Lorem ipsum dolor sit amet, consectetur adipiscing elit. Morbi eu nulla vehicula, sagittis tortor id, fermentum nunc. Donec gravida mi a condimentum rutrum. Praesent aliquet pellentesque nisi.
Image thumbnail

AIP – The Science


Research suggests that the contribution of genetics to the development of autoimmune disease is approximately a third, or 33%. That means that whilst a third of the predisposing factors for developing an autoimmune condition lie within the genes, the rest is entirely down to factors other than our DNA. Put another way, you can be born with the ‘predisposition’ to autoimmunity – but 66% of the factors which are going to make you develop autoimmune conditions are anything but genetically predetermined.

This might surprise you. Genetic analysis is currently so popular that you could be forgiven for thinking that interpreting genetics would hold the key to revealing the truth of our identities, our characteristics, our traits – and our illnesses. Figures suggest that the reality is far different. So whilst genetics is certainly a part of the manifestation of illness, it is far from the whole story.

You may have heard the phrase “genetics load the gun, the environment pulls the trigger.” This alludes to the fact that our DNA contains all of the information necessary for producing (and reproducing) every single cell in our entire body. But along with these deterministic factors, there are a lot of other variables and things which need to be switched ‘on’ in order to manifest. Much of our genetic code is just a predisposition until circumstances cause it to become ‘expressed’.

The term ‘genetic expression’ indicates what we are coming to understand about the manifestation and/or minimisation of certain parts of ourselves: both of our personality and our biology. Certain genes can be turned ‘on’ and ‘off’.


What turns these switches on or off (i.e. governs whether certain genetic traits or patterns are ‘expressed’) is referred to as the ‘exposome’, i.e. everything external and non-genetic that we go through in life.  And yes, we literally mean everything, from food to sleep, stress, emotions, relationships, chemicals, mood, nutrients etc. etc. etc…. for your entire life.


This is the realm of epigenetics – the manipulation of gene expression by factors which are not genetic. If you appreciate that DNA may not malleable, but certain parts of it are able to be influenced in terms of how brightly they shine, it demonstrates why only 33% of autoimmune disease is genetically determined: there is a whole world of ‘triggers’ and ‘activations’ that must happen in life for the genes which predispose to autoimmunity to come into effect in the life.

It gets even more nuanced than this. The exposome that surrounded our ancestors can also influence our own DNA and biochemistry. That means that the environment around the people that made us – from food to toxicity to societal norms and structures – can affect us in the now: this is thought to be how cultural norms affect genetic evolution.

This means that the way your mother and father ate, responded to stress, exercised and dealt with their epigenetic milieu will have, in part, played a role in the activation or repression of some of your genes’ expression.

Then they brought you up – and you went to school – and you lived in a certain community and at a certain socioeconomic level. Everything that you went through factors into the you that you become. Brain frontal cortex development isn’t even complete until age 25, so you literally aren’t even thinking like a fully formed adult until you are a quarter of a century old…


It seems that the elements of biology we believed were ‘fixed’ may actually be far more manipulated and altered than we imagined.


But what does any of this have to do with autoimmunity?


Guilt, Responsibility and Illness

One of the most pervasive and complex parts of any chronic illness, including autoimmune conditions, is the psychological distress that can come along with it. You will read elsewhere on this site how important mindset, perspective and attitude are in the process of attempting to effect change.


This is why we present an understanding of genetics – because understanding the ‘why’ behind any physical suffering or condition is a fundamental step in being able to accept the current situation. The heritability of genetics, coupled with the influences of the exposome of our ancestors, shows us that there is a many things that we could do nothing about that contributed to the evolution of any of our suffering.


But that said, this same understanding of genetics and the influence of the exposome also shows us that our fate is not written in our genetic code because we can, today, change our exposome – and in doing so we have the power to tackle our health conditions head on and really make improvements in our wellbeing.


So what is the genetic cause of autoimmunity?

Well, in truth, chronic illnesses are rarely, if ever, caused by one isolated ‘instigator’ or issue. Chronic illnesses arise due to a multitude of factors, the combination of which is often referred to as a ‘perfect storm’.

This perfect storm of lifestyle conditions may trigger illness, but a genetic predisposition is what determines its downstream impacts. When discussing autoimmunity, these downstream impact revolve around having an immune system which goes into overdrive.

Currently, autoimmunity is believed to be the result of the immune system malfunctioning in one of two ways (or possibly both):


  1. Either the immune system is hyper-sensitised and attacks too readily, perveiving anything and everything is a threat and thus engaging in pre-emptive strikes, during which the self tissue is mistaken for enemy tissue and becomes damaged,


  2. The immune system does not have the correct regulatory measures to turn itself off after an initial, appropriate, attack to a legitimate ‘antigen’. This means that  inflammatory cytokines and killer immune cells are constantly being released as if a threat were still present, despite it being long gone. The net effect is permanent inflammation and the system issues that result.




Some of the genetic Single Nucleotide Polymorphisms (or SNPs) which govern the way the immune system responds, and the way the immune suppression system  acts, have been identified. To understand this you need to understand that the immune system is built to create antibodies to enemy invaders all the time. It does this by a complex network of cells and complexes which are permanently scanning for foreign bodies, designing antibodies for anything vaguely suspicious and then pulling back after an attack, or after realising that an attack was unwarranted.

In the maelstrom of activity of a perfectly functioning immune system, even healthy individuals continually make so-called ‘auto-antibodies’ – or antibodies that can attack ‘self tissue’. These are kept in check by a regulatory system which either reformulates those auto-antibodies prior to release (after recognising that they would attack ‘self) or removes these auto-antibodies from circulation if they are discovered.


This regulation, reformulation, recall system has to be built by our genes – and there are SNPs which can affect and interfere with the whole, complex workings of immunity.


B cells (a type of immune cell created in the bone marrow) must be ‘checked’ prior to their release – like immunological quality control. Some of the most simple SNPs  affecting immunity change this checking process so that instead of faulty B cells being reformulated they are released into circulation, creating unintended inflammatory and immune responses.

One of the most complex, beautiful and intriguing parts of how our immune system works is coded by the Human Leukocyte Antigen (HLA) genes. These affect what is known as the major histocompatibility complex (MHC). The MHC governs the “presenting” of antigens to the adaptive immune system, the part of our immune system that learns what’s threatening to us as we go through life. SNPs in the HLA genes can affect what gets presented by the MHC to the adaptive immune system as a threat. This means that the immune system is taught by faulty HLA/MHC presentation to react to things that aren’t actually damaging – even some ‘self tissue’.

Mutations within the HLA-B coding have been linked to excess sensitivity (and reactivity) to some external products such as foodstuffs, toxins, chemicals or moulds. The number attached to the end of the HLA is correlated with the particular products your immune system will respond to – with HLA-B27 linked to autoimmunity, and several others linked to mould sensitivity, and two other HLAs, DQ2 and DQ8, being tied to the presence of coeliac disease.

Lastly, moving beyond the SNP-determined regulation of autoantibodies and HLA coding, our genes can also affect the strength and nature of our inflammatory responses themselves, not just what we react to. How many immune cells you make, where they are located, how much inflammatory material each cell contains and how easy it is to ‘set them off’ are all, in part, influenced by genetics.

And yet…


Not one of these SNPs is categorically causative of autoimmune conditions.  And, as with all genetic components, it is the epigenetics (everything mentioned in the first few paragraphs here) that will trigger the expression of these genes and the manifestation of extremes of illness as a result.


What the above-highlighted genetic factors do suggest is that if you have the wiring for autoimmunity or immune sensitivity then it is a deep part of you which must be accepted for what it is.

It doesn’t however, have to rule and dominate your life.

Just as epigenetic factors such as diet, lifestyle, stress, lack of sleep, emotional conflict and socio-economic struggles are able to trigger off the manifestation of autoimmunity, these same epigenetic factors are able to regulate the immune system, even when it is in a state of reactivity and self-attack.

Understanding the science of autoimmunity provides the backdrop to accepting the genesis of any autoimmune condition – but it also provides us with the understanding of the pieces of our exposome we can manipulate in order to reverse autoimmunity and place any health crises caused by it into remission.

In many cases this is perfectly possible, but it requires a foundational understanding and compassion. Any autoimmune condition is a perfectly reasonable response from an immune system that has, for some reason, spiralled out of hand. In attempting to keep us safe, our immune system has developed an overzealous response. More on this can be found in out AIP Mindset page.

But with this backdrop in mind, the rest of our AIP section will help you to understand the exposome manipulations which will down-regulate, re-educate and re-balance your immune system. But if you want to know the science behind immuno-modulation using nutritional manipulation, read on…


When faced with the prospect of all of the eliminations recommended on AIP there are some common reactions, amongst which are overwhelm, panic, dread and sorrow or grief. But another common reaction is to believe that the foods being eliminated are suddenly ‘enemies’ or ‘bad for us’.


In truth, the foods eliminated on any Autoimmune Protocol are not necessarily ‘bad foods’ – because there really are no ‘bad foods’.  Instead there are only foods which are healthy and not as healthy for each individual at each moment in time.


When it comes to AIP we are intentionally removing foods based on their known capacity to aggravate an immune system which is already hyper-alert. In context of the genetics information shared above, it should be clear that, in someone with the right genetics, the body itself is the target of an attack because the immune system is attacking anything that resembles something potentially toxic.

The foods eliminated on AIP are those known to aggravate the human immune system. Even in normal, functioning, healthy individuals the proteins, compounds and nutrients found in foods such as eggs, nightshade fruits and vegetables and nuts and seeds are slightly inflammatory and they elicit a minuscule release of inflammatory compounds.

In someone with a raging immune system this stimulates the release of inflammatory compounds – but this is ON TOP of an immune system already on high alert, creating more inflammation, which in turn stimulates further immune responses, further increasing inflammation – and the result is reaction compounded by reaction. Additionally, the presence of slightly triggering, mildly toxic foods reaffirms the message to the immune system that the body is in a state of threat and that it must remain on high alert.

The whole purpose of removing healthy but slightly aggravating or inflammatory foods from the diet is to circumvent the overreaction and constancy of inflammatory cascades. AIP advocates the restriction of otherwise perfectly healthy foods ONLY because they play a role in continuing inflammation and immune reactions in the body.

At its heart, therefore, the Autoimmune Protocol is not just about food. It is about removing inflammation. A large part of this revolves around food and nutrition – because ⅔ of our immune system surrounds our gastrointestinal tract, making food-based compounds a prime trigger.

However, it is mostly about removing all of the stressors and the stimulus to the immune system – so lifestyle, mindset, social relationships and work-life balance is utterly vital to quelling the fire of an autoimmune condition.

Whilst there are other Elimination Diets which remove different foods for different reasons, the science behind the the AIP approach specifically is all about turning off the immune overdrive – and keep reading for the ‘how’.


The majority of the science of Elimination Diets can be found on our AIP Reintroductions page – but the most important paragraphs are copied below.  The context of this process should now make sense in light of the ideas shared above:

The AIP Elimination Diet removes common, known and suspected antigens or inflammatory compounds from the body.

Whilst consuming these foods, the immune system has networked response of checks and balances to all foods eaten. This works on a see-saw of processes: the first being ‘react’ and the second being ‘calm the reaction’.

The initial inflammatory, immune response at the presence of an antigen comes from one branch of the immune system. This initial response is then brought down by a complementary branch of the immune system. (In fact, one theory (shared above) of autoimmunity is that it is this complementary, ‘calm the reaction’ branch which is ineffective.)

This bringing down of the reaction is simply done to avoid the body being reactive and hyper-inflammatory all of the time – but all of this means that the body is locked in a state of react/quell the reaction/react/quell the reaction – and while the immune system is on overdrive, you feel generally awful.


The AIP Diet removes reactionary foods, and hence removes the need for the immune system to ‘react’ in the first place. You therefore also remove the need for the ‘calm the reaction’ response. All of the immune cells involved in these paired processes start to diminish in the body on AIP, as the body no longer has the need for the specially made, targeted reactive T cells which fought the antigenic foods. It therefore no longer needs or makes the cells that match those T cell to bring the reaction down.


The magic of Elimination Diets is that the cells which suppress the ‘reaction’ T cells disappear far quicker than the memory T cells which create the reaction in the first place. i.e. the ‘react’ branch retains memory of antigens for a good while, just in case. But the ‘calm the reaction’ branch very quickly stops making its calming cells which seem clearly to be no longer needed.

This means that when eliminated foods are brought back into the diet after a period of time, if you have any reaction it will be more reflective of the things that truly aggravate your immune system. The ‘react’ cells are still there, waiting just in case – but you no longer have a ready supply of the ‘calm the reaction’ cells. You will get symptoms if you really cannot tolerate that food – and the symptoms are the clue to whether you personally are reactive to that foodstuff.


Here is a good place to reiterate… the AIP Diet is NOT a personalised regimen excluding all the foods you are intolerant or reactive to. It is a broad brush which eliminates all the foods known to trigger immune activity, generally.


This means that you are highly, highly unlikely to be truly reactive to every food eliminated on the AIP Diet. The reintroduction of certain foods may have no impact at all. Other foods may have a larger impact than they ever did when you consumed them prior to AIP.


THIS is how you know what foods are truly problematic for you personally, and how you personalise your diet going forward.


This is why Elimination Diets work. In the symptomatic fog of a highly inflamed state, whilst consuming a diet filled with foods that your immune system doesn’t like, living with the perpetual checks/balances, flare/suppression dance of reactivity it is very difficult to observe reactions for what they truly are.

Removal means that reintroduction will cause you to react more overtly to certain things that are real triggers for you personally. But it also empowers you to know the foods that you are absolutely, perfectly fine to eat going forwards.

Coping with the flares and reintroduction phases of the AIP Diet requires a mindful awareness of the following:


  1. If you do have a symptom flare on reintroduction, your foundations after several months of low-inflammation, AIP living will be far stronger than they were when you began this process. You will quieten the reaction and you will be able to move forward

  2. This is truly an information-gathering exercise in which you are the driver and the experimenter. You are learning everything you need to know about the reality of what affects – and doesn’t affect – your body. Whilst flares and reactivity during reintroductions might feel like failures, they are not completely backwards steps. They are knowledge-gaining, information-gleaning experiences which will continue to empower your journey going forward.


Life doesn’t start at reintroduction, nor does AIP disappear once you have your “crib-sheet” of foods. At Paleo in the UK we are firm believers that everything on both the AIP and Paleo sections of this websites are tools. These tools clear the reactivity in the body and foster the relationships of awareness between us and our food, our environment and our lifestyle practices. We can learn ourselves, and in so doing create an understanding of how we stay healthy in our lives.


If you have had any autoimmune condition take root in your life then the real way to get through it is to find any tools you need to modify the levels of threat your body feels it is experiencing on a moment-by-moment basis. A part of this is the dietary piece – but there are so many other fragments of life which affect and will hep to decrease immune reactivity.


Do continue to explore the rest of this site to discover more. And if you’re still scared and fear the AIP Reintroduction phases – reach out to us for help today.