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AMS 500, Responsible Conduct of Research and Scholarship (RCRS)
This course is designed to introduce students to the major issues in the ethics of science and research. Using a combination of readings - written and web-based - videos, and case discussion, students will investigate the moral values intrinsic to science and the professional and social values with which scientists must comply. Each class will begin with an introductory lecture or video followed by discipline-based, small group discussions with the participation of an AMS faculty member.

0 credits, S/U grading

Effective Fall 2013 Semester: This course will be offered in Fall and Spring semesters

Stony Brook University Policy P211: Responsible Conduct of Research and Scholarship (RCRS) ( requires that all faculty, graduate students, and post-docs complete the on-line training in RCRS. In addition, all faculty, Ph.D. students, M.S. students supported on research grants, and post-docs must also complete an in-person training in RCRS.  AMS 500 is the mechanism to satisfy this requirement for members of the Department of Applied Mathematics and Statistics.

AMS Ph.D. students, supported M.S. students, and post docs must take this course once each 4 years while at SBU. Faculty satisfy the requirement by teaching all modules of the course, accumulating 2 hours of module teaching each year. Attendance is required and reported to the Research Foundation.  Note that graduate students and post-docs in Computational Biology should take the spring semester of AMS 532 instead of AMS 500 to fulfill the in-person training of RCRS. 

Class Schedule
FALL 2023

AMS 500 - T01; WEDNESDAY, 1:00 - 1:55PM 

Class Meeting Faculty Week Location
August 30, 2023 Joseph Mitchell 1 Remote
September 6, 2023 Song Wu
Wei Zhu
2 Remote
September 13, 2023 Pawel Polak
Stan Uryasev
3 Remote
September 20, 2023 Haipeng Xing
Yan Yu
4 Remote
September 27, 2023 Eugene Feinberg
Roman Samulyak
5 Remote
October 4, 2023 Xiangmin Jiao
PeiFen Kuan
6 Remote
October 11, 2023 James Glimm
Hyunkyung Lim
7 Remote
October 18, 2023 Jiaqiao Hu
Xiaolin Li
8 Remote
October 25, 2023 Yuefan Deng
Evangelos Coutsias
9 Remote
November 1, 2023 NO CLASS Makeup Remote
November 8, 2023 NO CLASS   Remote
November 15, 2023 NO CLASS   ----
November 22, 2023 NO CLASS   ----


Class Syllabus


For weeks 2-9 the student must view the lecture and read the case study prior to coming to class.
Date Instructor Topic References
Week 1 Instructor #1 Additional requirements to fulfill RCRS training


  • View the Responsible Conduct of Research and Scholarship - Presentation given to department chairs by professor Michael Hadjiargyrou 2010.06.08_hadjiargyrou.pdf
  • Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at
  • Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics
Week 2 Instructor #2 Integrity in Scholarship (Introduction to Ethics and Science)

Readings (Nature articles)


  • Why is the class important?
  • How should we behave as scientists?
  • How is science a social enterprise?
Week 3 Instructor #3 Scientific Misconduct



  • From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?
  • From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?
  • How can the pressure to publish influence the conduct of research?
Week 4 Instructor #4 Mentoring



  • What qualities do you want in a mentor?
  • What are the challenges associated with being a mentor?
  • What does Professor Rubin mean when he says it is very important not to burn bridges?
Week 5 Instructor #5 Ownership and Authorship


Discussion (also from the above Columbia course)

  • Is it ever appropriate for authorship to change during a project or potential paper?
  • Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?
Week 6 Instructor #6 Plagiarism



  • Is plagiarism really that bad?
  • If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?
Week 7 Instructor #7 Data Management



  • From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?
  • From Case Study 2: Under what condition is copying allowed?
  • Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.
Week 8 Instructor #8 Journalism and Science

Readings (3 Case Studies)


  • From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?
  • From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?
  • From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly hospital which might violate patients privacy?
Week 9 Instructor #9 Responsible Conduct of Research Involving Human Subjects

Readings: (Background Information, Case Studies, Helsinki manuscript)


  • From Human Subjects handout, Background History: Why does the Helsinki Declaration limit the use of Placebo's?
  • From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?
  • From Helsinki manuscript: Do you agree with the authors that placebo-controlled trails are in many cases necessary ? Why ?


* Week 10 Instructor #10

* This will not be covered in AMS 500

Responsible Conduct of Research Involving Laboratory Animals

Readings (Case Studies)


  • From Case Study 1: What are some of the troublesome issues associated with this set of experiments?
  • From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?
  • From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?
  • From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?


Learning Outcomes:

1.) Ethics in using work of others; plagiarism. 
      * Proper citation, written permission, co-authorship; 
      * Restrictions on using ideas of others when reviewing grant proposals or journal submissions; 
      * When does lab director merit coauthor ship.

2.) Monitoring shortcomings in one's research. 
      * Do not pick and choose which data to use;
      * Acknowledging alternative interpretations;
      * Avoiding personal biases in project design;
      * Acknowledging negative results;
      * To wary of when pressure to publish and get grants cause ethical shortcuts.

3.) Ethical treatment of subjects.
      * Ethical choices of design, control group;
      * Working with campus Human/Animal Subjects committees

4.) Full disclosure of financial and familial conflicts of interest.
      * Conflict of interests with vested positions.

5.) Avenues for Reporting misconduct
      * How to report or seek advice about ethical concerns such as originality or conflict of interest