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Bugs: How not to recover your health

Our immune system is mind-bogglingly complex. The distinctions it is capable of making between the 99%+ of organisms that are vital to our health and the few that can undermine our health is subtle beyond belief. And of course, we are not talking about a standard catalogue, we are talking about rapidly evolving organisms that are trying to pretend they are benign and recognised in order to get access. Our immune systems are almost certainly the most rapidly learning part of us, and we don’t even know what is being learnt!

We can think of ourselves as hosts to more creatures than we have cells in our body, or we can think of ourselves as communities of collaborative organisms. The latter take is more helpful in getting a perspective on what the immune system is and does. If we kill or maim the wrong bugs, we die just as surely as if the “bad” bugs take over. And sometimes infection with bugs that seem merely harmful has side-effects that prove to be valuable. There is no escape from the need to select accurately who our micro friends are.

We need to have a gut feel (sic) for the statistics of this. The problem with Covid vaccines is easy to describe statistically: if Covid produces severe infection in less than 1% of a population, then a huge number of people approaching the other 99% of the population are going to need to be vaccinated when they were not really at risk. That means that it is easy for tiny problems with a vaccine to do more damage than the virus itself. Not a criticism of people or technology, just simple stats.

Subtle systems do not respond well to sledgehammers. We depend on massively complex ecosystems both inside and outside our body. But at the drop of a hat, we take anti-biotics to kill whole swathes of bacteria, both friend and foe. Or we shower away our skin colonies (or microbiomes), kill our oral colonies with mouthwash, sterilise the soil our food grows in — the list is endless. We never get to compare the person we would be if we did not use the sledgehammer to the person that did. In fascinating ways, they are not the same person.

To be a little cruel, this does correspond to our approach to education. Let’s kill off all ideas except a few sterile approved ones. Let’s determine standard catalogues of what counts as learning and what counts as deviance. This is just the same thinking problem as nearly wiping out a microbiome and expecting it still to learn and function in our defence as part of our immune system. We expect this infinitely subtle apparatus to still work for us after we have stamped on it. Real education requires real challenge which implies risk. We refuse the risk and we refuse the education: there is no other path.

And the problem with our ignorance is rooted in the same statistical trap. Almost all bacteria, fungi, algae, protozoa, actinomycetes are beneficial or even vital to us. And not only the groups and the myriad species within them, but of course their patterns of interaction in ecosystems, are what we literally depend on in ways we cannot even imagine. The patterns of interaction that “work” for us have evolved over thousands of years of novel challenges, and path that cannot be mapped let alone recreated as a learning set. If we choose simplistic “solutions” to statistically unimportant problems, the chance of damaging our futures is correspondingly huge.

If you doubt this, think of the beginnings of settled agriculture when it became possible to substitute nutritious hunted food with grains that stunted our growth, shrank our brains by 30%, and exposed us to diseases that left us deformed. And because we do not know this history, we are flirting with reliving it. This issue is so recursive that there is a body of study working to show how we will only learn to think straight by reforming our diets in the direction of high nutrient density foods. Meaning meat and especially organ meats. Really.

Maybe the image we need of the modern world is its continued flirtation with electro-convulsive therapy. ECT not surprisingly can result in permanent brain damage. The judgment about whether it “works” is in the hands of the professionals, not the patients. The mind of the patient is treated as diseased and therefore not capable of being part of the healing of that very mind! There is little in the way of informed consent, just an exasperation when patients do not respond to other treatments. An all too literal sledgehammer to deal with a “problem” that in other cultures is not even seen as a problem.


Ultimately, sudden flourishing of microorganisms capable of making us ill is a signal that the ecosystems concerned have become unbalanced. The systemic rebalancing is hindered if there is insufficient diversity in them to allow self-regulation. The serious studies of this effect show that we are likely to suffer from more and more severe “infections” as we erode the fundamental biodiversity in the world.

This is the same pattern we have been exploring but at the next level up. We use an exponentially rising amount of biocides in our agriculture. We mindlessly destroy the natural resources of the soil that provide support for the immune systems or plants, animals, and ourselves. We wreck the ability of the biosphere to regulate the atmosphere the way it always has. We think that randomly planting some trees will help rebalance things.

Like our damaged and damaging ideas about education, we think that biodiversity will be orderly and neat. I constantly have to mind myself to limit my tidying up of the smallholding here, to allow the wisdom of the ecosystems to function. I have yet to find the wisdom in myself or others to understand the role of nettles and thistles and bracken in rebalancing whatever is out of kilter.

What I have read reports of, is people managing habitats to allow biodiversity to expand and finding unlooked for benefits. Introducing ponds and wildlife “corridors” would be examples. Some of the principles of permaculture about seven different storeys of plants and about how edges are the richest environments would also count. Of course, these run counter to the conventional wisdom of “productive” and “efficient” farmers. But not in obvious ways.

How would we know whether the collection of “solutions” to agricultural and food “problems” is actually taking biodiversity over some tipping point from which there is no recovery for human health? 99% of people are going to look for another “solution” and totally miss the point that we are headed inexorably down the wrong road.

Right way up thinking

We typically think upside down. We think we are whole and in command of our faculties. From there we look for deficits or damage that we can address. We try to create order in our environment — food, exercise, social relations, education, whatever. But all the evidence is that we cannot know how we would be if we were part of an ecosystem that worked tolerably well.

There is absolutely no doubt that our gut microbiome affects our mental health, whatever that is! There are ways in which we are the product of the microorganisms we consist of and swim in. We are subject to their interaction and their rapid evolution and not in bad ways. We cannot conceive, except in principle as we do here, what the effects of flourishing in these support environments might be like for us.

So, thinking the right way up is to say, “hang on, I know that mountaintop and wilderness feeling when I am part of what is”. We do not know, or need to know, what it is that becomes right and whole and appropriate, but our life depends on recognising when it does. We need to forgo the hubris that another supplement, a magic food, a guru, a holiday will mend some essential me, put us in control again. Or that avoiding this poison or that stress will restore us to balance, a la organic food and yoga. Not that any of these things are a problem per se, but they are upside down thinking.

Upside down thinking merely complexifies the situation. In Deming management terms, it is meddling. It introduces changes designed to make adjustments to a system that is not understood and whose modes of operation are not even imagined. And conclusions are drawn about whether yoga or gym exercise “work”. I think we have to include the allopathic medicine that we are culturally obsessed with in the same category of meddling. For instance, a sane doctor would tell you that combining more than five medications becomes a complete lottery because of the interactions that will never be investigated. Our models are wrong: most of us know stories about how radical de-prescribing can have massive benefits. I know a lady who, at 102 years old, discharged herself from hospital and stopped most of her meds.

We can see how the education example works quite easily. When people are taught (upside down thinking) and what they are taught conflicts with what they know, the world becomes much more complex. You then have to compensate for what you are required to think is right in your reasoning and practice. You have to factor in that other people may genuinely believe the lies they have been taught or may be dissembling, as you are. Truth doesn’t come into it. There are lots of people who now simply say “there are conflicting research outcomes” so they don’t need to take a view.

Magnesium again

It seems most people are deficient in magnesium and that it causes health problems. Interestingly for our argument it seems that magnesium being out of balance with calcium allows calcium to do damage. The “solution” is to take a magnesium supplement, isn’t it?

Why does the great majority of the population have a magnesium deficiency? Basically, their diet is based on foods that are themselves deficient because soils are deficient and food is grown using artificial fertilisers. We can chart the decline of magnesium in food over the recent decades. So what?

Well, if magnesium is deficient because the soil is not properly mineralised anymore, what else might be deficient? Lots of things from major minerals like magnesium down to all sorts of poorly understood trace elements. So, taking a magnesium supplement (as I do) is only going to make the nutritional picture more complex and probably more dangerous. What is needed is to remineralise the soil our food is grown in (I do this too). If this understanding is right, then multiple benefits will flow from one simple correction — some volcanic rock dust on the soil. But of course, no commercial entity will go anywhere near this sort of response.

Why this approach? Well to go back to all the micro-organisms we depend on, and to follow up the food chain through insects and worms and plants and on, all these elements of the ecosystem are capable of correcting the deficiencies that can and do arise, if they can. When we damage the ecosystem support services (the soil and air and water but so much more too) then we prevent the intricate interdependent processes that will restore our health for us.

When we bemoan the decline in farmland bird species, most people think we like to see birds, and we do. But this is canary in coalmine stuff — the loss of birds is signalling something that threatens us directly. The only system competent to provide to complexity of support that we absolutely depend on is the system that was working as we evolved to use it. Try to change, “improve”, supplement, bypass, reinvent any of that at your peril. This, of course, is the correct context to try and understand how synthetic meat can destroy the health of whole populations.



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Aidan Ward

Aidan Ward


Smallholder rapidly learning about the way the world works