Course Details

Course Materials

Required Textbook: Coral Reefs in the Microbial Seas, by Forest Rohwer, 2010. Additional materials will be provided and include textbook chapters, current journal publications, rock and fossil specimens. Assigned materials will be available through the EAS E-341 Canvas site, and various websites.

Objectives of the Course

We will analyze and synthesize the ecologic and environmental context for long-term biotic associations in the reef ecosystem. By the semester’s end you will have up-to-date knowledge on the state of reefs through their natural geologic history to the present day, with scientific backing for predictions of future reef scenarios. The semester’s focus will be on developing critical thinking skills to augment your classroom learning and, if appropriate, your broader research objectives. Your writing goal will be to integrate concepts learned during the semester into your homework assignments, in-class exercises, and examination responses.

Lecture, in-class small group exercises, class discussions, videos, fossil samples, identification keys, and data from targeted websites and journal readings will comprise our course meetings. As will become clear during the semester, both writing and speaking skills will be sharpened. Bloom’s Taxonomy of Learning is an invaluable guide for tracking your progress from memorization through synthesis and evaluation of scientific material. Learning objectives will be assessed through a mid-term examination, coral identification examinations, in-class exercises and presentations, homework assignments, a scientific reflection using the scientific method, and a final comprehensive examination.

Student Learning Outcomes, CASE N&M Breadth of Inquiry

By the end of this course on the Natural History of Coral Reefs, you should be able to:

  1. Provide an understanding of physical, chemical, and biological factors affecting reef ecosystems
  2. Apply the scientific method to an investigation of reef evolution, and modern reef demise
  3. Present a review of the state-of-the-science related to reef ecosystem patterns and processes, and evidence supporting and refuting established hypotheses
  4. Establish the role and approaches of mathematics for reef ecosystem studies.

Assignment Due Dates and Make-up Work

  1. Assignments are due at the start of class OR at the date and time indicated on the weekly Agenda. Unexcused late assignments will not be given credit.
  2. Late work done under an excused absence is due within one week of original due date. Example of an excused absence is a doctor’s note or equivalent, and permission of professor.
  3. If you are participating in a university-sanctioned event, prior notification to professor and AI, and pre-approval by professor, are necessary to receive credit for late work. Assignments are due within one week of the original due date.

For extenced absences or any problems that affect your work, please check with professor and AI for assistance

Grading Policy, Major Assignments, Exam Dates

  1. 15%: 3 coral identification quizzes. Quiz dates are in the syllabus.
  2. 45%: in-class exercises, presentations, and homework assignments
  3. 20%: mid-term exam, date March 17, 2023
  4. 20%: final comprehensive exam, date May 2, 2023

Final Grade Distribution: A=90-100; B=80-89; C=70-79; D-60-69; F=59 & lower; marks of + and − will be added to the letter grades as follows (− assigned to 0, 1, 2; + assigned to grades of 7, 8, or 9; e.g., 87%=B+, 61%=D− 74%=C). Class grades are not curved.

Disability Services for Students (DSS).

Accommodation for Disabilities: Every attempt will be made to accommodate qualified students with disabilities (e.g. mental health, learning, chronic health, physical, hearing, vision, neurological, etc.). You must have established your eligibility for support services through Disability Services for Students. Note that services are confidential, may take time to put into place, and are not retroactive. Please contact Disability Services for Students using the link below, or call us at 812-855-7578 as soon as possible if accommodations are needed.

The process to establish accommodations for a student with a disability is a responsibility shared by the student and the DSS Office. Only DSS approved accommodations should be utilized in the classroom. After the student has met with DSS, it is the student’s responsibility to share their  accommodations with the faculty member.

Go to the Student Affairs website

Mental health services

Mental health services offered by CAPS and other support services are available to students.  Contact the Dean of Students’ Office using the button below for information on where to find a wide range of support services.

Please check in with Dr. Johnson or our AIs at any time that you need help.  We are here to help you learn the course materials.   

Contact the Dean of Students

Code of Student Rights, Responsibilities, and Conduct

Academic Integrity: As a student at IU, you are expected to adhere to the standards and policies detailed in the Code of Student Rights, Responsibilities, and Conduct (Code).

Academic misconduct is defined as any activity that tends to undermine the academic integrity of the institution. Academic integrity violations include: cheating, fabrication, plagiarism, interference, violation of course rules, and facilitating academic dishonesty. When you submit an assignment with your name on it, you are signifying that the work contained therein is yours, unless otherwise cited or referenced. Any ideas or materials taken from another source must be fully acknowledged. Students should not share their work with any other students. If plagiarism or other cheating occurs, both students involved will be considered responsible even if the student sharing their work was unaware that academic misconduct would occur or had occurred. Ignorance of what constitutes academic misconduct or plagiarism is not a valid excuse. In addition, submitting content generated by another person or via an artificial intelligence program (such as ChatGPT, Google Translate, etc.), and posting questions from quizzes/exams or assignments or downloading answers from online sources are all considered academic misconduct. All suspected violations of the Code will be reported to the Dean of Students (Office of Student Conduct) and handled according to University policies. Sanctions for academic misconduct in this course may include a failing grade on the assignment, a reduction in your final course grade, or a failing grade in the course, among other possibilities. If you are unsure about the expectations for completing an assignment or taking a test or exam, be sure to seek clarification from your instructor in advance.

Students Needing Additional Financial or Other Assistance. The Student Advocates Office (SAO) can help students work through personal and academic problems as well as financial difficulties and concerns. SAO also assists students working through grade appeals and withdrawals from all classes. SAO also has emergency funds  for IU students experiencing emergency financial crisis. Contact the Student Advocates Office

Sexual Misconduct and Title IX
As your instructor, one of my responsibilities is to create a positive learning environment for all students. IU policy prohibits sexual misconduct in any form, including sexual harassment, sexual assault, stalking, sexual exploitation, and dating and domestic violence. If you have experienced sexual misconduct, or know someone who has, the University can help. If you are seeking help and would like to speak to someone confidentially, you can make an appointment with the IU Sexual Assault Crisis Services at (812) 855-5711, or contact a Confidential Victim Advocate at (812) 856-2469 or cva@indiana.edu.
It is also important that you know that University policy requires me to share certain information brought to my attention about potential sexual misconduct, with the campus Deputy Sexual Misconduct & Title IX Coordinator or the University Sexual Misconduct & Title IX Coordinator. In that event, those individuals will work to ensure that appropriate measures are taken and resources are made available. Protecting student privacy is of utmost concern, and information will only be shared with those that need to know to ensure the University can respond and assist. I encourage you to visit  https://stopsexualviolence.iu.edu/index.html  to learn more.

Bias-Based Incident Reporting. Bias-based incident reports can be made by students, faculty and staff. Any act of discrimination or harassment based on race, ethnicity, religious affiliation, gender, gender identity, sexual orientation or disability can be reported through any of the options: 1) email biasincident@indiana.edu or incident@indiana.edu; 2) call the Dean of Students Office at (812) 855-8188; or 3) use the IU mobile App (m.iu.edu).

Reports can be made anonymously at this link:
Report a bias-based incident


Boost. Indiana University has developed an app, “Boost” to help students stay on top of their schoolwork in Canvas. The app is free to all IU students, and it integrates with Canvas to provide reminders about deadlines and  other helpful notifications.
Get the Boost app

Re: Note Selling: Several commercial services have approached students regarding selling class notes/study guides to their classmates. Selling the instructor’s notes/study guides in this course is not permitted. Violations of this policy will be reported to the Dean of Students as academic misconduct (violation of course rules). Sanctions for academic misconduct may include a failing grade on the assignment for which the notes/study guides are being sold, a reduction in your final course grade, or a failing grade in the course, among other possibilities.

Additionally, you should know that selling a faculty member’s notes/study guides individually or on behalf of one of these services using IU email, or via Canvas may also constitute a violation of IU information technology and IU intellectual property policies and additional consequences may result.