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Bechtel, William and Bollhagen, Andrew (2021) Active Biological Mechanisms: Transforming Energy into Motion in Molecular Motors. [Preprint]

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Bolinska, Agnes (2018) Synthetic versus Analytic Approaches to Protein and DNA Structure Determination. [Preprint]

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Bourrat, Pierrick and Lu, Qiaoying (2017) Dissolving the Missing Heritability Problem. [Preprint]

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Brigandt, Ingo (2009) The Epistemic Goal of a Concept: Accounting for the Rationality of Semantic Change and Variation. [Preprint]

Brigandt, Ingo (2011) Explanation in Biology: Reduction, Pluralism, and Explanatory Aims. [Preprint]

Brigandt, Ingo (2013) Systems Biology and the Integration of Mechanistic Explanation and Mathematical Explanation. [Preprint]

Brigandt, Ingo (2004) An alternative to Kitcher's theory of conceptual progress and his account of the change of the gene concept. [Preprint]

Brigandt, Ingo (2017) Explanation of Molecular Processes Without Tracking Mechanism Operation. [Preprint]

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Goddiksen, Mads (2014) Explanatory standards in biology and physics textbooks: The case of polymers. [Preprint]

Goldwasser, Seth (2023) Standard Aberration: Cancer Biology and the Modeling Account of Normal Function. [Preprint]

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Green, Sara and Serban, Maria and Scholl, Raphael and Jones, Nicholaos and Brigandt, Ingo and Bechtel, William (2016) Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity. [Preprint]

Griffiths, Paul and Gray, Russell (2002) The Developmental Systems Perspective: Organism-environment systems as units of development and evolution. [Preprint]

Griffiths, Paul and Tabery, James (2008) Behavioral Genetics and Development: Historical and Conceptual Causes of Controversy. [Preprint]

Griffiths, Paul E (2002) The Fearless Vampire Conservator: Philip Kitcher, Genetic Determinism and the Informational Gene. [Preprint]

Griffiths, Paul E (2002) The Fearless Vampire Conservator: Phillip Kitcher and Genetic Determinism. [Preprint]

Griffiths, Paul E and Stotz, Karola (2005) Gene. [Preprint]

Griffiths, Paul E and Stotz, Karola (2006) Genes in the postgenomic era. [Preprint]

Griffiths, Paul Edmund (2000) Genetic Information: A Metaphor in Search of a Theory. [Preprint]

Griffiths, Paul Edmund (2000) The Philosophy of Molecular and Developmental Biology. [Preprint]

Guttinger, Stephan and Love, Alan C. (2020) modENCODE and the elaboration of functional genomic methodology. [Preprint]

Hangleiter, Dominik and Carolan, Jacques and Thebault, Karim P Y (2021) Analogue Quantum Simulation: A New Instrument for Scientific Understanding. [Preprint]

Havstad, Joyce C (2020) Complexity Begets Crosscutting, Dooms Hierarchy (Another Paper on Natural Kinds). [Preprint]

Havstad, Joyce C (2021) Sensational Science, Archaic Hominin Genetics, and Amplified Inductive Risk. [Preprint]

Hicks, Daniel (2015) Epistemological Depth in a GM Crops Controversy. [Preprint]

Illari, Phyllis and Russo, Federica (2016) Information channels and biomarkers of disease. [Preprint]

Jantzen, Benjamin and Danks, David (2008) Biological Codes and Topological Causation. [Preprint]

Jones, Elizabeth (2019) Ancient Genetics to Ancient Genomics: Celebrity and Credibility in Data-Driven Practice. [Preprint]

Knuuttila, Tarja and Loettgers, Andrea (2013) Varieties of Noise: Analogical Reasoning in Synthetic Biology. [Preprint]

Korenić, Andrej and Perović, Slobodan and Cirkovic, Milan M. and Miquel, Paul-Antoine (2019) Symmetry breaking and functional incompleteness in biological systems. [Preprint]

Kostic, Daniel and Hilgetag, Claus and Tittgemeyer, Marc (2020) Unifying the essential concepts of biological networks: biological insights and philosophical foundations. [Preprint]

Krohs, Ulrich (2021) The epistemology of biomimetics: the role of models and of morphogenetic principles. [Preprint]

Kumar, Manish (2023) Precision Oncology, Signaling Pathways Reprogramming and Targeted Therapy: A Holistic Approach to Molecular Cancer Therapeutics. [Preprint]

Kumar, Manish (2023) Precision Oncology, Signaling Pathways Reprogramming and Targeted Therapy: A Holistic Approach to Molecular Cancer Therapeutics. [Preprint]

Kõiv, Riin (2023) Genetically caused trait is an interactive kind. [Preprint]

Lean, Christopher and Doolittle, W. Ford and Bielawski, Joseph (2022) Community-level evolutionary processes: Linking community genetics with replicator-interactor theory. [Preprint]

Lean, Oliver M (2019) Binding Specificity and Causal Selection in Drug Design. [Preprint]

Lean, Oliver M (2019) Chemical Arbitrariness and the Causal Role of Molecular Adapters. [Preprint]

Linquist, Stefan and Cottenie, Karl and Elliott, Tyler and Saylor, Brent and Kremer, Stefan and Gregory, T. Ryan (2015) Applying ecological models to communities of genetic elements: the case of neutral theory. [Preprint]

Linquist, Stefan and Saylor, Brent and Cottenie, Karl and Elliott, Tyler A. and Kremer, Stefan C. and Gregory, T. Ryan (2013) Distinguishing ecological from evolutionary approaches to transposable elements. [Preprint]

Lu, Qiaoying and Bourrat, Pierrick (2017) The Evolutionary Gene and the Extended Evolutionary Synthesis. [Preprint]

Luchetti, Michele (2018) Constitutive elements in science beyond physics: the case of the Hardy–Weinberg principle. [Preprint]

López-Rubio, Ezequiel and Ratti, Emanuele (2019) Data science and molecular biology: prediction and mechanistic explanation. [Preprint]

Malaterre, Christophe (2009) Can synthetic biology shed light on the origin of life? [Preprint]

Matthews, Lucas J. (2017) On mechanistic reasoning in unexpected places: the case of population genetics. [Preprint]

Meloni, Maurizio and Reynolds, Jack (2020) Thinking embodiment with genetics: epigenetics and postgenomic biology in embodied cognition and enactivism. [Preprint]

Meyer, Russell (2020) Dynamical Causes. [Preprint]

Meynell, Letitia (2024) Are There Two Sexes? Yes and No, But Mostly No (and Gender is Something Else Anyway—More or Less). [Preprint]

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Novick, Aaron and Scholl, Raphael (2017) Presume It Not: True Causes in the Search for the Basis of Heredity. [Preprint]

O'Malley, Maureen (2008) Exploratory experimentation and scientific practice: Metagenomics and the proteorhodopsin case. [Preprint]

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Veit, Walter and Browning, Heather (2022) Polygenic Scores and Social Science. [Preprint]

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Conference or Workshop Item

Baetu, Tudor (2010) A defense of syntax-based gene concepts in postgenomics: ‘Genes as modular subroutines in the master genomic program’. In: UNSPECIFIED.

Baxter, Janella (2015) Engineering Novel Proteins with Orthogonal tRNA: Artificial Causes that make a Difference. In: UNSPECIFIED.

Bechtel, William (2021) Discovering control mechanisms: The controllers of dynein. In: UNSPECIFIED.

Bolinska, Agnes (2024) Models of Information in Structural Biology. In: UNSPECIFIED.

Bollhagen, Andrew (2020) The "Inch-Worm Episode": Reconstituting the Phenomenon of Kinesin Motility. In: UNSPECIFIED.

Bourrat, Pierrick and Lu, Qiaoying (2016) Dissolving the missing heritability problem. In: UNSPECIFIED.

Burnston, Daniel (2016) Real Patterns in Biological Explanation. In: UNSPECIFIED.

Chen, Ruey-Lin (2018) Individuating Genes as Types or Individuals: Philosophical Implications on Individuality, Kinds, and Gene Concepts. In: UNSPECIFIED.

Fagan, Melinda B. (2012) The stem cell uncertainty principle. In: UNSPECIFIED.

Godfrey-Smith, Peter (2013) Sender-Receiver Systems Within and Between Organisms. In: UNSPECIFIED.

Goldwasser, Seth (2022) Finding Normality in Abnormality: On the Ascription of Normal Function to Cancer. In: UNSPECIFIED.

Green, Sara and Vogt, Henrik (2016) Personalizing medicine in silico and in socio. In: UNSPECIFIED.

Greslehner, Gregor P. (2018) What do molecular biologists mean when they say 'structure determines function'? In: UNSPECIFIED.

Hall, Melinda (2013) Mere Deviation, Critically Assessing Prenatal Testing. In: UNSPECIFIED.

Kieval, Phillip Hintikka and Westerblad, Oscar (2024) Deep Learning as Method-Learning: Pragmatic Understanding, Epistemic Strategies and Design-Rules. In: UNSPECIFIED.

Kistler, Max (2007) Mechanisms and Downward Causation. In: UNSPECIFIED.

Knuuttila, Tarja and Loettgers, Andrea (2010) Modeling and experimenting: The combinational strategy in synthetic biology. In: UNSPECIFIED.

Knuuttila, Tarja and Loettgers, Andrea (2012) Synthetic Modeling and Mechanistic Account: Material Recombination and Beyond. In: UNSPECIFIED.

Knuuttila, Tarja and Loettgers, Andrea (2011) Synthetic Modeling and the Functional Role of Noise. In: UNSPECIFIED.

Leonelli, Sabina (2008) On the Locality of Data and Claims about Phenomena. In: UNSPECIFIED.

Levy, Arnon and Bechtel, William (2016) Towards Mechanism 2.0: Expanding the Scope of Mechanistic Explanation. In: UNSPECIFIED.

Northcott, Robert (2008) Innateness and Science. In: UNSPECIFIED.

O'Malley, Maureen A. and Brigandt, Ingo and Love, Alan C. and Crawford, John W. and Gilbert, Jack A. and Knight, Rob and Mitchell, Sandra D. and Rohwer, Forest (2014) Multilevel Research Strategies and Biological Systems. In: UNSPECIFIED.

Ratti, Emanuele and López-Rubio, Ezequiel (2018) Mechanistic Models and the Explanatory Limits of Machine Learning. In: UNSPECIFIED.

Sarwar, Ameer (2020) Perspectives on Causal Specificity. In: UNSPECIFIED.

Schindler, Samuel (2007) Model, Theory, and Evidence in the Discovery of the DNA Structure. In: UNSPECIFIED.

Sheredos, Benjamin and Burnston, Daniel and Abrahamsen, Adele and Bechtel, William (2012) Why do biologists use so many diagrams? In: UNSPECIFIED.

Souto-Maior, Caetano (2022) Extraordinarily corrupt or statistically commonplace? Reproducibility crises may stem from a lack of understanding of outcome probabilities. In: UNSPECIFIED.

Sustar, Predrag (2006) Neo-Functional Analysis: Phylogenetical Restrictions on Causal Role Functions. In: UNSPECIFIED.

Tabery, James (2008) Difference Mechanisms. In: UNSPECIFIED.

Tabery, James (2008) Interactive Predispositions. In: UNSPECIFIED.

Weber, Marcel (2018) Causal Specificity, Biological Possibility and Non-parity about Genetic Causes. In: UNSPECIFIED.

Wieber, Frederic (2009) Theoretical technologies in an “experimental” setting: empirical modeling of proteinic objects and simulation of their dynamics within scientific collaborations around a supercomputer. In: UNSPECIFIED.

Yeh, Hsiao-Fan and Chen, Ruey-Lin (2018) Intervention as both Test and Exploration: Reexamining the PaJaMo Experiment based on Aims and Modes of Interventions. In: UNSPECIFIED.

Published Article or Volume

Abir-Am, Pnina Geraldine (2014) García-Sancho. 2012. Biology, Computing, and the History of Molecular Sequencing; From Proteins to DNA, 1945-2000. THEORIA. An International Journal for Theory, History and Foundations of Science, 29 (3). pp. 433-436. ISSN 2171-679X

Bartol, Jordan (2012) Re-Examining the Gene in Personalized Genomics.

Barwich, Ann-Sophie (2021) Fishing for Genes: How the Largest Gene Family in the Mammalian Genome was Found (and Why Idiosyncrasy in Exploration Matters). Perspectives on Science, 29 (4).

Barwich, Ann-Sophie (2018) How to be rational about empirical success in ongoing science: The case of the quantum nose and its critics. Studies in History and Philosophy of Science.

Barwich, Ann-Sophie (2020) What Makes a Discovery Successful? The Story of Linda Buck and the Olfactory Receptors. Cell, 181 (4). pp. 749-753.

Barwich, Ann-Sophie and Bschir, Karim (2017) The Manipulability of What? The History of G-Protein Coupled Receptors. Biology & Philosophy. ISSN 1572-8404

Barwich, Ann-Sophie and Bschir, Karim (2017) The Manipulability of What? The History of G-Protein Coupled Receptors. Biology & Philosophy. ISSN 1572-8404

Bechtel, William (2017) Analyzing network models to make discoveries about biological mechanisms. British Journal for the Philosophy of Science.

Bechtel, William (2017) Explaining features of fine-grained phenomena using abstract analyses of phenomena and mechanisms: two examples from chronobiology. Synthese.

Bechtel, William (2017) Using the hierarchy of biological ontologies to identify mechanisms in flat networks. Biology and Philosophy.

Birch, Jonathan (2012) Robust Processes and Teleological Language. European Journal for Philosophy of Science. ISSN 1879-4912

Buzzoni, Marco and Tesio, Luigi and Stuart, Michael T. (2022) Holism and Reductionism in the Illness/Disease Debate. From Electrons to Elephants and Elections: Saga of Content and Context. pp. 743-778. ISSN 978-3-030-92192-7

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

DiFrisco, James and Ramsey, Grant (2023) Adaptationism and Trait Individuation. Philosophy of Science, 90 (5). pp. 1234-1243.

Downes, Stephen M. (2021) The role of ancient DNA research in archaeology. Topoi, 40. pp. 285-293.

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.

Evans, Nicholas G. and Pence, Charles H. (2024) Gain of Function Research and Model Organisms in Biology. Journal of Medical Ethics, 50 (3). pp. 201-206. ISSN 1473-4257

Giroux, Élodie (2021) L’exposome : vers une science intégrative des expositions ? Lato Sensu, revue de la Société de philosophie des sciences, 8 (3). pp. 9-28. ISSN 2295-8029

Glynn, Luke (2010) Deterministic Chance. British Journal for the Philosophy of Science, 61 (1). pp. 51-80.

Grant, Ramsey and Cristina, Villegas (2024) Developmental Channeling and Evolutionary Dappling. Philosophy of Science. pp. 1-18.

Green, Sara and Vogt, Henrik (2016) Personalizing medicine in silico and in socio. Humana.Mente Journal of Philosophical Studies.

Haber, Matthew H. (2019) Species in the Age of Discordance. Philosophy, Theory, and Practice in Biology, 11 (021). ISSN 2475-3025

Haber, Matthew H. and Molter, Daniel J. (2019) Species in the Age of Discordance: Meeting Report and Introduction. Philosophy, Theory, and Practice in Biology, 11 (012). ISSN 2475-3025

Hazelwood, Caleb (2022) Review of Observing Evolution by Bruce S. Grant. History and Philosophy of the Life Sciences.

Hazelwood, Caleb (2021) The Species Category as a Scientific Kind. Synthese.

Hicks, Daniel (2017) Genetically Modified Crops, Inclusion, and Democracy. Perspectives on Science.

Ioannidis, Stavros and Psillos, Stathis (2017) In Defense of Methodological Mechanism: The Case of Apoptosis. Axiomathes. ISSN 1572-8390

Jodoin, Laurent (2014) Génétique des populations et mécanique statistique : stratégie explicative et analogie formelle. Lato Sensu, revue de la Société de philosophie des sciences, 1 (1). pp. 12-25. ISSN 2295-8029

Kesić, Srdjan (2019) Rethinking the pragmatic systems biology and systems-theoretical biology divide: toward a complexity-inspired epistemology of systems biomedicine. Medical hypotheses, 131. p. 109316.

Laplane, Lucie and Duluc, Dorothée and Bikfalvi, Andreas and Larmonier, Nicolas and Pradeu, Thomas (2019) Beyond the tumour microenvironment. International Journal of Cancer, 145 (10). pp. 2611-2618. ISSN 0020-7136

Laplane, Lucie and Duluc, Dorothée and Larmonier, Nicolas and Pradeu, Thomas and Bikfalvi, Andreas (2018) The Multiple Layers of the Tumor Environment. Trends in Cancer, 4 (12). pp. 802-809. ISSN 24058033

Lemoine, Maël and Pradeu, Thomas (2018) Dissecting the Meanings of “Physiology” to Assess the Vitality of the Discipline. Physiology, 33 (4). pp. 236-245. ISSN 1548-9213

Liu, Katherine E (2017) Rethinking Causation in Cancer with Evolutionary Developmental Biology. Biological Theory.

Malaterre, Christophe (2011) Making Sense of Downward Causation in Manipulationism. With Illustrations from Cancer Research. History and Philosophy of the Life Sciences, 33 (4). pp. 537-562.

Malinowska, Joanna Karolina and Serpico, Davide (2023) Epistemological Pitfalls in the Proxy Theory of Race: The Case of Genomics-Based Medicine. The British Journal for the Philosophy of Science. ISSN 1464-3537

Martens, Niels C.M. (2022) Dark Matter Realism. Foundations of Physics, 52 (1). ISSN 0015-9018

Meneganzin, Andra and Ramsey, Grant and DiFrisco, James (2024) What is a trait? Lessons from the human chin. JEZ-B Molecular and Developmental Evolution, 342 (2). pp. 65-75.

Meunier, Robert (2018) Project knowledge and its resituation in the design of research projects: Seymour Benzer's behavioral genetics, 1965-1974. Studies in History and Philosophy of Science Part A.

Ndhlovu, Andrew and Durand, Pierre and Ramsey, Grant (2020) Programmed cell death as a black queen in microbial communities. Molecular Ecology. pp. 1-10.

Nicholson, Daniel J. and Dupré, John (2018) Genidentity and Biological Processes.

Northcott, Robert and Piccinini, Gualtiero (2018) Conceived This Way: Innateness Defended. Philosophers' Imprint, 18 (18). pp. 1-16.

Osimani, Barbara (2014) Causing something to be one way rather than another: Genetic Information, causal specificity and the relevance of linear order. Kybernetes, 43 (6). pp. 865-881.

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Pradeu, Thomas and Laplane, Lucie and Prévot, Karine and Hoquet, Thierry and Reynaud, Valentine and Fusco, Giuseppe and Minelli, Alessandro and Orgogozo, Virginie and Vervoort, Michel (2016) Defining "Development". Current topics in developmental biology, 117. pp. 171-83. ISSN 1557-8933

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Open Access Book

Ramsey, Grant (2013) Human Nature. Elements in the Philosophy of Biology . Cambridge University Press, Cambridge, UK. ISBN 978-1-108-71606-2

Other

Chen, Ruey-Lin (2023) Scientific exploration of causation in biomedical research: The case of gene targeting on mouse embryonic stem cells. UNSPECIFIED.

Stotz, Karola (2006) 2001 and all that: a tale of a third science. UNSPECIFIED.

Wilkins, John S. (2009) A deflationary account of information in biology. UNSPECIFIED.