SYLLABUS - Ecology and Evolutionary Biology

Course title and number GEOL652: Biogeology
Term
Spring 2012
Meeting times and location TBA
Course Description and Prerequisites
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SYLLABUS
This course is designed to introduce early career graduate students to modern themes, theories, and
conceptual tools in geobiology. Students are expected to have diverse backgrounds in the geosciences, biology,
chemistry, and engineering. Completion of this course will provide the groundwork for more advanced courses in
paleobiology, environmental geosciences, landscape ecology and biogeochemistry, and biological oceanography,
as well as provide preparation for research in systems with significant biological and geological components.
Course topics: organism/environment interactions over time scales of seconds to billions of years and
spatial scales of nanometers to tens of thousands of kilometers; dynamical modeling of geobiological systems;
ecosystem cycling of energy and matter; ecological processes and evolution; case studies.
Prerequisite: permission of instructor
Recommended prerequisites: one year each of college-level earth science, chemistry, and biology, and
math through ordinary differential equations
Learning Outcomes
Students will be able to
1) identify and explain the uses of basic models and theories used for modeling complex geobiological
systems (e.g. population growth models, conservation laws, law of mass action, transport models,
evolution, etc.);
a. Students will be able to associate examples of physical/biological processes with corresponding
models or theories and, where appropriate, express these models/theories in mathematical
form.(Case study reflections and discussions; oral midterm and final)
b. Students will be able to explain the assumptions necessary for expressing these models in
mathematical form. (Case study reflections and discussions; oral midterm and final)
c. Students will be able to identify conditions under which these models/theories or their
mathematical expressions do not apply. (Case study reflections and discussions; oral midterm
and final)
2) identify likely processes occurring in real geobiological systems (e.g. soils, sediments, landscapes) based
on measured data;
a. Students will be able to analyze primary literature in geobiology using the “paired funnel”
scheme (i.e. for a given paper, they will be able to identify the context, specific question,
approach, hypotheses, analytical techniques, results, analyses, conclusions, and implications).
(Case study reflections and discussions)
b. Students will be able to discuss how each figure in a paper contributes to the overall logical
flow. (Case study reflections and discussions)
c. Students will be able to use basic models and theories to identify specific processes important in
producing measured data presented in figures or tables (e.g. use the slope and curvature of a
concentration profile to identify zones of production, consumption, and transport of solutes; use
population growth models to identify episodes of growth and stasis from substrate time series;
etc.). (Case study reflections and discussions; oral midterm and final)
3) develop conceptual models of geobiological systems based on predicted actors, processes, and interactions
and express those models through representations;
a. Students will be able to produce flow charts, box/flux diagrams, or other appropriate
representations capturing essential elements of geobiological systems in case studies drawn from
the primary literature. (Case study reflections and discussions; oral midterm and final)
4) convert conceptual models into simplified mathematical models and analyze their qualitative behaviors to
make simple predictions; and
a. Students will be able to apply basic models and theories to write appropriate mathematical

expressions describing processes and interactions in conceptual models. (Case study reflections
and discussions; oral midterm and final)
b. Students will be able to simplify models by identifying circumstances under which spatial or
temporal scales separate. (Case study reflections and discussions; oral midterm and final)
c. Students will be able to use dynamical systems theory to make qualitative predictions about the
behavior of their models. They will be able to predict the existence of fixed points and evaluate
their stabilities, predict the existence of limit cycles, identify critical parameters and predict
bifurcations and catastrophes, and understand the circumstances under which chaotic behavior
is possible. (Case study reflections and discussions; oral midterm and final)
5) discuss and critique geobiological models.
a. Students will use the reasoning outlined in goals 1–4 to evaluate the reasoning and assumptions
in modern integrative geobiological models. (Case study reflections and discussions; term
project and presentation)
Names
Telephone number
Email addresses
Office hours
Office locations
Mike Tice
845-3138
tice@geo.tamu.edu
TBA
Halbouty 314
Instructor Information
Textbook and/or Resource Material
There will be one reading from the primary literature each week which will be required for participation
in Friday case study discussions. In addition, there will be up to two short optional readings (tutorials) provided
each week that may be helpful background reading for the case studies. These tutorials will not be discussed in
class. There is no required textbook.
Grading Policies
Activities forming the basis for learning evaluations will be 1) participation in classroom discussions
(20%); 2) written summaries and reflections of weekly readings from the primary literature (20%); 3) a term
project analyzing a specific geobiological system (20%); and 4) a midterm (20%) and final exam (20%). Final
grades will be assigned based on weighted averages of graded activities rounded to the first decimal place (e.g.
89.84% → 89.8%) and the following distribution: A = 90-100%, B = 80-89.9%, C = 70-79.9%, D = 60-69.9%, F ≤
59.9%.
Case Studies. Each of the first 12 weeks will include analysis of one case study from the primary
literature. Students will work in groups to read one paper and analyze it using models and theories discussed in
class. Each student will individually write a short (1–3 page) first-person reflection on that paper explaining their
analyses in logical steps (e.g. “I didn’t find the authors’ approach obvious, so I reasoned in the following way in
order to identify it.”). These reflections should be type-written and will prepare students for case study discussions
each Friday. Discussions will be student-led, but discussion leaders will be selected by the instructors randomly
throughout the Friday session. Students are encouraged to add additional notes to their reflections in blue ink prior
to handing them in at the end of discussion.
Term Project. Each student will select a geobiological system to analyze and present to the class in a slide
presentation. The instructors will guide students in selecting topics appropriate for modeling using techniques
described in this class. Topics presented in term projects will form part of the material tested in the final.
Midterm and Final. Students will be given small geobiological models to analyze over the course of one
hour. They will then present their analyses orally to the instructors. The oral presentation and discussion will form
the basis for the test grades.
Course Topics, Calendar of Activities, Major Assignment Dates
Week Topic Required Reading
1 One-Dimensional Models in Geobiology: Population
growth; one-component reaction kinetics
Case Study: As(III)-oxidizing phototrophs
Tutorials: Oxidation/reduction reactions and
metabolism; measuring bacterial growth
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Kulp et al., 2008, Arsenic(III) fuels
anoxygenic photosynthesis in hot
spring biofilms from Mono Lake,
California, Science 321:967–970.

2 Two-Dimensional Models in Geobiology:
Competition; two-component reaction kinetics
Case Study: Evolution of cooperation
Tutorials: NA
3 N-Dimensional Models in Geobiology:
Metapopulation dynamics; biogeochemical cycles
Case Study: Mediterranean microbial communities
Tutorials: Chemostat growth
4 Networks in Geobiological Models: Structure of
networks
Case Study: Community detection
Tutorials:
5 Dynamics on Networks: Dynamical systems and
percolation on networks
Case Study: Stability of ecosystems
Tutorial:
6 Parameter Sensitivity in Geobiological Models:
Biogeochemical bifurcations; ecological catastrophes
Case Study: Desertification
Tutorials: Terrestrial nitrogen cycling
7 Continuous Models in Geobiology:
Reaction/diffusion dynamics; transport in turbulent
fluids
Case Study: Microbial mat growth and the diffusive
boundary layer
Tutorials: Anaerobic ammonium oxidation; the marine
nitrogen cycle
8 Scale Separation in Geobiology: Identifying physical
and temporal scales; developing coupled models
Case Study: Spatial organization in mats and
stromatolites
Tutorials: Stromatolites
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Griffin et al., 2004, Cooperation and
competition in pathogenic bacteria,
Nature, 430(7003):1024–1027.
Lebaron et al., 2001, Microbial
community dynamics in
Mediterranean nutrient-enriched
seawater mesocosms: changes in
abundances, activity and composition,
FEMS Microbiology Ecology,
34:255–266.
Girvan and Newman, 2002, Community
structure in social and biological
networks, PNAS, 99(12):7821–7826.
Neutel et al., 2002, Stability in real food
webs: weak links in long loops,
Science, 296:1120–1123.
McCann et al., 1998, Weak trophic
interactions and the balance of nature,
Nature, 395:794–798.
Schlesinger et al., 1990, Biological
feedbacks in global desertification,
Science, 247(4946):1043–1048.
Kuypers et al., 2003, Anaerobic
ammonium oxidation by anammox
bacteria in the Black Sea, Nature,
422:608–611.
Tice, et al., 2011, Archean microbial mat
communities, AREPS, 39:297–319.
9 MIDTERM NA
10 Tectonics vs. Life Lowe and Tice, 2007, Tectonic controls
on atmospheric, climatic, and
biological evolution 3.5–2.4 Ga,
Precambrian Research, 158:177–197.
Kopp et al., 2005, The Paleoproterozoic
snowball Earth: a climate disaster
triggered by the evolution of oxygenic
photosynthesis, PNAS,
102(32):11131–11136.
11 Fitness Landscapes; Frustration and Extraction Knoll, 2003, Life on a Young Planet,
chapter 7
Marshall, 2003, Nomothetism and
understanding the Cambrian
“Explosion”, Palaios 18(3):195-196.
12 The Gaia Hypothesis Lovelock, 1988, The Ages of Gaia,
chapter 4
Free and Barton, 2007, Do evolution and
ecology need the Gaia hypothesis?
TRENDS in Ecology and Evolution,
22(11):611–619.

13 Student Presentations
14 Student Presentations
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