Escape from Planet Earth: Psychedelics, religion, and outlaw scientist John C. Lilly

John C. Lilly
(Illustration by Alex Innocenti)

Most scientists don't include personal stories in their research reports, but for John Lilly, personal experiences and science experiments were the same thing. His ears, eyes, mouth, and nose were calibrated probes. His mind was the unbiased observer, the ideal model for dispassionate inquiry. Knowledge and experience led him to new sets of questions, not firmly held beliefs. But as anyone who has traveled into the psychedelic spaces knows, soon after arrival, one quickly finds out that the scientist's tool kit—language—is much too small and inadequate for the job. The scientist's reaction to the psychedelic experience is a set of questions that sound more like a seeker's. This is the crux of the enigma of John Lilly.

In the last two decades, Johns Hopkins University has renewed experiments with psychedelic drugs, a research frontier Lilly was drawn to as long ago as the '60s. In fact, Maryland has a long history of clinical and experimental psychedelic research stretching back to the earliest investigations into the psychedelic drug lysergic acid diethylamide, or LSD. Albert Hofmann accidentally discovered LSD in 1938 at Sandoz Labs in Switzerland. In 1947, Sandoz began offering it free of cost for psychiatric research, and the National Institutes of Health in Bethesda gave its researchers, including Lilly, free rein to investigate any potential use for the substance. The Maryland Psychiatric Research Center at Spring Grove Hospital in Catonsville also conducted extensive psychedelic research with LSD and psilocybin (the active compound in "magic mushrooms") for many years, ending in 1977. Psychedelics are now experiencing a renewed surge in interest, primarily due to the efforts of psychopharmacologist Roland Griffiths, who along with psychologist Bill Richards began volunteer research studies with psychedelics in 1999 at Johns Hopkins Bayview Medical Center.


That first study, the intriguing results of which were published in 2006, was crucial in restoring legitimacy to psychedelic research. "Two-thirds of the participants who received psilocybin rated their experiences as among the five most important events of their lives," Richards reported in his 2015 book "Sacred Knowledge." Since that first study, nearly 300 additional volunteers have passed through Hopkins in various studies involving psychedelics with very similar results. These studies rigorously designed and carried out at a conservative and distinguished medical center by a leading drug researcher with a reputation for excellence provided a green light to other researchers and institutions to pursue their own studies. Research studies with psychedelics are now underway at a dozen or more universities around the world.

It may be surprising to learn that the most striking, profound, and well-documented religious and mystical experiences are happening every week inside of a research center at Bayview in East Baltimore, rather than inside of a church or synagogue. Though mystical experiences do happen spontaneously, psychedelics are the most dependable trigger for profound religious and mystical experiences when used in the right setting. The use of mysticism for gleaning hidden knowledge is a long tradition going back to the beginning of written and oral history, and was the primary source of wisdom for the ancient philosophers Plato and Heraclitus, whose mystic insights were complimented by rational scientific minds. As the great British mathematician, philosopher, and social critic Bertrand Russell said in his 1976 "Mysticism and Logic": "The greatest philosophers have felt the need both of science and of mysticism." One of the most clearly written and insightful recent books on the relationship between mystical experiences and the therapeutic value of psychedelics is Bill Richards' "Sacred Knowledge." He has spent over 25 years of his professional life doing legal psychedelic research and he also worked with Lilly for a brief time at Spring Grove.


Lilly, who died in 2001, is not just an important historical figure in psychedelic research, though he is surely that as well. His research into LSD and ketamine and the conclusions he reached have been virtually ignored outside of the counterculture and the often ridiculed, mostly affluent and politically detached "New Age" scene. The breadth and density of his output, along with the technical nature of the language in which he wrote, have surely contributed to his obscurity as well. But despite this marginalization, the most recent studies into the brain, memories, the isolation tank, and psychedelics are providing new evidence that Lilly was far ahead of his time in understanding the science behind cognition and psychedelics, sparking a renewed interest and investigation into his work.

Lilly's work—scientific papers, lectures, and 12 books—took him in surprising directions. His first book, published in 1961, was "Man and Dolphin," which predicted that within 10 to 20 years, humans would establish communication with another species, most likely dolphins. He saw himself as working in the tradition of Aristotle, who had studied and written extensively about dolphins approximately 2,300 years earlier. "If we are to seek communication with other species we must first grant the possibility that some other species may have a potential (or even realized) intellectual development comparable to our own," Lilly suggested. He was skeptical of the vain assumption (or belief) that humans are the ultimate product of evolution, and believed that getting scientists to entertain the possibility of communication with other species was the first obstacle to pursuing this potentially valuable research. His book detailed efforts to establish communication with dolphins by teaching them English. Some of Lilly' recordings from his attempts to communicate with dolphins were released on an LP by Smithsonian Folkways in 1973 under the title "Sounds and the Ultra-Sounds of the Bottle-Nose Dolphin." His life and work seeped into other weird pop culture relics, inspiring both the 1980 film "Altered States" and 1973's "The Day of the Dolphin."

Lilly's most accessible book, "The Center of the Cyclone," published in 1972, is an autobiographical work documenting his personal search for the meaning of life. He describes his experimentation with different levels of consciousness using the isolation tank and psychedelic drugs, meditation, hypnosis, and psychoanalysis—all things that have gained widespread acceptance. "It is my firm belief that the experience of higher states of consciousness is necessary for survival of the human species," Lilly writes in the introduction. In 1977 "The Deep Self" was published, synthesizing Lilly's research into isolation and its effects on human consciousness. "Simulations of God: The Science of Belief" was released in 1975. In his most abstract work, Lilly assigns the term "God" to the underlying assumptions that construct the belief systems that control human behavior. He then outlines the consequences of those beliefs on our behavior, and describes the way societies function based on different cultural beliefs and values. "For many people the possession of money is equated with God. The belief that God is money and money is God is a powerful determinant of behavior in our Western society," Lilly writes.

His magnum opus, "Programming and Metaprogramming in the Human Biocomputer" received a proper publication in 1972, but it was initially leaked in 1967 after being favorably reviewed by the Whole Earth Catalog, a popular counterculture magazine of the time. At the request of Whole Earth, Lilly mimeographed 300 copies himself to be sold through the catalog, and it quickly became a much-discussed underground classic. Essentially a handbook on how to jailbreak the mind using LSD and the isolation tank, its circulation led to speculation and gossip within the science community that Lilly had lost his mind, leading to the termination of the government grants supporting his dolphin research. After his funding was pulled, Lilly decided to close the dolphin research labs and move to Catonsville to pursue clinical psychedelic research at Spring Grove Hospital—once again circling back to Maryland where he could research psychedelics legally.


Lilly liked to say that his own beliefs were unbelievable. His oft-repeated maxim: "In the province of the mind, what is believed to be true is true or becomes true, within limits to be found experientially and experimentally." Over the years, experimenting with different levels of consciousness, Lilly would go on to explore everything from interspecies communication and astral travel to mystical experiences, telepathy, and alien contact.

John Lilly found the scientist's toolkit too limited for his research on psychedelics.
John Lilly found the scientist's toolkit too limited for his research on psychedelics. (Wikimedia Commons)

The Origins of a Scientist


Born in 1915 in St. Paul, Minnesota, physician and biologist John Cunningham Lilly was what William S. Burroughs called a natural outlaw: "those dedicated to breaking the so-called natural laws of the universe foisted upon us by physicists, chemists, mathematicians, and biologists, and, above all, the monumental fraud of cause and effect, to be replaced by the more pregnant concept of synchronicity." Lilly's life story forms a virtual blueprint on how to escape the confines of the physical body, and he had a natural ally in Burroughs, who insisted that humans are "an artifact designed for space travel," no more designed to remain in our present biologic state "than a tadpole is designed to remain a tadpole."

Lilly, whose life has been well documented in hundreds of press interviews, some biographies, and his own books, says that he had his first vision at age seven. It was not well received. "Only saints have visions!" a sister scoffed, and few in his family believed him. Mystical experiences, he was told, were not spontaneously received by just anyone. Three years later, after achieving orgasm on his parent's "body shaker" (an antique exercise machine fitted with a vibrating belt), the boy collapsed on the floor into a state of "moist-eyed, wet-crotched post-orgasmic bliss." For him, it was a religious experience. But when his parents returned and found him slumped on the floor in front of the machine, they scolded him, and referred him to the family doctor and a Catholic priest. The experts told him that masturbation was a health hazard and mortal sin, too much of this "abuse" would eventually result in insanity. He did not understand why something so wonderful was associated with embarrassment and shame. The seeds of his scientific journey were sown, and he decided from there on out those ideas that conflict with experience must be abandoned. "If religion didn't agree with his own experience," Lilly deduced, "then religion itself must be wrong."


Lilly grew up in ideal conditions for a scientist. On a 160-acre farm outside St. Paul, the young scientist spent his nights studying the stars. During the day, he dug for fossils, played with bugs, and observed nature. His father, a successful banker and philanthropist, supplied Lilly with the financial independence required for a creative and risky scientific career. In a 1990 biography co-authored by Francis Jeffrey, Lilly said that money is a "psychotic system," describing it as "a form of forestalled violence waiting to pounce on anyone who weakens, as in a pack of wolves or a school of sharks." He never had to worry about the limits of money, and had the freedom to pursue whatever kind of research he wanted.

While still a teen, he read "Brave New World" and became captivated with Huxley's vision of people who were transformed into "ideal citizens" (i.e. consumers) through conditioning (i.e. media), learned limitations (i.e. laws, schools), and genetic engineering. He was struck by the way the characters escaped limited reality by ingesting "soma," a tranquilizing drug.

In 1940, he entered medical school at the University of Pennsylvania after spending two years at Dartmouth. His mentor at there, the physiologist H.C. Bazett, introduced the technique that would establish Lilly's maverick approach to drug research. Bazett told Lilly that a scientist should never conduct an experiment on someone that he had not done on himself first. Bazett had in turn learned from his own mentor, the noted Indian scientist J.B.S. Haldane. To obtain scientific data on the human respiratory system, Haldane acted as his own guinea pig and gassed himself with mustard gas and guzzled various dilutions of hydrochloric acid, calcium chloride, and other chemicals, often becoming violently ill in the process. In the spirit of objectivity, Haldane referred to himself in research notes in the third person, explaining that he thought of himself as he would anyone else.

Lilly drew from this and came to see his body as a sacrifice to science, a laboratory and crash test dummy. In his own "metaphysical autobiography," Lilly cops Haldane's approach and refers to himself in third-person as simply "The Scientist." His life story is written as a final report on a lifelong series of experiments on his own brain and the results, and he eschews justifications for his actions. The reason he did what he did was simple: he wanted to find out what would happen, as with any other experiment. The easiest and most effective way of investigating a drug is trying it yourself, he believed. He followed the rules of science—and then bent the rules—going on to become an officer in the United States Public Health Corps and a recipient of a Research Career Award from the National Institutes of Health.

He was brilliant, and he knew it.

Stepping Outside Convention

Lilly, a tall, thin man with a regal and bird-like chiseled face, reported for duty at the National Institutes of Health in Bethesda, Maryland in 1953. In a building used by the Navy to study underwater breathing apparatus for divers, he developed the isolation tank. At this time, there were two opposing beliefs about brain activity. One group of scientists believed that the brain needed external stimulation to stay awake, and the other group believed that the brain's systems continued to oscillate and be active at all times, regardless of whether the brain was conducting transactions with the external world. This group also believed that consciousness was derived from this ongoing activity in the circuitry of the brain. Over the next two years, Lilly shaped the tank to exclude external stimulation and answer this question.

Early prototypes of the isolation tank were difficult to use and involved being completely submerged in water inside of a horizontal tube with a breathing apparatus attached to your face like a diver. Over the years, such tanks continue to be used, but have been refined into large, enclosed bathtubs. Climbing inside through a front hatch, a person enters an environment of complete darkness and lies in water that is neither hot nor cold (93°F). The water is heavily concentrated with Epsom salt, making it easy to float on top, face-up, with no pressure on the body.

Floating in this dark cave, Lilly discovered that the isolated mind becomes highly active and creative. "I did not tend to go to sleep at all," Lilly explained in his 1972 book, "The Center of the Cyclone." "The original theory was wrong…. One did not need external stimulation to stay awake. After a few tens of hours of experiences, I found phenomena that had been previously described in various literatures. I went through dreamlike states, trancelike states, mystical states." By isolating the mind, Lilly also found that he could also harness the power of his heightened senses. "By cutting off the environment I could examine the self in stark relief from a perspective that simply wasn't available to those who were continually involved with the demands of the outside world."


Lilly believed that by becoming unconscious of the body you could reduce the size of your consciousness, or observer, to an incredibly small size, allowing travel on a quantum level to different universes and galaxies as a small feeling/recording device. "At these levels there seem to be 'doorways' into other universes, doorways of incredibly small size, but nonetheless doorways."

Renowned theoretical physicist John Archibald Wheeler (1911-2008), a graduate of Baltimore City College high school, possibly provided some complementary insight to Lilly's mystical observation. Wheeler pioneered the study of black holes, helped build the atomic bomb, collaborated with Niels Bohr and Albert Einstein, and earned his PhD in physics from Johns Hopkins University at the age of twenty-one. His colleagues described him as a visionary, one who pushed the frontiers of science forward by means of physical intuition. Wheeler believed that "wormholes" (a term he invented) could act as a kind of cosmic shortcut through space and time, essentially a bridge linking different universes and points across vast distances. Theoretically, if you were small enough to jump inside of one, it would allow you to travel forward or backward in time faster than the speed of light.

Wheeler's wormholes look a lot like Lilly's doorways. Wheeler later concluded, along with Einstein, that time and the separation between past, present, and future was only an illusion. He also never gave up the belief that consciousness, or the observer, was a participant in shaping physical reality. Though Wheeler explicitly dismissed using his theory for supporting telepathy and extrasensory perception, it's possible that the latest science behind psychedelics and consciousness may eventually prove both Lilly and Wheeler correct. Lilly liked to point out that magic was simply the outward appearance of science we don't yet understand, and that "radio was silent in the 1700's." With practice, Lilly could simply park his body in the isolation tank and disappear; directly observing the workings of other dimensions while the world around him scurried like buzzed ants.

Lilly's work in the isolation tank, which began during the Korean War when the government was interested in devising techniques of brainwashing, rejected the notion of using it for torture, opting instead to focus on its use as a tool of cognitive liberation—a time machine, magic mirror, and mental radio all in one—and laid the groundwork for the contemporary float tank industry, which is experiencing a surge in popularity among Americans seeking retreat from a culture constantly assaulting the senses with artificial noise (See Field Tripping, p. 26).

Over time, Lilly became obsessed with his vessel, and practically detached himself completely from the outside world and its commitments, including his crumbling marriage. He spent hundreds of hours in the tank studying himself and exploring other dimensions. Lilly's colleagues at NIH encouraged him to try LSD in the tank, but he refused. Though it was legal and easily attainable for researchers at the time, Lilly didn't want anything to contaminate his isolation research. But that would soon change. He resigned from NIH in 1958 and with government grants constructed research labs in the Virgin Islands and Florida to investigate another large-brained floating mammal: the dolphin. If humans were capable of meditating such extraordinary things, he wondered, what was the larger brain of the dolphin capable of?

Polaroid photograph taken Easter Sunday 1991, at the home of Dr. Oscar Janiger. From left: Allen Ginsberg, Timothy Leary, and John C. Lilly, M.D.
Polaroid photograph taken Easter Sunday 1991, at the home of Dr. Oscar Janiger. From left: Allen Ginsberg, Timothy Leary, and John C. Lilly, M.D. (Philip H. Bailey)

Exploring LSD

Immersed in his research efforts to communicate with dolphins, it would be five years before Lilly turned his sites on LSD. But in 1964, he began to consider how the psychedelic drug might help his research into the mind.

He knew that researchers were told not to take LSD alone, that it could make a person feel like he had gone temporarily insane, and that a guide was recommended to watch over the physical body while the mind was away. He knew that he would need courage to take LSD alone in his isolation tank because fear is not an ideal state of mind for seeing things clearly. Putting up a resistance would only attenuate and distort the channel, producing a bad reading of the experience, thus skewing his results, or data. He had to relax and become wide open to get the full experience.

In May 1964, Lilly picked up a bottle labeled "Delysid (LSD 25)" and pierced its rubber top with a hypodermic needle, drawing in 100 micrograms. He injected the substance into his right thigh and climbed into his isolation tank. LSD acts like rocket fuel when used in isolation and the combination blasted Lilly further out of his body and into the universe than he had ever imagined possible. It was terrifying, he recalled. "I moved into a region of strange life forms, neither above nor below the human level, but strange beings, of strange shapes, metabolism, thought forms, and so forth," he'd later write. He then traveled down into his own body as a single point of consciousness, of feeling and recording, and explored his systems and organs all the way down to the atomic level. He became a speck on the sunbeam of some other universe, one thought in a huge mind, and one program in a cosmic computer.

Psychedelics can disable time and space, allowing users to experience unfiltered reality down to the quantum level and so, while a very sobering experience, it can be incredibly freeing and healing, Lilly discovered.

Lilly was a sexually repressed Midwestern Catholic boy with Welsh and German roots. He had designed his life as a quest for knowledge, and that had given his life purpose and meaning, but it didn't provide for balance. His relationships with women were marred by detachment, infidelity, and, ironically, communication problems. Inside the isolation tank, he saw these issues in new light, he said. His psychedelic experiences were humbling and helped him to realize that letting his scientific mindset carry over into his personal life had made him a sometimes cold and arrogant person, uninterested in examining the bonds that tied him to other humans.


"It was the most punishing I had ever had in my whole life," he wrote in the "Center of the Cyclone" in 1972. "The pain, the terror, the paranoid feelings were of the maximum energy that my organism could possibly have sustained without burning me out. During the next few days I was to experience and feel love of the intensity that I had felt earlier in my childhood. I was to go through grief, through all sorts of emotions that I had been blocking off and refusing to recognize because of my "scientific" knowledge. For the first time I began to consider that God really existed in me and that there is a guiding intelligence in the universe. For the first time since childhood, life was precious: the sun, the sea, the air, all were precious."

Self-analysis on psychedelics is absolutely ruthless and life altering, Lilly discovered. The experience of seeing one's own life with complete objectivity is justifiably perceived as a religious experience, along with feelings of being "born again" into a world of restored meaning that gave Lilly a more fearless perspective on life and death. He noted how psychedelics tied into spirituality, exploring how these ideas shrouded in mystery and deeply interwoven into cultures, religions, arts, and sciences throughout history were difficult to explain, so metaphors were employed to condense research down into narratives and tales, making ancient knowledge more easily transmittable through the oral tradition. He wondered, were psychedelics then the missing link between science and spirituality? Lilly began to believe that religion was an area for experimental science. He converted over 20 years of intense research and hundreds of experiments into a system of diagrams, correspondences, flowcharts, and instructions creating, in essence, a techno-Kabbalah.

The Human Guinea Pig

Lilly's trademark look in the 1980's befitted a pioneer of the mind. He favored a Daniel Boone-style coonskin cap and maroon tracksuit, with a compass and Swiss army knife attached to the pockets. His left hand was bandaged from a third-degree battery acid burn he incurred flipping his Dodge Camper (license plate number: "DOLFIN") over in the middle of the Pacific Coast Highway in 1987 after falling asleep at the wheel.

On his way home one morning, he ran up an embankment on the right side of the road, flipping his camper. He claimed that if he had been wearing his seatbelt, he'd have been decapitated. He spent most of his time submerged in inner spaces, though could sometimes be found sauntering across the grounds of the Esalen Institute in Big Sur, California, wearing a robe like Obi Wan Kenobi, dispensing wisdom and lecturing on dolphins, isolation, and psychedelics. "Cosmic love is absolutely ruthless and highly indifferent," Lilly would tell acolytes. "It teaches its lessons whether you like them or not." By 1987, the elder scientist and sage was living with chronic pain from using his body as a laboratory and vehicle for discovery for almost 40 years.

After all, he had not limited his research to LSD. In fact, after being introduced to the dissociative psychedelic drug ketamine by a friend and fellow physician in 1973 as a possible cure for his migraine headaches, he became enthralled with the drug and embarked on a drug investigation that nearly took his life on several occasions.

Ketamine, a commonly used anesthetic in animal care, makes users completely unaware of their bodies when taken in high doses. Lilly described the drug as a "chemical isolation tank" and he nearly drowned after passing out in his hot tub under its influence one day. After standing up too fast, his blood pressure plummeted and he fell unconscious face down in the water. He was transported by helicopter to a hospital and treated for a cut to the head. But in Lilly's mind, he had traveled to a utopian future world. After recovering from his injury and spending several days in a psychiatric hospital to judge his mental competence, he was discharged.

He continued to do intensive research on the long-term effects of ketamine for years. For three weeks straight, in 1974, he injected 50 milligrams of ketamine into his thigh 20 times a day, taking four hours off for sleep. Lilly became convinced that he was a visitor from the year 3001. One night, while relaxing with his wife at home, he noticed a strange flickering on the television, while U.S. Attorney General Elliot Richardson was delivering a speech. Lilly imagined that entities from another galaxy were intervening in human affairs through extraterrestrial agents disguised as government officials. Solid state electronics, including his television, were their tools of manipulation. He knew that he must contact the White House to warn them of this conspiracy before it was too late. He flew to New York alone, injecting ketamine all along the way. From a hotel room off Central Park, he phoned the White House and asked for President Gerald Ford. "What do you wish to speak to the President about?" the voice on the other end inquired. "I wish to speak to him about a danger to the human race involving atomic energy and computers," Lilly replied. "I will have to have more details than that. Who are you?" Lilly introduced himself before a psychiatrist friend grabbed the phone, apologized, and hung up. Lilly was involuntarily checked into a New York State Psychiatric Hospital.

Soon after his release he re-initiated his research. In and out of the isolation tank, Lilly studied how different concentrations of ketamine in the blood corresponded to changes in levels of consciousness. But a near-fatal bicycle crash in 1974 finally ended this drug study. On a long, twisting canyon road near his home in Malibu, Lilly was blissfully zipping along on his ten-speed when he lost connection with the external world. His bicycle was moving at 30 mph when the chain fell off and the wheels locked. Lilly was launched over the handlebars onto the hard pavement shoulder-first. He spent nine days in the hospital, suffering a broken collarbone, scapula, several ribs, and a punctured lung. His reputation and credibility were also seriously injured as a result of these events. To some of his orthodox colleagues, Lilly spoke more like a space cadet than a scientist, and his unconventional approach to research was mistaken for addiction. "When one is doing research on a substance, one takes it so frequently that outside observers can say you're addicted, but that's a very bad definition of addiction. Any good research is obsessive and compulsive," Lilly explained. He spent the rest of the 1970s and '80s pursuing his research into ketamine (under safer conditions) and in isolation at his ranch in Malibu. He also reinitiated his efforts into dolphin communication in hopes of using newer and more sophisticated computers available at the time as an interface between man and dolphin. In the 1990s he relocated to Hawaii and continued to travel around the world giving talks on his dolphin research.


Lilly's Legacy

In Lilly's seminal 1972 book, "Programming and Metaprogramming in the Human Biocomputer," he explored how much of human behavior was genetically determined and how much was "installed" by experiences in life, laying the groundwork for future research on the topic. In essence, Lilly found a graveyard at the outer limits of consciousness, a place where bad experiences are buried and forgotten. These experiences are coded into belief systems or assumptions—the beliefs behind your beliefs, as he described it—that operate like background programs running in our subconscious and controlling our behavior. With isolation and LSD, Lilly said that he was able to hack into the control panel of the mind and reveal these hidden sets of beliefs. Once revealed, or brought into awareness, limiting beliefs could be worked out through self-analysis and positive changes in behavior, he said. Limiting beliefs might be assumptions about appearance, self-worth, or current situation. Lilly urged readers to clean out the attic of their minds—unpacking and going through boxes of old pictures—in order to relive the painful memories and move toward healing. This "re programming," he said, enables people to see things more objectively, to see more of the unfiltered reality. This attainment of higher states of consciousness was the only way to find mentally healthy paths to personal and social progress, he believed.


Beliefs, unlike morals, are temporary platforms that dissolve into more complex beliefs as your consciousness is raised—experience is gained and better questions are formulated. Lilly saw psychedelic drugs as a way of advance this process of self-awareness. "Too many intellectuals and scientists (almost unconsciously) use basic assumptions as defenses against their fears of other assumptions and their consequences," Lilly explained. Looking into our assumptions, or limits, about what is and isn't possible, can reveal new possibilities and paths to real progress, he said. "Freedom is in the unknown."

By using these sets of assumptions as tools of scientific investigation—setting them up, knocking them back down again, and moving them like scaffolding to navigate the mind in search of higher truths—Lilly was determined to reconfigure our perception of reality. With these thought experiments, he sought to obtain data from the nether regions of the mind and used the information he gathered on these forays to create a map of the subconscious.

But in 1968, Lilly was instructed that all experiments with psychedelics were to be stopped, and was told to send his reserves of Sandoz back to Switzerland. On the last day he could use the substance for research, Lilly took a powerboat out onto the sea, north of the British Virgin Islands. Shortly after injecting himself with LSD, he felt two presences near the boat. "Two dolphins," the skipper announced, as two dolphins emerged out of the water. Lilly then felt another, larger presence. "Whale!" the skipper added. A finback whale accompanied the two dolphins. They rowed the boat up next to them. "She (the whale) zapped me," Lilly reported. "I've never had such a powerful blast of mental telepathic information being shot into my brain….For twenty minutes she riveted my attention. She had one eye turned up looking at me, and then dropped down into 12,000 feet of water and just disappeared. I've never had such an experience since."

In 1970, Nixon signed the Controlled Substances Act making most psychedelics a Schedule One drug: those with "no currently accepted medical use in treatment in the United States." As federal research funding dried up and heavy restrictions were placed on obtaining substances for research purposes, the scientific community wound down its work. The last psychedelic research study in the United States was at the Maryland Psychiatric Research Center at Spring Grove Hospital in 1977, and the man who administered the last dose of psilocybin to the final volunteer was psychologist Bill Richards. It would be over two decades before clinical psychedelic research would resume.

When Lilly died in Los Angeles on September 30, 2001, he was 86 years old. Of Lilly, one of his former colleagues remarked, "there were those who thought he was brilliant, and there were those who just thought he was insane, I, of course, thought he was a little bit of both."