Advanced Topics in Marine Biology (BIOL 404)

Lecture Syllabus and Schedule

Fall 2017

Lectures/Discussions: TTh 9:00 - 10:15, Gartley Hall, Room 102 

Course Instructor:
Dr. Timothy C. Tricas, Professor, Department of Biology, Biomed A208
Phone: 956-8677, email:
Office hours: TTh 11:00-12:00, or by appointment

Teaching Assistant:
Chelsie Counsell,
Office hours: Sinclair Library, T 10.30-1:00, or by appointment

Course Overview:
This course will explore the great breadth of research and activities conducted by marine biologists in Hawaii.  We will hear presentations from experts in various subdisciplines, ranging from microbes to vertebrates, from taxonomy to global system science, and related professional/educational fields.  Most speakers will have a geographical focus on the Hawaiian Islands and the broader oceanic realm.  This course is Writing Intensive (WI), meaning that a substantial amount of written material is expected.  We will also work to develop your oral communication skills each week of the semester.

Course assignments:
Seminars - Tuesday mornings are reserved primarily for guest speakers. You will be assigned readings in advance which will prepare you for the topic of the lecture. You will then participate and be graded on your oral contributions to the question and answer period after each seminar.

Roundtable Discussions - On Thursday mornings, the class will prepare and conduct a “roundtable” discussion on the assigned readings, in the context of the presentation material from the previous class. Discussions are led by two students who will give a brief 5-10 minute summary of the assigned readings. Discussion leaders should be prepared to 1) query their class members to identify the specific scientific hypotheses presented in each paper, 2) challenge their classmates with questions that can stimulate a scientific debate, 3) be prepared to answer any technical questions on the readings that the class can not answer, and 4) help pace the discussion period so that all reading material is covered.

All other class members are expected to understand the assigned papers in detail, prepare questions and their scientific opinions, and communicate them to the class. See the document 'HOW TO LEAD AND PARTICIPATE IN A DISCUSSION' on Laulima for important details.

Note that 25% of your grade is based on your discussion and oral contributions on both days. Thus, it is important that you prepare, attend and participate actively in all classes.

Essay assignments - Students will prepare and submit four written essays (500 words each) that summarize the scientific merit of one week’s lecture/reading material. Essay subjects are clustered into four groups (choose 1 of 3 lectures in each group, see schedule). The essays will be graded on their scientific rigor, the logic of your arguments and grammar. More details on these assignments will be given in class, and see the document 'HOW TO WRITE A SCIENTIFIC ESSAY' on Laulima. Essays (in Word document format – no pdfs!) must be submitted by email to by Sunday night in the class schedule.

Research paper - The second writing assignment is a 1500 word minimum (6 page) research paper. These papers are to address a current topic in marine biology that has been approved by the instructor. Papers must address an important scientific question and your thesis/arguments supported by citations from the primary literature (not websites or blogs). A draft of the research paper is submitted for review and comments from the instructors, and is then returned to the student for further editing and improvement of the final version. The draft and final papers are graded for scientific rigor, logic and grammar. More details on these assignments will be given in class, and see the document 'SEMESTER RESEARCH AND GRFP PAPER' on Laulima. All writing assignments must be submitted as Word documents and emailed to by the deadlines in the class schedule.

Oral presentations - The last few weeks of the class are devoted to student presentations. You will give a professional oral presentation to the class on the topic of your research paper, and address questions from the class. More details will be given in class.

Course materials:
There is no required textbook for this course. All reading materials can be downloaded on the class site at Laulima: in Resource folder ‘BIOL-404-001’.

As detailed above, your grade will be determined by a collection of written and oral communicaiton assignments. The weightings are provided below. Final grades for the class are not curved: 90-100% = A, 80-89% = B, 70-79% = C, 60-69% = D, < 60% = F.


Grading schedule
4 Research Lecture Essays - 500 words each 100
Roundtable Discussions 100
Discussion Leader 25
Research Draft and Final Paper – 1500 words each 200
Oral Presentation 75
Total   500


Code of Conduct:
You are expected to abide by the University of Hawai'i Student Code of Conduct at all times ( All written work must be independent and original. You are responsible for any material covered during missed classes. Discussion participation grades cannot be made up for missed classes. Incomplete grades will not be assigned for this course.

Notes on Due Dates:
All written assignments must be received by their respective due dates for full credit eligibility. Receipt of an assignment after its due date will result in an automatic 20% point penalty per day, provided the assignment is submitted within one week of the due date. An assignment received more than five days after its due date will not be accepted and you will not receive any points for that assignment. This policy is intended to encourage you to plan ahead and to keep in mind the likely possibility of power outages, laptop crashes, etc. These inconveniences may be beyond your control, but are not valid reasons for turning work in back up your work often! We promise, too, to abide by deadlines, returning graded work promptly.

Student Learning Outcomes for BIOL 404 - Advanced Topics in Marine Biology:
By the completion of this course, you will be able to:

(1) explain numerous marine biological processes, including examples from Hawai ‘i. [Biological Knowledge: Synthesis and Application]

(2) demonstrate scientific literacy in marine biology by critically evaluating scientific evidence, identifying gaps in knowledge, and/or applying strong evidence-based biological arguments to real-world problems. [Critical Thinking and Reasoning Skills]

(3) apply the scientific method to marine biological problems to generate new hypotheses, formulate experimental approaches, and/or outline potential outcomes, applying logical and/or quantitative methods. [Critical Thinking and Reasoning Skills]

(4) demonstrate inquisitiveness and respect for the marine biological world. [Values]

(5) work ethically both as an individual and/or in teams, and demonstrate respect for a diversity of viewpoints. [Values]

(6) communicate marine biological information in written and oral form clearly and professionally. [Communication Skills]


Class Schedule
(rev 10-24-2017)

Week Date   Class Topic Papers Introduction/Discussion Leaders Assignments Due
1 Aug 22 Introduction - Students, course goals and expectations, hypothesis testing
24 Analysis of a scientific paper van Oppen et al. 2015 Class Sunday: Newspaper article (250 words)
2 29

Dr. Camilo Mora, Department of Geography, UHM, "We Punch Nature and It Will Punch Us Back: Human Impacts on Biodiversity and Their Feedback on People"

Cinner et al. 2016
Sweetman et al. 2017
 Phillipe Nicodemus
Alexa Gonzalez 
31 Discussion    "  
3 Sept 5 Dr. Bob Richmond, Director, Kewalo Marine Laboratory, "Coral Reefs, Climate Change and Atomic Bombs" Richmond et al. 2007
Richmond 2014
Amy Peterson
Sabrina Medina
7 Discussion   "  
4 12 Dr. Petra Lenz, Pacific Biosciences Reserch Center, "Predator-prey interactions in the plankton: copepods and larval fishes"

Peterson et al. 2014
Jackson and Lenz 2016

Kaitlin Scowen
Kalene Rogers
14 Discussion   " Sunday: Essay 1 due
5 19 Dr. Andrew Rossiter, Director, Waikiki Aquarium, “Waikiki Aquarium: Past, present and future” Sato 1986
Newman 1994
Brunner 2005
Moss et al. 2015
Rachel Ouye
Karla Balagso
21 Discussion   " Sunday: Declare research topic

6 26 Dr. Brian Bowen, Hawaii Institute of Marine Biology, "Phylogeography, Biogeography, and the Origins of Indo-Pacific Reef Fishes" Bowen et al. 2013
Bowen et al. 2016
Rachel Cox
Caitlin Manley
28 Discussion   " Friday: Finalize research topic
7 Oct 3 Dr. Melanie Hutchinson, NOAA, "Sharks and fisheries; designing studies to reduce mortality and inform conservation management" Rice and Harley 2013
Hutchinson et al. 2015
Moore et al. 2015
Louise Currie
Yuuki Niimi
5 Discussion   " Sunday: Essay 2 due
8 10 Dr. Eric Conklin, The Nature Conservancy, "Improving the Resilience of Reefs in Hawai‘i" Friedlander et al. 2017
Maynard et al. 2016
Alexander Lee
Alina Allen
12 Discussion   "  
9 17 Mark Heckman, Education Specialist, Hawaii Institute of Marine Biology, "Science and Education" Falk and Dierking 1997
Ballantyne et al. 2011
Chelsea Nolen
Travis Weaver
19 Discussion   "  
10 24 Dr. Randy Kosaki, Deputy Superintendent, Research and Field Operations, NOAA, "Mesophotic Coral Ecosystems: New Frontiers for Exploration in the Northwestern Hawaiian Islands" Semmler et al. 2016
Bongaerts et al. 2017

Sarah Albright
Jeremy Gasta
26 Discussion   " Sunday: Essay 3 due
11 31 Dr. Kelvin Gorospe and Paula Ayotte, NOAA, PIFSC, Coral Reef Ecosystem Division, "Coral Reef Ecosystem Monitoring for Science and Management: Current Research Directions and Career Paths" Williams et al. 2015
Gray et al. 2016
Alina Allen
Rachel Ouye
Nov 2 Discussion   "
12 7 Anke Kuegler, Marine Biology Graduate Program, "Ecology and acoustics of humpback whales in Hawaii" Herman et al. 2013
Noad et al. 2017
Jeremy Gasta
Caitlin Manley
9 Discussion   " Sunday: Draft of research paper due
13 14 Dr. Rosie Alegado, Department of Oceanography, UHM, "Marine microbe ecology" Biller et al. 2014
Lynch and Alegado 2017
Phillipe Nicodemus
Karla Balagso
16 Discussion   "

Sunday: Essay 4 due

14 21 Consultation on Research Papers/Presentations
23 Holiday
15 28 Presentation Day 1
30 Presentation Day 2
16 Dec 5 Presentation Day 3
7 Presentation Day 4 Sunday: Submit final research paper


December 18, 2017

Dear BIOL 404 Students: Below are the scores for your presenation and paper, and final grade for the course. You were a great class and showed substantial development in your ability for science-based argumentation.....keep up the good work and best of luck in your future endeavors in marine biology!

All the Best and Aloha, Dr. Tricas and Ms. Counsell


Oral Presentation
(75 pts)
Final Paper/GRFP
(100 points)
Final Course Grade