An Indiana-based company, set up by two professors from Albany Medical College, claims to have an effective alternative. You don't have to go further than your kitchen sink to understand the science.
Their company, Waste Reduction by Waste Reduction Inc., says that by using the kinds of chemicals that go into a drain-clearing product such as Drano, they can safely break down the suspected disease-causing proteins, known as prions.
Prions are miss-shaped proteins believed to cause bovine spongiform encephalopathy, or mad cow disease.
They eat at the brain tissue of cattle by forcing proteins performing other jobs to take their shape, resulting in a chain reaction.
Incineration has been the popular method to destroy the carcasses of afflicted cattle but researchers say tests have revealed that the prions - like the mythical phoenix - survive and can emerge from the ashes.
Waste Reduction claims its pressure cooker-like machine, known as a digester, not only breaks prions into harmless amino acids but emits no toxic gases and operates at a fraction of the cost of an incinerator.
The US Department of Agriculture bought a machine and started testing it in November, a month before the first US case of mad cow disease was discovered in a dairy cow in Washington state.
The Wisconsin Veterinary Diagnostic Laboratory in Madison is working with the USDA to test the digester on deer carcasses infected with a prion disease similar to mad cow.
"In the inactivation of abnormal prions, the digester has a leg up over incineration and we are able to do it at a third of the cost," Robert Shull, director of the Wisconsin laboratory, told Reuters.
The United States jolted the world meat industry on December 23 by announcing the first case of mad cow disease in US history.
The news rocked the cattle industry, the single largest sector of US agriculture, as two dozen countries halted US beef imports, which account for about 10 percent of annual production and $3.2 billion in sales.
USDA says the infected cow came from Canada. But it slaughtered about 450 bull calves in Washington state that were linked to the infected dairy cow as it strives to convince consumers that US beef is safe.
The agency has also announced sweeping measures to tag and test US cattle and other steps to boost confidence. Officials say the digester may help that process.
"At this point the USDA plans to hold test animals until we get test results back," said Linn Wilbur, a USDA veterinary surgeon.
"What we are anticipating is that the carcasses will be kept in coolers and, if we found any positives, they will go through the digesters, and the negatives will go through the normal rendering process," he said.
Rendering is the process of reducing the remains of cow carcasses into smaller pieces to be used in animal feeds.
In the digester, a big stainless steel container, a solution of sodium or potassium hydroxide is poured over the carcass. Heat is applied and the chemical reaction, which also produces heat, then reduces the mass into a slurry for tests.
Through this method, proteins, nucleic acids and infectious micro-organisms are converted into a sterile solution of sugars and small peptides, which are chains of amino acids that in turn form proteins.
Operating costs for the digesters, about 25 cents per pound of carcass, are lower than that of incinerators, which can cost 80 cents to a $1 a pound due to high fuel costs.
"The science of this method has been known for quite some time," said Giuseppe Legname, a neurology professor at the University of California San Francisco. Contaminated lab animals are frequently given a similar chemical wash under the influence of heat and pressure, he said.
"They have merely patented the process," Legname said of Waste Reduction by Waste Reduction.