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A Royalist clergyman from Brecon, Wales, Thomas was the twin brother of the poet Henry Vaughan, both being born at Newton, in the parish of St. Briget's, in 1621. He entered Jesus College, Oxford, in 1638, and remained there for a decade during the English Civil War.
Vaughan took part in the Battle of Rowton Heath in 1645. He became rector of the parish of Llansantffraed (St Bridget) Wales and took up medical studies, motivated by the lack of doctors in Wales. But in 1650, Vaughan was evicted from the parish because of his Royalist sympathies.
Vaughan later became involved with a plan of Robert Child to form a chemical club, with a laboratory and library, the main aim being to translate and collect chemical works. He married his wife Rebecca in 1651 and spent the next period of his life in London. His wife died in 1658.
Although he did not practice medicine, Vaughan sought to apply his chemical skills to preparing medicines in the manner recommended by Paracelsus. He corresponded with Samuel Hartlib, who by 1650 was paying attention to Vaughan as author, and established a reputation with his book Anthroposophia Theomagica, a magico-mystical work. Vaughan was the author of tracts published under the pseudonym Eugenius Philalethes, as is now generally agreed.
Vaughan was unusual amongst alchemists of the time in that he worked closely with his wife Rebecca Vaughan. He was a self-described member of the "Society of Unknown Philosophers", and was responsible for translating into English in 1652 the Fama Fraternitatis Rosae Crucis, an anonymous Rosicrucian manifesto first published in 1614 in Kassel.
Allen G. Debus has written that a simple explanation of Vaughan's natural philosophy, in its mature form, is as the De occulta of Cornelius Agrippa, in an exposition coming via the views of Michael Sendivogius. As a writer in the school of Sendivogius, Vaughan follows Jacques de Nuisement and Andreas Orthelius. He placed himself in the tradition of the Rosicrucian reformers of education, and of Johannes Trithemius, his teacher Libanius Gallus, and Pelagius of Majorca, teacher of Libanius (of whom the last two are not known to have been real people apart from what Trithemius relates of them).
According to some writers of catalogues of hermetic and alchemical treatises (such as John Ferguson, Denis Ian Duveen, Vinci Verginelli et al.), Thomas Vaughan could be the anonymous author of the treatise Reconditorium ac Reclusorium Opulentiae Sapientiaeque Numinis Mundi Magni, cui deditur in titulum CHYMICA VANNUS... Amstelodami... Anno 1666, i. e. a mysterious masterpiece of the hermetic tradition..
Vaughan quarrelled in print with Henry More. Their pamphlet war petered out, but More returned to the subject of alchemists in Enthusiasmus Triumphatus (1656). Another critic of Vaughan was John Gaule.
Vaughan fell out with an alchemical collaborator, Edward Bolnest, over money matters and alleged broken promises, and the matter came to litigation after Bolnest had threatened violence. Vaughan was accused as part of this affair of spending "most of his time in the study of Naturall Philosophy and Chimicall Phisick". He is reported as having confessed that he had "long sought and long missed... the philosopher's stone."
- "[Henry's] twin brother was THOMAS VAUGHAN (1621-1666). . ." Vaughan, Henry in Welsh Biography Online, at National Library of Wales
- The twins were the sons of Thomas Vaughan of 'Trenewydd', Newton . . . "who m. the heiress of Newton in Llansantffraed" VAUGHAN family, of Tretower Court in Welsh Biography Online, at National Library of Wales.
- Garrett A. Sullivan; Alan Stewart (1 February 2012). The Encyclopedia of English Renaissance Literature. John Wiley & Sons. pp. 1001–2. ISBN 978-1-4051-9449-5. Retrieved 7 June 2012.
- Donagan, Barbara. "Vaughan, Thomas". Oxford Dictionary of National Biography (online ed.). Oxford University Press. doi:10.1093/ref:odnb/28148. (Subscription or UK public library membership required.)
- Betty Jo Teeter Dobbs (29 April 1983). The Foundations of Newton's Alchemy, Or, "The Hunting of the Greene Lyon". CUP Archive. p. 66. ISBN 978-0-521-27381-7. Retrieved 7 June 2012.
- Peter Levenda The Tantric Alchemist: Thomas Vaughan and the Indian Tantric Tradition(2015)
- Allen G. Debus (2004). Alchemy and Early Modern Chemistry: Papers from Ambix. Jeremy Mills Publishing. p. 417. ISBN 978-0-9546484-1-1. Retrieved 7 June 2012.
- William R. Newman (15 February 2003). Gehennical Fire: The Lives of George Starkey, an American Alchemist in the Scientific Revolution. University of Chicago Press. p. 213. ISBN 978-0-226-57714-2. Retrieved 7 June 2012.
- Noel L. Brann (1999). Trithemius and Magical Theology: A Chapter in the Controversy Over Occult Studies in Early Modern Europe. SUNY Press. p. 109. ISBN 978-0-7914-3961-6. Retrieved 7 June 2012.
- Paola Zambelli (2007). White Magic, Black Magic in the European Renaissance. BRILL. p. 77. ISBN 978-90-04-16098-9. Retrieved 7 June 2012.
- Italian translation by Gerolamo Moggia and Vinci Verginelli, manuscript, 1921–1925, reviewed by Mario Marta and Giovanni Sergio, self-publishing www.youcanprint.it, 2018.
- Juliet Cummins (1 May 2003). Milton and the Ends of Time. Cambridge University Press. p. 34. ISBN 978-0-521-81665-6. Retrieved 7 June 2012.
- Betty Jo Teeter Dobbs (29 April 1983). The Foundations of Newton's Alchemy, Or, "The Hunting of the Greene Lyon". CUP Archive. p. 116. ISBN 978-0-521-27381-7. Retrieved 7 June 2012.
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