In 1476, just as Leonardo was becoming a master in his own right, probably functioning as a partner to Verrocchio, he was suddenly plagued by scandal. Along with three other young men, he was anonymously accused of sodomy, which in Florence was a criminal offense, even though in most cases the authorities looked the other way and the general culture attached little social stigma to homosexuality.

Leonardo was 24 years old at the time. The accusation specifically charged him with a homosexual interaction with one Jacopo Saltarelli, a notorious prostitute. The charges were brought in April, and for a time Leonardo and the other defendants were under the watchful eye of Florence's "Officers of the Night"–a kind of renaissance vice squad.

However, the charges were dismissed in June, due to a lack of witnesses and evidence. It is probable that the Medici family brought had something to do with this outcome, as another of the defendants was Lionardo de Tornabuoni, and Lorenzo de Medici's mother had been a Tornabuoni.

The period immediately following the case was a productive one for Leonardo. Sometime in the mid-1470s, he worked on the Portrait of Ginevra de Benci. In 1478, he received what was probably his first commission: a religious group wanted him to paint an Adoration of the Shepherds. He did a few preliminary sketches but then abandoned the project.

That same year, Leonardo wrote in his journals, "I have begun the two Virgin Marys." Critics agree that the Benois Madonna is one of them. Originally believed lost, it appeared out of the blue in the nineteenth century when a traveling musician sold it to a Russian in southern Italy, and was confirmed as a work of Leonardo in 1909. On Mary's lap the Christ Child plays with two small flowers; yet his aspect is serious. The shadows are such that it appears that the painting's light source shines from above the viewer's shoulder, as if from heaven. Both have halos; as his career progressed, however, Leonardo was less likely to endow his religious subjects with such ornamentation. The Virgin has a rounded, glowing face–this, too, is typical of Leonardo's earlier work. Her expression exemplifies part of what set Leonardo's work apart from that of his contemporaries: she looks winsome and fresh, and has none of the stodginess of other artists' madonnas from the time.

When he was about 30 years old and probably working quite independently from Verrocchio, Leonardo received a commission for The Adoration of the Magi. He soon left Florence for Milan, and thus it stands unfinished. Nonetheless, critics consider it a masterpiece. It shows Leonardo's ability to endow a familiar scene–here, the three wise men's adoration of Christ–with a fresh and lively spirit. The traditional manger has been removed to the rear side, to make room for a crowd of people reacting with emotion to the Child's Epiphany. Leonardo famously noted, "A good painter has two subjects of primary importance: man and the state of man's mind. The first is easy, the second difficult, since it must be conveyed by means of the gestures and movements of the various parts of the body." Here we see these "gestures and movements" in brilliant vibrancy. It was common for religious paintings to feature figures who stood placidly by, as if they, too, were separated from the scene's focal point by a gap of centuries. But Leonardo insists on realism, and the result is eminently more entertaining. His composition constitutes a pyramid with Mary at the apex; around it the crowd stands in a semi-circle. Anchoring the crowd stand two figures whose peculiar calmness at this miraculous sight may betray some lack of religious fire on Leonardo's part. The dueling men in the background could symbolize myriad things; most likely they are intended to contrast the calm of the coming Christian order with the vice and waste of the past.

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