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In 1831, devoutly religious Captain Fitzroy prepares for a voyage to survey places still untouched by humans, during which he hopes to prove the literalness of the Bible's Book of Genesis doctrine that asserts that living things were created in a certain moment of time and have not changed since. At the recommendation of Cambridge botanist Professor Henslow, Fitzroy invites twenty-two-year-old Charles Darwin, who has been trained as a naturalist and a theologian, to accompany him aboard his ship, the H.M.S. Beagle . Darwin suggests that to accomplish Fitzroy's mission, they would need to find evidence of the great flood mentioned in the Bible. The captain agrees with Darwin's premise and asserts that all life was derived from Noah's ark. Although Emma Wedgewood, Darwin's cousin, is sorry to see him take this five-year journey, his father Robert and his uncle, Josiah Wedgewood, who have been dissatisfied with his unpromising academic progress, hope that he will establish his future career in the church. They are enthusiastic about the opportunity, as they believe he will afterward settle down. In 1832, the Beagle travels to Bahia Brazil, where Darwin is amazed by the types of creatures he sees. Taking note of the violent tendencies in nature, he theorizes that some animals perish and that only the strongest survive. On the ship, while dining, Darwin tells Fitzroy about his first sight of a monkey, who seemed to welcome him as a long-lost relative. When Darwin mentions that man has bones, similar to those of the orangutan, that are reminiscent of a tail, Fitzroy becomes offended and reminds him that man's immortal soul differentiates him from the animals. Darwin writes to Emma and Henslow about his theories and sends specimens home, which Henslow uses in his classroom. In 1833, while in Baha Blanca, Patagon, Darwin and his assistant, Sullivan, find the ancient bones of a huge, extinct animal. Pleased, Fitzroy claims that the bones prove the story of Noah, because the animal drowned, as it was too large to be brought aboard the ark. Darwin disagrees, saying that the animal died long before the flood is supposed to have occurred. Upon finding fossilized ocean fish high in the Andes Mountains, Sullivan wonders if they have proven the occurrence of the flood, but Darwin says that earthquakes account for their presence. When he and Sullivan find fossilized trees, Darwin explains that the trees once stood near coastlines, and were submerged when the sea rose. He says that the trees became petrified, because they absorbed the water's minerals and that earthquakes thrust them upward. While in the jungle, Darwin is bitten by an insect and becomes ill, but Fitzroy, instead of leaving him in a coastal town to recuperate, keeps him on board and personally nurses him back to health. Although they argue about their theories, they have respect for each other. In Ecuador, Moreno, the governor of the Galapagos Islands, invites Fitzroy and Darwin to dinner and explains that each island has a different kind of tortoise. Darwin's research bears out his information, as he finds that each island has an idiosyncratic environment containing flora and fauna related to those on the other islands, but that have evolved differently. For instance, Darwin finds that all of the islands contain finches, but on each island the beaks of the finches have developed differently, according to the survival requirements on their particular island. Darwin theorizes that when the finches arrived in the area, their beaks were alike, but changed over the centuries to adapt to the situation. Darwin comes to believe that animals, as well as humans, were not created in a single instant, but evolved over centuries. Although Fitzroy vehemently disagrees with him, Darwin encourages discussion. Fitzroy feels that the Bible specifically says God created man as "perfect" and in his own image. In contrast, Darwin believes that there is a vital spark of life that is divine, but that humans evolved over time, beginning in a state more primitive than the ape. When Fitzroy expresses concern for Darwin's immortal soul, the younger man counters that he hopes answers will bring one closer to God than blind faith. When Darwin returns to England at the age of twenty-seven, his work receives academic accolades and he becomes secretary of the Geological Society in London. He marries Emma and, after the birth of their first child, marvels at the baby's reflexes and the way he clings like a monkey. Several years later, the Darwins have six children and are living in Kent. He now feels certain that species change and develop over time when the strongest members mate with each other and pass their survival abilities to their offspring. When his daughter tells him that Emma fears that God disapproves of his ideas, Darwin tells her that he believes God is too wise to be offended by the truth. Colleagues are eager for Darwin to publish his theories about the natural selection process, but Darwin remains reluctant to offend those close to him. Asked by Darwin where he stands on the issue, Henslow responds that if Darwin's work destroys the idea of "simple faith," he will never forgive him. Later, Darwin receives a letter from a young scholar who has come to similar conclusions about the theory of natural selection and asks for his help in getting published. Darwin's friends urge him at least to publish his own papers at the same time, but Darwin worries about the effects on Emma and the children of having his work made public. Emma, who has been unable to express her thoughts directly to him, writes Darwin a letter, offering support but explaining her concern that they be together in heaven after death. Eventually Darwin decides to publicize his theories and invites Fitzroy, who is now an admiral, to visit, in order to tell him his plans. Fitzroy, who agrees with theologians who have calculated that the first day of creation was Sunday, 23 October 4004 B.C. at 9 a.m., urges Darwin to cease publication of his "obscene thesis." Grateful to Fitzroy for the opportunity he gave him, Darwin is troubled by their estrangement, but Sullivan points out that neither will ever see the other's point of view. The Origin of Species is published in 1859 when Darwin is fifty. People who misunderstand his theory are troubled and joke about it. When the British Association schedules a meeting at Oxford to discuss the publication and its possible consequences, Thomas Huxley represents Darwin, who is too ill to attend, and the Bishop Wilberforce of Oxford attends in order to speak against the work. The debate is lively and the audience quick to react. While Huxley affirms Darwin's work, Wilberforce proclaims that Darwin's ideas are an attack on God, and other people speak out according to their convictions. Greatly troubled, Fitzroy confesses his feelings of responsibility and guilt for inviting Darwin on the Beagle . Feeling betrayed by Darwin, Fitzroy says he will forever regret his part in the development of Darwin's heretical theories. Meanwhile, the ill Darwin accompanies his family to a local fair, where monkeys, dressed in clothing, are on exhibit. His children tell Darwin that they were told his work will not last, because it is not the whole truth. "Perhaps," admits Darwin, but he adds that what is more important is that others continue to seek the truth.