The Nobel laureate who 40 years ago codiscovered the double-helix structure of DNA - the master molecule that contains the genetic code - is in his office over-looking the Pacific Ocean at the Salk Institute in La Jolla, California. Francis Crick is studying a postcard reproduction of William Blake's famous etching of Isaac Newton in which the great scientist is depicted naked, sitting in a cleft of rock. Newton is bent with his compass in hand, trying - rationally - to decipher the mysteries of our universe.

It was Blake, the eighteenth-century poet and artist, who warned that scientists, in trying to decipher that which should remain indecipherable, would "turn that which is Soul & Life into a Mill or Machine."

If Blake were alive today, it seems a fair bet that Crick, and his new book The Astonishing Hypothesis: The Scientific Search for the Soul, would surely provoke his ire. In the book, Crick, now 77, baldly sets out to discover whether what we commonly regard as soul or consciousness is actually a machine, a neural machine. And he implores the scientific community to tackle "the experimental study of consciousness and its relationship, if any, to the hypothetical immortal soul."

Crick's "astonishing hypothesis" declares that all of our interior states, joys and sorrows, our memories and ambitions, even our personal identity and the cherished notion of free will, are no more than the behavior of a vast assembly of nerve cells." And with an audacity that Blake would have found heretical, Crick also claims to have located the seat of free will inside the brain.

The desire to map what we call consciousness - what Crick also calls awareness - is not new. But with the publication of his book, Crick, one of the fiercest reductionists in science, has joined one of the hottest scientific debates of the decade. And his views, he admits, are a "head-on contradiction to the religious beliefs of billions of human beings alive today."

Crick comes to the consciousness wars armed, of course, with impressive credentials. However, at the age of 31, when Crick, having spent the war years designing mines to blow up German merchant ships, took stock of his scientific credentials, he found himself with, a "not-very-good degree," redeemed somewhat by his achievements at the Admiralty. "No published papers at all," he says.

Determined to get work in England's postwar science boom, he applied his "gossip test" to his own life. Crick's gossip test says that the things you are talking and thinking about, you should go to work on. The two subjects which he settled on in 1947 for his life's work touched on problems which, in many circles, seemed beyond the power of science to explain. "What attracted me to them was that each contained a major mystery - the mystery of life and the mystery of consciousness. I wanted to know what, in scientific terms, those mysteries were." Six years later, he and James Watson had discovered the structure of DNA, widely regarded as the most important biological discovery of the twentieth century, earning them both a share of the prestigious Nobel Prize in medicine. Fifteen years ago, after arriving at the Salk Institute, Crick turned his attention to the study of the second subject which he had chosen to investigate in 1947, the mystery of consciousness.

"What is the neural basis of consciousness?" he asks. "That's the problem. Obviously, it's very mysterious." But people have forgotten, Crick reminds us, how mysterious the nature of genes appeared as late as 1943. Molecular biology, at the time, was considered a sloppy field. "The phrase Watson uses is 'intellectual chaos.' That is exactly the state of our ideas of the brain - intellectual chaos. Lots of ideas rumbling around but nothing very clear. People arguing about things that will probably turn out to be pretty fatuous eventually - it's just chaotic."

To Crick, the key to understanding the mystery we call the soul does not lie in religion, philosophy, or psychology, but in neurons. Most current ideas about the brain, he argues, will not survive a detailed understanding of how it works; the idea of a soul or mind separate from the brain and not penetrable by our known scientific laws is probably an outdated myth, he says. Looked at in the perspective of human history, he argues, the main object of scientific research on the brain is not merely to understand and cure what may afflict us, but "to grasp the nature of the human soul." Whether this term is metaphorical or literal is exactly what Crick is trying to discover.

Unlike dualists, such as neuroscientist Sir John Eccles, who believe in the "ghost in the machine," Crick doubts whether there is any need for a spiritual concept of a soul to explain behavior. Religion, he claims, is "based on evidence which by scientific standards is so flimsy that only an act of blind faith makes it acceptable." In fact, he suggests, raising his white, prominent eyebrows that give him a devilish air, "if the members of a church really believe in a life after death, why do they not conduct sound experiments to establish it?"

The only way to understand what we regard as the soul, Crick argues, is to understand how nerve cells in the brain behave and interact. But with 100,000 neurons beneath every square millimeter of the brain's cortical sheet, and with the human cortex containing some tens of billions of neurons - comparable to all the stars in our galaxy - how does Crick suggest scientists go about this?

Experimentation on the living human brain is limited by ethical considerations. "Most people do not object to an experimenter fixing electrodes to their scalp in order to study their brain waves," Crick says, "but they do object to having a portion of their skull removed, even temporarily, so that electrodes can be stuck directly into living brain tissue." Crick suggests an alternative strategy, which seems, at first glance, deceptively simple. If you want to learn how consciousness works, concentrate your research on the visual system - on how we see. That our eyes are the windows to our soul is not just an aphorism to Crick.

"Visual awareness is an example of consciousness," Crick says, and as if to underscore his point, a yellow-and-blue hang glider drifts into view outside his office window, swooping and diving above the Pacific. He leans forward.

"We have a very vivid picture of the world. The question is how that is produced in the brain."

Visual perception combines attention with short-term memory, but by standards of exact sciences, Crick points out, we don't know how our brains produce the visual awareness that we take so much for granted. We can glimpse fragments of the processes involved - the way the eye responds to light - but we lack both the detailed information and the ideas to answer the most simple questions: How do we see color? What is happening when we recall the image of a familiar face?

Although the main function of the visual system is to perceive objects and events around us, the information available to our eyes "is not sufficient by itself to provide the brain with its unique interpretation of the visual world." In a recent special issue of Scientific American devoted to the mind and brain Crick and his collaborator for the past several years, Christof Koch, a computation and neural-systems specialist from the California Institute of Technology, speculated on how the brain uses past experience - "either its own or that of our distant ancestors, which is embedded in our genes" - to help interpret the information coming into our eyes. "Your eyes - or we will say - your brain," they wrote, "must find the best interpretation of visual symbols in the light of its past experience. Thus, what the brain has to build up is a many-level interpretation of the visual scene, usually in terms of objects and events and their meaning to us."

Crick suspects that visual awareness - and perhaps consciousness itself - involves the cortex and also the thalamus, which he calls the "organ of attention." All senses (except smell) have to pass through the thalamus, the gateway to the cortex. Consciousness, Crick says, depends "crucially on thalamic connections with the cortex."

The cortex consists of two separate sheets of nerve cells, one on each side of the head. These cortical sheets are, in Crick's words, "about the size of a man's handkerchief" and are folded so as to fit on either side of the skull. Often referred to as gray matter, the cortex consists mainly of neurons or nerve cells, which are electrical and chemical signalers.

The job of a neuron is to receive information, usually in the form of electrical pulses, from other neurons. Some of these connections are local - they on best, a few millimeters - but others leave the cortical sheet and travel some distance before entering another part of the sheet or going elsewhere, for example to the thalamus or the spinal cord. These longer connections are often covered by a fatty sheath, which enables the signal to travel faster and which gives this tissue a somewhat white, glistening appearance. Forty percent of our brain is made of this "white matter," and this is crucial to Crick's notion of just how much communication there is within the brain.

This communication system handles both explicit and implicit representations of the visual world. The explicit representation is symbolized without further extensive processing. An implicit one contains information but needs further processing to make it explicit. Crick hypothesizes that our brain must produce an explicit multilevel symbolic interpretation of the visual scene in order for us to "see" it.

Some people, Crick says, may find it difficult to accept that what we see is only a symbolic interpretation of the world - it all seems so like the "real thing." Unlike, for example, the Hindu belief that what we see is "maya," or illusion, and that nothing we see actually exists, Crick argues that the world does exist but that "we have no direct knowledge of objects in the world."

And though Crick believes that visual consciousness is, in part at least, about the very route information takes through the brain, and most importantly, where it gets to and which neurons are firing, he confesses, "I myself find it difficult at times to avoid the idea of the homunculus - a little man in our head directing it all. One slips into it so easily." And if all this sounds a bit complex, Crick sums it up neatly, grinning, "As Lewis Carroll's Alice might have phrased it, 'You're nothing but a pack of neurons.'"

Some of Crick's colleagues at the Salk Institute may have wondered if Crick himself had gone through the looking glass last year when he bounded into an afternoon faculty tea announcing that he'd located the seat of free will in the human brain. Crick describes free will as the "feeling that one is free to make personal choices."

What prompted this announcement was an account he'd read by his colleague Antonio Damasio, a well-known neurologist, of a woman who prior to recovery from brain damage had suffered a loss of will. The importance of studying cases of brain damage, Crick says, is that they show which parts of the brain are necessary for functions such as consciousness or free will. For a month, the woman appeared unresponsive, Iying in bed but with an alert expression. She could follow people with her eyes but did not speak spontaneously. She gave no verbal reply to any questions put to her, though she appeared to understand because of the way she nodded in reply. When the woman recovered, she said she had not been upset by her inability to communicate even though she'd been able to follow conversations; she hadn't talked because she had had "nothing to say." Her mind had been "empty."

Crick was intrigued. "I immediately thought she'd lost her will and wondered where the damage was." The damage turned out to be in or near the anterior cingulate sulcus, a region Crick was delighted to learn receives many inputs from higher sensory regions, and, as he had guessed, is at or near the higher levels of the motor system where movements are planned. "Take the complex act of swimming," he says. "How does the brain plan it all?" According to Crick, one of the functions of visual awareness is to plan movements. "What is the connection between seeing something and the part of the brain that plans and executes movements?" he asks. "Clearly, it's about neurons firing."

Reading more case histories, Crick stumbled upon the "alien hand" syndrome, a kind of brain damage in which one of the patient's hands makes simple movements, which the patient denies he or she willed. A patient's left hand, for example, might spontaneously grasp some object put near it, though the patient denies that he or she is responsible for the movement. In some cases, the patient is unable to get the hand to let go and has to use the right hand to detach the left hand from the object. One patient found that he couldn't make his "alien" hand let go by his own willpower, but he could make it release its grasp by saying, "Let go!" in a loud voice. These cases fascinated Crick, especially when he learned that the damage was again in or near the anterior cingulate sulcus, substantiating his theory that this is the seat of free will.

Some scientists have speculated that the seat of consciousness is located in the hippocampus, a small, sea-horse-shaped part of the brain that stores for a few weeks or more the codes for new long-term, episodic memories before the information is conveyed to the neocortex. Crick disagrees, citing the case of a patient who had his hippocampus system on both sides knocked out after an injury. While the patient couldn't remember anything that happened more than a minute before, he could see and talk perfectly well, which convinced Crick to rule out the hippocampal system as the seat of consciousness.

The trouble with speculation about consciousness, Crick admits,"is that the damage is rather crude. If we could make nicely controlled brain damage on people, we could find out how the brain works, but we're not allowed to do that - quite rightly."

A plastic model of the human brain is on a shelf nearby. When I asked Crick to show me the location of free will, he cautioned, back-pedaling a bit, "Now, this is still highly speculative." From the walls of his office, portraits of Einstein and Darwin stare down at us. He cradles the brain in his hands and says, rubbing the anterior cingulate sulcus with his forefinger, "Free will is most likely located here, but we think there probably is a frontal component as well. It certainly isn't at the back of the brain." He lays his thumb against the primary motor area: "Yes, it's definitely near here, but it may depend on interactions with this frontal region."

When reminded of the widespread belief in the existence of the soul separate from the body, he pauses, looks up from the model, and says flatly, with perfect timing, "Surely, if almost everyone believed it, that is in itself prima facie evidence for it. But then some 4,000 years ago, almost everyone believed the earth was flat."

Smiling now, Crick reminds me that his friend Leslie Orgel has teasingly suggested that there may be a religious peptide in the brain. Seeing that this speculation is going on the record, he settles back in his chair. "Oh, I don't think there is quite a religious peptide, but there is probably something in people's brains that makes some of them more susceptible to religion than others. Whether it's inherited or not or whether it's something produced by early training is like the question about homosexuality. There's no reason why all that shouldn't be found out."

Eight paintings of nude women line Crick's office at his quiet, airy home in La Jolla. They were painted by his wife, Odile, whose studio adjoins his office. It was Odile's drawing of a double helix that accompanied the now-legendary 700-word article in Nature, the British science magazine, announcing the 1953 discovery of the molecular structure of DNA.

The Cricks have been married 44 years. Odile, with bright hazel eyes and a quick laugh, says of their courtship, which began when she was translating captured German documents in London, "I'd never been with a scientist; it took some getting used to. When we went on our first picnic one very romantic afternoon, Francis gave me a lecture on gravity." They are both laughing now. "I simply asked," Cricks says, "if she knew how far up gravity went."

On Crick's desk is a home computer - nothing fancy, a simple workstation. Mostly he uses it for accounting and domestic functions. He finds computers, he says, "a bit obsessional" and prefers to work out his scientific theories in longhand. When the discussion turns to the comparison of the brain to a computer, Crick cautions that this parallel, if carried too far, leads to unrealistic theories. In the first place, he explains, a computer works much more quickly than the human brain. And while the operations in a computer are largely serial - one after another - the arrangements in the brain "are usually massively parallel. For example, about a million axons go from each eye to the brain, all working simultaneously." The loss of a few neurons is unlikely to alter the brain's behavior appreciably. "In technical jargon," Crick says, "the brain is said to 'degrade gracefully.' A computer degrades catastrophically - even small damage may cause havoc." A typical neuron in the brain can have anywhere from a few hundred to many tens of thousands of inputs, but a transistor - a basic unit in a computer - has only a few inputs and outputs. Yes, Crick argues, computers can be programmed for extensive number crunching, rigid logic, and playing on chess, but when faced with tasks that ordinary humans can do in a rapid and effortless way, such as seeing objects and understanding their significance, even the most modern computers fail. And yet in the storage and retrieval of information, the computer is much more precise, and it's clear that memory is stored in a computer in a different way. But for Crick, the fundamental difference is that while a computer has been deliberately designed by engineers, the "brain has evolved over many generations of animals under the pressures of natural selection."

The mysterious aspects of consciousness might disappear if we could build machines that had the "astonishing characteristics of the brain and if we could follow exactly how they worked," Crick says, but he does not hold much hope that in the near future such a machine will be built. "Perhaps they will be more like the brain of a frog or even that of a humble fruit fly. Until we understand what makes us conscious, we are not likely to be able to design the right sort of artificial machine nor to arrive at firm conclusions about consciousness in lower animals."

The problem of consciousness Crick believes, will be far more difficult to solve than DNA. "But you have to remember," he says, "that we didn't know how simple DNA was. For all we know, there may be a simple answer to this one, but it doesn't seem likely. The brain is a more complex system. DNA was much earlier in evolution - the answer had to be simpler or it wouldn't have got started. DNA has been here for three and a half billion years. Consciousness is relatively late. Don't forget, modern man has been here for only a hundred thousand years or so."

For Crick, the image of the brain as an impenetrable black box is outdated and self-defeating. "Most of the mysteries of life are not seeable - all of science depends on roundabout methods. If it were straightforward, it would be done straightaway." Our secret weapon in brain research, Crick suggests, may not be theorists and computation experts, but people who are using computers to solve practical problems. In the workplace, "people have to produce gadgets that work, which is what evolution has to do." For example, the post office had to produce a machine that can read handwritten zip codes. Gadgets like this "probably, will give us ideas of what happens in the brain, because evolution tends to produce gadgets as well. In that sense, evolution knows nothing about theory; it only knows how to build gadgets."

From San Diego, it's two hours over the mountains to the house Francis and Odile Crick have recently built in the Anza Borego desert. Driving down Montezuma's Grade toward the desert floor, the steep, boulder-strewn descent is reminiscent of the barren, atavistic landscape at the start of 2001: A Space Odyssey. In the distance is the dying Salton Sea, which historian Bill deBuys calls a "place where consequences collect."

This is where Crick goes to get away, his hermitage. And like his work in neurobiology, which he turned to after decades of pioneering work in molecular and developmental biology, he is slowly mapping the territory out here as well, walking trails each twilight through the desert with his wife, learning the names of wildlife and vegetation: creosote bush, ocotillo, elephant tree. It is to this desert in blistering afternoon sun that we have come to talk about the culture that Crick foresees if indeed scientists find that the soul is simply a machine.

He says he will be very surprised if developments in science "don't make radical changes in the way educated people think of themselves." And still, he knows, like the debate over evolution, vast numbers won't be influenced - "usually for religious reasons."

In Crick's culture, psychology will be a hard science, and philosophy departments will house researchers who also have degrees in biology or neurobiology. And words like conscious and unconscious, he suggests, may be replaced by processing unit or awareness unit. (Already, Patricia Churchland, one of the few philosophers in the world with a detailed knowledge of neurons and the brain and also of neural networks has, at Crick's urging, an adjunct appointment at the Salk Institute.)

"Many people think all things can't be explained by chemistry and physics, that it's explainable only as something outside science - a life force. That was also the view about our genetic inheritance before we knew about DNA. Most scientists believe there isn't anything else." But, he admits, "that's still a hypothesis." He knows at this point based on the scientific data, that he couldn't convince a skeptic. "They would just say, 'That is just your prejudice."' He adds, with a chuckle, "Which is not to say that your prejudice may not turn out to be right."

He admits that some people will be disturbed by the religious implications of the book, especially those who believe there is life after death. "The implication that it might not be true and that we might be able to show it scientifically will be disturbing." The others who will be disturbed, he says, are those "who don't actually believe in life after death but who haven't faced up to the implications of it yet." Though beliefs change slowly, the church in Crick's culture will increasingly have to reckon with science. "Scientifically, we know if you are out in a thunderstorm, the chances are increased that you may be struck by lightning. We no longer think that it's because we didn't sacrifice an ox recently to Jove. Look at the beliefs people had in the past. Do you really think it was sensible to look at the entrails of a chicken to predict what was going to happen in the future?"

He predicts that while scientists "are basically tolerant of religion, that may not last. There eventually will be conflict. We might even see religious science wars. One would hope that could be avoided." People outside the scientific culture, Crick says, "are naturally beginning to feel threatened by scientists. And they are wise to feel that. They will be threatened."

I venture to ask if Blake was right to warn of scientists turning that which is soul into machine? Are there some things that should remain undeciphered? Crick is smiling now - a mischievous, ironic smile. "You know," he says, "Blake used to sit outside naked in the garden with his wife and talk to angels. Now l've got nothing against sitting naked in the garden, but talking to angels - don't you find that a bit odd?"

The desert sun has begun to sink behind the Santa Ysidro Mountains, its nearly autumnal colors settling over Crick's face, softening his angular features. I wonder if, in his scientific view, there is room for mystery. "Well, what do you mean by mystery?" he asks. "It's a mystery how the darn thing behaves, whether it's in the activities of neurons or not." And as if he implicitly understands what the next question must be, for it is the universal question of an anxious and God-yearning people - If soul is only a metaphor, a story we tell to comfort ourselves, and if there is no ghost in the machine, then what does that leave us with? - Crick leans forward, his face reflecting the last light of this fading day, and says, "Think about the size of the universe. In Shakespeare's time they had no idea how big the universe was. Does our knowledge today remove the mystery of it? It seems to me what you lose in mystery you gain in awe."

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