Terrestrial Geobiology Course Website

 

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Spec Tpcs: Geology & Geophysics - GG 711 (Spring Semester, 2013)

 

Time: 12:30 to 2:30 pm on Fridays (occasionally we will go longer, but advance notice will be given)

Location: 312 Biomedical Sciences Building (click for map)

 

Instructor: Professor Hope Jahren jahren@hawaii.edu

Assisted by: Nancy Parker parkerne@hawaii.edu

 

Participants:

Lauren Deem deeml@hawaii.edu

Jan Kamenik kamenik@hawaii.edu

Whitney Ray wray524@gmail.com

 

Schedule:

 

Week 1: Friday, January 18, 2013

Lecture Topic: What is Life?

Required Reading (to be completed by the beginning of class):

(PDF for download) S.D. Wullschleger and M. Strahl. 2010. Climate Change: A Controlled Experiment. Scientific American (March 2010) 

Assignment (to be completed by the beginning of class):

(PDF for download) Three and Three worksheet to be completed for Wullshleger and Strahl, 2010.

Supplemental Reading (optional readings that give more detail on the subjects discussed in this lecture):

(PDF for download) B.A. Schubert and A.H. Jahren. 2011. Fertilization trajectory of the root crop Raphanus sativus across atmospheric pCO2 estimates of the next 300 years. Agriculture, Ecosystems, and Environment, 140(1-2) 174-181, doi: 10.1016/j.agee.2010.11.024.

 

Week 2: Friday, January 25, 2013

Lecture Topic: The Five Activities of Life: Growth, Maintenance, Storage, Reproduction, Defense

Required Reading (to be completed by the beginning of class):

(PDF for download) P. Rogers. 2008. Facing the Freshwater Crisis. Scientific American (August 2008)

Assignment (to be completed by the beginning of class):

(PDF for download) Three and Three worksheet to be completed for P. Rogers. 2008.

Supplemental Readings (optional readings that give more detail on the subjects discussed in this lecture):

(PDF for download) G. Mora and A.H. Jahren. 2003. Isotopic evidence for the role of plant development on transpiration in deciduous forests of the southern United States. Global Biogeochemical Cycles, 17(2), 2002GB001981.

(PDF for download) A.Y. Hoekstra and M.M. Mekonnen. 2011. The water footprint of humanity. PNAS doi/10.1073/pnas.1109936109.

 

Week 3: Friday, February 1, 2013

Lecture Topic: Autotrophy and Heterotrophy

Required Reading (to be completed by the beginning of class):

(PDF for download) Villarreal. 2004. Are Viruses Alive? Scientific American (December 2004)

(PDF for download) Kearney. 1996. Training the Olympic Athlete. Scientific American (June 1996); Pages 52-55 only

(PDF for download) Sagan. 1994. The Search for Extraterrestrial Life. Scientific American (October 1994)

Assignment (to be completed by the beginning of class):

(PDF for download) Three and Three worksheet to be completed for all required readings

 

Week 4: Friday, February 8, 2013

(Note: class will start at 1:15 pm this day.)

Lecture Topic: (Part I) Photosynthesis, Respiration and Fermentation

Required Reading (to be completed by the beginning of class):

No new material, see materials from previous week

Supplemental Readings (optional readings that give more detail on the subjects discussed in this lecture):

1.   Sections on ATP and NAD/NADP – H+ by Nelson and Cox (Principles of Biochemistry) (27.7 MB PDF)

2.   B. Khakh and G. Burnstock. 2009. The Double Life of ATP. Scientific American (December 2009) PDF

3.   J. De Keersmaecker. 1996. The Mystery of Lambic Beer. Scientific American (August 1996) PDF

4.   T.B. Causey et al. 2004. Engineering Escherichia coli for efficient conversion of glucose to pyruvate. Proceedings of the National Academy of Sciences 101:2235-2240 PDF

5.   Raven et al. 1992. Biology of Plants (excerpt). (17.4 PDF)

 

Week 5: Friday, February 15, 2013

Lecture Topic: (Part II) Photosynthesis, Respiration and Fermentation

Required Reading (to be completed by the beginning of class):

1.   C. de Duve. 1996. The Birth of Complex Cells. Scientific American (April 1996) PDF

2.   M.T. Madigan and B.L. Marrs. 1997. Extremophiles. Scientific American (April 1997) PDF

3.   W.F. Doolittle. 2000. Uprooting the Tree of Life. Scientific American (February 2000) PDF

Assignment (to be completed by the beginning of class):

(PDF for download) Three and Three worksheet to be completed for all required readings

 

Week 6: Friday, February 22, 2013

Lecture Topic: Single-celled versus Multicellular Organisms

(Note: Class starts at 12:30; plants will be harvested at the beginning of class.)

Required Reading (to be completed by the beginning of class):

No new material, see materials from previous week

Supplemental Readings (optional readings that give more detail on the subjects discussed in this lecture):

1.   D.M. Downs. 2006. Understanding microbial metabolism. Annual Review of Microbiology 60:533-59. PDF

2.   R. Kassen and P.B. Rainey. 2004. The ecology and genetics of microbial diversity. Annual Review of Microbiology 58:207-231. PDF

3.   D.A. Cowan and L.A. Tow. 2004. Endangered Antarctic environments. Annual Review of Microbiology 58:649-690. PDF

 

Week 7: Friday, March 1, 2013

Lecture Topic: Carbohydrates, Lipids, Proteins and Other Common Biological Compounds

Required Reading (to be completed by the beginning of class):

1.   B. Khakh and G. Burnstock. 2009. The Double Life of ATP. Scientific American (December 2009) PDF

2.   A.K. Dunker and R.W. Kriwacki. 2011. The Orderly Chaos of Proteins. Scientific American (April 2011) PDF

3.   N.Y. Kiang. 2008. The Color of Plants on Other Worlds. Scientific American (April 2008) PDF

4.   N. Sharon and H. Lis. 1993. Carbohydrates in Cell Recognition. Scienific American (January 1993) PDF

Assignment (to be completed by the beginning of class):

(PDF for download) Three and Three worksheet to be completed for all required readings

 

Week 8: Friday, March 8, 2013

Lecture Topic: Pigments and Enzymes

Class Presentations of Planned Experiments (this Worksheet explains what to include)

Required Reading (to be completed by the beginning of class):

No new material, see materials from previous week

Supplemental Readings (optional readings that give more detail on the subjects discussed in this lecture):

1.   Sections on ATP and NAD/NADP – H+ by Nelson and Cox (Principles of Biochemistry) (27.7 MB PDF)

2.   Sections on Enzymes and Pigments by Nelson and Cox (Principles of Biochemistry) (29.5 MB PDF)

3.   RCSP Protein Data Bank information sheet on RuBisCO (PDF)

4.   RCSP Protein Data Bank information sheet on Nitrogenase (PDF)

Homework DUE: 5 Talk-Block Worksheets due in class

 

Week 9: Friday, March 15, 2013

Activity: Week #1 of Planned Experiments (Start)

Lecture Topic: Evolution, Phylogenies, and Cladistics

Required Reading (to be completed by the beginning of class):

1.   W.P. Jacobs. 1994. Caulerpa. Scientific American (December 1994) PDF

2.   P.G. Falkowski. 2002. The OceanÕs Invisible Forest. Scientific American (August 2002) PDF

3.   M. Sturm. 2010. Arctic Plants Feel the Heat. Scientific American (May 2010) PDF

4.   3. D. Grossman. 2004. Spring Forward. Scienific American (January 2004) PDF

5.   4. P.A. Cox. 1993. Water-Pollinated Plants. Scienific American (October 1993) PDF

Assignment (to be completed by the beginning of class):

(PDF for download) Three and Three worksheet to be completed for all required readings

Handout: Simplified Plant Evolution (PDF)

 

Week 10: Friday, March 22, 2013

Activity: Week #2 of Planned Experiments (Continued)

FIELD TRIP TO LYON ARBORETUM

Directions: The field trip will take place at the Lyon Arboretum, which is walking distance from the University.

A City Map to the Arboretum is available HERE; a Trail Map within the Arboretum is available HERE). 

Materials: Bring a notebook and pen/pencil (calculator optional). Prepare for rain and shine. Bug spray optional.

In order to come along, you need to download and fill out this Risk Release Form (PDF)

Field Trip Assignment (due in class on Friday, April 5, 2012) (PDF)

Directions for Three-Essays Assignment (Draft #1 due in class on April 12; Final Draft due May 10) (Full Directions Here)

Handout: An Example of How to Write An Essay (PDF)

 

Week 11: Friday, March 29, 2013

Activity: Week #3 of Planned Experiments (Continued)

(Note: No Class - UH Spring Break)

 

Week 12: Friday, April 5, 2013

Activity: Week #4 of Planned Experiments (Harvest)

Lecture Topic: Guest SpeakerDr. Elena Bennett, McGill University

Required Readings (to be completed by the beginning of class):

1.   J. Foley. 2010. Living on a New Earth; Boundaries for a Healthy Planet Scientific American (April, 2010) PDF

2.   D.A. Vaccari. 2009. Phosphorous: A Looming Crisis. Scientific American (June 2009) PDF

3.   J. Elser and E. Bennett. 2011. A broken biogeochemical cycle. Nature v. 478 p. 29 PDF

4.   G.S. Metson et al. 2012. The role of diet in phosphorous demand. Environ. Res. Lettdoi:10.1088/1748-9326/7/4/044043 PDF

5.   G. MacDonald et al.  2011. Agronomic phosphorous imbalances across the world's croplands. PNAS doi: 10.1073/pnas.1010808108 PDF

Assignment (to be completed by the beginning of class):

(PDF for download) Three and Three worksheet to be completed for all required readings

Supplemental Readings (optional readings that give more detail on the subjects discussed in this lecture):

1.   C. Raudsepp-Hearne et al. 2010. Ecosystem service bundles for analyzing tradeoffs in diverse landscapes. PNAS doi:10.1073/pnas.0907284107 (PDF)

2.   Supplementary Information for the article above (PDF)

Homework DUE: Field Trip Assignment/Homework

 

Week 13: Friday, April 12, 2013

Lecture Topic: Elemental Cycles

Required Readings (to be completed by the beginning of class):

1. D.G. Hawkins, D.A. Lashof and R.H. Williams. 2006. What to do about Coal. Scientific American (September 2006) PDF

2. A.R. Townsend and R.W. Howarth. 2010. Fixing the Global Nitrogen Problem. Scientific American (February 2010) PDF

3. A.Y. Hoekstra and M.M. Mekonnen. 2011. The water footprint of humanity. PNAS doi/10.1073/pnas.1109936109 PDF

Note: Hoekstra and Mekonnen (2011) was included above as an optional supplemental reading; for this week it is required.

Assignment (to be completed by the beginning of class):

(PDF for download) Three and Three worksheet to be completed for all required readings

Homework DUE: Draft #1 of Three-Essays due in class

 

Week 14: Friday, April 19, 2013

Class Presentations of Data from Completed Experiments (this Worksheet explains what to include)

 

Week 15: Friday, April 26, 2013

(Note: last day of class.)

Class Presentations on What Makes a Good Talk? (this Worksheet explains what to include)

Homework DUE: 5 Talk-Block Worksheets due in class

 

End of Finals Week: Friday, May 10, 2013

Homework DUE: Final Draft of Essay due in Hope JahrenÕs mailbox (701 POST Building) or by email (Full Directions for Final Draft Here)

 

Grading:

Your grade for the course will be based on the following:

 

10% Talk-Block Worksheets (10 total)

10% Three-and-Three Worksheets for all readings

10% Field Trip Assignment (due April 5)

10% Presentation 1: Planned Experiments (March 8)

20% Presentation 2: Completed Experiments (April 19)

10% Presentation 3: What Makes a Good Talk (April 26)

30% Three-Essays (Rough Draft due April 12; Final Draft due May 10)

Total = 100%

 

Talk-Blocks:

You are required to attend 10 scientific research talks on campus during the course of the semester, and complete a Talk-Block Worksheet evaluation for each of the talks that you attend. 

Deadlines:

5 Talk-Block Worksheets due in class on Friday, March 8, 2013

5 Talk-Block Worksheets due in class on Friday, April 26, 2013

Talk-Block Worksheet is available here: (PDF for download)

 

BTW, What is Geobiology?

Geobiology is the understanding of biogeochemical systems in terms of the biological organisms that comprise them. It emphasizes biochemical and metabolic processes and an organismal agenda for global cycles. Through processes that result in growth and reproduction, living organisms contribute significantly to carbon cycling, weathering, pedogenesis and a wealth of other phenomena. This course makes clear the conversion of energy and matter during shared metabolic pathways, makes distinct the shared structures of organisms, and explores specifically geobiological phenomena such as the living root zone within soils, and the precipitation of minerals within cells.