The Origins of Life on Earth
Fall 2024
Universitat Autònoma de Barcelona and Georgia Tech Study Abroad

Professor Loren Williams
School of Chemistry and Biochemistry
Center for the Origins of Life
Georgia Tech

Around four billion years ago, prebiotic chemistry established the molecular keystones of biology, paving the path to life. Chemical and geological processes on the ancient Earth caused increases in size and functionality of organic molecules, leading ultimately to RNA, DNA, protein, polysaccharides, and membrane-forming amphipaths. The roots of biology present some of the most fascinating and difficult questions in the fields of chemical and biological sciences. In this course we will investigate the origins of life. We will introduce concepts, survey relevant literature, discuss recent advances, and identify and question assumptions and biases. There is no textbook. All course material will be supplied by the instructor.

Grades will be based on: (i) A short written report on a subject that is agreeable to the student and the professor, (ii) Presentations by groups of students (see below), (iv) Participation in class discussions, and (iv) Class attendance (you have to come to class). The structure of the class will be similar to that of a group meeting. Students are expected to participate in discussions.

Course Topics

Topic 1. On the Nature and Functioning of Science (Group 1 & 2)

Kuhn, 1997, The Structure of Scientific Revolutions (pdf)

LDW excerpts of Kuhn, Bigamist Hydrogen - A Protest

Newman, 1995, American Intransigence: The Rejection of Continental Drift in the Great Debates of the 1920's, Earth Sciences History, 62-83 (pdf)

Rousseau, 1992, Case Studies in Pathological Science, American Scientist, 54-63 (pdf)

Topic 2. Origins and Nature of our Universe, Solar System and Earth-Moon System (Groups 3 & 4)

The Universe

Timeline of the Universe

The Universe in a Year

What happened in the Early Universe?

What is the Big Bang Theory?

The Solar System

Kane et al., 2021, The Fundamental Connections between the Solar System and Exoplanetary Science, Journal of Geophysical Research: Planets (pdf)

The Earth-Moon System

Wada et al., 2006, High-resolution simulations of a Moon-forming impact and postimpact evolution, The Astrophysical Journal, 1180 (pdf)

Zellner, 2017, Cataclysm no more: new views on the timing and delivery of lunar impactors, Orig. Life Evol. Biosph., 261-280 (pdf)

Wogan et al., 2023, Origin-of-life Molecules in the Atmosphere after Big Impacts on the Early Earth, The Planetary Science Journal, 169 (pdf))

Topic 3a. Evolution

LDW Powerpoint 1

LDW Powerpoint 2

Topic 3. Origins of Life: Standard Models (Groups 5 & 6)

General Introduction

Lanier, 2017, The origin of life: models and data, J. Mol. Evol., 85-92 (pdf)

RNA Worlds

Neveu et al., 2013, The “strong” RNA world hypothesis: Fifty years old, Astrobiology, 391-403 (pdf)

Orgel, 2004, Prebiotic chemistry and the origin of the RNA world, Crit Rev Biochem Mol Biol, 99-123 (pdf)

Thermal Vents

Martin et al., 2008, Hydrothermal vents and the origin of life, Nat. Rev. Microbiol., 805-814 (pdf)

Barge, 2022, Diverse geochemical conditions for prebiotic chemistry in shallow-sea alkaline hydrothermal vents, Nature Geoscience, 976 (pdf)

Clays

Kloprogge & Hartman, 2022, Clays and the origin of life: The experiments, Life, 259 (pdf)

Compartments

Kahana, Dynamic lipid aptamers: Non-polymeric chemical path to early life, Chemical Society Reviews, 11741-11746 (pdf)

Topic 4. Biomolecules: Building Blocks of Life (Groups 4 & 5)

Nelson et al., 2021, Lehninger Principles of Biochemistry, 8th Edition,

Miller, 1953, A production of amino acids under possible primitive earth conditions, Science, 528-529 (pdf)

Aponte et al., 2020, Analysis of amino acids, hydroxy acids, and amines in CR chondrites, Meteoritics & Planetary Science, 2422-2439 (pdf)

Topic 5. Biomolecules: Polymers of Life - Emergence, Symbiosis, Recalcitrance and Persistence (Groups 6 & 1)

Nelson et al., 2021, Lehninger Principles of Biochemistry, 7th Edition (pdf)

Metange, 2024, Biological Polymers: Origins, Evolution and Significance (pdf)

Hud, 2013, The origin of RNA and “my grandfather’s axe”, Chem. Biol., 466-474

Edri, 2023, Assembly‐driven protection from hydrolysis as key selective force during chemical evolution, FEBS Lett., 2879-2896

Runnels, 2018, Folding, assembly, and persistence: the essential nature and origins of biopolymers, J Mol Evol, 598-610

Lanier, 2017, The Central Symbiosis of Molecular Biology: Molecules in Mutualism, J Mol Evol, 8-13

Topic 6. Water: Physics, Geology, Chemistry, and Biochemistry (Groups 2 & 4)

Forsythe, 2015, Ester-mediated amide bond formation driven by wet-dry cycles: a possible path to polypeptides on the prebiotic earth, Angew. Chem. Int. Ed., 9871-9875

Frenkel-Pinter, 2021, Water and Life: The Medium is the Message, J. Mol. Evol., 1-10

Topic 7. The Tree of Life: The Ribosome and the Last Universal Common Ancestor of Life (Groups 3 & 5)

Vetsigian et al., 2006, Collective evolution and the genetic code, Proc. Natl. Acad. Sci. USA, 10696-10701

Bowman et al., 2020, Root of the tree: the significance, evolution, and origins of the ribosome, Chem. Rev., 4848-4878

Topic 8. Evolution, Part 1: Darwinian, Lamarkian, and Constructive Neutral Processes (Groups 6 & 2)

Muñoz-Gómez et al., 2021, Constructive neutral evolution 20 years later, J. Mol. Evol., 172-182

Jacob, 1977, Evolution and tinkering, Science, 1161-1166

Topic 9. Evolution, Part 2: Trans-Darwinian Processes - Stellar, Mineral and Chemical Evolution (Groups 1 & 4)

Hazen & Ferry, 2010, Mineral evolution: Mineralogy in the fourth dimension, Elements, 9-12

Wong et al., 2023, On the roles of function and selection in evolving systems, Proc. Natl. Acad. Sci. USA, e2310223120

Matange et al., 2024, Evolution of Complex Chemical Mixtures Reveals Combinatorial Compression and Population Synchronicity, ChemRxiv, 10.26434/chemrxiv-22022-s26433cr26432-v26433

Topic 10. Evolution, Part 3. Exaptation, and the Inference of Ancestry

Gould & Vrba, 1982, Exaptation—a missing term in the science of form, Paleobiology, 4-15

Frenkel-Pinter et al., 2022, Adaptation and Exaptation: From Small Molecules to Feathers, J. Mol. Evol., 166-175

Topic 11. Definitions of Life

Gómez-Márquez, 2021, What is life?, Mol. Biol. Rep., 6223-6230

List of Students

Full Citations

Aponte, J. C., Elsila, J. E., Hein, J. E., Dworkin, J. P., Glavin, D. P., McLain, H. L., Parker, E. T., Cao, T., Berger, E. L., & Burton, A. S. (2020). Analysis of amino acids, hydroxy acids, and amines in CR chondrites. Meteoritics & Planetary Science, 55(11), 2422-2439.

Barge, L. (2016). From Geochemistry to Biochemistry: Simulating Prebiotic Chemistry Driven by Geochemical Gradients in Alkaline Hydrothermal Vents. 41st COSPAR Scientific Assembly, 41, F3. 1-40-16.

Bowman, J. C., Petrov, A. S., Frenkel-Pinter, M., Penev, P. I., & Williams, L. D. (2020). Root of the tree: the significance, evolution, and origins of the ribosome. Chem. Rev., 120(11), 4848-4878.

Edri, R., Fisher, S., Menor‐Salvan, C., Williams, L. D., & Frenkel‐Pinter, M. (2023). Assembly‐driven protection from hydrolysis as key selective force during chemical evolution. FEBS Lett., 597(23), 2879-2896.

Forsythe, J. G., Yu, S. S., Mamajanov, I., Grover, M. A., Krishnamurthy, R., Fernandez, F. M., & Hud, N. V. (2015). Ester-mediated amide bond formation driven by wet-dry cycles: a possible path to polypeptides on the prebiotic earth. Angew. Chem. Int. Ed., 54(34), 9871-9875. https://doi.org/10.1002/anie.201503792

Frenkel-Pinter, M., Petrov, A. S., Matange, K., Travisano, M., Glass, J. B., & Williams, L. D. (2022). Adaptation and exaptation: from small molecules to feathers. J. Mol. Evol., 90(2), 166-175.

Frenkel-Pinter, M., Rajaei, V., Glass, J. B., Hud, N. V., & Williams, L. D. (2021). Water and Life: The Medium is the Message. J. Mol. Evol., 1-10.

Gómez-Márquez, J. (2021). What is life? Mol. Biol. Rep., 48, 6223-6230.

Gould, S. J., & Vrba, E. S. (1982). Exaptation—a missing term in the science of form. Paleobiology, 8(1), 4-15.

Hazen, R. M., & Ferry, J. M. (2010). Mineral evolution: Mineralogy in the fourth dimension. Elements, 6(1), 9-12.

Hud, N. V., Cafferty, B. J., Krishnamurthy, R., & Williams, L. D. (2013). The origin of RNA and “my grandfather’s axe”. Chem. Biol., 20(4), 466-474.

Jacob, F. (1977). Evolution and tinkering. Science, 196(4295), 1161-1166. https://science.sciencemag.org/content/196/4295/1161.long

Kahana, A., Maslov, S., & Lancet, D. (2021). Dynamic lipid aptamers: Non-polymeric chemical path to early life. Chemical Society Reviews, 50(21), 11741-11746.

Kane, S. R., Arney, G. N., Byrne, P. K., Dalba, P. A., Desch, S. J., Horner, J., Izenberg, N. R., Mandt, K. E., Meadows, V. S., & Quick, L. C. (2021). The Fundamental Connections between the Solar System and Exoplanetary Science. Journal of Geophysical Research: Planets, 126(2).

Kloprogge, J. T., & Hartman, H. (2022). Clays and the origin of life: The experiments. Life, 12(2), 259.

Kuhn, T. S. (1997). The Structure of Scientific Revolutions (Vol. 962). University of Chicago press Chicago.

Lanier, K. A., Petrov, A. S., & Williams, L. D. (2017). The Central Symbiosis of Molecular Biology: Molecules in Mutualism. J Mol Evol, 85(1-2), 8-13. https://doi.org/10.1007/s00239-017-9804-x

Lanier, K. A., & Williams, L. D. (2017). The origin of life: models and data. J. Mol. Evol., 84(2), 85-92.

Martin, W., Baross, J., Kelley, D., & Russell, M. J. (2008). Hydrothermal vents and the origin of life. Nat. Rev. Microbiol., 6(11), 805-814. https://www.nature.com/articles/nrmicro1991.pdf

Matange, K., Rajaei, V., Costner, J. T., Robertson, A., Kim, J. S., Petrov, A. S., Bowman, J. C., Williams, L. D., & Frenkel-Pinter, M. (2024). Evolution of Complex Chemical Mixtures Reveals Combinatorial Compression and Population Synchronicity. ChemRxiv, 10.26434/chemrxiv-22022-s26433cr26432-v26433.

Miller, S. L. (1953). A production of amino acids under possible primitive earth conditions. Science, 117(3046), 528-529. http://www.ncbi.nlm.nih.gov/pubmed/13056598

https://science.sciencemag.org/content/117/3046/528.long

Muñoz-Gómez, S. A., Bilolikar, G., Wideman, J. G., & Geiler-Samerotte, K. (2021). Constructive neutral evolution 20 years later. J. Mol. Evol., 89, 172-182.

Nelson, D. L., Lehninger, A. L., & Cox, M. M. (2021). Lehninger Principles of Biochemistry, 8th Edition. Macmillan.

Neveu, M., Kim, H.-J., & Benner, S. A. (2013). The “strong” RNA world hypothesis: Fifty years old. Astrobiology, 13(4), 391-403. https://www.liebertpub.com/doi/pdfplus/10.1089/ast.2012.0868

Newman, R. P. (1995). American Intransigence: The Rejection of Continental Drift in the Great Debates of the 1920's. Earth Sciences History, 62-83.

Orgel, L. E. (2004). Prebiotic chemistry and the origin of the RNA world. Crit Rev Biochem Mol Biol, 39(2), 99-123. https://doi.org/10.1080/10409230490460765

Rousseau, D. L. (1992). Case Studies in Pathological Science. Am. Sci., 80(1), 54-63.

Runnels, C. M., Lanier, K. A., Williams, J. K., Bowman, J. C., Petrov, A. S., Hud, N. V., & Williams, L. D. (2018). Folding, assembly, and persistence: the essential nature and origins of biopolymers. J Mol Evol, 86(9), 598-610. https://doi.org/10.1007/s00239-018-9876-2

Vetsigian, K., Woese, C., & Goldenfeld, N. (2006). Collective evolution and the genetic code. Proc. Natl. Acad. Sci. USA, 103(28), 10696-10701.

Wada, K., Kokubo, E., & Makino, J. (2006). High-resolution simulations of a Moon-forming impact and postimpact evolution. The Astrophysical Journal, 638(2), 1180.

Wogan, N. F., Catling, D. C., Zahnle, K. J., & Lupu, R. (2023). Origin-of-life Molecules in the Atmosphere after Big Impacts on the Early Earth. The Planetary Science Journal, 4(9), 169.

Wong, M. L., Cleland, C. E., Arend Jr, D., Bartlett, S., Cleaves, H. J., Demarest, H., Prabhu, A., Lunine, J. I., & Hazen, R. M. (2023). On the roles of function and selection in evolving systems. Proc. Natl. Acad. Sci. USA, 120(43), e2310223120.

Zellner, N. E. (2017). Cataclysm no more: new views on the timing and delivery of lunar impactors. Orig. Life Evol. Biosph., 47, 261-280.