What is the omnivore's dilemma?
Basically, the omnivore's dilemma is "what should we have for dinner." Since human beings are omnivores, they can eat whatever they want. However, all the things that people might eat have implications both for the human beings themselves and for the planet on which we live. Having to take into account all these implications of what we eat creates the omnivore's dilemma.
The point of this book is to explore some of the implications of our food choices. Pollan uses the book to look at what we eat (for example, the fact that we eat so many things that are dependent on corn) and to discuss the ramifications of those choices. He looks at ways in which these choices affect our own health and he looks at the way they affect global trends such dependence on oil.
In short, then, the omnivore's dilemma is that omnivores must face that their food choices have major consequences.
The omnivore's dilemma is choosing what to eat since an omnivore can eat anything. This dilemma involves knowing what is safe to eat and what is safe to think. Omnivores need a variety of nutrients from a variety of sources. Therefore, humans don't have an innate ability to determine what is safe to eat. For instance, a koala eats only eucalyptus leaves so it has no dilemma; no doubt in what is safe to eat. Humans are born with tools, instead, to determine what is safe and what isn't.