Centre for Philosophy of Science Applied Evolutionary Epistemology Lab

Ilya Tëmkin


Course Description

This course introduces the application of hierarchy theory to evolutionary biology. Hierarchy theory is an approach to understand the way complex systems work by identifying levels of organization and their relationships in the context of scaling. As metatheory, it suggests that hierarchical systems have some common properties that are independent of their specific content and can be applied across physical, biological, or social sciences. Even though hierarchies have been an integral part of life sciences for centuries, the implications of hierarchical organization of nature for elucidating causes and mechanisms of evolution have not emerged until recently. Contemporary biological evolutionary theory is ontologically committed to the existence on nested hierarchies in nature and attempts to explain natural phenomena as a product of complex dynamics of real hierarchical systems. We will start with an overview of major concepts of hierarchy theory and a brief history of approaches to complexity that led to its emergence. Then we will explore the application of hierarchy theory to the biological world and, more specifically, to re-conceptualizing evolution as a product of integrating processes occurring at different levels of spatial and temporal biological hierarchies. We will focus on processes leading to the origin and sorting of variation in nature and how such processes produce evolutionary patterns and trends that evolutionary biologists attempt to explain. The course will conclude with an overviews of challenges that hierarchy theory of evolution faces and the directions of its future development.

Day-by-Day Program

Lecture 1: General Principles of Hierarchical Systems
Properties of Hierarchies; Individuality; Hierarchical Levels; Causation, Emergence

  1. Simon, H. A. 1962. The Architecture of Complexity. Proceedings of the American Philosophical Society 106: 467-482.
  2. Korn, R. W. 2005. The Emergence Principle in Biological Hierarchies. Biology and Philosophy 20: 137-151.


Lecture 2: Hierarchies in Biology
Defining Life; Levels of Biological Organization; Economic and Genealogical Hierarchies

  1. Eldredge, N. & Salthe, S. N. 1984. Hierarchy and Evolution. Oxford Surveys in Evolutionary Biology 1: 184-208.
  2. Grene, M. 1987. Hierarchies in Biology. American Scientist 75: 504-510.
  3. Miller, W., III (2001) What's in a Name? Ecologic Entities and the Marine Paleoecologic record. In: Evolutionary Paleoecology: the Ecological Context of Macroevolutionary Change, (Allmon, W. D. & Bottjer, D. J., eds.). pp. 15-33. Columbia University Press, New York.
  4. Pattee, H. H. 1970. The Problem of Biological Hierarchy. In Towards a Theoretical Biology, (Waddington, C. H., ed.). Aldine. Chicago.


Lecture 3: Hierarchies and Evolution
Locus and Limits of Evolution; Evolutionary Patterns and Trends

  1. Eldredge, N. & Gould, S. J. (1972) Punctuated equilibria: an alternative to phyletic gradualism. In: Models in paleobiology, (Schopf, T. J. M., ed.). pp. 82-115. Freeman, Cooper, San Francisco.
  2. Gregory, T. R. 2008. Evolutionary trends. Evolution, Education and Outreach 1: 259–273.
  3. Hull, D. 1980. Individuality and selection. Annual Review of Ecology and Systematics 11: 311-322.
  4. McShea, D. W. 2001. The minor transitions in hierarchical evolution and the question of a directional bias. Journal of Evolutionary Biology 14: 502-518.
  5. Vrba, E. S. & Eldredge, N. 1984. Individuals, hierarchies and processes: toward a more complete evolutionary theory. Paleobiology 10: 146-171.


Lecture 4: Proximal Evolutionary Processes: Origin and Sorting of Variation
Sorting; Selection; Drift; Constraints

  1. Grantham, T. A. 1995. Hierarchical approaches to macroevolution: recent work on species selection and the "Effect hypothesis". Annual Review of Ecology and Systematics 26: 301-321.
  2. Ghiselin, M. T. 1974. A radical solution to the species problem. Systematic Zoology 23: 536-544.
  3. Lewontin, R. C. 1970. The units of selection. Annual Review of Ecology and Systematics 1: 1-18.
  4. Jablonski, D. 2008. Species selection. Annual Review of Ecology and Systematics 39: 501–524.


Lecture 5: Process Integration of Across Hierarchies
Causality and Macroevolutionary Dynamics

  1. Cracraft, J. 1982. A Nonequilibrium Theory for the Rate-control of Speciation and Extinction and the Origin of Macroevolutionary Patterns. Systematic Zoology 31: 348-365.
  2. Cracraft, J. 1992. Explaining Patterns of Biological Diversity: Integrating Causation at Different Spatial and Temporal Scales. In: Systematics, Ecology, and the Biodiversity crisis, (Eldredge, N., ed.). pp. 59-76. Columbia University Press, New York.
  3. Eldredge, N. 2003 The Sloshing Bucket: How the Physical Realm Controls Evolution. In: Evolutionary Dynamics - Exploring the Interplay of Selection, Accident, Neutrality, and Function, (Crutchfield, J. P. & Schuster, P., eds.). pp. 3-32. Oxford University Press, Oxford.
  4. Eldredge, N., Thompson, J. D., Brakefield, P. M., Gavrilets, S., Jablonski, D., Jackson, J. B. C., Lenski, R. E., Lieberman, B. S., McPeek, M. A. & Miller, W. I. 2005. The Dynamics of Evolutionary Stasis. Paleobiology 31: 133-145.
  5. Jablonski, D. 2000. Micro- and Macroevolution: Scale and Hierarchy in Evolutionary Biology and Paleobiology. Paleobiology 26: 15-52.