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Yanomami hunting party
Much to the chagrin of creationists, no doubt, we can trace our evolution by the evolution of the obligate parasites and symbiont organisms that live on and in us - our microbiome. Just as with the evolution of our lice, the evolution of which and their diversification from the lice which live on the other African apes, maps exactly onto our diversification from a common ancestor with those same apes, so our microbiome can show how human groups are related and have diversified over history.
It has long been suspected that the number of different species in our microbiome declined as we became more hygienic and especially since we discovered antibiotics, so a team who studied the microbiome of the recently-contacted Amazonian tribe, the Yanomami, expected to find a high degree of biodiversity - which they did, finding some 60 unique genes. However, what they didn't expect to find was that a number of the Yanomami gut bacteria have already evolved antibiotic resistance, including resistance to man-made antibiotics.
The general view of antibiotic resistance is that this evolves in bacteria in the presence of antibiotics because the environment is favourable to those with mutations which convey resistance in a basic Darwinian evolution by natural selection. However, the Yanomami have no history of antibiotic use, at least not in the way antibiotics are used by modern medicines.
So, there are two ways to look at this - either antibiotic resistance has evolved in the Yanomami's gut bacteria in response to naturally occurring antibiotics or toxins (toxic to the bacteria) which resemble them, or they have been exposed to man-made antibiotics even though they have remained isolated. This latter seems the least likely and the team believe they eliminated it, so, if their bacteria evolved resistance to man-made antibiotics the probability is that our gut bacteria already had the capacity to 'switch on' resistance even before we began synthesising them. And that raises some worrying possibilities for future antibiotics in our continuing arms race with bacteria.
The probability is that natural antibiotics are far more common in the environment, particularly in soil, where fungi and bacteria compete for similar resources and it is the fungi which produce the antibiotics. Bacteria and fungi have been in this evolutionary arms race since fungi evolved so we should expect fungi to have evolved a whole range of antibiotics, and bacteria to have evolved a whole range of different forms of resistance to them, so it's highly likely that some of these will be similar enough to our synthetic ones for the same resistance to work against them too.
The explanation was that these are evolved in response to natural antibiotics produced by gut fungi in their ongoing arms race with bacteria. It was also suggested that phage viruses which infect bacteria could incorporate strands of bacterial DNA into their own genome and so act as a repository for resistance even when the bacteria themselves lose it as the micro-environment swings back to favour non-resistance.
Whatever the mechanism, the discovery of antibiotic resistance in 14th-century human fecal bacteria shows that man-made antibiotics are not necessary for bacteria to evolve resistance, so perhaps the discovery of resistance in the microbiome of the Yanomami isn't at all surprising. It raises the possibility that there may be a large number of antibiotics yet to be discovered occurring naturally in soil, for example.
It has been proposed for some time now that some of our diseases, such as autoimmune diseases like allergies, asthma and diabetes, Crohn's disease, celiac disease, and colitis may be due to our reduced microbiome in some way. Not to the organisms we still have but to the lack of those we have lost. One bacteria found in Yanomami, Oxalobacter, is already known to protect against kidney stones.
A reduced microbiome in industrialised societies has even been associated with obesity and heart attacks. The Yanomami, like other hunter-gatherers in Papua-New Guinea, Peru and Africa, suffer from few of these diseases, and appeared to be remarkably healthy, despite carrying around all those different bacteria - or maybe that should be because of all those different bacteria. The theory is that the presence of a wide diversity of organisms in their microbiome trains the immune system of children and so helps protect us against infections. This idea is counter-intuitive in that we tend to think of disease being caused by the presence of an organism, not to its absence.
It seems that we evolved our immune system in the presence of a wide diversity of organisms and part of that evolved process was a period of programming of our immune system in infancy to match our specific microbiome. Now we have changed that microbiotic environment with our evolution of modern, industrialised societies, we still have our old immune system which still needs programming to function properly simply because there has not been enough selection pressure to evolve a new, improved immune system. However, without the necessary compliment of organisms, this training is incomplete.
This is an example of how organisms don't evolve in isolation but as part of an evolving ecosystem. In this case an ecosystem consisting of our multicellular bodies providing an environment for a whole host of microorganisms to which we adapt as they adapt to us until we both become dependent to some extent on each other. It was mutually beneficial for our microbiome to provide us with a degree of protection.
In changing this environment for our microbiome we have actually harmed ourself in the process. Our memetic evolution, which has produced modern, industrial societies, has impacted on our microbiotic environment but not yet on our immune system. Memetic evolution works very much more quickly - maybe within a generation or two - but genetic evolution takes place very slowly over thousands of generations and tens or hundreds of thousands of years.
It's sheer infantile lunacy to think something like this was intelligently designed using magic, of course, but as the product of a utilitarian evolutionary process where the only test of effectiveness is in the number of successful descendants produced, it makes perfect sense.
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