The 1,500 Jersey cows that Nathan Chittenden and his family raise in upstate New York seem to lead carefree lives. They spend their days lolling around inside well-ventilated barns and eating their fill from troughs. Three times a day, they file into the milking parlor, where computer-calibrated vacuums drain several gallons of warm milk from their udders, a process that lasts about as long as a recitation of “The Farmer in the Dell.”

Mr. Chittenden, 42, a third-generation dairy farmer whose family bottle-feeds each newborn calf, expresses affection for his animals. It’s a sentiment they appeared to return one recent afternoon as pregnant cows poked their heads through the enclosure to lick his hand.

“I’m in charge of this entire life from cradle to grave, and it’s important for me to know this animal went through its life without suffering,” he said, stroking the head of one especially insistent cow. “I’m a bad person if I let it suffer.”

Animal rights activists have a markedly different take on farms like Mr. Chittenden’s that satiate the nation’s appetite for milk, cheese and yogurt. To them, dairy farmers are cogs in an inhumane industrial food production system that consigns these docile ruminants to a lifetime of misery. After years of successful campaigns that marshaled public opinion against other long-accepted farming practices, they have been taking sharp aim at the nation’s $620 billion dairy industry.

Some of their claims are beyond dispute: Dairy cows are repeatedly impregnated by artificial insemination and have their newborns taken away at birth. Female calves are confined to individual pens and have their horn buds destroyed when they are about eight weeks old. The males are not so lucky. Soon after birth, they are trucked off to veal farms or cattle ranches where they end up as hamburger meat.

The typical dairy cow in the United States will spend its entire life inside a concrete-floored enclosure, and although they can live 20 years, most are sent to slaughter after four or five years when their milk production wanes.

“People have this image of Old MacDonald’s farm, with happy cows living on green pastures, but that’s just so far from reality,” said Erica Meier, the president of the activist organization Animal Outlook. “Some farms might be less cruel than others, but there is no such thing as cruelty-free milk.”

The effort to demonize dairy as fundamentally cruel has been fanned by undercover farm footage taken by groups like Animal Outlook that often are widely viewed on social media. In October, the organization released a short video filmed undercover on a small, family-owned farm in Southern California that revealed workers casually kicking and beating cows with metal rods, and a newborn male calf, its face covered with flies, left to die in the mud. One segment showed an earth-moving bucket hoisting an injured Holstein into the air by its hindquarters.

Stephen Larson, a lawyer for the Dick Van Dam Dairy, described the images as staged or are taken out of context. Earlier this month, a judge dismissed a lawsuit against the farm filed by another animal rights organization, saying it lacked standing. “The accusation that they mistreated their cows is something that cuts the Van Dam family very deeply, because the truth is that they have always, for generations, cared about and cared for all of their cows,” Mr. Larson said.

Dairy industry experts and farmers who have viewed the footage expressed revulsion and said the abuses depicted were not the norm. “These videos make every dairy farmer and veterinarian sick to their stomach because we know the vast majority of farmers would never do such things to their cows,” said Dr. Carie Telgen, president of the American Association of Bovine Practitioners.

The effort to turn Americans against dairy is gaining traction at a time when many of the nation’s farms are struggling to turn a profit. Milk consumption has dropped by 40 percent since 1975, a trend that is accelerating as more people embrace oat and almond milk. Over the past decade, 20,000 dairy farms have gone out of business, representing a 30 percent decline, according to the Department of Agriculture. And the coronavirus pandemic has forced some producers to dump unsold milk down the drain as demand from school lunch programs and restaurants dried up.

During his Academy Awards speech last February for best actor, Joaquin Phoenix drew rousing applause when he urged viewers to reject dairy products.

“We feel entitled to artificially inseminate a cow and when she gives birth we steal her baby, even though her cries of anguish are unmistakable,” he said, his voice cracking with emotion. “And then we take her milk that’s intended for the calf and we put it in our coffee and cereal.”

The National Milk Producers Federation, which represents most of the country’s dairy 35,000 dairy farmers, has been trying to head off the souring public sentiment by promoting better animal welfare among its members. That means encouraging more frequent veterinarian farm visits, requiring low-wage workers to undergo regular training on humane cow handling, and the phasing out of tail docking — the once-ubiquitous practice of removing a cow’s tail.

“I don’t think you’ll find farmers out there who are not trying their best to enhance the care and welfare of their animals,” said Emily Yeiser Stepp, who runs the federation’s 12-year-old animal care initiative. “That said, we can’t be tone-deaf to consumers’ values. We have to do better, and give them a reason to stay in the dairy aisle.”

What scientists see

Among those caught in the battle to win the hearts and minds of dairy consumers is a small group of animal welfare scientists quietly working to answer knotty questions: Are cows that spend their entire lives confined indoors unhappy? Does the separation of a newborn calf from its mother result in quantifiable anguish? And are there ways to improve the life of a dairy cow that are both scientifically sound and economically viable?

Marina von Keyserlingk, a researcher at the University of British Columbia in Canada and a widely recognized pioneer in the field of animal welfare, has made some headway in trying to understand whether certain aspects of modern dairy farming lead to avoidable suffering.

Raised on a cattle ranch, Professor von Keyserlingk says she can empathize with farmers who resent being lectured by urbanites disconnected from animal husbandry. Still, part of her job is helping persuade dubious farmers to accept improvements in animal welfare backed by science.

“As a little girl, I castrated thousands of calves without pain-relieving drugs and never thought to tell my dad, ‘This isn’t OK,’” she said. “But would I castrate a calf now without pain mitigation? Absolutely not.”

Divining the inner life of animals is notoriously elusive, but scientists like Professor von Keyserlingk have created experiments that seek to quantify bovine desires and ascertain whether some farming practices lead to poorer health and subpar milk production.

The studies she and other scientists have designed include installing weighted swinging gates inside barns to gauge whether pregnant cows might prefer to remain in their climate-controlled enclosures and munch on their favorite food or push through the gate to reach pasture. They found that cows’ desire to go outside depends on the weather (they avoid rain and snow) and the time of day (they prefer the outdoors at night).

One experiment sought to determine whether housing two calves together, as opposed to keeping them isolated in pens, could improve their learning abilities. (They found it did, and that paired housing also made them less fearful and easier to manage.)

Another study highlighted the value of mechanical scratching brushes to a cow’s well-being. Using the same weighted gate setup, it found that cows were as interested in rubbing up against the spinning bristles as they were in gaining access to fresh feed. Although the brushes are not cheap, the findings have convinced a growing number of farmers that they are worth the expense.

“It’s really important that we don’t just anthropomorphize cows based on our human experience, but we do know that they can experience negative emotions like pain and fear that we want to minimize,” said Jennifer Van Os, an animal welfare scientist at the University of Wisconsin-Madison. “On the flip side, they can have positive experiences like pleasure, reward and contentment that we want to try to promote.”

Research by animal welfare scientists has led to a number of changes in the industry. Many large dairy farms have begun housing multiple cows together, abandoning the age-old tradition of keeping solitary cows tied up inside barn stalls, and a number of studies over the past two decades found there was no hygienic benefit to removing a cow’s tail, which they use to swat away flies.

(Until recently it was widely believed a swishing tail spread feces and bacteria, but farmers mostly found the tails to be annoying.)

Other changes promoted by scientists have led to the widespread adoption of pain-relief medication during dehorning, a process that has long angered animal rights activists but one that veterinarians say is necessary to protect both livestock workers and cows from being gored.

Mr. Chittenden’s farm is entirely populated by Jerseys, a smallish, tawny breed made incarnate by Elsie the Cow, the daisy-garlanded Borden Dairy mascot who provided generations of Americans with quaint notions of the happy, lovable milk cow. Jerseys are known for their gentle disposition, and for producing milk with a high butterfat content.

A loquacious man whose weather-beaten hands reflect a lifetime of toil, Mr. Chittenden said low prices, increasingly stringent environmental rules and heightened attention from animal rights groups had made the past five years especially stressful. He and other farmers say the allegations of widespread abuse from animal rights activists are exaggerated, contending that unhappy cows are poor milk producers.

“Fortunately for me, all the things that result from an animal being better cared for are better for my bottom line because these animals will never produce more milk than when they are well fed, well cared for and don’t have a single stress in the world,” he said.

He scoffed when asked about the practice of artificial insemination, which People for the Ethical Treatment of Animals has described as rape. Cows seldom resist artificial insemination, he said, and the alternative — being mounted by a 1,500-pound bull — is an often brutal act that can injure females. “When a cow is in heat, she is not looking for a relationship,” he said.

Spencer Fenniman, who helps manage Hawthorne Valley Farm, an organic milking operation in Ghent, N.Y., has a deep appreciation for cow horns. He loves showing visitors how the rings on a horn can reveal an animal’s age, and without them, he would also have a hard time identifying Nutmeg from Martha or any of the other 70 Normande and Brown Swiss cows that graze on the farm’s verdant fields. Though there have been a handful of injuries over the past decade, he said it was rare for a cow to wield her horns as weapons, and even Elvis the bull, the sole sire of the herd, was docile one recent afternoon as a group of humans moved through his fenced-in enclosure.

There’s another striking thing about his cows: Many of them spend months alongside their offspring. Allowing a calf to nurse decreases the amount of milk available for human consumption, but Mr. Fenniman said his cows largely repaid the debt by producing extra milk, which is notably richer and sweeter.

“I think we have to acknowledge that taking milk from mammals is inherently subverting a natural process,” he said. “But we can provide them a certain amount of freedom, which includes the light and air they get at pasture.”

With its acres of open space and a nonprofit operating structure, Hawthorne Valley’s model of dairy production isn’t easily replicable, Mr. Fenniman acknowledges. Another obstacle is the limited pool of consumers willing to pay as much as double for organic milk that has been certified as “high-welfare produced” by third-party auditing groups.

Soft-spoken and contemplative, Mr. Fenniman, 38, knows that some aspects of dairy farming — most notably the fate of male calves — will always upset animal lovers. A proponent of ethically raised veal, he says that getting more consumers to eat veal would help farms like Hawthorne Valley remain financially viable. The lack of demand means that two-thirds of newborn males are sold off to beef producers. “It’s a tough conversation to have, but if you can raise a veal calf on pasture with the herd, that’s a good thing,” he said.

Professor von Keyserlingk, the Canadian researcher, has similarly tough conversations with the farmers she meets across North America. Like many animal welfare scientists, she rejects the notion that dairy farming is fundamentally inhumane, but she says farmers have a responsibility to continuously improve the well-being of their herds. That means reconsidering — or at least talking about — some bedrock practices, like cow-calf separation.

Professor von Keyserlingk often tells recalcitrant farmers that ignoring the issue could come back to haunt them if enough consumers turn against dairy.

“We live in societies where people can make decisions about what they eat based on their values,” she said. “This is one of the biggest challenges facing all of animal agriculture because although the public doesn’t expect farming to change overnight, they expect that farmers give their cows a reasonably good life, even if it’s a short one.”

Correction: Dec. 29, 2020
An earlier version of the article misstated a quality of Jersey cows’ milk. It is high in butterfat, not buttermilk.

Andrew Jacobs is a health and science reporter, based in New York. He previously reported from Beijing and Brazil and had stints as a metro reporter, Styles writer and national correspondent, covering the American South. @AndrewJacobsNYT