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Much of the speculation about Steve Jobs’ rail-thin appearance at the unveiling of the new iPhone on June 9 has tended to be all or nothing.

Either his cancer has returned or he is recovering from a bout with a “common bug,” as his spokeswoman told the Wall Street Journal on Tuesday. “That’s all there is to it,” she said. (The talk may have unnerved investors a bit: Apple (AAPL) shares fell 4.1% on Thursday and another 2.4% by midday Friday.)

But this is not the first time Jobs’ appearance has raised concerns about his health, and the “common bug” doesn’t explain the weight loss that’s evident in a review of his keynote videos over the past few years.

There’s another possibility, one that is consistent with both Jobs’ medical history and the changes in his appearance. It stems directly from the type of cancer for which he was treated four years ago and the nature of that treatment.

In 2003 Jobs learned that he had a malignant tumor in his pancreas – a large gland behind the stomach that supplies the body with insulin and digestive enzymes. The most common type of pancreatic cancer – adenocarcinoma – carries a life expectancy of about a year. Jobs was lucky; he had an extremely rare form called an islet cell neuroendocrine tumor that can be treated surgically, without radiation or chemotherapy.

As Fortune reported in a March 5 cover story, (“The trouble with Steve Jobs“), Jobs tried various alternative therapies for nine months before the tumor was taken out on July 31, 2004, at the Stanford University Medical Clinic in Palo Alto, near his home.

“This weekend I underwent a successful surgery to remove a cancerous tumor from my pancreas,” Jobs wrote in an e-mail to Apple’s staff the next week. “I will be recuperating during the month of August, and expect to return to work in September.”

What Jobs didn’t tell the staff was that the operation he had undergone had radically rearranged his digestive organs and would permanently change the nature of his health.

The Fortune article reported – and Apple has not disputed – that his surgery was a variation on the Whipple procedure, or a pancreatoduodenectomy, the most common operation for pancreatic cancer.

Nobody who has a Whipple is ever quite the same.

The Whipple procedure, named for Allen Oldfather Whipple, the American doctor who perfected it in the 1930s, is a complex, Rube Goldberg-type operation in which surgeons remove the right-most section, or “head,” of the pancreas – as well as the gallbladder, part of the stomach, the lower half of the bile duct, and part of the small intestine – and then reassemble the whole thing in a new configuration. The severed surfaces of the stomach, bile duct, and remaining pancreas are stitched to the small intestine so that what’s left of the pancreas can continue to supply insulin and digestive enzymes.

These before-and-after diagrams, reposted with permission from the Mayo Clinic website, will give you a feel for what’s involved (e-mail subscribers click here):

A German study comparing the long-term effects of two variations of the Whipple procedure on 104 patients found an increase in diabetes and various degrees of gastric acid reflux, stomach ulcers, oily bowel movements, intolerance toward larger meals and aversion to certain foods. (Annals of Surgery, 2005)

Along with the digestive problems, patients often lose 5% to 10% of their body weight after the procedure. Weight stabilizes within the first year or two for the vast majority of patients, says Dr. Dilip Parekh, chief of tumor and endocrine surgery at the University of Southern California, who has performed more than 100 Whipple procedures. “There is a small group of people who tend to have persistent problems with weight loss and loss of energy and you often you are not able to pinpoint why,” he says. “But if they stay active and manage their nutrition well, there is no reason for them not to live a normal life.”

Jobs has never spoken publicly about what life is like after the Whipple, so we can’t be sure that he has any of the post-operative problems associated with the procedure. But they would go long way toward explaining why he looked the way did on Monday. And none of them would indicate that his cancer has returned, or that his capacity for work is diminished. Post-operative guides for patients suggest that there will be lifestyle changes but that they need not be drastic. And a survey of patients at Johns Hopkins Hospital found that the overall quality of life of long-term survivors of the surgery is nearly comparable to that of healthy people.

Apple was invited to comment on this story, but has so far declined.