The problem of distinguishing causes from effects is not a trivial one, as illustrated by the science fiction writer Isaac Asimov in a novel dedicated to an imaginary compound with surprising "chronochemistry" properties. The problem is particularly important when trying to establish the etiology of diseases. Here, we discuss how the problem reflects on our understanding of disease using two specific examples: Alzheimer's disease (AD) and Friedreich's ataxia (FRDA). We show how the fibrillar aggregates observed in AD were first denied any interest, then to assume a central focus, and to finally recess to be considered the dead-end point of the aggregation pathway. This current view is that the soluble aggregates formed along the aggregation pathway rather than the mature amyliod fiber are the causes of disease, Similarly, we illustrate how the identification of causes and and effects have been important in the study of FRDA. This disease has alternatively been considered as the consequence of oxidative stress, iron precipitation or reduction of iron-sulfur cluster protein context. We illustrate how new tools have recently been established which allow us to follow the development of the disease. We hope that this review may inspire similar studies in other scientific disciplines.