1 Course Information and Syllabus Stony Brook University College ...

CLASS TIMES AND LOCATIONS
Tuesday & Thursday 5:30 PM – 6:50 PM
Melville Library E4330
Course Information and Syllabus
Stony Brook University
College of Arts and Sciences
Department of Ecology and Evolution
BIO 336 Conservation Biology
Fall 2012
INSTRUCTOR AND TA CONTACT INFORMATION
Instructor: Professor Liliana Dávalos
Email: liliana.davalos-alvarez@stonybrook.edu
Office Location: Life Sciences Bldg, 6th floor, Room 630
Office Hours: Wednesday 10:30-12:30 and by appointment
Teaching Assistant: Jin Gao
Email: jingao@life.bio.sunysb.edu
Office Location: Life Sciences Bldg, 6th floor, Room 633A
Office Hours: Tuesday 10:00 AM – 12:00 PM and by appointment
COURSE DESCRIPTION
Society and individual lives are increasingly affected by environmental degradation at different
scales. From the decline of local fisheries to global climate change, multiple crises threaten the
biodiversity and ecosystems that sustain us humans. This course introduces the scientific
foundations of conservation biology, along with examples from real-world conservation. The
course reviews the biological concepts that underlie conservation including habitat
requirements, population dynamics, biogeography, and population genetics. Analysis of case
studies on the effects of human activities on biological diversity and ecosystem services will be
used to explore the interdisciplinary nature of the practice of conservation. This course will
prepare students for careers in environmental sciences and ecology.
Credits: 3
COURSE OBJECTIVES
This is an undergraduate/masters lecture course focusing on biological concepts and methods
underlying conservation practice. The course aims to:
1. Expand on fundamental concepts of ecology and evolution relevant to conservation.
2. Build quantitative and analytical skills, including the application of simple models of
population and community dynamics.
3. Develop writing skills through writing, re-writing, and peer review.
AMERICANS WITH DISABILITIES ACT
If you have a physical, psychological, medical or learning disability that may impact your course
work, please contact Disability Support Services, ECC (Educational Communications Center)
Building, room128, (631) 632-6748. They will determine with you what accommodations, if any,
are necessary and appropriate. All information and documentation is confidential.
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ACADEMIC INTEGRITY STATEMENT
Each student must pursue his or her academic goals honestly and be personally accountable
for all submitted work. Representing another person's work as your own is always wrong.
Faculty are required to report any suspected instances of academic dishonesty to the Academic
Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management,
Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their
school-specific procedures. For more comprehensive information on academic integrity,
including categories of academic dishonesty, please refer to the academic judiciary website at
http://www.stonybrook.edu/uaa/academicjudiciary/.
In this class we will treat Academic Dishonesty harshly. What constitutes Academic
Dishonesty? Academic dishonesty includes any act that is designed to obtain fraudulently,
either for oneself or for someone else, academic credit, grades, or other recognition that is not
properly earned or that adversely affects another's grade. The following represents examples of
this and does not constitute an exhaustive list:
• Cheating on exams or assignments by the use of books, electronic devices, notes, or
other aids when these are not permitted, or by copying from another student.
• Collusion: two or more students helping one another on an exam or assignment when it
is not permitted. This includes sharing answers with others.
• Ringers: taking an exam for someone else, or permitting someone else to take one's
exam.
• Submitting the same paper in more than one course without permission of the
instructors.
• Plagiarizing: copying someone else's writing or paraphrasing it too closely, even if it
constitutes only some of your written assignment, without proper citation.
• Submitting the same paper in more than one course without approval of the instructors.
• Falsifying documents or records related to credit, grades, status (e.g., adds and drops,
P/NC grading, transcripts), or other academic matters.
• Altering an exam or paper after it has been graded in order to request a grade change.
• Stealing, concealing, destroying, or inappropriately modifying classroom or other
instructional material, such as posted exams, library materials, laboratory supplies, or
computer programs.
• Preventing relevant material from being subjected to academic evaluation.
• Presenting fabricated excuses for missed assignments or tests.
If you are found to violate the Academic Honesty standards, you will receive a zero (no
credit) for any graded material and you will be reported to the Academic Judiciary. If you
are found to violate Academic Honesty standards a second time, you will receive a
penalty of 2 letter grades below your final grade, in addition to a zero on any graded
material.
CRITICAL INCIDENT MANAGEMENT
Stony Brook University expects students to respect the rights, privileges, and property of other
people. Faculty are required to report to the Office of Judicial Affairs any disruptive behavior that
interrupts their ability to teach, compromises the safety of the learning environment, or inhibits
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students' ability to learn. Faculty in the HSC Schools and the School of Medicine are required to
follow their school-specific procedures.
EMERGENCIES
If an emergency arises on campus during class, you are to remain in class until instructed to
leave. The university emergency mechanisms and policy will apply.
CLASS PROTOCOL
• Unless otherwise instructed, please turn off all personal electronic devices. This includes
cell phones and texting.
• Do not check your email, phone/text messages, etc. during lectures. If you are expecting
an urgent message or call, notify the instructor before the class.
• Feel free to ask a question at anytime, but please do not talk to other students during
lectures. It is disruptive and rude to other students.
• Blackboard will be used extensively in this course for communication and assignments.
You must have a Blackboard account with a valid, current email address. University
email access and addresses are free! You should log in as soon as possible and confirm
your e-mail address.
COURSE REQUIREMENTS
GRADING
Your grade will be based on:
Item Percent
Exam I 15
Exam II 15
Exam III 15
Blog writing and peer review 25
Assignments and exercises 25
Participation 5
COVERAGE OF EXAMS
Each exam will be based on all information presented in prior lectures, readings, discussions,
and exercises with the exception of the last lecture before the exam. The last exam will be
based on all information presented in lectures, readings, discussions, and exercises. Exams will
be designed to take 75 minutes.
ATTENDANCE AND EXAM MAKE-UP POLICY
If you miss an exam, or a take-home exercise because of an illness or emergency, you may be
allowed to take a make up exam or assignment. Not having registered for the course at the
time of a take-home exercise is not a valid excuse for not turning in the exercise. If you
register late for the course and miss an assignment, you will not get credit for the missed
assignment.
You will need to present documentation verifying your excused absence. This must include a
phone number and contact information. We will follow up with the information you provide.
If you provide a false excuse or falsified documentation, you will be reported to the academic
judiciary. You will also be given a zero (no credit) for the assignment or exam.
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BLOG WRITING
Each student will select 1 topic and develop a blog entry presenting 1 scientific article on the
relevant question, and communicating the findings to the public. You will be able to choose from
a set of class-sourced topics. The scientific state of the art comes from the primary scientific
literature, but the blog format is aimed at the general public (i.e., your retired relatives who did
not complete degrees in science). The article that you will synthesize for the public can ONLY
be found via Web of Science or Google Scholar.
This writing assignment is NOT a term paper and term paper standards such as
dictionary definitions, Wikipedia mining, and expounding on facts already reported in textbooks
will not do. Blog writing will be an individual exercise. First draft of the blog entry will be due
on 9/27, second draft on 10/18. Peer review of the drafts will begin immediately after
submission. You have 1 week to complete peer reviews. The final, revised blog is due before
the end of classes. Your blog entry can also count toward the writing requirement in the Biology
major.
PEER REVIEW
We will implement peer-review of the blog items. Peer-review means you review the work of
your peers, i.e., offer constructive criticism with the goal of improving their writing. Peer-review
will count for 20% of your blog points in the class. Register into this system
http://sword.lrdc.pitt.edu/sword/ and look for the class (BIO336 2012 at SBU). Use the class
password “PlasmodiumRules” to register for the class. The system will enable you to submit
your draft blog entries and review your peers’ work.
ASSIGNMENTS AND EXERCISES
Six individual take-home exercises with instructions will be posted on BB. The results and
interpretation of each exercise will be due one week after being assigned. A small number (4-5)
of in-class group exercises will also be collected and count toward 33% of this grade. Graded inclass
assignments will be announced during class.
LATE ASSIGNMENTS
It is imperative that you submit your work on time. Should you decide to submit your work late,
the penalty will be 15% for each day your work is late. Beyond 7 days your grade for the work
will be 0. This table does not apply to blog entries. Because those are peer-reviewed, they have
hard deadlines that you must adhere to.
PARTICIPATION
Participation on weekly online forums will be counted toward 5% of your final grade. You will
obtain the maximum score in this grade if you participate in the discussion forum posted with
each discussion reading (9 total).
EXTRA CREDIT OPPORTUNITY
You will get 5 bonus points if you complete ALL surveys and assessments for the class. Some
of the surveys and assessments will be posted online, and some will take place in class. Do
them all and you will get these bonus points.
DESCRIPTION AND SCHEDULE OF REQUIRED READINGS AND/OR ASSIGNMENTS
Lecture titles and readings are listed for each day of class. Check Blackboard (BB) for updates
and changes. Additional reading and web links will be found on BB. Check for updates, links to
these sites and tips for using these sites. You must have a Blackboard account and a valid,
current email address must be listed in your Blackboard account.
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Syllabus
The following is a schedule of lectures, exams, and assignments.
Date Topic Learning
objective
28-
Aug
30-
Aug
4-
Sep
6-
Sep
11-
Sep
13-
Sep
18-
Sep
20-
Sep
Course introduction
& student ethics.
Active learning &
blog topics.
No classes
Critical thinking
assessment.
Population:
survivorship curves.
Population: models
& density
dependence.
Population:
managing
populations.
Population:
stochasticity.
To identify ethical
actions, and
distinguish from
the opposite.
To contrast
learning via
traditional lectures
vs. active learning.
To evaluate
baseline critical
thinking in class.
To interpret and
plot survivorship
curves, and
calculate life
tables.
To model the
trajectory of
populations using
summary
demographic
parameters.
To design
management
strategies based
on population
models.
To evaluate the
effects of
stochasticity on
Textbook reading Discussion
reading
How to read a scientific article (pdf)
http://biology.kenyon.edu/Bio_InfoLit/index.html
http://www.nature.com/scitable/knowledge/library/survivorship-curves-
16349555
http://www.nature.com/scitable/knowledge/library/how-populations-grow-theexponential-and-logistic-13240157
http://www.eoearth.org/article/Carrying_capacity
http://www.nature.com/scitable/knowledge/library/population-ecology-at-workmanaging-game-populations-50937864
(Congdon et
al. 1993)
http://www.eoearth.org/article/Minimum_viable_population_size?topic=58074 (Frick et al.
2010)
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25-
Sep
27-
Sep
2-
Oct
4-
Oct
9-
Oct
11-
Oct
16-
Oct
18-
Oct
23-
Oct
Genetics: genetic
diversity.
Genetics: HWE &
mutation. First
draft blog entry
due.
Genetics: genetic
drift & migration.
Genetics: natural
selection. Reviews
of peers due.
Species
interactions:
infectious disease.
Exam I
Species
interactions:
competition.
Species
interactions: enemy
release & invasion.
Second draft blog
entry due.
Species
interactions:
consequences of
populations.
To relate genetic
diversity to
demography and
life history.
To infer departure
from equilibrium
from observed
gene frequencies.
To contrast the
effects of
demographic
processes on
genetic diversity
To assess the role
of genetic diversity
in future
conservation.
To model the
impact of
infectious disease
on population
dynamics.
To asses the role
of competition in
shaping
communities.
To relate species
interaction to
biological
invasion.
To measure
impact of invasion
on communities
http://www.nature.com/scitable/topicpage/mitosis-meiosis-and-inheritance-476
http://www.nature.com/scitable/knowledge/library/the-hardy-weinbergprinciple-13235724
http://www.nature.com/scitable/topicpage/genetic-drift-and-effectivepopulation-size-772523
(Hendrickson
et al. 2003)
http://www.nature.com/scitable/topicpage/negative-selection-1136 (Silva et al.
2006)
http://www.nature.com/scitable/knowledge/library/direct-and-indirectinteractions-15650000
http://www.nature.com/scitable/knowledge/library/ecological-consequences-ofparasitism-13255694
http://www.nature.com/scitable/knowledge/library/resource-partitioning-andwhy-it-matters-17362658
http://www.eoearth.org/article/Invasive_species (Hochachka
& Dhondt
2000)
http://www.nature.com/scitable/knowledge/library/conceptualizing-andevaluating-non-native-species-80060037
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25-
Oct
30-
Oct
1-
Nov
6-
Nov
8-
Nov
13-
Nov
15-
Nov
20-
Nov
22-
Nov
27-
Nov
29-
Nov
invasion. and ecosystems.
Biogeography:
biological
communities.
Reviews of peers
due.
No classes
No classes
Critical thinking:
Intervention.
Biogeography:
species-area
relationship.
Biogeochemistry:
carbon cycling.
Exam II
Biogeochemistry:
more carbon
cycling.
No classes
Economics: the
global commons.
Economics:
microeconomic
equilibrium
&environmental
To contrast
populations and of
communities.
To practice critical
thinking skills.
To calculate
species richness
in island and
island-like
habitats.
To diagram major
biotic components
of carbon flows.
To distinguish
environmental
goods from
rival/excludable
commodities.
To interpret and
plot supply and
demand curves,
and identify
http://www.nature.com/scitable/knowledge/library/sampling-biologicalcommunities-23676556
http://www.nature.com/scitable/knowledge/library/the-conservation-of-mass-
17395478
http://www.nature.com/scitable/knowledge/library/soil-carbon-storage-
84223790
http://www.eoearth.org/article/Tragedy_of_the_Commons_(historical)
pp. 52–54 in posted reading.
http://www.eoearth.org/article/Supply_and_demand?topic=49482
(Torchin et al.
2003)
(Brooks et al.
1999)
pp. 71-73 in posted reading. (Kindermann
et al. 2008)
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4-
Dec
6-
Dec
18-
Dec
externalities. Final
version blog entry
due.
Economics:
pollution markets.
Critical thinking
assessment.
Reviews of peers
due.
environmental
degradation as an
externality.
To design marketbased
correctives
to environmental
externalities.
To evaluate critical
thinking after
having taken the
class.
E4330 11:15 AM–1:45
PM
http://www.eoearth.org/article/Economics_of_climate_change?topic=49482
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Critical Thinking Rubric
Modified from the AAC&U VALUE Rubric by The Network of Conservation Educators & Practitioners (NCEP)
Critical thinking is a habit of mind characterized by the comprehensive exploration of issues, ideas, evidence, and events before
accepting or formulating an opinion or conclusion. Levels of achievement (1-4) range from Beginning to Exemplary.
Explanation of
issues to be
considered critically
Evidence
Selecting and using
information to
investigate a point of
view or conclusion
Influence of context
and assumptions
States the issue/problem without
clarification or description.
Selects evidence not relevant to
the issue.
1 2 3 4
Takes information from source(s)
without any
interpretation/evaluation.
Conflates cause and correlation,
facts and opinion. Takes
viewpoints of experts as fact,
without question.
Shows an emerging awareness
of assumptions and context.
Does not recognize context or
assumptions and underlying
implications, or does so
superficially.
States the issue/problem but
description leaves some terms
undefined, ambiguities
unexplored and/or backgrounds
unknown.
Selects evidence somewhat
relevant to the issue.
Takes information with some
interpretation/evaluation, but not
enough to develop a coherent
analysis or synthesis. Takes
viewpoints of experts mostly as
fact, with little questioning.
Identifies some ways in which
relevant contexts affect the
issue. Acknowledges various
sides of an issue. May be more
aware of others’ assumptions
than one’s own (or vice versa).
States, describes
and clarifies
issue/problem so
that understanding is
not seriously
impeded by
omissions.
Selects evidence
mostly relevant to
the issue.
Takes information
with enough
interpretation/
evaluation to
develop a coherent
analysis or
synthesis. Questions
viewpoints of
experts.
Identifies and
examines own and
other’s assumptions
and several relevant
contexts when
describing/
evaluating an issue.
Clearly states and
comprehensively
describes issue/problem
delivering all relevant
information necessary
for full understanding.
All evidence selected is
relevant to the issue.
Takes information with
enough interpretation/
evaluation to develop a
comprehensive analysis
or synthesis. Thoroughly
questions viewpoints of
experts.
Fully analyzes and
synthesizes own and
others' assumptions.
Carefully evaluates
relevance of contexts
when describing/
evaluating an issue.
Conclusions and Position is too simple or obvious. Position begins to acknowledge Position Position takes into
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elated outcomes
Ability to make
judgments and reach a
position, drawing
appropriate
conclusions based on
the available information,
its implications and
consequences.
Conclusion is inconsistently tied
to the information discussed.
Dismisses evidence without
adequate justification. Related
outcomes (consequences and
implications) are not mentioned,
or oversimplified.
complexity of an issue, such as
different sides, knowledge gaps,
or alternative solutions.
Conclusion is logically tied to
information, but evidence may
be selected to bolster own
arguments. Some related
outcomes (consequences and
implications) are identified
clearly.
acknowledges
complexity of an
issue; refers to
different sides,
knowledge gaps,
alternative solutions.
Conclusion is
logically tied to a
range of information,
including opposing
viewpoints.
Consequences and
implications) are
identified clearly.
account the complexity
of an issue.
Conclusions and related
outcomes
(consequences and
implications) are logical,
reflect student’s informed
evaluation and are
qualified as the best
available given evidence
and context.
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Bibliography
Brooks, T., J. Tobias, and A. Balmford. 1999. Deforestation and bird extinctions in the Atlantic
forest. Animal Conservation 2:211-222.
Congdon, J. D., A. E. Dunham, and R. C. Van Loben Sels. 1993. Delayed Sexual Maturity and
Demographics of Blanding's Turtles (Emydoidea blandingii): Implications for
Conservation and Management of Long-Lived Organisms. Conservation Biology 7:826-
833.
Frick, W. F., J. F. Pollock, A. C. Hicks, K. E. Langwig, D. S. Reynolds, G. G. Turner, C. M.
Butchkoski, and T. H. Kunz. 2010. An Emerging Disease Causes Regional Population
Collapse of a Common North American Bat Species. Science 329:679-682.
Hendrickson, S. L., R. Bleiweiss, J. C. Matheus, L. S. de Matheus, N. L. Jácome, and E. Pavez.
2003. Low genetic variability in the geographically widespread Andean Condor. The
Condor 105:1-12.
Hochachka, W. M., and A. A. Dhondt. 2000. Density-dependent decline of host abundance
resulting from a new infectious disease. Proceedings of the National Academy of
Sciences, USA 97:5303-5306.
Kindermann, G., M. Obersteiner, B. Sohngen, J. Sathaye, K. Andrasko, E. Rametsteiner, B.
Schlamadinger, S. Wunder, and R. Beach. 2008. Global cost estimates of reducing carbon
emissions through avoided deforestation. Proceedings of the National Academy of
Sciences, USA 105:10302-10307.
Luyssaert, S., E. D. Schulze, A. Borner, A. Knohl, D. Hessenmoller, B. E. Law, P. Ciais, and J.
Grace. 2008. Old-growth forests as global carbon sinks. Nature 455:213-215.
Silva, A., G. Luikart, N. Yoccoz, A. Cohas, and D. Allainé. 2006. Genetic diversity-fitness
correlation revealed by microsatellite analyses in European alpine marmots (Marmota
marmota). Conservation Genetics 7:371-382.
Torchin, M. E., K. D. Lafferty, A. P. Dobson, V. J. McKenzie, and A. M. Kuris. 2003.
Introduced species and their missing parasites. Nature 421:628-630.
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