some liquid
  23. 25. YouTube for demonstrating experimental set-up
  24. 26. Calculations Made Public on Google Spreadsheets
  25. 27. Revision History on Google Spreadsheets
  26. 28. Wiki Page History
  27. 29. Comparing Wiki Page Versions
  28. 30. Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX
  29. 31. Linking to Molecules in Chemistry Databases
  30. 32. Experimental Spectra and User-Deposited Data on ChemSpider
  31. 33. (Andy Lang, Tony Williams) Open Data JCAMP spectra for education (Andy Lang, Tony Williams, Robert Lancashire)
  32. 34. Database Curation via Game Playing
  33. 35. Over 100,000 spectrum views so far - worldwide
  34. 36. Link Spectral Game to Open Educational Content
  35. 37. The Ugi reaction: can we predict precipitation? Can we predict solubility in organic solvents?
  36. 38. Crowdsourcing Solubility Data
  37. 39. ONS Submeta Award Winners
  38. 40. ONS Challenge Judges
  39. 41. Teaching Lab: Brent Friesen (Dominican University)
  40. 42. Solubility Experiment List
  41. 43. Solubilities collected in a Google Spreadsheet
  42. 44. Rajarshi Guha’s Live Web Query using Google Viz API
  43. 45. WE ARE HERE How can the scientific process become more automated?
  44. 46. Semi-Automated Measurement of solubility via web service analysis of JCAMP-DX files (Andy Lang)
  45. 47. Solubility Measurement Requests: DoSol sheet <ul><li>Outlier Bot: flags measurements with high standard deviation to mean ratios </li></ul><ul><li>Google Analytics queries – new solvent/solute searches </li></ul><ul><li>Solubility request form – researcher in Israel requesting pyrene in acetonitrile solubility for environmental soil contamination study </li></ul><ul><li>Application based models – high priority Ugi reactants </li></ul>
  46. 48. Solubility Prediction (Andy Lang’s Model)
  47. 49. Understanding in addition to empirical modeling Missed in a prior publication on solubility for this compound
  48. 50. Data provenance: From Wikipedia to…
  49. 51. … the lab notebook and raw data
  50. 52. Including links to the literature
  51. 53. <ul><li>Concentration (0.4, 0.2, 0.07 M) </li></ul><ul><li>Solvent (methanol, ethanol, acetonitrile, THF) </li></ul><ul><li>Excess of some reagents (1.2 eq.) </li></ul>How does Open Notebook Science fit with traditional publication?
  52. 54. Paper written on Wiki
  53. 55. References to papers, blog posts, lab notebook pages, raw data
  54. 56. Paper on Journal of Visualized Experiments (JoVE)
  55. 57. Pre-print on Nature Precedings
  56. 58. ChemSpider Automated Mark-up of Chemical Names
  57. 59. BUT… Open Access: the Choice that Keeps Giving.. and Giving…
  58. 60. Beware of your addiction to metrics: redundancy will reduce them
  59. 61. Cameron Neylon’s Notebooks Other Open Notebooks
  60. 62. Anthony Salvagno’s Notebook (Steve Koch group)
  61. 63. Archiving Open Notebook Science Projects What is the role of the librarians, researchers and other parties? What are options for citing?
  62. 64. Librarians and Science 2.0 &quot;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.&quot; The internet Archive is not practical for practitioners of  Open Notebook Science  or  Science 2.0 
  63. 65. Good concept but.....
  64. 66. Most pages look like this....
  65. 67. Where We Began: The ONS backup spreadsheet and ONSPreserver
  66. 68. Publishing Google Spreadsheets as XLS
  67. 69. Where We Are Now
  68. 70. ONSArchive: Semi-Automated Snapshot of the Entire Scientific Record
  69. 71. Snapshot is Self-Contained and Live on the Internet
  70. 72. Data Disks
  71. 73. DSpace – Handle (hdl)
  72. 74. - ISBN Google Spreadsheets Google Documents Web Services ChemSpider & Indiana Real Time Linear Regression, Unit Conversions, Style Sheet, etc Data Book
  73. 77. Bradley, Jean-Claude; Lang Andrew. Solubilities Summary Sheet. Open Notebook Science Challenge. 2009-12-11. URL: Accessed: 2009-12-11. (Archived by WebCite® at )
  74. 78. Book Editions on Nature Precedings
  75. 79. More about the ONSarchive project:
  76. 80. 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
  77. 81. 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