ENVS316 Schedule, Assignments, Readings & Questions

Readings should be completed prior to the class, lab, or site visit for which they are assigned. The questions posted for each reading are designed to help you focus on the concepts most relevant to this course (these questions are also useful as a study guide for quizzes). Since the syllabus will undergo minor modifications and readings and questions may be added, you should check below before each reading. PDFs of all assigned readings, except those in J. Gordon’s Planning Research are in folders on Blackboard corresponding to each topic below.  Click on the headings below to navigate to each week’s readings and assignments. Unless a different time is specified, assignments are due by midnight on the date indicated.


I. BASIC PRINCIPLES OF SYSTEMS ECOLOGY

1. Week of 9/5/11: Intro to the Ecosystem Ecology and Ecosystem Forming Factors

2. Week of 9/12/11: Ecosystem Forming Factors in North East Ohio

3. Week of 9/19/11: Energy Flow from Biosphere to Physiological Scales

4. Week of 9/26/11: Biogeochemical Cycles

5. Week of 10/3/11: Ecosystem-Level Research

6. Week of 10/10/11: Ecosystem Development, Disturbance, Resilience & Biotic Regulation

 

II. SYSTEM ECOLOGY APPLICATIONS

7. Week of 10/17/11: Restoring and Engineering Ecosystems

Week of 10/24/11: Fall Break

8. Week of 10/31/11: Agroecosystems and Biosequestration

9. Week of 11/7/11: Landscape Ecology

10. Week of 11/14/11: Global Change #1: Climate Change

11. Week of 11/21/11: Methods of Data Analysis

12. Week of 11/28/11: Great Lake Ecosystem and Response to Phosphorous

13. Week of 12/5/11: Applying Systems Concepts to Human Habitat: The Ecology of the Built Environment

14. Week of 12/12/11: Poster Presentation


I. BASIC PRINCIPLES OF SYSTEMS ECOLOGY

1. Week of 9/5/11: Intro to the Ecosystem Ecology and Ecosystem Forming Factors

READINGS:

>”ENVS316 Course Structure & Function”

This is the text linked to the second button on the course Blackboard site.  Read this completely so that you understand the objectives, expectations and relationship between course structure and function.  Bring questions to class.

>Barrett et al. Transcending processes and the levels-of-organization concept. 1997. BioScience 47:531-535.

Terms to understand: hierarchy, reductionism, holism
Q: What is the "levels-of-organization concept" and how does it provide a framework for developing an integrated understanding ecosystems?
Q: What common properties do all levels of biological organization possess?
Q:
What do the authors argue is deficient with examining levels in isolation?
Q:
What is a hierarchy?
Q: What are emergent properties and how are they related to the concepts of reductionism and holism? 

>Chapin et al. Chapter 1. The ecosystem concept. 2002. 3-17.

Terms: pool (aka "stock"), flux (aka "flow"), process, scale, succession, climax, parent material, interactive controls, chronosequence, toposequence, functional type (aka functional group)
Q: How is ecosystem ecology distinct from other sub-disciplines of ecology?
Q: Which of the following are pools (stocks) and which are fluxes (flows): plant biomass, photosynthesis, rainfall, soil carbon, grazing, soil moisture? How do the units used for a pool differ from units used for flux?
Q: Of the five that Chapin identifies, which "state factor" is most important in determining the distribution of world biomes? What kind of study can be used to assess the importance of different state factors?

>Ulanowicz. Aristotelean causalities in ecosystem development. 1990. Oikos 57:42-48.

Focus on understanding the sections "The nature of causality" and "An origin of formal and final agency". Don't worry about the math in the section, "Quantifying the effects of formal and final causes", or about the concept of "ascendancy".
Q: How do the feedback principles outlined for ecosystem development apply to other types of systems and to your own experiences?
Q: Distinguish and identify examples of positive and negative feedback, what roles do each play in systems development? How is positive feedback "scale dependent"?
Q: Define cybernetics, holism, reductionism, and autocatalysis
Q: Be able to distinguish between, and provide an example of how the four levels of causality are responsible for experience in your own life

Optional

>Ford Causal loop diagrams. (Chapter 7:, Pages 69-87 in   1999.  Modeling the environment)

DISC/CASE: Conceptual models of causality: (click on “case studies” for examples from previous years)

ASSIGNMENT: a) Conceptual models of feedback and causality due 9/13 (see syllabus instructions on submitting electronically).  b) Complete the survey posted on our class web site Sunday by midnight so that I can set up lab/research working groups

LAB/FIELD: Introduction to Terrestrial Field Methods.  Review field methods of terrestrial analysis and, in Audubon pocket guide, review local trees for quiz including: red maple, sugar maple, silver maple, pin oak, white oak, black oak, black cherry, hickory, ash, eastern red cedar.  Be able to identify leaves by sight and know common name, genus and species names and something about ecological habitat (e.g. moisture light requirements/tolerance, and means of seed dispersal).

 

2. Week of 9/12/11: Ecosystem Forming Factors in North East Ohio

READINGS:

>Sherman: Intro & Rocks (C1 pgs 3-33), Water and Ice (C2, 35-55), Flora (C5, 111-141)

Terms: glacial till, lake till, glacial erratic, end moraine, ground moraine, kettle hole, Lake Maumee, Lake Whittlesey, Lake Warren, Canadian shield, Cincinnati arch, climax forest
Q: Imagine digging a well in Oberlin. Describe the series of materials you would pass through and their geologic origin. How might this differ if you were to drill closer to Lake Erie, on a beach ridge, or adjacent to a river?
Q: If a geologist describes material as being "Devonian" or "Pennsylvanian", what does this tell you about the age and mineralogy of the material?
Q: What sized particles produce sandstone, siltstone and shale? Explain how local geological history resulted in a clay rich soil in NE Ohio.
Q: Some regions of the US that were glaciated still have substantial topographic variation while other regions, like ours here, are very flat. Why?
Q: How does the advance and retreat of glaciers affect the depth of the oceans and the height of the land surface on which the glacier resides?
Q: How do glaciers advance and retreat and how and in what direction do they transport material?
Q: Compare the shape of a river flowing over steep and over slight topography -- which is likely to exhibit a straighter course and why?
Q: In Europe, the primary mountain ranges extend along an East-West direction (Alps and Pyrenees) whereas in North America and Asia they extend primarily in a North-South direction (Appalachians, Rockies). Explain how this fact might explain native species diversity in Europe relative to diversity in North America and Asia.
Q: What role do bogs play in elucidating the vegetative history of a glaciated region? What characteristics of bogs facilitate this? What is the natural ecological progression of a bog over time?
Q: It is believed that tree species in this region became established in the local post-glacial environment in the order: spruce, fir, pine, birch, oak, hemlock, hickory, beech. Why this order, what does it have to do with properties of the individual species?
Q: For species with equal climatic requirements, what type of seed strategy might lead to faster migration into newly available land?
Q: A number of characteristic vegetative forest formations are defined for this region: beech-sugar maple, elm-ash-red maple, oak-hickory, sycamore-cottonwood-red maple. Under what conditions does each of these formations come to dominate a site (think factors)?
Q: In what ways have humans affected the species composition of the local landscape?
Q: An "ecotone" is the relatively diverse region that forms as a gradient between two different kinds of ecosystems. How might one use a similar concept, but on a larger scale, to explain the relatively high plant diversity in this region of the country?

>Chapin et al. Chapter 3. Geology and soils. 2002. 46-67. (Geology and soils)

Terms: rock cycle, igneous, metamorphic, sedimentary, aspect, physical and chemical weathering, bulk density, gley, soil horizon (O, A, E, B, C), texture (clay, silt, sand), oxidation-reduction reaction, soil organic matter, cation exchange capacity, base cations [Don't bother memorizing the soil orders].
Q: What processes are responsible for the rock cycle?
Q: Chapin applies the concept of forming factors (he calls these "state factors") to soils. How do each of the five factors Chapin discuses influence soil formation?
Q: How do processes occurring within ecosystems (i.e. "interactive controls") affect soil development?
Q: What factors determine erosion rate? Which of these are most strongly influenced by human activity?
Q: What is a "soil profile", and what processes cause its development? Explain how differences in climate, drainage, and biota might affect profile development.
Q: What are the processes involved in physical and chemical weathering of soils? Give examples. How do plants affect these processes?
Q: What is soil texture? How and why does it affect ecosystem processes?
Q: What are oxidation-reduction reactions, how are they important in soils? From the perspective of capturing energy, which commonly occurring chemical species in soils are the best electron acceptors, which are the worst?  What are the implications?
Q: What is cation exchange capacity (CEC) and why is it important? What factors determine the CEC of a soil?
Q: If global climate change caused only an increase in average temperature, how would you expect this to affect soil development?

Optional:

>Sherman: People (C3, 57-83), Western reserve (C4, 85-109), Fauna (C6, 143-178)
>Forsyth. The geological setting of the Great Lakes. 1987. p. 11-17 in  The Great Lake Erie (under "Fortner" in Science Library Reserve)
>Furlow. Vegetation and plant geography of Lake Erie. 1987. p. 18-26 in The Great Lake Erie (under "Fortner" in Science Library Reserve)

DISC/CASE: Jones Farm data analysis, Read “Case: Interpreting data from Jones Farm ecosystems” before we meet.  Arrive with mechanistic hypotheses written down!

LAB/FIELD: Jones Farm forest/field/wetland comparison (Draft due 9/20, Final due 9/27)

>Review handouts notes in syllabus on site visit logistics. Each group must select one member who will focus on plants, one on geology & soils, one on humans and one on animals. Review sections of above readings relevant to your assigned role (e.g. geology people should carefully review material on soils, glaciation, etc.).

>Audubon pocket guide and web (e.g. Wikipedia, plants.usda.gov), review local trees for quiz including all trees from previous excursion and: cottonwood, black willow, elm, buckthorn, beech, hawthorn, apple, clover, broad-leaf cattail, sedge family, rush family.  Learn something about the ecological niches of these different plant species.  Be able to identify leaves by sight and know common name, genus and species names and something about ecological habitat (e.g. moisture light requirements, and means of seed dispersal).

 

>Soil Survey of Lorain County, OH (Hard reserve in Science library)
Locate the Jones Farm and determine soil series and properties

>Masi. Ecological Design Innovation Center: Land assessment and conceptual land-use plan. 2000.

>Fox. SARE proposal for Jones Farm forest development 2003 (posted with this week’s readings).  Skim through this to get a general idea of what the plans are for this site

>Petersen.  Example site reports 1990 and other site reports.  These are site reports from a course taught at Yale School of Forestry that should provide you with a good sense of my general expectations.

3. Week of 9/19/11: Energy Flow from Biosphere to Physiological Scales

NOTE: **Thursday’s class meets in the Science Center PC Lab (1st floor between S. entrance and foyer)**

QUIZ#1 due 9/22

READINGS:

>Chapin et al. Chapter 2. Earth's climate system. 2002. 18-45.

Note: This chapter goes into a bit more detail on the climatic system than I care that you know for this course. As always, use the questions as a study guide
Q: How does the energy that the earth receives differ from the energy that it emits?
Q: Explain how unequal heating of the earth by the sun and the resulting atmospheric circulation produce the major latitudinal climate zones.
Q: How does ocean circulation affect climate at global and continental scales?
Q: Specifically how do the greenhouse gasses (“radiatively active gasses”) affect radiative balance?
Q: How does the chemical composition of the earth’s atmosphere influence climate?
Q: Why are upwelling areas important for aquatic primary productivity in the ocean?
Q: How does land cover affect climate, and why is this important? How might land use changes in tropical and temperate forests alter local climates?
Q: What general factors are responsible for long term (millions – thousands of years), intermediate term (100s of years), short term (years), seasonal, and diel (24hr) variability in climate at the surface of the earth?

>Ricklefs 2007, Chapter 6.  Energy in the Ecosystem.  Pgs. 125-141. In The Economy of Nature

Terms: food chain, food web, trophic level, primary producers, primary productivity, gross primary productivity, net primary productivity, photosynthetic efficiency, transpiration efficiency, food chain efficiency (= trophic transfer efficiency), assimilation efficiency, exploitation efficiencies, residence time, biomass accumulation ratio, autochthonous vs. allochthonous inputs

Q: Why do ecologists use the element carbon to trace energy flow through ecosystems?
Q: What is the “reduced” form of carbon, what is the “oxidized” form?  Which one represents the higher energy state?
Q: What ecosystems are most productive?  What ecosystems are least productive?  What explains these differences in productivity?
Q: What is the relationship between trophic transfer efficiency and the number of trophic levels in a system?
Q: How would you expect the residence time of carbon in detritus to compare with the residence time of carbon in fresh leaf tissue?  Why?
Q: How does trophic transfer efficiency differ in planktonic ecosystems from forests?  What accounts for this?
Q: Under what conditions would you expect detritus based food chains to dominate over herbivore based food chains and why?

>Aquatic Ecosystem Metabolism Exercise Handout (click on “case studies” button)

Optional:

>Schlesinger. Redox potential: The basics. 1997. 226-242.
Provides a good explanation of redox potential
>Eichenlaub. The effect of Lake Erie on climate. 1987. 27-37. (Science Library Reserve)
How Lake Erie moderates local temperature and precipitation patterns
>Hagen, (p. 50-55 - Elton, 87-94 - Lindeman, 100-107, 140-142 - Whole system metabolism)
Fascinating historical account of development of energy analysis in ecosystems
>Odum. Energy in Ecological Systems.  2005.  77-139.  Chapter 3 in Fundamentals of Ecology.
Energetics explained by one of the grand fathers of ecology
>Hall and Moll. Methods of assessing aquatic primary productivity. 1975.
Good explanation of how to calculate primary productivity
>Lindeman. The trophic-dynamic aspect of ecology. 1942. Ecology 23:399-418.
THE classic paper that started energy analysis in ecology.

DISC/CASE: Whole system metabolism in aquatic ecosystems 

LAB/FIELD: Terrestrial methods (integrate soil analysis as appendix in final Jones farm report due 9/27)

>Terrestrial methods lab handout

>Brewer et al., Chapter 2C, focus on section 10.2. Also read Chapter 6a, sections on Dry Weight and Ash-Free Dry Weight (pgs. 200-201). (Science Library only)

 

4. Week of 9/26/11: Biogeochemical Cycles

READINGS:

>Leopold. Odyssey. 1966. 111-116 (in Ballantine Books 1970 edition).

The most eloquent essay on biogeochemical cycles ever written. To appreciate its subtleties, I suggest that you read Odyssey after the Ricklefs assignments. Savor this one!
Q: What elements might atom x be? How do you know? Does it change?
Q: Which specific components of the story embody conservation of matter and which the 1st and 2nd laws of energy?

>Ricklefs 2007, Chapter 7. Pathways of elements in ecosystems.  Pgs. 142-160. In The Economy of Nature

Terms: Mineralization, source, sink, compartment model, Nitrogen fixation, ammonification, nitrification, denitrification, photoautotrophs, chemoautotrophs
Q: Which reactions in the nitrogen cycle require energy, which give off energy? Which require an oxic environment, which require an anoxic environment? What two benefits do nitrogen fixing bacteria receive by living in a symbiotic association with plants?
Q: What are the principle forms of phosphorus? How does phosphorus cycling differ from N cycling? At what soil pH is P most available? Explain why.
Q: How could it be that a lake has lots of dissolved P and yet the phytoplankton remain P limited?
Q: Use biogeochemical transformations associated with the sulfur cycle to explain why the mining of fossil fuels often results in "acid mine drainage".
Q: Why is the production of N2O (laughing gas) considered of particular biogeochemical importance?
Q: Explain two alternate scenarios for the possible effects of elevated CO2 on arctic tundra ecosystems.
Q: Explain the energy source for organisms living in hydrothermal vents.

>Ricklefs 2007, Chapter 8. Nutrient Regeneration in terrestrial and aquatic ecosystems.  Pgs. 161-179. In The Economy of Nature

Terms: benthic, pelagic, littoral zone, epilimnion, hypolimnion, emergent vegetation, macrophyte, microbial loop, dissolved organic matter (DOM), nutrient spirals in streams, estuary, Redfield ratio, oxic, anoxic
Q: Explain the energy source for organisms living in hydrothermal vents.

Q: Describe the principle differences between nutrient cycling in terrestrial and aquatic ecosystems with respect to the physical proximity of dominant producers to nutrients and also with respect to the importance of anaerobic vs. aerobic processes in the soil or sediment.
Q: How does nutrient cycling differ in shallow and deep water columns and what are the implications? How does seasonal pattern of stratification in temperate lakes affect oxygen and nutrient dynamics in the hypolimnion and sediments?
Q: How does the oxidation state of the sediments affect both N and P dynamics (consider what happens to the important forms of these nutrients under oxidized and reduced conditions)? What role do the two important oxidation states of Fe play in P dynamics in aquatic sediments?
Q: Under what nutrient conditions do small phytoplankton dominate? Why? Use the "microbial loop" concept to explain the ecological effect on trophic dynamics.
Q: What does it mean for an ecosystem to be heterotrophic or autotrophic? As ecosystems, are streams and rivers typically heterotrophic or autotrophic? A certain stream has a narrow upstream, forested section and a wide downstream section. Speculate on the relative trophic status of these two sections.
Q: Explain why estuaries typically have such high rates of gross primary productivity.
Q: Why does a salt marsh have high rates of denitrification? In designing the Living Machine, how and why have we attempted to copy the biogeochemistry of nitrogen transformations in natural wetlands? (FYI, many years ago, John Todd, the designer of our LM, was a scientist at Woods Hole Oceanographic Institute).
Q: A large volume of pure carbohydrate (no N or P) is delivered to relatively oxic sediment. Explain how this might result in the release of dissolved phosphate into the water column.
Q: Many estuaries are thought to oscillate between nitrogen and phosphorous limitation seasonally. Assuming you have seasonal data on the concentrations of inorganic nitrogen and phosphorous, how could you use the "Redfield ratio" concept to create a graph depicting likely nutrient limitation over the course of the season?
Q: The so called "Geritol hypothesis" advocates fertilizing the southern oceans with iron in order to reduce the global concentration of atmospheric CO2. What assumptions about limiting nutrients and about carbon cycling are implicit in this hypothesis?
Q: The importance of N and P limitation are different in fresh and salt water environments. What principle mechanisms do scientists invoke to explain this difference?

Optional

>Chapin et al. The nature of nutrient limitation in plant communities. 1986. American Naturalist 127:48-58.
Discusses why concepts of nutrient limitation developed for crop plants don't necessarily work in ecosystems
>Chisholm. What limits phytoplankton growth? 1992. Oceanus 36-46.
>Herdendorf. Recovering from phosphorus enrichment. 1987. p. 127-135 in The Great Lake Erie (under "Fortner" in Science Library Reserve)
Describes the sequence of biological and legislative events that took place in Lake Erie between the '60s and today.
>http://www.epa.gov/glnpo/aoc/blackriver.html. This site provides excellent background on Black River watershed's contribution to pollution in Erie

LAB/FIELD: Aquatic methods (Data analysis due 10/6)

>Methods for Analyzing Aquatic Ecosystems (handout)

>Sinniah and Piers, Ion Chromatography: Analysis of ions in pond waters

We will run samples on the type of ion chromatograph described in this paper. Get a sense of how it works.

DISC/CASE: Nitrogen transformations in the Living Machine

 

5. Week of 10/3/11: Ecosystem-Level Research

QUIZ#2 due 10/6

NOTE: **For Thursday’s lab you should bring a laptop to class.  If you don’t have access, let me know well ahead of time and I will try to borrow one for you**

NOTE: **Lab will meet from 1:00-4:30 this week**

READINGS:

>Gordon.  2007,  Planning research guide for environmental and natural resource sciences. Yale University Press.pgs 1-80

Questions:

This assignment is a large page count, but pages in this exceptionally concise explanation of the research process are small and writing is easily digested.  Questions below are organized by chapters

1)     Importance of written plans

Q: what is it important to have a study plan?

Q: What are the key components of a study plan?

2)     Scientific method

Q: what are the distinctions between applied and basic research and qualitative vs. quantitative research?

Q: What are the key elements of the scientific method

Q: What is the distinction between inductive and deductive logic and what are some of the limitations of each?

Q: What is the null hypothesis and why isn’t it a mechanistic hypothesis?

Q: what is a mechanistic hypothesis?

3)     Useful views of science

Q: What criteria does Karl Popper use to distinguish between science and non-science?

Q: Explain what is meant by “normal science”.  From Thomas Kuhn’s perspective, what is a paradigm and what is a revolution?

Q: What factors induce a scientific revolution?

Q: What does Gordon see as the distinguishing features of ecological science from the rest of science, i.e. parts of the paradigm (end of chapter).

4)     Stating problems and objectives clearly

Q: explain the “gap-in-knowledge” and Decision-maker models for identifying problems to research

Q: What role to the objectives play in the research plan?

Q: What are the functions of the title of a research plan?

5)     Creating hypotheses and models

Q: explain the “gap-in-knowledge” and Decision-maker models for identifying problems to research

Q: What role to the objectives play in the research plan?

Q: What are the functions of the title of a research plan?

Creating hypotheses and models

Q: What is the value of hypothesis formulation?

Q: Explain the  rational for maintaining multiple working hypotheses.

Q: what, in Gorden’s view is a model and what are its values in research planning?

6)     Designing experiments

Terms to understand: Treatment, control, experimental unit, replication, randomization, experimental error, adaptive management

Q: distinguish between: laboratory experiments, field experiments, natural (i.e. “found”) experiments.

7)     Communicating study plans

>Lertzman. Notes on writing papers and theses. 1995. Bulletin of the Ecological Society of America 86-90.

Follow these good suggestions on writing!

>Loehle. A guide to increased creativity in research- inspiration or perspiration. 1990. BioScience 40:123-129.

This paper provides rare insight into the role of creativity in the Scientific process.
Q: According to Loehle, what are the four requirements for a successful career in science?
Q: What is the "Medawar zone"? How is this relevant to your research project?
Q: What roles do walking, sitting, staring out the window and procrastination play in Loehle’s research process?

>Petersen 2008 Research Proposal to the Great Lakes Protection Fund

This is an example of a successful research proposal (funded for $812K).  Not important that you understand the particular research, but I want you to flip through this to get a sense of what proposals look like.  The format was very constrained by the questions that that granting organization provided.

>Petersen et al. Multiscale experiments in coastal ecology: improving realism and advancing theory. 2003. BioScience . and Reviews, response and exchanges with editor

I would like you to take a quick look at the paper and at the exchanges with the editor.  I am not so concerned that you understand the content of the paper; focus instead on developing and understanding of the process of writing and publishing a manuscript as illustrated by this example.

Q: How do the two reviewer evaluations of this paper differ?

>Kuyper. Bringing up scientists in the art of critiquing research. 1991. BioScience 41:248-250.

Provides excellent general intro to the scientific process.
Q: What does IMRAD stand for? Specifically what does and does not go into each section of a traditionally constructed research paper?
Q: According to Kuyper, what are the critical traits of an effective paper describing research?

Optional

>Carpenter et al. Ecosystem experiments. 1995. Science 269:324-327.

DISC/CASE: Research questions & Literature search strategies  (bring laptop!)

LAB/FIELD: Chance Creek/Vermilion River (Site report due 10/18)

>Review Sherman readings - much of what he writes is based on his experiences at the spot we will visit.

>Johnson. Community classification, composition, and structure at Chance Creek Natural History Reservation, Ohio 1974-1998. 1999. 39. (Student thesis on Chance Creek)

Q: What did Amy Johnson find at the Vermilion river/Chance creek forest with respect to changes in tree species diversity and how does this relate to the patterns Chapin et al. discuss?

>Plummer et al. Chapter 10. Streams and floods. 2001. 221-240.

Review this (or some other surficial geology text) so that you are able to explain the processes by which rivers move over time and how they erode, transport and deposit sediments.

>Grame Lorain County Metro Parks, Vermilion River Reservation Natural Resource Management Plan. 1999

>Dupont.  How dynamite streamlines streams.  1935.  American Forests (optional)

Plant ID: Willow, sycamore, sassafras, cottonwood, white oak, red oak, sugar maple, red maple, silver maple, box elder, shagbark hickory, hemlock, white pine, tulip poplar, black cherry, ash, big toothed aspen, beech

PROJECT: Literature search summary and research ideas assignment (due 10/7)

 

6. Week of 10/10/11: Ecosystem Development, Disturbance, Resilience & Biotic Regulation

NOTE: **Class will not meet met on Tuesday 10/11 (AASHE conference)**

NOTE: **Class meets Sunday 10/16 4:00-6:00: Research Proposal Evaluation**

NOTE: **Lab will meet from 1:00-5:50 this week**

READINGS:

>Odum. The strategy of ecosystem development (Chapter 9, a revised version of classic Science paper from 1969). 2005. 336-373.

Q: First published in 1969, this remains one of the classic papers on ecosystem development. Most of Odum's generalizations on ecosystem development have stood the test of time, but some better than others. As you read this paper, consider how concepts and theories of ecosystem development are relevant to the field of restoration ecology.
Q: What general changes are evident during ecosystem development with respect to energetics, community structures, life history, nutrient cycling, and reproductive strategy?
Q: With respect to energy and biomass in particular, what trends in the ratio of GPP/R and GPP/biomass during ecosystem development and why?
Q: During what portions of ecosystem development would r and K selected species be expected to dominate?
Q: According to Odum, what role does biotic control over nutrient cycling play in ecosystem development?
Q: What do you make of the notion that an ecosystem might have a “strategy”?

>Jones et al. Organisms as ecosystem engineers. 1994. Oikos 69:373-386.

Q: What is an ecosystem engineer?
Q: How does the concept differ from keystone species?
Q: What are the differences between “allogenic” and “autogenic” engineers?

>Chapin et al. Biotic control over the functioning of ecosystems. 1997. Science 277:500-504.

Q: How might the introduction of mycorrhizal fungi into an ecosystem that had not experienced this group of organisms, or the removal of mycorrhizal fungi from a community that historically developed with these organisms alter ecosystem function?
Q: The authors site four key categories of effects that species can have on ecosystem function: resource dynamics, trophic structure, disturbance regime, and indirect effects. Explain each.
Q: What logical arguments are advanced to explain why species diversity should increase stability? Is a clear and consistent relationship between diversity and stability evident across ecosystems?
Q: So far, what general category of human activity has had the largest impact on species diversity? What other anthropogenic effect is likely to exert increasing effects on species diversity?
Q: "No two species are ecologically redundant, even if they appear similar in their ecosystem effects under one particular set of environmental conditions". Explain.
Q: Why might high latitude ecosystems be particularly vulnerable to damage from climate change?

Optional:

>deAngelis. The nature and significance of feedback in ecosystems. 1995. 450-467.
>Levin. Ecosystems and the biosphere as complex adaptive systems. 1998. Ecosystems 1:431-436.
>Patten and Odum. The cybernetic nature of ecosystems. 1981. American Naturalist 118:886-895.
>Petersen. Adding artificial feedback to a simple aquatic ecosystem: the cybernetic nature of ecosystems revisited. 2001. Oikos 94:533-547.
>Bormann and Likens. Chapter 1: The northern hardwood forest: a model for ecosystem development. 1979. 1-39.
>Clements. Plant succession: an analysis of the development of vegetation. 1916. 242:512
>Gleason. The individualistic concept of the plant association. 1926. Bulletin of the Torrey Club 53:7-26.
>Whittaker. A consideration of climax theory: the climax as a population and pattern. 1953. Ecological Monographs 23:41-78.
>Cowles. The ecological relations of the vegetation on the sand dunes of Lake Michigan. 1899. Botanical Gazette 27:95-117 (Part I).

PROJECT: Research proposals (must be posted on Blackboard by noon, 10/14), Peer Review of Research Proposals (must post to Blackboard by noon 10/16.  Print and bring hard copy to class for discussion!)

DISC/CASE: **(Sunday, 4:00-6:00, 10/16) Research proposal evaluation panel**

LAB/FIELD: Old Woman Creek (with Limnologist/Oceanographer Eddie Herdendorf) (Report due 11/1)

>Old Woman Creek web link (very useful for reports)

 

II. SYSTEM ECOLOGY APPLICATIONS

7. Week of 10/17/11: Restoring and Engineering Ecosystems

NOTE: **Tuesday’s class will be a field trip 8:30-10:50 and includes breakfast**

NOTE: **Thursday’s class meets in PC lab**

READING:

>Ehrenfeld and Toth. Restoration ecology and the ecosystem perspective. 1997. Restoration Ecology 5:307-317.

Q: Many restoration ecologists focus on techniques for establishing appropriate plant species. In what ways does an ecosystem perspective on restoration differ from this horticultural perspective?
Q: Restoration ecology is conceptually based on the notion that restored sites should be self-sustaining. How would a systems ecologist define sustainability?
Q: What key attributes (variables) might a systems ecologist focus on in considering the success of a restoration project? How would these differ from the success criteria of a more horticulturally oriented ecologist?
Q: Ehrenfeld and Toth emphasize the importance of boundaries and fluxes. What criteria might a systems ecologist apply in considering how a restored ecosystem interacts with surrounding ecosystems?
Q: What factors can be manipulated in order to control energy flow through a restored ecosystem?
Q: What important ecosystem-level research questions can be addressed through restoration ecology?

>Mitsch. Ecological engineering: a cooperative role with the planetary life-support system. 1993. Environmental Science and Technology 27:438-445.

Terms: Ecological engineering, self-organization (= self-design)
Q: Compare and contrast ecological engineering with traditional engineering. In what principle ways would an ecologically engineered system differ from one designed through traditional engineering approaches?
Q: Compare and contrast ecological engineering with biotechnology (genetic engineering).
Q: What role does self-design play in ecological engineering?
Q: Describe the range of scales in ecological engineering projects that have been undertaken. Which of these scales corresponds with our "living machine"?
Q: Mitsch argues that a conservation ethic is fundamental to ecological engineering. From a Q: strictly pragmatic perspective, explain why is this so.
Q: How does ecological engineering contribute to basic ecological knowledge?

>Zedler. Wetlands at your service: reducing impacts of agriculture at the watershed scale. 2003. Frontiers in Ecology and the Environment 1:65-72.

Q: What three key ecosystem services are provided by wetlands?
Q: What site attributes and restoration approaches optimize each of these three wetland services? Is it feasible to maximize all three on a given site? Explain.
Q: What have been the negative environmental impacts of large-scale conversion of natural ecosystems to farmland on aquatic ecosystems?
Q: How do restored ecosystems tend to differ from natural ecosystems in terms of both structure and function?
Q: What is "adaptive management" and how does Zedler suggest that it should be applied to wetland restoration?

Optional:

>Berryman et al. Ecological engineering - an idea whose time has come? 1992. Trends in Ecology & Evolution 7:268-270.
>Ewel. 1989. Restoration is the ultimate test of ecological theory. Restoration Ecology 31-33.
>Hobbs and Norton. Towards a conceptual framework for restoration ecology. 1996. Restoration Ecology 4:93-110.
>Jordan, Gilpin, Aber. Restoration Ecology: Ecological Restorations as a Technique for Basic Research. 1989. 3-21
>Mitsch and Cronk. Creation and restoration of wetlands: some design consideration for ecological engineering. 1992. Advances in Soil Science 17:217-259.
>Petersen. Alienation and ecotechnology: an ecologically designed landscape. 1992. Annals of Earth 10:16-18.
Provides social and ecological context for ecological engineering
>Bradshaw. Restoration: An Acid Test for Ecology. 1989. Restoration Ecology 23-29
>Bradshaw. The reconstruction of ecosystems. 1983. Journal of Applied Ecology 20:1-17.
>Todd and Josephson. Living machines: theoretical foundations and design precepts. 1994. Annals of Earth 12:16-25.

LAB/FIELD: Project lab#1: Scheduled conferences with each project group

DISC/CASE: Introduction to Simulation Modeling

 

Week of 10/24/11: Fall Break

 

8. Week of 10/31/11: Agroecosystems Biofuels and Biosequestration

QUIZ#3 due 11/3

READING:

>Matson et al. Agricultural intensification and ecosystem properties. 1997. Science 277:504-509.

TERMS: green revolution, monoculture, polyculture, intercropping, pest complex, planned diversity, no-till agriculture, integrated pest management (IPM), biological control
Q: Compare and contrast natural and modern agricultural systems in terms of each of the ecosystem forming factors.
Q: Compare and contrast soil in natural versus modern agricultural ecosystems in terms of both chemical, physical and biotic properties and regulation.
Q: What are the various effects of plant diversity in agro-ecosystems on ecological function?
Q: What effects do modern agricultural systems have on adjacent "natural" ecosystems, and what effects do the natural systems have on the agricultural ecosystems?
Q: Why is soil organic matter important and what practices can be use to increase it?
Q: Discuss environmental problems associated with increased use of irrigation.

>Foster and Magdoff. Liebig, Marx, and the depletion of soil fertility: relevance for today's agriculture. 1998. Monthly Review 50:32-45.

Q: Who was Justin von Liebeg, and how did his revolutionary insight relate to scale?
Q: What's wrong with having tenant farmers, or renting farmland out? How much of U.S. farmland is rented out?
Q; Why/how did WWII have a profound effect on agriculture? Come up with several examples.
Q: What are the environmental costs associated with the physical separation of population centers from agricultural centers and of plant from animal production?
Q; What specific problems with modern agriculture do Foster and Magdoff cite? What specific solutions do they offer?

>Altieri. Ecological impacts of industrial agriculture and the possibilities for truly sustainable farming. 1998. Monthly Review 50:60-71.

Q: What are the primary differences between old-style farming and modern farming in terms of inputs, pest control and nutrient cycles? Which type more closely matches the processes in natural ecosystems?
Q: What is "the green revolution", and what key technologies made it possible?
Q: Describe five important consequences of the specialization that has occurred in modern agriculture.
Q: What key risks does Altieri associate with the release of genetically engineered crops?
Q: What does Altieri view as the alternatives to modern agricultural practices. What are the goals? What are the primary obstacles to instituting alternatives?

>Beardsley.  2010.  Biological carbon sequestration.  BioScience BioScience 20(9): 671

This less than 1 pg editorial provides context for the Jansson paper below

>Jansson et al. 2010.  Phytosequestration: Carbon biosequestration by plants and the prospects of genetic engineering.  BioScience 20(9): 685-696

Terms Soil organic carbon (SOM), Soil inorganic carbon (SIC), sequestration, biochar
Q: from the perspective of the entire terrestrial portion of the biosphere, distinguish between the concepts of annual Gross Primary Productivity (GPP), Net Primary Productivity (NPP), Net Ecosystem Productivity (NEP) and Net Biome Productivity (NBP)
Q: How does NBP relate to climate change? 
Q: What is the difference between a C3 and C4 plant
Q: In what critical stock is most terrestrial organic matter stored?
Q: How/why could it be argued that new storage of carbon belowground in the soil is more important than storage of aboveground biomass?
Q: What are the properties of biochar?  Explain the potential role of biochar in sequestration
Q: How/why are photoliths, durable wood products and wood burrial potentially important to C sequestration?
Q: Why are biomass crops considered carbon neutral?
Q: From the perspective of phytoremediation, what plant attributes are targets for enhancement through genetic engineering?

>Ashley et al. 2011.  A brief history of phosphorus: From the philosopher’s stone to nutrient recovery and reuse

Skim the sections of this fine review of P and focus on those sections most relevant to human modifications of the P cycle and the importance of P in agriculture.  Use questions below to help you focus

Q: In what ways is P a key element for life?  In terms of biogeochemical cycling, how is it fundamentally distinct from other important biorelements?

Q: How was fire used by early agriculturalists to affect the P cycle?

Q: What did the Chinese learn 5,000 years ago as a mechanism for replenishing P in agricultural systems

Q: How did development of large permanent human settlements and the ‘Sanitation Revolution” associated with the industrial revolution fundamentally alter the global P cycle?

Q: How did the Green Revolution alter the global P cycles

Q: Explain why some people argue that phosphorous represents a greater constraint on the human population than fossil fuels.

Q: What are the options available for averting a phosphorus crisis?

Optional

>Morris.  The Carbohydrate Economy.  2006.  The American Prospect Magazine
>Pena.  Biofuels for transportation: A climate perspective.  2008.  Pew Center on Global Climate Change

DISC/CASE: Biofuels and Food or Peak Phosphorus

LAB/FIELD: Project lab #2: Scheduled conferences with each project group

 

9. Week of 11/7/11: Landscape Ecology

NOTE: **Both Wednesday’s Lab and Thursday’s class meet in PC Lab**

READING:

>Chapin et al. Chapter 14. Landscape heterogeneity and ecosystem dynamics. 2002. 305-331.

Terms/concepts: landscape, heterogeneity, patch, fragmentation, connectivity, metapopulation, shifting steady state mosaic
Q: What properties of patches are important in determining landscape-scale dynamics?
Q: Does the degree of fragmentation and connectivity influence function?
Q: Provide examples of spatial heterogeneity at different scales – e.g. what environmental variables are patchy at 1 m, 10 m, 1 km and 100 km scales and how does this patchyness affect function? If heterogeneity at each of these scales disappeared, how would the function of the systems change?
Q: What are the major natural and human induced processes that cause spatial heterogeneity? How do interactions among these processes affect landscape dynamics?
Q: What processes are most strongly affected by landscape pattern?
Q: What issues must be considered in extrapolating processes measured at one scale to larger scales of time and space?

>Wiens. Spatial scaling in ecology. 1989. Functional Ecology 3:385-397.

Terms: Grain, extent, ecological neighborhood, domain of scale
Q: Use the arguments presented by Wiens to explain why the "mosaic steady-state" concept is scale dependent (he does not discuss this concept by name, but you should be able to figure this out).
Q: "If we study a system at an inappropriate scale, we may not detect its actual dynamics and patterns but may instead identify patterns that are artifacts of scale. Because we are clever at devising explanations of what we see, we may think we understand the system when we have not even observed it correctly." (390) Explain.
Q: Two species of birds are negatively correlated on scales of 3-hectare plots (i.e. they are not often found together), yet positively correlated on a larger, regional scale (i.e. they ARE found together). What logical explains the scale-dependence of co-occurrence?
Q: Provide examples of phenomena in which variability at small scales gives rise to stability at larger scales.
Q: Explain how an organism may have several "ecological neighborhoods" (see page 391) associated with different functional attributes?

>Aronoff.  1. An introduction to geographic information systems.  & 2.  What is a geographic information system? 1995.  1-45 [Replace this reading?]

Q: Skim the first chapter to get a sense of the different contexts in which GIS has been used to manage and analyze landscapes.   Fig. 1.2 provides a good conceptual model of how GIS works.   What data maps would be used to generate a map of soil erodibility?

Q: What is "georeferenced data"?

Q: The author argues that, "the most important aspects of data quality are accuracy, precision, time, currency and completeness" (pg. 35).  Explain.

Q: "A good model is the simplest model that correctly and consistently predicts the behavior of the real world for the phenomena of interest." (pg 37).  Explain.

Q: What are the "two fundamental components" of geographic data

Q: What are the four components of a geographic information system?

DISC/CASE: Landscape ecology model of riparian zone

LAB/FIELD: Using GIS to explore watersheds, land use and stream water quality (PC lab)  

 

10. Week of 11/14/11: Global Change #1: Climate Change

READING:

Note: I assume that most of you have a decent basic grip on climate/global change issues.  The second and third articles below provide excellent (if slightly dated) summaries.  In recent years the issue of adaptation to climate change has become controversial.  The  first article below address some of the more recent thinking in terms of adaptation and its relationship to mitigation.

>Faze 2010.  Adaptation strategies for reducing vulnerability to future environmental change

Q: What three approaches do the authors see as critical to effective mitigation strategies for addressing rapid environmental change now underway?
Q: The authors argue that prior examples of human adaptation to environmental change have often addressed short term problems but created additional vulnerabilities over the longer term.  How do they propose avoiding this?
Q: The authors distinguish between “buffering adaptation” and “fully aligned” adaptation and be “techno-fixes” and behavioral changes. Explain these distinctions and why the authors see these as important.
Q: The authors argue that adaptations involving tech-fixes often eliminate short term ecological feedback in ways that increase vulnerability to longer term change.  Explain.

>Pew Center. 2006.  Climate change 101: Understanding and responding to global climate change.

Skim the Overview Section, focus on Science and Impacts section.  I am assuming that this is largely a review for most of you.  Glance through the rest of this excellent summary of the state of our knowledge to ensure you understand the basics. 
Q: What are the documented and predicted effects of elevated greenhouse gasses (GHGs) on: temperature, fresh water supply, sea level, storm intensity, agricultural productivity and disease, polar ice cap, glaciers, snow pack, ocean temperatures, and mosquito-borne disease?
Q: Figure 3 in the Overview section depicts the so-called “wedge” model published by Pacala and Socolow in 2004.  What is expected to happen to GHG emissions between 2005 and 2055 if no action is taken?  Explain the wedge concept of reducing GHG emissions.  What do the authors suggest as some of the possible wedges?
Q: How do per person emissions differ between U.S. citizens and citizens of Europe?
Q:  During what period have the ten warmest years in human history occurred?
Q: What is a “cap and trade” policy and how does it stimulate emissions reductions?
Q: What is the Kyoto protocol and to what extent is the U.S. participating in it?
Q: What two factors related to climate change explain rising sea levels?
Q: What are the three main greenhouse gasses?
Q: The authors write that, “the true costs of greenhouse gas emissions are not reflected in the market price.”  Explain what they mean.
Q: Activities that take place within the built environment (i.e. buildings) are responsible for about what fraction of the total CO2 emissions?  What fractions are due to transportation and industry?
Q: What does “carbon sequestration” mean and what role might it play in stabilizing GHGs?
Q: What are the primary options available for reducing the GHG emissions associated with buildings?
Q: What are the primary options available for reducing the GHG emissions associated with transportation?

>Vitousek et al. 1997.  Human domination of the earth’s ecosystems. Science 277 pgs. 494-499

Q: In what ways has human transformation of land affected biodiversity and climate?
Q: What are humans major impacts on the coastal zone and ocean?
Q: How do we know that most of the increase in CO2 in the atmosphere has resulted from burning fossil fuels?
Q: How have humans changed the nitrogen cycle and why is this important?
Q: What is meant by the term "biological invasion" and how and why are these invasions important?

DISC/CASE: Effects of elevated temperature on soil dynamics in North East forests

QUIZ#4 due 11/17

LAB/FIELD: Project lab #3: Open

 

11. Week of 11/21/11: Methods of Data Analysis

NOTE: **Tuesday’s class meets in PC lab**

NOTE: **No class Thursday (Thanksgiving)**

DISC/CASE: Methods of data analysis, (PC computer lab)

LAB/FIELD: Project lab #4: Open

 

12. Week of 11/28/11: Great Lake Ecosystem and Response to Phosphorous

NOTE: **I will be at a conference and unavailable for consultation between 11/30-12/2**

NOTE: **Discussion/Case will take place in Tuesday’s lab**

NOTE: **On Thursday guest speaker Limnologist Charles (Eddie) Herdendorf will discuss the changing ecology of Lake Erie**

READING:

>Herdendorf. Recovering from phosphorus enrichment. 1987. p. 127-135 in The Great Lake Erie (under "Fortner" in Science Library Reserve)

Q: What sequence of biological and legislative events have taken place in Lake Erie following restoration efforts initiated in the 1960s?

DISC/CASE: Methods of data presentation

>Guidelines for poster presentations (class handout, see project assignments)

>Ornes. Tips for effective communication in ecology.  2007.  Ecological Society of America Bulletin

LAB/FIELD: Project lab #5: Open

PROJECT: Research abstract due (posted on Blackboard) 11/30; Peer review of abstracts due by 6:00 on 12/2 (you review same two projects as for proposals); Two figures and figure legends for poster due by 6:00 12/3; First draft of poster due  by 6:00 12/4.

 

13. Week of 12/5/11: Applying Systems Concepts to Human Habitat: The Ecology of the Built Environment

READING:

>Wilson.  2001.  Buildings and the environment: The numbers, Environmental Building News 10(5), pgs1, 10-14

Note: PDF is an entire publication, but I only want you to read one paper in it

Context: This paper has become a bit of a classic in considering the environmental impact of buildings and human dominated landscapes.  It’s 10 years old now, but the numbers have not changed much. 

Q: I don’t expect you to memorize statistics, but get a good sense of the ecological impact of buildings and human activities and what the authors propose to do to minimize the ecological impacts of the built environment

> Petersen. 2007.  Dormitory residents reduce electricity consumption when exposed to real-time visual feedback and incentives

Context: This paper was published when Oberlin’s “Campus Resource Monitoring System” was first being developed.

Q: Considering this study, in what ways is the built environment, including human occupants of buildings, similar to and different from other kinds of ecological systems?

Q: How is feedback been employed?  How would you diagram the causal loop diagram that explains feedback loop employed in this study?

>Petersen.  2011.   The performance of the Adam Joseph Lewis Center at 10 yrs: Reflecting back, moving forward

Context: This is not a peer-reviewed journal paper, but an article I was recently asked to write for a magazine called “High Performance Buildings” that is published by the American Society of Heating, Refrigeration and Air-Conditioning Engineers.  HPB is targeted towards architects and engineers.

Q: In what ways is the AJLC similar to and different from other kinds of ecological systems?

Q: In what ways would you say that the AJLC is like an organism, in what ways is it like an ecosystem. 

Q: Assuming our goal is to create a more ecologically sustainable built environment, what are the features of ecological systems are most important for us to mimic within the built environment?

>Naeem et al. Biodiversity and ecosystem functioning: maintaining natural life support processes. 1999. Issues in ecology 4:1-11.

The Ecological Society of America (ESA) is a professional organization for ecologists that publishes the prestigious journals Ecology, Ecological Monographs, and Ecological Applications. This piece is part of a series, “Issues in Ecology” that ESA began publishing for lay audiences a few years back (“Issues” gets distributed to politicians and promoted for education). As the other reading for this week discusses, this particular volume of “Issues” generated considerable controversy within ESA.
Q: What are the primary factors responsible for loss of biodiversity?
Q: Explain the idea that there are several different levels of biodiversity.
Q: According to the authors, why is it challenging to use observational studies of existing ecosystems to assess the effect of biodiversity on ecological function?
Q: According to the authors, what conclusions can be drawn from experiments that have assessed the effect of decreased biodiversity on productivity?
Q Explain the difference between the proposed “sampling effect” and “complementarity effect” mechanisms.
Q: According to the authors, what conclusions can be drawn from experiments that have assessed the effect of decreased biodiversity on ecosystem stability and predictability? What mechanisms are invoked to explain this?

>Kaiser, Rift over biodiversity divides ecologists. 2000. Science 289:1282-1283

I am primarily interested in your understanding the dispute here - why are the authors of this paper so upset by the publication of the "Issues" paper?
Q: Explain the two schools of thought on the effect of biodiversity on ecological function
Q: What principle criticisms do the authors offer to discount experiments that have purported to demonstrate relationships between biodiversity and ecosystem function?
Q: The authors of this paper argue that the folks who wrote the "Issues" paper set up a house of cards that could ultimately damage attempts to preserve biodiversity. Explain the logic of this position.

Optional:

>McCann. The diversity-stability debate. 2000. Nature 405:228-233
>Symstad et al. Long-term and large-scale perspectives on the relationship between biodiversity and ecosystem functioning. 2003. BioScience 53:89-98.

QUIZ#5 due 12/8

PROJECT: Final draft of poster due by 8:00 PM Wednesday 12/7 

DISC/CASE: Biodiversity and ecosystem function

LAB/FIELD: Project lab #6: Final touches on posters

 

14. Week of 12/12/11: Poster Presentation

Oral poster presentations of posters and course evaluations will occur during our final class

PROJECT: Final written reports and project data due 12/14