Contents
Introduction
Chapter 1 Standard Adaptation
1.1 The three conditions necessary for observing natural selection. 1. Variation
1.2 The three conditions necessary for observing natural selection. 2. Heritability
1.3 The three conditions necessary for observing natural selection. 3. Fitness
1.3.1 Survivorship
1.3.2 Mating success
1.3.3 Fecundity
1.3.4 Interaction among the components of fitness
1.4 The <"force> " of natural selection is metaphorical
1.5 Sorting versus selection
1.6 Watch out for <"selection in constraint's clothing> "
1.7 Beware the ad hoc hypothesis
1.8 What constitutes a selective pressure? Generation time and recurrence
1.9 Measuring fitness empirically
1.10 The importance of energetic efficiency in postulating fitness differences
1.11 There can be multiple favored configurations and multiple <"functions> "
1.11.1 <"The> " favored configuration or configurations
1.11.2 <"The> " function of a biological feature
1.12 <"Continuous> " variation: the main reaction point for adaptationist evo-devo
1.13 Standard adaptation case studies 1.13.1 Standard selection case studies: mammalian long bone-body mass relations
1.13.2 Standard selection case studies: the human female orgasm
1.13.3 Standard selection case studies: developmental bias
1.13.4 Congratulations on expertly adaptationizing
1.14 Benefits of being an expert adaptationist (and dangers of not being one) 1.14.1 Macroevolution that isn't
1.14.2 Biological metaphors: interspecific <"competition,> " <"stress,> " and environmental <"filtering> "
1.15 Helpfulness is a helpful criterion Chapter 2 Developmental potential and adaptation
2.1 Motivating adaptationist evo-devo: limited variation
2.1.1 Examples of limited variation: Always odd segment number in geophilomorph centipedes
2.1.2 Examples of limited variation: The pentadactyl hand
2.1.3 Examples of limited variation: The mystery of synapomorphy
2.1.4 Examples of limited variation: Tradeoffs
2.1.5 Examples of limited variation: Shared developmental cascades
2.2 Developmental potential (evolvability)
2.3 Adaptationist evo-devo case studies: layers of evidence, not <"full proof> " in a single study
2.3.1 Arabidopsis directed mutagenesis
2.3.2 Radish flower artificial selection
2.3.3 Domesticated dogs
2.3.4 Domesticated goldfish
2.3.5 Domesticated and feral pigeon legs
2.3.6 The architecture of organismal circulatory systems 2.3.7 Fly micro-surgery
2.3.8 Mammalian long bone scaling
2.3.9 You can't get there from here: Erika Edwards's activation energy metaphor
2.3.10 Drosophila flight performance maneuvering around panadaptationism
2.3.11 Butterfly wing proportionalities
2.3.12 Eppendorf tube flowers, 3D printed insects, and virtual morphospaces
2.3.13 Seven cervical vertebrae
2.3.14 Drosophila sex combs
2.3.15 Carotenoid-based coloration in birds: selection acting in a finite space of possibilities
2.4 Toward complementarity Chapter 3 Evolution and developmental systems
3.1 Everyone knows that genes alone aren't sufficient for inheritance
3.2 Everyone knows that there is no straightforward connection between genotype and phenotype
3.3 The contradiction that sticks in the craw of the genes-aren't everythingers
3.4 If genes are causal agents, it should be possible to recognize them
3.4.1 Mitochondrial ATPase subunits 6 and 8 in humans and mice
3.4.2 Human and mouse INK4A/ARF
3.4.3 IP259/DUb80 in Drosophila 3.4.4 Gene expression in trypanosomes
3.4.5 Slowpoke in chickens, Dscam in fruit flies 3.4.6 The point of these examples
3.5 Moving toward common ground: unresolved phylogenies and missing heritability
3.5.1 Missing phylogenetic resolution
3.5.2 Missing heritability
3.6 Developmental resources and causal parity
3.6.1 Opn, photons, and eye development
3.6.2 Vitamin C
3.6.3 Carnivorous vs. <"proto-carnivorous> " plants
3.6.4 Duckling auditory development
3.6.5 Parity of necessariness
3.7 Distributed causation and three analogies of the genome
3.7.1 The automobile engine analogy
3.7.2 The analogy of the army general
3.7.3 The analogy of digital music files
3.8 DNA contains information: yes and no
3.9 No plan in development
3.10 Reliability of recruitment is what makes a resource
3.11 Natural selection as the biasing of development
3.12 Heritability as the reconstruction of the parental phenotype in development
3.13 Inheritance involving more than genes
3.14 Niche construction
3.15 The unit of inheritance as the developmental system and <"evolution> " as change in the developmental system 3.16 Order without bosses: Deborah Gordon's work on ants
3.17 The physical properties of biological materials in development: more common ground
3.18 A systems exercise
3.19 Systems biology
3.19.1 Systems biology insights: network architecture
3.19.2 Systems biology insights: modularity
3.19.3 Systems biology insights: robustness
3.19.4 Systems biology insights: causal parity, again
3.19.5 Systems: an attractor for all of biology
3.20 Genetic <"eppur si muove> "
3.20.1 Genetic causation residing in unseen antecedent steps
3.20.2 Genetic backfill
3.20.3 Environmental cues versus developmental resources
3.21 What a developmental systems perspective means for adaptationist evo-devo
3.21.1 Relaxing and expanding the notion of inheritance and the unit of inheritance
3.21.2 Where the limits of developmental systems lie
3.21.3 Expanding the causes of developmental potential and <"mutation> "
3.21.4 The term <"phenotype> "
3.22 A developmental systems view is not required for adaptationist evo-devo, and more common ground Chapter 4 Understanding phenotypic plasticity and its role in evolution
4.1 What phenotypic plasticity is
4.2 Phenotypic plasticity is exclusively adaptive 4.3 What is really meant by the plastic-genetic distinction
4.4 No species is maximally plastic
4.5 Clarifying <"maladaptive plasticity> " 4.6 Change in developmental system, change in outcome
4.7 <"Mere plasticity> ": when plasticity is important and when it isn't in a functional explanation
4.8 <"Phenotype> " and <"environment> " sensu lato
4.9 Phenotypic accommodation: the other side of the plasticity coin
4.9.1 Phenotypic accommodation in trees and termite mounds
4.9.2 Phenotypic accommodation and human stunting
4.10 Phenotypic plasticity and accommodation and novel phenotypes
4.11 Plasticity-first, genes-as followers evolution
4.11.1 Unusual developmental outcomes can also be assimilated
4.12 What does plasticity-first evolution mean for well-supported explanations of organismal form? Chapter 5 Building adaptationist evo-devo explanations of organismal form
5.1 The sources of empirical evidence: comparative, populational, optimality, and developmental potential
5.1.1 Source of empirical evidence: comparative method
5.1.2 Source of empirical evidence: population biology
5.1.3 Source of empirical evidence: optimality models
5.1.4 Source of empirical evidence: developmental potential
5.1.4.1 Manipulation
5.1.4.2 Embryology 5.1.4.3 The comparative method
5.2 Generative assumptions and complementarity between sources of empirical evidence
5.2.1 Populational weakness, comparative strength
5.2.2 Comparative weakness, populational strength
5.2.3 Essential complementarity of methods
5.2.4 A (spurious) case can be made for the supremacy of any method
5.3 Assumptions and just-so stories 5.4 Moving from assumptions to evidence
5.5 Untestable limits and historical assumptions
5.6 Assumptions are part of even the best-supported evolutionary explanation
5.7 Key clauses and loopholes in the fine print of evolutionary explanation
5.7.1 No smoking guns
5.7.2 The structure of a robust explanation--descriptive not proscriptive
5.7.3 Putting the <"deductive> " in the hypothetico-deductive method
5.7.4 Ceteris paribus
5.7.5 Teleology, licensed and not
5.7.6 <"Progress> " in phylogenies 5.7.7 Underdetermination
5.7.8 False dichotomies
5.7.8.1 Dichotomies as tools of convenience. 5.7.9 Managing metaphors
5.7.9.1 Metaphor diagnostics
5.7.9.2 The <"adaptive landscape> " metaphor
5.7.9.3 The <"genetic blueprint> " metaphor
5.7.10 Pattern versus process and the descriptive substitution fallacy: <"phylogenetic inertia> " and <"niche conservatism> "
5.8 Real macroevolution
5.9. <"Explained by selection> " or <"explained by developmental constraint> "
5.9.1 <"Explained by selection> " 5.9.2 <"Explained by constraint> " 5.9.3 Extremes of a continuum: convergence versus parallelism
5.9.4 <"Contingency> " versus selection
5.9.5 The adaptation-constraint/contingency dichotomies as a question of scale
5.10 Understanding the Spandrels paper
5.10.1 The central analogy of Spandrels was a perfect illustration of selection 5.10.2 True spandrels illustrate issues of trait delimitation, not <"constraint> "
5.10.3 Spandrels can be exapted, but not all exaptations are spandrels
5.11 Conclusion: explanation and complementarity Chapter 6 Conclusion: Working together to build better explanations of organismal form
6.1 Adaptationist evo-devo precepts
6.1.1 Standard adaptationist accounts are non-trivial
6.1.2 Exploring developmental potential is a key aspect of explanations of organismal form
6.1.3 Developmental systems: small to large changes in research programs
6.1.4 Phenotypic plasticity as an adaptive phenomenon
6.1.5 Building explanations of organismal form: working together
6.1.5.1 Common ground: Complementarity of methods
6.1.5.2 Common ground: Disputes over relative importance, not wholesale disqualification
6.1.5.3 Common ground: Systems biology
6.1.5.4 Common ground: Order for free
6.1.5.5 Common ground: What is possible and what it not in development
6.1.5.6 Common ground: Universal regard for empirical data
6.1.5.7 Common ground: The grain of research focus
6.1.6 Just-so stories can be developmental as well as adaptationist, and they're not so bad.
6.1.7 From buzzwords to bedrock
6.2 <"Adaptation vs. constraint> " and alternative vocabulary
6.3 The most useful false dichotomy Glossary
