Aquatic Ecology (BIOL 435)

Aquatic Ecology (BIOL 435)

Spring 2007

TR 9:20 – 10:35 PM

Lecture Room 107 MCB

Instructor: Matthew P. Hoch, Ph.D.E-mail:

Campus Phone: 4016Website:www2.yk.psu.edu/~mph13/

Office/Lab:Office Rm 131 MCB / Biology Lab Rm 124 MCB

Office Hours:MW 13:00 – 15:00, or by appointment

Required Textbook: Dodds. W.K., 2002.Freshwater Ecology: Concepts and Environmental Applications, 1st ed. Academic Press. 569 pgs.

Course Perspective:

Emphasis will be placed on the fundamentals of inland freshwater ecosystems. Topics cover physical processes related to water circulation and hydrology, the chemistry of inland waters and processes involved in nutrient cycling, the controls of biological productivity, and aquatic community interactions. Students will be exposed to field and laboratory protocols standardized by the US EPA and used by aquatic scientists at state agencies, private consulting firms, non-government conservation organizations, and academic researchers.

Lecture and Assignment Schedule:

Lecture # / Date / Topics / Assigned Chapter Reading†
1 / T, Jan 16 / Man and The Hydrologic Cycle / Ch 1
2 / R, Jan 18 / Aquatic Habitat Overview / ------
3 / T, Jan 23 / Properties of Water / Ch 2
4 / R, Jan 25 / Water Movement
5 / T, Jan 30 / Properties of Light in Water / Ch 3
6 / R, Feb 1 / Groundwater / Ch 4
7 / T, Feb 6 / Wetlands / Ch 4
8 / R, Feb 8 / Lake Origins and Morphometrics / Ch 6
9 / T, Feb 13 / Lake Circulation and Classification / Ch 5
EXAM 1 / R, Feb 15 (Monday)Covers content through Feb 13th, 2007.
Lecture and Assignment Schedule: (continued)
10 / T, Feb 20 / Stream Hydrodynamics / Ch 7
11 / R, Feb 22 / NSCD Restoration
12 / T, Feb 27 / Aquatic Decomposers / Ch 8
13 / R, Feb 29 / Aquatic Autotrophs / Ch 8
14 / T, Mar 6 / Aquatic Consumers / Ch 9
15 / R, Mar 8 / Aquatic Consumer (continued)
No classes Mar 13-15 / SPRING BREAK 2007
16 / T, Mar 20 / Biodiversity / Ch 10; part of 20
17 / R, Mar 22 / Aquatic Chemistry / partly of Ch 11
18 / T, Mar 27 / Aquatic Chemistry (continued) / Ch 12
19 / R, Mar 29 / Aquatic Element Cycling / Ch 13
EXAM 2 / T, Apr 3 Covers content through Mar 29th, 2007.
20 / R, Apr 5 / Primary Production / partly Ch 11; Ch 17
22 / T, Apr 10 / Nutrient Dynamics / Ch 16; partlyCh 20
23 / R, Apr 12 / Population Interactions / partly Ch 18; partly Ch 20
24 / T, Apr 17 / Stream Continuum Theory / Ch 22
25 / R, Apr 19 / Fish and Habitat Data Analysis / (Poster's Due)
26 / T, Apr 24 / Fish Ecology / Ch 21
27 / R, Apr 26 / Fisheries Management / Ch 21
28 / T, May 1 / Data Discussion
29 / R, May 3 / Poster Discussion
EXAM 3 / Finals Week Covers content through May 3rd, 2007.

* NOTE: Topics for particular lecture dates are tentative; although, we will try to keep to this schedule. Any change to the syllabus will be announced and presented in electronic format (e.g. website or Email).

† Chapters in your textbook by Dodds are given by the number; chapters from other references are given by the text author followed by chapter number. The later reading assignments will be given to students as handouts. Full references for readings other than your textbook can be found below.

Student Evaluation:

Your evaluation for this course will be based on your performance on three exams, a poster presentation, a research project report, and a participation journal for documenting responses to “thought assignments” on readings and entry of field and laboratory notes and data. Each is explained below in more detail.

Theory Exam I / 25 pts
Theory Exam II / 25 pts
Theory Exam III / 25 pts
Poster Presentation & Discussion / 15 pts
Group Data Presentations & Discussion / 10 pts
Total = / 100 pts

Theory Exams (3 x 25 pts = 75 pts): Your exams will be based on lecture notes and reading assignments. A note of caution for lecture notes. Please do not solely depend on my PowerPoint presentations, which will be posted at the end of each week. Take notes in class! Exams will include a diversity of question types, multiple choice, matching, fill-in blanks, true/false, short answer, and a technical essay. Exam essays will be written by each student individually. However, the technical essay question or topic options will be provided a few days in advance of the exam and I encourage you to brainstorm ideas and discuss it with your peers.

Poster Presentation & Discussion (15 pts): Each student will choose an article from the primary literature on a topic suggested by me. You will study the article, which may require additional background research in order to fully understand the contents. Together you will create a research presentation poster on the article. Basically you will pretend to be the author of work presented at a scientific meeting’s poster session. We will discuss poster criteria and look at examples of posters so you have an idea of what you’re making. You will be evaluated on the following: format; logical presentation; knowledge of the work presented; and added background knowledge on the broader topic you present. Posters will be due on Thurs. April 19th, and we will present and discuss the work in a conference-like format on Thursday May 3rd. Posters will be posted for peer review (evaluation) by all students between the deadline and presentation date.

Group Data Presentations (10 pts): We will schedule a field expedition to evaluate habitat and fish populations in the Codorus Creek Watershed. This mini-research project will be performed on either Saturday,April 7 or April 14, 2007. A component of the data set generated will be assigned for analysis by pairs of students and then presented and discussed in class on May 3, 2007. Students are responsible for understanding all field or lab protocols.

Extra Credit (6% maximum): There are two activities this semester that can generate up to 3 % extra credit each. First, I would also like to organize a trip to the StroudWaterResearchCenter, Avondale, PA ( This will need to be an all day trip on a Wednesday or Saturday. Second, a student may receive 3% extra credit for each time they volunteer with educational outreach activities through the Codorus Creek Restoration Efficacy Program in partnership with the Watershed Alliance of York (WAY) and Codorus Creek Improvement Partnership (CCIP) , Joint Watershed Education Program. Two contributions to educational outreach activities will earn 6% extra credit and should make you feel goodabout serving your community in a professional capacity. See Dr. Hoch for details on how to get involved.

Grades:

Letter grades are based on the total percentage of course marks accumulated as indicated below. Plus (+) or minus (-) designations will be assigned only at final grade submission, and will be based on the distribution of marks, i.e. "the curve", within each posted letter grade range.

A / 89 - 100 %
B / 77 - 88 %
C / 65 - 76 %
D / 53 - 64 %
F / < 52 %

"Make-Up" and Testing Policy:

Missed evaluation elements (exams, lab sessions, field sessions, paper discussions and other assignments) can only be made-up, or waived, by prior arrangement and/or with proof of an excusable absence (e.g., documented medical reason, sanctioned University function). A different set of questions or criteria may be used for any make-up assignment or exams. Any evaluation element waived by the instructor will have its percentage deducted from the total course percentage of 100%., and that value will be used as the denominator in calculating your numerical grade upon which a letter grade will be assigned. (e.g. An exam is waived; your final numerical grade will be the sum of all other work as a percentage of 100-25=75.)

Exams will be administered at the beginning of class on their scheduled dates. Late arrival to class on an exam day is extremely disruptive and inconsiderate to your other classmates. You also run the risk of not being allowed to take the exam. If any student completes and submits the exam prior to your arrival in class, you will not be permitted to take the quiz or exam, and you will forfeit your grade (receive a 0%). Please show up on time!

Course Requirements:

Participate class and bring your most positive attitude.
A PSU Access Account. Go to IST Rm 106 and make the request for your user-ID and password. It will take about 24 hours for activation, at which time I recommend you change your password.
A single Email address. I will send all course announcements and notes to your PSU user-ID address. This is also the easiest address for other PSU students to use in reaching you, as it is on the PSU Directory. If you prefer using another Email address, it is your responsibility to have mail sent to your PSU address forwarded to your preferred alternate address. Contact the campus computer helpdesk to inquire how to do this.
You will keep in touch with me and other students in the class by Email. Check your Email frequently (i.e. daily) so you don’t miss important announcements.
The ability to save computer work to permanent space on the network, a diskette, CD, or zip-disk. You will have to supply the disc or CD.

Class Guidelines:

I would like everyone to participate in making our class times a nice comfortable place to learn throughout the next fifteen weeks. To this end, please, let us all adopt the following guidelines on appropriate and considerate behavior.

Unless you are waiting for an organ transplant, or a birth is imminent, please turn off all electronic devices (e.g. cell phones, pagers, etc) that could generate distracting noises prior to entering class.
I encourage you to fill the room with questions and discussion on the topic at hand. Please ask questions freely, and if not in class then out of class, either verbally or via Email. When others ask, or answer, questions in class, please give them your full attention and respect.
If you have a comment or complaint regarding any aspect of the course other than the course content or activity being discussed, please wait to speak with me until after class, outside of class, or by Email. This saves valuable class time and is much more discrete, particular on issues of grade disputes or any other potential misunderstanding.
Please don’t study or read other course material in class. If you find yourself in a time management crises come see me before class instead.
Also, refer to “Promoting a Vibrant Learning Culture” at

Academic Integrity:

Academic dishonesty, a.k.a. cheating, is not something you want on your record, nor do you want to lower your grade or fail the course. Students that cheat are not challenging themselves, and such cowardly behavior now, will leave them even more ill prepared for their future. If you ever feel the urge to cheat in any form, then that is your signal to seek help from your peers, instructor, and/or the learning center. Faculty will have great respect for the hard working honest student that feels they have learned something, regardless of any grade outcome. Preservation of a high standard of academic integrity is, for many individuals, a source of self-confidence and pride.

To possess academic integrity means you don’t cheat. So what is cheating?

Copying someone else’s assignment and submitting it as yours.
Referring to another student or sources during a quiz or exam.

It is NOT cheating to work with other students while studying for quizzes and exams. It is NOT cheating to seek assistance from another student, a tutor, or your instructor, in order to understand an in-class activity or out-of-class assignment.

If the instructor suspects you of cheating, they will immediately notify you to meet informally after class or at some other time outside of class. At that time, the instructor will inform the student of the accusation and its circumstances, and the student will have the opportunity to explain their view point or situation. The instructor will then decide whetherto proceed with a formal academic sanction. Notification of an academic sanction will involve a formal meeting between accused student and instructor. At this formal meeting, the student will be presented with an academic sanction form that explains the accusation and the sanctions, such as a failing grade on an assignment, quiz, or exam. The formal meeting will be arranged by e-mail or phone call. The student may agree and sign the form or contest the allegations through the university authorities. If a student is absent from the formal meeting time, they will be given three additional days to contact and meet with the instructor. Failure to formally meet with the instructorwill be deemed as the student's acceptance of academic sanction, and waives the student's right to contest the allegations of academic dishonesty. Note, that any student(s) assisting or facilitating others in cheating will be subject to equal penalty and treated according to these same guidelines The official guideline on this policy can be found in the Academic Administrative Policies Manual, which is available on the PSU website: or refer to menu item G-9 at

Disability Statement:

Please see me immediatelyafter the first class if you have a document disability that may require special accommodations for this course. I will do all I can to accommodate your needs and/or arrange to get you any additional required assistance. See below for the CommonwealthCollege official statement:

CommonwealthCollege Disability Statement

PennState is committed to providing access to a quality education for all

students, including those with documented disabilities. If a student has a

disability and wishes an accommodation for a course, it is the student's

responsibility to obtain a University letter confirming the disability and

suggesting appropriate accommodation. This letter can be requested from the York

campus Disability Contact Liaisons, Dr. Sharon Christ, Student Affairs (ALL); Dr. Cora Dzubak, LearningCenter (LEARNING); and Nan Flesher, Admissions (PHYSICAL).