Contents

• THE NATIONAL ACADEMIES
• Arthur M. Sackler, M.D.
  1913–1987
• Preface to the In the Light of Evolution Series
• Preface to In the Light of Evolution, Volume I: Adaptation and Complex Design
• I. INTRODUCTORY ESSAY
  • 1. Darwin’s Greatest Discovery: Design Without Designer
    FRANCISCO J. AYALA.
    • INTELLIGENT DESIGN: THE ORIGINAL VERSION
    • ARGUMENT AGAINST CHANCE
    • PALEY’S IRREDUCIBLE COMPLEXITY
    • DARWIN’S “MY THEORY”
    • WALLACE: A DISTINCTION WITH A DIFFERENCE
    • DARWIN’S EXPLANATION OF DESIGN
    • MUTATION AND NATURAL SELECTION
    • DESIGN WITHOUT DESIGNER
    • CHANCE AND NECESSITY: NATURAL SELECTION AS A CREATIVE PROCESS
• II. EPISTEMOLOGICAL APPROACHES TO BIOCOMPLEXITY ASSESSMENT
  • 2. Functional Information and the Emergence of Biocomplexity
    ROBERT M. HAZEN, PATRICK L. GRIFFIN, JAMES M. CAROTHERS, and JACK W. SZOSTAK.
    • SYSTEMS AND THEIR FUNCTIONS
    • QUANTIFYING COMPLEXITY
    • FUNCTIONAL INFORMATION AS A MEASURE OF SYSTEM COMPLEXITY
    • THE FUNCTIONAL INFORMATION OF LETTER SEQUENCES
    • THE FUNCTIONAL INFORMATION OF AVIDA POPULATIONS
    • MEASURES OF AVIDA FUNCTION
    • AVIDA RESULTS
    • ISLANDS OF FUNCTION
    • FUNCTIONAL INFORMATION AND RNA POLYMERS
    • FUNCTIONAL INFORMATION IN HIGHER-DIMENSIONAL SYSTEMS
    • CONCLUSIONS
    • METHODS
  • 3. The Theory of Facilitated Variation
    JOHN GERHART and MARC KIRSCHNER.
    • CONSERVED CORE COMPONENTS: RAW MATERIAL OF PHENOTYPIC VARIATION
    • WEAK REGULATORY LINKAGE
    • EXPLORATORY PROCESSES
    • ROBUSTNESS AND ADAPTABILITY
    • FAVORABLE SOURCES AND PATHS OF PHENOTYPIC CHANGE
    • COMPARTMENTATION
    • EXPERIMENTAL EVIDENCE FOR FACILITATED VARIATION
    • FACILITATED VARIATION AND EVOLUTION
  • 4. Between “Design” and “Bricolage”: Genetic Networks, Levels of Selection, and Adaptive Evolution
    ADAM S. WILKINS.
    • EVOLUTIONARY METAPHORS AND THINKING ABOUT GENETIC NETWORKS
    • MOLECULAR CONSTRAINTS ON EVOLUTIONARY TINKERING
    • BUT IS A NETWORK PERSPECTIVE TRULY NECESSARY TO UNDERSTAND ADAPTIVE EVOLUTIONARY CHANGES?
    • USING GENETIC NETWORKS TO ASSESS RELATIVE PROBABILITIES OF MICROEVOLUTIONARY TRAJECTORIES
    • CONCLUSIONS
  • 5. The Frailty of Adaptive Hypotheses for the Origins of Organismal Complexity
    MICHAEL LYNCH.
    • NOTHING IN EVOLUTION MAKES SENSE EXCEPT IN LIGHT OF POPULATION GENETICS
    • INTERNAL VERSUS EXTERNAL EVOLUTIONARY FORCES
    • THE PASSIVE EMERGENCE OF GENOME COMPLEXITY BY NONADAPTIVE PROCESSES
    • ARE THE ORIGINS OF ORGANISMAL COMPLEXITY ALSO ROOTED IN NONADAPTIVE PROCESSES?
    • THE PASSIVE EMERGENCE OF MODULAR GENE INTERACTIONS
    • EVOLVABILITY
    • CLOSING COMMENTS
• III. FROM INDIVIDUAL ONTOGENY TO SYMBIOSIS: A HIERARCHY OF COMPLEXITY
  • 6. Emerging Principles of Regulatory Evolution
    BENJAMIN PRUD’HOMME, NICOLAS GOMPEL, and SEAN B. CARROLL.
    • PIGMENTATION PATTERNS AND GENE EXPRESSION AS MODELS OF REGULATORY EVOLUTION
    • USING AVAILABLE GENETIC COMPONENTS TO GENERATE NOVELTY
    • CIS-REGULATORY EVOLUTION MINIMIZES FITNESS PENALTIES
    • INTERACTION MAY EVOLVE BETWEEN ANY TRANSCRIPTION FACTOR AND DOWNSTREAM CRE
    • LOSSES ARE EASY, GAINS ARE HARDER
    • CONNECTING THE DOTS FROM PIGMENTATION PATTERNS TO BODY PLAN DIVERSIFICATION: THE COMPOUNDING OF REGULATORY CHANGES OVER EONS
    • CONCLUSION
  • 7. Evolution of Individuality During the Transition from Unicellular to Multicellular Life
    RICHARD E. MICHOD.
    • ORIGIN OF REPRODUCTIVE ALTRUISM
    • COST OF REPRODUCTION
    • COVARIANCE EFFECT
    • HOW DOES A GROUP BECOME AN INDIVIDUAL?
  • 8. Insect Societies as Divided Organisms: The Complexities of Purpose and Cross-Purpose
    JOAN E. STRASSMANN and DAVID C. QUELLER.
    • THE ROCK, THE CLOCK, AND ORGANISMAL COMPLEXITY
    • A HOUSE DIVIDED
    • HOW ARE COLONIES ORGANISMAL?
    • THE SUCCESS OF SOCIAL INSECTS
    • AN INORDINATE FONDNESS FOR KINSHIP
    • THE HAPLODIPLOID HYPOTHESIS
    • KIN SELECTION AND SYNERGISM: LIFE INSURANCE AND FORTRESS DEFENSE
    • RELATEDNESS IS STILL IMPORTANT
    • AN EVEN MORE INORDINATE FONDNESS FOR SELF
    • WORKER REPRODUCTION AND POLICING
    • CONCLUSIONS
  • 9. Symbiosis as an Adaptive Process and Source of Phenotypic Complexity
    NANCY A. MORAN.
    • DISPARATE GENE SETS CONFER DISTINCT CAPABILITIES
    • ACQUISITION OF FOREIGN GENES AND CAPABILITIES
    • SYMBIOSIS AS A MECHANISM OF ADAPTATION AND AS A SOURCE OF PHENOTYPIC COMPLEXITY
    • BACTERIOPHAGE AS GENE VECTORS AND SYMBIONTS OF BACTERIA
    • SYMBIOTIC MICROBIAL CONSORTIA
    • SYMBIOSIS AS A ROUTE TO ADAPTATION AND COMPLEXITY IN EUKARYOTES
    • FORCES FAVORING SYMBIOSIS IN ANIMALS
    • HEREDITARY SYMBIOSIS IN ANIMALS
    • MULTIPARTITE SYMBIOSES WITHIN INSECT LINEAGES
    • GENOME SEQUENCES ELUCIDATE COMPLEMENTARY FUNCTIONAL ROLES OF SYMBIONTS AND HOST
    • GENOMIC DECAY IN OBLIGATE SYMBIONTS AND HOST DEPENDENCE
    • ANIMAL SYMBIONTS RETAINING GENOME PLASTICITY
    • CONCLUSIONS
• IV. CASE STUDIES: DISSECTING COMPLEX PHENOTYPES
  • 10. Adaptive Evolution of Color Vision as Seen Through the Eyes of Butterflies
    FRANCESCA D. FRENTIU, GARY D. BERNARD, CRISTINA I. CUEVAS, MARILOU P. SISON-MANGUS, KATHLEEN L. PRUDIC, and ADRIANA D. BRISCOE.
    • NYMPHALID BUTTERFLIES COMPRISE A USEFUL SYSTEM FOR STUDYING COLOR VISION
    • ABSORBANCE SPECTRA AND OPSIN SEQUENCES OF LIMENITIS L PHOTOPIGMENTS
    • POPULATION GENETIC AND MOLECULAR EVOLUTIONARY ANALYSES SUGGEST L OPSINS ARE UNDER POSITIVE SELECTION
    • CONCLUSIONS
    • MATERIALS AND METHODS
  • 11. Plant Domestication, a Unique Opportunity to Identify the Genetic Basis of Adaptation
    JEFFREY ROSS-IBARRA, PETER L. MORRELL, and BRANDON S. GAUT.
    • IS ARTIFICIAL SELECTION ANALOGOUS TO NATURAL SELECTION? A HISTORICAL PERSPECTIVE
    • TWO APPROACHES TO FINDING ADAPTIVE GENES
    • FROM THE TOP DOWN: QTL AND LD MAPPING
    • FROM THE BOTTOM UP: MOLECULAR POPULATION GENETICS
    • PERSPECTIVE: TOP-DOWN VS. BOTTOM-UP
  • 12. An Experimental Test of Evolutionary Trade-Offs During Temperature Adaptation
    ALBERT F. BENNETT and RICHARD E. LENSKI.
    • RESULTS
    • DISCUSSION
    • METHODS
  • 13. Two Routes to Functional Adaptation: Tibetan and Andean High-Altitude Natives
    CYNTHIA M. BEALL.
    • POTENTIAL AND ACTUAL POINTS OF ADAPTATION TO HYPOXIA
    • ARE THESE FUNCTIONAL ADAPTATIONS HERITABLE?
  • 14. On the Origin and Evolutionary Diversification of Beetle Horns
    DOUGLAS J. EMLEN, LAURA CORLEY LAVINE, and BEN EWEN-CAMPEN.
    • A NATURAL HISTORY OF BEETLES WITH HORNS
    • THREE STEPS TO BUILDING A BEETLE HORN
    • A DEVELOPMENTAL MODEL FOR THE ORIGIN AND EVOLUTIONARY DIVERSIFICATION OF BEETLE HORNS
    • CONCLUSIONS
• v. CONCLUDING ESSAY
  • 15. Biological Design in Science Classrooms
    EUGENIE C. SCOTT and NICHOLAS J. MATZKE.
    • HISTORICAL BACKGROUND: FUNDAMENTALIST OPPOSITION TO EVOLUTION EDUCATION IN THE UNITED STATES
    • INTELLIGENT DESIGN ARGUMENTS
    • THE ARTIFACT ANALOGY AND DESIGN
    • DESIGN IN CREATION SCIENCE
    • SPECIAL CREATION
    • THE EMERGENCE OF INTELLIGENT DESIGN
    • INTELLIGENT DESIGN AND EDUCATIONAL POLICY
• References