3.3 The Nested Holarchy of Life

Evolution complexifies into nested levels from life’s origin to symbiotic cells and on to global ecosystems.

3.3.1 Emergent Communities of Life


Geophysical Domains

Diego, Perugini, and Poli Giampiero. “Chaotic Dynamics and Fractals in Magmatic Interaction Processes: A Different Approach to the Interpretation of Mafic Microangular Enclaves.” Earth and Planetary Sciences Letters. vol. 175, nos. 1–2 (30 January 2000): 93–103.

Quattrochi, Dale A., and Michael F. Goodchild, eds. Scale in Remote Sensing and GIS. Boca Raton, Fla.: Lewis Publishers, 1997.

Rodriguez-Iturbe, Ignacio, and Andrea Rinaldo. Fractal River Basins: Chance and Self-Organization. Cambridge: Cambridge University Press, 1997.

Rowan, Linda, and Jessie Smith. “The Terrestrial Web.” Science. vol. 288, no. 5473 (16 January 2000): 1983.

Teisseyre, Roman, and Eugeniusz Majewski, eds. Earthquake Thermodynamics and Phase Transformations in the Earth’s Interior. San Diego, Calif.: Academic Press, 2001.

Werner, Brad T. “Complexity in Natural Landform Patterns.” Science. vol. 284, no. 5411 (2 April 1999): 102–104.

Origin of Life

Brack, Andre, ed. The Molecular Origins of Life: Assembling Pieces of the Puzzle. New York: Cambridge University Press, 1998.

Davies, Paul. The Fifth Miracle: The Search for the Origin and Meaning of Life. New York: Simon & Schuster, 1999.

de Duve, Christian. Vital Dust: Life as a Cosmic Imperative. New York: Basic Books, 1995.

Dokholyan, Nikolay, et al. “Expanding Protein Universe and Its Origin from the Biological Big Bang.” Proceedings of the National Academy of Sciences. vol. 99, no. 22 (29 October 2002): 14132–36.

Ingber, Donald E. “The Origin of Cellular Life.” BioEssays. vol. 22, no. 12 (December 2000): 1160–70.

Lahav, Noam. Biogenesis: Theories of Life’s Origins. New York: Oxford University Press, 1999.

Morowitz, Harold J. Beginnings of Cellular Life: Metabolism Recapitulates Biogenesis. New Haven, Conn.: Yale University Press, 1992.
_______. “A Theory of Biochemical Organization, Metabolic Pathways, and Evolution.” Complexity. vol. 4, no. 6, (July/August 1999): 39–53.

Rizzotti, Martino, ed. Defining Life: The Central Problem in Theoretical Biology. Padova, Italy: University of Padova Press, 1996.

Schopf, J. William, ed. Life’s Origin: The Beginnings of Biological Evolution.Berkeley, Calif.: University of California Press, 2002.

Wills, Christopher, and Jeffery Bada. The Spark of Life: Darwin and the Primeval Soup. Cambridge, Mass.: Perseus Books, 2000.

Microbial Colonies

Ben-Jacob, Eshel. “Bacterial Wisdom, Godel’s Theorem and Creative Genomic Webs.” Physica A. vol. 248, nos. 1–2 (1 January 1998): 57–76.

Ben-Jacob, Eshel, et al. “Cooperative Self-Organization of Microorganisms.” Advances in Physics. vol. 49, no. 4 (2000): 256–80.

Bown, J. L., et al. “Evidence for Emergent Behaviour in the Community-Scale Dynamics of a Fungal Microcosm.” Proceedings of the Royal Society of London B. vol. 266, no. 1432 (1999): 1947.

Brown, Sam P., and Rufus A. Johnstone. “Cooperation in the Dark: Signalling and Collective Action in Quorum-Sensing Bacteria.” Proceedings of the Royal Society of London B. vol. 268, no. 1470 (2001): 961–65.

Crespi, Bernard J. “The Evolution of Social Behavior in Microorganisms.” Trends in Ecology and Evolution. vol. 16, no. 4 (1 April 2001): 178–83.

Maree, Athanasius, and Paulien Hogeweg. “How Amoeboids Self-organize into a Fruiting Body.” Proceedings of the National Academy of Sciences. vol. 98, no. 7 (27 March 2001): 3879–83.

Shapiro, James A. “Thinking about Bacterial Populations as Multicellular Organisms.” Annual Review of Microbiology. vol. 52 (October 1998): 81–104.

Wakeford, Tom. Liaisons of Life: From Hornworts to Hippos, How the Unassuming Microbe Has Driven Evolution. New York: Wiley, 2001.

The Symbiotic Cell

Dyson, Freeman. “The Evolution of Science.” In Evolution: Society, Science, and the Universe, ed. Andrew C. Fabian, 118–35. Cambridge: Cambridge University Press, 1998.

Frank, Steven A. “The Origin of Symbiotic Symbiosis.” Journal of Theoretical Biology. vol. 176, no. 3 (7 October 1995): 403–10.

Harold, Franklin M. The Way of the Cell: Molecules, Organisms, and the Order of Life. Oxford: Oxford University Press, 2001.

Margulis, Lynn. Symbiosis in Cell Evolution: Life and Its Environment on the Early Earth. 2d ed. San Francisco, Calif.: W. H. Freeman, 1993.

Margulis, Lynn, and Rene Fester, eds. Symbiosis as a Source of Innovation in Evolution: Speciation and Morphogenesis. Cambridge, Mass.: MIT Press, 1991.

Rizzotti, Martino. Early Evolution: From the Appearance of the First Cell to the First Modern Organisms. Basel: Birkhauser, 2000.

Ryan, Frank. Darwin’s Blind Spot: Evolution Beyond Natural Selection. Boston, Mass.: Houghton Mifflin, 2002.

Sapp, Jan. Evolution by Association: A History of Symbiosis. New York: Oxford University Press, 1994.

Schwemmler, Werner. Symbiogenesis: A Macro-Mechanism of Evolution: Progress Towards a Unified Theory of Evolution Based on Studies in Cell Bilogy. Berlin: Walter de Gruyter, Inc., 1989.

Seckbach, Joseph, ed. Symbiosis: Mechanisms and Model Systems. Dordrecht: Kluwer Academic Publishers, 2002.

Woese, Carl. “On the Evolution of Cells.” Proceedings of the National Academy of Sciences. vol. 99, no. 13 (19 June 2002): 8742–47.

Multicellular Organisms

Bonner, John. First Signals: The Evolution of Multicellular Development. Princeton, N.J.: Princeton University Press, 2000.

Buchman, Timothy G. “The Community of the Self.” Nature. vol. 420, no. 6912 (14 November 2002): 246–51.

Conway Morris, Simon. “Evolution: Bringing Molecules into the Fold.” Cell. vol. 100, no. 1 (7 January 2000): 1–11.

Eldredge, Niles. The Pattern of Evolution. New York: W. H. Freeman and Co., 1999.

Furusawa, Chikara, and Kunihiko Kaneko. “Complex Organization in Multicellularity as a Necessity in Evolution.” In Artificial Life VII: Proceedings of the Seventh International Conference on Artificial Life, eds. Mark Bedau, et al., 1–12. Cambridge, Mass.: MIT Press, 2000.

Gilbert, Scott F., and Jessica A. Bolker. “Homologies of Process and Modular Elements of Embryonic Construction.” Journal of Experimental Zoology. vol. 291, no. 1 (April 2001): 1–12.

Ingber, Donald E. “The Architecture of Life.” Scientific American. vol. 278, no. 1 (January 1998): 48–59.

Kaiser, Dale. “Building a Multicellular Organism.” Annual Review of Genetics. vol. 35 (2001): 103–23.

Kingsland, Sharon. “Neo-Darwinism and Natural History.” In Science in the Twentieth Century. eds. John Krige and Dominique Pestre, 417–37. Amsterdam: Harwood Academic, 1997.

Klein, Jan, and Naoyuki Takahata, eds. Where Do We Come From?: The Molecular Evidence for Human Descent. Berlin: Springer, 2002.

Michod, Richard, and Denis Roze. “Transitions in Individuality.” Proceedings of the Royal Society of London B. vol. 264, no. 1383 (1997): 853.

Raff, Rudolf A. The Shape of Life: Genes, Development, and the Evolution of Animal Form. Chicago, Ill.: University of Chicago Press, 1996.

Ridley, Mark. Evolution. 2d ed. Boston, Mass.: Blackwell Scientific, 1993.

Schopf, J. William. Cradle of Life: The Discovery of Earth’s Earlier Fossils.Princeton, N.J.: Princeton University Press, 1999.

Wilkins, Adam S. The Evolution of Developmental Pathways. Sunderland, Mass.: Sinauer Asociates, Inc., 2002.

Woese, Carl. “Interperting the Universal Phylogenetic Tree.” Proceedings of the National Academy of Sciences. vol. 97, no. 15 (18 July 2000): 8392–96.

Zimmer, Carl. At the Water’s Edge: Macroevolution and the Transformation of Life. New York: The Free Press, 1998.

Human Development

Bergman, Lars, et al., eds. Developmental Science and the Holistic Approach. Mahwah, N.J.: Lawrence Erlbaum Associates, 2000.

Cairns, Robert. “The Making of Development Psychology.” In Handbook of Child Psychology. 5th ed., vol. 1: Theoretical Models of Human Development, ed. Richard Lerner, 25–105. New York: Wiley, 1998.

Courage, Mary L., and Mark L. Howe. “From Infant to Child: The Dynamics of Cognitive Change in the Second Year of Life.” Psychological Bulletin. vol. 128, no. 2 (March 2002): 250–77.

Kelso, Scott. “Principles of Dynamic Pattern Formation and Change for a Science of Human Behavior.” In Developmental Science and the Holistic Approach, eds. Lars Bergman, et al., 63–84. Mahwah, N.J.: Lawrence Erlbaum Associates, 2000.

Lewis, Marc D. “The Promise of Dynamic Systems Approaches for an Integrated Account of Human Development.” Child Development. vol. 71, no. 1 (January 2000): 36–43.

Lewis, Marc D., and Isabela Granic, eds. Emotion, Development, and Self-Organization: Dynamic Systems Approaches to Emotional Development. Cambridge: Cambridge University Press, 2000.

Thelen, Esther, and Linda B. Smith. A Dynamic Systems Approach to the Development of Cognition and Action. Cambridge, Mass.: MIT Press, 1994.

Organic Societies

Axelrod, Robert. The Complexity of Cooperation: Agent-Based Models of Competition and Collaboration. Princeton, N.J.: Princeton University Press, 1997.

Boehm, Christopher. Hierarchy in the Forest: The Evolution of Egalitarian Behavior. Cambridge, Mass.: Harvard University Press, 1999.

Bonabeau, Eric, et al. “Scaling in Animal Group-Size Distributions.” Proceedings of the National Academy of Sciences of the United States of America. vol. 96, no. 8 (13 April 1999): 4472–77.

Buck, Ross, and Benson Ginsberg. “Communicative Genes and the Evolution of Empathy.” In Empathic Accuracy, ed. William Ickes, 17–43. New York: Guilford Press, 1997.

Caporael, Linda, and Reuben Baron. “Groups as the Mind’s Natural Environment.” In Evolutionary Social Psychology, eds. Jeffry A. Simpson and Douglas T. Kenrick, 317–43. Mahwah, N.J.: Lawrence Erlbaum Associates, 1997.

Casti, John L., and Anders Karlqvist. Cooperation and Conflict in General Evolutionary Processes. New York: Wiley, 1995.

Chase, Ivan D., et al. “Individual Differences Versus Social Dynamics in the Formation of Animal Dominance Hierarchies.” Proceedings of the National Academy of Sciences of the United States of America. vol. 99, no. 8 (16 April 2002): 5744–49.

Corning, Peter A. “Holistic Darwinism: ‘Synergistic Selection’ and the Evolutionary Process.” Journal of Social and Evolutionary Systems. vol. 20, no. 4 (1997): 363–400.

Couzin, Iain, et al. “Collective Memory and Spatial Sorting in Animal Groups.” Journal of Theoretical Biology. vol. 218, no. 1 (7 September 2002): 1–11.

de Waal, Frans B., and Peter L. Tyack. Animal Social Complexity: Intelligence, Culture, and Individualized Societies. Cambridge, Mass.: Harvard University Press, 2003.

Dugatkin, Lee. Cooperation Among Animals: An Evolutionary Perspective. Oxford: Oxford University Press, 1997.

Fehr, Ernst, et al. “Strong Reciprocity, Human Cooperation, and the Enforcement of Social Norms.” Human Nature. vol. 13, no. 1 (2002): 1–25.

Johnson, Craig R., and Marten C. Boerlijst. “Selection at the Level of the Community: The Importance of Spatial Structure.” Trends in Ecology and Evolution. vol. 17, no. 2 (1 February 2002): 83–90.

Michod, Richard E. Darwinian Dynamics: Evolutionary Transitions in Fitness and Individuality. Princeton, N.J.: Princeton University Press, 1998.

Ridley, Matt. The Origins of Virtue: Human Instincts and the Evolution of Cooperation. New York: Viking, 1997.

Sober, Elliott, and David Sloan Wilson. Unto Others: The Evolution and Psychology of Unselfish Behavior. Cambridge, Mass.: Harvard University Press, 1998.

Wilson, David Sloan. “Introduction: Multilevel Selection Theory Comes of Age.” American Naturalist. vol. 150, no. S1, Supplemental Multilevel Selection (July 1997): S1–S4.
_______. “Animal Movement as a Group-Level Adaptation.” In On the Move: How and Why Animals Travel in Groups, eds. Sue Boinski, and Paul A. Garber, 238–58. Chicago, Ill.: University of Chicago Press, 2000.

Wilson, Robert A. “Group-Level Cognition.” Philosophy of Science. vol. 68, no. 3 Supplement (2001): S262–S273.

Wright, Robert. Nonzero: The Logic of Human Destiny. New York: Pantheon, 1999.

Dynamic Ecosystems

Dynamic Ecosystems are intricate natural domains do not seek an equilibrium or balance as once thought but are in constant flux over many similar scales from microbes to bioregions.

Allen, T. P. H., and Thomas N. Hoekstra. Toward a Unified Ecology. New York: Columbia University Press, 1992.

Andrea, Rinaldo, et al. “Cross-Scale Ecological Dynamics and Microbial Size Spectra in Marine Ecosystems.” Proceedings of the Royal Society of London B. vol. 269, no. 1504 (2002) 2051–59.

Atkinson, R., Christopher I. Rhodes, David W. Macdonald, Roy M. Anderson, eds. “Scale-Free Dynamics in the Movement Patterns of Jackals.” OIKOS. vol. 98, no. 1 (2002): 134–40.

Bascompte, Jordi, and Ricard V. Sole. Modeling Spatiotemporal Dynamics in Ecology. New York: Springer-Verlag, 1997.

Brown, James H. Macroecology. Chicago, Ill.: University of Chicago Press, 1995.
_______.“Macroecology: Progress and Prospect.” OIKOS. vol. 87, no. 1 (1999): 6–9.

Enquist, Brian J., et al. “General Patterns of Taxonomic and Biomass Partitioning in Extant and Fossil Plant Communities.” Nature. vol. 419, no. 6907 (10 October 2002): 610–12.

Harte, John. “Toward a Synthesis of the Newtonian and Darwinian Worldviews.” Physics Today. vol. 55, no. 10 (October 2002): 29–34.

Harte, John, et al. “Self-Similarity in the Distribution and Abundance of Species.” Science. vol. 284, no. 5412 (19 April 1999): 334–36.

Higgins, Paul, et al. “Dynamics of Climate and Ecosystem Coupling.” Philosophical Transactions of the Royal Society of London B. vol. 357, no. 1421 (29 May 2002): 647–55.

Holling, Crawford S. “Understanding the Complexity of Economic, Ecological, and Social Systems.” Ecosystems. vol. 4, no. 5 (August 2001): 390–405.

Jorgensen, Sven F., ed. Thermodynamics and Ecological Modelling. Boca Raton, Fla.: Lewis Publishers, 2001.

Kaitala, Veijo, et al. “Self-organized Dynamics in Spatially Structured Populations.” Proceedings of the Royal Society London B. vol. 268, no. 1477 (2001): 1655–60.

Kawanabe, Hiroya, et al., eds. Mutualism and Community Organization: Behavioral, Theoretical, and Food-Web Approaches. New York: Oxford University Press, 1993.

Kay, James J., et al. “An Ecosystem Approach for Sustainability: Addressing the Challenges of Complexity.” Futures. vol. 31, no. 7 (September 1999): 721–42.

Keitt, Timothy, et al. “Scaling in the Growth of Geographically Subdivided Populations.” Philosophical Transactions of the Royal Society of London B. vol. 357, no. 1421 (29 May 2002): 627–33.

Lassig, Michael, et al. “Shape of Ecological Networks.” Physical Review Letters. vol. 86, no. 19 (7 May 2001): 4418–21.

Lek, Sovan, and J.-F. Guegan, eds. Artificial Neuronal Networks: Application to Ecology and Evolution. Berlin: Springer, 2000.

Levin, Simon A. “Ecosystems and the Biosphere as a Complex Adaptive System.” Ecosystems. vol. 1, no. 5 (September/October 1998): 431–43.
_______. Fragile Dominion: Complexity and the Commons. Reading, Mass.: Perseus Books, 1999.
_______. “Complex Adaptive Systems.” Bulletin of the American Mathematical Society. vol. 40, no. 1 (2003): 3–19.

Margalef, Roman. “Information Theory and Complex Ecology.” In Complex Ecology: The Part-Whole Relation in Ecosystems, eds. Bernard C. Patten and Sven E. Jorgensen, 40–50. Englewood Cliffs, N.J.: Prentice Hall, 1995.

Marquet, Pablo A. “Of Predators, Prey, and Power Laws.” Science. vol. 295, no. 5563 (22 March 2002): 2229–30.

Montoya, Jose M., and Ricard V. Sole. “Small World Patterns in Food Webs.” Journal of Theoretical Biology. vol. 214, no. 3 (7 February 2002): 405–12.

Mouillot, David, et al. “The Fractal Model.” OIKOS. vol. 90, no. 2 (September 2000): 333.

Naveh, Zev. “Ten Major Premises for a Holistic Conception of Multifunctional Landscapes.” Landscape and Urban Planning. vol. 57, nos. 3–4 (15 December 2001): 269–84.

Nielsen, Soren Nors. “Thermodynamics of an Ecosystem Interpreted as a Hierarchy of Embedded Systems.” Ecological Modelling. vol. 135, nos. 2–3 (5 December 2000): 279–89.

Pahl-Wostl, Claudia. The Dynamic Nature of Ecosystems: Chaos and Order Entwined. Chichester: Wiley, 1995.

Pimm, Stuart. The Balance of Nature?: Ecological Issues in the Conservation of Species and Communities. Chicago, Ill.: University of Chicago Press, 1991.

Recknagel, F. “Preface.” Ecological Modelling. vol. 146, nos. 1–3 (2001): 1–2.

Ricotta, Carlo. “From Theoretical Ecology to Statistical Physics and Back: Self-Similar Landscape Metrics as a Synthesis of Ecological Diversity and Geometrical Complexity.” Ecological Modelling. vol. 125, nos. 2–3 (2000): 245–53.

Rinaldo, Andrea, et al. “Cross-Scale Ecological Dynamics and Microbial Size Spectra in Marine Ecosystems.” Proceedings of the Royal Society of London B. vol. 269, no. 1504 (2002): 2051–59.

Schneider, David. “The Rise of the Concept of Scale in Ecology.” BioScience. vol. 51, no. 7 (July 2001): 545–53.

Wu, Jianguo, and Danielle Marceau. “Modeling Complex Ecological Systems: An Introduction.” Ecological Modelling. vol. 153, nos. 1–2 (July 15, 2002): 1–6.

A Living Planet
The evolution of the biosphere appears to be a self-regulated process so as to sustain favorable geochemical and atmospheric conditions for life.


Benner, Steven A., et al. “Planetary Biology.” Science—Paleontological, Geological, and Molecular Histories of Life. vol. 296, no. 5569 (3 May 2002): 864–68.

Bunyard, Peter, ed. Gaia in Action: Science of the Living Earth. Edinburgh: Floris Books, 1996.

Downing, Keith “Exploring Gaia Theory.” In Artificial Life VII: Proceedings of the Seventh International Conference on Artificial Life, eds. Mark A. Bedau, John S. McCaskill, Norman H. Packard, and Steen Rasmussen, 90–102. Cambridge, Mass.: MIT Press, 2000.

Ernst, Walter G., ed. Earth Systems: Processes and Issues. New York: Cambridge University Press, 2000.

Lenton, Timothy, and Marcel van Oijen. “Gaia as a Complex Adaptive System.” Philosophical Transactions of the Royal Society of London B. vol. 357, no. 1421 (29 May 2002): 683–95.

Lovelock, James. Gaia: A New Look at Life on Earth. New York: Oxford University Press, 1979.
_______. Healing Gaia: Practical Medicine for the Planet. New York: New York: Harmony Books, 1991.

Margulis, Lynn. Symbiotic Planet: A New Look at Evolution. North Ponfret, V. M.: Trafalgar Square Books, 1998.

Margulis, Lynn, Clifford Matthews, Aaron Haselton, eds. Environmental Evolution: Effects of the Origin and Evolution of Life on Planet Earth. 2d ed. Cambridge, Mass.: MIT Press, 2000.

Schneider, Stephen H., and Penelope J. Boston, eds. Scientists on Gaia. Cambridge, Mass.: MIT Press, 1991.

Schwartzman, David. Life, Temperature, and the Earth: The Self-Organizing Biosphere. New York: Columbia University Press, 1999.

Skinner, Brian J., et al. The Blue Planet: An Introduction to Earth System Science. 2d ed. New York: Wiley, 1999.

Smil, Vaclav. The Earth’s Biosphere: Evolution, Dynamics, and Change. Cambridge. Mass.: MIT Press, 2002.

Staley, Mark. “Darwinian Selection Leads to Gaia.” Journal of Theoretical Biology. vol. 218, no. 1 (7 September 2002): 35–46.

Volk, Tyler. Gaia’s Body: Toward a Physiology of Earth. New York: Copernicus Books, 1998.

Williams, George R. The Molecular Biology of Gaia. New York: Columbia University Press, 1996.