Captivity
Captivity is the subject that Ishmael professes to teach. Having been raised in captivity, he considers it his area of expertise. He complicates the issue, however, by refusing to feel resentful of his captors. Largely, this complication reflects his larger feelings of pity for his captors; he believes that Mother Culture holds all of society captive. The planet's salvation comes in realizing that the “Taker Prison” holds most of us captive, and then working to dismantle those limitations.
Identity
Identity is a major theme, especially in the early portions of the novel. Ishmael's first given name is Goliath, which makes him aware of the importance and value of individual identity. However, he discovers how fully a name forces an identity on someone when he gets his new name, Ishmael. Eventually, in realizing that we need not simply accept the identity we are given, Ishmael discovers that social labels can be misleading. Titles and names are often simply another way in which Mother Culture serves to imprison us within society.
Evolution
Evolution, as Ishmael reasons, has stalled because of mankind’s actions. When people lived in the “hands of the gods,” evolution was inevitable, since mankind had to adapt to a changing world in order to survive. Now that man has completely taken control of the food supply, there is no need to change or adapt, and evolution is no longer taking place. The stakes of a such a cessation are high, however, since a lack of diversity could spell impending disaster for the planet.
Food
The human relationship to food is central to Ishmael's lesson. Quinn draws a contrast between the way food is handled and distributed in civilization, and how it is done in the wild. In the wild, food is plentiful and free for the taking, even though humans are subject to natural rules of population control, unable to expand past their means. Before "totalitarian" agriculture, earth was a paradise, with food free for the taking. As the Takers have forced agriculture on the rest of the world, the natural balance between food and population has been disrupted.
Religion
The treatment of religion is a controversial issue in Ishmael. Quinn essentially denounces prophets, claiming that they enforce arbitrary laws on how to live. By providing definitive models for life, prophets allow humans to ignore the more important laws, which are provided by nature. Religion gives humans license to do whatever they please with the world, blaming the gods for any natural problems. This approach is also reflected in Ishmael's treatment of the Genesis origin stories, which he considers allegories for the more important conflict between Taker and Leaver societies.
Philanthropy
Philanthropy is another controversial topic in Ishmael, especially as it relates to hunger and starvation around the world. In the novel, Ishmael suggests that philanthropy is part of the reason that population is expanding beyond earth’s capacity to hold it. Instead of moving food to feed starving populations, those populations should be moved to where the food is. Otherwise, they will continue to reproduce and create more starving individuals. Implicitly, Ishmael criticizes mis-considered philanthropy as another means through which Mother Culture enslaves us and distracts us from the more important questions.
Inherent Goodness of Man
Quinn debates the assumption that man is fundamentally flawed. Most religions attest that man is an imperfect being, but Quinn argues that these beliefs are simply justifications for our destructive behavior. On the contrary, he believes that man's fundamental flaw is simply that we do not realize how we "ought to live," even though the answer is clearly provided by nature. His implicit point is that man is capable of living in harmony with the Earth, provided we take responsibility for our own treatment of it.
Human Supremacy
Quinn argues against the idea of human supremacy on the planet. Humans, he claims, are the most evolutionarily advanced species on Earth, yet they are not entitled by nature to rule all other species. Instead, they are subject to the same “peace keeping law” that allows for competition, but not the elimination, of other species. By stressing the supremacy of humans, Mother Culture enables the behavior that is causing the Earth's imminent destruction. As counterpoint, Quinn argues that humans should afford other species the opportunity to evolve and develop, possibly to the point of self-awareness.
Civilization
Quinn argues that the need for agriculture and modern civilization is egregiously overvalued. This view is in line with the “new tribalist” movement that Quinn birthed. The new tribalists use the term "tribalism" not in its widely-used derogatory sense, but to refer to what they see as the defining characteristics of tribal life: an open, egalitarian, classless and cooperative community. For Ishmael, facilitating such a world requires us to first recognize that life before civilization was not a constant struggle for survival, but rather a harmonious co-dependence between all life. Quinn essentially calls into question the idea that modern civilization is the best and only way to live.
Mother Culture
Quinn introduces the idea of Mother Culture into Ishmael, as the driving force behind the accepted Taker theory of how things came to be in the world. In effect the antagonist of the novel, Mother Culture actively brainwashes us from birth, through everything including teachers, television, and money. That Quinn personifies this force is important, since it stresses that the ultimate danger comes not from any one person in power, but rather from a powerful force that humanity has created and to whom we are now enslaved. To break free requires us first to recognize the nature of our captivity.
