In mammals, adaptive transcription is a crucial mechanism to connect environmental stimulation to changes in gene expression and subsequent organism remodeling. Adaptive transcriptional programs are central to various organism functions, such as learning and memory, immune system plasticity and muscular remodeling, and their activation increases cellular resilience and prevents various diseases. Yet, they also form the basis for many maladaptive processes and are crucially involved in the progression of addiction, depression, cancer, cardiovascular disorders, autoimmune conditions and metabolic dysfunction among others. They are implicated in mediating the therapeutic effects of major treatment modalities such as antidepressants and can have negative effects on treatment efforts such as in radiotherapy resistance in cancer. The present work examines the universal role of adaptive transcription as a mechanism for the induction of cell state transitions in health and disease and explores how some of humanity’s gravest disorders can be seen as adaptive logic errors. It also considers underlying principles in the basic structure of adaptive transcriptional programs such as their division into a core and a directional program and analyses how one might best reprogram cells via complex stimulation patterns to achieve concrete adaptation goals and optimal health of the whole organism.