Bowdler was born near Bath, the son of a gentleman of independent means. He studied medicine at St. Andrews and at Edinburgh, where he took his degree in 1776, but did not practice, devoting himself instead to the cause of prison reform.

He was a strong chess player for his day, and played eight recorded games against the best chess player of the time, François-André Danican Philidor, who was confident enough of his superiority to Bowdler that he played with handicaps. Bowdler won twice, lost three times, and drew three times; Philidor was usually blindfolded and playing multiple opponents simultaneously, and sometimes started without one pawn. The first recorded game to feature a double rook sacrifice was played between Bowdler (white) and H. Conway at London in 1788.

In 1818, after retiring to the Isle of Wight, he published his Family Shakespeare, which had considerable success. He subsequently attempted to do the same with the works of historian Edward Gibbon, a project which was not as successful. Bowdler's edition of Gibbon's work was published posthumously in 1826. His sister Jane was a poet and essayist, and his sister Harriet was the editor of Bowdler's publications.

He later settled in south Wales, where he died, and is buried at Oystermouth in Swansea. His large library, consisting of (unexpurgated) volumes collected by his ancestors Thomas Bowdler (1638—1700) and Thomas Bowdler (1661—1738), was donated to the University of Wales, Lampeter.

In 19th-century households, a popular family pastime was reading aloud from the Bible, the classics or major works of English literature. In Bowdler's childhood, his father had entertained his family with dramatic readings of extracts from Shakespeare. Later, Bowdler realised his father had been extemporaneously omitting or altering passages he felt unsuitable for the ears of his wife and children. Bowdler felt it would be worthwhile to present an edition which might be used in a family whose father was not a sufficiently "circumspect and judicious reader" to accomplish this expurgation himself.

In 1807, the first edition of the Family Shakespeare was published, in four duodecimo volumes, containing 24 of the plays. In 1818 was published The Family Shakespeare, in Ten Volumes; in which nothing is added to the original text; but those words and expressions are omitted which cannot with propriety be read aloud in a family. Each play is preceded by an introduction where Bowdler summarises and justifies his changes to the text. The editions were actually edited by Bowdler's sister, Harriet, rather than by Thomas. However, they were published under Thomas Bowdler's name, because a woman could not publicly admit that she understood Shakespeare's racy passages. By 1850, eleven editions had been printed.

Bowdler was not the first to undertake such a project, and despite being considered a negative example, his efforts made it more societally acceptable to teach Shakespeare to new audiences. The poet Algernon Charles Swinburne said, "More nauseous and foolish cant was never chattered than that which would deride the memory or depreciate the merits of Bowdler. No man ever did better service to Shakespeare than the man who made it possible to put him into the hands of intelligent and imaginative children."

Bowdler's commitment not to augment Shakespeare's text was in contrast to many earlier editors and performers. Nahum Tate as Poet Laureate had rewritten the tragedy of King Lear with a happy ending. In 1807, Charles Lamb and his sister Mary published Tales from Shakespeare specifically for children, with synopses of 20 of the plays, but seldom quoting the original text directly.

Changes to Shakespeare

Some examples of alterations made by Bowdler's edition:

• In Hamlet, the death of Ophelia was referred to as an accidental drowning, omitting the suggestions that she may have intended suicide.
• In Macbeth, Lady Macbeth's famous cry "Out, damned spot!" was changed to "Out, crimson spot!"
• "God!" as an exclamation is replaced with "Heavens!"
• In Henry IV, Part 2, the prostitute Doll Tearsheet is omitted entirely; the slightly more reputable Mistress Quickly is retained.

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