History of the Earth Systems - Fall 2012
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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
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
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.
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
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?
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.