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As Lawrence Principe points out in his Secrets Of Alchemy, Alchemy was in fact the precursor to our modern notion of 'Chemistry'. The alchemists had theoretical foundations for their work which were inspired by and often incorporated 'unscientific' notions of divinity. At the same time however it's very important to remember that in contemporary terms this wasn't unusual, it's only in hindsight that we can say Newton's mathematical work was more scientific than his theological or alchemical work. (Having read this scholarly book on the subject which spares the bullshit, I quite recommend it.)

To people with the 'Magicians Mindset' as Keynes might put it, the world has a rational soul underlying it which can be teased out by careful study of all things. If you're a Christian and start with this prior belief, then it makes perfect sense that you should expect your theological studies to inform your understanding of the natural world and your understanding of the natural world to inform theological studies. This is a mindset where metaphors and abstract connections are not of the human mind. Rather, they represent features of the territory showing us God's divine authorship of the world.

Another good book that outlines some of this is Hall's The Secret Teachings Of All Ages, which discusses the essentially Aryan (Indo-Iranian) thesis that all theological traditions discuss the same underlying esoteric doctrine which itself descends from one civilization. Having been written in 1928, Hall speculates Atlantis. (Naturally, you should take this text with perhaps more than just a grain of salt.) As far as I know the modern version of this thesis usually places the ultimate originating civilization in India.



These alchemical principles you mention are probably derived from the Neoplatonic philosophy of Plotinus and Proclus, which is a pretty fascinating school of metaphysics with a significant mystical component. These Platonic influences are highly visible in Catholic and Orthodox churches today, having been transmitted through Augustine, Pseudo-Dionysius, and Origen. Hundreds of years ago, it made perfect sense for one person to be both a scientist and a theologian.

Also, "The Secret Teachings Of All Ages" sounds quite similar to the perennial philosophy.

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