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He was the eldest son of John Dee, by his second wife, Jane, daughter of Bartholomew Fromond of East Cheam, Surrey, and was born at Mortlake on 13 July 1579. He accompanied his father in travels through Germany, Poland, and Bohemia. After his return to England he was placed at Westminster School, 3 May 1592, under the tuition of Grant and Camden. Anthony Wood was informed that he subsequently studied at Oxford, but he took no degree, and his college is unknown.
Settling in London with the intention of practising 'physic' (medicine) he exhibited at the door of his house a list of medicines which were said to be certain cures for many diseases. The censors of the College of Physicians summoned him to appear before them; but it is not known with what outcome. Proceeding to Manchester, Dee married Isabella, daughter of Edward Prestwych, justice of the peace.
Through the recommendation of James I he was appointed one of the physicians to the Tsar Michael I of Russia. He remained in Russia for about fourteen years, principally at Moscow. There he wrote his Fasciculus Chemicus, a collection of writings on alchemy.
Returning to England upon the death of his wife in 1637, Dee became physician to King Charles I. Upon his retirement Arthur Dee resided in Norwich, where he became a friend of Sir Thomas Browne. Arthur Dee died in September or October 1651, in Norwich and was buried in the church of St. George, Tombland. He had seven sons and six daughters. Dee's relationship to Browne has been little explored, but on his death it was to Browne that the bulk of Arthur Dee's alchemical manuscripts and books were bequeathed.
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- The most informative detailed biography of Arthur Dee remains that of Charlotte Fell-Smith, published in 1909 .
- Fasciculus Chemicus or Chymical Collections. Expressing the Ingress, Progress, and Egress, of the Secret Hermetick Science our of the choicest and most famous authors London, 1650.