The roots and routes of cultural evolution are still a mystery. Here, we aim to lift a corner of that veil by illuminating the deep origins of encultured freedoms, which evolved through centuries-long processes of learning to pursue and transmit values and practices oriented toward autonomous individual choice. Analyzing a multitude of data sources, we unravel for 108 Old World countries a sequence of cultural evolution reaching from (a) ancient climates suitable for dairy farming to (b) lactose tolerance at the eve of the colonial era to (c) resources that empowered people in the early industrial era to (d) encultured freedoms today. Historically, lactose tolerance peaks under two contrasting conditions: cold winters and cool summers with steady rain versus hot summers and warm winters with extensive dry periods (Study 1). However, only the cold/wet variant of these two conditions links lactose tolerance at the eve of the colonial era to empowering resources in early industrial times, and to encultured freedoms today (Study 2). We interpret these findings as a form of gene-culture coevolution within a novel thermo-hydraulic theory of freedoms.