The following account is taken primarily from Ray Audette’s ‘Neanderthin’ but the words and, thus, the interpretation is mine
The theory centres on disorders of the immune system - how they are caused and what their effects may be.
• as human body composition is also diverse and its physiology complex, our immune systems must distinguish invaders from those that make up the host’s body and beneficial bacteria
• our immune systems distinguish invaders by their protein structures
• the attacking invaders continue to evolve and our defending immune system also evolves - as a species through natural selection; as individuals through sexual reproduction
• evolution, sexual reproduction and natural selection have given each of us our own distinct and possibly unique immune systems
• immune system disorders occur when the immune system mis-identifies a particular protein structure as either an alien and, therefore, a target for attack or benign or beneficial
• the amount and frequency of alien protein exposure that an individual can withstand varies by individual
• alien proteins frequently confront our immune systems in the food we eat. These foods have their own unique protein structures, often differing between (a) varieties - let alone at the species level, (b) cooked and uncooked, (c) ripe and unripe specimens from the same plant (d) the same food eaten occasionally or eaten as a staple.
• the ingestion of an alien protein profile may cause the immune system to attack itself - resulting in one of the numerous immune system diseases
• such alien proteins are less likely to come from foods that have been eaten for thousands of generations than they are from unaccustomed foods. Unaccustomed foods are more likely to be manufactured, processed or otherwise not part of our evolutionary inheritance
• given the slow rate of human evolution, it is unlikely that our species would evolve a complete compatibility with foods it had been consuming for only 15,000 years (tomatoes), 8,000 years (wheat), 500 years (cane sugar), 80 years (hydrogenated fats) or just a few years (many of the new ‘chemical additives’)
• complete adaptability could, however, be achieved by a species within a generation given (a) enough breeding stock who had evolved that compatibility, and (b) a sufficiently severe natural selection pressure to cause those without that compatibility to die off before reproducing
• alien protein theory stands in contrast to the more generally accepted assumption that, for example, 'a fruit is a fruit is a fruit'. This assumption maintains that, a fruit (such as a tomato), will - unless it is toxic or otherwise unsuitable for human consumption - be an acceptable Paleo food if the only characteristic ruling it out is that it is native to a continent (like Australia or the Americas) in which the forebears of Homo sapiens did not undergo the vast majority of their evolution from the Australopithecine line.
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