The Problem with CAFOs: Why They Are an Unsustainable System for Raising Livestock
What are CAFOs?
Three times a day you can make a world of difference, and that's by choosing what you put on your plate.
You may be (surprised/dismayed/motivated), to learn that one of the most important ways you can reduce your impact on the planet is to eat less meat and dairy and more plant-based food. Fact: the raising of livestock contributes 18% of humanity’s total impact on climate change, more than the emissions from cars, trains, and planes combined.
Animals do play an important role when incorporated into farms: they recycle nutrients by eating grass (not digestible by humans), insects (chickens can help keep down pests in this way), and food waste (especially pigs), and turn it into manure - a fertilizer for feeding food crops.
But in our current industrial agriculture system, most livestock is not raised on farms, but in CAFOs (Confined Animal Feeding Operations). In the 1970s, agricultural policies led to smaller farms consolidating into big monocultures (single crop). Animals were taken off the farm and squeezed into these animal “factories,” and instead of using manure for fertilizer we increased our usage of synthetic fertilizers. CAFOs allowed us to raise many more animals cheaply; we produce enough meat for every American to eat half a pound of meat a day, or 190 pounds a year. But it comes with steep ecological, health, and humanitarian costs.
 Steinfeld, H., P. Gerber, et al. (2006). Livestock's Long Shadow: Environmental Issues and Options. (Rome, Food and Agriculture Organization of the United Nations.)
The Meatrix is a short, informative, and funny cartoon exposing the truth about where our meat comes from.
Reason Why CAFOs Are Bad #1: they are inhumane
CAFOs aren’t farms at all, they’re animal factories. Hundreds of thousands of livestock or millions of chickens are grown in tight quarters where movement is restricted and the animals don’t have access to the outdoors. The tails are chopped off of pigs and the chickens’ beaks are clipped without receiving pain killers.
Furthermore, the animals did not evolve to eat the diet of corn and soy fed to them in CAFOs, and they certainly did not evolve to eat blood and chicken manure, which are sometimes added to factory farm animal feed to bolster the quantity and protein content of the meat.
Reason #2: CAFOs are a human health hazard
We eat what our meat ate, and what our CAFO produced meat ate is nothing good.
Disease spreads easily in the crowded unsanitary conditions found in CAFOs, so animals are routinely fed antibiotics even though they aren't sick. According to the Department of Agriculture, 80% of all antibiotics in the US are given to farm animals, most of them healthy and not needing drugs!
This overuse of antibiotics can create "superbugs" that pose serious health hazards. When bacteria are exposed to small doses of antibiotics over a long period of time, they evolve and become resistant, turning these antibiotics useless. These strains of "super-bacteria" can reach the human population and spread disease when we eat infected meat or drink water that has been contaminated by CAFO pollution.
Reason #3: CAFOs make a lot of waste
Historically animal waste was looked at as a precious resource that provided fertility to the farm. By removing the animals from the farms and increasing livestock production, this fertilizer turns into waste, and CAFOs produce enormous amounts: fully 130 times more animal waste than human waste is produced, or 5 tons of animal waste for every US citizen! The urine and feces are mixed with water and kept in open ponds called “liquid manure lagoons,” which occasionally leak into the surrounding groundwater systems and contaminate our drinking supply and natural ecosystems. The manure lagoon sludge may also be sprayed on crops, but this is often done excessively and turns into runoff that pollutes natural water systems.
Reason #4: CAFOs contribute to climate change
As we said, livestock production contributes about 18% of anthropogenic greenhouse gas emissions.
This is largely because it requires fossil fuels to grow the massive amounts of grain that is fed to livestock in CAFOs; cattle must be fed 10 to 16 pounds of grain to result in just one pound of beef! Eating higher on the food chain is an inefficient use of resources when you raise livestock on food that could have been fed directly to humans. One study found that it took 35 calories of fossil fuel energy to produce one calorie of food energy on a cattle feedlot.
 From Roberts, P. (2008). The End of Food. Boston, Houghton Mifflin Company. p. 293. See also Lappé, F. M. (1991). Diet for a Small Planet. New York, Ballantine Books.
Sustainable Alternatives: less meat, or organic, pasture raised meat
No doubt about it, if everyone in the world ate as much meat as Americans...well, we'd be sitting in a manure lagoon right about now. It's absolutely necessary that we reduce our consumption of meat - the experts say to just a few times a week, and in smaller portions.
When you do choose to eat meat, make it quality stuff: buy from small, organic, pasture raised or free range meat operations. This kind of product you're more likely to find at farmers markets than grocery stores.
Organically raised livestock are fed organic grains and feed, and have not received the heavy doses of antibiotics that CAFO raised animals were given. These high doses of antibiotics can create drug-resistant bacteria that can be passed on to humans through the consumption of non-organic meat, and thus contribute to the spread of disease. 
Organic meat production can also significantly reduce GHGs. A 2006 life cycle assessment of three modes of Irish beef production – conventional (CAFOs), pasture-raised, and organic – found that both pasture-raised and organic systems generate fewer GHGs than the conventional system, with the organic system producing 17 percent less than conventional.  Organic and/or environmentally sustainable farming systems can also reduce nitrous oxide emissions by avoiding overproduction of manure because animal stocking densities are typically limited to the land available for manure application.
 Walsh, Brian. 2009. Getting Real About the High Price of Real Food. Time. August 21st . http://www.time.com/time/magazine/article/0,9171,1917726,00.html
 Casey JW and Holden NM. 2006a. Greenhouse gas emissions from conventional, agri-environmental scheme, and organic Irish suckler-beef units. Journal of Environmental Quality 35:231-239.
 Kotschi J and Müller-Sämann K. 2004. The Role of Organic Agriculture in Mitigating Climate Change: A Scoping Study. Bonn, Germany: International Federation of Organic Agriculture Movements.