The Body Keeps the Score —
How Trauma Becomes Terrain

I have sat across from clients in consultation and asked about sugar cravings and muscle stiffness — entirely routine intake questions — and felt something shift in the room. A particular quality of stillness. An answer that came too quickly or too slowly. A story about a loss, a relationship, a period of sustained fear or grief, offered almost as an aside. And I would think: I have a strong expectation about what the mineral analysis will show. Which is worth naming for what it is. An expectation formed before the test is exactly the thing that makes a practitioner see what they came to see, and “test, don’t guess” has to apply to me before it applies to anyone else. I record the expectation and then read the result on its own terms.

The calcium shell. Elevated calcium and magnesium relative to sodium and potassium on a hair tissue mineral analysis, indicating a pattern of mineral dysregulation associated with chronic emotional stress and psychological withdrawal — often described as the body building a wall of calcium around itself as a defence. That description is a metaphor, not a demonstrated mechanism, and I want to separate the two. What I can say is that I have repeatedly observed this mineral pattern alongside a history of sustained stress or loss. What I cannot say is that the calcium is doing what the metaphor implies — nobody has shown that. There is also a measurement problem worth knowing: hair tissue mineral analysis has documented reproducibility difficulties, with identical samples sent to different laboratories returning materially different results and interpretations. I use it as a pattern-generating observation rather than as a measurement I would build a protocol on. The term comes from the hair-mineral interpretive tradition, not from controlled research. And the risk of the pattern is the one I named above: once you have seen it enough times, you start to recognise the person before you see the numbers — which is exactly when the numbers need reading on their own terms.

This post is about what trauma — physical and emotional — actually does to the biological terrain. Not as a psychological observation but as a physiological one. Because the body does not distinguish between a car accident and a bereavement, between a surgical procedure and the end of a marriage, between a childhood defined by unpredictability and a decade of sustained occupational stress. The HPA axis responds to threat. It does not ask what kind.

Three Books That Changed How I Think About This

The Cell Danger Response — When the Body Never Gets the All-Clear

Robert Naviaux's cell danger response (CDR) framework (Naviaux, Mitochondrion 2020) is the most useful model I know for thinking about how threat — physical or psychological — could become chronic biological dysfunction. It is a model, not a settled mechanism. Its cellular biology rests on laboratory work; its extension to psychological trauma in people is a hypothesis that has not been directly tested.

The CDR is an ancient, evolutionarily conserved programme that activates in response to any threat to cellular integrity — infection, toxin exposure, physical injury, or sustained psychological stress. When the CDR is activated, cells shift from their normal metabolic mode into a defence mode: energy production shifts from the mitochondria toward the cytoplasm, cellular communication changes, the extracellular environment becomes more protective, and the immune system is placed on heightened alert.

In an acute threat that resolves — an infection that clears, an injury that heals — the CDR deactivates and the cell returns to normal function. The problem arises when the threat does not resolve, or when the cell's danger detection system cannot register the resolution. In chronic stress, sustained trauma, or unresolved grief, the CDR remains partially activated indefinitely. The cell is permanently in a low-grade state of emergency. Its metabolic resources are continuously diverted toward defence rather than repair, growth, and optimal function.

The cell danger response is the body's answer to the question: is it safe? When that question cannot be answered with a clear yes — when the threat is chronic, or when the nervous system cannot find the signal that says the danger has passed — the answer defaults to no. Indefinitely.

If the model is right, this is how unresolved trauma becomes chronic illness. Not through weakness, not through imagination, not through a failure of will — but through a cellular programme that is doing exactly what it is designed to do, in a situation where the design is not adequate to the circumstances.

Physical Trauma — The Structural Story

Physical injuries, accidents, and surgical procedures create structural changes that persist long after the acute phase has resolved. The most clinically important — and most consistently overlooked — are the neurological consequences of structural trauma.

Emotional Trauma — The Mineral Signature

One of the most consistently revealing findings in my clinical practice has been the relationship between significant emotional events and specific mineral patterns on hair tissue mineral analysis. I want to be exact about the status of that observation. Sustained psychological stress has well-documented effects on the HPA axis. That those effects show up as a specific, reliable hair mineral pattern is my clinical observation and the claim of the HTMA interpretive literature — it has not been established by controlled research, and the test itself has the reproducibility problems described above.

The Calcium Shell

In a state of chronic emotional stress — sustained grief, unresolved loss, prolonged relationship difficulty, or the accumulated weight of caring responsibilities over years — the pattern I most often see is calcium and magnesium elevated relative to sodium and potassium. The HTMA interpretive model reads this as a biochemical buffer zone — reduced cellular permeability, slower metabolism, emotional flattening, withdrawal from engagement with the world. That reading is the model’s, not a measured result.

In the interpretive literature, the personality expression of this pattern is described as a kind of protective numbness — the person who does not feel the full weight of their situation. The clinical picture that tends to accompany it is: sugar cravings, muscle stiffness, fatigue that is not improved by rest, and a subjective sense of being behind glass — present in the room but not fully connected to it. The explanations usually offered for each (the body “penetrating the calcium barrier” with sugar, for example) are part of the model and are untested.

I have sat with clients who have recently lost a partner, a parent, or a child, and seen this pattern on their mineral analysis so consistently that I have learned to ask about significant losses as part of the interpretation conversation. Not because loss causes disease in any simple causal sense, and not because the mineral pattern proves anything about grief — but because the physiological load of grief is real, and a programme that ignores it tends to underperform.

Zinc, B6 and a Construct I No Longer Use

An earlier version of this post had a section on pyroluria — the idea that elevated urinary pyrroles bind zinc and B6 and drive anxiety and poor stress tolerance. I have retired pyroluria as a clinical construct, and this post now says so. The test has not been shown to be reliable: a systematic review of 73 articles found only three showing higher levels in a psychiatric population than in controls, no placebo-controlled trials of the zinc-and-B6 protocol, and concluded that testing is not recommended for screening or treatment (Warren et al., 2021). A 2024 review of the underlying chemistry questioned what the test is even measuring (Sherwin & Shaw, 2024). The full account is in my pyroluria correction.

What survives is simpler and testable. Zinc and B6 status are real, measurable, and worth checking in someone under sustained stress — zinc through plasma zinc read alongside albumin and alkaline phosphatase, rather than through a urinary pyrrole test or a hair sample. Low zinc and a high copper-to-zinc ratio have been associated with anxiety and mood symptoms in observational studies, but the evidence is mixed and does not show which comes first (grade: mixed, observational). The point stands in a narrower form: a client with poor stress tolerance deserves to have the basic nutrient picture checked, not only to be handed a psychological tool.

How Trauma Shapes the Approach to Healing

This is the dimension that is most absent from functional medicine education and most consequential in clinical practice. Trauma does not just alter the terrain biologically. It alters the relationship the person has with their own body — and therefore with the process of addressing their health.

The person who has lived in a body that has been a source of pain, shame, or threat does not approach a health programme with the same openness as someone whose relationship with their body has been broadly positive. The client with a history of disordered eating does not fill in a food response form the same way as someone who has a straightforward, uncomplicated relationship with food. The client who has been repeatedly told by medical professionals that there is nothing wrong with them — that their symptoms are stress, that their results are normal — arrives with a different level of trust in clinical investigation than someone for whom the medical system has been a source of answers rather than dismissal.

Albert Bandura's concept of self-efficacy — the specific belief in one's ability to organise and execute the actions needed to succeed in a particular situation — is directly relevant here. It is distinct from general self-belief. A person may believe they are capable and worthwhile in general terms, while having very low self-efficacy for changing their eating, for maintaining an exercise habit, or for following a supplement protocol consistently. This specific self-efficacy is shaped by prior experience. If previous attempts to improve health have failed — because the biochemical terrain was not addressed, because the protocol was not personalised, because the trauma driving the pattern was not acknowledged — the self-efficacy for the next attempt starts lower than it might appear from the outside.

Paul Chek articulated something that has stayed with me: that you have to have your own dream, or you will live someone else's. The health goals that come from external pressure — a partner's concern, a GP's warning, a social ideal — have different staying power than the goals that come from a genuine internal sense of what this person's health and life could be. Part of clinical work is finding that internal driver. Not manufacturing it — finding it. It is usually there, often buried under the weight of accumulated experience that has made believing in it feel dangerous.

The Small Victory and the Snowball

I have coached clients who said they had never been able to do a press-up. Not for lack of trying — for lack of believing it was possible. I have worked on their core stability, their hand placement, their hip strength, their scapulo-humeral rhythm, their breathing pattern and tempo. I have built the component parts separately and then reassembled them. And when the press-up happens — really happens, with control and range and repeatability — something shifts in that person that is not about the press-up at all.

The body has done something it believed it could not do. That is a different kind of evidence than being told you are capable. It is embodied evidence — felt in the nervous system, stored as a new reference experience that the self-efficacy for the next challenge is built upon.

I have watched clients stand on a Swiss ball — not because standing on a Swiss ball is especially useful for leg strength or caloric expenditure, but because overcoming the fear of that physical challenge produces a psychological shift that snowballs into other areas. The person who stood on the Swiss ball is not the same person who walked in believing their body was something that happened to them rather than something they inhabited and could trust.

These small movement victories are not separate from the clinical programme. They are part of it. The nervous system that has learned through embodied experience that it is capable of more than it thought it was, is a more receptive nervous system for every other intervention that follows. The person who leaves a session with a skip in their step is more likely to choose well at their next meal — not because the exercise burned calories but because their relationship with their body has shifted, fractionally, toward something more collaborative and less adversarial.