I am a philosopher of science specializing in philosophy of biology. My approach is both practice-focused and sensitive to the many roles of values in scientific research.
My PhD dissertation is about experimental systems in biomedical research. I focus on contexts where the following two features are true: (1) the research target is a complex phenomenon (e.g., the impact of the human genital tract microbiome on HIV acquisition risk) and (2) the research object is a complex experimental system (e.g., involving multiple modes, such as observational clinical trials, animal models, in silico modeling, &etc.). I hope to provide an account of what makes for a good experimental system in these contexts.
My MA dissertation is about mate choice and sexual selection and argues that shifting research emphases in biology research have resulted in improved understanding of sexually-reproducing organisms. The abstract is below, but this work is not yet published. Please email me if you are interested.
Other research interests of mine include: applied ethics (especially bioethics and environmental ethics), philosophy of medicine, public philosophy, climate change, and community/citizen science.
Vaynberg, E, Hoffman, KN, Wallis, JM, & Weisberg, M. (2024). Dimensional versus conceptual incommensurability in the social and behavioral sciences. Behavioral and Brain Sciences, 47(e64). https://doi.org/10.1017/S0140525X23002182
Wallis, JM & Detlefsen, K. (2022). Philosophy, Academic and Public: Lessons from the Graduate Certificate in Public Philosophy at the University of Pennsylvania. Precollege Philosophy and Public Practice, 4, 91–109. https://doi.org/10.5840/p4202233022
Wallis, JM. (2020). Is it ever morally permissible to select for deafness in one’s child?. Med Health Care and Philos, 23, 3–15. https://doi.org/10.1007/s11019-019-09922-6
Ronai, I, Greslehner, GP, Boem, F, Carlisle, J, Stencel, A, Suárez, J, Bayir, S, Bretting, W, Formosinho, J, Guerrero, AC, Morgan, WH, Prigot-Maurice, C, Rodeck, S, Vasse, M, Wallis, JM & Zacks, O. (2020). “Microbiota, symbiosis and individuality summer school” meeting report. Microbiome, 8, 117. https://doi.org/10.1186/s40168-020-00898-7
Biology Babu, TM, Srinivasan, S, Magaret, A, Proll, S, Stankiewicz Karita, H, Wallis, JM, Selke, S, Varon, D, Pholsena, T, Fredricks, D, Marrazzo, J, Wald, A, & Johnston, C. (2023). Genital HSV-2 suppression with valacyclovir is not associated with changes in Nugent score or absolute abundance of key vaginal bacteria. Open Forum Infectious Disease, 10(3), ofad099. https://doi.org/10.1093/ofid/ofad099
Dela Cruz, EJ, Fiedler, TL, Liu, C, Munch, MM, Kohler, CM, Oot, AR, Wallis, JM, Wang, J, Frishman, A, Garcia, K, Wiser, A, Balkus, JE, Srinivasan, S, Golob, JL, Sycuro, LK, Marrazzo, JM, Hawn, TR, & Fredricks, DN. (2021). Genetic Variation in Toll-Like Receptor 5 and Colonization with Flagellated Bacterial Vaginosis-Associated Bacteria. Infect Immun, 89(3), e00060–20. https://doi.org/10.1128/IAI.00060-20
Carter, KA, Srinivasan, S, Fiedler, TL, Anzala, O, Kimani, J, Mochache, V, Wallis, JM, Fredricks, DN, McClelland, RS, & Balkus, JE. (2021). Vaginal Bacteria and Risk of Incident and Persistent Infection With High-Risk Subtypes of Human Papillomavirus: A Cohort Study Among Kenyan Women. Sex Transm Dis, 48(7), 499–507. https://doi.org/10.1097/OLQ.0000000000001343
Jarrett, OD, Srinivasan, S, Richardson, BA, Fiedler, T, Wallis, JM, Kinuthia, J, Jaoko, W, Mandaliya, K, Fredricks, DN, & McClelland, RS. (2019). Specific vaginal bacteria are associated with increased risk of Trichomonas vaginalis acquisition in women. The Journal of Infectious Diseases, 220(9), 1503–1510. https://doi.org/10.1093/infdis/jiz354
MA Dissertation
Mate Choice and Sexual Selection: How shifting research emphasis in biology is improving understanding of sexually-reproducing organisms Sexual selection research is one of the most controversial areas of evolutionary biology. The controversies have historical origins with the views of Charles Darwin and Alfred Russel Wallace and have persisted, albeit transformed, to the present. Scientists continue to disagree over precise definitions of sexual selection and how best to account for the evolution of so-called exaggerated traits. Advances in the biology of mate choice, however, are providing new guidance on some of the long-prominent debates. Furthermore, these scientific trends challenge widespread intuitions about how sexual reproduction influences evolution by natural selection. In this dissertation I explore the shifting research emphasis from sexual selection (via exaggerated traits) to mate choice (via mating preference mechanisms). This shift to what I term ‘mate-choice thinking’ has ramifications – all related to biological investigations of sexually-reproducing organisms – for scientific, conceptual, and philosophical problems. My arguments attempt a philosophical overview to (i) outline and explain the shift and (ii) show how mate-choice thinking provides advantages over narrower emphasis on sexual selection. Advised by Samir Okasha
Papers in progress
[under review] A biology paper on vaginal bacteria and HIV (with S.S. and colleagues).
[under review] A paper on life cycle diagrams (with M.S. and K.N.H.).
[under review] A paper on community science (with J.H.). [in prep] A philosophy paper on bioinformatics methods in microbiome science.
[in prep] A paper on translation in biomedical research.
[in prep] A paper on improving decision-making for climate change adaptation.