I had been thinking about doing work on optical illusions with Alex ever since I was at the MIT Media Lab. In the summer of 2005, I teamed up with Patrick Cavanagh, a psychology professor at Harvard, to put the idea into practice. The human brain plays many tricks on us, so we sometimes see things not as they are. Patrick and I planned to ask a simple but profound question: Does Alex literally see the world as we do? That is, does his brain experience the optical illusions just as our brains do?

I envisaged this work as the next horizon in my journey with Alex, beyond naming objects or categories or numbers. Bird and human brains diverged evolutionarily some 280 million years ago. Does that mean that bird and mammalian brains are so different structurally that they operate very differently, too?

Until a landmark paper [pdf] by Erich Jarvis and colleagues in 2005, the answer to this question had been a resounding yes! Look at a mammalian brain and you are struck by the multiple folds of the massive cerebral cortex. Bird brains, it was said, don’t have such a cortex. Hence, their cognitive capacity should be extremely limited. This, essentially, was the argument I had faced through three decades of work with Alex. He was not supposed to be able to name objects and categories, understand “bigger” and “smaller,” “same” and “different,” because his was a bird brain. But, of course, Alex did do such things. I knew that Alex was proving a profound truth: brains may look different, and there may be a spectrum of ability that is determined by anatomical details, but brains and intelligence are a universally shared trait in nature—the capacity varies, but the building blocks are the same.

By the turn of the millennium, my argument was beginning to gain ground. It wasn’t just my work with Alex but others’ work, too. Animals were being granted a greater degree of intelligence than had been previously allowed. One sign of this was that I was asked to co-chair a symposium at the 2002 annual meeting of the American Association for the Advancement of Science, called “Avian Cognition: When Being Called ‘Bird Brain’ Is a Compliment.” The preamble read as follows: “This symposium demonstrates that many avian species, despite brain architectures that lack much cortical structure and evolutionary histories and that differ so greatly from those of humans, equal and sometimes surpass humans with respect to various cognitive tasks.” Even five years earlier, such a symposium would have been a difficult sell. That was progress. Jarvis’s paper three years later effectively said that bird and mammalian brains are not so very structurally different after all. More progress.

When Patrick and I submitted our grant proposal to the National Science Foundation in July 2006, we were expecting that, in some respects at least, Alex would see our world as we do. We didn’t wait to hear whether we would be funded before we embarked on some preliminary work. We chose a well-known illusion as the first test. You have probably seen it in psychology textbooks and popular articles: two parallel lines of equal length, both with arrows at the ends, one with the arrows pointing out, the other with the arrows pointing in. Despite being the same length, the line with the arrows pointing in looks longer to human eyes. That’s the illusion. We had to modify the test a little so as to use Alex’s unique abilities; we varied the color of the two lines, keeping the arrows black. We then asked, “What color bigger/smaller?” Right away, and repeatedly, Alex selected the one that you or I would choose. He did see the world as we do, at least with this illusion. That was a very promising step.

By June 2007, Patrick and I were pretty sure that we would get our grant, and by the end of August we learned that it would start on September 1, a Saturday. We would have money for a year. The following Monday we threw a party to celebrate, on the seventh floor of Harvard’s William James Hall. I was especially happy, and relieved to see my financial woes lessen.

Alex was a little subdued that week, though nothing out of the ordinary. The birds had had some kind of infection the previous month, but they were now fine. The vet had given them all a clean bill of health. On the afternoon of Wednesday the fifth, Adena Schachner joined me and Alex in the lab. She is a graduate student in the psychology department at Harvard, researching the origins of musical abilities. We thought it would be interesting to do some work with Alex. That evening, we wanted to see what types of music engaged him. Adena played some eighties disco, and Alex had a good time, bobbing his head in time with the beat. Adena and I danced to some of the songs while Alex bobbed along with us. Next time, we promised ourselves, we would get more serious about the music work.

The following day, Thursday the sixth, Alex wasn’t much interested in working on phonemes with two of the students during the morning session. “Alex very uncooperative in the task. Turned around,” they wrote in Alex’s work log. By midafternoon he was much more engaged, this time with a simple task of correctly selecting a colored cup, underneath which was a nut.

At six forty-five the supplemental lights went on, as usual, a signal that we had a few minutes left to clean up. Then the main lights went off, and it was time to put the birds in their cages: Wart first, then Alex, then the always reluctant Griffin.

“You be good. I love you,” Alex said to me.

“I love you, too,” I replied.

“You’ll be in tomorrow?”

“Yes,” I said, “I’ll be in tomorrow.”

The following morning, after checking my e-mail, I poured myself a cup of coffee. While I was savoring the coffee’s rich aroma, a thought crossed my mind, as it did from time to time, something that my friend Jeannie once said: Had I gotten a different Grey parrot that day back in 1977, Alex might have spent his life, unknown and unheralded, in someone’s spare bedroom. I didn’t, of course, and here we were with a history of astonishing achievements behind us, and poised to journey to the next horizon and beyond in our work together. And we had the resources we needed. I allowed myself to savor all this, too, a sense of happiness, excitement, and security that had eluded me since the heady days at the Media Lab. Yes! I then returned to my computer.

In the interim, another e-mail had arrived. In the subject line was a single word: “Sadness.” My blood turned to ice as I read the message. “I’m saddened to report that one of the parrots was found dead in the bottom of his cage this morning when Jose went to clean the room...not sure which?...in the back left corner of the room.” It was from K.C. Hayes, the chief veterinarian in the animal care facility at Brandeis University.

I was in raw panic. No...no...no! Back left corner of the room. That’s Alex’s cage! I was gasping for breath, trying to stave off rising terror. Maybe he’s mixing up his right and his left. Maybe he made a mistake. Maybe it’s not Alex. It can’t be Alex! Even though I clung to that feeble hope as I snatched at the phone, I knew K.C. had not made a mistake. I knew Alex was dead. Even before I could dial, a second e-mail from K.C. chimed onto the screen. The message was simple. “I’m afraid it is Alex.”

I reached K.C., barely able to speak through my tears and pain. He told me he had wrapped Alex in a piece of cloth and put him in the walk-in cooler, down the hall from the lab. I threw on jeans and a shirt and jumped in my car. I’ll never know how I managed to drive, given my state. I called Arlene Levin-Rowe [our lab manager], because I didn’t want her to walk into the lab unprepared. She was just driving into the parking lot down the hill from the lab when I reached her. “Alex is dead, Alex is dead,” I wailed. “But maybe, maybe they made a mistake. Maybe it isn’t Alex. Please go find out, Arlene.” What was I saying? I knew K.C. hadn’t made a mistake. I knew Alex was dead.

When I arrived in the lab almost an hour later, Arlene and I held each other and sobbed for quite some time. Wave after wave of pain and despair washed over us, a torrent of shared disbelief. “Alex can’t be dead,” Arlene whispered through her tears. “He was larger than life.”

NULL | Illustration by Scott Bakal

We knew that we had to take Alex to the vet for an autopsy. Karen Holmes, one of the veterinarians at the practice, greeted us with hugs of sympathy. She led us to the mourning room, where we placed Alex, still wrapped, still in his carrier, next to us on the sofa. Karen asked if I wanted to see Alex one last time, but I didn’t. Years ago I had seen my father-in-law in his casket. For a very long time I couldn’t dispel the image of him lying there, drained of life. I determined then never to look at death again, and I stuck to that determination, even when my mother died.

I wanted to remember the Alex I’d put in the cage the previous night. Alex, full of life and mischief. Alex, who had been my friend and colleague for so many years. Alex, who had amazed the world of science, doing so many things he was not supposed to be able to do. Now he had died when he was not supposed to, two decades before the end of his expected life span. Damn you, Alex.

I wanted to remember the Alex whose last words to me were, “You be good. I love you.”

I stood, put my hand on the door, and whispered, “Goodbye, little friend.”

Scientifically speaking, the single greatest lesson Alex taught me, taught all of us, is that animal minds are a great deal more like human minds than the vast majority of behavioral scientists believed—or, more importantly, were even prepared to concede might be remotely possible. Now, I am not saying that animals are miniature humans with somewhat lower-octane mental powers, although when Alex strutted around the lab and gave orders to all and sundry, he gave the appearance of being a feathery Napoleon. Yet animals are far more than the mindless automatons that mainstream science held them to be for so long. Alex taught us how little we know about animal minds and how much more there is to discover. This insight has profound implications, philosophically, sociologically, and practically. It affects our view of the species Homo sapiens and its place in nature.

We once thought only humans used tools; not so, as Jane Goodall discovered her chimps using sticks and leaves as tools. OK, only humans make tools; again not so, as Goodall and later others discovered. Only humans had language; yes, but elements of language had been discovered in nonhuman mammals. Each time nonhuman animals were found doing what was the supposed province of humans, defenders of the “humans are unique” doctrine moved the goalposts.

Eventually, these defenders conceded that evolutionary roots of certain cherished human cognitive abilities could indeed be found in nonhuman animals, but only in large-brained mammals, particularly in apes. By doing the things he did, Alex taught us that this, too, was untrue. A nonprimate, nonmammal creature with a walnut-sized brain could learn elements of communication at least as well as chimps. This new channel of communication opened a window onto Alex’s mind, revealing to me and to all of us the sophisticated information processing—thinking—going on inside that little grey-and-white feathered head.

By implication, a vast world of animal cognition exists out there, not just in African Grey parrots but in other creatures, too. It is a world largely untapped by science. Clearly, animals know more than we think, and think a great deal more than we know. That, essentially, was what Alex (and a growing number of research projects) taught us. He taught us that our vanity had blinded us to the true nature of minds, animal and human; that so much more is to be learned about animal minds than received doctrine allowed. No wonder Alex and I faced so much flak!

We faced a flurry of goalpost moving, too. Birds can’t learn to label objects, they said. Alex did. OK, birds can’t learn to generalize. Alex did. All right, but they can’t learn concepts. Alex did. Well, they certainly can’t understand “same” versus “different.” Alex did. And on and on.

Alex was teaching these skeptics about the extent of animal minds, but they were slow, reluctant learners.

From Alex & Me: How a Scientist and a Parrot Discovered a Hidden World of Animal Intelligence—and Formed a Deep Bond in the Process, by Irene Pepperberg. Copyright© 2008 by Irene Pepperberg. Reprinted by arrangement with HarperCollins Publishers.