The author shows that the genesis of the science associated with the transition from sensual-specific to the rational knowledge. The first philosophers were the first scientists, experts in the field of engineering, construction, etc. The author analyzes attempts of the naturally scientific explanation for the origin of the universe, space, animals and humans made by ancient philosophers and scientists. The particular attention is paid to the modern reading of Pythagoras’ ideas, who saw the key to understanding the Universe in mathematics, philosophy, and also the first scientific program of Leucippus, Democritus, that laid the basis of mechanicalism. Based on the analysis of philosophy and science by Aristotle, the author shows that science and philosophy in antiquity were in unity, however, at this stage the premises of their difference are already coming up.