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The Raw and the Cooked

Why We Process Our Food—and How Our Gut Microbes Respond

If someone asked you to list the organs that help you digest your food, chances are you would stick to what lies between your nose and the bottom of your torso. You would probably mention your stomach, which churns food with acids and enzymes; your small intestine, which breaks food down with more digestive juices and absorbs most of the component nutrients in its elaborate folds; and your colon, where the digestive process wraps up. You might mention organs that make and store digestive juices, such as your pancreas, liver, and gallbladder. Moving up, you might add your esophagus, that chute to the stomach, and your mouth, that maelstrom of chomping jaws and salivary glands. And moving down, you might even mention your rectum, the antechamber to the exit. But there’s one vitally important organ you probably wouldn’t think of: your brain.

Compared to chimps, our nearest living relatives, and to australopithecines, the ancestors of our genus, Hominidae, humans have puny digestive systems. We have smaller teeth, weaker chewing muscles, and shorter gastrointestinal tracts. But we also have higher energy needs. Our bigger bodies require more calories to run. We travel farther than chimps as we go about our days (or at least we did, before modern societies invented the couch potato). And we have far bigger brains, about three times the volume of those of Australopithecus, and even more than that compared to chimps’. Big brains make a big difference, because brains use more energy than any other human organ. So how do we get enough calories to support our energy-hungry bodies and lifestyles?

"In the course of our evolution, we used [our brains] to outsource digestion, moving part of the process outside our bodies."

human and chimp skull and skeleton comparison
Compared to chimps, humans have shorter digestive tracts, weaker jaws, and smaller teeth. So how do we get enough calories to run our bigger bodies and energy-greedy brains?

The answer, says Harvard human evolutionary biologist Rachel Carmody, lies in those big brains. In the course of our evolution, we used them to outsource digestion, moving part of the process outside our bodies. When you cook a hamburger or a yam, you’re not just making it more delicious—you’re actually kickstarting digestion, breaking down the muscle or plant cells so that your body has easier access to the nutrients. 
Carmody points to a dramatic change that took place two million years ago, between Australopithecus and the rise of Homo, our own genus. Bodies and brains grew bigger suddenly. Because early humans’ physical digestive systems were so puny, Carmody knew they couldn’t just be eating more of the same food; they had to be eating something fundamentally different, something that provided more calories per bite. She says, “As a graduate student, I started exploring whether food processing techniques—first, say, smashing foods, pounding them with a rock or grinding them against a stone, and then subsequently, with the control of fire—would have shaped the kind of energy gain that we got from the diet.”
To her surprise, nobody had actually measured the difference, so Carmody performed experiments with mice. She fed the mice lean beef or sweet potato in four forms: raw and whole, raw and pounded, cooked and whole, or cooked and pounded. She chose beef and sweet potatoes to echo the meat and tubers our ancient ancestors would have eaten. Since mice aren’t particularly good at digesting this unusual (for mice) fare, Carmody expected them to lose weight—but she also expected the cooked version to provide them with more calories. Sure enough, the mice lost weight on the raw diet. When the food was cooked, however, they had no trouble maintaining their body mass. Pounding made a difference too, though not nearly as much. (Interestingly, studies of people who eat a completely raw diet show that they, like Carmody’s mice, have trouble maintaining their body weight.)
Something to chew on
Carmody points to four changes that take place when we eat cooked or processed food: Changes in the food’s chemical and physical structure; changes in the energy our bodies must expend digesting it; changes in where in our digestive tracts it’s processed; and changes in our microbiome, the vast community of microscopic organisms that live in our colons and help us digest. 
Cooking, along with other forms of processing such as grinding, blending, and fermenting, transforms food both chemically and physically. The transformations make it easier for our bodies to digest the three major food components, called macronutrients: carbohydrates, proteins, and fats. Take that sweet potato, for example. Most of the calories it offers are in the form of starch, which comes in a tightly latticed crystalline structure. We use enzymes called amylases to break down starch, cleaving off smaller sugar molecules that our bodies can absorb.

Enzymes break up proteins
Amylase, a digestive enzyme, breaks up starches into small sugar molecules.

“Raw starch is very resistant to digestion in the small intestine, but when we cook that starch, it causes that crystalline structure to wiggle and loosen a little bit, and then it swells with water in a process called gelatinization. In that gelatinized form, it’s very easy for our amylases to get in and to cleave off the sugars,” says Carmody. She compares the process to a toy her three-year-old son loves: “You’ve got those sponge animals that shrink down to a little pill. It’s so hard and dry, you couldn’t possibly dig into it. But you throw it into water, and that tight structure begins to swell and soften. So now you could poke into the center of that sponge dinosaur very easily.” 

Similarly, proteins in raw meat take the form of long molecules tangled up tight, like a snarled ball of yarn. Cooking denatures the proteins, loosening the tangles so our enzymes can reach more of the molecule.

A tangle representing molecules in raw meat unfolds. Protein molecules in raw meat loosen up when they are cooked, making them more accessible to digestive enzymes.



In a fatty plant food like peanuts, the fat is encased in cells, protected by cell walls made of a material called cellulose, which our enzymes can’t break down. To get at that fat, we need to physically break open the cells. Cooking weakens the cell walls, and processes like grinding crush them further, releasing the fat; think of the layer of oil at the top of a jar of natural-style peanut butter. When our digestive juices can easily reach the macronutrients in our food, we can break more of them down into components that our small intestines absorb, such as sugars, amino acids, and fatty acids. That means we get more calories from a cooked carrot than a raw one, more from a medium-well hamburger than from the same meat served as steak tartare.


Not only do we get more calories out of the cooked food, we expend fewer calories digesting it, too. Digestion is an energetically costly process, and all this loosening up of food that happens on the cookstove or in the blender saves our bodies a lot of work. Eating raw, unprocessed food requires a lot of vigorous, calorie-expending activity: chewing in the mouth, and churning and pushing in the stomach and small intestine. 

And even with all that internal work, plenty of food passes into the colon without first being broken down. The less food is processed before we take a bite, the less of it will be digested by the time it leaves the small intestine, and the more will end up in the colon. That’s the home of a crucial, yet inhuman component of our digestive system: our microbiome. 
Going with the gut

Illustration showing human digestive system
Human digestive system

A teeming community of microbes thrives in the colon, all ultimately feeding on our leftovers. These tens of trillions of individual bugs belong to many different species. Our microbial communities vary enormously from person to person, but there’s a lot of what Carmody calls “redundancy in function”: different microbes can play the same roles. “At a functional level, we’re more similar than we would appear to be when we just look at the different bugs that are present,” she says. 
There about 150 times as many independent genes in our microbiome as we have in our own bodies, which gives our microbes a vast metabolic range—much bigger than ours. They can perform a whole bunch of functions that we can’t, says Carmody, such as breaking down materials we can’t digest, including cellulose.

Animation nutrients absorption
Most of our digestion takes place in the small intestine, where most fats (yellow), and proteins (red) are broken down and absorbed. We lack the enzymes to break down cellulose, also called fiber (green). Everything we can’t break down ourselves passes into the colon, where it becomes food for our microbes (purple). They break down protein and fiber into short-chain fatty acids, which are absorbed by the microbes themselves or the colon walls. The leftovers leave our body in our feces.

That functional range “has driven really profound, but very visible changes in biodiversity across animals that are linked to diet,” says Carmody. For example, unlike humans and other primates, who carry our microbiomes at the rear end of our intestinal tracts, ruminants like cows and sheep have evolved to keep theirs at the beginning, in four-chambered stomachs. This allows microbes to break down the ruminants’ cellulose-rich, grassy plant meals, through a process called fermentation, into nutritional components that are easily absorbed in the small intestines. [[ck]] 
Although we lack cows’ stomachs, we too benefit from gut microbes that digest cellulose. They break it down into short-chain fatty acids, which we can absorb in our colons and use for energy—though they’re nearly not as rich a source of calories as sugars, proteins, or fats. When our microbes break down cellulose, they also release the nutritious contents of the cells. When you eat a raw peanut, for example, you will release some of the oil from its cells in your mouth by chewing and in your stomach by churning, but lots of cells will be left with their cellulose walls intact until your microbes break the structure down in the colon. But because this fermentation happens after the food has passed out of the small intestine, our bodies’ main nutrient-absorption center, we don’t get to absorb as much of these nutrients. Instead, they feed the microbes themselves. “On the raw diet, you’ve got greater energy return in the colon, but not greater energy return overall, because you’ve lost the ability to have first dibs on that food,” says Carmody. 
When we change what we feed our microbes by changing what we eat, that will change the entire microbial ecosystem. “From the microbial communities’ perspective, on the raw diet the microbial community in the colon is seeing a large influx of starch. On the cooked diet, it’s not really seeing much starch come in at all,” says Carmody. “And so on the raw diet, evolution is going to select for microbes that are very good at processing and metabolizing that starch, causing them to proliferate in number at the expense of those who can’t really take advantage of that starch.” 
Now we’re cooking!
Carmody’s research on how the body digests raw and cooked food illuminates weaknesses in nutritional labeling. Current labels are based on measurements of what nutrients go in and what comes out. They don’t take into account where in the digestive tract the nutrients are digested; the same amount of starch or protein is worth twice as many calories when digested in the small intestine than in the colon, for example. They don’t take into account whether the food is whole or blended, or the degree and temperature of cooking. And they don’t take into account the makeup of the eater’s microbiome. 
In her current research, Carmody is looking at host-microbial interactions and how they affect metabolism, focusing on the effects of human diet and exercise. The work could have implications for our health: for example, it could help medical researchers understand and treat malnutrition and obesity by manipulating the microbes. Learning what’s unique about the human microbiome could help researchers build better animal models for studying the vast array of diseases and conditions affected by the microbiome, which Carmody says include “not just energy metabolism, but behavior and immune function and growth.”  
Beyond the applications, Carmody loves her the sheer wonder of her research subject. “It gets us to an answer about another way humans are the way we are, and why we are unique. And that’s just intellectually satisfying.”