Lec13 Scientific Papers and Communications


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Lec13 Scientific Papers and Communications

  1. 1. Scientific papers and communications. Phil 133 – Ethics in Science San José State University
  2. 2. Lecture overview: <ul><li>How does scientist-to-scientist communication fit into knowledge-building and scorekeeping? </li></ul><ul><li>Anatomy of a scientific paper </li></ul><ul><li>Peer review </li></ul><ul><li>Communication and credit </li></ul>
  3. 3. “ It’s not scientific knowledge if it stays in your notebook.” <ul><li>A crucial step in the scientific knowledge-building activity is communicating findings. </li></ul><ul><li>Norm of communism – shared body of knowledge as a resource for the whole tribe. </li></ul><ul><li>Those who paid for the research (e.g., the public) have an interest in seeing the results. </li></ul>
  4. 4. Articles in peer-reviewed journals as important mode of communication. <ul><li>Official reports of scientists to other scientists in their field. </li></ul><ul><li>Permanent record of the most recent findings. </li></ul><ul><li>“ The literature” with which scientists are supposed to keep up. </li></ul>
  5. 5. Dual nature of scientific publishing: <ul><li>Communicating important scientific information (including theories, techniques, findings) to other scientists. </li></ul><ul><li>How scientists “keep score”. (Priority for discovery; track-record for grant decisions and evaluation of job performance.) </li></ul>
  6. 6. What goes into a scientific paper? <ul><li>AUTHORS: </li></ul><ul><li>Who is responsible for the intellectual labor that led to these findings? (Institutional affiliations, contact information.) </li></ul><ul><li>Not just credit, but responsibility to be available for follow-up discussions around methods and results. </li></ul>
  7. 7. What goes into a scientific paper? <ul><li>INTRODUCTION: </li></ul><ul><li>A brief description of the question the present work answers, how the answer or the approach to the problem is new, and why is matters. </li></ul>
  8. 8. What goes into a scientific paper? <ul><li>BACKGROUND: </li></ul><ul><li>Crucial prior work on the system or problem investigated in the present work; </li></ul><ul><li>theoretical understanding; </li></ul><ul><li>empirical techniques others have used. </li></ul><ul><li>Citation of relevant published work. </li></ul>
  9. 9. What goes into a scientific paper? <ul><li>MATERIALS AND METHODS: </li></ul><ul><li>Detailed description of how to set up the system being studied, how measurements were made, etc. </li></ul><ul><li>Ideally, enough information that a reader could set up the experiment/study and replicate your results. </li></ul>
  10. 10. What goes into a scientific paper? <ul><li>DATA ANALYSIS: </li></ul><ul><li>Detailed description of how the raw data were analyzed, justification for these analyses rather than alternatives. </li></ul><ul><li>Relevant information about error bars, power analyses, etc. </li></ul>
  11. 11. What goes into a scientific paper? <ul><li>RESULTS: </li></ul><ul><li>What we observed. </li></ul><ul><li>Sometimes quantitative, sometimes qualitative. </li></ul><ul><li>Often includes graphs or images (e.g. of specimens, or gel separations) as well as numerical data. </li></ul>
  12. 12. What goes into a scientific paper? <ul><li>DISCUSSION: </li></ul><ul><li>What our results could mean. What issues are still not fully resolved. How future research could resolve those issues. </li></ul><ul><li>Nice to have evidence of some organized skepticism from authors here – dealing with weaknesses as well as strengths. </li></ul>
  13. 13. What goes into a scientific paper? <ul><li>CONCLUSION: </li></ul><ul><li>What we know after this research that we didn’t know before. </li></ul><ul><li>Understood to be tentative, but also supported (more than alternatives) by findings and the rest of what’s known from the literature. </li></ul>
  14. 14. What goes into a scientific paper? <ul><li>ACKNOWLEDGMENTS: </li></ul><ul><li>Who contributed essential labor to the research, or essential insights that guided the authors’ understanding of what they did, or vital reagents, or funding. </li></ul><ul><li>Contributions that don’t rise to level of authorship but are still important. </li></ul>
  15. 15. What goes into a scientific paper? <ul><li>REFERENCES: </li></ul><ul><li>Accurate and complete bibliographic information for the works cited. </li></ul><ul><li>Readers may need to be able to find them. </li></ul><ul><li>Should only cite sources you’ve actually read! </li></ul>
  16. 16. Is there something fraudulent about presenting results this way? <ul><li>“ The scientific paper in its orthodox form does embody a totally mistaken conception, even a travesty, of the nature of scientific thought.” </li></ul><ul><li>--P. B. Medawar, &quot;Is the Scientific Paper Fraudulent?&quot; Saturday Review , 1 August 1964, 42-43. </li></ul>
  17. 17. Medawar’s complaint: <ul><li>The format of the scientific paper suggests that research is more linear, predictable than it usually is in real life. </li></ul><ul><li>Medawar’s focus is on Results and Discussion. </li></ul>
  18. 18. Medawar’s complaint: <ul><li>“ The section called ‘results’ consists of a stream of factual information in which it is considered extremely bad form to discuss the significance of the results you are getting. You have to pretend that your mind is, so to speak, a virgin receptacle, an empty vessel, for information which floods into it from the external world for no reason which you yourself have revealed. ” </li></ul>
  19. 19. Medawar’s complaint: <ul><li>“ You reserve all appraisal of the scientific evidence until the ‘discussion’ section, and in the discussion you adopt the ludicrous pretense of asking yourself if the information you have collected actually means anything. ” </li></ul>
  20. 20. Medawar’s complaint: <ul><li>Obviously, the authors think the results mean something, or they wouldn’t publish them. </li></ul><ul><li>Something artificial about separating Results and Discussion. </li></ul>
  21. 21. Medawar’s complaint: <ul><li>“ What is wrong with the traditional form of the scientific paper is simply this: that all scientific work of an experimental or exploratory character starts with some expectation about the outcome of the inquiry. This expectation one starts with, this hypothesis one formulates, provides the initiative and incentive for the inquiry and governs its actual form.” </li></ul>
  22. 22. Medawar’s complaint: <ul><li>“ It is in the light of this expectation that some observations are held relevant and others not; that some methods are chosen, others discarded; that some experiments are done rather than others. It is only in the light of this prior expectation that the activities the scientist reports in his scientific papers really have any meaning at all.” </li></ul>
  23. 23. Medawar’s complaint: <ul><li>Not reading the conclusions straight off the empirical results. </li></ul><ul><li>What you measured, how you measured it, how you distinguished good data from noise, etc., connected to what you expected to see. </li></ul><ul><li>Pretending otherwise is assuming more objectivity than may be possible (at least without help from the community) </li></ul>
  24. 24. In defense of the scientific paper. <ul><li>Standardized format makes it easier for the scientists reading the papers to find the information they’re looking for. </li></ul><ul><li>Separate Discussion section recognizes that results are interpreted – and that others might interpret them differently. </li></ul>
  25. 25. Peer review. <ul><li>Before being published, scientific papers are evaluated by other scientists. </li></ul><ul><li>Pre-publication quality control: is this a reasonably well-supported scientific argument? </li></ul>
  26. 26. Peer reviewers may ask: <ul><li>Does this work discuss the relevant findings of other scientists in the field? </li></ul><ul><li>Sufficient detail on materials and methods? </li></ul><ul><li>Reasonable analysis of data? </li></ul><ul><li>Enough support for authors’ interpretations? </li></ul><ul><li>Further experiments, analyses required to resolve ambiguity? </li></ul><ul><li>Are these results important? </li></ul>
  27. 27. Peer reviewers generally can’t: <ul><li>Set up and replicate authors’ experimental system. </li></ul><ul><li>Recreate full analysis of raw data. </li></ul><ul><li>Detect fabricated results, images that look plausible. </li></ul>
  28. 28. Authors get reviews and respond. <ul><li>Sometimes major rewrites (or new data analyses, or additional experiments) are required to address critiques. </li></ul><ul><li>Sometimes authors can make persuasive arguments to journal editors that the reviewer’s critique is off-base. (Include that argument in paper or not?) </li></ul><ul><li>Sometimes send paper, unrevised, to a different journal. </li></ul>
  29. 29. Editors decide when peer review is done. <ul><li>Sometimes revisions undergo additional round of review. </li></ul><ul><li>Sometimes editor decided when article has addressed critiques sufficiently. </li></ul><ul><li>In some cases, editors may override normal peer review expectations (which can lead to problems). </li></ul>
  30. 30. Publication isn’t the last step. <ul><li>Once a paper is published, other scientists will discuss it. </li></ul><ul><li>Might disagree with it (and find convincing way to show the conclusion is wrong). </li></ul><ul><li>Might accept results but draw different conclusions from them. </li></ul><ul><li>Might contact authors for information on how to set up similar experiments. </li></ul><ul><li>Scientific literature as an ongoing discussion. </li></ul>
  31. 31. Dual purpose of scientific papers brings dual ethical considerations. <ul><li>Contributing to shared body of reliable knowledge about the world honesty </li></ul><ul><li>Keeping score for distribution of career rewards fairness </li></ul>
  32. 32. Dual purposes can make communication complicated. <ul><li>Tendency not to communicate negative results. But see Journal of Negative Results http://www.jnr-eeb.org/index.php/jnr http://www.jnrbm.com/ </li></ul><ul><li>Tendency to prejudge (and prioritize) importance of a finding. </li></ul>
  33. 33. Dual purposes can make communication complicated. <ul><li>Stretching meanings: </li></ul><ul><li>&quot;It has long been known&quot; = I don't know the original reference. </li></ul><ul><li>&quot;Typical results are shown&quot; Either means the only results are shown or the best results are shown. </li></ul><ul><li>&quot;A trend is evident&quot; Okay, a trend does seem apparent to me, but no statistical analysis in the world will support it. </li></ul><ul><li>(from http://chemistry.about.com/cs/chemists/a/researchpaper.htm) </li></ul>
  34. 34. Other modes of scientific communication: <ul><li>Presentations at professional conferences (talks, posters) </li></ul><ul><li>Presentations at department seminars </li></ul><ul><li>Discussions at group meeting </li></ul><ul><li>Private communications (letters, email, phone calls, chats at the bar) </li></ul><ul><li>Preprint depositories (e.g., arXiv) </li></ul><ul><li>Listservs, blogs </li></ul>
  35. 35. Other modes of scientific communication considered. <ul><li>How public? (Who can access, who’s left out?) </li></ul><ul><li>How official? (Enough to establish priority? Can someone else take your idea and run with it?) </li></ul><ul><li>How permanent or ephemeral? </li></ul><ul><li>How reliable? (Speaking carefully vs. handwaving or blowing off steam?) </li></ul><ul><li>Is it citable? </li></ul><ul><li>Does it count? </li></ul>
  36. 36. Dangers of free communication: <ul><li>You could get scooped. Case of Armando Córdova ( Chemical & Engineering News , March 12, 2007; Volume 85, Number 12, pp. 35-38 ) </li></ul><ul><li>You could violate policies of the journal where you want to publish. Slides of data on dark matter from PAMELA scientists photographed by data paparazzi ( Nature , September 2, 2008) </li></ul>
  37. 37. Problem: scientific work depends on effective and honest communication! <ul><li>How to set up conditions where scientists who communicate with each other don’t get punished by the reward system? </li></ul><ul><li>How to set up conditions where scientists are willing to share useful information? </li></ul>