Autoimmunity part 2: The autoimmune paleo diet - The Pro's and Cons

Where's the ice cream?!.jpg

 In this post I’m going to explore the mechanisms of the recommended autoimmune paleo diet (AIPD)  and suggest why it has very useful short term applications which are a mixed bag of interventions, reductionisms and shouldn’t be considered as a long term solution.

 In the last autoimmunity post you might remember how scientists like Polly Matzinger give an insight of auto immune disease that’s often not given enough credit. In summary of the danger theory, which is the body recognising self and the potentially damaged self. These damaged tissues be they thyroid or another tissue, is marked for removal from the system to prevent more damage occurring. The body is a pretty impressive organism that should be credited with being able to recognise its own tissues and respond with an effective response to restore best working order. So why should we discount this theory?  It’s essential to remember that a significant driver of autoimmunity is the increased prevalence of the disease in females (some 10 x more than males)  is driven by estrogen, estrogen like compounds and their ubiquity in the environment. Recently I’ve seen more people in the preceding months with vitiligo than I have seen in my entire lifetime but then I do live in a very polluted city.

 The recommendations for the autoimmune paleo diet protocol has some positives but the thought process behind such a diet has shortcomings and it’s important to tease out why it can be successful for some. I’ve always found the idea that a paleo lithic diet be entertained for health somewhat problematic. Archaeological specimens of older adults are generally lacking, suggesting mortality ranges commonly found between 20-40 year old samples (Trinkaus, 2011). That’s not to say that there weren’t older adults, ,but to base the efficacy of a diet strategy on a previous era without any data is problematic.

 There are several reasons why the AIPD might have some positive outcomes.

1.     It removes many offending compounds that are known to irritate the digestive tract. Sweeteners,  emulsifiers and thickeners are well documented to increase intestinal inflammation. Gums like guar, locust bean and Irish sea moss (carrageenan) can cause substantial damage over time and is also implicated in blood sugar regulation and diabetes. http://diabetes.diabetesjournals.org/content/67/Supplement_1/770-P?fbclid=IwAR1W8LRbx1fSu02Tr3b19ANtu2qpkZRhnwySvCj8uUC4TpRhvzypNH6lERg

2.     Alcohol is restricted. It should come as no surprise that alcohol has the capacity to affect multiple aspects of function. Most forms of alcohol contain phytoestrogens and just like long term soy consumption has the capacity to influence the body as a source of external estrogens . Additionally, many other additives like yeasts, colorants and preservative like sulphites appear equally problematic. Drinking alcohol in moderation isn’t necessarily problematic but the more susceptible that one is to estrogen issues, alcohol will often be problematic. I have seen many old ladies in their 90’s have been prone to a tipple of sherry or whiskey.

3.     Nuts, seeds and oils which are high in unstable unsaturated fatty acids are also restricted ,decreasing lipid/fat oxidation and improve mitochondrial function. The restriction of grains can also be useful for a similar reasoning and grains like millet, sorghum and barley are known to slow metabolism, but the action of seeds and grains can promote increased intestinal serotonin and histamine production, increasing the burden and damage to digestive function. Both poly and monounsaturated fats appear to promote compromised liver function, degrade metabolism and contribute to obesity.

4.     Nightshades, legumes, egg whites and gluten are well known for their role in irritability of the digestive system.

When all is said and done, there’s every reason why many people should feel better when removing these usual suspects. But there are problems with the AIPD and I have seen individuals who despite following this protocol still present with both digestive and energy issues, primarily because deficits in energy still arise and potential autoimmune reactions persist. Given some of the problems associated with determining cause and effect of specific interventions. It would be easy to speculate why someone who was prone to eating lots of fast food, high in unstable oils, high fructose corn syrups, preservatives, binding agents and suffering autoimmune, digestive, energy and other hormone disturbances might respond well to this in the short term?


There’s another plus to the AIPD - it includes fruit but there’s a caveat that natural sugars which include fructose should be kept to a minimum. There’s also an emphasis on eating fruits that are high in intestinal irritating seeds like berries. Carbohydrate is essential for optimal energy production. It promotes adequate carbon dioxide production and allows more efficient energy production and oxygenation of tissues that you just don’t get with sustained fat oxidation. Even refined table sugar shouldn’t be frowned upon and would only be problematic if your diet contained large amounts of refined sugar and devoid of other key nutrients like fats, proteins, and lack of potassium or magnesium as an example.


So is the AIPD useful? Yes, but it’s extremely limited. So how about a strategy that allows function to improve systemically rather than in isolation? Studies are limited on the effectiveness of AIPD. Whilst not autoimmune as such, a study that utilised the AIPD in patients with IBD (irritable bowel disease) completed remission in 11/15patients or 73% (Konijeti et al., 2017). That’s great, but it shouldn’t be surprising, if you’re removing all the intestinal irritants and this reasoning should extend to some improvements in autoimmune patients, resolving digestive function should follow. Gut function improved but markers of inflammation such as CRP did not, and one participant withdrew due to irritation from raw food consumption.


Aspects of the autoimmune and or autointoxication theory of disease is derived from Elie Metchnikoff’s work on immunology, bacteria and gut function (Metchnikoff & Metchnikoff, 1908). Metchnikoff proposed that death and disease started in the colon. Whilst there’s little doubt  that optimising gut function has many beneficial effects, problems arise beyond the digestive tract that might occur in otherwise healthy diets. The bowel can be a hospitable place for problematic bacteria when hydrochloric acid is low, and motility is slow induced by a low energy/thyroid state. Metchnikoff proposed that beneficial strains of bacteria can be useful to prevent unwanted maladies related to bowel function. However he was keen to point out that animals blessed with longevity often shared features of high metabolic rates and low levels of gut bacteria. This may explain why supplemental probiotic studies are not consistent in results and may simply act as a competing factor against more problematic bacteria (Goldenberg et al., 2015). The AIPD preference for more fermented goodies might be useful, but more is definitely not better. As food is poorly digested and bacterial metabolites increase so does endotoxin, intestinal hyperpermeability (leaky gut) and changes to biochemistry and hormones.

 I won’t discuss dairy produce here as it’s rarely the issue, the stressed digestive system has a problem with dairy products. I have seen countless clients return to eating dairy products like cheese, ice cream and  milks.

Eating ice cream & walking in the sunshine is an easy way to lower aspects of autoimmunity.jpg

It’s rarely the dairy that’s at fault, it’s usually the stressed digestive system that’s the real issue.

The AIPD, well there’s plenty that can be improved upon to create longer lasting function without the need for reductionist notions like the greener, the more natural, the better. Especially the problems that have been known for many decades that cruciferous/brassica vegetables high in isothiocyanates and glucosinolates, are well known to increase levels of cyanide in tissues and are anti-metabolic in nature disrupting thyroid function.

Siri what is broccoli?.jpg

Broccoli was not a palaeolithic food

Brassica vegetables may have very little place in resolving autoimmune diseases.

The most effective form of preventing autoimmunity might be to keep metabolism at its best working order rather than slowing it down. The fascination of broccoli in the modern diet is not without paradox.  Broccoli certainly wasn’t consumed in the palaeolithic era, although other cruciferous vegetables may have been (Buck, 1956). It’s elevation to farmed commodity and food stuff appeared to take place in Hellenic culture and more rapidly promoted to support the invading Roman army.

Promoting a diet that has easily digested nutrients, energy and facilitates available thyroid hormone, addressing internal and external sources of estrogen, without increasing stress responses may be the most pragmatic approach of any diet to decrease autoimmune responses. Eating plenty of fruit, sugars and honey combined with good quality proteins, moderate saturated fat and low in unsaturated fats, seeds might be the best autoimmune diet.

Another problematic aspect of the AIPD is the emphasis on Omega 3 fatty acids such as DHA to lower inflammation and this isn’t limited to poorly constructed diets but a common error in autoimmune and inflammatory protocols (Constantin et al., 2018). Many studies and review such as this invoke the antioxidant effect properties of omega 3s due to their ability to lower markers such as triglycerides, cholesterol and crease metabolism. Surprisingly when you decrease metabolic rate, you decrease metabolic function, therefore inflammatory and oxidative markers are reduced. Sustained omega 3 and other unsaturated fatty acids accumulate in the brain and liver and decrease aerobic metabolism through sustained lipid peroxidation, especially so when carbohydrate metabolism is lost.

‘ Calorific restriction and well established diet supplementation with omega 3 regulates total cholesterol, LDL-C and triglycerides.’ (Constantin et al, 2018).

 In essence this has as much benefit as taking medication to lower cholesterol. Of course eating less calories produces less inflammation and if calories are restricted below a certain threshold, this lowers metabolism, giving the impression of less oxidation. If you’re going to support the notion that taking omega 3s lowers inflammation and as many espouse, lowers cardiovascular risk, the net effect will be degraded cholesterol that’s prone to oxidation and left with an excess of fatty acids also prone to lipid peroxidation. If we’re going to help more people with a so called autoimmune disease, perhaps we need to be thinking a little more holistically? If estrogen is a main driver of a perceived autoimmune state then improving its excretion through adequate energy, liver function and robust biology should be the answer. There’s no doubt that improving digestive function is helpful but the current zeitgeist, promoting plenty of undercooked vegetables in their most natural state, high in metabolic inhibitors is restrictive to decreasing aspects of autoimmunity.


Buck, P. A. (1956). Origin and taxonomy of broccoli. Economic Botany. http://doi.org/10.1007/BF02899000

Constantin, M., Nita, I., Olteanu, R., Constantin, T., Bucur, S., Matei, C., & Raducan, A. (2018). Significance and impact of dietary factors on systemic lupus erythematosus pathogenesis (Review). Experimental and Therapeutic Medicine. http://doi.org/10.3892/etm.2018.6986

Goldenberg, J. Z., Lytvyn, L., Steurich, J., Parkin, P., Mahant, S., & Johnston, B. C. (2015). Cochrane Database of Systematic Reviews. The Cochrane database of systematic reviews (Vol. 12). http://doi.org/10.1002/14651858.CD004827.pub4

Konijeti, G. G., Kim, N., Lewis, J. D., Groven, S., Chandrasekaran, A., Grandhe, S., … Torkamani, A. (2017). Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease. Inflammatory Bowel Diseases. http://doi.org/10.1097/MIB.0000000000001221

Metchnikoff, E., & Metchnikoff, I. I. (1908). The Prolongation of Life: Optimistic Studies. Our post human future. Consequences of the biotechnology revolution. Retrieved from http://books.google.com/books?hl=en&lr=&id=U8bgKGvZJV0C&pgis=1

Trinkaus, E. (2011). Late Pleistocene adult mortality patterns and modern human establishment. Proceedings of the National Academy of Sciences. http://doi.org/10.1073/pnas.1018700108


Osteoporosis- could your exercise, nutrition and medical advice be better?

Osteoporosis and bone health, like many other aspects of optimal biology is a product of an organisms inputs and reactions to environmental stimulus. Osteoporosis is a condition like others, where prevention is often easier than the cure but perhaps the cure has been overcomplicated? Osteoporosis is a multifactorial musculoskeletal disease that is usually associated with the ageing process, decreased bone mineral density (BMD) and its tendency to fracture easily.       It’s clear that a number of factors that can be maintained throughout life to reduce the incidence of Osteoporosis in both men and women. Before we review those and compare with current guidelines, here’s some background info on the subject.

Primary Osteoporosis is the age related decline in men at around 70 and suggested as being a postmenopausal state, induced through the decreased production of estrogen in females. This last point is accepted in medical literature as the main cause of osteoporosis in females but may be severely flawed (more on this point later).

Secondary osteoporosis can be related to the following factors

Hypogonadism - testosterone/estrogen deficiency
Endocrine disease - Cushing’s syndrome, acromegaly, thyrotoxicosis, Addison’s disease and hyperparathyroidism
Dietary or assimilation deficiencies of calcium, vitamin K, vitamin D and other nutrients
Inflammation-rheumatoid arthritis, systemic lupus and ankylosing spondylitis
Neoplasms- Myleoma, lymphoma and leukaemia
Reduced physical activity
Medical drugs - corticosteroids, antiretroviral, antipsychotic, chemotherapy, hormone therapy, nicotine and excessive alcohol
Family history/genetics

The financial burden from osteoporosis generally, will increase from 98 Million Euros to 121 billion with proportional increases of 27.5 million to approximately 34 million people between the years 2010 to 2025 (Hernlund et al., 2013). Despite these huge burdens there appears to be a lack of well-designed educational programs that are geared at prevention of osteoporosis through non-pharmacological means.

The supplementation of vitamin D and calcium are well documented in osteoporosis strategies but a strategy to avoid these states are diets containing adequate calcium, vitamin A, K, magnesium (and others) adequate sunlight and moderate exercise.

Ok, so there’s a problem, it’s big business and there’s a lot of great info on how to avoid it right? Well no and here are the major points why I believe its not.


 Dual energy X-ray absorptiometry (DEXA) is the recommended choice for osteoporosis diagnosis, serum calcium, phosphate, creatinine (with GFR) alkaline phosphatase, liver function, 25 OHD, total testosterone, estrogen CBC and 24 urinary calcium excretion are recommended for the interpretation of secondary causes of osteoporosis (Watts et al., 2012).


Estrogen loss is touted as the most significant factor in decreasing BMD yet it’s action only retards resorption, or the removal of calcium from bone. Estrogen tends to inhibit the action of osteoclasts which ultimately reduce BMD. It’s the main reason the introduction of hormone replacement therapy (HRT) was considered as the primary treatment until its long-term use was found to induce clotting and cancer in women. So estrogen does not reverse Osteoporosis, it prevents further bone loss.

A variety of studies have suggested little influence of testosterone in males on BMD and that low estradiol levels combined with elevated sex hormone binding globulin appear to increase the loss of BMD (Cauley et al., 2010). A point worth noting from the correlation associated with higher estradiol levels and decreased BMD loss is that all participants in the study were recorded as having increased weight and BMD, which may influence skeletal modelling due to increased bone-loading parameters. Perhaps too much emphasis has been given to the suggestion that estrogen and its primary role of tissue proliferation amongst others, which should follow the course of age related decline?

Progesterone on the other hand has been shown to be a bone trophic or building factor that increases mineralisation of BMD, via osteoblasts (Prior, 1990). Stress increases cortisol and decreases progesterone binding at the receptor, with a preference for the glucocorticoid. Ray Peat (1997) points out that cortisol causes bone loss and its widely accepted that progesterone has an “antiglucocorticoid” action, it is reasonable to think that progesterone should protect against bone loss, and that it is a progesterone deficiency after menopause which is a major factor in the development of osteoporosis.

Thyrotoxicosis has been suggested as a mechanism of bone resorption but this appears inaccurate-  Ray Peat does a much better job at explaining this.

Medical treatment

Bisphosphonates are the first line medical treatment for treating osteoporosis and show modest changes to hip and vertebral BMD over 3 years. There use may come at a risk. Gastro intestinal side effects are well documented and in some the increase of osteonecrosis of the jaw has been observed. In some, the long-term use has been shown not only to increase the rate of fragility fracture but also to inhibit the healing process. It should be noted that adequate calcium and vitamin D in the diet are essential for bisphosphonate effectiveness


 There tend to be two well-known stances to the fitness industries approach to nutrition. One, the transformation approach, where limiting of nutrients, particularly dairy and carbohydrates and intermittent fasting are the norm. Another, the holistic warrior whose consumption of chia seeds and all things green, raw and limiting of dairy and sugar again,  may be a factor into lowering BMD in later life. Calcium is an essential nutrient for bone health and dairy is indeed a great source of calcium. Here’s an old blog on the subject.

 It’s clear that adequate vitamin D is a nutrient that is important in BMD maintenance. It regulates calcium levels, decreases the production of parathyroid hormone, which is a potent resorption factor of skeletal calcium when calcium or vitamin D are low. Here are the main points that relate to diet.

  • Vitamin D in isolation and particularly high doses increases fracture rates (Janssen, Samson, & Verhaar, 2002)
  • Unless vitamin D is accompanied by adequate calcium, BMD can decrease further.
  • Vitamin K2 can prevent the calcification of soft tissues and help improve blood calcium levels (Masterjohn, 2007)
  • High meat and diets high in pulses and beans can have a negative effect on calcium levels due to their high phosphate levels.
  • Unless you assess other key nutrients like magnesium and the factors discussed above
  • Low diary intake can be associated with poor bone health.
  • The low carbohydrate, raw green and seed eating diet suggested by holistic health practitioners may contribute to lower BMD.


Regular exercise has been touted as a significant factor in maintaining muscle mass and increasing BMD. But is the type of exercise that people are doing, increasingly in their younger years, contributing to better or worse outcomes to BMD. For bone to form adequate carbon dioxide (CO2 ) is essential. Some exercise regimes are so challenging, they contribute to excess levels of metabolic acidosis (lactic acid) and passing of CO2 from the body (worth noting that sugar consumption can also help to increase CO2 production) . Perhaps for exercise to be effective it should be light to moderate, with adequate rest periods that don’t mean that the participant is lying in a pool their sweat and vomit.

Walking, strength training with adequate rest, yoga, Pilates and other modes of moderate exercise appear most suitable for modest improvements to bone health but the diet and hormone factors are key.

It’s clear that osteoporosis is in the rise but it can be reversed. But instead of heading advice like cutting out dairy, eating lots of uncooked vegetables and training to complete exhaustion. There are more suitable mechanisms for improving bone health


Cauley, J. A., Ewing, S. K., Taylor, B. C., Fink, H. A., Ensrud, K. E., Bauer, D. C., … Orwoll, E. S. (2010). Sex steroid hormones in older men: longitudinal associations with 4.5-year change in hip bone mineral density--the osteoporotic fractures in men study. The Journal of Clinical Endocrinology and Metabolism, 95(9), 4314–23. http://doi.org/10.1210/jc.2009-2635

Hernlund, E., Svedbom, a, Ivergård, M., Compston, J., Cooper, C., Stenmark, J., … Kanis, J. a. (2013). Osteoporosis in the European Union: medical management, epidemiology and economic burden. Archives of Osteoporosis, 8(1–2), 136. http://doi.org/10.1007/s11657-013-0136-1

Janssen, H. C. J. P., Samson, M. M., & Verhaar, H. J. J. (2002). Vitamin D deficiency, muscle function, and falls in elderly people. The American Journal of Clinical Nutrition, 75(4), 611–5. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/11916748

Masterjohn, C. (2007). Vitamin D toxicity redefined: Vitamin K and the molecular mechanism. Medical Hypotheses, 68(5), 1026–1034. http://doi.org/10.1016/j.mehy.2006.09.051

Peat, R. (1999). Thyroid Therapies, Confusion and Fraud. Retrieved from www.raypeat.com/articles/articles/thyroid.shtml

Prior, J. C. (1990). Progesterone as a bone-trophic hormone. Endocrine Reviews, 11(2), 386–398. http://doi.org/10.1210/edrv-11-2-386

Watts, N. B., Adler, R. A., Bilezikian, J. P., Drake, M. T., Eastell, R., Orwoll, E. S., & Finkelstein, J. S. (2012). Osteoporosis in men: an Endocrine Society clinical practice guideline. The Journal of Clinical Endocrinology and Metabolism, 97(6), 1802–1822. http://doi.org/10.1210/jc.2011-3045

Calcium- Don't ditch the dairy.

Calcium - don’t ditch the dairy. Like every nutrient that we have consumed over the last millennia or ten, there are reasons why some foods appear more beneficial than others. Using poor tests like Igg4 sensitivity/allergy analysis many ‘experts’ have convinced us that one of our most potent foods is causing us more harm than good. I am on the bandwagon that as far as my food goes (meat and dairy) grass fed, free range and organic remain a better choice for all concerned. Hormesis can only take us so far when it comes to pesticide and pollutant exposure and the individuality of tolerance and adaptation remains a knife-edge for many.

Don't ditch the dairy

Without getting into the arguments of which type of cows produce what compounds. This topic is merely aimed at why people have issues with calcium uptake and is the problem really a dairy issue?

Many people who have had blood tests are often told to take extra calcium supplements in response to presenting with low serum calcium. However the issue of lowered calcium in the blood may have nothing to do with the amount of calcium that they are ingesting. Here are some potential mechanisms:

• Low levels of vitamin D: Vitamin D is a well-known nutrient/hormone like substance that allows for the adequate uptake of calcium into bones and teeth. amongst many other functions which include immune system function. (This synergistic relationship can be observed in reverse also) • High phosphorus/phosphate diet. In addition to the added phosphates to foods and crops. Current recommendations suggest increasing portions of grains, beans and peas, which not only contain phosphates but also contain phytates, which can block mineral uptake. Low magnesium is also an issue. • Increased estrogens and xenoestrogens that increase the stress response and cause calcium to leach from the bones into soft tissues. A decrease in available progesterone can decrease bone density. • Poor reabsorption factors such as low intake of vitamin K2 • An actual calcium deficiency from low calcium intake • Excessive exercise which can be due to inadequate calcium and poor carbon dioxide retention. • Inability to absorb calcium from the digestive tract, low stomach acid levels/hypochlorhydria and damage to villi/intestinal lining, which can be observed in celiac but increasingly with intestinal hyper-permeability, endotoxin and chemical induced damage. • Decreased blood albumin levels which bind calcium. Digestion and dehydration issues mainly. • Regulation of PTH or parathyroid hormone.

Osteoporosis is on the rise but its increasing prevalence is not due to low calcium intakes but due to many complex interactions, between stress, pollutants, low sunlight exposure, excessive exercise and nutrient levels. The common reductionist approach is to throw the same nutrient at the problem in larger amounts and hope that this so called ‘deficiency’ is corrected.

It's worth noting that elevated serotonin levels in the blood are responsible for bone less. An increase in serotonin  can be viewed with both a temporary spasticity of smooth muscles tissues and loose or watery stools. The role of serotonin is to increase evacuation of the bowel, mediated by an increase in its production from the entero chromaffin cells in the digestive tract, where some 95% of the bodies own supply is created. A diet high in nuts and seeds, which contain serotonin are likely to irritate the digestive tract. From an evolutionary survival perspective, this allows for seeds to be passed out from the bowel without being digested, ensuring plants survival. Increased aggression and irritability have been noted in elevated serotonin levels, which also correlates with a decrease in bone density. Ensuring adequate calcium in the diet during these times is therefore essential.

When phosphorus increases and there is a lack of vitamin D, PTH increases to balance out the need for increased calcium, which is taken from bones and teeth. In essence much of the calcification of arteries and soft tissues can be attributed to this situation. Some of the signs that can be observed with low calcium levels are:

• Muscle cramps • Nose bleeds • Soft fingernails • Frequent cold sores, rashes • High or low blood pressure • Irritability • Fevers with mild colds

Administering calcium supplements to those with calcium deficiency is much like talking over someone before they have a chance to speak. You only here there initial words but fail to here what they are truly saying.

Much of the marketing and sales of supplements these days are suggestive that our food does not give us the nutrients that we need and that we need to stay plugged in to the rattle of supplement bottles opening daily. When in fact if we just strive to improve digestion and cofactor optimisation this simply isn’t the case. In the case of dairy, when we flippantly talk about super foods, when you look at the nutrients provided from dairy, it is indeed a food with plenty to say for itself, particularly in the situations of growth, stability and anti-stress.


1. Christodoulou, S. , Goula, T., Ververidis, A., and Drosos, G. Vitamin D and Bone Disease. Volume 2013 (2013), Article ID 396541, http://dx.doi.org/10.1155/2013/396541 2. Weatherby, D. Blood Chemistry Analysis. Bear Mountain Publishing. 2002.