TABLE OF CONTENTS
Introduction: The Checkered Career of Hierarchical Thinking in Evolutionary Biology - Niles Eldredge
DOI: 10.7208/chicago/9780226426198.003.0001
[species concepts;individuality;Giambattista Brocchi;Jean Baptiste Lamarck;Charles Darwin;punctuated equilibria;macroevolution;hierarchy theory;speciation;natural selection]
This article reconstructs the history and significance of hierarchical thinking in evolutionary theory, suggesting further development of hierarchical approaches in evolutionary biology. Darwin’s intellectual background was imbued with ideas on the nature of species and on the causal mechanisms of species origin and extinction. Important in informing Darwin's hierarchical thinking was Giambattista Brocchi's analogy between species and organisms with respect to individuality, birth, and death. This imprint shined through Darwin’s observations on differential extinction rates, geographic replacements, and other biogeographical patterns. Following the discovery of natural selection, Darwin came to consider species as ephemeral entities whose apparent individuality was an artifact of the imperfections of the fossil record. The subsequent gradualist nonhierarchical view of evolution was challenged in the 1930s by Dobzhansky and then Mayr, who resurrected hierarchical thinking by pointing out the reality of species as distinct biological entities. The 1972 punctuated equilibria hypothesis by Eldredge and Gould suggested the connection between the process of allopatric speciation and the pattern of apparent species stability and abrupt origin as documented by the fossil record. Today hierarchy theory accommodates strong empirical evidence for stasis and speciation and against exclusive gradualism, improving our understanding of structure and dynamics of the biological world. (pages 1 - 16)
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Part 1. Hierarchy Theory of Evolution
Linking Section: General Principles of Biological Hierarchical Systems - Ilya Tëmkin, Emanuele Serrelli
DOI: 10.7208/chicago/9780226426198.003.0002
[biological hierarchies;network theory in biology;complex behavior;stability;replicators;hierarchy theory of evolution;evolution and ecology;change;interactors]
This contribution sets the stage for the following selection of articles addressing general aspects of the hierarchy theory of evolution. It does so by reviewing basic principles of hierarchical systems in general and biological nested hierarchies in particular. More specifically, the article provides formal definitions of a hierarchy, levels of organization, and considers the nature of emergence that arises as a consequence of a hierarchical architecture. The overall dynamics of the hierarchical systems is best described by the synergy between intra-level interactions (best approached using the network theory) and the inter-level relationships (interpreted as emergent constraints). These basic properties of hierarchical systems are then used to represent the overarching model of the structure of the organic world, consisting of two interacting systems: the economic (ecological) hierarchy of interactors and the genealogical hierarchy of replicators. This model is at the heart of the hierarchy theory of evolution, providing a novel ontological framework for inferring causality of a great diversity of evolutionary phenomena. (pages 19 - 25)
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Chapter 1: Pattern versus Process and Hierarchies: Revisiting Eternal Metaphors in Macroevolutionary Theory
DOI: 10.7208/chicago/9780226426198.003.0003
[contingency;macroevolution;nomothetic;phylogenetics;Turnover Pulse Hypothesis;punctuated equilibria;hierarchy]
A topic extensively debated is whether sciences that focus on historical entities are somehow fundamentally different from those sciences that are not concerned with the history of the entities they study. This duality has been treated when authors have discussed the difference between contingent and nomothetic approaches, between historical and functional approaches, and between pattern and process based approaches The history of thought on these concepts will be considered here, with special emphasis placed on writings in macroevolutionary theory and phylogenetics. A central focus will be documenting how these “dualities” should not be viewed as truly distinct.Furthermore, it is argued that repeated analysis of contingent histories is the key to discovering the nomothetic principles that exist in the history of life. This is in fact a central tenet of the hierarchical view of evolution. (pages 29 - 46)
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Chapter 2: Lineages and Systems: A Conceptual Discontinuity in Biological Hierarchies
DOI: 10.7208/chicago/9780226426198.003.0004
[Niles Eldredge;ecological hierarchy;genealogical hierarchy systems;lineages]
Systems and lineages are two kinds of individuals whose differences must be recognized and understood in order to comprehend a sort of ontological discontinuity that exists between the two major biological hierarchies appropriately distinguished by Eldredge: the genealogical hierarchy and the ecological hierarchy. By itself, that ontological discontinuity does not need to be problematic, but the relations between these two hierarchies and the epistemic articulations between the discourses that refer to them cannot be properly viewed without considering the distinction between systems and lineages. Overlooking the distinction can complicate the discussion and treatment of multiple biological problems, and it can also promote the proliferation of many epistemological issues motivated by the mere and avoidable confusion between two different grammatical orders: one ruling lineages lineages talk, the other ruling systems talk. This paper clarifies the distinction between lineages and systems and explains its significance for properly stating some issues in Philosophy of Biology. (pages 47 - 62)
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Chapter 3: Biological Organization from a Hierarchical Perspective: Articulation of Concepts and Interlevel Relation
DOI: 10.7208/chicago/9780226426198.003.0005
[biological organization;composition;constraint;level of organization;interlevel relation]
The purpose of this chapter is twofold. The first objective is to offer an articulation of ideas in the form of a model with five kinds of relations (composition, integration, emergence, regulation, organization). The model should help to ground the concept of level of organization onto an explicit analysis of the specific inter-level relations involved. This analysis will especially focus on a detailed account of thecompositionrelation, that will further be useful for the second goal. This second goal, on the other hand, is to defend the idea of biological organization being inherently hierarchical, not limited to a compositional view. In this view, the fully operative upward and downward inter-level relations are essential and supported by the presence of specific material constraints, within the context of a plural and complex understanding of causation and causality. (pages 63 - 85)
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Chapter 4: Hierarchy: The Source of Teleology in Evolution
DOI: 10.7208/chicago/9780226426198.003.0006
[evolution;hierarchy;natural selection;teleology;upper direction]
Teleological systems in biology are structured hierarchically. They consist of a smaller entity whose movements or changes are directed by a larger structure or “field” within which the entity is immersed. For example, a bacterium moving up a food-molecule concentration gradient appears goal-directed, correcting for down-gradient deviations whenever they occur. It can do this because it is directed by an enveloping field, the gradient, which is present wherever the bacterium wanders. The same hierarchical structure underlies all organismal teleology, including physiological homeostasis and development. All of these teleological systems are the product of natural selection, but the connection between selection and teleology runs deeper. The selective process itself is hierarchically structured. Adaptation is change in a species phenotype that is directed by an ecological context, by the ecological field within which the species is immersed. When drift leads to non-adaptive change, the enveloping ecological field corrects the trajectory, redirecting the phenotype back toward greater adaptedness. This view offers a kind of conceptual unity, revealing processes at very different scales - organismal behavior, physiology, and development on the one hand and adaptation on the other – to share a common physical structure. (pages 86 - 102)
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Chapter 5: Three Approaches to the Teleological and Normative Aspects of Ecological Functions
DOI: 10.7208/chicago/9780226426198.003.0007
[functional diversity;ecosystem functions;ecological functions;natural selection;hierarchy;closure of constraints;organization;etiology;causal role;pluralism]
Ecosystem function is the central use of function in ecology. In this work we examine the light that can be shed on ecosystem functions by three philosophical analyses of the concept of function: the causal role theory, the teleological theory, and the organizational theory. While the causal role theory provides a natural explication of many of the uses of ecosystem function, it does not underwrite either the teleological or normative aspects of functional discourse. The etiological approach has the potential to account for the teleology and normativity of ecosystem function but presupposes that ecosystem properties are, in some sense, shaped by natural selection. It is not obvious that this presupposition can be satisfied. The organizational approach has much in common with the causal role approach and also offers an alternative strategy for grounding teleology and normativity. Perhaps the biggest challenge for the organizational approach stems from the necessity to reach a historical accountof how functional systems come into existence in the first place that is in sufficient agreement with a Darwinian understanding of evolution. Given the strengths and weaknesses of the various approaches, we suggest that a pluralistic approach might have some attraction. (pages 103 - 124)
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Part 2. Hierarchical Dynamics: Process Integration across Levels
Linking Section: Information and Energy in Biological Hierarchical Systems
DOI: 10.7208/chicago/9780226426198.003.0008
[biological information;energy;sorting;natural selection;hierarchy theory of evolution;selection;biology]
The dual hierarchical framework of the hierarchy theory of evolution proposes information transfer and matter-energy exchange as two distinct and fundamental organization principles of the biological world. This contribution attempts to provide operational definitions of information and energy. Evolution processes the information-bearing states of biological systems at various levels, from individual development to inter-organism sorting such as natural selection to sorting among more inclusive systems. Evolution also shapes the mechanisms of coding and interpretation of information. Energy has an intimate relationship with the stability of organization of biological systems, and energy transformations affect the fate (origin, transformation, and loss) of information at multiple levels. (pages 127 - 136)
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Chapter 6: Why Genomics Needs Multilevel Evolutionary Theory
DOI: 10.7208/chicago/9780226426198.003.0009
[genome;transposable elements;multilevel selection;selfish DNA;junk DNA]
Less than 2% of the human genome is made up of the ~20,000 protein-coding genes. The remainder consists primarily of non-coding sequences of numerous types, such as introns, highly repetitive satellite DNA, defunct pseudogenes, and especially transposable elements (TEs). The latter make up at least half of the human genome sequence, with some TEs present in enormous numbers of copies; the primate-specific TE known as Alu, for example, is present in more than 1 million copies per genome. Any complete account of genome evolution therefore requires an understanding of transposable element biology and evolution. Unfortunately, there is a tendency to consider TEs largely from the level of the organism, especially whether or not they are “functional”. Here we discuss the need for a multi-level perspective that recognizes TEs at their own level, including their unique biological features, evolutionary histories, and interactions with the host and with each other. (pages 137 - 150)
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Chapter 7: Revisiting the Phenotypic Hierarchy in Hierarchy Theory
DOI: 10.7208/chicago/9780226426198.003.0010
[hierarchy theory;phenotypic evolution;homology;somatic hierarchy;Modern Synthesis;evolutionary transitions;biological information;evolutionary developmental biology]
The hierarchy theory at its onset was primarily committed to vindicate the distinctness of macro-evolutionary phenomena from micro-evolutionary processes, minimizing the explanatory relevance of levels and entities below the organism and above the gene. The current focus on phenotypic evolution, however, suggests a refinement and revision of the role of the so-called “somatic” or “phenotypic hierarchy”, and the evolutionary bearing of its structured variability at different levels. The paper reviews some theoretical reasons and implications of such reassessment. (pages 151 - 173)
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Chapter 8: Multilevel Selection in a Broader Hierarchical Perspective
DOI: 10.7208/chicago/9780226426198.003.0011
[group selection;multilevel selection;major transitions;double hierarchy;exaptation;crosslevel byproducts]
Since Darwin, multilevel selection has been the key concept of the hierarchical approach to evolution. The debate around the significance of group selection as an evolutionary phenomenon (in both an early controversial version and subsequent mathematical definition) has been the main entrance to multilevel selection theories. We present here a historical sketch of the debate prior to the formalization proposed by Samir Okasha. We also consider two extensions of Okasha’s multilevel theory: the diachronic perspective made possible by the study of major evolutionary transitions; the cross-level exaptive by-products. The double hierarchy, first proposed by Niles Eldredge and Stanley Salthe is a different kind of multilevel approach to evolution that avoids some theoretical impasses produced by a strictly selection-centered approach to extend the levels of evolutionary change. We argue that a dual hierarchical approach has a major heuristic power in order to embrace the complexity of evolutionary phenomena, from molecules to ecosystems, and is a candidate for an updated and unifying meta-theory of evolutionary patterns. (pages 174 - 201)
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Chapter 9: Systems Emergence: The Origin of Individuals in Biological and Biocultural Evolution
DOI: 10.7208/chicago/9780226426198.003.0012
[emergence;individuality;homology;biocultural epicycle;robustness]
Starting from Deacon’s three-level hierarchy of emergent systems—simple aggregates, cases of local historicity, and systems with information transfer and heredity—we focus on the third level. We argue that any form of third-order emergence involves the origin of novel individuals, that is, historically contingent systems that form a lineage of descent and may eventually go extinct. We further argue that at all levels, from the beginnings of cellular life to biocultural systems, individuals and their origins share deep structural similarities, including robustness, self-maintenance and feedback. We illustrate these similarities by exemplifying them in two cases: the origin of novel body parts (homologues) and the origin of biocultural epicycles. In emphasizing the structural similarities among different emergent individuals we intend to encourage the development of an abstract theory of the behavior and origins of emergent systems. (pages 202 - 224)
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Part 3. Biological Hierarchies and Macroevolutionary Patterns
Linking Section: Ecology and Evolution: Neither Separate nor Merged
DOI: 10.7208/chicago/9780226426198.003.0013
[ecology;hierarchy theory of evolution;ecosystem;community;evolutionary ecology;interaction;Modern Synthesis;ecological stage;evolution]
Since the 1970s, frequent attempts were made to bridge the gap between ecology and evolution. Ecology was divided into community ecology, that studies the composition and assembly of populations, communities, and metacommunities, and ecosystem science, that studies organisms and their environment as parts of interactive systems characterized by various “functions” (e.g., productivity, decomposition) and efficiency measures (e.g., food chain efficiency). Following the Modern Synthesis, evolutionary biology, on the other hand, was focused on genealogical processes (natural selection, drift, speciation) and came to consider ecological assemblies as aggregations characterized by secondary, derived patterns, or even to imagine them as a rather uninteractive 'stage' for the evolutionary play. Paleobiological macroevolutionary studies, models of niche construction and evolutionary ecology are attempts towards greater integration between ecological and genealogical patterns. The hierarchy theory of evolution is suggested to provide the most appropriate theoretical framework for the multiscale integration between the two disciplines. (pages 227 - 242)
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Chapter 10: Unification of Macroevolutionary Theory: Biologic Hierarchies, Consonance, and the Possibility of Connecting the Dots
DOI: 10.7208/chicago/9780226426198.003.0014
[macroevolution;large ecologic systems;punctuated equilibria;Turnover Pulse Hypothesis;Sloshing Bucket Model;macroevolutionary consonance;metatheory]
Modern macroevolutionary theory can be viewed as an expansion of the Modern Synthesis involving the interpretation of patterns and processes above the organizational level of organisms packaged in local populations, including modes and processes of speciation and the emergence and development of clades. New interpretations of the fossil record (punctuated equilibria, species selection, regional and global mass extinctions and recoveries) are the empirical and conceptual building blocks in this theoretical expansion. But as in most microevolutionary thinking, macroevolutionary theory has rarely placed ecologic processes on equal footing with evolutionary processes: ecology is seen as the stage, backdrop or product of adaptive evolution; all the important action actually involves evolutionary transformations. Several new movements in macroevolutionary theory (Turnover Pulse Hypothesis, Coordinated Stasis, the Sloshing Bucket Model), however, require attention to be focused on patterns of stability and reorganization/replacement of large ecologic systems in order to understand patterns of evolutionary stasis and turnover (invasion/abandonment, extinction, bouts of adaptive speciation) recorded in the fossil record. Connecting macroevolutionary patterns to macroecologic dynamics (the Theory of Macroevolutionary Consonance) could lead on to discovery of further conceptual connections and a more complete explication of large-scale patterns in the history of life. (pages 243 - 259)
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Chapter 11: Coming to Terms with Tempo and Mode: Speciation, Anagenesis, and Assessing Relative Frequencies in Macroevolution
DOI: 10.7208/chicago/9780226426198.003.0015
[anagenesis;cladogenesis;tempo;mode;punctuated equilibrium;speciation]
In 1944 Simpson suggested that in studying evolution, there are “two topics in particular” on which “the paleontologist enjoys special advantages”: estimation of evolutionary rates (“tempo”), and “the way, manner, or pattern of evolution” (“mode”). He described tempos as varying from very slow to very rapid, and the “basic modes of evolution” as “speciation, phyletic evolution, and quantum evolution”. Gould and Eldredge (1977) restricted “mode” to phyletic evolution (anagenesis) and speciation (cladogenesis), and claimed that mode could be inferred “from the empirical distribution of tempos”. Punctuated equilibrium (PE), they said, “is a hypothesis about mode”. Recent literature often takes a looser approach to these terms. Evolutionary “modes” now regularly refer to 3 patterns of anagenesis: directional, random walk, and stasis, and analyses of the relative frequency of these are taken as evidence of the relative frequency of PE, and/or other macroevolutionary patterns. But the evolution of life has proceeded by some combination of anagenesis and cladogenesis. Phyletic change has varied along a continuum, with and without involving lineage splitting. Compilations of “tempo and mode” from the fossil record need to keep this in mind. (pages 260 - 281)
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Chapter 12: Niche Conservatism, Tracking, and Ecological Stasis: A Hierarchical Perspective
DOI: 10.7208/chicago/9780226426198.003.0016
[Devonian;ecological stasis;ecological evolutionary subunits;gradient analysis;hierarchy theory;niche conservatism;sloshing bucket hypothesis]
At the heart of the concept of ecological stasis is the general hypothesis that ecological niches, broadly defined as positions of species along environmental gradients, remain relatively stable over time. To further investigate this concept, we designed a hierarchical sampling strategy for a well-studied interval of previously documented evolutionary-ecological stability, the Middle Devonian of New York State. Fossil assemblages were sampled at the scale of members, and formations; i.e., at timescales of tens of thousands to about a million years. In each case, gradients of fossil assemblages were diagnosed using detrended correspondence analysis and these gradients were used to parameterize the niches of individual taxa. In a seeming paradox, members exhibit minor niche modification, whereas formations appear more conservative. We attribute this to either an incomplete representation of environments within members or fluctuations in parameters that are not reflected in the environmental gradients studied here. Overall, the results indicate a tendency toward niche conservatism over the millions of years duration of the Hamilton Group, despite minor local and regional fluctuations over the shorter timescale of members. This result is consistent with a model of habitat tracking by taxa and may explain the pattern of prolonged stability known as "coordinated stasis". (pages 282 - 306)
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Chapter 13: The Stability of Ecological Communities as an Agent of Evolutionary Selection: Evidence from the Permian-Triassic Mass Extinction
DOI: 10.7208/chicago/9780226426198.003.0017
[Permian-Triassic mass extinction;community stability;transient dynamics;selection]
A series of six terrestrial communities spanning the Middle Permian to the M. Triassic from the Karoo Basin of South Africa display greater stability, both in terms of transient dynamics and resistance to secondary extinction, than do hypothetical communities of equal richness but alternative structures. Moreover, patterns of turnover before, during, and after the Permian-Triassic mass extinction suggest that there was selection for community stability. This selective force may have constrained the ecological evolution of species by increasing probabilities of extinction for species that caused instability in a community, and also promoted differential persistence of metacommunities across the landscape, such that more stable communities would gradually replace less stable ones. Evidence for the selection of more stable communities during times of background extinction and mass extinctions suggests that stability is an important determinant of the ecological properties of species and community structures. (pages 307 - 333)
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Chapter 14: Hierarchy Theory in the Anthropocene: Biocultural Homogenization, Urban Ecosystems, and Other Emerging Dynamics
DOI: 10.7208/chicago/9780226426198.003.0018
[biocultural;homogenization;Anthropocene;Homogeocene;urban ecology;invasive species;novel ecosystems]
While the increasingly large global impacts of humanity on the biosphere are often referred to as the “Great Acceleration,” it is perhaps more informative to call them the “Great Blending,” as this term describes not only the rate of change, but also the kind of changes. Humans are on a trajectory that increasingly intermixes many units and levels of biological organization, ranging from genes to ecosystems and even social groupings (e.g., tribes and ethnic groups). Looking at this emerging transformation from the viewpoint of hierarchy theory provides a useful historical and theoretically rich framework. For example, it is clear that the current changes, driven by urbanization, are causing massive alterations in all biospheric domains: genealogical (hybridized taxa), ecological (novel ecosystems), and socio-cultural (cosmopolitan or “McDonaldized” cultures). This chapter will examine to what extent the blending occurring in those domains will, if continued, drastically restructure the hierarchies of the biosphere, manifested in a more homogenized world with often high levels of local biocultural diversity, but with a greatly reduced level of overall global biocultural diversity. (pages 334 - 350)
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Conclusion: Hierarchy Theory and the Extended Synthesis Debate
DOI: 10.7208/chicago/9780226426198.003.0019
[hierarchy theory;heuristics;hominin phylogeny;evolutionary ecology;Extended Evolutionary Synthesis;niche construction;gene culture coevolution]
In the closing remarks we propose a theoretical watermark that connects all the chapters of this volume. After a short summary about Eldredge’s twin hierarchies as a possible unifying frame for evolutionary biology, with different levels of organization above and below the organismic level, we stress the point the each level should be considered autonomous, and at the same time interdependent with the others. Hierarchy theory is a non-reductionist Darwinian research programme, with a heuristic and a theoretical relevance. In the first sense, Hierarchy Theory is a useful framework in order to understand the rapid advancements in specific evolutionary disciplines, such as paleo-anthropology. In the second sense, Hierarchy Theory aims at enlarging the standard neo-Darwinian theory of evolution through a more ecological and multilevel framework if compared to the so-called Extended Evolutionary Synthesis. The theory of evolution is still evolving, and this is what a healthy research programme should do. (pages 351 - 364)
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List of Contributors
Index