San José State University
Department of Geology
Geology 285: Mass Extinction Seminar (27808), Spring 2013
Instructor:
Jonathan Hendricks
Office Location:
307 Duncan Hall
Telephone:
(408) 924-5279
Email:
[email protected]
Office Hours:
Tuesdays 1:30-3:30 PM, or by appointment
Class Days/Time:
Wednesdays, 1:30-3:20pm
Classroom:
309 Duncan Hall
Course Description
Overview of the environmental causes and biotic consequences of ancient massive
extinction events, including impactions for future life on Earth.
Course Goals and Student Learning Objectives
By the end of the semester, students are expected to understand hypotheses and
pertinent evidence concerning the causes and consequences of the “big 5” massive
extinction events that occurred during the Phanerozoic eon of geological time. This
goal will be achieved through analysis and discussion of the primary scientific
literature. Students will also apply their knowledge of past mass extinction events to
predicting the ecological consequences of current and future human-driven impacts
on the environment.
Additionally, the following Department of Geology graduate program learning
objectives will be addressed by your participation and involvement in the course:
1. Demonstrate scientific writing of acceptable quality.
2. Demonstrate ability to present results of scientific research orally.
3. Develop skills and knowledge to make use of scientific data and
resources to support investigations.
4. Develop ability to think analytically.
Geology 285 (Mass Extinction Seminar), Spring 2013
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Desire 2 Learn (D2L)
Important announcements and some course materials will be distributed
electronically using Desire 2 Learn (D2L), which may be accessed online at
http://sjsu.desire2learn.com. It is recommended that students check D2L for
announcements once per day. Students may also use D2L to check their grades
throughout the semester. See the following website for details on how to access
D2L: http://www.sjsu.edu/ecampus/students/.
Textbook (Required)
Raup, David M. 1991. Extinction: Bad Genes or Bad Luck? W. W. Norton &
Company, New York, 210 pp. The SJSU bookstore should have copies, though this
book may also be purchased online. Expect to pay $15 or less. ISBN10: 0393309274 | ISBN-13: 978-0393309270
Other Readings
Numerous other readings are assigned and listed in the schedule and bibliography
at the end of this greensheet. Students are expected to attain their own electronic
(PDF) copies of these papers using the SJSU library (http://library.sjsu.edu/; search
for publication names under “eJournals”).
Classroom Protocol
Students are expected to actively participate in classroom discussions; a portion of
the final grade will be based on participation (see below). Discussions must be kept
civil; students must not talk over one another, nor dominate class time if other
students are trying to speak. Arrive on time and don’t play with your cell phone,
laptop, etc. during class unless you are using it to look at an electronic version of a
paper that we are discussing.
Dropping and Adding
Students are responsible for understanding the policies and procedures about
add/drops, academic renewal, etc. Information on add/drops are available at
http://info.sjsu.edu/web-dbgen/narr/soc-fall/rec-324.html . Information about late
drop is available at http://www.sjsu.edu/sac/advising/latedrops/policy/ . Students
should be aware of the current deadlines and penalties for adding and dropping
classes.
Geology 285 (Mass Extinction Seminar), Spring 2013
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Assignments and Grading Policy
There will be a total of 350 points available in the course:
• Quizzes: 195 pts. (~56%)
• Participation: 70 pts. (20%)
• Paper: 50 pts. (~14%)
• Presentation: 35 pts. (10%) (Will be delivered to the class during the final
exam period on May 21)
Final grades—based upon percentages of the total points available—will be
calculated using the following distribution:
99% to 100% A+
93% to <99% A (excellent)
90% to <93% A87% to <90% B+
83% to <87% B (good)
80% to <83% B77% to <80% C+
73% to <77% C (adequate)
70% to <73% C65% to <70% D+
60% to <65% D (poor)
50% to <60% D<50% F (failure)
You will be able to track your progress throughout the semester on Desire 2 Learn.
Quizzes (15 pts. per week; 195 pts. total)
There will be a 10-15 minute quiz at the start of each class period (beginning at
1:30pm, prompt) that will address your understanding of the required readings for
the week. In preparation, focus on the major points of the paper. What hypothesis
or question was addressed? How (generally speaking) was the hypothesis/question
methodologically studied? (Hint: don’t get bogged down in the minutiae of methods;
rather, understand the main approach taken). What was the relevant evidence?
What were the major conclusions of the paper? Some quiz questions will have to
do with interpretation of key figures.
Each quiz will be worth 15 points and there will be a total of 14 such quizzes. These
quizzes will be “open book”, though you must work independently. Laptops may be
used during the quiz to look at notes and papers, but NOT to communicate with
other students (this would be considered academic misconduct). Your single lowest
quiz score will be dropped when computing final grades. Except in cases of
documented serious illness or family emergency, make-ups of missed quizzes will
not be permitted.
Geology 285 (Mass Extinction Seminar), Spring 2013
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Participation (5 pts. per week, 70 pts. total)
This course is a seminar, which cannot function without active student-driven
discussion and participation. As such, a portion of the grade will be based on
participation. Minimally, students should thoughtfully answer a prompted question
or raise a new thoughtful point of discussion at least twice during each class period
(2.5 pts x 2 = 5 discussion points per class period).
Each assigned reading will also be formally introduced by a student who is in
charge of briefly summarizing the paper (~5 minutes) at the front of the classroom
and then initiating and leading the following discussion (e.g., by asking prepared
questions). Responsibility for individual papers will be assigned on the first day of
class.
Paper (50 pts.) and Presentation (35 pts.)
A “term paper” will be due at the beginning of the final class period on May 8. The
late penalty will be 10 points/per day (20%) that it is late (no exceptions). A
corresponding presentation will be delivered to the class during the final exam
period on May 21. Failure to give a presentation on May 21 will result in a
presentation grade of zero.
Both the term paper and presentation will relate to this question: “Given current and
probable future human impacts on the environment, as well as paleontological
insights derived from the study of past mass extinction events, how might life on
Earth differ 200 years from now relative to its current state?”
Additional details on both the paper and presentation will be provided later.
University Policies
Academic integrity
Students should know that the University’s Academic Integrity Policy is availabe at
http://www.sa.sjsu.edu/download/judicial_affairs/Academic_Integrity_Policy_S072.pdf. Your own commitment to learning, as evidenced by your enrollment at San
Jose State University and the University’s integrity policy, require you to be honest
in all your academic course work. Faculty members are required to report all
infractions to the office of Student Conduct and Ethical Development. The website
for Student Conduct and Ethical Development is available at
http://www.sa.sjsu.edu/judicial_affairs/index.html.
Instances of academic dishonesty will not be tolerated. Cheating on exams or
plagiarism (presenting the work of another as your own, or the use of another
person’s ideas without giving proper credit) will result in a failing grade and
sanctions by the University. For this class, all assignments are to be completed
by the individual student unless otherwise specified. If you would like to include in
your assignment any material you have submitted, or plan to submit for another
Geology 285 (Mass Extinction Seminar), Spring 2013
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class, please note that SJSU’s Academic Policy F06-1 requires approval of
instructors.
Campus Policy in Compliance with the American Disabilities Act
If you need course adaptations or accommodations because of a disability, or if you
need to make special arrangements in case the building must be evacuated, please
make an appointment with me as soon as possible, or see me during office hours.
Presidential Directive 97-03 requires that students with disabilities requesting
accommodations must register with the DRC (Disability Resource Center) to
establish a record of their disability.
SJSU Writing Center
The SJSU Writing Center is located in Room 126 in Clark Hall. It is staffed by
professional instructors and upper-division or graduate-level writing specialists from
each of the seven SJSU colleges. Our writing specialists have met a rigorous GPA
requirement, and they are well trained to assist all students at all levels within all
disciplines to become better writers. The Writing Center website is located at
http://www.sjsu.edu/writingcenter/about/staff//.
Expectations and Success
Expect to do a lot of reading for this class (2-4 reading assignments per week). Set
aside time in your schedule for this. Be aware that some seemingly short papers
(especially in “high-profile” journals like Science, Nature, and PNAS) are densely
written and may take as much time to read and understand as some longer-format
journal articles. Come to class ready to discuss papers and to answer related quiz
questions (see notes above regarding quizzes).
SJSU mandated text: “Success in this course is based on the expectation that
students will spend, for each unit of credit, a minimum of forty-five hours over the
length of the course (normally 3 hours per unit per week with 1 of the hours used for
lecture) for instruction or preparation/studying or course related activities including
but not limited to internships, labs, clinical practica. Other course structures will
have equivalent workload expectations as described in the syllabus.”
Geology 285 (Mass Extinction Seminar), Spring 2013
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Geology 285 (Spring, 2013) Course Schedule
This schedule is subject to change with fair notice during class time or via an
announcement on D2L.
Week
1
2
3
4
5
6
7
8
9
10
11
12
13
Date
Jan. 23
Jan. 30
Feb. 6
Feb. 13
Feb. 20
Feb. 27
Mar. 6
Mar. 13
Mar. 20
Mar. 27
Apr. 3
Apr. 10
Apr. 17
Topics, Readings, Assignments, Deadlines
Topic: Introduction to the Seminar
Readings: None.
Topic: Introduction to Extinction
Readings: Raup (1991a, Introduction & Ch. 1-3); Gould (1993,
Ch. 3)
Topic: Mass Extinctions
Readings: Raup (1991a; Ch. 4); Raup and Sepkoski (1982);
Bambach (2006)
Topic: The Kill Curve, Selectivity, and Causes of Extinction
Readings: Raup (1991a; Ch. 5-8); Raup (1991b)
Topic: Periodicity
Readings: Raup and Sepkoski (1984); Lieberman and Melott
(2012)
Topic: The End Cretaceous Mass Extinction 1: The Alvarez
Hypothesis
Readings: Raup (1991a, Ch. 9-10; Alvarez et al. (1980);
Fellman (1988)
Topic: The End Cretaceous Mass Extinction 2: Thirty Years
After Alvarez et al. (1980)
Readings: Schulte et al. (2010); Schulte et al. (2010) critics
Topic: The End Cretaceous Mass Extinction 3: Selectivity and
Recovery
Readings: Wilf et al. (2006); Meredith et al. (2011); Longrich et
al. (2012)
Topic: End Ordovician Mass Extinction
Readings: Sheehan (2001); Finnegan et al. (2012)
Spring Break
Topic: The Late Devonian Crisis
Readings: Bond and Wignall (2009); Stigall (2010)
Topic: The End Permian Mass Extinction
Readings: Payne and Clapham (2012); Irmis and Whiteside
(2012)
Topic: The End Triassic Mass Extinction
Readings: Whiteside et al. (2010); Lindstrom et al. (2012)
Week
14
15
16
Final
Exam
Period
Date
Apr. 24
May 1
May 8
May 21
(12:152:30)
Topics, Readings, Assignments, Deadlines
Topic: Sixth Mass Extinction 1: Pleistocene Megafauna
Readings: Barnosky (2008); Johnson (2009)
Topic: Sixth Mass Extinction 2: Historical and Modern Impacts
Readings: Jackson et al. (2001); Harnik et al. (2012)
Topic: Sixth Mass Extinction 3: Conservation Paleobiology and
Epilogue; Term Papers Due
Readings: Raup (1991a, Ch. 11 and Epilogue); Dietl and Flessa
(2011)
Presentations
Readings
Note:
EJ = Electronic Journal article accessible @ http://library.sjsu.edu
ER = Electronic Reserve article accessible @ http://library.sjsu.edu/coursereserves/course-reserves
Alvarez, L.W., W. Alvarez, F. Asaro, and H. V. Michel. 1980. Extraterrestrial
cause for the Cretaceous-Tertiary extinction. Science 208: 1095-1108. (EJ)
Bambach, R. K. 2006. Phanerozoic biodiversity mass extinctions. The Annual
Review of Early and Planetary Science 34:127-155. (EJ)
Barnosky, A. D. 2008. Megafauna biomass tradeoff as a driver of Quaternary and
future extinctions. Proceedings of the National Academy of Sciences of the
United States of America 105: 11543-11548. (EJ)
Bond, D. P. G. and P. B. Wignall. 2008. The role of sea-level change and marine
anoxia in the Frasnian-Famennian (Late Devonian) mass extinction.
Palaeogeography, Palaeoclimatology, Palaeoecology 263: 107-118. (EJ)
Dietl, G. P. and K. W. Flessa. 2011. Conservation paleobiology: putting the dead
to work. Trends in Ecology & Evolution 26: 30-37. (EJ)
Fellman, B. 1988. Shootout at the K/T Boundary. The Scientist. http://www.thescientist.com/?articles.view/articleNo/9830/title/Shootout-At-The-K-TBoundary/ (Web)
Finnegan, S., N. A. Heim, S. E. Peters, and W. W. Fischer. 2012. Climate
change and the selective signature of the Late Ordovician mass extinction.
Proceedings of the National Academy of Sciences of the United States of
America 109:6829–6834. (EJ)
Gould, S. J. 1993. Chapter 3: Losing a Limpet. In: Eight Little Piggies: Reflections
in Natural History. W.W. Norton, New York. Pp. 52-60. (ER)
Harnik, P. G. et al. 2012. Extinctions in ancient and modern seas. Trends in
Ecology and Evolution 27: 608-617. (EJ)
Irmis, R. B. and J. H. Whiteside. 2012. Delayed recovery of non-marine tetrapods
after the end-Permian mass extinction tracks global carbon cycle.
Proceedings of the Royal Society B 279: 1310-1318. (EJ)
Jackson, J. B. C. et al. 2001. Historical overfishing and the recent collapse of
coastal ecosystems. Science 293:629-638. (EJ)
Johnson, C. N. 2009. Ecological consequences of Late Quaternary extinctions of
megafauna. Proceedings of the Royal Society B 276: 2509-2519. (EJ)
Lieberman, B. S. and A. L. Melott. 2012. Whilst this planet has gone cycling on:
what role for periodic astronomical phenonmena in large-scale patterns in the
history of life? In: Talent, J. A. (Ed), Earth and Life, pp. 37-50.
http://link.springer.com/content/pdf/10.1007%2F978-90-481-3428-1_3
Lindstrom et al. 2012. No causal link between terrestrial ecosystem change and
methane release during the end-Triassic mass extinction. Geology 40: 531534. (EJ)
Longrich, N. R., B.-A. S. Bhullar, and J. A. Gauthier. 2012. Mass extinction of
lizards and snakes at the Cretaceous-Paleogene boundary. Proceedings of
the National Academy of Sciences of the United States of America 109:
21396-21401. (EJ)
Meredith, R. W. et al. 2011. Impact of the Cretaceous terrestrial revolution and
KPg extinction on mammal diversification. Science 334(6055): 521-524. (EJ)
Payne, J. L. and M. E. Clapham. 2012. End-Permian mass extinction in the
oceans: an ancient analog for the twenty-first century? Annual Review of
Earth and Planetary Sciences 40: 89-111. (EJ)
Raup, D. M. 1991a. Extinction: Bad Genes or Bad Luck? W.W. Norton, New York,
210pp. (Required book – purchase.)
Raup, D. M. 1991b. A kill curve for Phanerozoic marine species. Paleobiology 17:
37-48. (EJ)
Raup, D. M. and J. J. Sepkoski. 1982. Mass extinctions in the marine fossil
record. Science 215: 1501-1503. (EJ)
Raup, D. M. and J. J. Sepkoski. 1984. Periodicity of extinctions in the geologic
past. Proceedings of the National Academy of Sciences of the United States
of America 81: 801-805. (EJ)
Schulte et al. 2010. The Chicxulub asteroid impact and mass extinction at the
Cretaceous-Paleogene boundary. Science 327: 1214-1218. (EJ)
Schulte et al. 2010 critics. Archibald et al. 2010. Courtillot and Fluteau (2010).
Keller et al. (2010) and response by Schulte et al. (2010). Science 328: 973976. (EJ)
Sheehan, P. M. 2001. The late Ordovician mass extinction. Annual Review of
Earth and Planetary Sciences 29:331-364. (EJ)
Stigall, A. L. 2010. Invasive species and biodiversity crises: testing the link in the
late Devonian. PLoS ONE 5(12): e15584. (Web)
Whiteside, J. H., P. E. Olsen, T. Eglinton, M. E. Brookfield, and R. N. Sambrotto.
2010. Compound-specific carbon isotopes from Earth’s largest flood basalt
eruptions directly linked to the end-Triassic mass extinction. Proceedings of
the National Academy of Sciences of the United States of America 107: 67216725. (EJ)
Wilf, P., C. C. Labandeira, K. R. Johnson, and B. Ellis. 2006. Decoupled plant
and insect diversity after the end-Cretaceous extinction. Science 313:11121115. (EJ)