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Parts of Chatwin's book In Patagonia mirror the key plot device of TheRime of the Ancient Mariner, namely, the Mariner's journey southward to the South Pole as a metaphor for hell. Both Chatwin and Coleridge, the author of The Rime of the Ancient Mariner, were well-read students of classic literature, and both stories bear similarities to Dante's Inferno, about a journey deeper and deeper into the circles of hell, with each circle bearing its own strange and terrible features.
The excerpt you are probably referring to from Chatwin's book—where he recounts John Davis's naval journey as part of his discovery of the Falkland Islands—closely recalls Coleridge's poem, especially the key moment involving the slaughter of birds. The Mariner's killing of the albatross seems to trigger the hellish experiences later in the poem, as does Davis and his crew's slaughter of the penguins. Both feature fateful and...
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grim comeuppances, and both characterize the southern seas as a dangerous, fog- and storm-ridden landscape filled with terrors.
In contrast, Chatwin's account is based on a real historical event, and the elements of fatefulness and dramatic tension are narrative devices on his part. He is also using the story as part of a larger travelogue about Patagonia, whereas Coleridge's poem is much more focused and completely fictional.
Chatwin, in section 45 of In Patagonia, describes the 1593 voyage of the Desire to South America, and points out some similarities between Davis's experiences and Coleridge's poem. In Davis's case, he was driven by hunger to land on a remote island on the tip of South America, where his men slaughtered thousands of penguins for food. The meat of the birds contained a parasitic worm that killed almost all the men aboard. The ship became a "rotten hulk" that finally drifted into port with only Davis and four other men alive.
Chatwin connects this story with the section of Coleridge's poem in which the Mariner's lies adrift in the tropics. In the poem, the death of the ship's crew is caused by the sin of killing the albatross, which was done out of spite or whim, rather than hunger, as was the case with Davis and the penguins. It can be argued, however, that in both stories the ships are doomed by circumstances outside their control. In the same way that the Mariner's actions unleash a series of events he could not have foreseen, Davis could not know that the meat that he thought would save his life would ultimately be the cause of their gruesome death of almost all his men.
In the extract that I assume you are referring to, Bruce Chatwin narrates a harrowing voyage taken in 1593 that was similar in some respects to the voyage in The Rime of the Ancient Mariner. Some argue in fact that this voyage inspired the poem by Coleridge. The ship of John Davis was separated from the others in his fleet and sailed to Penguin Island close to the tip of South America. There, the crew wantonly slaughtered thousands of birds. The birds, however, took their revenge through a "worm" that the bodies carried which nearly destroyed the ship and killed almost everyone on board.
This rather repugnant story mirrors many of the key themes of The Rime of the Ancient Mariner, mainly in that both stories narrate an act of brutal destruction of nature and an apparent punishment that occurs as a result. However, it is important to note that in the poem, the Mariner kills on a whim, for no apparent reason, whereas it is clear that the sailors in the extract kill systematically and with intent for food. Likewise we can compare the worm in the dead birds to the Polar Spirit of the poem. Both of them are responsible for the revenge or punishment of the people that acted against Nature, but obviously the worm is a natural phenomenon and has no intelligence or feeling, whereas the Polar Spirit in the poem is presented as a supernatural force which wills its actions.