The 2012 publication of the results of the ENCODE program generated an acrimonious debate about the role of junk DNA. This debate is a symptom of the difficulties of dovetailing functional and evolutionary descriptions of genomes. This essay argues that extant genomes are the result of a progressive evolutionary construction. To the basic function that gives rise to RNA and proteins have been successively added additional functions, such as regulation by microRNA and epigenetic marks. This process of complexification was the result of evolutionary history, and different for the different genomes. Better knowledge of the evolutionary history of genomes would help to understand these structures and their functions.