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Later years, 1851–1862

In 1851, Thoreau became increasingly fascinated with natural history and narratives of travel and expedition. He read avidly on botany and often wrote observations on this topic into his journal. He admired William Bartram and Charles Darwin 's Voyage of the Beagle. He kept detailed observations on Concord's nature lore, recording everything from how the fruit ripened over time to the fluctuating depths of Walden Pond and the days certain birds migrated. The point of this task was to "anticipate" the seasons of nature, in his word.

He became a land surveyor and continued to write increasingly detailed observations on the natural history of the town, covering an area of 26 square miles (67 square kilometers), in his journal, a two-million-word document he kept for 24 years. He also kept a series of notebooks, and these observations became the source of his late writings on natural history, such as "Autumnal Tints", "The Succession of Trees", and "Wild Apples", an essay lamenting the destruction of the local wild apple species.

With the rise of environmental history and ecocriticism as academic disciplines, several new readings of Thoreau began to emerge, showing him to have been both a philosopher and an analyst of ecological patterns in fields and woodlots. For instance, "The Succession of Forest Trees", shows that he used experimentation and analysis to explain how forests regenerate after fire or human destruction, through the dispersal of seeds by winds or animals. In this lecture, first presented to a cattle show in Concord, and considered his greatest contribution to ecology, Thoreau explained why one species of tree can grow in a place where a different tree did previously. He observed that squirrels often carry nuts far from the tree from which they fell to create stashes. These seeds are likely to germinate and grow should the squirrel die or abandon the stash. He credited the squirrel for performing a "great service... in the economy of the universe."

He traveled to Canada East once, Cape Cod four times, and Maine three times; these landscapes inspired his "excursion" books, A Yankee in Canada, Cape Cod, and The Maine Woods, in which travel itineraries frame his thoughts about geography, history and philosophy. Other travels took him southwest to Philadelphia and New York City in 1854 and west across the Great Lakes region in 1861, when he visited Niagara Falls, Detroit, Chicago, Milwaukee, St. Paul and Mackinac Island. He was provincial in his own travels, but he read widely about travel in other lands. He devoured all the first-hand travel accounts available in his day, at a time when the last unmapped regions of the earth were being explored. He read Magellan and James Cook; the arctic explorers John Franklin, Alexander Mackenzie and William Parry; David Livingstone and Richard Francis Burton on Africa; Lewis and Clark; and hundreds of lesser-known works by explorers and literate travelers. Astonishing amounts of reading fed his endless curiosity about the peoples, cultures, religions and natural history of the world and left its traces as commentaries in his voluminous journals. He processed everything he read, in the local laboratory of his Concord experience. Among his famous aphorisms is his advice to "live at home like a traveler".

After John Brown's raid on Harpers Ferry, many prominent voices in the abolitionist movement distanced themselves from Brown or damned him with faint praise. Thoreau was disgusted by this, and he composed a key speech, " A Plea for Captain John Brown ", which was uncompromising in its defense of Brown and his actions. Thoreau's speech proved persuasive: the abolitionist movement began to accept Brown as a martyr, and by the time of the American Civil War entire armies of the North were literally singing Brown's praises. As a biographer of Brown put it, "If, as Alfred Kazin suggests, without John Brown there would have been no Civil War, we would add that without the Concord Transcendentalists, John Brown would have had little cultural impact."