SANTA CLARITA, California—Cesar Millan crosses the road to meet me. Two pit bulls, a Chihuahua, and a Yorkshire terrier—named Junior, Taco, Alfie and Kaley Cuoko—follow. Off leash and at heel, the dogs are calm, almost languid. If Millan communicates with them, I do not notice.

For the past few minutes, I have been paying my respects to Millan’s pit bull, Daddy. He died in 2010 and his simple grave marker depicts a sleeping dog and the words, “Forever loved and missed,” set among the rocks of Millan’s training and rehabilitation clinic, dubbed the Dog Psychology Center. Millan sits in the spot where Daddy spent his final years, watching the wilderness of Santa Clarita’s hill country, an hour north of Los Angeles. He tears up when he talks about his dog. “This is a bed that I did for Daddy. He pretty much lived the rest of his years watching the llama and the horse. Nobody was allowed to be here except him. So we kept it this way. This is his place.”

2010 was a terrible year for Cesar Millan. Besides Daddy’s death, he went through a divorce and discovered he had no rights to the name, “Dog Whisperer,” the title of his television show on National Geographic Channel. He tried to kill himself by swallowing a bottle of Xanax. It was almost the end of an American dream for a man who grew up in Mexican drug country, and escaped when he was 21 by crawling through a tunnel in Tijuana with no money. He spoke no English and worked his way to Los Angeles by washing cars. He started a dog-walking business and scored a few celebrity clients. He landed a TV show, eventually becoming a celebrity himself as the world’s most famous dog behaviorist. He churned out books, videos, even a magazine.

Then things fell apart.

His personal life was hardly the only source of trouble. The criticism of Millan’s work has been steady and voluminous. He was described on the opinion pages of the New York Times as a “one-man wrecking ball directed at 40 years of progress in understanding and shaping dog behavior.” At the core of the condemnation by dog trainers and experts is that Millan bullies, intimidates, and scares dogs into behaving, and—most controversially—uses a move called an “alpha roll,” where he forces a dog onto its back to make it submissive. Most of his opponents believe that positive reinforcement such as giving a dog praise and treats is both kinder and more effective. They say Millan’s mistakes are grounded in a simplistic, out-of-date misunderstanding of animal science.

Who is right?

To answer that, we need history as well science. And a lot has changed for dogs recently—as well as in our understanding of them as a species. A century ago, there were about 1 million dogs in America, one for every hundred people. Fifty years ago, there were 30 million dogs, one for every six people. Today, there are 80 million dogs, one for every four people. Eight million (one in 10) of these animals are in shelters.

A most unnatural selection: Dogs became our babies

The role of dogs has changed, too. People have moved from rural lives to urban lives. A few decades ago, most dogs lived outside and were never allowed in the house. Today, the opposite is true. A hundred years ago, dogs worked as herders, hunters, or fighters. Today they are companions and family members.

The change in purpose has been matched by a change in perception. After Charles Darwin highlighted the power of selection in breeding, in 1859 with The Origin of the Species, his distant cousin Francis Galton popularized the idea of eugenics, or racial purity, in 1869, with a book called Hereditary Intelligence. Galton’s misunderstanding of Darwin is a big reason the idea of “purebred dogs” emerged. Not coincidentally, the British Kennel Club was founded in 1873, and the American Kennel Club followed in 1884. Both organizations created registers of “pure” dogs, based on subjective judgments about appearance and performance, and established “pedigree” to manage breeding and genetic inheritance. Meanwhile, the idea of breeding pure people reached its gruesome peak under Hitler’s reign—not coincidentally, the Nazis also led the world in purebred dogs. The German Shepherd, developed in 1899, was the official dog of the Third Reich. At the start of World War II, Hitler’s army boasted 200,000 dogs. He owned three himself, the last of which was allowed to sleep in his bed—unlike his girlfriend, Eva Braun. After the war, “pure breeds” such as German Shepherds proliferated in Europe and America.

This matters because all the dogs in the world actually descended from a few gray wolves. And their evolution occurred relatively recently. While dogs lived with humans for tens of thousands of years, all these lines died out—except for one or two gray wolves in Asia. They made, according to UCLA biologist Robert Wayne, a “profound adaptation” by mutating to digest grain as well as meat. (This revelation was published earlier this year by Swedish geneticist Erik Axelsson.) Wayne established that every dog’s mitochondrial DNA is 99.9% the same as a gray wolf’s—so close they are the same species. One-third of that 0.1% difference is in the genes for fat and carbohydrate digestion. Half is in the brain and the tiny remainder—so little it surprised even Wayne—controls the time and rate of physical development and accounts for the vast differences in size and shape between breeds. Basically, dogs are wolves that adapted to eat rice and be nice.

Both the transition from working outdoors to living indoors and the inbreeding of pure-blooded pedigrees—for example, all German Shepherds are descended from one dog that lived a hundred years ago—are highly unnatural. Today’s dogs find themselves in an environment, and often a body, very different from they the one in which their species evolved. What is not unnatural for dogs is being with people. The difference in dog brains and wolf brains—half of that minuscule genetic difference—is a sophisticated interface for interacting with humans.

This too is a recent discovery. Only a few academic papers about dog behavior were published in the 1970s and 1980s. In the 1990s, this number started to increase, and, by the turn of the century, it skyrocketed. One big reason was the opening of what was probably the world’s first dog behavior lab at Eötvös Loránd University in Budapest in 1994. Led by biologist Ádám Miklósi, the lab conducted sophisticated experiments with dogs and made a series of remarkable discoveries. Notably, dogs become attached to people. Wolves—even when raised as cubs in a home—do not.

Richard Schultz for Quartz Dogs look to humans for answers—and leadership.

This is true to an extraordinary extent. A dog put in a stressful situation will relax if a familiar human is there, but a familiar dog, even his mother, will make no difference. Dogs, even ones raised without human company, understand what it means when a person points, even if the pointing is done with a leg, and even if the object being pointed at it is far away. Dogs have an ability to read and interpret human faces that is unique among all animals. Their first instinct when faced with a problem is to look to a human for guidance, something wolves do not do. Dogs will also communicate by looking at a human, then at a target object, then back again. Wolves are not very vocal: they generally reserve howling and barking for long distance communication with out of sight animals. Dogs bark far more frequently than wolves. They do it to communicate aggressiveness, fear, despair, playfulness, and happiness. But, in most cases, dogs do not bark to communicate with each other, they bark to communicate with us.

Dog needs man

A dog, then, expects us to tell it what to do—to be what Cesar Millan calls a “pack leader.” This role (and the science behind it) is so important to him that his new TV show is called Leader of the Pack. The phrase is also the focus of a lot of the attacks on his methods. This is because, for a long time, scientists believed a wolf pack was a competition for hierarchical dominance between a breeding “alpha” pair and lower order “beta” and “omega” wolves. In the 1990s, wolf expert David Mech and others realized they had been wrong: this was only true of wolves that were not related to one another and were held in captivity. In the wild, a typical gray wolf pack is a family group consisting of a father, a mother, and several generations of siblings. “Leader” displaced “alpha” as the wolf expert’s term of art.

Similarly, the word “alpha” appears to be becoming a thing of Millan’s past. For example, it appeared in his first book four times: Not because he had learned about dogs from the old wolf theory—his understanding of dogs comes from experience and intuition and his rearing on a Mexican farm amid plenty of working dogs— but because it was a word some English speakers used when talking about dogs. He does not use it now. It does not appear at all in his latest book, and he did not use it once in the few hours we were together. As it fell out of favor among experts, he returned to the simpler word he has always preferred: “leader.”

Millan showed me what he means by “leader” as we walked around his property with Junior, Taco, Alfie, and Kaley Cuoko. “Here we’re going to have a chicken coop,” he said. “Inside we’re going to build a little church. It’s called ‘The Little Brown Church,’ and it’s where the chickens are going to go because they give life. I’m going to open it so they can just mingle with the dogs everywhere. My job as a pack leader to give direction and protection. My direction will be: We don’t kill chickens.”

Most of this direction comes from presence and body language—what Millan, somewhat mystically, calls “energy.”

We have five senses; they have a million

There is no scientific mystery about how this works. The dog’s dominant sense organ is its nose: smelling is to dogs what seeing is to us. Depending on breed, a dog gets up to 100 million times more information from scent that we do. We cannot easily conceive of all the things a dog learns about us through its nose. By smell alone a dog can tell, among many other things, whether or not we have malignant melanoma, bladder, breast, ovarian, prostate or lung cancer, long before any medical tests. Our scent goes with us everywhere: we are constantly shedding microscopic particles of dead skin that weigh 200-millionths of an ounce and are shaped like cornflakes. Each particle is laden with a unique scent—from our skin, from the four bacteria each one typically carries, from our bodily secretions and from vapors that surround us. These scent-carrying particles do not fall to the ground. They fly up, carried by air currents surrounding our bodies at 125-feet-a-second—even faster in hot weather or if we are wearing certain clothes. They change direction depending on how we move and eventually disperse 18 inches about our head. They broadcast our unique smell for many hours. Once emitted they decay, signaling time like a ticking clock.

Dogs can smell things that are far away and, because of their wet nose, detect the direction it is coming from. They can smell what has happened in the recent past. Most importantly, because of the chemical changes emotions cause and the way air flows around our body when we move, they can smell how we feel. In short, when a person has what Millan calls “calm assertive energy,” dogs can smell it. They can also smell fear, nervousness, sadness, and stress. They can see it too.

A dog’s vision is as different from ours as its sense of smell. Among other things, dogs have up to 270 degrees of peripheral vision. They can see us from over their shoulders without turning their head. Pretty much the last thing a dog does is listen. Millan: “Scent before sight before sound.”

Dogs that are already calm and paying attention can understand words they have learned in context—more than a thousand in at least one case—but verbal commands are unlikely to be effective otherwise. They will almost never work, even in obedient dogs, if the dog cannot see the face of the person talking. This is really easy to prove. When your dog is calm and relaxed, look into her eyes and tell her to “sit.” She will probably sit. Wait until she gets up. Turn your back to her and say “sit.” She almost certainly won’t. To put it another way, yelling at your dog makes no sense.

This is why Millan, despite being the “dog whisperer,” seldom talks to dogs. The closest he comes is an occasional clipped hiss—it sounds like “sssssst!”—to get their attention. Taco starts chewing on a plastic fork. “Ssssst!” says Millan. Taco looks at Millan for leadership. Millan gently removes the fork and resumes the conversation.

Wolves have each other, but dogs just have you

Our understanding of wolves was not overturned by the realization that wild packs are families. What we learned was that there were two models of social behavior: one for captive, unrelated wolves, and another for wild, related, wolves. One is more aggressive, and the other is more cooperative, but both are still hierarchical. Anyone who thinks there is no pecking order in a family has never been in a family.

The question at the center of the Cesar Millan controversy—and at the heart of understanding dog behavior in general—is which model applies to dogs? How best to train them? Their natural social group is humans, not related dogs, and even if they are with relatives, the lab in Budapest has shown that, once dogs are a few months old, they are almost completely indifferent to other family members. And their modern environment is inside a house. Is that like being in captivity, or like being in the wild?

For his part, Millan does not address his critics and cautions that there are many ways to train dogs. But the answer to this question is clear: People are the boss. Millan’s methods only have been bolstered by the spate of research on dogs and wolves. A dog’s pack, or family, is a unique interspecies group that must include people and may include other dogs. And a dog’s first instinct—unlike a wolf’s—is to look to the people for leadership. Only when it does not find that, either because its human is too abusive, affectionate, or unstable, does it start to behave more like a captive wolf with no family—aggressively questing for dominance, out of insecurity more than anything else. All along, this has been Millan’s secret to well-behaved dogs.

What humans are doing to dogs

This aggressive questing is more likely today, because we keep dogs indoors and may treat them like friends or infants, rather than giving them the reassurance that they are safe because we are in charge. Even when we do provide leadership, our dogs will organize themselves hierarchically. The process is normally peaceful, but sometimes there is a little nipping and growling. Wolves, and therefore dogs, test each other—and us—to see who should be pack leader. This is essential, evolved behavior: just as the strength of the wolf is the pack, so the strength of the pack is the leader. Anybody with more than one dog knows they sort themselves into an order, not a group of equals, typically with tests of dominance exactly the same as the ones wolves use in the wild. Millan’s explanation on how this plays out:

There are three positions: the back, the middle and the front. The guys in the back are the most timid ones. At the same time they are very sensitive, so they’re going to alert you for everything. If you want somebody to tell you when an earthquake is coming, that’s that guy. You don’t expect the rest of the guys to be as sensitive. Everybody in the pack is just as valuable. The guys in the front, those are the police dogs. They’re constantly at alert. And then the happy-go-lucky guys are in the middle. These are the guys that make sure the guys in the front and the guys in the back co-exist.

When he says this, he mimics body language for three positions: looking around timidly as the dog at the back (where Kaley Cuoco lives), thrusting forward assertively as the dog at the front (like Junior), pimp-rolling as the dog in the middle (like Taco). Millan has dog body language down cold. He does not just copy it, he reads it.

Scott Grover for Quartz No need to whisper: Cesar Millan is the leader of the pack.

He is so good at it that if you slow down his TV shows, you will frequently see Millan reacting to what a dog does before the dog does it. He will reach for a dog’s collar frames before it lunges. He will start to correct a dog a fraction of a second before it misbehaves. He can read a dog as if he himself is a dog.

This also debunks the argument that Millan is out of touch and that positive reinforcement is the new, better way. The truth is the opposite. What dog trainers call “positive reinforcement” is an example of something called “operant conditioning,” a method of learning that relies on reward or punishment. One of positive reinforcement’s earliest incarnations was “clicker training,” developed by Marian Kruse and Keller Breland in the 1940s. In clicker training, a dog or any other animal—Kruse and Breland used the technique with more than a hundred species including bears, chickens, and humans—is given a reward and hears the sound of a click whenever it does something the trainer wants it to repeat. In time, the treat is eliminated leaving only the click, and eventually the click can be removed too, leaving only the training. Kruse and Keller were students of B.F. Skinner, who, along with Ivan Pavlov of salivating dogs fame, was a founder of the school of psychology called “behaviorism.” In Skinner’s view, living things, including humans, were “organisms” that do what they do merely as a result of response to stimulus. It was not necessary to understand their goals or motives—only to condition them to provide the desired response on command. This approach shaped dog training for decades.

An obedient dog is not always a happy one

When dogs first became urban pets instead of rural hunters and herders, the first wave of dog trainers, influenced by Skinner, Pavlov and others, taught dogs to perform tricks like “sit” and “roll-over” by using command-based conditioning. The goal was not happiness but obedience. Behaviorism, like breed purity, dates back to the late 19th century. By the end of the 20th century, it had been displaced by a more complete, humane understanding of what living creatures do and why, called “cognitive psychology.” Cognitive psychology treats people and animals as complicated, sentient thinkers, with behaviors that result from instinct, intuition and reason, and are often directed by goals. Behaviorists train dogs to be obedient. Cognitivists lead dogs to be happy. Millan is in this latter category, the ultimate dog cognitivist. He seeks to understand what dogs need and think and why. He is not behind the times, but way ahead of them. It is the positive reinforcers who are out of date.

Now, three years after he tried to kill himself, Millan is rebuilding. He is in a serious relationship, has a new TV show, and a new dog psychology center, where he is getting back to his roots by recreating his grandfather’s farm in Mexico—a humble place with livestock and adobe that is about as far from Hollywood as it could be, permanently occupied by the immortal spirit of his favorite dog, Daddy. Of the vital function that dogs perform, Eckhart Tolle says:

They keep millions of people sane. They have become guardians of being.

Tolle is a spiritualist, but his observation is more than mystical. It is supported by science. The findings are not as simple as dogs improving human life. It depends on the dog, and most of all, it depends on you. But for all the proof that dogs need humans, a fairly consistent body of research does show benefits of the reverse. People with dogs feel more relaxed, less lonely, exercise more, and are even less likely to have infants with allergies. Some of the biggest impacts of dog ownership are felt by two types of people in particular: women and single men. A single man with a dog is much less likely to suffer from depression than a single man without one.

Cesar Millan knows this firsthand. The man he is today results not from what he learned about dogs, but what he learned from them. The Dog Whisperer died in 2010. Cesar Millan and his radical ways did not. While he was saving dogs, dogs were saving him.