Switching Off the Alarm

After losing an arm or a leg, most people go on to feel the missing limb, and many feel pain in it: a clenched fist that won't open, a burning foot that isn't there. There is no tissue left to be injured, yet the pain is completely real.¹ Phantom limb pain shows something remarkable about how we work. Pain, and many other symptoms, are made by the brain, as its best judgement of what the body needs to know.² Usually that judgement is accurate. But sometimes the brain's alarm system becomes stuck on high alert, and keeps sounding long after the danger has passed.

The alarm that won't switch off

Every moment, your brain is quietly predicting what is happening inside your body and deciding whether anything needs your attention.³ Two areas are central to this. The amygdala, a small almond-shaped cluster deep in the brain, scans constantly for threat. The insula gathers signals from the heart, gut, muscles and immune system and builds our felt sense of the body: whether we feel well, tired, sore or sick.⁴

When something genuinely threatens us, such as a virus, an injury, mould exposure or a long period of stress, this system rightly turns up the volume. Symptoms like pain, fatigue and sensitivity are protective: they make us rest, withdraw and recover. The trouble comes when the system learns the lesson too well. Nerve pathways that fire together repeatedly become stronger and quicker to fire again, and the threshold for raising the alarm drops lower and lower.

Scientists call this central sensitisation: an amplification of signals within the nervous system, so that ordinary sensations are felt as pain, and small triggers produce large responses.⁵ It's now recognised as a cause of pain in its own right. In 2017, the International Association for the Study of Pain added a new term, nociplastic pain, for pain that arises from this changed processing in the nervous system rather than from ongoing damage in the tissues.⁶ Researchers increasingly see a similar process behind other persistent symptoms too, including fatigue, dizziness, gut upset and sensitivity to light, noise, food and chemicals, as the brain's predictions about the body become locked in a pattern of danger.⁷

What's learned can be unlearned

The same neuroplasticity that allows the alarm to become stuck also allows it to be reset. Research on fear shows that the brain doesn't simply erase an old danger signal. Instead, it learns a new, stronger message of safety that gradually overrides it, a process called extinction learning.⁸ That new learning needs repetition, just as the old pattern did. Each time we notice the alarm and calmly teach the brain "this is safe", we strengthen the new pathway a little more. (For how meditation reshapes the brain, see The Sound of Stillness.)

A striking trial in back pain

Some of the clearest evidence comes from chronic back pain. In a randomised trial published in JAMA Psychiatry, 151 adults with long-term back pain received either four weeks of pain reprocessing therapy, a placebo injection, or their usual care. Pain reprocessing therapy teaches people to understand their pain as a false alarm from an overprotective brain, and to respond to sensations with safety rather than fear.⁹ (See The Belief Effect.)

The results were remarkable. After treatment, 66% of people in the therapy group were pain-free or nearly pain-free, compared with 20% of the placebo group and 10% of the usual-care group, and most of the benefit was still there a year later. Brain scans showed reduced activity in pain-processing regions, including the insula. The trial included people whose pain had no clear structural cause, and the authors stress that it isn't a treatment for pain from active injury or disease.

The brain that learned danger can learn safety.

The Gupta Program

One of the best-known brain retraining programmes was created by Ashok Gupta, a British researcher who recovered from ME/CFS himself. In 2002, he proposed that in some people with chronic fatigue syndrome, the amygdala becomes conditioned into a state of chronic alert after an initial trigger, keeping the body in a cycle of symptoms and further alarm.¹⁰ From this idea he developed an approach now known as Amygdala and Insula Retraining (AIR), or the Gupta Program.

It's delivered through an app and online course, with daily practice of around 20 minutes. The core is a simple series of steps for spotting the moments when the alarm is firing, through symptoms, worry or monitoring the body, then gently interrupting the pattern and redirecting the brain towards feelings of safety, calm and health. Alongside this sit guided meditations, breathwork, work with the vagus nerve, lifestyle guidance, live group sessions and a supportive community.

What the research shows so far

The Gupta Program has now been studied in several small randomised trials:

• Fibromyalgia and chronic fatigue (2012). At a specialist US clinic, patients who added amygdala retraining to standard care showed significant improvements in physical health, energy, pain, symptom distress and fatigue compared with standard care alone. Many participants dropped out, however, leaving 21 of the 44 who began.¹¹
• Fibromyalgia (2020). In a Spanish trial of 41 women, mindfulness combined with amygdala and insula retraining reduced functional impairment, anxiety and depression more than relaxation therapy, with benefits that grew at follow-up. For every three women treated, one more halved her fibromyalgia symptom score than with relaxation alone. Markers of inflammation in the blood didn't change.¹² (See Where Body Care Meets Mind.)
• Long COVID (2023). Compared with a similar-length health and wellness programme, three months of AIR led to a reduction in fatigue around four times greater, and twice the improvement in energy.¹³

A survey of people using the programme for a wide range of conditions, from Lyme disease and mould illness to mast cell activation, also reported large improvements in overall health,¹⁴ though as a survey without a comparison group, it can only point towards what larger trials should test.

As with any new approach, the research is still growing. The trials so far are small and rely on people's own reports of how they feel, which is natural when the symptoms themselves are felt rather than measured. In some trials, a number of participants didn't complete the programme. Like any daily practice, from meditation to physiotherapy, brain retraining works best for those who can commit to it regularly, and it won't suit everyone; for those who do engage, the results can be life-changing. What gives the findings weight is how well they fit the wider science: the growing understanding of central sensitisation, the strong results of pain reprocessing therapy, and decades of research on fear learning and mindfulness. Larger trials are now under way, and they will help show who benefits most.

Retraining alongside the roots

From a naturopathic point of view, the brain's alarm rarely stuck for no reason. It's more easily calmed when the body's genuine stressors are also addressed, so that the brain has less to be alarmed about:

• The gut, whose bacteria and lining constantly signal the brain and immune system. (See The Master Regulator.)
• Nutrient status, especially iron, B12, vitamin D and magnesium, which the nervous system and energy production depend on. (See You Are What You Absorb and Living by the Sun.)
• Blood sugar swings, which release stress hormones and can mimic anxiety. (See Balancing the Sugar Seesaw.)
• The stress hormone rhythm and sleep, the foundations of nervous system repair. (See The Cortisol Clock and The Art of Sleep.)
• Toxic exposures, such as damp and mould at home. (See Lightening the Load.)

If you have ME/CFS or long COVID, pacing remains essential. Brain retraining isn't about pushing through: activity that triggers a crash after exertion can set recovery back, and the UK's NICE guidance advises carefully managing energy within your limits.¹⁵ The aim is to gently widen the window of what feels safe, not to override the body's signals.

Simple ways to begin

• Name the alarm. When a symptom flares or worry spirals, try noticing it kindly: "That's my alarm system, trying to protect me." Labelling it creates a little distance.
• Slow the breath. A long, slow out-breath is one of the quickest ways to signal safety to the nervous system. (See The Healing Breath.)
• Savour safety. Several times a day, pause to notice what feels comfortable, calm or good, even briefly: warm hands on a mug, sunlight, a friend's voice. This is how the new pathway is built.
• Less body-scanning. Constantly checking for symptoms keeps the alarm primed. Gently turn your attention outward, towards people, nature and things you love.
• Small, safe steps. Reintroduce gently what the brain has learned to fear, whether a food, a walk or an activity, in steps small enough to feel safe.
• Stay connected. Feeling understood and supported is one of the strongest safety signals of all. (See Social Resonance.)

At Rootwise, we see the nervous system and the body as one. We look for the physical drivers that may have set off the alarm in the first place, from gut health and nutrient levels to blood sugar, hormones and environmental exposures, and support your nervous system as it learns to feel safe again. A Rootwise consultation can help you find where to begin.