In the continuing effort to understand the human brain, the mysteries keep piling up. Consider what scientists are up against. Stretched flat, the human neocortex -- the center of our higher mental functions -- is about the size and thickness of a formal dinner napkin.

With 100 billion cells, each with 1,000 to 10,000 synapses, the neocortex makes roughly 100 trillion connections and contains 300 million feet of wiring packed with other tissue into a one-and-a-half-quart volume in the brain.

These cells are arranged in six very similar layers, inviting confusion. Within these layers, different regions carry out vision, hearing, touch, the sense of balance, movement, emotional responses and every other feat of cognition. More mysterious yet, there are 10 times as many feedback connections -- from the neocortex to lower levels of the brain -- as there are feed-forward or bottom-up connections.

Added to these mysteries is the lack of a good framework for understanding the brain's connectivity and electrochemistry. Researchers do not know how the six-layered cortical sheet gives rise to the sense of self. They have not been able to disentangle the role of genes and experience in shaping brains. They do not know how the firing of billions of loosely coupled neurons gives rise to coordinated, goal-directed behavior.

They can see trees but no forest.

They do think they have solved one longstanding mystery, though. Most neuroscientists are convinced the mind is in no way separate from the brain. In the brain they have found a physical basis for all our thoughts, aspirations, language, sense of consciousness, moral beliefs and everything else that makes us human. All of this arises from interactions among billions of ordinary cells. Neuroscience finds no duality, no finger of God animating the human mind.

So what have neuroscientists been doing? Like a child who takes apart his father's watch, they have dissected the brain and now have almost all the pieces laid out before them. There are thousands of clues about what makes the brain tick.

But how to put it back together? How to understand something so complex by examining it piecemeal? Even harder, how to integrate the different levels of analysis? Some brain events occur in fractions of milliseconds while others, like long-term memory formation, can take days or weeks. One can study molecules, ion channels, single neurons, functional areas, circuits, oscillations and chemistry. There are neural stem cells and mechanisms of plasticity, which involve how the brain changes with experience or recovers from injury.

New research tools continue to drive progress. In the late 1970's, researchers mostly placed sharp-tipped electrodes into single cells and measured firing patterns. By the 1990's, they had machines that could take images of brain activity while people spoke, read, gambled, solved moral dilemmas or, in a recent study, had orgasms.

Unfortunately, studies like these, while fascinating, tend to feed the fires of a huge disagreement within the brain sciences: is the brain made up of discrete modules that pass information among themselves? Or is it more loosely organized so that varied pockets of distant neurons fire together when called upon to perform a particular task? In mapping the brain, some researchers say that areas dedicated to aspects of language, arm movements or face recognition are hard-wired modules.

Other researchers say that such areas are surprisingly flexible. For example, the human face recognition area is where expert bird watchers distinguish features of closely related species or car experts decide if a 1958 or 1959 Plymouth had bigger fins.

While the two sides in this debate agree that the brain is prewired to some degree at birth, the nature of that prewiring is uncertain. What do genes expressed in the brain do? How do genes influence behavior? What is innate and what is flexible? What is the role of culture in shaping a brain?

While lacking a coherent framework, scientists are nevertheless making progress in mapping the correlations between brain activity and behavior. New imaging tools reveal circuits and overall patterns of activity as people solve problems or reflect on their feelings. Genes expressed in mouse brain cells are being mapped so that researchers can begin to find out if neurons that look alike have different proteins and functions. A magnetic device can knock out human brain regions, safely and temporarily, to learn what those regions do.

A lively debate continues over the nature of time in brain function. In the absence of stimulation from the outside world, neurons remain active; they are filled with electrical currents that give them a propensity to oscillate and, on interacting, create spiking patterns of activity. Do the spikes carry precise information? Or do such spikes average out over large areas? How is information carried in the brain?

One of the most exciting developments is the recent exploration of the frontal lobes. Located behind the forehead, the frontal lobes help create the social brain, melding emotions, cognition, error detection, the body, volition and an autobiographical sense of self. Special circuits containing spindle cells appear to broadcast messages -- this feels right, this does not feel right -- to the rest of the brain. Researchers are finding that emotions arise from body states as well as brain states, confirming that the supposed distinction between mind and body is illusory.

Others are delving into individual differences. What makes one person empathic, another mean or shy or articulate or musical? How do genes relate to temperament and how is a baby's brain constructed from early experience? Specialized cells called mirror neurons seem to help babies imitate the world to learn gestures, facial expressions, language and feelings.

Brain chemistry is no longer the study of neuromodulators as ''juices'' that make us feel good or awake. Substances like serotonin, dopamine and norepinephrine play crucial roles in learning, updating memories and neuropsychiatric disease.

The question of free will is on the table. Some of our behavior is conscious, but most of it is notoriously unconscious. So although we make choices, is free will mostly an illusion? And what is consciousness? In seeking an explanation, a new mystery has emerged. Many scientists now believe that the brain basically works by simulating reality. The sights, sounds and touches that flow into the brain are put in the framework of what the brain expects on the basis of previous experience and memory.

In the words of many neuroscientists, all these mysteries are terrific job security.