What was Caravaggio's black-winged deity of love? What insights this masterwork uncovers about the rebellious artist

A young boy cries out as his skull is forcefully held, a massive thumb pressing into his face as his parent's mighty hand grasps him by the neck. This scene from The Sacrifice of Isaac appears in the Florentine museum, creating distress through Caravaggio's chilling rendition of the suffering youth from the biblical account. It appears as if the patriarch, instructed by God to kill his son, could snap his spinal column with a solitary turn. However the father's preferred approach involves the metallic steel knife he grips in his remaining hand, prepared to cut Isaac's neck. One definite aspect stands out – whoever posed as Isaac for this astonishing piece demonstrated remarkable expressive skill. Within exists not only fear, shock and pleading in his darkened eyes but also deep sorrow that a guardian could abandon him so completely.

The artist took a well-known scriptural story and made it so vibrant and raw that its horrors seemed to happen directly in front of the viewer

Viewing in front of the painting, viewers identify this as a actual face, an precise record of a adolescent model, because the same boy – identifiable by his tousled locks and almost black eyes – appears in two other paintings by the master. In each instance, that highly emotional visage dominates the composition. In John the Baptist, he peers mischievously from the darkness while embracing a ram. In Victorious Cupid, he grins with a toughness acquired on Rome's streets, his black plumed wings sinister, a unclothed child running chaos in a affluent residence.

Amor Vincit Omnia, presently displayed at a British museum, represents one of the most discomfiting artworks ever created. Observers feel completely unsettled gazing at it. The god of love, whose darts fill people with often agonizing longing, is portrayed as a extremely real, vividly lit unclothed form, straddling toppled-over items that comprise stringed devices, a musical score, metal armour and an architect's ruler. This heap of items echoes, intentionally, the mathematical and architectural equipment scattered across the floor in Albrecht Dürer's print Melencolia I – save in this case, the gloomy mess is caused by this smirking Cupid and the mayhem he can release.

"Love looks not with the vision, but with the mind, / And thus is winged Cupid painted blind," penned Shakespeare, just before this work was produced around the early 1600s. But Caravaggio's Cupid is not blind. He stares directly at you. That face – sardonic and ruddy-cheeked, looking with bold assurance as he struts naked – is the same one that screams in terror in Abraham's Test.

When Michelangelo Merisi da Caravaggio painted his three images of the same distinctive-looking kid in the Eternal City at the dawn of the seventeenth century, he was the most acclaimed religious painter in a city ignited by religious renewal. The Sacrifice of Isaac demonstrates why he was sought to decorate churches: he could adopt a scriptural story that had been portrayed numerous times previously and make it so fresh, so unfiltered and visceral that the terror appeared to be happening immediately in front of the spectator.

Yet there was another aspect to the artist, evident as quickly as he came in Rome in the winter that ended 1592, as a artist in his initial 20s with no teacher or supporter in the urban center, only skill and boldness. The majority of the works with which he caught the sacred city's eye were everything but holy. What could be the absolute first resides in London's National Gallery. A youth opens his crimson mouth in a yell of pain: while stretching out his filthy digits for a cherry, he has instead been bitten. Youth Bitten by a Reptile is sensuality amid squalor: viewers can see the painter's gloomy chamber mirrored in the murky liquid of the transparent vase.

The boy wears a pink flower in his coiffure – a symbol of the erotic commerce in early modern art. Venetian artists such as Titian and Jacopo Palma depicted courtesans grasping flowers and, in a work lost in the WWII but documented through photographs, the master represented a famous female courtesan, holding a bouquet to her chest. The meaning of all these floral indicators is clear: intimacy for purchase.

How are we to interpret of the artist's sensual depictions of youths – and of a particular boy in particular? It is a inquiry that has split his commentators ever since he achieved mega-fame in the twentieth century. The complicated historical reality is that the artist was neither the queer hero that, for example, Derek Jarman presented on film in his twentieth-century movie about the artist, nor so completely pious that, as some art historians improbably claim, his Youth Holding Fruit is in fact a likeness of Christ.

His early paintings do make explicit erotic suggestions, or including propositions. It's as if Caravaggio, then a destitute youthful creator, aligned with Rome's prostitutes, selling himself to survive. In the Uffizi, with this idea in mind, viewers might turn to another early work, the 1596 masterwork the god of wine, in which the deity of alcohol gazes coolly at you as he starts to undo the black sash of his garment.

A few years after the wine deity, what could have motivated the artist to create Amor Vincit Omnia for the art patron the nobleman, when he was finally becoming nearly respectable with prestigious ecclesiastical projects? This profane non-Christian deity revives the erotic challenges of his initial paintings but in a increasingly intense, uneasy manner. Fifty years afterwards, its secret seemed obvious: it was a representation of the painter's lover. A English traveller viewed the painting in about 1649 and was informed its figure has "the body & face of [Caravaggio's|his] own youth or servant that laid with him". The name of this adolescent was Francesco.

The artist had been dead for about forty annums when this story was recorded.