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So there's this young guy named Martin Arrowsmith and he really loves pure science, meaning that he loves the quest for truth. He thinks curing disease and making life more comfortable is all well and good, but it's capital-t Truth that really interests him. Unfortunately, the world around him doesn't care about Truth as much as it cares about fancy products, money, and cures for disease.
When he gets into medical school, Arrowsmith is charmed by a crabby old professor named Max Gottlieb, a man who cares about science purely for its own sake. All of Martin's medical classmates, though, are much more interested in making a lot of money once they become doctors. Martin constantly criticizes them for being "commercialists" and loses more than a few friends in the process. By the end of medical school, though, he realizes that he'll have to compromise a little if he ever plans on making a living.
After becoming engaged to two women at once, Martin marries a girl named Leora and settles in her hometown of Wheatsylvania, South Dakota. Little does Martin know, though, that his scientific point of view will end up making a lot of people hate him. He eventually has to pull up stakes and move to another town with Leora after he alienates practically everyone in her hometown.
Martin's next gig doesn't go so well, either. He knows his science, but he doesn't play politics well enough to hold a good job. As a Director of Public Health, he shuts down people's businesses for being hazardous and ends up making powerful enemies. Again, he's driven out of his town by people who aren't interested in hearing the truth unless it benefits them in some way. Now without a job, Martin gets a letter from his former mentor, Max Gottlieb, inviting him to become a scientist at the McGurk Institute in New York. It sounds like a dream job where Martin will be able to pursue his scientific interests without having to worry about money or political pressure…
But that would all be a little too convenient, wouldn't it? During his time at McGurk, Martin discovers a type of organism that can cure strep throat and all kinds of other diseases. Unfortunately, he's so dedicated to good science and due diligence that he drags his feet on publishing his findings and eventually gets beaten to the punch by a guy in France. He ends up losing his chance for money and recognition, and his bosses become unhappy with him.
The only way for Martin to recover his bosses' good favor is to travel to a Caribbean island that has become infected with plague and test some of his institute's vaccines to see if they can stop the disease. The only way to test the vaccine, though, is only to treat half of the infected population. In other words, Martin has to let half of the island's inhabitants die in order to determine whether his vaccine really works. Along the way, his wife Leora dies of plague and Martin loses his resolve. He ends up giving everyone the vaccine out of pity and returns home with nothing to show for his efforts but a dead wife.
With his wife gone, Martin marries a young, rich woman who takes him to a bunch of upper class parties. But he can't stand hanging around superficial people, and he eventually retreats to a homemade lab in Vermont to spend the rest of his life pursuing science for its own sake. He abandons both his wife and his new son in the process. At the end of the day, there's nothing that can compete with science for his heart.