A

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

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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]

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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

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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

Figdor, Carrie (2022) What Could Cognition Be, If Not Human Cognition?: Individuating cognitive abilities in the light of evolution. [Preprint]

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

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

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G

Ginnobili, Santiago (2022) Darwinian functional biology. THEORIA. An International Journal for Theory, History and Foundations of Science, 37 (2). pp. 233-255. ISSN 2171-679X

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.

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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)

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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.

M

Molter, Daniel J (2022) On the ontology of vernal orange slime. Mushroom: The journal of Wild Mushrooming, 28 (4). pp. 6-10. ISSN 0740-8161

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]

Ronai, Isobel and Greslehner, Gregor P. and Boem, Federico and Carlisle, Judith and Stencel, Adrian and Suárez, Javier and Bayir, Saliha and Bretting, Wiebke and Formosinho, Joana and Guerrero, Anna C. and Morgan, William H. and Prigot-Maurice, Cybèle and Rodeck, Salome and Vasse, Marie and Wallis, Jacqueline M. and Zacks, Oryan (2020) "Microbiota, symbiosis and individuality summer school" meeting report. Microbiome, 8. p. 117.

Roughgarden, Joan (2020) 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 (2020) Fitness and the Twins. Philosophy, Theory, and Practice in Biology, 12 (001). ISSN 2475-3025

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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

Watkins, Aja (2021) Multi-Model Approaches to Phylogenetics: Implications for Idealization. [Preprint]

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]

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

Wilkins, John (2022) The Good Species. [Preprint]

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