2013 (invited). "The Structure of Scientific Theories" for Stanford Encyclopedia of Philosophy. [Check SEP Projected Contents here. Email me for a draft - article entry deadline is rapidly approaching and significant progress is being made.]
2012. Mathematical Modeling in Biology: Philosophy and Pragmatics. Frontiers in Plant Evolution and Development. [Open Access Publication: Download Here.]
2012 Interweaving Categories: Styles, Paradigms, and Models. Studies in History and Philosophy of Science, Part A 43: 628-639. [Download PDF from philpapers.com.]
2011. Part-Whole Science. Synthese 178: 397-427. [Download PDF.]
2011. Darwin's Pluralism, Then and Now. Review of David N. Reznick's The Origin Then and Now. An Interpretative Guide to the Origin of Species (Princeton UP, 2009). Metascience. [Download PDF]
2011. "Una revisión crítica de los estilos de investigación científica: Teoría, práctica y estilos," in Historia, prácticas y estilos en la filosofía de la ciencia. Hacia una epistemología plural. (S. Martínez, X. Huang, and G. Guillaumin, eds.), Universidad Autónoma Metropolitana, Mexico City, pp. 259-287 (in Spanish). [Download PDF from philpapers.com.]
2011. Consciousness Modeled: Reification and Promising Pluralism. Pensamiento (Madrid, Spain) 67 (254): 617-630. [Download PDF from philpapers.com.]
2011. "¿La cosificación genética de la 'raza'? Un análisis crítico", in Genes (&) mestizos. Genómica y raza en la biomedicina mexicana. (C. López-Beltrán, ed.), UNAM, Mexico City, pp. 237-258 (in Spanish).
[Email me for a copy.]
2011 (forthcoming). "Evo-Devo as a Trading Zone" in Conceptual Change in Biology: Scientific and Philosophical Perspectives on Evolution and Development. (A. Love, ed.), Springer Verlag, Boston Studies in the Philosophy of Science. [Download PDF from philpapers.com.]
2009a. Schaffner's Model of Theory Reduction: Critique and Reconstruction. Philosophy of Science 76: 119-142. [Download PDF]
2009b. Prediction in Selectionist Evolutionary Theory. Philosophy of Science 76: 889-901. [Download PDF]
2009c. Character Analysis in Cladistics: Abstraction, Reification, and the Search for Objectivity. Acta Biotheoretica 57: 129-162. [Download PDF]
2009d. Introduction: From a Philosophical Point of View. Acta Biotheoretica 57: 5-10. [Download PDF]
2009e. Missing in Action: On Science and Constructivism in the Realism Debates. A Dialogue. Review of Kyle Stanford's Exceeding Our Grasp. Science, History, and the Problem of Unconceived Alternatives (Oxford UP, 2006), Metascience. (pp. 16-25). [Download PDF]
2008. Systemic Darwinism. Proceedings of the National Academy of Sciences (USA). 105 (33): 11833-11838. [Download PDF]
2007. "Estilos de investigación científica, modelos e insectos sociales", in Variedad Infinita. Ciencia y representación. Un enfoque histórico y filosófico (E. Suárez, ed.). UNAM and Editorial Limusa, pp. 55-89. [Download PDF]
2006a. Parts and Theories in Compositional Biology. Biology and Philosophy 21: 471-499. [Download PDF.]
2006b. On the Dangers of Making Scientific Models Ontologically Independent: Taking Richard Levins' Warnings Seriously. Biology and Philosophy 21: 703-724. [Download PDF.]
2006c. Fisherian and Wrightian Perspectives in Evolutionary Genetics and Model-Mediated Imposition of Theoretical Assumptions. Journal of Theoretical Biology 240: 218-232. [Download PDF from philpapers.com.]
2005a. An Obstacle to Unification in Biological Social Science: Formal and Compositional Styles of Science. Graduate Journal of Social Sciences 2: 40-100. [Download PDF from philpapers.com.]
2005b. "Evolutionary Developmental Biology Meets Levels of Selection: Modular Integration or Competition, or Both?" in Modularity: Understanding the Development and Evolution of Complex Natural Systems (W. Callebaut and D. Rasskin-Gutman, eds.), MIT Press, pp. 61-97. [Download PDF from philpapers.com.]
2001a. Varieties of Modules: Kinds, Levels, Origins, and Behaviors. Journal of Experimental Zoology (Molecular and Developmental Evolution) 291: 116-129. [Download PDF from philpapers.com.]
2001b. August Weismann on Germ-Plasm Variation. Journal of the History of Biology 34: 517-555. [Download PDF from philpapers.com]
2001c. Review of Deborah Gordon's Ants at Work: The Organization of a Social Insect Colony (Free Press, 1999). Philosophy of Science 68: 268-270. [Download PDF]
2000. Darwin on Variation and Heredity. Journal of the History of Biology 33: 425-455. [Download PDF from philpapers.com.]
Co-Authored Publications (Professional):
Vergara-Silva F, Winther RG. 2009. Editorial: Systematics, Darwinism, and the Philosophy of Science. Acta Biotheoretica 57: 1-3. [Download PDF]
Wade MJ, Winther RG, Agrawal AF, Goodnight CJ. 2001. Alternative Definitions of Epistasis: Dependence and Interaction. Trends in Ecology and Evolution 16: 498-504. [Download PDF from philpapers.com.]
van Syoc RJ, Winther R. 1999. Sponge-Inhabiting Barnacles of the Americas: A New Species of Acasta (Cirripedia, Archaeobalanidae), First Record from the Eastern Pacific, Including Discussion of the Evolution of Cirral Morphology. Crustaceana 72: 467-486. [Download PDF]
Theses:
2004. A Molecular and Evolutionary Study of the Obligate Endosymbiont Wolbachia in Tribolium confusum. [Masters Thesis in the biological sciences; download PDF]
2003. Formal Biology and Compositional Biology as Two Kinds of Biological Theorizing. [PhD Thesis in philosophy of science; PDF from philpapers.com.] In Progress:
I am also working on various general public "mini-essays", which have received positive feedback and praise. Feel free to email me about these.