- "Organisms, Traits, and Population Subdivisions: Two Arguments against the Causal Conception of Fitness?"
- On the "On the 'Transmission sense of information'"
"Capturing the superorganism: a formal theory of group adaptation"
Group adaptation, formal darwinism and contextual analysis
- "Idealized, inaccurate but successful: a pragmatic approach to evaluating models in theoretical ecology"
"The Structure of Idealization in Biological Theories: The Case of the Wright-Fisher Model"
- Convergent evolution and the limits of natural selection
Convergence and Parallelism in Evolution: A Neo-Gouldian Account
- "Computability, Gödel’s incompleteness theorem, and an inherent limit on the predictability of evolution"
"Transcriptomic analysis of avian digits reveals conserved and derived digit identities in birds"
- "Wayward Modeling: Population Genetics and Natural Selection"
"Upper-Directed Systems: A New Approach to Teleology in Biology"
- "Type-Selection versus Token-Selection"
"Testing for treeness: lateral gene transfer, phylogenetic inference, and model selection"
- "Species Are Not Uniquely Real Biological Entities"
Darwinian Populations and Natural Selection ch. 6 & 7
- "Beyond area relationships: Extinction and recolonization in molecular marine biogeography"
"Group selection or group physiology? Filling in the Gaps of Multi-level Selection Theory to Explain Cultural Variation"
- "The Strength of Phenotypic Selection in Natural Populations"
"Signatures of Selection in the Human Genome"
- "Contingency and Determinism in Replicated Adaptive Radiations of Island Lizards"
"What determines biological fitness? The problem of the reference environment"
- "Reproductive Social Behavior: Cooperative Games to Replace Sexual Selection"
"IS CONVERGENCE MORE THAN AN ANALOGY? APPEALING TO THE FREQUENCY OF HOMOPLASY AS EVIDENCE FOR A NON-CONTINGENTLY CONSTRAINED ADAPTATIONAL DESIGN SPACE"
- "The Empirical Non-Equivalence of Genic and Genotypic Models of Selection: A (Decisive) Refutation of Genic Selectionism and Pluralistic Genic Selectionism"
"THE PRINCIPLE OF DRIFT: BIOLOGY’S FIRST LAW"
- 'Adaptive Evolution' in "Developmental Plasticity and Evolution"
'Plasticity' in "Developmental Plasticity and Evolution"
- 'Material for a Synthesis' in "Developmental Plasticity and Evolution"
"SHIFTING THE NATURAL SELECTION METAPHOR TO THE GROUP LEVEL"
- "A Universal Generative Tendency toward Increased Organismal Complexity"
"Genetic Relatedness and the Evolution of Altruism"
- "Adaptive Phenotypic Plasticity: Target or By-Product of Selection in a Variable Environment?"
"The Ressurection of Innateness"
- "Epistemological and Practical Aspects of the Developmental Synthesis:Streamlining the Naturalistic Agenda"
"Modularity in animal development and evolution: Elements of a conceptual framework for EvoDevo"
- "Calvinism: An Argument from Design"
"What's Wrong with the Emergentist Statistical Interpretation of Natural Selection and Random Drift?"
- "Two Ways of Thinking about Fitness and Natural Selection"
"The Trials of Life: Natural Selection and Random Drift"
- "Functional and Generative Constraints on Life Cycle Evolution: an Attempt on the Architecture of Constraints"