This paper explores how dogs in Victorian experimental physiology sparked a fundamental ethical and epistemological crisis through their embodied resistance to mechanistic reduction. Using archival evidence from Claude Bernard’s laboratory notebooks, feminist antivivisection literature and the public controversy surrounding the Brown Dog memorial, it argues that canine subjects challenged the conceptual foundations of experimental science through persistent agency and interspecies recognition. The analysis highlights three interconnected acts of resistance: Bernard’s private struggles with ‘uncooperative’ experimental subjects that undermined his mechanistic doctrine; the feminist witnessing practices of Lizzy Lind-af-Hageby and Leisa Katherina Schartau, whose documentation of prolonged experiments exposed the systemic violence masked by claims to scientific objectivity; and the Brown Dog Affair, where a terrier’s transformation from laboratory subject to contested political symbol crystallised intersecting politics of species, gender and class in Edwardian London. Theoretically, the paper develops the concept of felt reality—the embodied, affective dimension of experimental practice that persistently challenged positivist frameworks. Through feminist animal studies, it examines how dogs’ ‘absent referent’ status required elaborate discursive and psychological mechanisms to suppress evidence of their consciousness and agency. This interdisciplinary inquiry contributes to medical humanities by foregrounding animal agency, ethical witnessing and the limitations of biomedical rationality. Ultimately, it argues that Victorian experimental dogs participated as active agents in historical debates over knowledge, ethics and human dominion. Their resistance shaped a counter-history of science—one that evaluates progress not by dominating life, but by the bravery to confront the irreducible otherness of conscious beings and acknowledge, in that vulnerable exchange, the basis for more compassionate scientific practice.