But, he said, serious respiratory cases might be easier to detect if soldiers had a record of their breathing capacity beforehand.
"Everybody that is deployed should get a pulmonary function test before deploying, said Miller. "If we have baseline breathing test on everybody we were seeing, then that would limit the amount of biopsies."
Weakley said his wife was the first to notice that something was wrong. Weakley recalled calling her within a week of his first exposure to the burn pits in Pakistan.
"She wondered why I was having a tough time talking," said Weakley, who was not one of the cases reported by the Vanderbilt researchers. "She recognized something was wrong over the phone."
Although Weakley felt short of breath, he chalked it up to exhaustion from long hours and little sleep.
"I was trying to decipher the reality and the psychological," said Weakley.
At the time, Weakly said, doctors told him he may have asthma, a common diagnosis among many soldiers deployed to Iraq and Afghanistan.
"When I got home [in July 2005], my wife from the get-go said I don't care who you see, something is wrong," he said. "It didn't hit me until I got home."
Post-deployment lung diseases like Weakley's sometimes mirror less serious respiratory infections, because it's unclear what's causing the condition, said Miller.
"There's pigment in the lung area, but we don't know exactly what that chemical or exposure is yet," he said.
Miller said he is now working with Weakley's pulmonologist at National Jewish Health in Denver, Dr. Cecile Rose, who will examine the biopsies to find the exact chemical that is causing the condition among soldiers.
Weakley, who could once run two miles in less than 13 minutes, found that he had to stop and catch his breath. In 2008, after five deployments in more than 20 years of service, Weakley received a medical discharge from the Army.
Now Weakley said he struggles to keep up with his 8-year-old and 11-year-old children.
"Before I left, I could do anything and everything," said Weakley. "I never thought I would have to brush the idea of a lung transplant."