The Brain Stem

The Brain Stem

The base of your brain

The brain stem sits lower in the brain and is often considered the “primitive” part of the brain. This may be an oversimplified way of describing this part of the brain – but it does control many life-sustaining functions so without it we are goners!

Brain stem

The parts of the brain stem

The brain stem is often referred to as the “primitive” part of the brain or famously the “reptilian brain”. This terminology was proposed by neuroscientist MacLean who wrote in his book, on the evolution of the brain, how different parts of the brain could be ascribed an evolutionary function. This “triune model” has become a simplified model of the brain and because of its appealing simplistic nature has been used and abused by many people including Daniel Goleman one of the father’s of emotional intelligence. I have also used it often. Neuroscientists and I know that this is a very simplified model of the brain. But we also know that there is some truth to it and so for the sake of ease of explanation and appeal to lay audiences this is still often used.

The language is also intuitive and easy to grasp. The logic goes that all organisms have a version of the brain stem, and this is what most simple brains are in essence – the equivalent of the brain stem often in miniature form in simple organisms. Also, in the development of the brain the brainstem forms first and then the structures grow out of this, and the cerebrum is formed last. So, the standard logic goes that the brain stem houses our primitive living functions. Let’s review briefly.

The brain stem is categorised into three sections:

  • Medulla Oblongata
  • Pons
  • Midbrain

What is also important is that 10 of the 12 cranial nerves target or sources form the brain stem.

The medulla oblongata (normally just called the medulla) is the transition zone of the brain into the spinal cord. It houses a number of critical functions such as two of the three respiratory groups controlling breathing and monitoring this. Also, cardiac control and regulation, controlling heartbeat and monitoring this and also controlling blood pressure.  The vomiting reflex is also controlled in the medulla through a region called the area postrema that monitors chemicals in the blood.

Above the medulla sits the pons which is dense in cranial nerve nuclei and connects the medulla to the thalamus but also coordinates activity in the hemispheres of the cerebellum (I covered the fascinating cerebellum in lbR-2021-01). It also houses the respiratory centre that coordinates with the other two respiratory centres in the medulla. The locus coeruleus is also located here which is a major centre for the synthesis of norepinephrine and a key part of attention and also curiosity circuits.

Above the pons sits the midbrain which has the other five cranial nerve nuclei but also a number of other important regions that crop up again and again in neuroscientific research. The periaqueductal gray is an area of neurons that are involved in multiple processes including pain desensitisation. The substantia nigra and also the ventral tegmental area are also located here and these are two key dopamine synthesising centres. Similarly, the rostro medial tegmental nucleus is a GABAergic centre. But is also houses the reticular formation (with the pons) and this is involved in arousal and consciousness systems. There are also strong connections to the lower motor neurons which is why regions her are also implicate d in Parkinson’s disease.

So, we can see that the brainstem does indeed house a whole host of living critical functions without which we cannot survive. This is why damage to this part of the brain is particularly disruptive and more often than not life threatening e.g. snapping the neck at the top of the spinal cord as we see in many old spy films.

On one hand though we can also see that some things which we consider primitive such as aggression are not actually driven from this region of the brain but more the critical life reflexes are such as heartbeat, breathing, arousal, and attention.

Though you may think that the brain stem is all we need to survive, a condition known as anencephaly shows this is not the case. Anencephaly is a condition in which babies are born without a cerebrum. These babies die shortly after birth which is a stark reminder that the brain does operate as a whole, and functions are spread over the brain.

So that simplified version of what the brain stem is does hold true, but we shouldn’t forget that the brain is incredibly complex and, particularly in human beings, has developed to operate across regions whether “lower” or “higher” – these regions often do not grab the neuroscience and popular science headlines. But without them you would surely not be here



Kolb, B. & Whishaw, I. Q. (2009). Fundamentals of human neuropsychology: Sixth edition. New York, NY: Worth Publishers.

MacLean, P. D. (1990). The triune brain in evolution: Role in paleocerebral functions. New York: Plenum Press.

Singh, Vishram (2014). Textbook of Anatomy Head, Neck, and Brain ; Volume III (2nd ed.). p. 363. ISBN 9788131237274.

Haines, D; Mihailoff, G (2018). Fundamental Neuroscience for Basic and Clinical Applications (5th ed.). ISBN 9780323396325.

 “Brainstem | Definition, Structure, & Function”. Encyclopedia Britannica.

“Cranial Nerve Nuclei and Brain Stem Circulation”. Neuroanatomy Online.



The mood modulator

Selective serotonin reuptake inhibitors (SSRI) may sound like gibberish to many but are in fact one of the most common drugs on the planet. These SRIs are used in mood disorders, particularly depression. The theory is that block the reuptake of serotonin leaves more between synapses and this in turn can control mood or alleviate a negative mood. Is it really that simple?

serotonin in the brain

Serotonin the brain’s mood modulator


Serotonin is associated with mood more than anything and particularly with alleviating depression and anxiety. But as with all things in the brain it is not quite so simple. Serotonin, or 5-hydroxytryptamine (5-HT), if you want to be technically correct, is known as a monoamine neurotransmitter. However, as Wikipedia put it “Its biological function is complex and multifaceted, modulating mood, cognition, reward, learning, memory, and numerous physiological processes such as vomiting and vasoconstriction.”

Serotonin is after all present in many parts of the body but of particular note is that of its role and production in the enteric nervous system, basically the gastrointestinal tract (digestive system). 90% of the body’s serotonin is produced in the GI tract a further 8 % is stored in platelets in the blood (which absorb this from the GI tract) and only 1-2% is present in the brain. However, the brain and body serotonin systems can be seen is separate systems with little to no influence on each other (the brain and body always exert some influence on each other).

In the body it has numerous functions but of interest is its role in wound healing one acting as a vasoconstrictor helping to close vein and arteries in wounds but also stimulating cell growth. Directly in the gut serotonin has an expellatory effect and can lead to diarrhoea- serotonin in present in many seeds which is why they also have a healthy effect on bowel movements. Interesting to note is also that serotonin is present in many insect and animal venoms, and this helps stimulate pain!

But back to our area of interest, the brain. What does serotonin do in the brain. Well, we have noted that it is considered the neurotransmitter related to mood. By mood we mean a general feeling of positivity and negativity rather than the ups and down of everyday life which may be more related to other transmitters such as dopamine. Hence its role in anti-anxiety drugs and that famous class of SSRIs such as Prozac. It is also negatively associated with aggression – that is lower levels lead to greater aggression. On closer inspection it is impulsive aggression that is increased rather than aggression in general. This I also noted in my feature article on love in last month’s issue whereby when in love serotonin levels decrease leading to mood swings and obsessive-compulsive behaviour.

serotonin dopamine pathway brain

Dopamine and serotonin pathways

Serotonin therefore seem to be a moderator more than anything in line with its roles as a general mood chemical or rather it takes the edge of impulsive or environmental swings. Its role though is still complex and further research has noted that of two tales of serotonin. This is better termed two receptors of serotonin as noted in a paper in 2017 by Carhart-Harris and Nutt. As I have noted previously neurotransmitters and modulators dock into receptors on neurons and it is this that triggers a response in the neuron. However, neurons have different types of receptors, and these can have different and sometimes opposing effects.

In the case of serotonin there are two receptors that seem to stimulate different pathways and responses. Type one receptors trigger a passive coping response to stress, i.e. moderating the impact of stress inputs, smoothing that curve of emotional stimuli, making the highs lower, and the lows higher. Type two receptors are responsible for active coping in response to stress by enhancing plasticity and learning. The latter has been less focused on in the literature and the general view of serotonin – but it is an important one, as in wound healing in the body whereby serotonin triggers receptors on cells to regenerate, this is also function of serotonin in the brain.

Now, I have said that serotonin in the body and serotonin in the brain can be considered separate systems. But as I also noted there are mutual influences on each other and particularly on the gut-brain axis as I have reported on in many other places. There has also been some interest of how to increase serotonin levels naturally – without pharmacological interventions. And these have some backing:

  • Mood induction: actively focusing on positive aspects and positive moods does lead to better moods and higher serotonin in the brain
  • Natural light: lack of natural light in known to be one of the major causes of Seasonal Affective Disorder – the winter blues. Light has multiple benefits and stimulates the brain in multiple ways. But bright natural daylight is associated with higher serotonin levels in the brain.
  • Exercise: this is again a general good health advice and exercise affects multiple pathways that I have also written about many times. But in this case, it also impacts serotonin and specifically through a precursor, tryptophan, an amino acid which is essential for the processing of proteins. This is elevated particularly when fatigued in the brain.
  • Diet: though many food stuffs contain serotonin such as bananas and many seeds these do not cross the blood-brain barrier. Similarly consuming foods high in tryptophan may not have an effect because they also elevate other amino acids and so serotonin synthesis is not elevated above other protein synthesis. However, some evidence points to milk but especially chickpeas and corn which improve the bioavailability of tryptophan and can hence increase serotonin synthesis.
  • Massage: in one study by Field et al. depressed pregnant women who received a massage twice a week from their partner, felt less anxious, less depressed, and had higher serotonin levels after 16 weeks.

So, to summarise serotonin is a key chemical transmitter in the human body and brain. In the brain it has a calming and moderating effect on stress moderating mood swings and keeping us in the positive. It also has a key adaptive function increasing plasticity and learning. Its synthesis can be elevated by doing those healthy things that we should be doing through multiple pathways and there appears to be a clear loop with mood. Daylight, exercise, nutrition, and positivity lead to higher serotonin levels which enables you to better manage the stresses of life avoiding a negative loop or vicious circle and also enhancing learning.

So, keep healthy for healthy brains. Obvious, right?




Kolb, B. & Whishaw, I. Q. (2009). Fundamentals of human neuropsychology: Sixth edition. New York, NY: Worth Publishers.

MacLean, P. D. (1990). The triune brain in evolution: Role in paleocerebral functions. New York: Plenum Press.

Singh, Vishram (2014). Textbook of Anatomy Head, Neck, and Brain ; Volume III (2nd ed.). p. 363. ISBN 9788131237274.

Haines, D; Mihailoff, G (2018). Fundamental Neuroscience for Basic and Clinical Applications (5th ed.). ISBN 9780323396325.

 “Brainstem | Definition, Structure, & Function”. Encyclopedia Britannica.

“Cranial Nerve Nuclei and Brain Stem Circulation”. Neuroanatomy Online.



A Central Switch for Everything

The Thalamus is one of those brain areas that crops up in everything – it is considered a central relay station for the brain and therefore is critical to everything we do and think.

thalamus brain neuroleadership


The thalamus is quite unusual in that it is a large brain area at least in surface because it surrounds one of the ventricles in the brain. You often hear about ventricles in passing, and they would, and will, be worth a review at another time. The ventricles are cavities in the brain filled with brain, or spinal fluid, and essential therefore to brain function – but not having a function, such as passing electrical signals, are therefore only studied by neurologists in any detail. Anyhow the thalamus sits at the top of the brain stem and surrounds the third ventricle and sits at a crucial junction.  

It’s first and foremost function seems to be like a junction, an electrical relay station connecting the brains sensory and motor signals to the brain and body. The thalamus is therefore a highly connected brain region and has direct connections to sensory regions, excepting the olfactory region (and interesting observation and may be why the sense of smell is, actually, and amazingly, the fastest sense of all.

brainstem thalamus brain neuroleadership


But it doesn’t just do sensory and motor control it also connects to associative parts of the brain and limbic centres so in effect function as a central station for majority of cognitive functions. These are:

  1. Reticular and intralaminar nuclei dealing with arousal and pain regulation
  2. Sensory nuclei regulating all sensory domains except olfaction
  3. Effector nuclei governing motor language function
  4. Associative nuclei connoting cognitive functions
  5. Limbic nuclei encompassing mood and motivation

Given that the thalamus is involved in so much it is almost strange that it does not get more press. The amygdalae have become superstars because of their role in fear and emotion processing.

Even more so when we consider that, as we mentioned above, the thalamus is involved in pain and arousal, pretty important functions, but also wakefulness and alertness.

In fact, the thalamo-cortico-thalamic circuits are though to be heavily involved in consciousness itself – it must be – after all the integration of sensory input into the cerebrum goes directly through the thalamus. Maybe its function is too diffuse and too non-specific to be a clear centre for anything spectacular – those parts of the brain which have clear functions seem to attract more attention and research. But we do also know that damage to the thalamus gives significant risk of coma.

So, it remains that the thalamus is one of the critical brain areas through which just about everything in the brain passes for processing – so we should probably be a bit more thankful for it than we are!


Habas, C., Manto, M., and Cabaraux, P. (2019). The Cerebellar Thalamus. Cerebellum 18. doi:10.1007/s12311-019-01019-3.

Haber, S. N., and Calzavara, R. (2009). The cortico-basal ganglia integrative network: The role of the thalamus. Brain Res. Bull. 78, 69–74.

Hwang, K., Bertolero, M. A., Liu, W. B., and D’Esposito, M. (2017). The human thalamus is an integrative hub for functional brain networks. J. Neurosci. 37. doi:10.1523/JNEUROSCI.0067-17.2017.

Redinbaugh, M. J., Phillips, J. M., Kambi, N. A., Mohanta, S., Andryk, S., Dooley, G. L., et al. (2020). Thalamus Modulates Consciousness via Layer-Specific Control of Cortex. Neuron 106. doi:10.1016/j.neuron.2020.01.005.

Wolff, M., and Vann, S. D. (2019). The cognitive thalamus as a gateway to mental representations. J. Neurosci. 39. doi:10.1523/JNEUROSCI.0479-18.2018.

Yen, C. T., and Lu, P. L. (2013). Thalamus and pain. Acta Anaesthesiol. Taiwanica 51. doi:10.1016/j.aat.2013.06.011.



Hormones and the Brain

A short primer to understand differences between transmitters and hormones and how hormones are directly controlled through the brain.

hormones brain neuroleadership


Hormones are often used colloquially to refer to the changes teenagers go though in adolescence and in reference to sex hormones, often in combination with teenagers. Yes, and there are large impacts on sexual function and related aspects such as fertility and pregnancy. But this interplay with hormones is strongly regulated by the brain, and for the brain, in a loop with stimulation, and secretion of various hormones.

First off, what is a hormone and how do these differ to neurotransmitters and modulators?

Hormones are chemical messengers, communicating to different parts, and organs, of your body. They travel in your bloodstream to tissues or organs. They work slowly, over time, and affect many different processes, including:

  • Growth and development
  • Metabolism – how your body gets energy from the foods you eat
  • Sexual function
  • Reproduction
  • Mood

Endocrine glands, which are special groups of cells, make hormones. The major endocrine glands are the pituitary, pineal, thymus, thyroid, adrenal glands, and pancreas. In addition, men produce hormones in their testes and women produce them in their ovaries.

So, what is the difference to neurotransmitters? Neurotransmitters are released in neurons at the synaptic junctions. They are the messenger between neurons. The most common by far are glutamate and GABA. However, there are also modulators which affects groups of neurons and often act through secondary messengers. Hormones can also be transmitters and modulators. For example, oxytocin, already outlined in lbR-2021-06 is a hormone, a neuromodulator, and a neurotransmitter. This means its effects can be quick, over longer times, and impact many organs in the body.

From this we can see the importance of hormones on brain function and indeed many of the key sites that trigger hormone release sit in the brain notably the pineal gland, the pituitary gland, and the hypothalamus, sitting next to the previously described thalamus. These create feedback loops with the brain and body. In fact, this is a very good reason not to see the brain and body as completely separate entities but as part of a brain-body system, or more accurately a brain-body-environment system.

And which specific hormones are released or triggered from the brain?


  • Kisspeptin
  • Oxytocin
  • Gonadotrophin Releasing Hormone


  • Melatonin
  • Serotonin


  • Adrenocorticotropic Hormone (ACTH)
  • Growth Hormone
  • Human Chorionic Gonadotropin
  • Luteinizing Hormone
  • Prolactin

Each of these is fascinating in their own right but what you will notice is that a few are probably well known such as Melatonin involved in sleep wake cycles, or oxytocin as we have reviewed previously. Others are more obscure, and others create loops such as ACTH which is triggered by stress reactions stimulating the adrenal gland on the liver to release cortisol which in turn can also have dramatic consequences on brain function.

For this short review it is important to understand that hormones operate within and without the brain. They trigger circuits in the body which in turn influences the brain, or further circuits in the brain which also influences the body – and each of these can have dramatic impacts on function, and notably on long-term health. And this is particularly important over our lifetimes and no less so in older age.


Essential guide to hormones:

Hormones: Communication between the Brain and the Body:

McEwen, B. S. (2020). Hormones and behavior and the integration of brain-body science. Horm. Behav. 119. doi:10.1016/j.yhbeh.2019.104619.



Colloquially called adrenaline – a powerful activator in the brain

When we speak of adrenaline we think of high stress situations, positive and often negative. Norepinephrine is the neurotransmitter that is related to adrenaline, but not to be confused with the hormone, and it is related to attention, action, but also plasticity and learning.

adrenaline brain

The Sabre-Toothed Tiger jumps out from behind a bush and turns its large yellow eyes onto our friendly cavemen. The tiger gives a low rumbling growl and takes a cautious small step forward, seemingly ready to pounce at an instant. Our caveman, shocked, stands focusing on the tiger his whole body has been rocketed into a high state of alert and tension. His heartbeat has accelerated, his pupils have dilated, his senses have all pricked up and he has laser sharp vision. At this precise moment he is frozen waiting for the slightest abrupt movement which will spur his body into action. Either to launch is rudimentary spear at the tiger or evade and try to escape.

This is often how the primitive roots of our flight or fight response are portrayed – with a threat scenario. Slightly unrealistically: Neolithic man did not live in the same time period as sabre-toothed tigers, and we are adapted to live in the savannah, more likely, than the jungle. Nevertheless, it is easy to imagine, and we have all experienced these periods of shock or tension from simple activities like being surprised by a person jumping from behind a wall, to having a near car crash, to receiving shocking news. Our system activates and all sorts of bodily functions kick off a string of automated reactions. They sympathetic nerve system preparing the system, in very short periods of time, for heightened vigorous activity.

Adrenaline is usually associated with this, it is. But I’d like to give you a brief review of another major neurotransmitter and modulator, norepinephrine also known as noradrenaline. Whereas adrenaline is the hormone signalling responses across the body stimulated by the hypothalamic-pituitary-adrenocortical system norepinephrine is the neurotransmitter that may or may not be associated with the adrenaline response. Chemically they are similar.

norepinephrine brain

So, what does norepinephrine do in the brain? Well, if we take a quick sidestep into ADHD, we can see that there are a number of approaches to deal with ADHD but there are two main classes of drugs to help with attention deficits. One is related to the dopamine system which includes the famous, or infamous, Ritalin, a selective dopamine reuptake inhibitor. The others are related to stimulation and often target the norepinephrine system such as atomoxetine.

Norepinephrine is released mostly in the brain stem specifically in the Locus Coeruleus. Some of you may remember that this is an area that we focused on way back in lbR-2021-01 and is involved in attention. This norepinephrine circuit basically projects throughout the whole cortex as you can see from the diagram above. However, what you will also notice is that there are some similarities to Dopamine which I reviewed in last month’s issue lbR-20201-09.

So, the question is are dopamine and norepinephrine similar, different, or collaborative in their function?

The answer seems to be an irrevocable – probably interrelated! A review in 2020 noted how their functions are similar and they seem to operate in parallel on similar topics – however, we saw last month that dopamine is very strongly involved in the encoding of reward and motivation. It is therefore suitable to conjecture that adrenaline has an arousal and attention function and this complements dopamine. This thereby also stimulates encoding of significance be that of positive or particularly of negative and stressful events which are particularly powerful in the brain. The review also notes norepinephrine’s importance in plasticity and how this also functions in parallel with dopamine.

So, in summary, norepinephrine is a key transmitter that has wide-reaching impacts on the brain and operates closely with dopamine to guide attention, encode and interpret emotional significance, and in guiding learning



Mather, M., Clewett, D., Sakaki, M., and Harley, C. W. (2016). Norepinephrine ignites local hotspots of neuronal excitation: How arousal amplifies selectivity in perception and memory. Behav. Brain Sci. 39. doi:10.1017/S0140525X15000667.

Moret, C., and Briley, M. (2011). The importance of norepinephrine in depression. Neuropsychiatr. Dis. Treat. 7. doi:10.2147/NDT.S19619.

Saboory, E., Ghasemi, M., and Mehranfard, N. (2020). Norepinephrine, neurodevelopment and behavior. Neurochem. Int. 135. doi:10.1016/j.neuint.2020.104706.

Schwarz, L. A., and Luo, L. (2015). Organization of the locus coeruleus-norepinephrine system. Curr. Biol. 25. doi:10.1016/j.cub.2015.09.039.

van der Linden, D., Tops, M., and Bakker, A. B. (2021). The Neuroscience of the Flow State: Involvement of the Locus Coeruleus Norepinephrine System. Front. Psychol. 12. doi:10.3389/fpsyg.2021.645498.

Dopamine vs Norepinephrine

Ranjbar-Slamloo, Y., and Fazlali, Z. (2020). Dopamine and Noradrenaline in the Brain; Overlapping or Dissociate Functions? Front. Mol. Neurosci. 12. doi:10.3389/fnmol.2019.00334.

The Amygdala

The Amygdala

Fear, or emotions, or attention?

The Amygdala is one of those brain areas that gets a lot of attention. A lot. In fact, it may be one of the most famous areas of the brain – in no short part due to its role in fear and what Daniel Goleman called the “Amygdala Hijack” to describe situations in which emotionality takes over your brain – or supposedly at least. But the amygdala is a little misrepresented – let’s clear up its reputation.

amygdala brain

SM are the initials of a patient, who according to the case in a well-cited paper by Feinstein et al. in 2010, exhibits little to no fear. What is special about SM is that she has severe damage to both her Amygdalae. And though at the time there was known to be a strong relationship between fear and Amygdala function, SM’s rare condition enables the study of this in real world scenarios.

She was put through a series of situations and her fear measured. For example, she had consistently expressed a fear of spiders and snakes in previous interviews and so she was taken to an exotic pet store and presented with snakes and spiders to document her response. Surprisingly despite her insistence she is “afraid “ of these, she showed no fear at all. In fact, she showed the opposite: curiosity, reaching out to touch the snakes and spiders and stroke them!

In addition to this she was taken to, ostensibly, America’s most haunted house. The Waverly Hills Sanatorium Haunted House, showing no fear on a tour in contrast to other participants, and researchers, on the same tour. Her fear and emotional response were also collected systematically in everyday life with an emotional diary and through structured interviews. She indeed seemed to show no fear or to experience threat.

One notable experience also points to a key role of the Amygdala or absence of this in SM. She lived in a city and one of her walking routes home passed through a parking lot. On one occasion she was held up at knifepoint and robbed. For many this may have been a traumatic experience – but moreover it would almost certainly have led to avoiding this parking lot or walking home at night through this place. Also, the place would be expected to trigger negative memories. Not so with SM. She continued to walk across the parking lot unabated and unaffected by her negative experience there. This shows a key role of the Amygdala, and maybe underestimated with the focus on fear processing, namely that of learning.

In fact, a recent study did just this. They attempted to connect the amygdala to learning and not through triggering the emotional impact. Emotions trigger large networks in the brain and so it is difficult to disentangle the effects of different regions in the brain. In these experiments by Bass et al. in 2021 they used Deep Brain Stimulation to simulate the Amygdala (or not) in rats when encountering objects. They showed that the stimulation increased the memory of objects without observably activating emotions.

fear brain amygdala

Illustration such as this are used in research into Fear – just looking at this picture consistently shows activation patterns in the amygdala.

Illustration such as this are used in research into Fear – just looking at this picture consistently shows activation patterns in the amygdala.[/caption]This puts the Amygdala at the crossroads of memory and learning and particularly Pavlovian conditioning – so relating positive or aversive stimuli with contexts. This was clearly missing in SM whose experience in the parking lot did not lead to her having aversive reactions to said parking lot. Though we have outlined this clear relationship to fear there have been just as many relationships to positive emotions and the Amygdala. This is why many researchers see it as a salience processing unit rather than a fear centre. It shows us what is important and hence where to focus our attention, or not, and what to learn or not.

However, though there is also strong activation in the Amygdala to positive or appetitive cues, cases such as in SM do not show much dysfunction of positive emotions. So, it seems the Amygdala is involved in all emotional processing, but rewarding and positive experiences rely on other networks whereas fear and threat are strongly related to, or even dependent on, the Amygdala.

This key function of the Amygdala can be seen in its location and connections: it sits in the limbic system close to the hippocampus, itself considered a memory centre, but also close to the thalamus and prefrontal cortex. It is split into different subsections, simply three. The medial, the middle bit, is connected strongly to the olfactory centres (smell), the basolateral, to the frontal and cerebral cortex, and the central & anterior to the brain stem, hypothalamus, and sensory centres.

brain amygdala

Amygdala and neighbouring structures


All of these seem to make sense – connecting sensory input to emotional and hormone release in the hypothalamus, and to the frontal regions to control attention and close to the hippocampus to guide learning, not to mention sensory centres to build associations. Of notable interest, and little discussed is the connections to the olfactory centre. Though the majority of research is into visual stimuli, particularly of faces to which the amygdala can be more responsive than other areas of the brain supposedly specialised in faces (the FFA reviewed in lbR-2021-08).

A recent piece of research shows why – the sense of smell is one of our fastest systems to respond – harking back to a time when our sense of smell was much more important in everyday life and more than in modern society. Iravani et al. from the Karolinska Institute in Sweden showed in a recent piece of research that the olfactory system is a high-speed circuit and particularly to aversive smells which influence our avoidance behaviours. This is often also unconscious.

So, this paints a clearer picture of the function of the Amygdala as an emotional attention centre that is especially reactive and necessary for threat and aversive contexts and drives learning, memory, and conditioning. However, the role of the Amygdala may have unintentionally been tainted by Daniel Goleman’s 1995 description of the “Amygdala Hijack”. This term has been used by many an aspiring neuroleadership expert or coach.

Simply put, Goleman, at the time, painted picture whereby the amygdala reaction essentially hijacked the rational brain and rendered us at the whims of our emotionality. This is an oversimplified description which is appealing to a broader audience but does have some truth in it. Even as an aspiring neuroleadership expert I found the term a little oversimplified – however, it was also useful to describe to lay audiences how emotionality can take over the brain. The fact is, threat is a basic survival instinct and so can, and will, activate many stress systems in the body. However, how to engage and deal with this and is not clearly identified with the term amygdala hijack.

The SCOAP model that regular readers will be familiar with, goes some way to explain this in more detail – Firstly, different concepts can trigger a negative reaction (e.g. self-esteem threat but also loss of control or loss of orientation). Secondly, this can be very individualised. Thirdly, some people respond to threats much stronger than others. Fourthly, many of these are also conditioned responses. Fourthly we are looking at broad networks in the brain and body. So yes, the Amygdala hijack could be a way to describe the emotional response we have, but is too simplified to be useful and misconstrues how the amygdala and brain functions together. SCOAP is a much better way to formulate this and explore – for those who want to learn more.

But back to our two almond-shaped structures in our brain. They are widely researched, seem to have an oversized influence on brain functions, do activate strongly to threat and fear, and control response to this, and control aversive and avoidance behaviours – in fact so much so that political affiliation can be accurately predicted by looking at amygdala activation as I outline in the earlier article on fear in society.

So, the amygdala it is a powerful brain region related to primal networks – and also positive learning, and sometimes being afraid and cautious of threat is very good thing. As SM didn’t learn, sometimes it is good to avoid dangerous places. But too much fear is not good thing either. So, we may need to use our prefrontal to exert some top-down influence on our amygdala or at least refocus on positives. And that will also lower stress. And lead to higher wellbeing


Case of SM

Feinstein, J. S., Adolphs, R., Damasio, A., and Tranel, D. (2010). The Human Amygdala and the Induction and Experience of Fear. Curr. Biol. 21, 1–5. doi:10.1016/j.cub.2010.11.042.

Olfactory response

Iravani, B., Schaefer, M., Wilson, D. A., Arshamian, A., and Lundström, J. N. (2021). The human olfactory bulb processes odor valence representation and cues motor avoidance behavior. Proc. Natl. Acad. Sci. U. S. A. 118. doi:10.1073/pnas.2101209118.

Amygdala and memory and learning

Bass, D. I., Partain, K. N., and Manns, J. R. (2012). Event-specific enhancement of memory via brief electrical stimulation to the basolateral complex of the amygdala in rats. Behav. Neurosci. 126. doi:10.1037/a0026462.

Article on DANA website:

Steinberg, E. E., Gore, F., Heifets, B. D., Taylor, M. D., Norville, Z. C., Beier, K. T., et al. (2020). Amygdala-Midbrain Connections Modulate Appetitive and Aversive Learning. Neuron 106. doi:10.1016/j.neuron.2020.03.016.


LeDoux, J. (2007). The amygdala. Curr. Biol. 17, R868-74. doi:10.1016/j.cub.2007.08.005.

Amygdala and fear

Hardee, J. E., Thompson, J. C., and Puce, A. (2008). The left amygdala knows fear: laterality in the amygdala response to fearful eyes. Soc. Cogn. Affect. Neurosci. 3, 47–54.

Murray, E. A. (2007). The amygdala, reward and emotion. Trends Cogn. Sci. 11, 489–497. doi:10.1016/j.tics.2007.08.013.

Michely, J., Rigoli, F., Rutledge, R. B., Hauser, T. U., and Dolan, R. J. (2020). Distinct Processing of Aversive Experience in Amygdala Subregions. Biol. Psychiatry Cogn. Neurosci. Neuroimaging 5. doi:10.1016/j.bpsc.2019.07.008.

Behaviour and stress

Zhang, W. H., Zhang, J. Y., Holmes, A., and Pan, B. X. (2021). Amygdala Circuit Substrates for Stress Adaptation and Adversity. Biol. Psychiatry 89. doi:10.1016/j.biopsych.2020.12.026.

Yang, Y., and Wang, J. Z. (2017). From structure to behavior in basolateral amygdala-hippocampus circuits. Front. Neural Circuits 11. doi:10.3389/fncir.2017.00086.

Gründemann, J., Bitterman, Y., Lu, T., Krabbe, S., Grewe, B. F., Schnitzer, M. J., et al. (2019). Amygdala ensembles encode behavioral states. Science (80-. ). 364. doi:10.1126/science.aav8736.

Krabbe, S., Gründemann, J., and Lüthi, A. (2018). Amygdala Inhibitory Circuits Regulate Associative Fear Conditioning. Biol. Psychiatry 83. doi:10.1016/j.biopsych.2017.10.006.

Šimić, G., Tkalčić, M., Vukić, V., Mulc, D., Španić, E., Šagud, M., et al. (2021). Understanding emotions: Origins and roles of the amygdala. Biomolecules 11. doi:10.3390/biom11060823.

Kim, J., Zhang, X., Muralidhar, S., LeBlanc, S. A., and Tonegawa, S. (2017). Basolateral to Central Amygdala Neural Circuits for Appetitive Behaviors. Neuron 93. doi:10.1016/j.neuron.2017.02.034.