Environment and Community

 Sandpiper, foraging for larval mole crabs and other zooplankton

Kitty Hawk, North Carolina

 photograph by the author

We are used to the idea of mankind altering his environment to make it more suitable for him. We not only build houses; we landscape areas, dig ditches, build highways, and so on. But it may come as a surprise to readers to hear that microorganisms routinely alter their own environment to make it suitable for themselves. The creatures that depend on them — ourselves, for example — also alter their own environments, believe it or not, to make them more suitable for the microorganisms that they need.

We're going to take one of the most striking examples of that today, although there will be more to look at later on. We've already explained that human beings require a healthy, and wide variety, of microorganisms in their gut in order to digest foods properly. Without them, we die.

Where do we get those microorganisms? Well, of course, we swallow some from our environment. But more importantly, we inherit some of them — quite literally inherit them, since we acquire them from our mother during the process of natural birth.

As peculiar as it may seem, the birth canal — the vagina — is a rich environment for bacterial growth, and in the days just before birth, it turns out, this environment is heavily populated with bacteria from the mother's own gut bacteria community. She has, in other words, a range of all the microbes that the child will need for its digestive system waiting for it in her birth canal. When the child finally leaves the sterile environment of the amniotic fluid — when the water breaks and birth begins — the infant moves through the vagina, opening and closing its mouth, and inevitably swallows billions — perhaps even trillions — of the bacteria that it will need to populate its gut with. So the first organisms it needs other than its mother are, logically enough, bacteria. And the very first act of its life, before it even leaves the birth canal, is to set up housekeeping with them.

Obviously, children that are born by cesarean section don't get this benefit. The rising tide of children born in this matter in modern Western societies is leading to a large number of children who don't start life out with the correct gut bacteria populations. This has long-term implications, since the developmental well-being of the child depends in large part on making sure it has the right gut bacteria from the moment it begins to ingest foods. Otherwise, it's digestive processes don't work properly, and, in addition, the immune system doesn't develop properly. This can lead to all kinds of overreactive immune system situations in later life, and may well lead to diseases such as autism, diabetes, and other maladies such as bipolar disorder and other psychological deficits.

Oddly enough, this could all be corrected by taking children born by cesarean, swabbing the mother's vagina, and making sure that some of that liquid was put in the child's mouth. But no one seems to think of things this obvious.

It gets a little more complicated than that. Breast milk, it turns out, has essential proteins in it which, although they don't do much for the child — it can't digest them — are in fact perfect for the gut bacteria developing the child's intestines. And it furthermore carries an additional wide population of bacteria that are absolutely necessary for the well-being of the child. Follow the links for some fascinating insights into this.

The point is that there is nothing passive about the way that bacteria are delivered to an infant so that it's gut bacteria populations develop properly. Nature is arranging things specifically so that the bacteria are not only present, but have exactly the right environment to support the growth of the organism. So you human beings don't just have bacteria; nature makes certain that they have bacteria, and it makes certain they have the right bacteria. It creates conditions ideal for those bacteria, delivers them, and then nurtures them. This is an example of bioengineering that goes to the root of what community means. Nature, and life, is a community, not a collection of individuals who act independently of one another. The perception of independent action is largely illusory, yet we endorse it as one of the foundations of our social contract.

Nature teaches us otherwise.

 Of course, human beings are far from the only organisms that do this. Think about this: every single organism with a gut has bacteria in it, and every single one of them undoubtedly has similar mechanisms to ensure that it has the right bacteria in it. The entire animal world is engaged in this activity — unseen, and underappreciated. Unfortunately, the action of chemicals in the environment and the accelerating spread of foreign bacteria into new environments is guaranteeing greater and greater disruption of this system, which leads to all kinds of diseases. Because we don't understand how the  system is constructed, many of these diseases don't, at least at first, appear to be linked to the microbial population, but most of them are, in one way or another. The situation becomes more serious every decade, with disturbing diseases such as psychological and immune system disorders becoming more and more prevalent.

We keep looking for the causes of these diseases in our genes; but it may well be that the causes of them lie in our microbial populations, a place we have only just recently started to look at more seriously.

 These arrangements do not stop with animals, which we will discuss in the next post.

The microbial atmosphere

Empire State Building, New York, Sept. 2013

Photograph by the author

You can't see them, but you are currently surrounded by a sea of microbes. Not just trillions of them; googols of googols of them (googol being the number one followed by one hundred zeros.) There are so many bacteria and microbes on the surface of the planet, in fact, that they form what is more or less an atmosphere, a living medium through which all life "swims." This medium is breathed in constantly by all breathing creatures; it is swallowed. It lives on, in, and around every living creature. The presence of microbes is 100% constant from the day an animal is born until the day it dies.

If we were deprived of this microbial medium, we'd all die. Everything would die. These are the fundamental and essential conditions that life exists under and is supported by: a sea of life through which we constantly swim.

Any impoverishment of the environment can lead to issues. Killing off microbes protects us, to some extent, from disease; but the negative consequences can be disastrous. Polio, for example, was rarely a problem before the twentieth century. Poor water quality very nearly guaranteed that infants were exposed to it; for reasons yet to be fully understood, the virus has little effect on infants, so the virus-rich water supply conferred immunity on the majority of the population. It was only when water supplies were cleaned up that children began to reach young adulthood without immunity; the results were disastrous. Although cleaning up the water supply has bee a good thing in many ways, it is definitely possible to have too much of a good thing; and the steady pace of extermination of microbes in the child-rearing environment is leading both to a host of old diseases on the rise and new, emergent diseases.

The bottom line is that we need the microbial communities we inhabit. Cleaning them up too much, sterilizing the environment, turns out to directly affect the development and responses of our immune system, with sometimes disastrous results.

Although I'm sure it sounds like a reach, it's useful to think of the microbial environment we inhabit as an atmosphere. Like air, it invisibly surrounds us, and like air it's a medium that we absolutely require for daily life. We literally and figuratively breathe it in and out.

Interestingly, science has readily identified and embraced the chemical atmosphere of air and water as essential to the support of life, but the microbial atmosphere has been largely ignored, even though it comprises a living atmospheric medium for all larger life forms. Found in the air, soil, and water, one might argue that bacteria and fungi bridge the gap between the these chemical media and macrobiotic life forms. They are, seen from a slightly different but analogous perspective, a tissue that holds the macrobiota of the planet together by translating chemical constituents into usable forms.

So we live in an atmosphere of microbiota; and we depend on them so much that it becomes apparent symbiosis is, on the whole, a more prevalent lifestyle than competition.

This is so much the case that larger organisms don't juts host microbes; they go out of their way to create situations that favor the microbes they need for their own survival. More, quite literally, than meets the eye goes on in this regard; and we'll discuss that in the next post.

Man and microbe

Here we are at the tangled, integrated end of a process that began about three billion years ago with bacteria and other microbes, evolved from them, and carried them along through billions of years of evolution... only to discover each one of us is the unwitting repository for trillions of microbes, without whom we could not survive.

To cast an even more interesting light on it, one of the possible—and credible—origin-of-life theories is that life came from outer space. Yes... life may be alien. The theory is more accepted than the idea that God created life out of thin air, at least in standard scientific circles.

One of the reasons this theory is considered credible is that DNA is an incredibly sophisticated, highly evolved and optimized molecule. It's so good at what it does that it just doesn't seem as though there was enough time after the molten fireball of earth cooled off enough to support life for it to have evolved to the state we find it in in the earliest fossil records... about 3.4 billion years ago.  The question of how life evolved at all in the hostile environment of early earth is still actively puzzling scientists.

The earliest fossils are recognizably similar to organisms still around today, which just about guarantees they shared a version of the same DNA we find in ourselves. DNA, it turns out, is so very, very good at what it does that many of the structures it uses to create specific proteins, molecules, and body structures are preserved as analogs to one another in creatures that diverged five hundred million years ago or more.

Bodies change... niches change... but although in some ways DNA changes a lot, in other ways, it's actually a very, very conservative molecule. It rarely, if ever, re-invents if what it already has can be reconfigured to work in a new way. Organisms (we can think of DNA, in a broad sense, as an evolving organism) this highly developed, consistent, and durable probably took hundreds of millions of years to reach that level of sophistication; and this is, to be sure, rather unlikely to have taken place at an accelerated pace under the hostile conditions provided on the early earth.

In a certain sense, man himself is a collection of microbes, since each cell—fully integrated and cooperative though they may be—functions as an individual organism. We're reminded of this in unpleasant ways when we get cancer—this, after all, is the ultimate example of just how independent and, in fact, malevolently autonomous cells can still be under the right circumstances. White blood cells (macrophages)  wander around acting on behalf of our defensive systems; cancerous cells act something like that, only when they crawl between tissues, they are looking for places to metastasize—settle down, set up house, and... eventually... kill us, if we're unlucky.

So we're communities of microbes, hosting larger communities of biota. It's estimated there may be as many as 100 trillion "foreign" microbes in the average human being. Multiply that by a planet of 6 billion people... we're up to six billion trillion microbes, and that's just the ones resident in us humans. In contrast, consider that there are probably about ten trillion of our own cells in a human body. The microbes we carry outnumber us by about 10 to 1... or 100 trillion to one, if you want to count our conscious self as one, and our microbes as being on the other side of that fence.

We live, furthermore, in a sea of microbes, one so dense as to give people with OCD the willies.

The point of this excursion is to explain that we depend on our microbial population for survival. We don't just have the microbes; we need them, and the vast majority of them have been evolving in conjunction with animals... first arthropods, then amphibians and fish, then reptiles, and mammals, until finally they ended up here with us. Each microbe we host is exquisitely tuned to living on or in our body.

It isn't just this way for humans. All of life on earth is ultimately arranged this way; everything depends on microbes to function.

We'll take that up in the next post.

Why microbes?

In order to gain a deeper understanding of why microscopic lifeforms are so important to the existence of life in general, we need to begin with the fact that these were the very first life forms.

Not only did all other forms of life develop from them, because they formed the initial communities from which all further developments in life evolved, all these developments in life ultimately built their livelihood directly on the foundations laid by this community of organisms.

Growth depends on the acquisition of nutrients, and in any given environment—especially, perhaps, the most primitive ones on early earth— the total amount of nutrients is quite limited. It furthermore always costs something in terms of energy to acquire nutrients and concentrate them. This is what microscopic life — the first cells — did. In doing so, they created richer, far more concentrated repositories of nutrients.

It turns out that one of the best ways to acquire richer sources of nutrients is to exploit pre-concentrated ones that already exist—that is, steal them, which usually takes less energy than doing the work of concentrating them. And indeed, very early on, lifeforms began not only to compete with each other for the available raw nutrient resources; they learned how to take them from one another. In other cases, they learned to cooperate with one another and share resources; but in either strategy, it became expedient to lock the nutrient resources up in one way or another so that they couldn't be easily shared or stolen. The idea was to make the cost of acquiring these richer sources of nutrients – that is, the bacteria themselves – high enough that it wasn't worth it to others, unless they were willing to give something in return. That could include anything from a mutually beneficial exchange of valuable substances up to the taking of the other party's life in order to get what they had. Cooperation and competition.

Locking these nutrients up took two obvious directions. One of them was to develop body shapes and forms that had strong defensive capabilities. Groups of cells cooperating were better able to defend themselves than single cells; and so one of the first steps in life was the advent of cellular communities, which developed into what we now call organisms. The organism is the microbiological equivalent of individuals and societies banding together to form an army. Communities of cells were better able to defend their resources; they were also, it turns out, better able, in many instances, to acquire them. It wasn't long, in fact, before they began actively altering the environment around them to favor their survival. This took a number of forms—still with us today—which we'll talk about later.

The second line of defense for nutrient resources was to lock them up in chemical forms that couldn't be used by adversaries. One of the best examples of this chemical defense mechanism is cellulose, which is incredibly effective at taking nutrients and locking them up in an unavailable form. It works so well that almost every plant on earth now builds its life around the production of cellulose. This has forced the many larger organisms that want to feed on it—after all, it is incredibly abundant!— to develop mechanisms that can defeat the chemical "locks" on cellulose by digesting it.

The mechanisms that allow animals to digest cellulose are all primarily microbiological. Because it's difficult to attack cellulose in any other than a chemical way, digestive juices of various kinds must process it, all the way from the macrobiotic (gut) level to the microbiotic (fermentation) one.

Despite several billion years of evolution since the advent of the first single cell organisms, everything on the planet is still arranged in exactly this way. Cells lock nutrients up to make them unavailable; and animals and plants which choose to acquire them have to use chemical tools to unlock those nutrients. Even the largest creatures with the biggest teeth and the most powerful muscles can only do the initial job of acquiring the foods; microbiotic forces have to unlock them and make them available. And in the vast majority of cases, in fact, probably all cases, larger organisms have recruited their own colonies of microorganisms to help them do this. (The whole process of decay is deeply tied to this activity.)

This means that when you get a meal for yourself, the meal isn't just for you. It's for the microbes in you as well; you need to feed them, or they can't feed you. Eating the wrong things for them will ultimately lead to bad results for you as well, because it will favor the development of microorganisms that aren't beneficial to your digestive process.

Although forms and sizes have changed over billions of years, the fundamental underpinnings of the food chain have never changed. Given the strong persistence of DNA throughout life as we know it, it's very likely that not only DNA, but also the nutrient-storing molecular forms it encodes for, are much the same as they were billions of years ago. We know, for example, that there were plants of one kind or another using chlorophyll that long ago. They are still doing it today — and so we exist in an unbroken chain that relies on chlorophyll and its molecular productions for energy. Without it, sunlight couldn't be converted; and without the sugars that it converts molecules into, pretty much nothing on the surface of the planet could live. (There is, of course, another chapter to this story—creatures under the surface.)

In a certain sense, then, microbes are running the show; all of us are just vehicles for their action and dispersal. The more efficiently an organism interacts with the microbial community it supports, the more effectively it competes in the acquisition of nutrients. So the microbiological community actually fuels the process of evolution in ways that are still not well understood.

Because of our general ignorance in these matters—and the impression that we can do little or nothing to intelligently manage such things—we have, on the one hand, blithely ignored our relationship with microbes and, on the other, attempted to exterminate the ones that we know cause disease. Both approaches have turned out to have their drawbacks; the one, because we cause harm we don't know about, and the other, because our short-term management of infectious disease in both livestock and humans has led to unforeseen problems in microbe evolution.

Microbe evolution is taking place all around us, all the time, and at a much more rapid pace than our own. 

We'll take that up next. 

the long timescale — a schematic

 Although this post may not seem to relate directly to biology in the subject at hand, I want to say a bit more about this subject of the long timescale, and how our perception of ourselves affects the way we treat the landscape and the biology around us.

 Because the damage to man's perception of the long timescale took place primarily because of a science-related event we refer to as the Age of Enlightenment, the subject is an important one.

In  the interests of further clarifying the question of the cycle of myth, the human perception of time, and the man's knowing of the place he is at, I have created the above diagram, which can also be found and shared at the following link: the long time scale.

 This schematic uses simple visual devices to contrast the way that ancient societies thought about time and themselves, versus the way we do. Time, on both sides of its blue line, is framed by the unknowable — which we will call God or the Gods. This unknowable property was entirely tangible to ancient societies, because they saw how little they understood about the way the world worked.

The result of this was a proportional allocation of perception to temporal forces and their relative importance. Gods, which represented unknowable but immensely powerful qualities, loomed the largest in the landscape, although they lay outside of time itself.

Ancestors, who did have some knowledge — often, it was considered to be better than and more important than contemporary knowledge — were highly valued. This was because of the knowledge base that they imparted to their descendants.

Individuals saw themselves as small players in a vast universe, the fortunate inheritors of a large body of knowledge that had been passed down to them which they could make only incremental contributions to.

Their descendants were considered to have high value, because individuals understood through the instrument of myth and tradition that they were playing the role of ancestors to them, and that the degree to which they performed this function would have an immediate and important impact on the future of their own families, cultures, geography, and civilization itself.

A modern reallocation of perception began during the Age of Enlightenment, when human beings — consequent to a set of admittedly important scientific discoveries —began to devalue everything that reminded them of their ignorance. The dawn of new sciences and the scientific method itself, along with a rise in belief in the ultimate triumph of rationalism, caused men to believe that earlier societies were primitive, and to be held in contempt.

This devalues ancestors dramatically. It also devalues God or the gods, because the perception becomes that all mysteries can be penetrated— often, very soon.  It's not even uncommon for this idea to be accompanied by the delusion that everything is already known, a premise that fundamentalists of various stripes adopt with great fervor.

 In this "system of the moment," descendants became relatively worthless, because one doesn't really owe them anything, and they are unable to contribute to the power structures du jour, which are the only things that matter.

It must be noted, however, that in absolute terms, virtually nothing has changed between the first and the second case. 

Measured against the total sum of knowledge about the universe that can be acquired, man's position is exactly the same as it was in ancient times. All of the knowledge he has acquired (and, in some cases, lost) since ancient times amounts to a zero sum measured against the total sum of the unknown: a fraction so small that one would be typing zeros after the decimal place for millennia in order to define it.

Nonetheless, humans, in a stunning display of hubris, have assumed that their gains are very major ones against the sum total of the unknown, and have consequently discounted it in their psychological landscape.

 The fact that man's total base of knowledge remains, essentially, unchanged from ancient times when measured as a percentage of all the knowledge in the universe is completely forgotten. The individual has now become the one with the power, not the universe and the gods. Modern societies are continually reminded of the fact that this isn't the case at all when natural catastrophe strike them, but they don't see the psychological and perceptual discontinuity that is given birth to their astonishment. Because they have forgotten the cycles of myth, the long timescale, and the essential on knowability and mystery of the universe, they have fallen victim to delusions in which they believe they actually know a great deal, when, in fact, we are profoundly ignorant.

The modern misperception of the long timescale leads to drastic mismanagement of future events and circumstances, since the perception of "now" becomes primary, and everything is seen exclusively as an opportunity for exploitation and personal gain. Because one no longer plays a role in a vast cycle where one owes a debt both to one's ancestors and one's descendants, one perceives one's self as fully licensed to act in a selfish manner.

 As I pointed out in one of the earlier essays on this, the long timescale is actually a dialectic between the transcendent and the immanent. In the first case, the transcendent — the mystery, the unknowable ability, of the universe and of life itself — is the powerful, formative, and transformational force that dominates the transaction between the individual and Being. In this arrangement, the ego is subordinate, even if only by the strength of social form and tradition.

 In the second case, the immanent, the known, and the materially tangible, is the powerful, formative, and transformational force that influences and forms the transaction between individual and Being. This arrangement is a direct affirmation and validation of ego at the expense of mystery and unknowability. It is the dominant form our society has assumed in the present day.

 We have reversed the psychological arrangement that evolved in man from the earliest time in which he formed societies, and we have done so in a few brief centuries. This essentially destructive reversal, which focuses us almost exclusively on our own self-importance, is gradually being seen for the mistake that it was from the beginning. Unfortunately, it is unleashing equally reactionary and divisive forces which — like many over aggressive immune system reactions — may do more harm than the good they attempt to bring.

Understanding these forces from this macroscopic point of view may help us to find sympathy for others, and create a different form of harmony that can include both what we know, and what we don't.

May your soul be filled with light.

A gut feeling

 Microbial communities are highly interactive, and extremely fluid, within the ranges they inhabit. They create whole complex ecosystems of their own, which are largely invisible and entirely incomprehensible to us at our current state of development in microbiology. Teasing apart some of the relationships between various microbial communities will have a major impact on understanding a wide range of human diseases, many of which are caused, directly or indirectly, by imbalances in gut bacteria. Diabetes, autism, cancer, obesity, and heart disease have all been implicated. This means that a wide range of the major killers in the disease community have important links to the way that our microbes are balanced, and their interaction with one another and our body.

Even more disturbingly, imbalances in gut bacteria can definitely lead to macroscopic psychological manifestations, as has been proven repeatedly in laboratory experiments with lower mammals. this means that microbes don't just affect the way your body functions; they affect the way you think. As bizarre as it may sound, microbes may make you smarter.

Or they may make you go out and buy a gun and shoot a bunch of people at a movie theater. We just don't know; and that's what ought to worry us more.

All of this is part of an emerging science of emergence — that is to say, a deepening of our understanding of the properties of emergence itself. Put very briefly, and in layman's terms, emergence is the property whereby an aggregate population of simple elements — whether it be molecules, bacteria, cells, or organisms such as bees or ants — that, by themselves, display consistent and easily predictable behaviors, reach a critical mass of synergistic interaction whereby they suddenly display completely unforeseeable new agencies and an entirely different level of organizational abilities.

Put simply, intelligence itself— and the property of consciousness — are emergent properties of matter. You cannot, for example, take a look at a DNA molecule and predict by looking at that molecular structure that it will create a creature that does what a human being does. But if you put enough DNA together, and it tells enough other material elements what to do, you do get that extraordinary and unusual creature. Much has been made of this by prominent scientists such as Robert Ulanowicz (A Third Window: Natural Life Beyond Newton and Darwin) Stuart Kauffman (Reinventing the Sacred) and Simon Conway Morris (Life's Solutions),  all of whom argue, for various — and very good — reasons, that biology as it manifests displays inexplicable phenomena which cannot be grasped by reductive scientific analysis alone.

 These books are far from simple — although well worth reading — but the point they make is that we live in extremely complex biological systems which display properties science cannot fully understand under any current, or future, set of circumstances. We may create some good approximations of some small fraction of the world we live in, but that fraction will always be necessarily small, because of the enormous complexity and the extraordinary behaviors of biosystems.

 These systems are so complicated that we are not going to fix them by tinkering with them; but we can most assuredly alter and even ruin them by dumping chemicals into them willy-nilly. Every massive, wholesale alteration of the environment — whether it is an environment outside of a man's body, or inside of it — causes the potential wholesale collapse of the inner or outer ecosystem. A huge assembly of maladies ranging from the inconvenient — for example, IBS, irritable bowel syndrome — to the catastrophic — such as Crohn's disease and stomach cancer — are directly attributable to microbial disruption in human digestive systems and other parts of the body. It turns out, for example, that atherosclerosis— the leading cause of heart attacks — is, without any doubt, directly linked to long-term inflammation in the linings of blood vessels, which has been directly associated with periodontitis, the bacteria that cause gum disease.

 We depend, in other words, on the microbial communities that support our bodily functions. In the same way, the outside ecosphere depends on microbial communities that support every single function we observe. Our health and well-being are vitally depended on these systems, but, unlike the macroscopic biological events we can have an effect on — for example, you can operate on a heart to fix a valve — we are very nearly unable, and probably always will be unable, to affect the long-term changes in these microbial systems, because they are vast, complex, and operate in porous environments with little or no control on the influence of outside events such as weather, temperature, influx of an excessive or foreign materials, community interactions, and so on.

You can slow down a heart or stop it beating to perform an operation on it, because it's large enough to see, you know where it is, and you know what needs to be done to it. That description can't possibly be applied to any microbial community we are currently aware of, and it probably never will be. Heart operations are scalable; microbial ecosystem management is not.

 Most of what we deal with in terms of internal and external ecosystems must, of necessity, apply itself to macro solutions. Micro solutions, while they can be engineered for specific instances such as cancers, become much more difficult to implement. It's been discovered, for example, that every single cancer is somewhat different in each individual. If you and I both have, for example, prostate cancer, although they share many of the same characteristics, what works to cure my prostate cancer won't necessarily work to cure yours. Microscopic ecosystem solutions are almost certainly going to turn out to have the same unique and individual characteristics, but they will be far more complex, thus far less susceptible to outside management. This is compounded by the fact that they are tiny, invisible, far more subject to contamination by foreign agencies, and inherently unpredictable because of the fluidity of their interactions.

This is why having negative effects on microbe populations, wherever they reside, has long-term implications that ought to be of far more concerned to human beings than they currently are. We are already engaged in the largest reengineering of the microbial communities on the planet in its history, because we are introducing foreign agents that have never before existed on the planet, in the form of tens of thousands of different chemical products that are contaminating our waters, our air, and our soil.

 This question needs to be re-examined over and over again in more detail, because it is not being discussed enough in environmental communities. The idea that we can tacitly accept the proliferation of chemical products without restraint needs to be retired.

Underpinnings, part two

 Human beings rarely stop to think about the fact that every single thing they look at which is alive and growing — animal or plant — is absolutely and utterly, completely and irrevocably, dependent on the microbial communities that support it.

 If all the microbes on the planet died, or even a significant fraction of them, nearly every life process we are aware of would be disrupted in one way or another. Plants would stop growing; animals would die. Animals have been extraordinarily dependent on microbial communities for survival ever since they developed guts; without the microbes in their guts, they wouldn't make it.

 In order to understand this, we have to understand that the gut — a tube in which food substances are broken down into constituent molecular components — has existed since the cambrian explosion, perhaps earlier. Ever since creatures began to eat surrounding organic material — including each other — there has been a need to break down the walls of cells in order to get at the nutrients inside them. In many cases, the walls of cells, which are microscopic, can't be so easily affected by the action of larger structures like teeth — which many creatures, let's remember, don't even have — and the chemistry of the foods inside the cells was bound up by molecular relationships that lock the energy into inaccessible structures — for example, and perhaps most typically, cellulose, the primary form of cell wall in green plants.

In order to avail themselves of these rich reservoirs of nutrient, animals needed microscopic organisms that could act on the structures to break them down. Bacteria, it turns out, are ideally suited for this, for a number of reasons. First of all, they are small enough to act on a microbiotic scale; big things may be able to eat little things, but other little things need to help digest them. Second, due to their short life cycles, they evolve very quickly, so they can quickly develop new responses to new foodstuffs as new evolutionary developments make them available to creatures foraging in new areas. Third, they are capable of one of the most extraordinary acts in the animal world, one that is functionally impossible at larger levels — that is, the inter-species exchange of genes through plasmids. This gives them a developmental edge that has vexed medical scientists for several generations now, since it allows them to rapidly develop resistance to antibiotics across a wide range of species.

But let's get back to what this meant to early life, because it's fun and exciting. A quick trip to the American Museum of Natural History –  or any museum, for that matter, that has a good collection of large  herbivorous dinosaurs such as apatosaurus— will treat the reader to the sight of creatures that evolved massive bodies with huge guts. These gigantic intestinal reservoirs developed with only one purpose in mind; they were massive housing units for gut bacteria, which fermented and dissolved the huge amounts of plant materials these dinosaurs ingested. Just looking at the skeletons and the shape and size of the guts verifies that by 150 million years ago, the digestion of food stuffs by gut bacteria had been taking place for additional hundreds of millions of years, and had reached what may well be a zenith. It is standard operating procedure in any creature with a gut. The gut is a portable toolkit for microbial digestion, exactly like a set of cookware people bring on camping trips.

Humans aren't any different in this regard. We have skeletal structures, much like the dinosaurs, that support an abdominal cavity that carries around a very neatly organized, species-specific package of bacteria that acts as a bioactive Swiss Army knife. Gut bacteria have been evolving for millennia and are supremely adapted for the diet and lifestyle of the creature that has them. Creatures exist in lockstep with their gut populations; and the gut population itself is a very complex structure that includes both microbiotic creatures such as yeasts, bacteria, and fungi, and macrobiotic creatures such as worms.

 These populations, moreover, have existed in such exquisite balance for so many hundreds of millions of years that changing any of it changes the fundamental nature of the organism itself, since all of its inner workings are highly dependent on the balance of these communities.

 Anyone who doubts this needs to spend a few hours browsing the articles I've collected at my gut bacteria page. You will come away with a completely new appreciation of what not only human beings, but all species, consist of — a commensal and symbiotic community of organisms that must have one another in order to survive.

 We may think we are different than the species of ants who have a parasitic fungus that alters their behavior, causing them to undertake activities that helps the fungus spread; but we are not. The bacteria in us have a direct effect on our psychology, remarkable though that might sound, and the laboratory evidence supporting this contention mounts with every passing day.

There will be more details about this to discuss as we move forward.