High-throughput data are extremely variable. The variability is such that it does not appear to represent deviation around a mean, with samples drawn from a single distribution – it appears more consistent with multiple distinct subtypes or states within the population. “Precision medicine” requires we treat this variability and complexity “not as a glitch but as a feature”. In this regard we view the genome, and thus cell phenotype, as highly adaptive, dynamic in response to changing environment. Our approach is to use the transcriptome, defined as RNA and RNA regulatory proteins, as a surrogate for phenotype, and to both analyze and drive the variability in neuronal phenotype. We take the transcriptome as a summary record of the unique experience of the organism, and indeed of each cell, over its history in the environment – and as not an end state but as highly malleable, including responses leading to disease. Thus, our goal is to develop a molecular physiology that incorporates variability. We study the neural regulation of visceral homeostasis and take regional, pooled cell, and single cell samples in the central neural control system involved. We assay these neural samples at rest and in response to elevated blood pressure. Analysis of the resulting high-dimensional dataset reveals a remarkable complexity and heterogeneity of the samples and of their response to changes in blood pressure. These results demonstrate differential expression modules for each anatomically distinct neuronal group and neuronal type. We have been able to analyze the variability in a way that connects it to higher-level neurophysiological and neuroanatomical features of the system. The results suggest a novel concept of neuronal regulation of cardiovascular homeostasis arising from variability in the molecular physiology. Our view is this approach may now enable a mechanistic molecular physiology of neural function and disease, involving constrained gene regulatory network models and multiscale models. Our multiscale models include the several cell types comprising brain tissue as they interact in innate neuroimmune inflammatory responses during the development of hypertension. We are developing the approach with the aim of discovering the adaptive responses involved in the development of neurogenic hypertension, thought to underlie the vast majority of all hypertension.