A Practical Guide to How Your Brain Works

Given that our brain is where the thoughts, feelings, ideas, beliefs and decisions that guide our whole life arise I think it's helpful to have a rudimentary understanding of how it works so we can use it more effectively.

Your brain is the most complex system in the known universe. Over eighty billion massively interconnected neurons form the most complex parallel-processing biological computer imaginable, and it's right there in your head controlling your every move. Nobody fully understands how it works, which isn't at all surprising when you consider that we're using our brain to try to understand itself. That's like a computer trying to understanding itself. So I can hardly do it justice in a single article but here's a rough guide to the features I think are most important.

Consciousness and The Mind

The mind is a function of our brain. When people talk about “the mind”, they are usually referring the conscious mind. Consciousness is that sense that we all have that we are awake, aware and alive. It causes us to notice the passing of time. We lose it when we are asleep or unconscious, like when we faint or are in a coma. Conscious thought has such a dominating influence on us that we naturally overlook the fact that most of what goes on in our brain actually happens unconsciously.

The way our brain regulates our heartbeat and most internal body functions is totally unconscious. Other functions like breathing are mostly unconscious, but can also be controlled consciously. Memory and emotions operate subconsciously, until specific memories and feelings are brought into conscious awareness. Our subconscious has a massive impact on the way we think and act, without us being aware of it.

We assume that other people experience consciousness the same way we do. There's no way to tell for sure, because we can't get into someone else's head, and consciousness is difficult to describe. Other animals clearly also experience consciousness, which is why we anaesthetise them at the vet for operations. The more developed the brain, the more deeply they are likely to experience consciousness. Apes certainly have it, bacteria probably don't; in between is a spectrum.

Pattern Matching

At all levels, our brain is as a massive pattern-matching machine. The way our neurons are wired together, the way they fire in response to input from our senses and from other neurons, and their ability to learn from previous input creates a pattern-matching system which operates at all levels in the brain and the central nervous system. The optical character recognition (OCR) software that came with your scanner is based on a simplified model of the neural networks in our brains.

This pattern-matching ability is going on both in our conscious mind and our subconscious all the time. It is key to our survival, and is particularly attuned to identifying danger. Subconscious pattern-matching filters the massive amount of information from our senses down to a manageable level so that our conscious mind isn't constantly overwhelmed. For the most part, we don't notice this. Our conscious thoughts are capable of pre-programming our subconscious pattern-matching abilities to look for danger or opportunity. This is why we start noticing red cars everywhere as soon as we go to buy one, even though the red cars have been out there all along. It's also why the law of attraction described in The Secret works. It's not that the universe provides for us magically, it's that we program our subconscious to start recognising opportunities that have always been there.

Co-incidences have a profound effect on us because they make it through the pattern-matching filter all the way to our conscious mind where they take precedence over our current train of thought. This leads us to infer a connection between co-incidental events simply because the occurred together. We end up believing that unrelated events are connected, which can have unfortunate consequences. One example is the myth that childhood vaccination causes autism, because the symptoms of autism appear at approximately the same age as the vaccination is done; and given the emotional charge associated with this, and you have all the ingredients for a deeply held yet false belief.

The flip side of this is our ability to ignore patterns which don't match, without even noticing. Our brains are wired to alert us to things which are dangerous or interesting, and to let everything else pass us by unnoticed; when in fact there is an overwhelming amount of stuff going on around us constantly. We think of someone we haven't spoken to in years, and they ring the same day. Amazing? Not really; we're actually thinking of other people constantly, but most of these thoughts are forgotten almost immediately. When a pattern matches in our brain, it reinforces our memory of it. We forget that we even thought of the many people who didn't happen to end up ringing that day.

Most of us vastly underestimate the power of our subconscious pattern-matching abilities, and attribute seemingly extraordinary coincidences to some higher power or external supernatural force. This explains why prayer seems powerful: it raises our awareness of both the situation we pray for, and the outcome. We routinely downplay the ordinary (the person we pray for dies of cancer), and highlight the extraordinary (someone else makes a miraculous recovery), when in fact these are all natural occurrences. All supernatural phenomenon and even the most mind-boggling of coincidences are really just the result of underestimating our brain's amazing pattern-matching abilities.

Emotions and Thoughts

Emotions are deeply wired into our brains and have a powerful effect on us. They exist in our subconscious, and are our its way of notifying our conscious mind that there is something we need to pay attention to. We don't think our emotions; we feel them. Their impact on our thoughts and behaviour is enormous. They are key to our survival, our social success, and our ability to reproduce.

Western society places a huge emphasis on our ability to think, and we spend many years at school and university learning factual information and developing our analytical thinking skills. We learn little about dealing with our feelings. We become self-conscious about them and many of us tend to bottle up and internalise them, contributing to the epidemic of depression and anxiety in western societies.

Our brains' ability to think analytically is a relatively recent evolutionary development. It's what sets us apart from other animals, and has led us to the top of the food chain even though we're slower and weaker than some of our potential predators. This rational ability is built atop a more primitive and powerful emotional brain. Our thoughts are able to suppress our emotions to some degree for short periods. Do this consistently, and we end up repressing our feelings. But emotions are more primitive and ultimately more powerful than thoughts. Emotion will always win over thoughts in the end.

Powerful emotions can arise spontaneously and often unexpectedly from our subconscious. They are poorly understood and their effect can be overwhelming. This is why some people attribute their effects to “energy” forces that don't really exist, or give a supernatural or spiritual interpretation to strong emotional experiences. Strong emotions like grief release natural narcotics in the brain which can lead to hallucinations, causing people grieving after a death to think they see their loved one everywhere.

We tend to feel an emotion first, and then think of a reason why we feel that way. The process happens so fast that often we think it happens the other way around, and in fact both reinforce each other. The way we think influences the way we feel, and fundamentally changing the way we think about an event can have a huge impact on how we feel about it. But changing the way we feel purely by changing the way we think is hard, which is why purely cognitive therapy and psychoanalysis that neglects emotion take such a long time.

We make all our decisions on an emotional basis, then come up with a rational justification for them. This is why effective salespeople give their sales pitch in terms that appeal to our emotions showing how buying their product will either make you feel good, or stop you feeling bad.

For more about the importance of emotions in our lives, I recommend the book Emotional Intelligence by Daniel Goleman.

Emotional repression is at the root of a great deal of mental suffering. The solution is to learn to feel and express the emotion that has been repressed. For a practical workshop on dealing with difficult emotions, go to The Mental Toolbox.


Fear is one of our most primal emotions, and deserves special attention because it's so powerful. In fact, there are specific circuits in our brain for dealing with it. The purpose of fear is to alert us to danger. It activates quickly because the circuits dedicated to it bypass a lot of the higher processing areas of the brain. As a result, our fear response tends to be inaccurate. We can easily became afraid of things that represent no danger. We're also prone to fear and anxiety about things that represented dangers to our ancestors, but no longer do so in the modern world.

Fear is paralyzing because it activates our brain's fight-or-flight response, which affects every organ in our body. We lose the ability to think clearly and to remember things, which is what happens for performers during stage fright. Getting the heck out of there or ceasing movement like a deer in the headlights in the hope that a predator doesn't notice us, becomes our only priority.

We can learn to become afraid of things by experiencing traumatic events, and we can undo this learning by dissipating the emotional charge that these events leave in our brain. The most powerful way of doing this is to systematically desensitize ourselves by exposing ourselves to a weak version of the stimulus that causes only mild (but not overwhelming) anxiety in an environment where we get a positive reward; then gradually increasing the stimulus.

Fear is a good thing because without it we would kill ourselves off almost immediately without it, but we generally notice most the fears that bother us by holding us back. You don't want to desensitize yourself to the fear of playing in oncoming traffic, for instance.

To learn more about how fear operates, read The Emotional Brain by Joseph Ledoux.

Mind and Body

The distinction between mind and body is a relatively recent idea, and is somewhat misleading. The mind is a function of the brain, and the brain is an not only an organ of the body, it's also massively interconnected with every other part of our body via the central nervous system. There are as many neurons connecting our brain to our body, as there are in our brain itself. Stop thinking of mind and body as separate; they're completely interdependent.

Our brain has a controlling influence over every part of our body, and again this is mostly unconscious. The connection between them is two way: what happens in our body effects our brain, and what happens in our brain effects our body. This is why chronic stress, which is an emotional condition generated in our brain, can cause physical disease in our body. When we are stressed, our fight-or-flight response activates: Our body tenses up physically and systems which are not essential to escaping a predator, like our immune system, are shut down or suppressed temporarily. That's fine in the short term to escape a predator, but leave yourself in that state for an extended period, and you'll have a problem.

We have relatively little conscious control over the interaction between our mind and body. Anything that relieves emotional stress will reduce to load that the fight-or-flight response puts on the body, allowing it to heal more quickly. This is why meditation help cure physical illness. It's also why the placebo effect occurs, and why homeopathy, kinesiology, reflexology and other alternative health treatments with no therapeutic benefit still work for people who believe in them.


There isn't any one centre of memory in the brain; memory is distributed throughout every neuron in our brain and central nervous system. All neurons have a simple biochemical mechanism for remembering what stimulus they fire in response to, and this mechanism is reinforced each time they fire in response to the same stimulus. The way our neurons are wired together creates our capacity for subconscious memory, and our ability to bring memories into consciousness.

Memory and emotion are tightly linked: Heightened emotional states cause memories to be reinforced more strongly. This is why you remember where you were on September 11, but not August 11 the same year; and why traumatic events can sometimes cause overpowering memories as in the case of Post Traumatic Stress Disorder.

The association between memory and emotion is two way, which is why a particular memory of the past can evoke an emotion even in the present, and why experiencing any particular emotion can bring back memories of other times when we felt the same way. Emotional baggage from prior experiences can colour our reaction to new situations and cause us ongoing grief and frustration. Therapy and other emotional healing techniques work by dissipating the stored emotional charge in our brain that we remember associated with painful or difficult memories.


When we are first born, our brain is like a mostly-blank slate. It is pre-loaded with only basic survival instincts compared to other animals, primarily the ability to learn what we need to know from other people and from our interactions with our environment. As the most intelligent animal on the planet, our ability and need to learn is much more dominant than our instinctual abilities. Our brain is literally wired to learn.

Our first 5 to 7 years are a particularly rapid time of learning. During this period our brains are still developing at a rapid rate, and the interconnections formed between our neurons depend on what we learn from our interactions with the environment and people around us. Neural plasticity is at its highest during these early years, and what we see, hear, feel and experience literally shape the structure of our brain. This is why childhood trauma has such a long-lasting effect on us. After this time, our rate of learning slows down, but we continue to learn by experience throughout our whole lives.

We tend to feel good when we're learning something new, provided it seems relevant and interesting to us, and builds on a foundation of something we already know. We need enough of our brain's existing pattern-matching circuitry to be firing in order for us to incorporate the new knowledge. Attempt to learn advanced calculus before you've mastered basic arithmetic, and you'll feel overwhelmed, confused and unhappy. But learning to play a challenging new song on guitar once you've already mastered the basics, is intrinsically rewarding. Our desire to learn and grow is a by-product of our brain's survival instinct for adaptability.

Repetition Feels Good

The biochemical mechanism that occurs when our brain matches a pattern causes that pattern to be reinforced. It also secretes chemicals that make us feel good. So doing some familiar task over and over is pleasurable, and as we build competence it feels better and better over time. Familiarity feels good to us, and makes us feel safe. This is why our brains are wired to reinforce our existing beliefs. It's also why we generally feel good when we chant a mantra over-and-over, when we hear a favourite song again, see an old friend, or participate in some religious ritual like going to church each week. It explains why people with an obsessive-compulsive disorder get some relief from their anxiety by repetitive tasks such as hand-washing; although it's not dealing with the underlying anxiety which returns once they stop.

Learning something new requires repetition and building competence through practise makes us feel good too. Even our reflexes can learn by repeated training. When dancers talk about “muscle memory”, they're referring to the memory in the nerves that control the muscles they are developing via repeating the same dance steps over and over. Musicians develop fine motor skills required to play instruments by repeated practice which trains both the muscles and the nerves that control them. Sports people develop faster reflexes by repetitive training to reduce the time they take to respond to a starter's gun or an approaching tennis ball.


There are specific neural circuits in our brain that facilitate empathy, which make emotions contagious between people. Empathy gives us a subconscious sense of how other people feel, by directly triggering the same emotional response in ourselves even though our circumstances may be different. We evolved to live in groups and the capacity for empathy developed in our brain as a survival mechanism.

Neural circuits take information from our senses and are tuned to notice cues like facial expressions or tone of voice which our conscious mind may be unaware of. Our brain is connected to the brains of every other person we interact with via our senses, actions, and behaviours.

Women are generally better at this than men, because they've learned the skill through more empathic relating to other people in their lives. Empathy is a key social skill which help us relate to each other at a deeper level. Close relationships are based on the sharing of emotions and our capacity for empathy.

Empathy is why a great movie, great actors in a play, or a stirring song or poem can move us so profoundly. It's also why we tend not to like people who are fearful: because their fear is contagious to us. If a public speaker is visibly nervous, it makes us uncomfortable because we take on their fear, and fear is an unpleasant emotion. This is why nervous guys appear creepy to women, even if a woman can't put her finger on exactly why.

Sadness, excitement and anxiety are all contagious due to empathy. This is why we get swept up in the excitement at mass sporting events even to the point of mass hysteria, and explains charismatic religious group experiences like speaking-in-tongues and collective visions.

It's not just emotions that are contagious either: Thoughts, feelings, ideas, and behaviours are all contagious. This explains a great deal of group dynamics including the Mexican wave at the football, and why many people blindly follow charismatic leaders. Peer pressure combines with empathy to have an enormously strong influence on us because it stems from a social survival mechanism in the brain.

We naturally take on the emotions of those around us. This has some handy consequences: If you want to be happier, the most powerful way to do that is to hang around happy people.

The Need To Socialise

Our brains are wired for social interaction with other people because we evolved to live in groups, and we reproduce sexually. So we have an incredible drive to connect with other people where we feel safe and protected. If we don't socialise, our brains remind us to do so via the unpleasant emotion of loneliness, which is one of the worst experiences we can have. The deeper and more emotionally engaging our interactions with others are, the less lonely we feel. This is all part of our basic survival and reproduction instincts essential to our genetic survival. This need for social interaction in our brain is the reason social networking sites like Facebook are so compelling.

We tend to underestimate how strong this biological drive wired deeply into our brain is. This basic need to connect with any consciousness outside of ourselves is so strong that it overflows into other areas of our lives and can give rise to a great spiritual yearning. Jung's need for a collective consciousness is a reflection of it. Over the centuries we have created many gods to fulfil this need for our connection to a higher power outside ourselves that will also protect us. Even despite our modern-day understanding of the world, many people still intuitively feel that there must be a God out there; which is really just a by-product of our powerful biological drive to socialise.

Social Grouping and Prejudice

We evolved living in relatively small tribes who competed with each other, so we prefer to socialise with other people who are “like us”. Yet now most of us live in overwhelmingly large cities. We need to exclude the people who aren't “like us” in order to reduce the size of our tribe back down to a manageable level. The distinguishing factor between who is in and who is out doesn't matter, but our brain comes up with a reason to make it appear important: race, skin colour, religious beliefs, fashion sense, gender, sexual orientation, whatever.

This causes our prejudice and racism. It explains everything from political factions to religious denominationalism and infighting between religious groups whose beliefs are essentially identical. Any time our “tribe” grows beyond a few hundred, our brains start to find arbitrary reasons to distinguish “us” from “them” to identify what we think are potential threats and help keep us feeling safe.


We are constantly projecting our ideas, thoughts, biases, judgements and prejudices onto other people and situations in the world. There is nothing wrong with this per-se; it's just the way we work, but it's worth being aware of if we want to be able to look past our own prejudices and connect with people and experiences we would otherwise miss out on. We notice this projection least when it comes from our dark side; anything about ourselves that we haven't dealt with gets projected onto other people because this is easier than dealing with parts of ourself that we're ashamed of.

Our brain only has it's own internal model to work on, so it assumes that other people are like us, or are like other people who we have encountered before. Our ability to project attributes of ourselves and other people who we have trusted in the past onto new people or groups of people helps us determine who we can and can't trust. We tend to distrust anything too new or different.

It can also work the opposite way: we tend to assume that ancient people were like us, even when they lived in a very different culture. We assume that people in ancient or biblical times were as objective, well educated and informed as we like to think we are, despite the obvious advances in human understanding since that time. Projecting our modern-day understanding onto them, we accept their interpretation of events as gospel even though they only had a primitive understanding of how their brain, body and the world around them functioned. The realisation that the earth is not flat, and that we are not at the centre of the universe all came later. Something as commonplace today as electricity or television would have been interpreted as supernatural had they stumbled across it in the desert by the originators of today’s mainstream religions.


Our brain is inherently creative. The western education system does a fairly good job of repressing individual creativity in order to train us to fit into a fairly uniform workforce, but our inherent creativity is still there. We like to feel in control, and part of that is to understand what is going on around us. When we understanding the things we fear, we tend to feel less fearful. In the absence of a good explanation for what goes on around us, we naturally tend to use our creativity to come up with an explanation. This makes us feel more in control, and more at ease in an uncertain world.

Our brain is constantly active. In the absence of sensory input, we will create stimulus, thoughts, ideas, and even hallucinations to fill the void. Our nervous system turns up the volume until we hear something, even if it's just background noise. This is why we dream, why people in extended isolation hallucinate, and why amputees experience phantom sensations in missing limbs.

The creativity of our minds is most powerful when it operates as a group process. Creative groups tend to be more powerful than individuals. Each person's creativity sparks something in the other people, which then sparks the creativity of other members.

All great ideas in religion and science are the result of a group creative process. Theologians base their ideas on those who have gone before, and scientists base the hypothesis for their experiments on the current understanding of the scientific community. Both are ultimately attempts to assuage our collective anxiety about living in a sometimes-hostile universe, by trying to master our understanding of how it operates. Religious teachings about God, supernatural phenomenon, the spirit world, karma, heaven and hell, angels and demons are all projections of our inner creativity onto an unseen outer world.


Our brain has inherent limitations based on the attributes that were important for survival in the environment that existed over the extremely long period during which human brain structure evolved. The modern urban environment has changed rapidly in such a short time that we haven't had time to fully adapt. This is another reason why depression, anxiety and stress are becoming increasing problems: we aren't particularly well suited to our new environment in some respects.

While our brain is particularly good at solving problems which relate to our direct survival, it's not so good at other tasks like complex mathematical problems. We don't have a particularly good intuitive feel for cumulative probability or forecasting events which are statistically unlikely. We can deal with 50/50 just fine, but we don't handle one-in-a-million so well and we often tend to underestimate the likelihood of seemingly remote co-incidences. Ask a random group of strangers to guess the chance that another person in the group has the same birth month and day as someone else, and we routinely underestimate it. It just wasn't relevant out on the savannah. This is why so many people get sucked into gambling, large state lotteries, astrology, numerology, and unnecessarily attribute many natural coincidences to supernatural causes.

We are well adapted to thinking of time scales that are not too short nor too long, like seconds, hours, minutes, days, weeks, months or years. But we have a poor intuitive feel of nanoseconds, milliseconds, centuries, millennia or epochs. These sort of time scales haven't been important to our survival until very recently .This is why many religious people discount the possibility of a complex system including living creatures such as ourselves evolving over just a few billion years. We don't have a good intuitive feel for just how staggeringly long such a period of time is.

I hope this guide to your brain has helped you understand how you operate a little better. I'm keen to hear your ideas and feedback, so leave a comment and share your thoughts.

About Graham

I combine trauma awareness, emotional healing and comedy to heal painful events from your past, so you can live a future life you love.
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4 Responses to A Practical Guide to How Your Brain Works

  1. Ira Allen says:

    What a great article! I am in agreement with what you have so clearly written. I have Idiopathic Pulmonary Fibrosis and am at a totally peaceful state of mind. I have been told that my state of mind is beyond description and I've been encouraged to explore Enlightenment, Transcendentalism and Entanglement which I have been doing. I'd be interested in communicating with you regarding what you'd think of what I've come up with.

  2. Ralph says:

    Great post. You've described it in terms everyone can understand. "Blink" by Malcolm Gladwell is another great book related to this subject.

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