John Baptist van Helmont created for Hale the basis of a Christian natural science, a means of re-describing various natural events as motions in obedience to God's will. The Helmontian ferments were ranged along a spectrum, from life in all its forms, through such phenomena as fires and magnets, to mere propensities like gravitation; they spanned the ‘qualitative’ gap between the falling stone and human minds. Hale never quite decided if a ferment was a kind of spiritual substance, or just an unexplained activity. The concept's ambiguity was the feature which made it so useful, but there was an evident danger in blurring the distinction that separated matter from immaterial things. In giving religious importance to trivial natural events, Hale tended to naturalise God's interventions. His talk of a spectrum of ferments brought even man's immortal part to the edge of the natural sphere, at a time when Christianity was being reduced to a message about the existence of a ‘future state’. His ‘biological’ treatises merged seamlessly with writings about the human soul. They were more than a support for his religion; they constituted a theology.

The continuities within Hale's thought can be seen from the closing pages of The primitive origination of mankind. At the conclusion of his book, Hale turned to ‘a farther enquiry touching the end of the formation of Man, so far as the same may be collected by natural light and ratiocination’.