Chapter 4 Notes

The Origin of Life

The Nature of Selection

There are a number of good general references on the origin of life. See Knoll (2003), Fenchel (2002), Gesteland and Atkins (1993), Gesteland et al. (1999, 2006), and Orgel (1998).

In the chapter introduction, we provide a definition of life, which is based upon what is referred to as the “NASA definition of life.” For more information on this and other definitions of life, see Joyce (1994), Luisi (1998), Fenchel (2002), and Rasmussen et al. (2004).

When Did Life Begin on Earth?

Radioisotope Dating

An excellent web resource is available from the United States Geological Survey at http://pubs.usgs.gov/gip/geotime/, including a chapter on radiometric dating at http://pubs.usgs.gov/gip/geotime/radiometric.html.

Other good web resources about determining the age of rocks and fossils are “Clocks in the Rocks,” by C.R. Nave at http://hyperphysics.phy-astr.gsu.edu/hbase/nuclear/clkroc.html; “Fossils, Rocks and Time,” by Lucy Edwards and John Pojeta at http://pubs.usgs.gov/gip/fossils/contents.html; “The Earth through Time,” by Harold L. Levin at http://www3.interscience.wiley.com:8100/legacy/college/levin/0470000201/chap_tutorial/ch01/chapter01-3.html.

Estimates of the Age of the Earth Place a Lower Boundary on When Life Began

More information on the geological approach using gneiss and zircon dating is available at http://pubs.usgs.gov/gip/geotime/age.html.

For more on the planetological approach, see http://pubs.usgs.gov/gip/geotime/age.html.

Additional information can be found in Chapter 3 of Life on a Young Planet: The First Three Billion Years of Evolution on Earth, by Andrew Knoll (2003).

Fossil Evidence and Comparisons of Modern Organisms Suggest That Life Evolved Soon after Earth Was Hospitable

Various views on the fossil evidence for early cellular life are presented in Brasier et al. (2006) and Schopf (2006).

For a discussion of early photosynthesis, see Olson (2006).

Chapters 3 and 4 from Knoll (2003) are a good presentation of what life may have been like on a young planet.

How Did Life Begin on Earth?

We outlined the essential steps for the origin of life (see p. 92ff). These are based largely on a review paper by Joyce (2002). For additional discussions on this topic, see de Duve (1987) and Orgel (1998).

Many Molecules Required for Life Can Be Created by Chemical or Physical Means

A general discussion of this topic is in Chapter 3 of The Origin and Early Evolution of Life by Thomas Fenchel (2002).

Wohler’s work on urea synthesis in 1828 is summarized in The Centenary of Wöhler’s Synthesis of Urea (1828–1928), by Frederick Gowland Hopkins (1928).

The original paper describing the synthesis of alanine is Strecker (1850).

Both Oparin and Haldane wrote about the early conditions on Earth, including the presence of a reducing atmosphere. Their presentations set the stage for the classic experiments of Miller and Urey, and others. See Oparin (1924, 1976) and Haldane (1929).

Miller and Urey’s classic papers on their prebiotic synthesis experiments include Miller (1953) and Miller and Urey (1959a,b).

As noted on p. 93, recent studies have reexamined the early conditions on Earth and the types of chemical reactions that may have taken place under those conditions. A good review on this subject is Bada and Lazcano (2003). Also see Lazcano (2001).

An exploration of the reducing environment in outer space and analyses of the Murchison meteorite as a site of prebiotic synthesis are discussed by Lerner and Cooper (2003) and Peltzer and Bada (1978).

Modern deep sea environments are discussed in Van Dover et al. (2002) and Van Dover (2000).

More general discussions on the where and how of prebiotic molecular syntheses are discussed in Orgel (1998) and Wächtershäuser (1992). Whether life arose on Earth under high temperature conditions has been explored by examining the impact of temperature on RNA folding in Moulton et al. (2000).

Chemical Reactions Can “Evolve” to Produce Complicated Molecules and Primitive Metabolism

For more on this topic, see Chemical Evolution by Melvin Calvin (1961), an older reference that still has some good material.

The polymerization of DNA from RNA is from Lewis and Hanawalt (1982). Nucleation of monomers is based on Maynard Smith and Szathmáry (1995). More on the evolution of metabolism is in Wächtershäuser (1988).

Orgel (2000) has a discussion of closed cycles. Hanczyc et al. (2003) report on the role of clays in accelerating the spontaneous conversion of fatty acid micelles into vesicles. Also see Hazen (2001) for a discussion of the roles rocks and clays could have played as sites of primitive metabolism.

Self-Replication Is Necessary for Evolution

Our discussion of self-replication is based in large part on The Major Transitions in Evolution, by Maynard Smith and Szathmáry (1995). Additional information on self-replicating molecules can be found in Rebek (1994) and Eigen et al. (1981).

Compartmentalization Facilitates Self-Organization and Accelerated Evolution

Maynard Smith and Szathmáry (1995) contains a general discussion of compartmentalization and its role in prebiotic evolution. Hanczyc and Szostak (2004) provide a review on replicating vesicles as models of primitive growth and division. Hazen (2001) discusses the role of iron sulfide rocks in self-organizing systems in an article for general audiences.

Manfred Eigen’s original papers on self-organization include Eigen (1971a,b). For an example of experimental studies on compartmentalization, see Hanczyc et al. (2003).

The Chicken-and-Egg Problem Solved: RNA Can Serve a Dual Role as Information Carrier and Catalyst

For a general discussion of the dual roles of RNA in the pre-DNA world, see Joyce and Orgel in The RNA World (1993). A good review of RNA catalytic possibilities is by Doudna and Cech (2002). The antiquity of RNA-based evolution is considered by Joyce (2002).

Leaving the RNA World Required the Evolution of the Translation System and the Genetic Code

General discussions on this topic include Schimmel and Ribas de Pouplana (1999), Di Giulio (2005), Schimmel et al. (1993), and Cedergren and Miramontes (1996).

More on Francis Crick’s important contribution to our understanding of the genetic code is in Crick (1968). Carl Woese’s sterochemical theory is discussed in his book The Genetic Code (1967). The origin of the genetic code is reviewed by Knight et al. (1999).

DNA Replaces RNA

The evolutionary transition from RNA to DNA in early cells has been studied by a number of investigators; see Lazcano (1988) and Forterre (2005, 2002).

References

Bada J.L. and Lazcano A. 2003. Prebiotic soup: Revisiting the Miller experiment. Science 300: 745–746.

Brasier M., McLoughlin N., Green O., and Wacey D. 2006. A fresh look at the fossil evidence for early Archaean cellular life. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361: 887–902. Freely available at http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16754605.

Calvin M. 1961. Chemical evolution. Oregon State System of Higher Education, Eugene, Oregon.

Cedergren R. and Miramontes P. 1996. The puzzling origin of the genetic code. Trends Biochem. Sci. 21: 199–200. Erratum in: Trends Biochem. Sci. 21: 396.

Crick F.H. 1968. The origin of the genetic code. J. Mol. Biol. 38: 367–379.

de Duve C. 1987. Selection by differential molecular survival: A possible mechanism of early chemical evolution. Proc. Natl. Acad. Sci. 84: 8253–8256.

Di Giulio M. 2005. The origin of the genetic code: theories and their relationships, a review. Biosystems 80: 175–184.

Doudna J.A. and Cech T.R. 2002. The chemical repertoire of natural ribozymes. Nature 418: 222–228.

Eigen M. 1971a. Molecular self-organization and the early stages of evolution. Q. Rev.Biophys. 4: 149–212.

Eigen M. 1971b. Self organization of matter and the evolution of biological macromolecules. Naturwissenschaften. 58: 465–523.

Eigen M., Gardiner W., Schuster P., and Winkler-Oswatitsch R. 1981. The origin of genetic information. Sci. Am. 244: 88–92, 96, et passim.

Fenchel T. 2002. The origin and early evolution of life. Oxford University Press, Oxford. (Whole book and also Chapter 4, “What is life?”, pp. 22–44.)

Forterre P. 2002. The origin of DNA genomes and DNA replication proteins. Curr. Opin. Microbiol. 5: 525–532.

Forterre P. 2005. The two ages of the RNA world, and the transition to the DNA world: A story of viruses and cells. Biochimie 87: 793–803.

Gesteland R.F. and Atkins J.F. 1993. The RNA world. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

Gesteland R.F., Cech T.R., and Atkins J.F., eds. 1999. The RNA world: The nature of modern RNA suggests a prebiotic RNA world, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

Gesteland R.F., Cech T.R., and Atkins J.F., eds. 2006. The RNA world, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

Gowland Hopkins F. 1928. The centenary of Wöhler’s synthesis of urea (1828–1928). Biochem J. 22: 1341–1348. See http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1252269.

Haldane J.B.S. 1929. The origin of life. The Rationalist Annual 148: 3–10.

Hanczyc M.M. and Szostak J.W. 2004. Replicating vesicles as models of primitive growth and division. Curr. Opin. Chem. Biol. 8: 660–664.

Hanczyc M.M., Fujikawa S.M., and Szostak J.W. 2003. Experimental models of primitive cellular compartments: Encapsulation, growth, and division. Science 302: 618–622.

Hazen R.M. 2001. Life’s rocky start. Sci Am. 284: 76–85.

Joyce G.F. 1994. Foreword. In Origins of life: The central concepts (ed. D.W. Deamer and G.R. Fleischaker), pp. xi–xii. Jones and Bartlett, Boston.

Joyce G.F. 2002. The antiquity of RNA-based evolution. Nature 418: 214–221.

Joyce G.F. and Orgel L.E. 1993. Prospects for understanding the origin of the RNA world. In The RNA world: The nature of modern RNA suggests a prebiotic RNA world (ed. R.F. Gesteland and J.F. Atkins), pp. 1–25. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

Knight R.D., Freeland S.J., and Landweber L.F. 1999. Selection, history and chemistry: The three faces of the genetic code DNA replacing RNA. Trends Biochem. Sci. 24: 241–247.

Knoll A.H. 2003. Life on a young planet: The first three billion years of evolution on Earth. Princeton University Press, Princeton, New Jersey. (Whole book; also in Chapter 3, “Life’s signature in ancient rocks,” pp. 32–49; Chapter 4, “The earliest glimmers of life,” pp. 50–71.)

Lazcano A. 2001. Prebiotic chemistry. In Encyclopedia of life sciences. John Wiley & Sons, Ltd., London.

Lazcano A., Guerrero R., Margulis L., and Oró J. 1988. The evolutionary transition from RNA to DNA in early cells. J. Mol. Evol. 27: 283–290.

Lerner N.R. and Cooper G.W. 2003. Imino acids in the Murchison meteorite: Evidence of Strecker reactions. Lunar and planetary science XXXIV. Ames Research Center, Moffett Field, California. Document ID: 20030111393.

Lewis R.J. and Hanawalt P.C. 1982. Ligation of oligonucleotides by pyrimidine dimers—A missing “link” in the origin of life? Nature 298: 393–396.

Luisi P.L. 1998. About various definitions of life. Orig. Life Evol. Biosph. 28: 613–622.

Maynard Smith J. and Szathmáry E. 1995. The major transitions in evolution. W.H. Freeman, Oxford.

Miller S.L. 1953. A production of amino acids under possible primitive earth conditions. Science 117: 528–529.

Miller S.L. and Urey H.C. 1959a. Organic compound synthesis on the primitive earth. Science 130: 245–251.

Miller S.L. and Urey H.C. 1959b. Origin of life. Science 130: 1622–1624.

Moulton V., Gardner P.P., Pointon R.F., Creamer L.K., Jameson G.B., and Penny D. 2000. RNA folding argues against a hot-start origin of life. J. Mol. Evol. 51: 416–421.

Olson J.M. 2006. Photosynthesis in the Archean era. Photosynth Res. 88: 109–117.

Oparin A.I. 1924. The origin of life. Izd. Moskovshii Rabochii, Moscow. English translation in Oparin A.I. 1967. The origin of life (ed. J.D. Bernal), p. 199–234. Weidenfeld & Nicolson, London.

Oparin A.I. 1976. Evolution of the concepts of the origin of life, 1924–1974. Orig. Life 7: 3–8.

Orgel L.E. 1998. The origin of life—A review of facts and speculations. Trends Biochem. Sci. 23: 491–495.

Orgel L.E. 2000. Self-organizing biochemical cycles. Proc. Natl. Acad. Sci. 97: 12503–12507.

Peltzer E.T. and Bada J.L. 1978. α-hydroxycarboxylic acids in the Murchison meteorite. Nature 272: 443–444.

Rasmussen S., Chen L., Deamer D., Krakauer D.C., Packard N.H., Stadler P.F., and Bedau M.A. 2004. Transitions from nonliving to living matter. Science 303: 963–965.

Rebek J., Jr. 1994. Synthetic self-replicating molecules. Sci. Am. 271: 34–40.

Schimmel P. and Ribas de Pouplana L. 1999. Genetic code origins: Experiments confirm phylogenetic predictions and may explain a puzzle. Proc. Natl. Acad. Sci. 96: 327–328. Erratum in Proc. Natl. Acad. Sci. 96: 5890.

Schimmel P., Giegé R., Moras D., and Yokoyama S. 1993. An operational RNA code for amino acids and possible relationship to genetic code. Proc. Natl. Acad. Sci. 90: 8763–8768.

Schopf J.W. 2006. Fossil evidence of Archaean life. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361: 869–885. Freely available at http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16754604.

Strecker A. 1850. Ueber die künstliche Bildung der Milchsäure und einen neuen, dem Glycocoll homologen. Ann. Chem. Pharm. 75: 27–45.

Van Dover C.L. 2000. The ecology of deep-sea hydrothermal vents. Princeton University Press, Princeton, New Jersey.

Van Dover C.L., German C.R., Speer K.G., Parson L.M., and Vrijenhoek R.C.. 2002. Evolution and biogeography of deep-sea vent and seep invertebrates. Science 295: 1253–1257.

Wächtershäuser G. 1988. Before enzymes and templates: Theory of surface metabolism. Microbiol. Rev. 52: 452–484.

Wächtershäuser G. 1992. Groundworks for an evolutionary biochemistry: The iron-sulphur world. Prog. Biophys. Mol. Biol. 58: 85–201.

Woese C.R. 1967. The genetic code. Harper & Row, New York.

WWW Resources

http://hyperphysics.phy-astr.gsu.edu/hbase/nuclear/clkroc.html Nave C.R. 2006. Clocks in the rocks. Department of Physics and Astronomy, Georgia State University, Atlanta, Georgia 30303-3088. Email: RodNave@gsu.edu

http://pubs.usgs.gov/gip/geotime/ Newman W.L. Geologic time—Online edition. U.S. Geological Survey Publications Services, Washington, D.C.

http://pubs.usgs.gov/gip/geotime/about.html Last updated July 28, 1997.

http://pubs.usgs.gov/gip/geotime/radiometric.html Newman W.L. Radiometric time scale. In Geologic time—Online edition. U.S. Geological Survey Publications Services, Washington, D.C. Last updated June 13, 2001.

http://pubs.usgs.gov/gip/geotime/age.html Newman W.L. The age of the earth. In Geologic time—Online edition. U.S. Geological Survey Publications Services, Washington, D.C. Last updated July 9, 2007.

http://pubs.usgs.gov/gip/fossils/contents.html Edwards L.E. and Pojeta J. Jr. 2007. Fossils, rocks, and time. USGS Geological Survey, Publications Services, Washington, D.C.

http://pubs.usgs.gov/gip/fossils/about.html. Last updated 14 August 1997.

http://www.astrobio.net/news/article344.html Mullen L. Defining life. Astrobiol. Mag. December 30, 2002.

http://www3.interscience.wiley.com:8100/legacy/college/levin/0470000201/chap_tutorial/ch01/chapter01-3.html Levin H.L. 2006. Introduction to Earth history (Chapter 1). In The Earth through time, 7th ed. John Wiley, New York.