History of the Earth Systems - Fall 2008

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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.)
Waller Hall (WAL), Room 203, Cook Campus
Class Time: TTh 2:15 - 3:35 PM

Instructor: Dr. Paul Falkowski
Email: falko@imcs.rutgers.edu
Office hours: by appt. – call 732-932-6555 ext. 244
Office location: Institute of Marine and Coastal Science bldg. Rm. 318D

Syllabus for Fall 2008 (word document)

Class Lecture Slides and Assigned Reading - Fall 2008
(Adobe Acrobat Required to View Files)

Week 1 - Sept 2
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

Week 1 - Sept 4
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

Week 2 - Sept 9

Katye Altieri's Lecture Slides (powerpoint)

Introduction to Earth’s early atmosphere, radiation budget and the “faint Sun” paradox (part I).

Week 2 - Sept 11
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

Week 3 - September 16

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 - September 18
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 - September 23
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

Week 4 - September 25

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

Week 5 - Supplement

Week 5 - September 30
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.

Week 5 - October 2
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

Week 6 - October 7

more slides- October 7
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

Week 6 - October 9 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 14
The hydrological cycle, oceanic heat transport and thermohaline circulation.
The role of the ocean in climate dynamics.

Week 7 - October 16 Hardy-Weinberg Law
Aeolian fluxes, mineral transport, weathering and feedbacks on biogeochemical fluxes.
Time scales of element cycling.

Week 8 - October 21, 2006 Mid-term Examination - no lecture

Week 8 - October 23 The Big Five -- Bas van de Schootbrugge
Extinctions: The “big five”. The Permuian extinction & the resetting of the ocean redox system.

Week 9 - October 28
The Triassic recovery – The “tempo” and “mode” of evolution – Theories of evolution.
The concepts of natural selection and introduction to population biology.

Week 9 - October 30

* Natural Selection Notes
Introduction to plate tectonics and role in genetic drift.

Week 10 - November 4
Rates of evolution and selection mechanisms in the Cretaceous – Darwin, and neoDarwinism.

Week 10 - November 6
The K/T boundary and the post impact world - Evolution of mammals and the evolution of intelligence.

Week 11 - November 11
Glacial and interglacial cycles/ Milankovich cycles.

Week 11 - Supplement

Week 11 - November 13 Ken Miller's Presentation (pdf, 4.79 MB)
CO₂ since the beginning of the Industrial Revolution.

Week 12 - November 18
Primary production and carbon sequestration in the contemporary world.
The solubility and biological pumps, higher plant sensitivity to CO₂.

Week 12 - November 20
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.

Week 13 - November 25 (will have class - Thursday Schedule)
Bio-diversity, ecological homogenization, extinction / human interactions with the environment; The evolution of intelligence

Week 13 - November 27 - NO CLASS - Thanksgiving Recess

Week 14 - December 2

more slides Evolution of Speech
The evolution of language and post-evolutionary theories of Earth System Science.

Week 14 - December 4 - Last Class Meeting before Final
Discussion of term papers; Oral Summaries

Last set of slides - from last 2 weeks lectures

** Final Exam - Dec. 9 (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. 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. 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.