Why you are sick and
how to get better

The hygiene hypothesis, the old friends hypothesis, and some context for beginners

The Short Version

Because of things like antibiotics, chlorinated drinking water, refrigeration, the elimination of many infectious diseases via vaccination and increased hygiene your immune system never learns to distinguish properly between real threats and benign environmental components it comes into contact with.

In addition it evolved to exist in an ecosystem, one defined by your body, that was constantly parasitised.

Parasites that feed on us, that attach to our tissues like hookworm and whipworm do to feed, have to dial down the host immune response, particularly inflammation, that would otherwise be directed at them and that would kill them before they can reproduce. We evolved to account for that to some extent, so absent that dialing down effect we become more prone to inflammation in their absence.

The Hygiene Hypothesis/Old Friends Hypothesis/Depleted Biome Hypothesis propose that modern levels of hygiene involving the elimination of most of the microorganisms, good and bad, that used to infect or infest us throughout our lives prevents our immune systems from learning by doing.

By eliminating universal “old friends” we end up with "depleted biomes", a fancy phrase for intestinal tracts that define impoverished ecosystems, all due to excessive "hygiene" and the result is poorly educated immune systems.

Immune systems that because they do not get much practice are misdirected, and that react much more violently and vigorously than they could when parasites were present and moderating the immune system’s response.

The parallels with modern humans, out of shape and on the couch reacting with outrage to some distorted information emanating from the television or internet are stark.

The result is an immune system that cannot distinguish friend from foe and that goes immediately to the “nuclear” option, reacting violently.

Inflammation is a helpful adaptation necessary for a functional immune system. When you get a cut or an infection inflammation is the immediate and first response of your immune system. It occurs to make tissues porous to things like white blood cells. 

Some white blood cells, the early responders, are sent to work out what is going on and to report back so that other appropriate immune system components can be sent, as well as signalling for the development of antibodies specific to the pathogen. Inflammation is a good thing.

Except when it is not a response to a real pathogen and instead of stopping when the infection resolves either by getting better or the subject dying, it goes on indefinitely.

If it is attacking something that can not be killed or beaten, dander, or pollen or you, the mis directed immune response never stops.

If instead of being a short-lived healthy part of a normal immune response inflammation a chronic never-ending reaction it becomes a cause of pathology, and potentially a route to secondary effects like “leaky gut”. By making tissues porous to elements of the immune system tissues are also made porous to other things, which in the digestive tract can cause other issues.

Helminthic therapy is an attempt to restore health by remediating the ecosystem defined by your body, particularly in the intestinal tract.

Helminths have to moderate the host’s (in this case the host is you) inflammatory and immune response to survive long enough to reproduce.

They also change the make up of the microbial population in your intestinal tract (this is the cause of gas for some as a side effect with early doses), which also has an effect on your immune system. In the case of whipworm they also increase mucous production which probably has a protective effect, since that is why mucous is produced. To act as a protective barrier against any irritant.

The changes to our diet also have a direct effect on the microbes inhabiting our intestines. By increasing the proportion of calories we consume from carbohydrates so much, from about 10% to about 30%, we have radically changed the proportions of microbes in our intestines. Those that eat carbohydrates or starches, or some of their break down products, have proliferated. While those that fed on the foods grains and the like have replaced have diminished in number. 

When as a species we adopted agriculture our average stature and life expectancy both dropped substantially. No population recovered those things until the latter half of the 20th Century, in the USA. That's about fifteen thousand years. The evidence of our maladaptation to agriculture is there to see in lactose intolerance and coeliac disease, but to think agriculture's impact on our health is restricted to just those few things is, in my opinion, naive.

Other changes to the daily routine we evolved for that affect immunological health and your tendency for chronic inflammation are the usual culprits, obesity, lack of exercise, doing all the sensible, boring and unpleasant things we all put off and avoid, or lie to ourselves about.

You evolved to be much more active than you are, to eat a radically different diet and to deal with a very large variety of infectious organisms and parasites throughout your life.

Every aspect of your daily routine is radically different from that you are evolved for.

Your body is an ecosystem and your health depends on that ecosystem being in good shape.

That, in turn, depends on your daily routine, almost every aspect of it.

No one is going to make you well, the medical system isn't helping. No one except you.

No magic supplement, no "super-food", no magic pill, nor any fad diet is going to do it. Not alone, it's not.

If you take responsibility and reorder your life around the principle of being healthy then you very likely will regain your health and massively improve the quality of your life.

But this is not a quick fix. Not from this side of the task anyway.

Looking back you will wonder how you ever got in this state in the first place, and you will be amazed at how fast and complete the transformation was. The years will pass whatever you do after all.

You have spent years screwing your body up. Yes, you got a lot of help, but you have to take responsibility in order to take charge, to make things change.

You can expect things to improve gradually, it may be months before you notice a difference. But as you lose weight, get in shape, improve your diet, and remediate you the ecosystem you will regain your energy, vitality and joy.

The Long Version: You are an ecosystem

Modern medicines greatest areas of success are in fixing structural damage like fractures, organ failures like appendicitis, and in curing infectious diseases. Particularly bacterial ones.

As a result we and the practitioners of modern medicine have a bias towards viewing the workings of the body in very mechanistic terms.

That disease arises out of contamination and impurity.

That our bodies are enormously complex machines and that problems arise when a component fails or is damaged, and disease arises out of infection. Out of something being out of place, from contamination.

But diseases of the immune system have proved largely intractable to medical research and even the most modern of its’ drugs are crude, ineffective, very expensive, and dangerous.

By approaching the body as a machine, with parts and components to be identified, catalogued and understood in terms of how they work and interrelate medical research set itself an enormous task. One many orders of magnitude larger when it is the immune system that is the focus of research.

Nor does the science’s devotion to the Scientific Method, which has produced all the wonders of the modern world, making such devotion easy to understand, serve our or science’s interests when it comes to understanding the immune system, because of its complexity.

We have not identified all of the components of our immune system never mind how they work.

Based on this far from complete understanding of our immune system modern medicine's approach to allergy, autoimmunity and chronic inflammatory disorders arising out of immune system dysregulation is also based on a view of the body as a very complex machine.

Medical research on this basis has developed a series of treatments, of drugs, that just knock out this or that portion of the immune system to stop it from causing damage. Drugs like the TNF-Alpha blockers.

This without any real understanding about the cause of allergies or autoimmunity. Modern medicine's approach is based on this view of the body as a very complex machine. So instead of fixing the underlying problem they just "remove" that part of the immune system that is "causing" the problem. If your car was making a lot of noise you would not remove the engine, would you?

Your immune system is misconfigured because it is getting bad information. As a result it is reacting to things it should not, and reacting in ways it should not. 

It is misconfigured because for your entire life, including right now, the environmental signals it depends upon to develop properly and to learn how and when to react and what to react to and what not to react to are absent or incomplete.

The source of those signals throughout your life have been removed by excessive hygiene, and perhaps worse those signals that remain have grown louder.

By depriving your immune system of challenges throughout your life, thanks to sterile food and water, and in particular because of antibiotics, it has not been exposed to the types of challenges it requires to learn what to react to, and how to react.

In fact if you have an autoimmune, allergic or a disease involving chronic inflammation due to immune dysregulation you have one of the latest models of immune system, a top-of-the-line model.

An analogy you may find helpful is to think of your body and your immune system as a car. It was built to run on well maintained roads. Nice smooth, flat roads. The roads are the environment in this analogy. Now imagine your car, your immune system, in a country where all the roads are dirt tracks. Bumpy. Potholes everywhere. Wet and muddy. Big rocks everywhere. Your "car" is going to struggle without the roads it was built for.

So it is for your immune system. You and your immune system evolved for environments spectactularly dirtier than the one you inhabit, the one we have created. Your immune system evolved to deal with that long gone environment, and ones we created along the way even filthier than the original one.

We don't have the immune systems of hunter gatherers, we killed those off long ago. We have the immune systems required of filthy medieval cities.

Your genes made it from the dawn of our species, through hunter gathering, through the adoption of agriculture, through the filthy medieval cities, through migrations and wars and famines. You are very well built.

So, you can safely get rid of the hand sanitiser, doing so will help you be healthier in the long run.

As you may have read humans are changing the environment so fast we are exterminating species faster than at any time in history. Many are afraid, me included, that our own extinction may be a consequence.

What people fail to realise is that those environmental changes are damaging human health on an astonishing and growing scale already.

Your immune system evolved for an environment we have profoundly changed in the developed world and increasingly in the developing world. We have created environments which because of excessive hygiene and changes to our diet, increased stress, much lower levels of physical activity and reduced sunlight exposure, as well as other factors our immune systems are maladapted and confused.

Digressing a little, if you think the only thing affected is physical health, think again.

We can assume our immune systems have dealt with all those challenges from birth for every generation before you given your existence very well. So again, get rid of the hand sanitiser.

But without those challenges your immune system does not develop properly. It does not have to deal with infections and diseases.

As a result it is miscalibrated. It does not learn to distinguish real threats from things like cat dander or pollen because it never really has to deal with anything.

Vaccinations, sterile food and water and particularly antibiotics prevent it from learning. It evolved for a succession of different environments where your ancestors were under constant assault.

So it evolved for an environment where it was constantly active.

But thanks to modern hygiene nothing much happens as "expected". It does not learn from a series of encounters with a variety of microbes, and so it cannot distinguish a real threat from something benign, and it does not develop the capacity for proportionate response.

Your immune system is not the problem, your environment is.

As a result your immune system is pointed in the wrong direction and acting disproportionately to threats that are not really threats.

How can pollen or food or your own tissues be a threat? And why do so many doctors believe more antibiotics are the solution?

You are not a machine

Medicine doesn't see it like that, though. Modern medicine takes a very mechanistic approach to health. If your immune system is attacking something it should not most of the time the answer is simply to disable that part of the immune system causing the problems, say TNF-Alpha blockers like Remicade or Humira.

If you don't understand what I mean by your body is an ecosystem consider this: 90% of the cells in and on you are not you. They and you form an ecosystem that you encapsulate, one lacking the biodiversity it evolved for because of excessive hygiene, primarily because of antibiotics.

Particularly important are your intestines, which is an external surface, a wet porous external surface covered in microbes varying along its entire length.

You are like a donut, but with a very thin, long hole in the middle. One which is semi-permeable, it has to be to allow in food and water. For that reason a large proportion of your immune system is located there, to keep the bad stuff out and allow the good stuff in.

The immune system is in many ways a signalling system. It is listening and watching all the time, and it is listening for and to microorganisms. Bacteria, yeasts, viruses.

By eating sterile food, drinking sterile water, taking antibiotics and being vaccinated the ecosystem or zoo that is your intestinal tract is incomplete, many, many animals are missing from your ecosystem. Many are in the wrong places, and many are present in numbers far higher than they should be.

Up to half the bacteria which would ordinarily be there have been killed by antibiotics even if you last took them many years ago. Those ecological niches they occupied are not left vacant. Into those empty niches proliferate microorganisms that were it not for antibiotics killing that niche's "normal" occupants could never survive there.

As a result all the immune system components there are receiving signals it is not evolved for up and down your intestinal tract.

Microbial variety in your colon is so important humans evolved a reservoir to preserve that microbial variety in the event of dysenteric illnesses, cholera, etc.

The appendix. The organ that medicine said was a vestigal remnant from when we ate a lot more fiber in our diet for centuries. That organ.

Unfortunately for us the appendix evolved before antibiotics showed up. So the appendix is no refuge for bacteria from antibiotics.

How you got sick

Your immune system never learned how to behave thanks to excessive hygiene. Which resulted in the absence of many of the micro organisms, like helminths, we coevolved with as an ecosystem/organism we call homo sapiens.

One day you caught an infectious illness, perhaps something as banal as a cold. Or you had an accident, physical trauma. Or, you experienced an extreme emotional shock, grief or bereavement. Some trauma. Maybe you took some antibiotics, that's a common trigger. Sometimes it isn't apparent what the trigger was. Perhaps in some people this environment given enough time makes them sick.

But something upset your immune system.

It was ready and had been waiting all your life to do what it evolved to do, fight. A fight it was expecting in an alleyway in Medieval London or Shanghai perhaps. Your immune system is a badass.

But because it has never learned to discern good from bad, it has not encountered the millions of microbes every drink of water used to bring, or dealt with semi rancid meat or the contents of a prey's stomach which were eaten by our ancestors, it attacks something that cannot be defeated. That cannot be destroyed. Whether its pollen, or dander, or the breakdown products of a food, or self-tissues like the mylein sheaths around your nerves, this is a battle it cannot win, but that you will definitely lose.

So it keeps fighting, it did not evolve to stop until it had won or you had died.

You are now chronically sick, a person with a misdirected immune system causing chronic acute inflammation, or autoimmunity.

You are a person modern medicine has no answers for. If you present with something they do not understand they very likely will tell you that your experiences are imaginary, that you are not sick. They know best, and your experiences and observations do not appear in their textbooks, so they have no meaning or value. In fact, the louder and more insistent you are the harder it is for you.

You are a person modern medicine says will never be well again, who will experience a steady or bumpy decline, perhaps even long periods of remission. But you will never be healthy again.

They may provide you some relief from your symptoms. But it won't be much, unless you like taking drugs that on average simply move the curve describing your physical decline out into the future by about three years, if they don't kill you.

It is not just antibiotics

You evolved to be active, out of doors, and to eat very, very different foods than the ones you eat every day, in different quantities and proportions. Stress was something that happened in short, intense bursts.

Caffeine, upon which Western Civilisation depends was not part of the picture, and it induces a mild stress response every time you use the most popular drug in world.

Stress is a major contributor to immune disorders of all kinds. A cup won't hurt, but what about three cups a day for twenty, thirty, forty or fifty years?

This is not about additives, although they play a part no doubt. Eating organic might help you be healthy in other respects, but as far as your immune system goes it isn't going to do you much good unless you are allergic to or triggered by one of the many contaminants in modern food. I have not seen much evidence that eating organic does much good, sorry.

It is much more about the fundamental make up of your diet. Of what you do every day, how you do it, where you do it and even when you do it.

You are almost certainly malnourished, and if you are not you are getting your calories and nutrients from foods you are not well adapted for. Agriculture is, in genetic terms, a very new arrival.

You never go hungry for more than a few hours, but you evolved to withstand famine. Metabolic syndrome anyone?

You are what you eat, but so are your companions in your intestinal tract. What you eat is what they eat, and by changing our diets from those we evolved for, we profoundly change the denizens in our intestines. Some of those microbes do "better" from it, and they are more common. Others are much diminished in number, perhaps they are absent altogether? If they have nothing they evolved to eat they will starve to death. So even if you are well fed, if your ecosystem is not, and it is not, then there is another factor affecting you, you the ecosystem in a negative way. Simply by changing our diets so profoundly thanks to agriculture we have changed our ourselves, us the ecosystem.

History shows that agriculture was not kind to those who adopted it. Life expectancy, height, bone density and vitality all diminished substantially as soon as agriculture dominated diets.

Life expectancy is estimated to have fallen by over twenty years, average height by up to two feet. It also made our environments a great deal dirtier. It was common practice to live with one’s domesticated animals, from goats and pigs to dogs and cows. It was from the animals that we domesticated and lived with that came all the major diseases that by killing humans in massive numbers throughout history changed our immune systems.

That is the harsh truth of natural selection. Killing large proportions of any population before they are able to breed and pass on their genes is what drives evolution. By exerting intense selection pressure over many generations our immune systems became much more reactive and aggressive in response to the sudden arrival of all the diseases and parasites our newly domesticated animals brought with them. You can see other evidence for this idea in things as diverse as Taye-Sachs (an adaptation to Tuberculosis), Sickle Cell Anaemia (an adaptation to Malaria), and in lactose intolerance (a failure to adapt to continuing to eat milk after infancy) and coeliac disease (ditto for grains which only became part of our diet in any quantity with agriculture).

There is even evidence for this in various cultures. Pigs being the most similar to humans in many respects of all the animals we domesticated were the carriers of most of the diseases and parasites we were subjected to as a result of agriculture. Hence the pig, owning them and eating them, is proscribed in the Jewish and the Islamic traditions because of the enormous health impact resulting from their domestication.

Our immune systems became much stronger and violent in response to disease thanks to adopting animals and living in close proximity to them (as in the same buildings), and to the diseases we had not been exposed to before domesticating them. So we evolved thanks to agriculture and the animals we domesticated for a filthier environment still. The effect was amplified by ceasing to be nomadic at the same time.

By remaining in one place we created increasingly concentrated reservoirs of infectious or parasitic pathogens in our immediate environments, and in ourselves.

So our immune systems adapted to environments in which infection and infestation were a certainty and where parasite burdens over a relatively short proportion of a potential lifetime became lethal. As a result some of the adaptations did not have to account for the possibility of even low levels of parasite burden, never mind their absence. As a consequence some adaptations, which manifest in our modern environment as Crohn’s and Colitis, in the absence of their targets which are hookworms, roundworms, whipworms and protozoa, lack an “off” switch. In cultures which encourage or demand marrying within that culture or religion these effects over time have been amplified. It is no accident that Crohn's and Colitis are much more common in Jews and Muslims who prohibit marrying outside of their faith.

Then came medieval cities, in Europe and in China and South East Asia and Japan. Cities which for hundreds of years increased in population despite the fact that in many years it is estimated that up to a third, a third, of the resident population died from infectious diseases and parasite burdens.

After a few centuries, and the enormous evolutionary impact of that on their immune systems they got into boats and took their diseases and their immune systems with them.

While the European colonialists of the sixteenth Century and onwards were murderous, barbaric and waged terrible wars killing millions it is the diseases they brought with them that killed the estimated 90%+ of residents prior to contact with Europeans in the Americas who died within a century or two of the European's arrival.

The result is a kind of monoculture of immune systems, ones adapted to medieval cities, to a kind of agriculture where people lived with their animals. An environment many magnitudes more "dirty" in terms of exposure to pathogenic microorganisms than those hunter gatherers had to deal with.

Then we adopted modern standards of hygiene, and moved those immune systems, yours and mine, in a generation or four into environments more sterile than any our genes, many we share with things like bacteria, onions and horses, old genes, had ever encountered.

As a result we are spectacularly maladapted to the environment we have created.

To give you an idea how maladapted it was not until the last half of the twentieth century that humans, in America at least, regained the life expectancy and stature taken from us by agriculture up to fifteen thousand years previously.

Most of the rest of the world is still waiting, life expectancy in Cameroon where I first went to obtain hookworms is forty-seven years.

I was almost forty-two when I arrived there, an old man by local standards. 

There is one thing to be said for a poor country that is abundunt and fertile (well fed), there aren't many ugly people.

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