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6. Why the rules apply to us

Updated: Jun 1, 2021

(This section finishes the background info that I feel is necessary before we dive into the microbiome itself. It's important to understand that human endeavors and our society sometimes create roadblocks to deeper understanding of who we are biologically. This is not trivial. Once we get on a certain path for solving a problem, we find it hard to deviate or even think about other paths and that makes it hard to recognize underlying factors that contribute to the larger problems.)


Living within the rules

When we are faced with a biological problem, we rarely think about the biological underpinnings and what sort of disruption may have led to the problem. Instead, our thought process, more often than not, is to consider what sorts of technological approaches could be called upon to fix the problem. This very human approach tends to ignore the fact that the “problem” is very likely a response to a disruption in the system, which is often the presence and activities of humans. That is, human activity creates stress within the environment and the “problem” we recognize and wish to fix is the response of the system to that stress.

Prior to our disturbance of the environment, the problem did not exist which implies that the undisturbed system suppressed or controlled the problem, even if it did exist. For example, the incredible number of deer-car collisions in the eastern US is a result of very high populations of deer which is a result of the elimination of wolves (by humans), the natural predators of deer. So, is the growing deer population the real problem? No, the underlying problem is the lack of a biological control on the deer population in a simplified ecosystem. But the human solutions, though many and various, never deal with the root problem of the lack of a natural deer predator.

The biological solution is obvious (reintroducing wolves), but not simple or acceptable so we resort to technological solutions (e.g., hunting, contraception, sterilization, relocation, and automobiles). The result? The problem is not fixed. In fact, when the reduction in deer numbers is successful, the response by the deer will be higher reproduction rates. That is, as numbers of deer go down and population pressure on the environment is eased, female deer fertility goes up because of plentiful resources, and the result is a cyclical and never-ending problem.

Complex biological systems are more stable than simple systems and can respond to imbalances. This fundamental characteristic of a complex system has tremendous implications for you, me, humans, food, culture, and the persistence of the environment as we know it. The ability to regulate, to maintain equilibrium, is the ability to survive. It should come as no surprise then that all biological entities are actually biological systems.

That is, if survival is predicated on the ability to maintain a stable internal environment and stability is a quality of a complex system, then we should expect that all stable systems are actually very complex. What does that mean? It means that you and I are systems, very complex ecosystems, even though we think of ourselves as individuals. It means that every organism is a system because survival in this world means possessing the ability to make rapid and complex adjustments to the external environment and, by doing so, maintaining an internal equilibrium.

But it reaches further than that. Throughout time, every organism has had to deal with the challenges of the environment or die. In a population facing severe stress, the majority of individuals will die and only the strong will survive. Survival means being able to tolerate the stress long enough to produce offspring who will also be tolerant of the stress. In that way, populations adapt to the stress because each new generation is comprised of tolerant individuals and the intensity of the stress on the population is thereby reduced over time.

We can view all adaptations as responses to environmental challenges and over millions of years all species have faced (and survived) innumerable environmental challenges. The variety of adaptive mechanisms that decrease stress and increase survival is also innumerable. Until recently, we assumed the most important mechanism for adaptation was natural selection for beneficial genetic mutations, but it is now very apparent that there may be more effective and more rapid modes of adaptation that do not involve the serendipitous occurrence of a random event such as a mutation.

Although we’ve long known about the mutualistic associations between animals and microbes (such as the cellulose-digesting microbes in the gut of the termite), we only attributed positive functions for such associations in species other than humans. We knew that the human colon harbored an incredible density and diversity of bacteria, but this was considered an unavoidable and undesirable contamination problem from living in an unclean world.

We are just beginning to appreciate how important those bacteria are to our physiological equilibrium. That is, we are beginning to understand that our physiological and even our personal happiness as individuals depends in very large measure on the happiness of the bacteria in our digestive system. Their influence goes well beyond regular bowel movements and can range from developing our nervous system as toddlers to modifying our vitamin and protein balance to enhancing the strength of our immune system. Each of us is an extraordinarily complex system; we harbor communities and those communities interact with each other. Our internal communities also interact with communities in the external environment.

Thus, while we tend to think about the food we eat as being food for just the one of us, we are feeding tremendously diverse communities of species at the same time. And the community I am feeding with my food may not be quite the same as the community you are feeding. The composition of my gut community is similar to that in my immediate family and it decreases in similarity with people I don’t live with or closely interact with. In addition, our genetic profiles determine to some extent what bacteria we’re comfortable with and which we cannot tolerate.

Each of us reacts differently to different foods and this is due in part to the reactions of our gut communities to those foods and in part to our genetic constitution. Indeed, as we progress from toddlers through the teen years to adulthood and beyond, those communities change. The community in my 60-year-old gut is similar, but not the same as that of my 20-year-old self. I’ve had many experiences in my life with sickness, drugs, foods, and geography that changed and shaped my microbiome composition. Where I might have had a microbiome composition that was very similar to my siblings before I left my parent’s house, after 40 years of separation, our gut communities are assuredly very different now.

Perhaps most importantly, the health of our internal ecosystem is dependent on the health of an external ecosystem that is increasingly influenced by human technology. As we ingest a greater proportion of processed foods, as we take more and more drugs and antibiotics, as we consume things the human body has no prior exposure to or adaptive history with, we are relying more and more on our bacterial community to help us.

Some of the chemicals we consume are toxic to the bacteria and we should wonder how they are able to cope with the technological wonders we keep swallowing. How do they cope with a lack of fiber or fresh vegetables or cope with foods that are entirely digested in the small intestine with only table scraps left for the large intestine? We have to hope that the external environment is able to come to the rescue when a strong antibiotic wipes out the bacterial community in our digestive system. We depend on the external environment for providing new immigrants when the internal environment is laid waste by medical technology. And this is only likely to be true IF the external ecosystem is healthy and diverse and capable of providing replacements. The speed and reliability of that rescue is something that has not yet been determined.


Each of us (and every other multi-cellular organism on this planet) is an ecosystem that is maintained by our external environment. As we damage and simplify the environment around us, we compromise the ability of the environment to support our internal environment, and our lives depend on that environment. If it is given the resources it needs, our internal ecosystem is very capable of maintaining itself and, in the process, of assisting our ability to maintain an internal equilibrium.

The symbiotic relationship between us and our internal communities is so close and so intertwined that we may well lose the ability to withstand the challenges of the external environment without the presence of a healthy internal environment. What we will find through research in the very near future is that we cannot maintain our internal environment without assistance from the external environment. Our internal ecosystem is nested within the larger ecosystem and there is constant flux and necessary exchange between them.

We exist in a macro-biome made up of innumerable micro-biomes and all of those ecosystems are interacting with each other to different degrees that we do not understand. Because ecological principles apply to all complex living systems, we can neither pretend that we are not complex nor that we are isolated from the rest of the world.

It is also very important to appreciate that our understanding is very poor concerning the strength of the interactions between our body and our microbiome as it relates to our health. Just as losing a species of frog or butterfly or large carnivore can have ramifications for the larger ecosystem, until we know more, we must be careful about the loss of any part of our personal ecosystem, no matter how insignificant it might appear to be. And perhaps more than anything else, if we acknowledge the we are biological systems, it will be in our best interest to treat ourselves as such and be very cautious about applying technology fixes to biological problems we do not understand.


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