Fate and Prophecy
Dune explores themes of fate and prophecy, seemingly occupying a middle ground as to whether fate is real or free will reigns. On the anti-fate side, there's the Missionaria Protectiva: everything about Paul's interaction with the Fremen, from earning their acceptance to becoming their leader, is thanks to superstitions spread by the Bene Gesserit to protect themselves hundreds of years ago. The "prophecies" that Paul fulfills are manufactured by the Bene Gesserit. The future sight that Paul possesses isn't because he's the messiah; it's thanks to extensive training and exposure to spice. Paul's story, and the Bene Gesserit narrative in general, can be read as a crafty generations-long capitalization on resources, power, and an effective eugenics program.
On the pro-fate side, Paul can see the avenues of the future, having prescient dreams before he's even tested by the gom jabbar. He fulfills Fremen prophecies without knowing about them, seemingly impossibly, like his choice of Muad'Dib as a name without knowing the word "muad'dib," just having seen desert mice. The sandworm that he rides is the largest one in memory. His actions do result in a religious war in his name, as he predicted. By trying to prevent that jihad, he ensures that it will happen, which seems to indicate that fate will run its course regardless of free will.
Though later books in the series explore these concepts much further, Dune lays the groundwork for an interesting look at fate and prophecy—and whether a foretold hero who isn't actually foretold is still the chosen one.
Fear
Every character in Dune (with the exception of Alia, who's repeatedly called strange for this reason) is afraid of something. The Emperor fears the Landsraad; Jessica fears for Leto and Paul's lives; the Reverend Mother Gaius Helen Mohiam fears Alia and Paul; even the sandworms, mighty makers of the desert, are driven by fear for their lives, their young, and their resources. In a book preoccupied with ecology (which is explored as a theme below), the relationship between an organism and its environment is paramount, and fear is clearly a driving factor in every character's relationships.
Dune features a recurring litany against fear, which Paul, Jessica, and presumably other Bene Gesserit use as a mantra to control their natural fear response. Those who are governed by fear are destroyed by it (perhaps this is something that separates "human" from "animal," another theme discussed below). Using tools like the litany, characters allow their fear to pass through them, being strengthened by it instead of overwhelmed. The only non-Bene Gesserit character to display such a tool is Chani, who is able to "submerge her fears in thought," perhaps indicating that the Fremen have a fear-mastering tool similar to the litany but much less formal in practice.
Leadership
Dune follows many characters that have made an impact on history—Duke Atreides, Baron Harkonnen, Paul-Muad'Dib, Stilgar—and in doing so explores a theme of good leadership. The Duke tries to teach his son Paul how to lead men, and while his lessons help Paul, Paul's leadership is also shaped by the power of the desert and the lifestyle of the Fremen. Fremen leadership is passed down through combat and is only viable if it's for the betterment of the tribe—a harsh contrast to Landsraad Houses like the Harkonnens, who are led by a sadistic, greedy inherited leader who's certainly not for the betterment of his tribe.
While Paul-Muad'Dib is admired as a good leader, Dune begins to explore the risk of extreme fanaticism associated with a powerful religious/political leader. Later books in the series will explore this further—good leadership is not always good.
Scarcity
At a luxurious state dinner in Arrakeen, Liet-Kynes explains to Paul the Law of the Minimum: Growth is limited by that necessity which is present in the least amount. This means that the least favorable condition controls the rate of growth in any given situation. On Arrakis, water is the least-present necessity, so it determines how quickly things can grow and develop.
This theme—scarcity—can be seen throughout the novel, and not just in the obvious water shortage of the Fremen. Various characters struggle with their own Law of the Minimum. Jessica perceives a scarcity of allies as Paul's primary challenge after the fall of House Atreides. Thufir Hawat, poisoned, has to follow the commands of Baron Harkonnen, since the antidote to that poison is now his least-present necessity. Paul manipulates the least-present necessity for the Guild (spice) and uses it as leverage to become the Emperor. Paul's understanding of the Law of the Minimum helps him expand his power. By explaining scarcity and then demonstrating it repeatedly to the reader, Herbert encourages consideration of the ecological rules that govern daily life, and how least-present resources can be protected.
Animal versus Human
One of the primary questions pitched by Dune centers on the relationship between animal and human, and what that relationship really is. When the Reverend Mother tests Paul with the gom jabbar, she "sifts people to find humans," separating them from animals. Baron Harkonnen frequently thinks of humans as animals, either predators or prey, and perhaps this manner of thinking is the source of his sadism. In Paul's final battle with Feyd-Rautha, Gurney calls Feyd a "Harkonnen animal," to which Paul replies that "this being has human shape...and deserves human doubt."
These are merely a few examples of Dune's preoccupation with the line between human and animal, and though the novel seems at some points to suggest that humans are superior to animals, it contradicts this as well. If Baron Harkonnen is any indication, thinking of some humans as animals—and of animals as disposable—is a pathway to cruelty.
Ecology
Dune explores ideas drawn from ecology, a branch of science that looks at the relationship between organisms and their environment. Frank Herbert's son, Brian Herbert, writes in the afterword to Dune that Herbert understood ecology as "the science of understanding consequences." The novel features literal ecologists, like Dr. Kynes and his remembered father, and it depicts one part of a generations-long attempt to use finite resources to create a paradise on Arrakis. Fremen use dew collectors and expend enormous resources (both water and spice) to make minuscule changes to the surface of Arrakis, hoping that in generations to come, that small change will have a great consequence.
Other parts of Dune look at the interaction between organisms and environment as well—for example, the harsh prison planet Salusa Secundus is where men are trained to become Sardaukar by their harsh environment. Caladan, a water planet, is a paradise for human life, but it doesn't create "strong organisms" the way that Arrakis or Salusa Secundus can.
Gender
Remarkably for a novel written in the 1960s, when the field of popular science fiction was even more male-dominated than it is today, Dune explores concepts of gender. The Bene Gesserit, a purely female society, have been controlling human breeding for thousands of years, looking for the one man who can see into both "male" and "female" past and futures: the Kwisatz Haderach. Paul is able to do this, and he sees the dark place within where no Bene Gesserit can go. He describes it as the ancient forces of giving and taking; he explains that women have more access to giving, and men have more access to taking. He says that he stands at the fulcrum, unable to give without taking and vice versa. The book takes an essentialist view of sex and gender, and it portrays a rigid society dominated by class and function; however, in Paul and sometimes in others, the firm lines of their sexist, eugenicist, and violent world is questioned.
The ending line of the novel is delivered by Lady Jessica. She talks to Chani about how while they might technically be concubines, history will call them wives. While this might seem like a random note for the end of Dune, it allows the reader to focus not on the small events on the climax, but on the overarching themes of the novel: what we preserve, and how; who we respect, and why; and how to look at the bigger picture as well as the more intimate details.
