Understanding Thought – Part 1




This series of blogs is taken from my book Hold That Thought: Reappraising the work of Dr Caroline Leaf. We will look at some basic neurobiology first, then look at the neurobiology of thought itself. We’ll discuss some psychological models of our thought processing, and finally we’ll discuss the common brain states and functions that are usually confused with thought.

Neurobiology 101

The nerve cell

At the most fundamental level of our thought process is the nerve cell, also called a neuron. Nerve cells, like all cells in the body, have a nucleus containing the genetic material. The nucleus is surrounded by cytoplasm, a watery chemical soup that contains the functional proteins that make the cell run. A thin lipid layer called the cell membrane envelopes the nucleus and cytoplasm. The cell membrane contains important protein structures such as receptors that help the cell receive signals from other cells, and ion channels, which help the cell regulate its internal chemistry.

Compared to other cells, nerve cells have three unique structures that help them do their job. First are dendrites, which are spiny branches that protrude from the main cell body, which receive the signals from other nerve cells. Leading away from the cell body is a long thin tube called an axon which helps carry electrical signal from the dendrites, down to the some tentacle-like processes that end in little pods. These pods, called the terminal buttons of the axon, and then convey the electrical signal to another nerve cell by directing a burst of chemicals towards the dendrites of the next nerve cell in the chain.

In order for the signal to be successfully passed from the first nerve cell to the second, it must successfully traverse a small space called the synapse.

The synapse

Despite being very close to each other, no nerve cell touches another. Instead, the spray of chemicals that’s released from the terminal button of the axon floats across a space of about 20-40nM (a nanometre is one billionth of a metre).

There are a number of different chemicals that traverse synapses, but each terminal button has its own particular one. The most well known are serotonin, noradrenaline and dopamine.

If the signal from the first nerve is strong enough, then a critical amount of the chemical is released and will make it across the gap to the dendrites of the second nerve cell on the other side. The chemical interacts with specific receptors on the new dendrites, which cause them to open up to certain salts like sodium and potassium. As sodium and potassium move in and out of the cell, a new electrical current if formed in the second nerve cell, passing the signal down the line.

To prevent the chemicals in the synapse from over-stimulating the second nerve cell, enzymes breakdown the chemicals to clear the space before the next signal comes past.

Nerve pathways

Combining nerve cells and synapses together creates a nerve pathway, where the input signal is received by specialised nerve endings and is transmitted down the nerve cell across a synapse to the next nerve cell, across the next synapse to the next nerve cell, and on and on until the signal has reached the destination for the output of that signal.

And that’s it. The entire nervous system is just a combination of nerve cells and the synapses between them.

What gives the nervous system and brain the near-infinite flexibility, and air of mystery, is that there are eighty-six billion nerve cells in the average adult (male) brain. Each nerve cell has hundreds to thousands of synapses. It’s estimated that there are about 0.15 quadrillion (that’s 150,000,000,000,000) synapses throughout the average brain [1]. And that’s not including the nerve cells and synapses in the spinal cord, autonomic nervous system and throughout the body. Each of these cells and synapses connect in multiple directions and levels, and transmit signals through the sum of the exciting or inhibiting influences they receive from, and pass on to, other nerve cells.

Single nerve cells may have the appearances of trees with their axon trunks and dendritic branches. But altogether, the billions of connections would more resemble a box of cobwebs.

Higher order brain structures

But unlike a box of cobwebs, the brain has precise organisation to the myriad of connections. These areas can be defined either by their structure, or by their function.

Structurally, there are areas in the brain that are dominated by nerve cell bodies, formed into a little cluster, called a nucleus (different from the nucleus of each cell). Then there are groups of axons bundled together, called a tract, which behave like a data cable for your computer. Nuclei process multiple sources of signal and refine them. The refined signals are sent into the appropriate tract to be transmitted to either another set of nuclei for further refinement, or to distant structures to carry out their effect. The axons of the nerve cells that make up the tracts are usually covered in a thick white material called myelin. Myelin acts like insulation on a wire, improving the speed and accuracy of the communicated signal. Parts of the brains with lots of myelinated cells are described as “white matter”. The nuclei and the cerebral cortex (the outer covering of the brain) are unmyelinated cells, and are referred to as “grey matter”.

On a functional level, the brain is divided into parts depending on what information is processed, and how it gets processed. For example, the cerebral cortex is divided into primary areas for the senses and for motor functions, secondary areas and tertiary association areas. The primary sensory areas detect specific sensations, whereas the secondary areas make sense out of the signals in the primary areas. Association areas receive and analyze signals simultaneously from multiple regions of both the motor and sensory areas, as well as from the deeper parts of the brain [2]. The frontal lobe, and specifically pre-frontal cortex, is responsible for higher brain functions such as working memory, planning, decision making, executive attention and inhibitory control [3].

Everything our senses detect is essentially deconstructed, processed then reconstructed by our brains. For example, when reading this page, the image is decoded by our retina and sent through a number of pathways to finally reach the primary visual cortex at the back of our brain. The primary visual cortex has 6 layers of nerve cells which simultaneously encode the various aspects of the image (especially colour, intensity and movement of the signals) and this information is sent to the secondary association areas that detect patterns, both basic (lines are straight, curved, angled) and complex (two diagonal intersecting lines form an ‘x’). One part of the secondary association areas in the visual cortex (the Angular Gyrus) processes these patterns further into the patterns of written words. The information on the various patterns that were discerned by the secondary association areas then get sent to the tertiary association area for the senses where those visual patterns are combined with patterns processed from other sensory areas (hearing, touch and internal body sensations) to form a complex pattern of multimodal association [2]. In the case of reading, the tertiary association area allows comprehension of the written words that were previously only recognised as words by the secondary association areas.

In the recent decades, with the widespread adoption of non-invasive methods of studying the active living brain such as PET scanning and fMRI, researchers have discovered that rather than discrete parts of the brain lighting up with a specific task, entire networks involving multiple brain regions are activated. This has lead to the paradigm of neurocognitive networks, in which the brain is made up of multiple interconnected networks that “are dynamic entities that exist and evolve on multiple temporal as well as spatial scales” and “by virtue of both their anatomical and functional architectures, as well as the dynamics manifested through these architectures, large-scale network function underlies all cognitive ability.” [4]

Emotions and feelings


I’ll discuss emotions further in chapter 2, but for now, it’s easiest to think of our emotional state as the sum total of our different physiological systems, and feelings are the awareness, or the perception of our emotional state.

Different parts of the brain are responsible for the awareness of these feelings. The amygdala is often considered the seat of our fears, the anterior insula is responsible for the feeling of disgust, and the orbitofrontal and anterior cingulate cortex are involved in a broad range of different emotions [6].

Different emotional states are linked with different neurotransmitters within the brain. For example, a predisposition to anxiety is often linked to variations in the genes for serotonin transport [7] while positive and negative affect (“joy / sadness”) are linked to the dopaminergic system [8].


Memories, like thoughts, are something that we’re all familiar with in our own way.

Memory is quite complicated. For a start, there’s more than one form of memory. You’ve probably heard of short term and long term memory. Short term memory is further thought of as sensory memory and working memory. Long term memory is divided into semantic and episodic memory. Memory is also classified as either declarative memory, also called explicit memory, and nondeclarative memory, also called implicit memory.

Squire and Wixted explain, “Nondeclarative memory is neither true nor false. It is dispositional and is expressed through performance rather than recollection. These forms of memory provide for myriad unconscious ways of responding to the world. In no small part, by virtue of the unconscious status of the nondeclarative forms of memory, they create some of the mystery of human experience. Here arise the dispositions, habits, and preferences that are inaccessible to conscious recollection but that nevertheless are shaped by past events, influence our behavior and mental life, and are an important part of who we are.” [9]

On the other hand, declarative memory “is the kind of memory that is referred to when the term memory is used in everyday language. Declarative memory allows remembered material to be compared and contrasted. The stored representations are flexible, accessible to awareness, and can guide performance in a variety of contexts. Declarative memory is representational. It provides a way of modeling the external world, and it is either true or false.” [9]

Working memory is a central part of the memory model. Information from feelings, stored memories and actions all converge in working memory. The model of working memory initially proposed by Baddeley involves a central executive, “a control system of limited attentional capacity that is responsible for the manipulation of information within working memory and for controlling two subsidiary storage systems: a phonological loop and a visuospatial sketchpad.”[10] Baddeley later added a third subsidiary system, the episodic buffer, “a limited capacity store that is capable of multi-dimensional coding, and that allows the binding of information to create integrated episodes.” [10]

Working memory is known to be distinct from other longer term memories that are dependent on part of the brain called the hippocampus, because patients with severe damage to the hippocampus can remember a small amount of information for a short time, but are not able to push that information into longer term memory functions to retain that information. Information in working memory doesn’t last for any more than a few minutes [9].

So, there are many forms of memory that are important to our lives and influence our behaviour that are “inaccessible to conscious recollection”. But even declarative memory, which is accessible to thought, doesn’t actually make up the thought itself. Memories are stored representations.

When memories are formed or retrieved, the information is processed in chunks. As Byrne pointed out, “We like to think that memory is similar to taking a photograph and placing that photograph into a filing cabinet drawer to be withdrawn later (recalled) as the ‘memory’ exactly the way it was placed there originally (stored). But memory is more like taking a picture and tearing it up into small pieces and putting the pieces in different drawers. The memory is then recalled by reconstructing the memory from the individual fragments of the memory.” [11] Recalling the original memory is an inaccurate process, because sometimes these pieces of the memory are lost, faded or mixed up with another [12]. This is why what we perceive and what we recall are often two different things entirely.

Why do we have memory then, if it’s so flawed at recalling information? Because memory is less about recalling the past, and more about imagining and planning the future. As Schacter writes, “The constructive episodic simulation hypothesis states that a critical function of a constructive memory system is to make information available in a flexible manner for simulation of future events. Specifically, the hypothesis holds that past and future events draw on similar information and rely on similar underlying processes, and that the episodic memory system supports the construction of future events by extracting and recombining stored information into a simulation of a novel event. While this adaptive function allows past information to be used flexibly when simulating alternative future scenarios, the flexibility of memory may also result in vulnerability to imagination-induced memory errors, where imaginary events are confused with actual events.” [13]


  1. Sukel, K. The Synapse – A Primer. 2013 [cited 2013, 28/06/2013]; Available from: http://www.dana.org/media/detail.aspx?id=31294.
  2. Hall, J.E. and Guyton, A.C., Guyton and Hall textbook of medical physiology. 12th ed. 2011, Saunders/Elsevier, Philadelphia, Pa.:
  3. Stuss, D.T. and Knight, R.T., Principles of frontal lobe function. 2nd ed. 2013, Oxford University Press, Oxford ; New York:
  9. Squire, L.R. and Wixted, J.T., The cognitive neuroscience of human memory since H.M. Annu Rev Neurosci, 2011. 34: 259-88 doi: 10.1146/annurev-neuro-061010-113720
  11. Byrne, J.H. Learning and Memory (Section 4, Chapter 7). Neuroscience Online – an electronic textbook for the neurosciences 2013 [cited 2014, Jan 3]; Available from: http://neuroscience.uth.tmc.edu/s4/chapter07.html.
  13. Schacter, D.L., et al., The future of memory: remembering, imagining, and the brain. Neuron, 2012. 76(4): 677-94 doi: 10.1016/j.neuron.2012.11.001

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