Syllabus for Science 2.0

Course Outline:

This seminar will deal with some “big picture” topics in modern science. There are 12 topics that we’ll discuss (one per week). Each of you will be responsible for a moderately short (25-30 minute) presentation to the rest of the class on one of these topics. The order of assigned presentations was chosen at random. You may swap topics with one of your classmates, but please keep me informed of any swaps. The day before your assigned presentation, you’ll be expected to email a brief (1 page) abstract to the rest of the class.

Following each of the presentations, we’ll discuss how that topic bears on the work and interests of various “stakeholders” in the scientific enterprise. These roles include (but are not limited to): principal investigators (PIs), reviewers, funding agencies, members of the public, journal editors, graduate students, undergraduates, amateur scientists, and corporate researchers.

Your grades for this course will be based on the quality of your presentation (50%) as well as your contributions to the discussions of other topics (50%).

The course materials are posted on Sakai. The course page includes a set of URLs that link to a set of interesting essays, papers, blog posts, and online resources to get you started. These links should not be the only reading you do on these topics; they are just there to get you started on your research.


  1. What is Science? How is Science different from Research? What makes an explanation Scientific? Is science predictive? Is science “right” or just self-correcting? Why does it work so well? Why is reproducibility a good standard? Reproducible by whom? What is the reproducibility crisis?
  2. Publish or Perish: What goes in to a scientific publication? What doesn’t go in? What goes in supporting materials? What are the stages of publication? Why submit to one journal instead of another? Is it OK to use a paper as a chapter of your thesis? What is scooping?
  3. Peer review, preprint services (arXiv, ChemRxiv, biorxiv, institutional repositories), and post-publication peer review. The following equation appears to be true on YouTube comment streams:
    (poorly socialized individuals + anonymity + audience) = bad group behavior
    Is this necessarily true for scientific papers? How do you get honest feedback without anonymity?
  4. Supporting science: Grants, Funding models, industrial research and sustainability. Is popular science necessarily good science? Why were there so many Hydrogen storage grants in the 2000s? How is a grant different from a contract? What happened to Bell Labs? What is overhead? How much does a graduate student cost? How much does a paper cost to produce?
  5. Simulation, the third “leg” of science: Predictive weather and climate modeling has become very good in the past few years. Do computers change anything about science? Is there really a third leg? What does a simulation actually test? Do simulations of approximate models for chemicals teach us anything? If not, why do we do them?
  6. Big Data, the fourth “leg” of science: informatics, big data and other “-omics”. Do large data sets change anything about science? What can you learn from the statistics of a entries in a large data set like the protein data bank? What kind of discoveries have been made by proteomics, genomics, and other omics?
  7. Open Data: public science databases / accession IDs, data licenses, Does scientific data have copyright protection? What is CC0? Who owns scientific data? Machine readability & searching, Hierarchies vs. Annotation & Tagging.
  8. Open Source scientific software: licenses, advantages, disadvantages. Should you cite your plotting program? Should you trust your plotting program? Should you trust your quantum chemistry program? Who owns scientific code?
  9. Open Access Publishing (PLoS, PubMed Central). Copyright issues and The Journals vs. The Public. Who owns a scientific paper? Why don’t more scientists put their papers in PubMed Central? What is Sci-Hub? Is Sci-Hub ethical? Why are scientific publishers so profitable? Who pays for their raw goods and labor? Are scientific publishers behaving ethically?
  10. Scholarly metrics (h-index, citation count, publication count, journal impact factors). Can you measure quality of science, or just quantity? Who calculates impact factors? What is the formula? Why do we use it for measuring individuals?
  11. Conferences. What are they for? What goes into a conference presentation? What goes in to a poster? The danger of out-of-band conference communications. Examples of good talks. Examples of bad talks.
  12. Social networking for collaborative science. Why would a “Facebook for Science” be a good idea? Why would it be a bad idea? How much science is done on Twitter?

Stakeholder Roles:

  1. Principal Investigator (PI)
  2. Competing PI
  3. Skeptical reviewer
  4. Funding Agency
  5. Interested member of the public
  6. Professional Society journal editor
  7. For-profit publisher
  8. Graduate student in competing group
  9. Future graduate student in the same group
  10. Amateur / Public scientist
  11. University administrator
  12. Pharma or specialty chemicals researcher