Biology 211A, General Ecology, Spring 2015
Lecture and Monday Lab Instructor: Betsy Kirkpatrick; TH 223G, x3739; (kirkpatrick@pugetsound.edu)
Tuesday Lab Instructor: Stacey Weiss; TH 223H; x2744; (sweiss@pugetsound.edu)
Wednesday Lab Instructor: Amy Replogle; TH 117H; x2829; (areplogle@pugetsound.edu)
IAs: Monday – Amanda Johnson (aejohnson@pugetsound.edu), Tuesday – Lucy Banta
(lbanta@pugetsound.edu), Wednesday – Cole Jackson(cjackson@pugetsound.edu)
Office Hours: Mon 10:00-12:00 & Tues 11:00-12:00; You are also welcome to schedule an appointment
with me at other times by phone, by email, or in class.
Your Biology Liaison Librarian: Eli Gandour-Rood (egandourrood@pugetsound.edu)
Lectures: MWF 9:00 – 9:50 in TH193; Labs: Mon, Tues, or Wed; 1pm – 5pm. TH 221
Required Materials:
Molles, M.C. Ecology: Concepts and Applications. 6th Edition. McGraw Hill.
WARNING: Multiple students in previous semesters who bought the book online ended up with a pirated
copied that had multiple typos and errors. If you buy online, be sure it is from a reputable buyer with a
good return policy!
SimUText Ecology Collection: Chapters on Population Growth, Competition, & Predation ($27)
Pechenik, J. A Short Guide to Writing about Biology. Pearson-Longman
Clicker: Available new from the bookstore ($40) or used from last fall’s 112 and some Cell Bio students?
Carol may still have some that we didn’t sell last fall ($25).
Optional: Rite-in-the-Rain notebook (several kinds are available at the bookstore).
WEB RESOURCES
Class Moodle site: http://moodle.pugetsound.edu/
Statistics For Ecology site: http://stat.pugetsound.edu/ecology/
Library Course Guide: http://research.pugetsound.edu/BIOL211
What is Bio 211-General Ecology?
Bio 211 is an introduction to the theories and practice of Ecology. You will gain an overview of the history
of the field and of the current ideas and methods in ecological research. In addition to building on the skills
you learned in Biology 111 and 112, you will be learning and using new skills relating to the analysis and
interpretation of data. You will learn statistical skills in labs, and then apply these skills to data analysis in
your labs and independent projects. We will continue to strengthen your skills in graphical data
presentation, clear writing, and good use of literature from earlier courses.
Understanding any field involves knowing what we know and how we know it. I emphasize the
presentation of data from real studies and the use of primary literature. In class and in assignments, you
will use ecological knowledge to evaluate other people’s experiments, design your own experiments, and address real ecological problems. In both lecture and lab, the practice of ecology is as important as the
ideas and theories.
Lectures
Check the Moodle page before each lecture for the lecture slides and other postings. You are welcome to
print these slides and bring them to class to facilitate your note-taking.
Lectures will include discussion and group problem-solving exercises, so come to class awake.
 Assignments are due via EMAIL by 9 am on the due date. Let me know if you have a problem.
 Quizzes will be given at 9 am and will last about 10 minutes. If you are late, you will have less time.
Bio 211A Syllabus — 2
Labs

Attendance in your assigned lab section is mandatory. Temporary attendance in the other lab section is
possible only under extraordinary circumstances and with prior permission. It is not possible to make
up labs.

It is your responsibility to be on time to lab – vans for field trips will leave on time, whether or not you
are there. If you miss a van, try to get to the site on your own. Directions will be on Moodle.

You are responsible for downloading and reading the lab handout before lab each week. Handouts will
be posted on the class Moodle page by the Friday before the lab takes place.

Labs will involve field studies, computer simulations, and in-lab manipulations with fun things. For field
labs we will work outdoors, rain or shine, so DRESS APPROPRIATELY. Wear solid (closed) walking shoes,
sneakers, or hiking boots. Long pants and layers are important as we will have to walk through wet
vegetation or remain stationary (to count organisms) for periods of time. Raingear is a good idea (clear
plastic ponchos are great because you can still take data under them, and they are relatively cheap).
Biology 211: Learning Objectives
The American Association for the Advancement of Science (AAAS, the publishers of the journal Science) and
the National Science Foundation (NSF) have developed a list of core concepts and skills in which every
science undergraduate should be literate. Here is a very brief statement of their vision with the areas
underlined that we will teach or rely on in Ecology. As you can see, Ecology hits almost every part of what
AAAS and NSF deem important for scientific literacy.
“Most faculty agree that to be scientifically literate, students need to understand a few
overarching core concepts:
(1) Evolution,(2) Pathways and transformations of energy and matter,(3) Information flow,
exchange, and storage, (4) Structure and function, and (5) Systems.
As important, undergraduates need to understand the process of science, the interdisciplinary
nature of the new biology, and how science is closely integrated within society. Students also
should be competent in communication and collaboration, as well as have a certain level of
quantitative competency, and a basic ability to understand and interpret data.
To be current in biology, students should also have experience with modeling, simulation,
and computational and systems-level approaches to biological discovery and analysis, as
well as with using large databases.” --AAAS & NSF Vision and Change Executive Summary
Ecology presents questions relevant to our current environmental challenges. It also gives context to other
biological disciplines. Molecules and cells function in the context of whole organisms, populations,
communities and ecosystems; and becoming familiar with these higher levels will increase your
understanding of other aspects of biology.
Our ecology course also offers significant experience with experimental design, data collection, quantitative
and statistical data analysis, scientific writing, conceptual and mathematical modeling and simulation.
These skills will be developed largely in the lab, but we will do some modeling in lecture as well.
Content Objectives
Students will be able to:
1. Describe the levels of ecological hierarchy.
2. Explain global climatic patterns and the mechanisms generating them, as well as describe
biomes and predict their occurrences based on structure-function adaptations to climate.
Bio 211A Syllabus — 3
3. Describe the growth of a single population verbally and mathematically, factors that affect
that growth, and evolutionary implications of population size and growth potential.
4. Explain how populations interact in systems using both verbal and mathematical models.
5. Explain the structure and function of communities, the transformation of energy through
community systems and the pathways cycling nutrients within community systems.
6. Integrate into their explanations current and historical theories about ecological processes
and patterns and important questions in the field of ecology.
Skill Objectives
Students will be able to:
1. Ask interesting ecological questions, design experiments to test them, collect relevant data,
use statistics to analyze data, and present the results effectively.

Experimental design and statistical analysis are both important aspect of all areas of biology, and
the skills you learn in this class will benefit you in many future classes.

Understanding statistical tests is critical to your ability to evaluate your results and the results of
studies presented by other scientists….statistical training makes you an informed reader.

Understanding statistical tests is also important in everyday life, as it allows you to critically
evaluate information presented to you by the media, politicians, and your professors.

Presenting results effectively gets your message out to other scientists, the media, and the public.
Statistics Lectures and Labs: An essential part of the Biology 211 curriculum is training in statistics.
There are 5 laboratories in which you will learn to use the program “R” to statistically analyze data sets.
To prepare you for these labs, I will introduce the relevant statistical subject matter in lecture. Because
the only way to learn statistics is to use them, material presented in these lectures will be on lecture
quizzes and exams. You will use the knowledge you gain in these lectures and labs to analyze the data
you collect in lab and for your independent project.
Scientific reports: For several assignments, you present your results in writing. This will give you
experience both in the execution of the statistical tests and the presentation of your analyses to your
readers. These assignments are designed to build your skills toward the analysis of your IP data at the
end of the term.
Primary literature: The primary literature articles that we read in class were selected because they are
interesting topics, and because they will be useful to you in building your understanding of the
considerations of experimental design and statistics.
Independent Project: Especially in this project, you will pose your own questions and come up with an
experimental design that addresses your hypotheses. You and a partner will design and carry out an
original investigation of an ecological question of your choosing. Projects can be observational studies,
experimental manipulations, or a combination of the two. In week 5, you and your partner will meet
with me and your IA to discuss your ideas. In week 6, you will submit individually written project
proposals, and you will begin your research. This research will mostly be done outside of lab time, but
you will also have several lab periods dedicated to independent project research. In the last lab period
of the course you will present your project to the rest of the lab section in a 10-minute talk. You will
submit INDIVIDUALLY WRITTEN final written reports by 4:00 pm on May 7.
Start thinking about project ideas early. Talk to me about your ideas as soon as you can.
Keep it simple; plan to address a specific, limited question. You can approach it in many
different ways. Do you really like sea stars? Read up on the organism and come up with
some questions to address. Are you fascinated by the intermediate disturbance
hypothesis or optimal foraging predictions? Design a study to test a question or
Bio 211A Syllabus — 4
assumption. Make sure that the project can be completed in the time allowed, and that
the materials are either already available or inexpensive and easy to obtain. Coordinating
with Susan in the stockroom is your responsibility. Remember that ordering supplies
involves a time-lag. Also remember that several other classes (and all your classmates)
will be using the same limited pool of on-campus supplies. Use the many resources
available to you to help you get started on this important project.
2. Refine your scientific writing skills.



As scientists, we have a duty to communicate our research findings to our peers.
Science writing is fundamentally different from writing in other disciplines.
The only way you can improve your writing skills is by practicing and receiving constructive
criticism.
Scientific papers describing laboratory exercises: As you know, this course culminates with a large
writing project, in which you communicate the methods, results, and relevance of your independent
study project. To prepare you to write this large paper, we will work through several smaller papers
throughout the term. Some papers will concentrate on particular sections of the scientific paper (e.g.
methods and results) in order to allow you to spend time on these sections and fully appreciate the
feedback you receive on your work. Some papers will be very short (1-page papers similar to your 112
lab papers) which will allow you to get feedback on very general aspects of paper writing such as
phrasing and figures. And other papers will be full papers on labs designed to prepare you for the full
IP paper.
The goals of science writing include:
 clearly presenting your study design so that it can be replicated by other researchers,
 convincing your reader of your point by showing them your DATA, not through an abundance of
words…
 clearly putting your study into context with other research on the subject so that the reader
understands how your work fits into the larger field of ecology.
We will work with you throughout the term to help you master the skills of science writing.
3. Become familiar with primary literature detailing research in the field of Ecology.




Primary literature gives you examples to guide you when writing your own scientific papers:
consider how these authors reference and cite the work of other authors, describe the methods of
their study, present their results to the reader, and put the work in a broader context in the
discussion.
Primary literature allows you to review your statistical knowledge – as you read papers, make sure
you understand the statistics they use: what are they actually testing? Why did they use the
statistical test that they did? What does the p-value tell you?
Primary literature gives you thought-provoking examples that can help you conceive of and design
your independent project.
Primary literature gives you a broader exposure to the field than you could get by only reading a
text or listening to lectures.
In-Class Primary Literature Discussions in which you will participate in collectively analyzing and
critiquing other scientists’ work.
Primary Literature Analysis: Over the term, you will read and summarize 3 primary literature papers
that are relevant to material we cover in lecture. The idea is to get you to read articles, think about the
data they present, and concisely state the main points. Each analysis will be due the day we discuss the
Bio 211A Syllabus — 5
paper in lecture. The articles have been selected because they are interesting, relevant to course
material, reasonably well-written, and have statistical analyses that you will be able to interpret.
Required references for written work: For your final independent project report, you will be required
to correctly and carefully reference at least 5 papers from the primary literature. Citing literature in
your written work requires preparation (remember, it takes time to find relevant articles, read them,
and figure out how you will use them in your paper). You will work up to the task of the ‘final 5’ throughout the term. For your IP proposal due week 6, you will be required to cite 2 (of the final 5)
sources. In week 8, our Science Library Liaison will come to the labs to guide you through the process of
finding additional references in the library and using citation software. In the Foraging or Duckweed
lab report, you will need to incorporate 3 outside references (due week 10). Along with the IP
Introduction and Methods that is due in week 12, you will turn in an annotated bibliography that cites
all 5 of your references and presents a sentence or two about how you will use that reference in your
final paper.
Classroom Emergency Response Guidance
Please review university emergency preparedness and response procedures posted
at www.pugetsound.edu/emergency/. There is a link on the university home page. Familiarize yourself
with hall exit doors and the designated gathering area for your class and laboratory buildings.
If building evacuation becomes necessary (e.g. earthquake), meet your instructor at the designated
gathering area so she/he can account for your presence. Then wait for further instructions. Do not return
to the building or classroom until advised by a university emergency response representative.
If confronted by an act of violence, be prepared to make quick decisions to protect your safety. Flee the
area by running away from the source of danger if you can safely do so. If this is not possible, shelter in
place by securing classroom or lab doors and windows, closing blinds, and turning off room lights. Stay low,
away from doors and windows, and as close to the interior hallway walls as possible. Wait for further
instructions.
Academic and Scientific Integrity
Academic honesty is a fundamental principle of intellectual endeavor. Scientific integrity is an integral part
of the scientific process. Simply put - cheating sucks. It is unfair to others, cheats the cheater of learning,
and ends up consuming way too much time and emotion. Cheating is a waste of your time and mine. You
will learn nothing and I will have to waste my time dealing with it.
It is your responsibility to make sure that you know and completely understand what constitutes academic
dishonesty and plagiarism. It is your responsibility to read and understand the UPS policies on Academic
Integrity. If you haven’t already been through the new Academic Integrity tutorial on the library’s website, you should familiarize yourself with it: http://alacarte.pugetsound.edu/subject-guide/6-Academic-IntegrityPuget-Sound.
When you sign the student contract for this course, you are stating that you have read the information on
the UPS web page and that you fully understand what constitutes plagiarism and the penalties for
academic dishonesty.
Several forms of academic dishonesty are especially relevant to this class:
 Cheating on exams or quizzes
 Alteration, fabrication or misrepresentation of data
 Plagiarism on any assignment including questions and comments and lab exercises. Note that
plagiarism includes paraphrasing that uses the original wording or sentence structure.
Even when lab work is performed in groups, you must complete all written work individually unless the
assignment specifically states otherwise. To avoid problems, never collaborate with classmates when you
are actively writing your labs, papers or other assignments. I encourage you to discuss assignments with
Bio 211A Syllabus — 6
your colleagues, but do not take notes during those discussions because that can lead to answers that are
suspiciously similar between individuals. I ran across this quote on George Gilchrist’s Diversity of Life Web Page. It captured my sentiments so thoroughly that I have reprinted it for you – complete with quotes:
“Remember that you are here to learn, not to get a good grade. Cheating will not help you learn, [nor] will it help you get into medical school or graduate school. It will not help you get a
good job nor will it help you obtain happiness with your life. Cheating is for losers and I don’t think anyone here falls into that category. If you decide that maybe you really want to be a
loser and that cheating might be just the ticket to get you there, I will help you in every way I
can. If you are caught cheating, you will fail this course and may be ejected from the university.
More importantly, you will have cheated yourself out of the education you have been working
and paying to obtain."
Course sanctions range from, at a minimum, losing credit for the assignment plus 100 points to being
dismissed from the course with an F. Depending on the situation, further sanctions can be imposed by the
University administration.
Bio 211 Grading Scale
≥ 93%
90 – 93%
87 – 90%
83 – 87%
A
AB+
B
80 – 82%
77 – 80%
70 – 77%
67 – 70%
BC+
C
C-
64 – 67%
60 – 64%
57 – 60%
< 57%
D+
D
DF
Bio 211 Assignment Overview
Assignment
Quizzes and Exams
Quizzes (5@15 ea: drop lowest of 6*)
Midterm Exams (3 @ 100 pts each)
Final Exam (comprehensive)
Homework
Primary Lit Summaries (3 @ 15 pts each)
SimUText: Population Growth
SimUText: Competition
SimUText: Predation
Labs
Pre-lab questions (10 @ 5pts each)
Reserve Design Simulation
Statistics Problem Sets (5)
Lichen Report: Methods & Results w/ Figures
Foraging Report OR Duckweed Report: Abstract, Intro, Methods,
Results w/Figures, Discussion, Literature Cited
Independent Project
IP Proposal
IP Progress Reports (4)
IP Introduction, Methods & Annotated Bibliography
IP Written Report
Participation (Clickers)
TOTAL POINTS
*If you take all 6 quizzes, I will drop your lowest score.
Point Value
525
75
300
150
85
45
10
15
15
210
50
20
65
25
50
160
20
20
20
100
20
1000
General Ecology Spring 2015
Biology 211
Betsy Kirkpatrick
Tentative Schedule
Date
Jan
(1)
Lecture (TH 193)
21 (1) Course goals & ideas
23 (2) Ecological Methods
26 (3) Stats I-Testing hypotheses
(2)
Feb
(3)
(4)
(5)
(6)
Mar
(7)
(8)
Mar 17-21
(9)
Ecology of Individuals
28 (4) Evolution & Optimality
30 (5) Evolution & Altruism
2 (6) Stats II
4 (7) Discussion: 1o Lit 1
6 (8) Climate I
9 (9) Climate II
11 Q1 (10) Responses to temp & water
13 (11) Behavior: Optimal foraging
16
18
20
23
Ecology of Populations
(12) Populations: distrib’‛n and growth
EXAM 1 (through Feb 13)
(13) Population growth
(14) Demography
25 Q2 (15) Life History Theory
27 (16) Introduction to competition
Species interactions
2 (17) Competition models
4
6
9
11
13
Q3 (18) Coexistence of species
(19) Experiments for competition
Catch up/Review
EXAM 2 (through Mar 7)
(20) Pollination stories from Israel
SPRING BREAK!
23 (21) Mutualisms & Pollination
25 (22) Discussion: 1o Lit 2
27 (23) Positive Interactions
Reading in Molles (6th ed)
*GB = Green boxes (pg #)
Ch 1
Ch 1, GB* 9, 18, 106, 168,
299
GB 88, 188, 236, 314-315,
419
Ch. 8, GB 188-189
Ch 8
GB 402-403, 419, 450451, 466
Parker & Burkley 2009
11-16
16-42
Ch 5 & 6
165-170
Ch 9 & 11
Ch 10
SimUText Pop. Growth
(10 pts);Ch 12
Ch 12
282-288
SimuText Competition
(15 pts)
289-292;
292-301
---
--SPRING BREAK!
Gaskett et al. 2008
Ch. 15
Lab (TH 221)
No lab
Field lab: Quantifying
Ecological Patterns
Stat skills: Descriptive stats,
Intro to Excel & R
Field lab: Lichen distributions
Stat skills: t-test, regression
Focus on Statistics – I
Stat skills: paired t-test,
Wilcoxon test, 1-way ANOVA
Lab exp’‛t: Duckweed growth 1
& IP conferences
Field exp’‛t: Foraging behavior,
Stat skills: Chi-square tests
& Duckweed Experiment 2
Focus on Statistics – II
Stat skills: 2-way ANOVA,
ANCOVA & Duckweed Experiment 3
Assignments due
Download and install “R”
(see Moodle Course Info)
Pre-lab questions (5 pts)
Patterns, Questions and
Stats Problems 1 (20 pts)
Pre-lab questions (5 pts)
Stats Problems 2 (10 pts)
1o Lit Summary 1 (15 pts) F
Pre-lab questions (5 pts)
Stats Problems 3 (10 pts)
Pre-lab questions (5 pts)
Lichen Report (25 pts) F
Pre-lab questions (5 pts)
Stats Problems 4 (10 pts)
IP Proposals (20 pts) F
Pre-lab questions (5 pts)
Stats Problems 5 (15 pts)
Literature Searching and Citing Tools
& Duckweed Growth 4
SPRING BREAK!
Open Lab
Work on IPs
Pre-lab questions (5 pts)
IP Progress Report 1 (5 pts) F
SPRING BREAK!
Pre-lab questions (5 pts)
1o Lit Summary 2 (15 pts) F
IP Progress Report 2 (5 pts) F
Date
Lecture (TH 193)
(10)
30 (24) Predation: patterns & models
Apr
(12)
1
3
6
8
10
13
15
(13)
17 (31) Biodiversity
20 (32) Island Biogeography
22 (33)Disturbance, Succession & Stability
(14)
May
(15)
May
24
27
29
1
4
6
May
15 FINAL EXAM Friday 8-10 am
(11)
Q4 (25) Predation: Models & exp’‛ts
(26) Herbivory: plant defenses
(27) Herbivory: defense strategies
Q5 (28) Herbivory: defense strategies
(29) Indirect interactions
(30) Discussion: 1o Lit 3
EXAM 3 (through Apr 11)
Ecology of Communities
Ecology of Ecosystems
*GB = Green boxes
303-319; SimUtext
Predation (15 pts)
319-327
--Ch 17
Roemer et al. 2002
250-362, 491-501
481-491
Ch 20 & 362-368
(34) Energy flow
(35) Nutrient cycling
Q6 (36) Your choice!
(37) Your choice!
(38) Your choice!
Wrap up/Review
Ch 18
Ch 19
TBA
TBA
TBA
Lab (TH 221)
Assignments due
Open Lab
Work on IPs
Field lab: Intertidal Diversity
IP Progress Report 3 (5 pts) F
Duckweed/Foraging Rprt (50 pts)
Pre-lab questions (5 pts)
IP Progress Report 4 (5 pts) F
Open Lab
Work on IPs
Reserve Design Simulation
1o Lit Sum 3 (Lec; 15 pts) F
IP Intro, Meth & Bib (20 pts) F
Pre-lab questions (5 pts)
Reserve Design (Lab; 20 pts)
IP Abstract (10 pts) F
IP presentations
No Lab
Final IP Reports (90 pts) W
Visit the course Moodle Site for…
 course syllabus and schedule updates
 guidelines for scientific writing
 lecture Powerpoints
 guidelines for oral presentations
 primary literature papers
 guidelines for independent projects
 practice problems (with answers) for each unit
 previous independent project titles and abstracts
 keys to this year's quizzes and exams
 links to other interesting web sites