As Pollan points out, there are alternatives to the government subsidized and sanctioned food system. His primary focus is on Joel Salatin's Polyface Farm, one of the world's leading models for a self-contained, sustainable, local food system. In Salatin's model each animal is given the right to act on its own instincts, eat the food God designed it to eat, and work in symbiosis to not only create meat and eggs, but to invest in the land itself.
Cows are moved to new pasture each day, and three or four days later are followed by chickens. The chickens eat the grub larvae in the cow patties, and in doing so spread the cow patties which fertilize the pasture. The chickens fertilize the pasture themselves with their own manure. The managed grazing and animal manure create a rich, healthy topsoil which in turn supplies more healthy, nutritious grass for the cows to come back and feed upon. He also uses pigs to aerate soil and compost. Salatin doesn't have to worry about sick animals because they are getting the diet God intended their bodies to eat, and consequently their immune systems are healthy.
The system is actually humane and healthy for all involved. There is no pollution, and the only feed introduced into the farm is corn for the poultry. The result is meat that exceeds the nutritional quality of its feedlot competitors. Pollan explains,
"…meat of grass-fed livestock not only had substantially less fat than grain-fed meat but that the type of fats found in grass-fed meat were much healthier. (Grass-fed meat has more omega 3 fatty acids and fewer omega 6, which is believed to promote heart disease; it also contains betacarotine and CLA, another ''good'' fat.) A growing body of research suggests that many of the health problems associated with eating beef are really problems with cornfed beef. In the same way ruminants have not evolved to eat grain, humans may not be well adapted to eating grain-fed animals. Yet the U.S.D.A.'s grading system continues to reward marbling -- that is, intermuscular fat -- and thus the feeding of corn to cows."
This alternative food system is typically local, as it not well suited for industrial sized operations. Industrial feedlots are unnatural, full of pollution, they rape the health of the land, and are not focused on health or nutrition, but their purpose is to provide mass quantities of cheap meat.
Pollan points out in the book that the typical American household spends approximately 10% of its discretionary spending on food, half of what it once was. Americans are conditioned to think that all food is equal, there is no such thing as a "better egg" or "better beef." Grocery stores advertise the best price on the same foods as their competitors. Our food system is meant to be cheap, not nutritious. This is a paradigm shift that is difficult to overcome. After all, our food is subsidized by the government, not only directly through farmer subsidies, but by tax breaks, tax incentives, and lack of accountability to produce a healthy product. These are unseen, unconsidered costs that cloak the costliness of our food, not to mention the costs of obesity, heart disease, diabetes, cancer, and so on.
So the fact that the alternative food system which receives little or no subsidy from the government costs more than the conventional system. But again, consider the costs of the unintended consequences of the conventional system.
My family has just joined a CSA (community shared agriculture) for meat. We'll receive eggs, chicken, beef, and pork from a local family farm that follows the ideas of the alternative, clean food system.
Our first experience with the alternative system was with a whole chicken that was raised on a pasture. While we noticed little difference in the taste, the chicken itself was unlike any other I've encountered. The bones, tendons, and ligaments were considerably stronger than any I've ever carved. It was actually difficult to remove the leg from the body! We have also tried eggs, which, as advertised, had a different color yolk. I encourage you to study these issues and learn more for yourself.