How to Think about the Brain

The brain is a complex biological system. It is the unity of a massive set of cooperating, interacting, and interdependent biological parts and chemical processes. Unlike other biochemical systems, the brain exhibits a persistent epiphenomenon: the mind. The mind represents the flow of all those things—behaviors, sensations, thoughts, reasoning, emotions, communications, dreams—that reflect what the brain is doing. It is challenging, and in some cases apparently impossible, for some people to grasp that brain and mind are, literally, intertwined as a singular complexity.  Neither the living brain nor mind can exist without the other. The brain is made up of biological entities and has physical boundaries, albeit exceedingly complex; the mind, the entirety of that which we witness as brain processes, is abstract and boundless.

In order to think about the brain accurately and comprehensively, it is essential to inseparably tie the biological and mental parts and processes together. A unifying, comprehensive set of premises is herein offered for how to think about the brain/mind in a way that reveals and respects its magnificent and true nature. Because of its overwhelming scope, the brain is often described in fragmented form as a simplified aid for how it might be understood. Adopting some guiding principles for how to think about the brain will preserve its intriguing complexity, and make understanding it more inclusive.

The human brain has been called the most complex biological system known, more vast and complex than the cosmic universe. It has captivated its possessors’ zeal to understand it, cure its ills, and use it well. Trying to figure out how to comprehend its, literally, uncountable parts, connections, and processes—and the mind these yield—often results in fragmented, reductionistic, or metaphorical descriptions. While we need to understand the trees, the greatness of the forest should not be undermined.

Is there a way to think about the brain that might engage a broad, conceptually encompassing focus about what the brain is and does without resorting to reductive simplicity, or incomplete or erroneous metaphor or analogy? The brain performs massive calculations in complex manners unparalleled, and likely unimaginable, in computer hardware. The brain ensnares unceasing noise and randomness and yields conscious regularities (understandable patterns and perceptions) unlike any other known biological or technological object. The brain intervenes between atoms and cultures, turning a massive environment of chaos into ordered consciousness and mental activity.

To provide grounding, consider that the human brain is roughly two million years old—an evolving biological product that sifts perceptual grain from chaff; weaves momentary experiences into cohesive and temporal memories; assembles and executes bodily responses on the fly, selecting from most easily accessible and pertinent information; and creates thought trajectories that yield ideas, communications, and social cooperation. The brain accomplishes all these things extremely fast and with numerous operations performed in parallel. The brain has evolved as, and is becoming, the consummate multi-tasker.

The brain was the “black box” of a half century ago, dismissed for scientific study because of insufficient technology required to explore it. With sophistication in broad areas of neuroscience and biotechnology, however, the brain may now be appreciated well beyond that of an elusive psychological or behavior-producing organ. The brain is emerging as an understandable biological system composed of atoms, molecules, and  proteins, constantly changing and interacting, producing all the psychology one may ever observe or experience. Understanding, exactly, how and why this happens is the on-going challenge of modern neuroscience.

Underlying virtually every aspect of mind and behavior is both the nanometric goings-on of quadrillions of atoms joining forces to produce trillions of molecules and billions of proteins, all interacting and interdependent. The brain is created out of these basic entities, yielding billions of neural cells and trillions of ever-changing inter- and intraneural connections. The purpose of these entities and their processes is to establish and maintain cooperation for the sake of brain-environment interactions. While seemingly overwhelming, thinking about this mass of biological entities and dynamics yields a rich understanding of how mind is the observable product of unseen biological entities. A rich understanding of the biological brain yields more insight into behavior than can any reified psychological concept or incomplete metaphor.

The brain is a dynamic, self-organizing biological construction that uses recursive externally- and internally-generated stimuli that yields both simple and complex interaction with its environment. Each response orchestrated by the brain feeds back into itself, providing historical grist for the stimulus mill that will yield the next round of responses. This self-organizing process happens on scales of quanta and eons, dimensions that humans are not used to imagining. In addition to its moment-by-moment molecular changes in response to massive amounts and kinds of stimuli, the brain is also an on-going individual, social, and cultural product, changing and evolving over large time scales.

Here are several premises that may be useful in order to maintain a comprehensive encapsulation of brain and mind. These premises are not mutually exclusive but reflect aspects of the greater whole.

The brain is a molecular colloquy. Molecular conversation is the fundamental, back-stage level from which the grand dance may be appreciated and on which every behavioral and psychological on-stage phenomenon emerges. Understanding this molecular colloquy requires thinking about things that are very small, very fast, and very versatile. Uncountable atoms are ever in phases of building up and breaking down molecules and proteins in response to environmental influences, genetic activations, and energy demands. Perturbations abound, constantly modifying the processes, yet allowing the dance to thrive, change, and grow as a beautiful, rhythmic, and entrancing biological/psychological experience.

By virtue of their ability to communicate with one another through electrochemical attractions and repulsions, the array of proteins constantly changes patterns of intermolecular associations and movements. These dynamics are not normally chaotic, but self-organize into functional processes that serve some down-stream electrochemical, and ultimately mental, purpose. Each effect in the dynamic goings on is a consequence of the past and a constituent for the future. Over time, success of down-stream purposes feed back to more elementary processes, encouraging stronger and more predictable self-organization. Perturbations that challenge the organization of the dance at any instant will be responded to in the brain’s best available manner to protect the grand scheme of the dance, all held together by a common (but, no surprise, extremely complex) playbook—the individual genome.

The brain is a complex system. The molecular colloquy that develops from the zygote emerges into super-systems of proteins, cells, tissues, brain and other organs, and body, all within and in response to an ever-changing environment. The brain-as-system simultaneously integrates physiology, emotion, behavioral responses, thoughts, and social exchange, producing diverse mental experiences. The parallel processing among the components, pathways, and connections and their interrelationships within the brain is not linear; interactive trajectories flow in many directions simultaneously and interact with each other as multiple systems and hierarchical subsystems. Nonlinearity—a hallmark of complex systems—can be appreciated as the emergent properties of a system: the product being greater than the sum of its parts.

If a person can wrap one’s mind around the concept of a complex system—an interconnectivity of a massive number of components, internal and external stimulus perturbations, and vast biological and chemical processes, changing over exceedingly brief and exceptionally long time spans—then thinking about the brain can proceed without resort to reductionist simplification or mysterious voodoo.

The brain functions on the basis of evolutionary purpose and self-organization. Without evolutionary purpose, chaos would drive the brain into disorder and extinction. Through multiple simultaneous and sequential developmental processes, the atoms, molecules, and so forth of the brain stumble on regularities and irregularities of electrochemical interaction, out of which emerge processes that are (eventually) supportive in sustaining better overall functioning in order to optimally sustain and reproduce life.

Accepting this premise instills in one the admonishment that nothing is simple in understanding the brain-as-system. Simple linear causal relationships rarely exist at any level of the brain. Simplistic or fragmental explanations never tell the whole story.

The electrochemical processes of the brain represent synergistic interactions. Just as when we take a medication targeted for a specific purpose, numerous “side effects” occur as well. This is an example of how genes and intrinsic molecules work in the brain. The nonlinear, synergistic interactions constantly evolve in a self-organizing manner, effecting multiple subsystems in order to optimally support life and reproduction.

The brain functions on the basis of recursive influence. Behavioral, cognitive, and emotional responses also produce internally-generated stimuli that flow back into the brain. The brain depends on current, historical, and predictive stimuli in order to manage an elaborate continuity of stimuli, responses, memories, and predictions. Simultaneously, externally-generated stimuli provide an ever fanatical bombardment to the body which brain machinations must sort, concatenate, accept, reject, or delay, depending on the brain’s time-molecular state at the moment. The uncountable sources of internal and external inputs could easily overwhelm the brain, but emergent organized molecular processes can (usually) manage to avoid or restrict chaos.

The molecular dance is not strictly rule-bound but is also spontaneous. The brain abides by evolutionary purpose and genetic guidelines but is also influenced by massive amounts of data from elsewhere in the brain, body, and environment. Nothing in the brain happens in isolation but happens within the context of memory of past biological states, and simultaneous stimulation from innumerable molecular states. Biological organization of future responses and states becomes constrained such that future responses become more efficient and conform to patterns of past influences.

Every gene or set of genes that is expressed in the brain may potentially influence thousands of molecular structures and processes (as well as other genes), improving or diminishing their properties and actions based on molecular history and context. However much we have been taught that the genetic code is a blueprint, it absolutely is not. Genes are not linear in their influence but provide the foundation for complexly interactive molecules and proteins, all in the service of optimizing life and reproductive success.

The nature of the complex brain system, through multiple interacting, simultaneous, and sequential molecular processes, creates cascades of results. Any action or thought produced by the system feeds back on the system itself as new stimulus influence on how the next cascades of molecular processes will play out. Virtually any concept from behavioral psychology is no longer seen in the traditional fixed S->R paradigm, but in both an ever constraining and elaborated S->->S->R-> … paradigm.

Brain functions are partly stochastic. The state of the brain, moment-by-moment, is the product of both predictable and deterministic (purposeful and influenced) processes as well as stochastic (random and probabilistic) processes. The brain has only a semblance of a guidebook—the genetic code—for how the molecular dance is played out. The system utilizes random, unpredictable, probabilistic, and accidental actions as elements to be integrated, repeated, or eliminated within the organizational state the system exhibits at any given moment. The dance includes dancers constantly entering and leaving the somewhat improvised performance. Sometimes the dance is improved by this exchange, occasionally not. The fundamental underlying process which emerges in the brain is neural self-organization.

The brain is a chronology. The brain works on both fast and slow time scales. The brain can be thought of as exhibiting processes reflecting clear temporal qualities as well as representing things. The processes that accomplish the brain’s functions do so through modular neural entities and distributed interconnections. The brain changes these configurations moment-by-moment on one scale within the individual, and over the course of thousands of years on the scale of the species. The brain binds bits of information within its electrochemical dynamics into wholes that subjectively hang together in unified temporal trajectories. Through the process of pulling together simultaneous and ever-changing states of the brain’s modules (i.e., protein states, nuclei states, pathway states, and response states), actions taking place (either predictable or stochastic) constrain future trajectories. Thus, self-organization is always a developing and emerging state improving (except under atypical conditions) and adding to itself rather than deteriorating into chaos.

Our sense of time (past, present, and future) is an epiphenomenon of neural representations (i.e., memory). As brain states occur and morph into regularities, highly influenced by recursive information and on-going organization, patterns of information processes gain strength and become available to consciousness. The level of interactive and recursive brain states includes, as one trajectory in the complex system, links across concrete and abstract representations that add a sense of when to all experiences.

Consciousness is a product of neural states and recursive representations. Billions upon billions of molecular states in billions upon billions of neural cells interconnected by trillions of nodes of communication are presented in the brain as small isolated events and large inclusive events. Consciousness is the representation of large, inclusive events that become (or have the potential to become) memory that also exhibits temporal awareness.

Consciousness is another epiphenomenon of brain states that achieves certain configurations of molecular and neural connection thresholds. Only a tiny fraction of the brain states that run the brain moment-to-moment have the potential to be available as consciousness. Consciousness, because its exact mechanisms and thresholds are so poorly understood, is typically associated with complicated and vague constructs such as free will and self-determination. Nevertheless, as a premise for how to think about the brain, the concept of consciousness is useful for revealing the dimensions (size, nature, and time) of biological phenomena that coalesce into a representation of something of which we are aware and can think about.

Each brain is a unique and individual creation. The final premise for how to think about the brain is probably, by now, an understatement. Although members of a species have incredible similarity in structure and function, each member possesses its own peculiarity and personality. Personality is, like consciousness, an epiphenomenon of a unifying thread that binds together the complex, stochastic, temporal, and unique genetically-influenced molecular makeup of an individual. Personality emerges as a product of the process of each unique self-organized brain.

Humans are bent on identifying “normal distributions” of traits that make up the collective characteristics that define the species. However, individual members of the species’ population fall at different places on distribution curves representing hundreds or thousands of different traits and characteristics. This demonstrates, further, the observable uniqueness (and mind) of each member of the species. However, a super-distribution of all the conceivable trait distributions would, theoretically, yield a single point, the mean of the means. This underscores the diversity among members of the species and, simultaneously, the unity of the species brought about as a collective result of its common operating principles.

The molecular colloquy in each person is so incredibly diverse that a population of trillions would never yield two alike.


The brain is a complex dynamical system of structures and functions that involves configurations of molecules, proteins, genes, cells, networks of cells and pathways, interactions with other body systems, and interactions with the environment. The ever-changing nature of neural connections, pathways, and chemical arrays exists on moment-to-moment, lifespan developmental, and evolutionary timeframes. The brain is gene-dependent for gross development. Interacting with genes, experience and environment yield idiosyncratic development. The combination of multi-causal components to the complex brain system yields idiosyncratic presentation of a broad spectrum of physical, behavioral, and psychological characteristics (i.e., the physical person and his or her personality).

If attempting to think about the brain in the manner described herein does not overwhelm you at least a little bit (like when you think about infinity), then you likely have not yet grasped the scope and complexity of the brain. To summarize, it is absolutely necessary to comprehend the forest, the trees, and the marvel of all the biology that creates the trees and the forest. Too often we forget the biology—usually because of its overwhelming panoply—and invent reified names for things to “explain” the brain (which, of course, don’t). Intelligence, creativity, pathology, memory, socialization, even personality are such reified concepts that, in themselves, ultimately explain nothing, biologically.

Look deep into who you are and you will find in the brain the greatest show on Earth.

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