The obituaries of Koko the gorilla, who died Tuesday at the age of 46, tell all the same kind of wistful, aspirational stories. They explain how Koko’s trainers, Francine “Penny” Patterson and her colleagues, taught her to “speak” American Sign Language from the tender age of 1. There are mentions of how Koko graced the cover of National Geographic and became the star of a documentary. There are stories of numerous encounters with the rich and famous, from an extremely friendly exchange with William Shatner to a celebrated meeting with the eponymous star of Mister Rogers’ Neighborhood. But there’s one creepy and uncomfortable story the obits aren’t telling—which is a shame, because of all the stories about Koko and the research she was involved in, it’s the most revealing.

That story: the sexual harassment suit.

As celebrities are sometimes wont to do, Koko had developed a few antisocial tendencies. By the time she was in her 20s, for example, Koko had begun to show signs of nipple fetish. In 2005, Kendra Keller and Nancy Alperin, who had been employed by the Gorilla Foundation the previous year, took Patterson to court because, they alleged, “Patterson instructed Keller and Alperin to engage in the sexual act of removing their clothing to expose their breasts to Koko, in particular, their nipples.” The lawsuit alleged that in response to signing from Koko, Patterson pressured Keller and Alperin to flash the ape. “Oh, yes, Koko, Nancy has nipples. Nancy can show you her nipples,” Patterson reportedly said on one occasion. And on another: “Koko, you see my nipples all the time. You are probably bored with my nipples. You need to see new nipples. I will turn my back so Kendra can show you her nipples.”

The suit was settled out of court a few months later, sparing the court system the indignity of figuring out how to administer an oath to a gorilla. But the story is nevertheless crucial to understanding the arc of the scientific field of animal linguistics and Koko’s place within it.

Reports of animals that could talk, read, and even do complex calculations have appeared and reappeared over the years. At the beginning of the 20th century, for example, every day at noon, crowds in Berlin gathered to watch an amazing spectacle: an elegant stallion that could communicate in German. His owner, Wilhelm von Osten, was a retired schoolmaster—the aging pedant had convinced himself that his rigid teaching method could make even animals literate.

His horse, Clever Hans, certainly looked the part. He could nod or shake his head yes or no, and he could tap with his hoof to indicate numbers—or even more impressive, letters of the alphabet. With his hoof taps, Hans was able to demonstrate, over and over, that he had mastered the German language.

It didn’t take long for scientists to figure out that something was amiss. Clever Hans was only able to respond correctly when the questioner knew the answer ahead of time. When the interrogation was “blinded”—that is, eminent professors sidled up to the horse and whispered questions in its ear instead of standing in front of him—Clever Hans didn’t live up to his name.

It turned out that Hans was picking up subtle, involuntary cues from his questioners. When someone would ask a question of the horse, he would tense up and lean forward almost imperceptibly, which Hans took as a signal to start tapping his hoof. When the horse had tapped out the correct number, the questioner (or someone else in the audience) would raise his head slightly—the sign to stop tapping.

This wasn’t a case of fraud—von Osten honestly believed that his pedagogical technique had given a horse the gift of language. It was self-deception. Von Osten and the Clever Hans fans were guilty of performing intellectual backflips to ignore contrary evidence to keep their beliefs alive.

Whenever Hans didn’t behave as a learned horse should, the discrepancy was always neatly explained away. If Hans flubbed an easy question, van Osten explained that his steed was deliberately making errors, willfully answering the easiest questions wrong. Bored by the simple problems, the horse was telling the questioners, in his own way, that he wanted more challenging fare. Hans’ incorrect answers were a sign of Hans’ extraordinary abilities and a manifestation of Hans’ stubbornness—and his sense of humor. The desire to believe crowded out the skepticism that is necessary for good science.

This isn’t to say that studying animal cognition is a bogus science. Far from it. Ivan Pavlov’s dogs and B.F. Skinner’s pigeons and rats have led to deep new understandings about how brains—both human and nonhuman—function. But animal language in particular? That’s a fraught subject. Even from a philosophical perspective.

On one hand, there’s a deep-rooted principle in science that says there’s nothing unique about us—about the planet, about the solar system, and about humanity itself. Yet, for a long time, it seemed that humans alone had the ability to communicate in a deep, semantically complex, syntactic language. Starting in the ’50s, researchers started trying to resolve that seeming contradiction by teaching language to primates. In the late ’60s, two researchers at the University of Nevada claimed they had taught American Sign Language—more than 300 words’ worth—to a chimp named Washoe. If true, they had not just opened up a whole new avenue for understanding the animal mind; they had shown that humans were not unique after all.

Linguists like Noam Chomsky went bananas. The concept of language is a philosophically sticky subject—even defining it properly is not such an easy task. Chomsky imagined a Skinner-type experiment in which a pigeon would learn to press four buttons in order—say, red, green, blue, and then yellow—to dispense a pellet of food. Nobody would be terribly surprised. “Suppose that we label these buttons, successively, ‘please’, ‘give’, ‘me’, ‘food,’ ” he wrote. “Do we now want to say that pigeons have been shown to have the capacity for language, in a rudimentary way?” Language acquisition was something deeper than mere Skinnerian or Clever Hans-ish conditioning, but telling the difference between the two would be exceedingly difficult.

Koko’s desperate pleas for nipple access even undermined Penny’s fundraising attempt.

The immediate response to Chomsky’s gauntlet was a new experiment, a more rigorous version of the Nevada experiment starring a chimpanzee named, naturally enough, “Nim Chimpsky.” The project ended badly—Nim injured a few of his teachers and wound up confined and neglected. But the leader of Project Nim, Columbia’s Herbert Terrace, felt he had enough data to conclude that Chomsky was right: The ape’s gestures showed no syntax, no semantic regularities that seemed truly language-like. He was largely parroting back what his teachers were signing to him.

Koko started her linguistic journey a year before Nim Chimpsky was born. According to Patterson, once her training began, Koko started acquiring signs at a blistering rate: It only took a few weeks of training before she was signing “food.” Less than six weeks after Patterson first met Koko, the gorilla was signing rudimentary two-word sentences like “gimme food.” (It’s unclear when she learned to demand that her trainers disrobe.) Luckily for her, demanding that people show their nipples is not the sort of offense that gets a gorilla locked up. But Koko’s nipple fetish was a graphic illustration of the fundamental conflict at the heart of the tale of Noam and Nim and Washoe—and at the core of the scientific endeavor. How can we be sure that we’re not fooling ourselves?

The nipple fetish has a long enough history that we can examine its context. Take this 1998 AOL chat with Koko and her keeper, Penny Patterson.

PENNY: Hey, Cutie. Let me explain what we’re doing. KOKO: Fine. PENNY: We’re going to be on the phone with a lot of people who are going to ask us questions … KOKO: Nipple.

Even as Penny and her AOL audience tried to steer the conversation in other directions, over and over again, Koko turned the conversation back to her favorite subject.

AOL: What will she do now when we get off the phone? What does she eat for dinner? KOKO: Candy hurry … candy. PENNY: She’ll probably be very pleased to have her dinner. She’s asking me for ‘candy’ right now. After dinner. KOKO: Candy hurry. PENNY: She has vegetables for dinner … raw vegetables… KOKO: Nipple. PENNY: Yes, like a big salad.

Koko’s desperate pleas for nipple access even undermined Penny’s fundraising attempt.

PENNY: … that we’re trying very hard to raise the money that it will take to build the preserve and make it habitable for them. That’s going to take about $7 million, and we’re less than halfway there. So we’re hoping that corporations, the public at large, foundations will help us with that project. And we are now approaching them and asking, so we’re asking here, too. KOKO: Hurry give-me mouth nipple.

Penny explained to the audience that by “nipple,” Koko means “people,” and that the gorilla was somehow rhyming, even though she used sign language to communicate.

Yet it’s not at all clear that she really meant “nipple” when she used the sign, in which she gestured to her own nipple. Koko’s signings tended to be incredibly malleable. According to Patterson and her colleagues, “nice” could be interpreted as meaning “rice.” “Foot” could be interpreted as “man.” “Lip” as “woman.” “Bean” as “cookies.” Or “shoes.” Or “artichokes.” Or a “toy tiger.” Or “Jell-O.” When all else fails, an out-of-context word could be interpreted as an insult. (“Bird,” “nut,” “toilet,” and “devil” were supposedly favorites.) Or interpreted as boredom. Or as bizarre gorilla humor. Even when transcribed by a sympathetic stenographer, Koko’s signing seemed to be littered with non sequiturs, even gibberish. Instead of seeing Koko’s inconsistencies as a sign that the gorilla hadn’t truly acquired language, advocates had to go through more and more intricate—and bizarre—intellectual backflips to try to project a meaning upon them.

And while it’s not as warm and fuzzy a story as some of the other ones you’ll hear about Koko, the tale of her purported nipple fetish is the one that truly speaks to her lasting legacy. If we don’t believe that she ordered her handlers to undress, then we have to question the fundamental basis of her fame: her language. In other words, we have to confront the fact that when we were gazing into her dark brown eyes, we weren’t seeing her; we were seeing ourselves.