History of the Earth Systems

Course Syllabus for Fall 2012

01:460:476:01 (Geological Sciences-Undergrad.)
11:628:476:01 (Marine and Coastal Sciences – Undergrad.)
16:712:560:01 (Oceanography-Grad.)
Lipman House (LP), Room 102, Cook Campus
Class Time: TTh 2:15 - 3:35 PM

Instructor: Dr. Paul Falkowski

Email: falko@imcs.marine.rutgers.edu
Office hours: by appt. – call (848) 932-3426
Office location: Institute of Marine and Coastal Science bldg., Rm. 318D

Supplemental Reading: Earth System History by: Steven Stanley

Grading: Mid-Term Exam (Oct. 23) 30%

Term Paper (Dec. 4) 40%
Final Exam (Dec. 11) 30%
100%
Term Paper: Undergraduates: 15 page referenced overview of any topic related to Earth System
Science or History of Earth Systems
Graduates: Different format; Paper will be in a research grant proposal style
** More detail will be discussed about these term papers

Overview:
This course integrates atmospheric, oceanographic, geological and biological concepts in an historical
perspective to introduce the student to the major processes that have shaped Earth's environment. The
course will examine climatic processes on geological time scales, the evolution of organisms, the cycling of
elements, and the feedbacks between these processes. Prerequisites: Introductory courses in Chemistry,
Biology, and Physics (or by consultation with the Instructor).

Goals:
The primary goal of this course is to introduce upper level undergraduate and graduate science majors to
the complexity of Earth as a physical/biological system. The course is aimed at challenging the student to
think about connections between various science disciplines (e.g. Molecular phylogeny and climatic
variability). The course will emphasize learning rigorous, fundamental concepts in science (e.g. Stefan-
Boltzmann equation, the Poisson probability function, the Nernst equation) as applied to understanding
radiative transfer, rates of genetic change, etc.

Philosophy:
The course will be taught as a lecture series, building from an historical perspective, and noting the
contributions of specific scientists to our knowledge of Earth System Science. The course will use one
primary text with supplemental reading from other texts and review articles in the primary literature.
Course grades will be based on a mid-term exam (short answer and essay questions - 30% of total), a
comprehensive final - (short answer and essay 30% of total), and a term paper that reviews a specific topic
in Earth System Science (40% of total). The term paper for the 400 level course will be 15 page review of
literature in a course topic. At the 500 level, the term paper will be modeled as an NSF style Research
Proposal, and focus on an examination of competing hypotheses in Earth System Science with a detailed
research plan that would reconcile the hypotheses. The course will be modeled on similar courses taught at
Berkeley in Integrative Biology.
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Month Day Topic

September 4 Description of course structure/goals. Introduction to planetary origins/accretion/
origin elements & their distribution, the origin of the ocean.

6 Early Earth, theories of the origin of organic matter in the universe & on Earth.

11 Introduction to Earth’s early atmosphere, radiation budget and the “faint Sun” paradox (part
I).
13 Introduction to Earth’s early atmosphere, radiation budget and the “faint Sun”
paradox (part II).
Introduction to origins of life concepts: definition of life, the initial conditions redox
chemistry and early metabolic sequences, the formation of organic polymers & cells.

18 Fossils and geochemical biomarkers from the Archea & Proterozoic epochs - the
geological record. Molecular clocks and the biological inference of origins of life.

20 The evolution of the carbon cycle/ modes of Nutrition I. The evolution of the N 2 cycle

25 Modes of Nutrition II / the Redfield ratios Introduction to bioinorganic chemistry.

27 The role of trace elements in regulating biogeochemical cycles.

Month Day Topic

October 2 Concepts of biological limiting processes in geochemistry. Molecular phylogeny &
origin of eucaryotes / lateral gene transfer and the origins of plastids and
mitochondria. The organization of metabolic sequences.

4 TERM PAPER Discussed

Oxygen & the evolution of photosynthesis – signs of life on the planet. The impact of
oxygen evolution on trace element distributions. The origins of animals and the
Cambrian “explosion” / role of oxygen in the evolution of macrofauna.

9 TERM PAPER Discussed (Cont'd)

Isotopic fractionation, Paleothemometers, paleobarometers, and paleo
“depositometers”. The pre-Cambrian extinctions and the “missing” pieces of the
fossil record – Darwin’s dilemma.

11 Earth’s radiation budget II, greenhouse gases, clouds and ice (Earth’s
albedo). Steffan-Boltzmann equation, climate feedbacks, and energy balance.

16 The hydrological cycle, oceanic heat transport and thermohaline circulation. The role
of the ocean in climate dynamics.

18 Aeolian fluxes, mineral transport, weathering and feedbacks on biogeochemical

fluxes. Time scales of element cycling.
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23 MID-TERM EXAM

25 Extinctions: The “big five”. The Permuian extinction & the resetting of the ocean
redox system.

30 The Triassic recovery – The “tempo” and “mode” of evolution – Theories of

evolution. The concepts of natural selection and introduction to population
biology.

Month Day Topic

November 1 Introduction to plate tectonics and role in genetic drift.

6 Rates of evolution and selection mechanisms in the Cretaceous – Darwin, and

neoDarwinism.

8 The K/T boundary and the post impact world - Evolution of mammals and the
evolution of intelligence.

13 Glacial and interglacial cycles/ Milankovich cycles* (taught by Ken Miller or Bob
Kopp)

15 CO2 and other greenhouse gases since the beginning of the Industrial Revolution.

20 Primary production and carbon sequestration in the contemporary world. The

solubility and biological pumps, higher plant sensitivity to CO2. The search for an
“off ramp”

22 NO CLASS – Thanksgiving Recess

27 Mapping biogeochemical cycles to the evolution of functional proteins - an

introduction to structural biology and problems in contemporary evolutionary
theories - the problems of predicting outcomes of climate change on biological
systems
29 Bio-diversity, ecological homogenization, extinction / human interactions with the
environment; The evolution of intelligence.

Month Day Topic

December 4 TERM PAPERS DUE
The evolution of language, horizontal information transfer. Have humans escaped the
“Red Queen” constraint. Post-evolutionary theories of Earth System Science.
(Last Class Meeting before Final)
Discussion of term papers; Oral Summaries

6 NO CLASS

11 Exam
If you need to meet with me, please make an appointment by calling 848 932 3426
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History of the Earth Systems - Fall 2012

Back to EBME main site

01:460:476:01 (Geological Sciences-Undergrad.)

11:628:476:01 (Marine and Coastal Sciences – Undergrad.)
16:712:560:01 (Oceanography-Grad.)
Lipman House (LP), Room 102, Cook Campus
Class Time: TTh 2:15 - 3:35 PM

Instructor: Dr. Paul Falkowski

Email: falko@imcs.rutgers.edu
Office hours: by appt. – call 848-932-3426
Office location: Institute of Marine and Coastal Science bldg. Rm. 318D

Syllabus for Fall 2012 (word document)

Class Lecture Slides and Assigned Reading - Fall 2012

Week 1 – Sept. 4
Description of course structure/goals. Introduction to planetary origins/accretion origin elements & their
distribution, the origin of the ocean.
Assigned Reading for next time (pdf files):
1) Reading list
2) Lineweaver, Science 1999
3) Ziurys et al., Nature 2007
4) Drake & Righter, Nature 2002
5) Bhattacharjee, Science 2010

Week 1 - Sept. 6
Early Earth, theories of the origin of organic matter in the universe & on Earth.
Assigned Reading for next time (pdf files):
1) Cowan & Thielemann, Physics Today 2004
2) Drake & Righter, Nature 2002
3) Kasting, Science 1993
4) Palme, Science 2004
5) Robert, Science 2001
6) NASA map image
7) Figure 1.4
8) Nance, Worsely, Moody, Scientific American 1988
9) Lunine, Philosophical Transactions: Biological Sciences 2006

Week 2 – Sept. 11
Katye Altieri's Lecture Slides (powerpoint)
Introduction to Earth’s early atmosphere, radiation budget and the “faint Sun” paradox (part I).

Week 2 – Sept. 13
Introduction to Earth’s early atmosphere, radiation budget and the “faint Sun” paradox (part II).
Introduction to origins of life concepts:
definition of life, the initial conditions redox chemistry and early metabolic sequences, the formation of
organic polymers & cells.
Assigned Reading for next time (pdf files):
1) Anbar & Knoll, Science 2002
2) Bada & Lazcano, Science 2002
3) Benner et al., Science 2002
4) Kwok, Nature 2004
5) Mojzsis, Harrison & Pidgeon, Nature 2001
6) Pace, Science 1997
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7) Watson & Harrison, Science 2005

8) Williams & da Silva, J. Chem. Ed. 2004
9) Martin & Russell, Phil. Trans. R. Soc. Lond. B., 2002

Week 3 – Sept. 18
Additional Lecture Slides (powerpoint) (source: Tracy Quan)
Fossils and geochemical biomarkers from the Archea & Proterozoic epochs - the geological record.
Molecular clocks and the biological inference of origins of life.
Assigned Reading for next time (pdf files):
1) Canfield et al., Roy. Soc. B. 2006
2) Farquhar et al., Science 2000
3) Zahnle et al., Geobiology 2006
4) Knoll et al., Ch.8 (available here) (published in The Evolution of Aquatic Photoautotrophs. 2007.
Academic Press)
5) Summons et al., Nature 1999

Week 3 – Sept. 20
The evolution of the carbon cycle/ modes of Nutrition I. The evolution of the N2 cycle
Assigned Reading for next time (pdf files):
1) Falkowski, Nature 1997
2) Falkowski et al., Science 2008
3) Graur & Martin, TRENDS in Genetics 2004
4) Hayes et al., Chem. Geology 1999
5) Hedges, Nature 1998

Week 4 – Sept. 25
Modes of Nutrition II / the Redfield ratios Introduction to bioinorganic chemistry.
Assigned Reading for next time (pdf files):
1) Fennel et al., Am. J. Sci. 2005
2) James Farquhar, et al., Science 2000
3) Falkowski, PowerPoint 2009
4) Pavlov & Kasting, Astrobiology 2002

Week 4 – Sept. 27
The role of trace elements in regulating biogeochemical cycles.
Assigned Reading for next time (pdf files):
1) Falkowksi & Godfrey, Phil. Trans. R. Soc. B 2008
2) Redfield, Am. Sci. 1958
3) Quan et al., Global Biogeochem. Cycles 2008
4) Falkowski, PowerPoint 28Sept2010

Week 5 - Supplement

Week 5 – October 2
Dr. Silke Severmann's lecture handout (pdf)
Concepts of biological limiting processes in geochemistry.
Molecular phylogeny & origin of eukaryotes / lateral gene transfer and the origins of plastids and
mitochondria.
The organization of metabolic sequences.
1) Williams, The Royal Society 1981
2) Falkowski & Isozaki, Science 2008
3) Arnold, Anbar, Barling, Lyons, Sciencexpress 2004
4) Falkowski et al., Science 2008
5) Falkowski, PowerPoint-A 2009
6) Falkowski, PowerPoint-B 2009
7) McDaniel et al., Science 2010

Week 5 – October 4
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TERM PAPER Discussed

Oxygen & the evolution of photosynthesis – signs of life on the planet.
The impact of oxygen evolution on trace element distributions.
The Cambrian “explosion” / role of oxygen in the evolution of macrofauna.
Assigned reading for next time (pdf files):
1) Anbar et al., Science 2007
2) Canfield, Nature 1998
3) Des Marais, Science 2000
4) Falkowski, J. Phycol. 2000
5) Kappler et al., Geology 2005
6) Walker, Nature 1987
7) Smith & Peterson, Annu. Rev. Earth Planet. Sci. 2002
8) Falkowski, PowerPoint

Week 6 - October 9
more slides- October 9
Additional Lecture Slides (PowerPoint) (source: Paul Falkowski)
TERM PAPER Discussed (Cont'd)
Isotopic fractionation, Paleothemometers, paleobarometers, and paleo “depositometers”.
The pre-Cambrian extinctions and the “missing” pieces of the fossil record – Darwin’s dilemma.
Assigned reading for next time (pdf files):
1) Isozaki et al., Science 1997
2) Hoffman et al., Science 1998
3) Kopp et al., PNAS 2005
4) Martin & Russell, The Royal Society 2002
5) S.L. Baldauf, et al., Science 2003
6) Canfield et al., Science 2010

Week 6 - October 11 International Stratigraphic Chart

Earth’s radiation budget II, greenhouse gases, clouds and ice (Earth’s albedo).
Steffan-Boltzmann equation, climate feedbacks, and energy balance.

Week 7 - October 16
The hydrological cycle, oceanic heat transport and thermohaline circulation.
The role of the ocean in climate dynamics.
Review: Old midterm exam sample (word document)
Assigned reading for next time (pdf files):
1) Kerr, Science 2002
2) Olsen, Science 1999
3) Chen et al., Science 2004
4) Wray et al., Science 1996
5) Ayala et al., PNAS 1998
6) Falkowski, PowerPoint 2003
7) Bambach, Paleobiology 1993

Week 7 - October 18 Hardy-Weinberg Law

Aeolian fluxes, mineral transport, weathering and feedbacks on biogeochemical fluxes.
Time scales of element cycling.
Assigned reading for next time (pdf files):
1) Baldauf et al., Science 2003
2) Chahine, Nature 2002

Week 8 - October 23, 2012 Mid-term Examination - no lecture

1) Examples of Mid-term Examination Questions

Week 8 - October 25 The Big Five -- Bas van de Schootbrugge

Extinctions: The “big five”. The Permuian extinction & the resetting of the ocean redox system.
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Additional Lecture Slides (powerpoint) (source: Livia Montone)

Assigned reading for next time (pdf files):
1) Baldauf, Trends in Genetics 2003
2) Felsenstein, Annu. Rev. Genet. 1988
3) Wray, Genome Biology 2001

Week 9 - October 30
The Triassic recovery – The “tempo” and “mode” of evolution – Theories of evolution.
The concepts of natural selection and introduction to population biology.
Additional Lecture Slides (powerpoint) (source: Debashish Bhattacharya)
Assigned reading for next time (pdf files):
1) Boyd et al., Science 2007
2) Isozaki, Science 1997
3) Raup & Sepkowski, Science 1980
4) Alvarez et al., Science 1980
5) Purcell, Am. J. Phys. 1977
6) Planavsky, Nature 2010
7) Van Valen, Evol.Theory 1973

Week 9 - November 1
* Natural Selection Notes
Introduction to plate tectonics and role in genetic drift.

Week 10 - November 6
Rates of evolution and selection mechanisms in the Cretaceous – Darwin, and neoDarwinism.
Assigned reading for next time (pdf files):
1) Rasmussen et al., Nature 2008
2) Delwiche, The American Naturalist 1999
3) Heckman et al., Science 2001
4) Berner, Science 1997
5) Keeling & Palmer, Nature Reviews 2008
6) Bambach, Paleobiology 1993
7) Kenrick & Crane, Nature 1997

Week 10 - November 8
The K/T boundary and the post impact world - Evolution of mammals and the evolution of intelligence.
Assigned reading for next time (pdf files):
1) Van Valen, Evol. Theory, 1973

Week 11 - November 13
Glacial and interglacial cycles/ Milankovich cycles.
Assigned Reading for next time (pdf files):
1) Falkowski et al., Science 2005
2) Appenzeller, Science 1999
3) Xu et al., Nature 2003
4) Falkowski, PowerPoint 2003

Week 11 - Supplement

Week 11 - November 15 Ken Miller's Presentation (pdf, 4.79 MB)

CO2 since the beginning of the Industrial Revolution.
Assigned Reading for next time (pdf files):
1) Charlson et al., Nature 1987
2) Falkowski et al., Science 1992
3) Falkowski et al., Science 2000

Week 12 - November 20
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Primary production and carbon sequestration in the contemporary world.

The solubility and biological pumps, higher plant sensitivity to CO2.
Guest lecture by Dr. Tracy Quan: Slides from lecture (pdf)
Assigned Reading for next time (pdf files):
1) Berger, Reviews of Geophysics 1988
2) Hayes et al., Science 1976
3) Sigman & Boyle, Nature 2000

Week 12 - November 25 - NO CLASS - Thanksgiving Recess

Week 13 - November 27
Mapping biogeochemical cycles to the evolution of functional proteins -
an introduction to structural biology and problems in contemporary evolutionary theories -
the problems of predicting outcomes of climate change on biological systems.
Assigned Reading for next time (pdf files):
1) Barton & Harvey, Nature 2000
2) Nowak et al., Nature 2002
3) Molnar, Irish J. Earth Sciences 1990

Week 13 - November 29
Bio-diversity, ecological homogenization, extinction / human interactions with the environment; The
evolution of intelligence
Assigned Reading for next time (pdf files):
1) Carroll, Nature 2003
2) Petit et al., Nature 1999
3) Kaas & Collins, Nature 2001
4) Engard et al., Nature 2002

Week 14 - December 4 -Term Papers Due

Last Class Meeting before Final
more slides Evolution of Speech
The evolution of language and post-evolutionary theories of Earth System Science.
Additional Lecture Slides (powerpoint) (source: Falkowski)
Assigned Reading for next time (pdf files):
1) Vitousek, Science 1997
2) Norenzayan, et al., Science 2008
3) Falkowski & Tchernov, Chapter 11
4) http://blogs.sciencemag.org/origins/2009/11/on-the-origin-of-religion.html
5) Hardin, Science 1968
6) Cohen et al, Science 2003

Week 14 - December 6 - No Class

Last set of slides - from last 2 weeks lectures

** Final Exam - Dec. 11(during class period)**

SAMPLE FINAL EXAM QUESTIONS

Sample types of questions:
There will be some short answer questions of the following general type (you will not have options to
select questions):

1. What appears to be the "pacemaker" for glacial/interglacial cycles for the past 2.5 million
years of Earth's history?

2. What is one proxy for wind speed that can be inferred from ice core records? What is the
rationale for using it as a proxy?
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3. How does metabolic rate scale with body size in metazoans?

4. What is one difference between human induced changes to the Earth System compared
with natural changes?

5. How has the evolution of language helped humans to escape the Red Queen constraint?

There will be short essays of the following general form:

E1. There are two carbon cycles on Earth – a “slow cycle” and a “fast cycle”. Describe the basic
features of both cycles (you can use a diagram if you like) and explain how human activities have
disrupted the cycle(s).

E2. Explain how mass extinctions differ from “normal” extinction processes, and why mass
extinctions are always followed by major radiations. In addressing these issues choose specific
examples, whenever possible.