Theories in early embryology: close connections between epigenesis, preformationism, and self-organization

In current biological and philosophical literature, the use of the terms epigenesis and epigenetics has increased tremendously. As these terms are often confused, this paper aims at clarifying the distinction between them by drawing their conceptual and historical evolutions. The evolution of the term epigenesis is situated in the context of early embryological studies. Departing from Aristotle's natural philosophy, it is shown that epigenesis gained alternating attention from the 17th century onwards, as it was introduced into neo-classical embryology and considered to be the opposite of the preformationist tradition. Where preformation stated that the germ cells of each organism contain preformed miniature adults that unfold during development, epigenesis held that the embryo forms by successive gradual exchanges in an amorphous zygote. Although both traditions tried to explain developmental organization, religious and metaphysical arguments on the conception of embryonic matter as either active or passive determined the scope of their respective explanations. It is shown that these very arguments still underlie the use of gene-centric metaphors in the molecular revolution of the 20th century.