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At a remarkable 2004 conference, the Food and Agriculture Organization of the United Nations, the World Health Organization and the World Organization for Animal Health (OIE) put their tremendous resources together to evaluate the available information on "emerging zoonotic diseases" or those spread by humans-to- animals and animals-to-humans.

At the time of the conference, H5N1 and SARS topped the list of feared emerging zoonotic diseases. Today, the H1N1 swine flu would be the pathogen enemy No. 1.

The scientists distinguished between "primary risk factors" for zoonotic diseases and mere "amplification risk factors," which affect only the rate at which a disease spreads. Their examples of primary risk factors were "change to an agricultural production system or consumption patterns." What particular agricultural and consumer changes did they have in mind?

First in a list of four main risk factors was "increasing demand for animal protein," which is a way of saying that demand for meat, eggs, and dairy is a "primary factor" influencing emerging zoonotic diseases. This demand for animal products, the report continues, leads to "changes in farming practices." Lest we have any confusion about the "changes" that are relevant, poultry factory farms are singled out.

Similar conclusions were reached by the Council for Agricultural Science and Technology, which brought together industry experts and experts from the WHO, OIE and USDA. Their 2005 report argued that a major impact of factory farming is "the rapid selection and amplification of pathogens that arise from a virulent ancestor (frequently by subtle mutation), thus there is increasing risk for disease entrance and/or dissemination."

Breeding genetically uniform and sickness-prone birds in the overcrowded, stressful, feces-infested and artificially lit conditions of factory farms promotes the growth and mutation of pathogens. The "cost of increased efficiency," the report concludes, is increased global risk for diseases. Our choice is simple: cheap chicken or our health.

Today, the factory farm-pandemic link couldn't be more lucid. The primary ancestor of the recent H1N1 swine flu outbreak originated at a hog factory farm in America's most hog-factory-rich state, North Carolina, and then quickly spread throughout the Americas.

It was in these factory farms that scientists saw, for the first time, viruses that combined genetic material from bird, pig and human viruses. Scientists at Columbia and Princeton Universities have actually been able to trace six of the eight genetic segments of the most feared virus in the world directly to U.S. factory farms.

Perhaps in the back of our minds we already understand, without all the science, that something terribly wrong is happening. We know that it cannot possibly be healthy to raise such grotesque animals in such grossly unnatural conditions. We know that if someone offers to show us a film on how our meat is produced, it will be a horror film.

We perhaps know more than we care to admit, keeping it down in the dark places of our memory -- disavowed. When we eat factory-farmed meat, we live on tortured flesh. Increasingly, those sick animals are making us sick.

The opinions expressed in this commentary are solely those of Jonathan Safran Foer.