Defining and revising the structure of evolutionary theory : Theories need both essences and histories ; The structure of evolutionary theory: revising the three central features of Darwinian logic ; Apologia pro vita sua : A time to keep ; A personal odyssey. Epitomes for a long development : Levels of potential originality ; An abstract of one long argument -- The history of Darwinian logic and debate : The essence of Darwinism and the basis of modern orthodoxy: an exegesis of the Origin of Species : A revolution in the small ; Darwin as a historical methodologist : One long argument ; The problem of history ; A fourfold continuum of methods for the inference of history. Darwin as a philosophical revolutionary : The causes of nature's harmony : Darwin and William Paley ; Darwin and Adam Smith. The first theme: the organism as the agent of selection ; The second theme: natural selection as a creative force : The requirements for variation : Copious ; Small ; Undirected. Gradualism ; The adaptationist program. The third theme: the uniformitarian need to extrapolate: environment as enabler of change. Judgments of importance -- Seeds of hierarchy : Lamarck and the birth of modern evolutionism in two-factor theories : The myths of Lamarck ; Lamarck as a source ; Lamarck's two-factor theory: sources for the two parts : The first set: environment and adaptation ; The second set: progress and taxonomy ; Distinctness of the two sets. Lamarck's two-factor theory: the hierarchy of progress and deviation ; Antinomies of the two-factor theory. An interlude on Darwin's reaction ; No allmacht without hierarchy: Weissman on germinal selection : The allmacht of selection ; Weismann's argument on Lamarck and the allmacht of selection ; The problem of degeneration of Weismann's impetus for germinal selection ; Some antecedents to hierarchy in German evolutionary thought : Haeckel's descriptive hierarchy in levels of organization ; Roux's theory of intracorporeal struggle. Germinal selection as a helpmate to personal selection ; Germinal selection as a full theory of hierarchy. Hints of hierarchy in supraorganismal selection: Darwin on the principle of divergence : Divergence and the completion of Darwin's system ; The genesis of divergence ; Divergence as a consequence of natural selection ; The failure of Darwin's argument and the need for species selection : The calculus of individual success ; The causes of trends ; Species selection based on propensity for extinction. Postscript: solution to the problem of the "delicate arrangement". Coda -- Internalism and laws of form: pre-Darwinian alternatives to functionalism : Prologue: Darwin's fateful decision ; Two ways to glorify God in nature : William Paley and British functionalism: praising God in the details of design ; Louis Agassiz and continental formalism: praising God in the grandeur of taxonomic order ; An epilog on the dichotomy. Unity of plan as the strongest version of formalism: the pre-Darwinian debate : Mehr Licht on Goethe's leaf ; Geoffroy and Cuvier : Cuvier and Conditions of Existence ; Geoffroy's formalist vision ; The debate of 1830: foreplay and aftermath. Richard Owen and English formalism: the archetype of vertebrates : No formalism please, we're British ; The vertebrate archetype: constraint and nonadaptation ; Owen and Darwin. Darwin's strong but limited interest in structural constraint : Darwin's debt to both poles of the dichotomy ; Darwin on correlation of parts ; The "quite subordinate position" of constraint to selection -- The fruitful facets of Galton's polyhedron: channels and saltations in post-Darwinian formalism : Galton's polyhedron ; Orthogenesis as a theory of channels and one-way streets: the marginalization of Darwinism : Misconceptions and relative frequencies ; Theodor Eimer and the ohnmacht of selection ; Alpheus Hyatt: an orthogenetic hard line from the world of mollusks ; C.O. Whitman: an orthogenetic dove in Darwin's world of pigeons. Saltation as a theory of internal impetus: a second formalist strategy for pushing Darwinism to a causal periphery : William Bateson: the documentation of inherent discontinuity ; Hugo de Vries: a most reluctant non-Darwinian : Dousing the great party of 1909 ; The (not so contradictory) sources of the mutation theory ; The mutation theory: origin and central tenets ; Darwinism and the mutation theory : Confusing rhetoric and the personal factor ; The logic of Darwinism and its different place in de Vries' system. De Vries on macroevolution. Richard Goldschmidt's appropriate role as a formalist embodiment of all that pure Darwinism must oppose --
Pattern and progress on the geological stage : Darwin and the fruits of biotic competition : A geological license for progress ; The predominance of biotic competition and its sequelae. Uniformity on the geological stage : Lyell's victory in fact and rhetoric ; Catastrophism as good science: Cuvier's Essay ; Darwin's geological need and Kelvin's odious spectre : A question of time (too little geology) ; A question of direction (too much geology) -- The modern synthesis as a limited consensus : Why synthesis? ; Synthesis as restriction : The initial goal of rejecting old alternatives ; R. A. Fisher and the Darwinian core ; J. B. S. Haldane and the initial pluralism of the synthesis ; J. S. Huxley: pluralism of the type. Synthesis as hardening : The later goal of exalting selection's power ; Increasing emphasis on selection and adaptation between the first (1937) and last (1951) edition of Dobzhansky's Genetics and the Origin of Species ; The shift in G. G. Simpson's explanation of "quantum evolution" from drift and nonadaptation (1944) to the embodiment of strict adaptation (1953) ; Mayr at the inception (1942) and codification (1963): shifting from the "genetic consistency" to the "adaptationist" paradigm ; Why hardening?. Hardening on the other two legs of the Darwinian tripod : Levels of selection ; Extrapolation into geological time. From overstressed doubt to overextended certainty : A tale of two centennials ; All quiet on the textbook front : Adaptation and natural selection ; Reduction and trivialization of macroevolution -- Segue to part II -- Towards a revised and expanded evolutionary theory : Species as individuals in the hierarchal theory of selection : The evolutionary definition of individuality : An individualistic prolegomenon ; The meaning of individuality and the expansion of the Darwinian research program : Criteria for vernacular individuality ; Criteria for evolutionary individuality. The evolutionary definition of selective agency and the fallacy of selfish genes : A fruitful error of logic ; Hierarchical vs. genic selectionism : The distinction of replicators and interactors as a framework for discussion ; Faithful replication as the central criterion for the gene-centered view of evolution ; Sieves, plurifiers, and the nature of selection: the rejection of replication as a criterion of agency ; Interaction as the proper criterion for identifying units of selection ; The internal incoherence of gene selectionism ; Bookkeeping and causality: the fundamental error of gene selectionism ; Gambits of reform and retreat by gene selectionists. Logical and empirical foundations for the theory of hierarchical selection : Logical validation and empirical challenges : R. A. Fisher and the compelling logic of species selection ; The classical arguments against efficacy of higher-level selection ; Overcoming these classical arguments, in practice for interdemic selection, but in principle for species selection. Emergence and the proper criterion for species selection : Differential proliferation or downward effect ? ; Shall emergent characters or emergent fitnesses define the operation of species selection?. Hierarchy and the sixfold way : A literary prologue for the two major properties of hierarchies ; Redressing the tyranny of the organism: comments on characteristic features and differences among six primary levels : The gene-individual : Motoo Kimura and the "neutral theory of molecular evolution" ; True genic selection. The cell-individual ; The organism-individual ; The deme-individual ; The species-individual : Species as individuals ; Species as interactors ; Species selection as potent. The clade-individual. The grand analogy: a speciational basis for macroevolution : Presentation of the chart for macroevolutionary distinctiveness ; The particulars of macroevolutionary explanation : The structural basis ; Criteria for individuality ; Contrasting modalities of change: the basic categories ; Ontogenetic drive: the analogy of Lamarckism and anagenesis ; Reproductive drive: directional speciation as an important and irreducible macroevolutionary mode separate from species selection ; Species selection, Wright's rule, and the power of interaction with directional speciation ; Species level drifts as more powerful than the analogous phenomena in microevolution ; The scaling of external and internal environments ; Summary comments on the strengths of species selection and its interaction with other macroevolutionary causes of change --
Punctuated equilibrium and the validation of macroevolutionary theory : What every paleontologist knows : An introductory example ; Testimonials to common knowledge ; Darwinian solutions and paradoxes : The paradox of insulation from disproof ; The paradox of stymied practice. The primary claims of punctuated equilibrium : Data and definitions ; Microevolutionary links ; Macroevolutionary implications : Tempo and the significance of stasis ; Mode and the speciational foundation of macroevolution. The scientific debate on punctuated equilibrium: critiques and responses : Critiques based on the definability of paleontological species : Empirical affirmation ; Reasons for a potential systematic underestimation of biospecies by paleospecies ; Reasons for a potential systematic overestimation of biospecies by paleospecies ; Reasons why an observed punctuational pattern might not represent speciation. Critiques based on denying events of speciation as the primary locus of change ; Critiques based on supposed failures of empirical results to affirm predictions of punctuated equilibrium : Claims for empirical refutation by cases : Phenotypes ; Genotypes. Empirical tests of conformity with models. Sources of data for testing punctuated equilibrium : Preamble ; The equilibrium in punctuated equilibrium: quantitatively documented patterns of stasis in unbranched segments of lineages ; The punctuations of punctuated equilibrium: tempo and mode in the origin of paleospecies : The inference of cladogenesis by the criterion of ancestral survival ; The "dissection" of punctuations to infer both existence and modality : Time ; Geography ; Morphometric mode. Proper and adequate test of relative frequencies: the strong empirical validation of punctuated equilibrium : The indispensability of data on relative frequencies ; Relative frequencies for higher taxa in entire biotas ; Relative frequencies for entire clades ; Causal clues from differential patterns of relative frequencies. The broader implications of punctuated equilibrium for evolutionary theory and general notions of change : What changes may punctuated equilibrium instigate in our views about evolutionary mechanisms and the history of life? : The explanation and broader meaning of stasis : Frequency ; Generality ; Causality. Punctuation, the origin of new macroevolutionary individuals, and resulting implications for evolutionary theory : Trends ; The speciational reformulation of macroevolution : Life itself ; General rules ; Particular cases : Horses as the exemplar of "life's little joke" ; Rethinking human evolution. Ecological and higher-level extensions. Punctuation all the way up and down? The generalization and broader utility of punctuated equilibrium (in more than a metaphorical sense) at other levels of evolution, and for other disciplines in and outside the natural sciences : General models for punctuated equilibrium ; Punctuational change at other levels and scales of evolution : A preliminary note on homology and analogy in the conceptual realm ; Punctuation below the species level ; Punctuation above the species level : Stasis analogs: trending and non-trending in the geological history of clades ; Punctuational analogs in lineages: the pace of morphological innovation ; Punctuational analogs in faunas and ecosystems. Punctuational models in other disciplines: towards a general theory of change : Principles for a choice of examples ; Examples from the history of human artifacts and cultures ; Examples from human institutions and theories about the natural world ; Two concluding examples, a general statement, and a coda. Appendix: a largely sociological (and fully partisan) history of the impact and critique of punctuated equilibrium : The entrance of punctuated equilibrium into common language and general culture ; An episodic history of punctuated equilibrium : Early stages and future contexts ; Creationist misappropriation of punctuated equilibrium ; Punctuated equilibrium in journalism and textbooks. The personal aspect of professional reaction : The case ad hominem against punctuated equilibrium ; An interlude on sources of error ; The wages of jealousy : The descent to nastiness ; The most unkindest cut of all ; The wisdom of Agassiz's and von Baer's threefold history of scientific ideas ; A coda on the kindness and generosity of most colleagues
The integration of constraint and adaptation (structure and function) in ontogeny and phylogeny: historical constraints and the evolution of development : Constraint as a positive concept : Two kinds of positivity : An etymological introduction ; The first (empirical) positive meaning of channeling ; The second (definitional) positive meaning of causes outside accepted mechanisms. Heterochrony and allometry as the locus classicus of the first positive (empirical) meaning; channeled directionality by constraint : The two structural themes of internally set channels and ease of transformation as potentially synergistic with functional causality by natural selection: increasing shell stability in the gryphaea heterochronocline ; Ontogenetically channeled allometric constraint as a primary basis of expressed evolutionary variation: the full geographic and morphological range of cerion uva ; The aptive triangle and the second positive meaning: constraint as a theory-bound term for patterns and directions not built exclusively (or sometimes even at all) by natural selection : The model of the aptive triangle ; Distinguishing and sharpening the two great questions : The structural vertex ; The historical vertex. An epitome for the theory-bound nature of constraint terminology.
Deep homology and pervasive parallelism: historical constraint as the primary gatekeeper and guardian of morphospace : A historical and conceptual analysis of the underappreciated importance of parallelism for evolutionary theory : A context for excitement ; A terminological excursus on the meaning of parallelism : The nine fateful little words of E. Ray Lankester ; The terminological origin and debate about the meaning and utility of parallelism. A symphony in four movements on the role of historical constraint in evolution: towards the harmonious rebalancing of form and function in evolutionary theory : Movement one, statement: deep homology across phyla: Mayr's functional certainty and Geoffroy's structural vindication : Deep homology, archetypal theories, and historical constraint ; Mehr licht (more light) on Goethe's angiosperm archetype ; Hoxology and Geoffroy's first archetypal theory of segmental homology : An epitome and capsule history of hoxology ; Vertebrate homologs in structure and action ; Segmental homologies of arthropods and vertebrates: Geoffroy's vindication : Rediscovering the vertebrate rhombomeres ; More extensive homologies throughout the developing somites ; Some caveats and tentative conclusions. Geoffrey's second archetypal theory of dorso-ventral inversion in the common bilaterian groundplan. Movement two, elaboration: parallelism of underlying generators: deep homology builds positive channels of constraint : Parallelism all the way down: shining a light and feeding the walk : Parallelism in the large: pax-6 and the homology of developmental pathways in homoplastic eyes of several phyla : Data and discovery ; Theoretical issues ; A question of priority. Parallelism in the small: the origin of crustacean feeding organs. Pharaonic bricks and Corinthian columns. Movement three, scherzo: does evolutionary change often proceed saltation down channels of historical constraint? ; Movement four, recapitulation and summary: early establishment of rules and the inhomogeneous population of morphospace: Dobzhansky's landscape as primarily structural and historical, not functional and immediate : Bilaterian history as top-down by tinkering of an initial set of rules, not bottom-up by adding increments of complexity ; Setting of historical constraints in the Cambrian explosion ; Channeling the subsequent directions of bilaterian history from the inside ; An epilog of Dobzhansky's landscape and the dominant role of historical constraint in the clumped population of morphospace
The integration of constraint and adaptation (structure and function) in ontogeny and phylogeny: structural constraints, spandrels, and the centrality of exaptation in macroevolution : The timeless physics of evolved function : Structuralism's odd man outside ; D'Arcy Thompson's science of form : The structure of an argument ; The tactic and application of an argument ; The admitted limitation and ultimate failure of an argument ; Odd man in (D'Arcy Thompson's structuralist critique of Darwinism) and odd man out (his disparagement of historicism ; An epilog to an argument. Order for free and realms of relevance for Thompsonian structuralism. Exapting the rich and inevitable spandrels of history: Nietzsche's most important proposition of historical method ; Exaptation and the principle of quirky functional shift: the restricted Darwinian version as the ground of contingency : How Darwin resolved Mivart's challenge of incipient stages ; The two great historical and structural implications of quirky functional shift ; How exaptation completes and rationalizes the terminology of evolutionary change by functional shifting ; Key criteria and examples of exaptation. The complete version, replete with spandrels: a revisit to San Marco ; Three major reasons for the centrality of spandrels, and therefore of nonadaptation, in evolutionary theory. The exaptive pool: the proper conceptual formula and ground of evolvability : Resolving the paradox of evolvability and defining the exaptive pool ; The taxonomy of the exaptive pool : Franklins and Miltons, or inherent potentials vs. available things ; Choosing a fundamentum divisionis for a taxonomy: an apparently arcane and linguistic matter that actually embodies a central scientific decision ; Cross-level effects as Miltonic spandrels, not Franklinian potentials: the nub of integration and radical importance. A closing comment to resolve the macroevolutionary paradox that constraint ensures flexibility whereas selection crafts restriction
Tiers of time and trials of extrapolationism, with an epilog on the interaction of general theory and contingent history : Failure of extrapolationism in the non-isotrophy of time and geology : The specter of catatrosphic mass extinction: Darwin to Chicxulub ; The paradox of the first tier: towards a general theory of tiers of time. An epilog on theory and history in creating the grandeur of this view of life.
