Despite how mad cow disease (bovine spongiform encephalopathy) and avian influenza have been in the news for years, I've never seen any coverage that explicitly makes the connection between industrial factory farming and the emergence of these diseases. While things like close human-animal contact in the developing world seem to be important when considering outbreaks of influenza, it is entirely a product of an industrial farming system that turns cows into cannibals that BSE has emerged as a threat to human health at all. BSE is a prion illness that spreads between cows when they are fed portions of the brains and spinal cords of their dead brethren. The fact that it keeps cropping up suggests that this is continuing to happen, though it is possible that BSE cases are the result of infections dormant since before bans on feeding ruminant byproducts to cows.
I don't doubt that if people were aware of the realities of where the bulk of humanly consumed meat comes from, there would be a lot more people wary about eating it - on environmental, health, and hygienic grounds. On the disease front, people should at least acknowledge the dangers inherent to keeping thousands of closely packed animals together, all of them on hormones and other drugs to make them grow faster. Additionally, the constant use of antibiotics to try to suppress disease among populations of factory farmed animals contributes to the emergence of bacterial strains resistant to antibiotics. Food animals have also been genetically weakened over time as they have been both 'standardized' so as to produce single definitive variants and bred for qualities like the quantity of a certain kind of meat they produce, rather than being able to resist diseases or even function on their own.
A lot of people seem to take the attitude that "given that I want to eat meat, and I am dimly aware that learning about where it comes from may put me off it, I will resist learning about where it comes from." While psychologically understandable, such approaches do not live up to the standard of good sense, or due diligence with regards to how we behave as individuals and societies.
This entry is also posted on my blog, at: http://www.sindark.com/2006/04/diseases-and-factory-farming.html