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How is alchemy considered an occult practice / esoteric?

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Philosophical alchemy on the historiographic record starts popping up around the 3rd and 4th century. The oldest philosophical alchemist with extant writings is Zosimos of Panopolis, an egyptian hermeticist, who's works greatly influenced hermetic practice and alchemy as a spiritual discipline.

It is important to recognize that in this time period and for the following centuries philosophers were scientists, astronomers were priests, and the line between religion and science was incredibly blurred. The forces of Natural Physics could be approached through ontology by metaphysicians, and a successful lab experiment for a proto-scientist was physical proof for a loving and miraculous God.

We can see in the Golden Tractate (4th Century) of Hermes Trismegistus outlining very clearly a hermetic ascent ritual and magical operations using chemistry as the symbol set for the description of the procedure interspersed with mythic symbolism. This sets the tone for philosophical alchemy moving forward. The Zosimos tradition was pushed even further by the Arabs/Muslims during the Abassayid Caliphate where we see Muslim and Sufi mystics using the hermetic alchemical symbols to describe the dissolution and mystical conjunction with Allah (see Ibn Umayil). During this same time period alchemy is trickling into mideval Europe through Byzantium and Al-Andalus (Muslim Spain) and this is where the puffers (those obsessed with physical gold) take it to an extreme by interpreting the philosophical alchemy the same way as laboratory alchemy.

After the fall of Constantinople and the Spanish reconquest of the Iberian Peninsula, Muslim/Arabic literature flooded into Europe and became a part of the Rennaissance. The Muslim literature preserved much of the Hermetic and Zosimos tradition of Arabic alchemy and this is when European alchemists began getting really familiar with the spiritual branch. You can see this pop up with the alchemist Ripley (15th century) where we see an extremely Christianized version of alchemical symbolism that is encouraging the alchemist to practice this same type of spiritual transformation and engraved and emblemized in monuments such as the Porto Alchemica (there is an astrological and hermetic tinge to this) and most famously the front porch of Notre Dame (where there were symbols of Mithraic initiatory rites).

During the late Rennaissance this got consolidated into its own European flavored Philosophical alchemy through the Rosicrucian project in which the performance of the work promised immortality, or something like it with the perfectly preserved body of Christian Rosenkreuz (this echos Alchemy's egyptian roots as we can see here the beliefs of the Egyptian funerary rites clearly embedded in this goal). The influence of the Rosicrucians further embedded into the the Freemasons during the 18th century during the reconstruction of their esoteric symbol sets and made its way into the many magical lodges of the 18th and 19th centuries.

So philosophical/spiritual alchemy has always been there, atleast, hard evidence for it goes back to the 3rd century. Its evolved over time from its hermetic roots, appearing in formats used by muslim and christian mystics. There is confusion though, as there is alchemical literature that is purely laboratory alchemy and then there is alchemical literature that is obviously philosophical/spiritual alchemy. The puffers got caught in the middle confusing the two with each other, which is where we get the radical stories of black magicians chasing a philosophers stone that could turn lead into gold.
 
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