A

Amitani, Yuichi (2015) Prototypical Reasoning about Species and the Species Problem. [Preprint]

Austin, Christopher J. (2020) Organisms, Activity, and Being: On the Substance of Process Ontology. [Preprint]

Austin, Christopher J. (2017) Recent Work in The Philosophy of Biology. [Preprint]

B

Barker, Matthew J. and Velasco, Joel D. (2012) Deep Conventionalism about Evolutionary Groups. In: UNSPECIFIED.

Barker, Matthew J. (2018) Species and Other Evolving Lineages as Feedback Systems. Philosophy, Theory, and Practice in Biology, 11 (013). ISSN 2475-3025

Brigandt, Ingo (2008) Natural Kinds in Evolution and Systematics: Metaphysical and Epistemological Considerations. [Preprint]

Byron (formerly Baker), Jason M. (2005) Adaptive speciation: The role of natural selection in mechanisms of geographic and non-geographic speciation. UNSPECIFIED.

C

Cabrera, Frank (2017) Cladistic Parsimony, Historical Linguistics and Cultural Phylogenetics. Mind and Language, 32 (1). pp. 65-100.

Campero, María Belén and Favre, Cristián and Saborido, Cristian (2020) Dying to live. Cell death as a regulatory process. THEORIA. An International Journal for Theory, History and Foundations of Science, 35 (2). pp. 197-215. ISSN 2171-679X

Conix, Stijn (2019) Measuring evolutionary independence: A pragmatic approach to species classification. Biology & Philosophy. ISSN 1572-8404

Currie, Adrian (2020) Comparative Thinking in Biology. [Preprint]

D

DiFrisco, James and Jaeger, Johannes (2021) Homology of process: developmental dynamics in comparative biology. [Preprint]

Doolittle, W. Ford (2018) Speciation without Species: A Final Word. Philosophy, Theory, and Practice in Biology, 11 (014). ISSN 2475-3025

Dunn, Cory D. (2017) Some Liked It Hot: A Hypothesis Regarding Establishment of the Proto-Mitochondrial Endosymbiont During Eukaryogenesis. Journal of Molecular Evolution, 85. pp. 99-106.

E

Esfeld, Michael (2005) The causal homogeneity of biological kinds. [Preprint]

F

Finkelman, Leonard (2019) Crossed Tracks: Mesolimulus, Archaeopteryx, and the Nature of Fossils. [Preprint]

Finkelman, Leonard (2018) De-extinction and the Conception of Species. [Preprint]

Fuerst, John (2017) Lineage population: A concept needed by an observer of nature? [Preprint]

G

Gouvea, Devin (2018) Reframing the Homology Problem. In: UNSPECIFIED.

Green, Sara and Wolkenhauer , Olaf (2013) Tracing organizing principles: Learning from the history of systems biology. History and Philosophy of the Life Sciences, 35. pp. 553-576.

Griffiths, Paul (2005) Function, Homology and Character Individuation. [Preprint]

Griffiths, Paul E (2006) Function, Homology and Character Individuation. [Preprint]

Griffiths, Paul Edmund (2005) Function, Homology and Character Individuation. [Preprint]

H

Haber, Matthew H. (2012) Multilevel Lineages and Multidimensional Trees: The Levels of Lineage and Phylogeny Reconstruction. In: UNSPECIFIED.

Hamilton, Andrew and Haber, Matt (2004) Coherence, Consistency, and Cohesion: Clade Selection in Okasha and Beyond. In: UNSPECIFIED. (In Press)

Hamilton, Andrew and Haber, Matt (2004) Coherence, Consistency, and Cohesion: Clade Selection in Okasha and Beyond. In: UNSPECIFIED. (In Press)

Havstad, Joyce C (2019) Let Me Tell You ‘Bout the Birds and the Bee-Mimicking Flies and Bambiraptor. [Preprint]

Houkes, Wybo (2010) Tales of Tools and Trees: Phylogenetic analysis and explanation in evolutionary archaeology. In: UNSPECIFIED.

Houkes, Wybo (2010) Tales of Tools and Trees: Phylogenetic analysis and explanation in evolutionary archaeology. In: UNSPECIFIED.

J

Jones, Nicholaos (2016) Strategies of Explanatory Abstraction in Molecular Systems Biology. In: UNSPECIFIED.

K

Kendig, Catherine (2010) An ontogenetic-ecological conception of species: a new approach to an old idea. In: UNSPECIFIED.

Kunz, Werner and Werning, Markus (2009) The Biological Species as a Gene-Flow Community. Species Essentialism Does Not Imply Species Universalism. In: UNSPECIFIED.

N

Nathan, Marco J. (2018) Pluralism is the Answer! What is the Question? Philosophy, Theory, and Practice in Biology, 11 (015). ISSN 2475-3025

O

Osimani, Barbara and Poellinger, Roland (2020) Osimani B., Poellinger R. (2020) A Protocol for Model Validation and Causal Inference from Computer Simulation. In: Bertolaso M., Sterpetti F. (eds) A Critical Reflection on Automated Science. Human Perspectives in Health Sciences and Technology, vol 1. Springer, Cham. https://doi.org/10.1007/978-3-030-25001-0_9. [Preprint]

Otsuka, Jun (2018) Species as models. In: UNSPECIFIED.

P

Pedroso, Makmiller (2018) Forming Lineages by Sticking Together. Philosophy, Theory, and Practice in Biology, 11 (016). ISSN 2475-3025

Pence, Charles H. (2019) Locating Uncertainty in Stochastic Evolutionary Models: Divergence Time Estimation. Biology & Philosophy, 34. p. 21. ISSN 1572-8404

Pradeu, Thomas and Kostyrka, Gladys and Dupré, John (2016) Understanding viruses: Philosophical investigations. Studies in history and philosophy of biological and biomedical sciences. ISSN 1879-2499

Q

Quinn, Aleta (2019) Diagnosing Discordance: Signal in Data, Conflict in Paradigms. Philosophy, Theory, and Practice in Biology, 11 (017). ISSN 2475-3025

R

Roffé, Ariel Jonathan (2020) Dynamic Homology and Circularity in Cladistic Analysis. [Preprint]

Roughgarden, Joan (2019) Holobiont Evolution: Mathematical Model with Vertical vs. Horizontal Microbiome Transmission. Philosophy, Theory, and Practice in Biology, 12 (002). ISSN 2475-3025

S

Sarma, Gopal P. (2016) Collecting Systematic, Introspective Reports of Pharmacological Effects and Side-Effects. [Preprint]

Sarma, Gopal P. and Faundez, Victor (2017) Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices. Cellular Logistics, 7 (4).

Slater, Matthew (2013) Natural Kindness. [Preprint]

Sober, Elliott (2019) Fitness and the Twins. Philosophy, Theory, and Practice in Biology, 12 (001). ISSN 2475-3025

Sterner, Beckett and Witteveen, Joeri and Franz, Nico (2019) Alternatives to Realist Consensus in Bio-Ontologies: Taxonomic Classification as a Basis for Data Discovery and Integration. [Preprint]

Suárez, Javier (2016) Bacterial species pluralism in the light of medicine and endosymbiosis. THEORIA. An International Journal for Theory, History and Foundations of Science, 31 (1). pp. 91-105. ISSN 0495-4548

Suárez, Javier (2021) The holobiont/hologenome as a level of selection: An approach to the evolution of multispecies systems. THEORIA. An International Journal for Theory, History and Foundations of Science, 36 (1). pp. 81-112. ISSN 2171-679X

Suárez, Javier and Stencel, Adrian (2020) A part‐dependent account of biological individuality: why holobionts are individuals and ecosystems simultaneously. Biological Reviews of the Cambridge Philosophical Society, 95. pp. 1308-1324.

T

Taylor, Henry (2019) Whales, fish and Alaskan bears: interest-relative taxonomy and kind pluralism in biology. [Preprint]

Turner, Derek (2019) In Defense of Living Fossils. [Preprint]

V

Velasco, Joel (2008) Species concepts should not conflict with evolutionary history, but often do. [Preprint]

Velasco, Joel (2009) Species, Genes, and the Tree of Life. [Preprint]

Velasco, Joel (2009) When monophyly is not enough: Exclusivity as the key to defining a phylogenetic species concept. [Preprint]

Velasco, Joel D. (2012) The Future of Systematics: Tree-Thinking Without the Tree. [Preprint]

Velasco, Joel D. and Sober, Elliott (2010) Testing for Treeness: Lateral Gene Transfer, Phylogenetic Inference, and Model Selection. [Preprint]

W

Wilkins, John S. (2007) The Concept and Causes of Microbial Species. [Preprint]

Wilkins, John S. (2009) Species are not theoretical objects, or, On what there is in biology. [Preprint]

Wilkins, John S. (2010) What is a species? Essences and generation. [Preprint]

Wilkins, John S. and Nelson, Gareth J. (2008) Trémaux on species: A theory of allopatric speciation (and punctuated equilibrium) before Wagner. UNSPECIFIED.

Wilkins, John S. and Nelson, Gareth J. (2008) Trémaux on species: A theory of allopatric speciation (and punctuated equilibrium) before Wagner. [Preprint]

Witteveen, Joeri (2014) Naming and contingency: the type method of biological taxonomy. [Preprint]