In 1822 a musket went off by accident at a fur trading post on Mackinac Island, in what is now Michigan, and a young French Canadian voyageur named Alexis St. Martin took the blast in his side. He survived, but the wound healed into a permanent opening into his stomach. The army surgeon who treated him, William Beaumont, spent years using that opening as a window. He lowered food on silk strings into the stomach and pulled it out to see how far it had broken down, and he drew off stomach juice and found it could dissolve meat in a glass jar. Beaumont showed that stomach juice digests food chemically, even outside the body. His work also raises hard questions. St. Martin, who could not read, signed a contract binding him to Beaumont's service, and historians still debate how freely he took part. Modern rules of informed consent exist partly because of cases like his.

Breaking food down

Digestion has two parts. Mechanical digestion, such as chewing and churning, breaks food into smaller pieces. Chemical digestion uses enzymes, proteins that split large food molecules into small ones the gut can absorb. It starts in the mouth: amylase in saliva begins breaking starch into sugars, which is why bread chewed for a long time starts to taste sweet. When you swallow, waves of muscle contraction called peristalsis push food down the esophagus, strongly enough to work even if you are upside down.

The stomach

The stomach lining releases hydrochloric acid, making its contents about as acidic as lemon juice or stronger. The acid kills many microbes and unfolds proteins so the enzyme pepsin can start cutting them apart. A thick layer of mucus keeps the stomach from digesting itself.

For decades doctors blamed stomach ulcers on stress and spicy food. In the early 1980s two Australians, the pathologist Robin Warren and the physician Barry Marshall, found a spiral bacterium, Helicobacter pylori, living in the stomachs of ulcer patients. Many experts were reasonably skeptical, since few believed bacteria could thrive in such acid. In 1984 Marshall drank a culture of the bacterium and developed stomach inflammation. Further studies confirmed that most stomach ulcers are caused by this bacterium and can be cured with antibiotics. The pair won the Nobel Prize in 2005. Some ulcers do have other causes, especially regular use of painkillers such as aspirin and ibuprofen.

The small intestine

Most digestion and nearly all absorption of nutrients take place in the small intestine, a tube several meters long. The pancreas pours in enzymes that work on carbohydrates, proteins and fats, along with bicarbonate that neutralizes stomach acid. The liver makes bile, stored in the gallbladder, and bile breaks fat into tiny droplets so enzymes can reach it, much as dish soap breaks up grease. The inner wall is folded into millions of fingerlike villi, each covered in microscopic microvilli, giving an enormous surface for absorption.

Sugars and amino acids pass into the blood, and blood from the intestines goes first to the liver through the hepatic portal vein. The liver stores some nutrients, processes others and neutralizes many toxins before the blood reaches the rest of the body. Digested fats take a different route, entering lymph vessels before joining the blood.

The large intestine and its residents

The large intestine absorbs water and salts and forms what remains into feces. It is also home to trillions of bacteria, the gut microbiota. They ferment dietary fiber that our own enzymes cannot digest, producing useful fatty acids, and some make vitamin K. A widely repeated claim said bacteria outnumber human cells ten to one, but a 2016 estimate found that bacterial cells roughly equal human cells in number. Research on gut microbes is booming, and some links to health look strong, but many popular claims run ahead of the evidence.

What food provides

Food supplies energy and building materials. Carbohydrates and proteins each provide about 4 kilocalories per gram, while fat supplies about 9 kilocalories per gram, more than twice as much. Proteins also provide amino acids for building and repairing tissue. Vitamins and minerals are needed in small amounts, and lacking them causes specific diseases: scurvy from too little vitamin C, rickets from too little vitamin D. Fiber feeds gut bacteria and keeps food moving.

Worked example: a cheese sandwich

Take a bite of a cheese sandwich. As you chew, salivary amylase starts on the starch in the bread. In the stomach, acid unfolds the cheese's proteins and pepsin begins cutting them, while churning muscles turn everything into a thick liquid. Squirted in small doses into the small intestine, the mixture meets bicarbonate and pancreatic enzymes. Bile breaks the cheese's fat into droplets so fat-digesting enzymes can work. Glucose from the bread and amino acids from the cheese cross the villi into the blood and travel first to the liver, while the fat enters the lymph. The bread's fiber, which no human enzyme can break, travels on to the large intestine, where bacteria ferment it and water is reclaimed. The whole journey, from bite to toilet, commonly takes one to three days.