Chickens stand in their cages at Maine Contract Farming, Thursday, July 1, 2010, in Turner, Maine. New England's largest egg farm is taking steps to show it has improved care of its hens after reaching a settlement over allegations its birds were mistreated. (AP Photo/Robert F. Bukaty)

Earlier this month, John Clifford, the Chief Veterinary Officer for the U.S. Department of Agriculture, said something many people might not like.

At a hearing organized to discuss the impact of the avian flu, which has affected nearly 50 million birds in the United States, he suggested that farmers could have killed infected chickens and turkeys more efficiently by shutting off ventilation systems at poultry barns. "It's the fastest way and probably the most humane way to take care of this," Clifford said during the hearing, which was held on July 7.

Many disagree—chief among them, the Humane Society (HSUS), which likened the method to "baking the birds to death en masse" in a letter sent to the USDA on Thursday. The animal rights group holds that there are other ways to depopulate flocks that cause less pain.

Paul Shapiro, HSUS's vice president, said that several other organizations, including the American Veterinary Medical Association, World Health Organization, and the USDA itself, don't recommend killing chickens this way. "It's very troubling that the possibility is even being discussed," he said. "It can take as long as three hours for the birds to die."

It's also very telling. The mere fact that the method is being proposed—by the U.S.'s chief veterinary officer no less—is a testament to how thoroughly the avian flu has terrified the poultry industry. The crisis has given rise to a necessary but uncomfortable question: What is the most responsible way to kill millions of infected birds at once?

The only method of euthanasia that is currently approved by the USDA for egg-laying hens is by exposure to carbon dioxide gas, which puts the birds to sleep before killing them. The method most commonly used for turkeys and broiler chickens involves the use of a water-based foam, which kills the birds within approximately one minute.

The problem with these methods, Clifford explained during the hearing, is that a farmer can use them to kill only so many chickens at once.

"You can only take out about 100,000-plus birds a day out of one house and C02 those," he said, when there are farms with millions of birds that have to be euthanized.

"We need to allow all tools to be used in the toolbox," Clifford said. "Any delay in putting birds down puts more virus into the environment."

Ventilation shutdown, he reminded, can be used to kill as many birds as fit in a single barn.

Shapiro sees it differently. "The only reason anyone would want to do a ventilator shutdown is simply for the ease and the cost," he said. "All it takes is flicking a switch.

All things being equal, cutting off ventilation to more than a million birds at once is largely considered a crueler way to kill chickens. Without ventilation, temperatures rise, air becomes still, and chickens suffer; their organs eventually fail, they become lethargic, and they eventually die of either heat or suffocation or both. It's the sort of thing that happens by accident—like it did earlier this year at a battery farm in China, where some 6,000 chickens died, rather than by choice.

But these are not normal circumstances.

Poultry farms across the United States have been decimated by the avian flu, which was first detected in the country last December. Each time an infection has been discovered, the entire surrounding flock has had to be killed. And some of those flocks have been enormous—a single farm in northwest Iowa, for instance, had to euthanize almost 4 million chickens.

The flu, which has slowed in recent weeks, has already caused egg prices to double, and there's a fear the virus could return with a vengeance in this coming fall or spring, when temperatures dip. If it does, the challenge for the industry will be to manage it better than it did this past spring. And that means moving much faster to stunt the spread of the disease.

"The main thing is figuring out how to deal with chicken houses where there are so many birds, and there’s a real value in depopulating quickly," said Dustin Vande Hoef, the communications director for the department of agriculture in Iowa, where the bird flu has affected more birds than any other state. "I think they're just evaluating different options."

Vande Hoef explained that farms in Iowa where the flu has been identified reach out to the local department of agriculture, but that the USDA is in charge of everything thereafter, which includes the depopulation of infected flocks. Ultimately, the federal body will have the final say on whether ventilation shutdown is the optimal way to contain the virus if it breaks out once again and should therefore be used.

And that's exactly what has animal welfare activists so worried.

"Avian influenza is a serious problem that merits a serious response, but not one that causes the unnecessary and grotesque suffering of potentially millions of animals," the HSUS said.

Shapiro reiterated the stance by invoking a more immediate analogy. "Think of all the dogs and babies that have accidentally been left in cars over the years," he said. "They suffocate, they slow-burn alive—it's a terrible thing. Now imagine multiplying that by hundreds of thousands or even millions of animals. Does that sound humane?"