Biological Oceanography: OCNG 620

Syllabus and Course Synopsis for Spring 2008

Tues 1/15: I'll overview topics, course organization, and I'll give selected examples of how our understanding of biological processes has proceeded. General topic of this 1st week of class is "Special Properties Affecting Life in the Sea".

• read the first three sections 1.1, 1.2 & 1.3 in the 15-page PDF file that's on e-reserves (from the supplemental text by Lalli & Parsons, 2nd ed, 1997). Skim/read these three sections before class begins, if possible.
• I'll assign Hmwk#1; this is due before next class begins on 17 Jan.

Thurs 1/17: I'll continue with selected history of biological oceanography -- we'll see how 19th Century expeditions explored "The Edge of An Unfamiliar World"

• read sections 1.4 & 1.5 in the PDF file from Lalli & Parsons that's on e-reserves.
• I'll assign Hmwk#2; this is due before next clas begins on 22 Jan.

2nd Week: Week of 21 January :

Tues 1/22: Forcing Functions: Light, Temperature, & Salinity

• read sections 2.1, 2.2 & 2.3 from Lalli & Parsons (1997) before class, if possible.
• I'll assign Hmwk#3; this is due 24 Jan.

Thur 1/24: More Forcing Functions: Density, Pressure, & Currents

• read sections 2.4, 2.5 & 2.6 from Lalli & Parsons (1997)
• and I'll introduce Biology in the Physical Vernacular -- read section 2.7 in Lalli & Parsons (1997) on e-reserves and also the paper by Mackas et al (1985) on e-reserves.
• I'll assign Hmwk#4; this is due 29 Jan.

3rd Week: Week of 28 January :

Tues 1/29: The Spring Phytoplankton Bloom

• read Miller, Chapter 1
• I'll assign Hmwk#5; this is due 31 Jan.

Thurs 1/31: The Microbial Loop

• read Miller, Chapter 5)
• I'll assign Hmwk#6; email this to reach me before class begins on 5 Feb.
• I'll distribute Take-Home EXAM #1 for you to work on while I'm gone next week; exam is due when class begins on 12 Feb.

4th Week: Week of 4 February : I'll be out of town this week.  I've invited two collegues to give guest lectures:

Tues 2/5: The Phycology of Phytoplankton

• read Miller, Chapter 2: I've requested a guest lecture by Dr. Lisa Campbell

Thur 2/7: Habitat Determinants of Primary Production in the Sea

• read Miller, Chapter 3: I've requested a guest lecture via TTVN from TAMUG by Dr. Rainer Amon

5th Week: Week of 11 February :

Tues 2/12: Global Phytoplankton Productivity

• read sections 3.6 & 3.7 from Lalli & Parsons (1997) in the PDF file on e-reserves
• I'll assign Hmwk#7; this is due 2/16.

Thur 2/14: Remote Sensing of Ocean Color Climatology from Space

• you'll read some papers from the primary literature by Muller-Karger and others that I'll put on e-reserves
• we'll look at CZCS, SeaWiFS, and MODIS websit3es that are hosted by USF Institute for Marine Remote Sensing.

6th Week: Week of 18 February :

• Tues 2/19: The Zoology of Zooplankton (read Miller, Chapter 6)
• Thur 2/21: Biogeography of Pelagic Habitats (read Miller, Chapter 9)
• 2/21: I'll distribute Take-Home EXAM #2; this is due 4 March

7th Week: Week of 25 February :

Tues 2/26: Biome and Province Analysis

• read Miller, Chapter 10

Thur 2/28: Production Ecology & Population Biology of Zooplankton

• read Miller, Chapters 7 & 8

8th Week: Week of 3 March :

Tues 3/4: Food Chains and Food Webs

• I'll put supplemental stuff on e-reserves
• I'll assign Hmwk#8, due 6 March.

Thurs 3/6: Numerical Models: The Standard Form of Theory in Pelagic Ecology

• read Miller, Chapter 4
• I'll assign replacement Hmwk#6, due 18 March

9th Week: Week of 10 March: yippee no class (Spring Break)

10th Week: Week of 17 March :

Tues 3/18: Fisheries Oceanography and Mariculture

• read Miller, Chapter 15
• I'll assign Hmwk#9, due 20 March

Thurs 3/20: Ocean Ecology and Global Climate Change

• read Miller, Chapter 16

11th Week: Week of 24 March :

Tues 3/25: Fauna of Deep Sea Sediments

• read Miller, Chapter 12
• I'll assign Hmwk#10, due 27 March.

Thurs 3/27: Benthic Community Ecology

• read Miller, Chapter 13)
• I'll distribute Take-Home EXAM #3; this is due 10 April

12th Week: Week of 31 March :

Tues 4/1: Overview of Port Aransas and Corpus Christi Bay

• I'll put PDF materials on e-reserves

Thurs 4/3: Special-Case Benthic Environments: Coral Reefs

• After class ends on 3 April, vans will take OCNG-620 and OCNG-420 students who wish to participate in an optional field trip to Port Aransas.  See "Optional Field Trips" for more information about this opportunity.

13th Week: Week of 7 April:

Tues 4/8: Pelagic-Benthic Coupling

• I'll put PDF materials on e-reserves; also skim Miller, Chapter 11

Thurs 4/10: Special-Case Benthic Environments: Hot Vents and Cold Seeps

• read Miller, Chapter 14

14th Week: Week of 14 April :

Workshop on Human Impacts and the Biological Health of the Ocean: Critical discussion of the Pew Foundation Oceans Commission Report (2003) and US Ocean Commission Report (2004): Four of you will be presenting on aspects of the recommendations of one or both Commission Reports on Tuesday 4/15 and four of you on Thursday 4/17.

15th Week: Week of 21 April:

Workshop (continued) on Human Impacts and the Biological Health of the Ocean: Critical discussion of the Pew Foundation Oceans Commission Report (2003) and US Ocean Commission Report (2004): Four of you will be presenting on aspects of the recommendations of one or both Commission Reports on Tuesday 4/22 and four of you on Thursday 4/24.

Dead Week (Week of 28 April):

On Tues 29 April, there will be a group discussion meeting that can serve as a review session in lieu of regular class.

The FINAL EXAM is scheduled for 1-3 PM on Monday 5 May. This will be a two-hour, in class, closed book and closed notes exam. Review questions/answers to exams 1-3 to study for this exam; see also Final Exam from Spring 2006 that I will put on e-reserves.

ATTENDANCE: I expect you to come to class when you're not away on university business. If you know you will be at sea or at a meeting or on other university business travel especially during any week in which a take-home exam is distributed, please let me know at least 2 weeks before you plan to leave and I'll work with you to allow you to take the exam earlier or later.

GRADING: Your grade will be based on the numerical average of your scores on the three take-home exams (each counts 15% of your semester average), your scores on homework problems (which together count 20%) and on your presentation of an aspect of the Oceans Commission reports (which counts 15%), and your score on the Final Exam (which counts 20% of your semester average).

HOMEWORK: You'll use data collected on R/V Gyre Training & Research cruises, or other field programs, to calculate mixed layer depth versus compensation depth versus critical depth; extinction coefficient; specific growth rate; grazing rate; diversity; etc, etc. You'll do ten hmwk problem sets over the course of the 15 week semester. You can send me your answers to these questions by email .

OPTIONAL FIELD TRIP:  Grad students taking OCNG-620 and undergrads taking OCNG-420 will have the opportunity to go on an optional field trip to Port Aransas TX, to get out on UT small boat for "hands on" biological collecting in Corpus Christi Bay.  Dates for this combined class optional trip to Port Aransas are 3-5 April.  We'll drive to Port Aransas the afternoon of 3 April and go out for 4 hours of collecting in the area around Port Aransas on UT-MSI vessel "Katy", on the afternoon of Friday 4 April. We'll return on Saturday 5 April.

TEXTBOOK: Biological Oceanography, by C. B. Miller (2004; Blackwell Publishing; paper, 402 pp.)

For my lectures, I'll supplement your text with material from scientific journals and from nine supplemental reference texts:

• Connell, S.D., and D.M. Gillanders (editors). 2007. Marine Ecology. Oxford University Press. 630 pp. [QH541.5/S3/C62/2007]
• Robinson, A.R., J.J. McCarthy, and B.J. Rothschild (editors). 2002. Biological-Physical Interactions in the Sea. The Sea, Volume 12. [GC11/S4/v.12/2002].
• Bertness, M.D., S.D. Gaines, and M.E. Hay. 2001. Marine Community Ecology. Sinauer Associates, Inc. 550 pp. [QH541.5/S3/M256/2001].
• Longhurst, A. 1998. Ecological Geography of the Sea . Academic Press. 398 pp. [QH541.5/S3/L66/1998].
• Lalli, C.M., and T.R. Parsons. 1997. Biological Oceanography, An Introduction (2nd edition). The Open University. 314 pp. [I've put the 1st edition, QH91/L35/1993, as well as the 2nd edition, QH91/L35/1997, on reserve]; I've also copied the first two chapters of the 2nd edition of this undergraduate textbook for you to read on e-reserves.
• Valiela, I. 1995. Marine Ecological Processes, 2nd ed. Springer-Verlag. 686 pp, hardback [QH541.5/S3/V34/1995]. A 3rd edition is anticipated sometime this year 2008.
• Jumars, P.A. 1993. Concepts in Biological Oceanography . Oxford University Press. 348 pp, hardback [QH541.5/S3/J85/1993].
• Mann, K.H., and J.R.N. Lazier. 1991. Dynamics of Marine Ecosystems: Biological-Physical Interactions in the Oceans. Blackwell Scientific Publications, paperback, 466 pages. [QH541.5/S3/M25/1991]. NOTE: a 3rd edition was published lin 2006 and I've requested this 3rd edition be put on reserve when available, to supplement the 1996 edition.
• Parsons, T.R., M. Takahashi, and B. Hargrave. 1984. Biological Oceanographic Processes, 3rd ed. Pergamon Press. 330 pp {QH/541.5/S3/P37/1984].

I will put the Evans Library's copy of Miller (QH541.5/S3/M55/2004) on reserve as soon as it gets returned by borrower who had it over winter break and I've put copies of each of the supplemental texts on reserve as well, in the 2nd floor Course Reserves area. These reference books are on 4 h check out; these reference books are shelved there by call number.

WORKSHOP TOPIC: Each of you will have the opportunity to select one of the topic areas which constitute "Human Impacts on Biological Communities" as you summarize one or more of the recommendations of the Pew Oceans Commission Reportand/or US Ocean Commission Report for oral presentation to the class during the weeks of 14 April and 21 April. You'll each give a 13 minute (AGU or ASLO style) oral presentation, after which each of you should be prepared to respond to follow up questions from me or from your fellow students.

You'll summarize this oral presentation by turning in a 2 page written synopsis of your topic.

Please remember the University's policy on plagarism as you prepare your oral and writen synopses, and as you work on take-home exams:

Plagarism is passing off as your ideas the ideas, words, and writings which belong to another. You commit plagarism if you copy the work of another and turn it in as your own without acknowledging (referencing) the source of the material. Plagarism is one of the worst academic sins, for a plagarist destroys the trust among colleagues without which research cannot be safely communicated.

COPYRIGHT:  All materials generated for this class, which include but are not limited to this syllabus, outlines and notes that you can link to using this syllabus, powerpoint lectures on e-reserves, and exams, are copyrighted.  You do not have the right to  redistribute  any of these unless I expressly grant permission.

ADA STATEMENT: The Americans with Disabilities Act (ADA) is a federal anti-discrimination statute that provides comprehensive civil rights protection for persons with disabilities. Among other things, this legislation requires that all students with disabilities be guaranteed a learning environment that provides for reasonable accommodation of their disabilities. If you believe you have a disability requiring an accommodation, please contact the Department of Student Life, Services for Students with Disabilities in Room 126 of the Koldus Building. The phone number is 845-1637.

ACADEMIC HONESTY: Aggie Honor Code
Students in this class are expected to abide by the honor code: cheating will be penalized by loss of points or worse, in accordance with the University policies. The Honor Code, based on the long-standing affirmation that "An Aggie does not lie, cheat, or steal, or tolerate those who do", is fundamental to the value of the A&M experience. Know the Code!