What if the very basis of what a human is was radically different from what we were taught as children? On one hand it could be challenging. After all, the majority of my life is past, and I went through it merrily thinking I had humans pretty much figured out. But no. It turns out that I was wrong about the most basic and fundamental concept of what a human is. I am not alone.
Our instruction about what it means to be human usually begins in childhood. It covers both the inherent nature of humans and their biology. Mostly this instruction comes from our schools. But often it is also connected to church or religious gatherings. And of course, daily we get ideas about humans from family members. A parent or sibling might ask such probing questions as “Why would you do that?” or “What on earth were you thinking?” There were questions around my house presaging the idea of the superorganism such as “What part of you thought that was a good idea?”
Our communities and even government organizations may weigh in on the nature and/or biology of humans. School, church, and family presented me with rather complete ideas on what I was as a human being and how I fit into the world as we know it. My childhood teachings from these different sources did not always align precisely. Even the people I looked up to the most had different views. And that was fine. In my own case, none of the sources of information on humans insisted that my view had to be theirs. Well, with the exception of having a grasp of Darwin’s view of evolution for biology exams in school—that was mostly required.
School presented me with an evolutionary view that humans represent the pinnacle of life on earth, honed from earlier life forms and proven to be biologically fit through a rigorous selection process. It was an extension of Charles Darwin’s general view of biology and how species are challenged and change. That was the academic mantra I encountered throughout much of my education in biology.
I remember being drawn to an often overlooked book by Theodosius Dobzhansky, a very famous plant geneticist, an evolutionary biologist, and the scientist most credited with updating Darwin’s ideas in the light of the discovery of genes in the twentieth century. While I appreciated his work in genetics and evolutionary biology, the book that attracted my interest was not one of his evolutionary biology tomes. Instead, it was a perspective on genetics and human nature titled The Biological Basis of Human Freedom (1954). In this book, Dobzhansky moved beyond the narrow study of genetics to tackle more holistic topics such as man’s kinship with nature and the relationships between genes, environment, and culture. He espoused the benefit of cooperative behavior for the fitness and natural selection of humans. Of course, Dobzhansky was thinking about cooperation among humans. In this book I am thinking about cooperation within a human. We are the village. Dobzhansky’s unique and broader worldview was part of what led me to major in genetics in college, and those research credentials in genetics eventually secured my faculty position at Cornell University. I admired the fact that Dobzhansky was thinking more broadly about the possibilities of how his science applied to humans as both individuals and as a society.
Near the end of my formal education a brilliant mind added a fascinating idea to Darwin’s theory of evolution. Former Oxford University professor Richard Dawkins published The Selfish Gene in 1976. In it he proposed that human beings are essentially “gene machines” whose biological operation is determined as a result of their carefully selected human genes. It was a tight argument. It was based on a general twentieth-century understanding of mammalian biology, and that has turned out to be its flaw. If we are robots controlled by genes, what genes control us exactly? Some of your genes never switch on; some never switch off; some switch off for a while, then switch on again. Should we only count the ones that are on? But then who or what is doing the switching?
These insights from the field of epigenetics made the gene robot or selfish gene idea a bit outdated. But perhaps even more important, we now know that 99 percent of the genetic information within the space we call “you” is not from your genome. Your genes only account for 1 percent of what is guiding cells in and on your body. The problem is that every time we think we know what is going on in biology, someone discovers something that we are missing, and sometimes it is something really big. To rethink the selfish gene idea, it might be more accurate to say, if we were built as anything, we are microbial storage machines designed to pass our microbes along to future generations.
When I was growing up, the church presented me with a creationist view of humans as a heavenly designed, newly installed organism on the previously unpopulated earth. It also provided guidance about how humans should operate in the world. I picked the parts that resonated with me, and became flexible in my consideration of exactly how life’s creation might have occurred.
My far-from-atheist family was somewhere in the middle of the range of various scientific and religious concepts concerning humans. Fortunately, they gave me the space to work out how I would grapple with these different views while forming my own perspective about humans, other species, the earth, and the universe. By age twenty-five, I was rather stable in this merged Darwinian-church view, and that continued on for decades. I was even content that I had an operational view of humans and life on earth. Satisfied, I continued on with this understanding of humans until recently.
Almost no one understood the real biological secret about humans. The best minds—the pillars of biology, including Charles Darwin, Theodosius Dobzhansky, Richard Dawkins, James Watson, and Francis Crick—were missing a key piece of fundamental information about human biology. Namely, we are not what everyone thought we were, starting with our own DNA, our genome. We are far from alone even in our own bodies.
James Watson and Francis Crick discovered the nature of DNA in 1953, winning the Nobel Prize in Physiology or Medicine in 1962. Just fewer than fifty years after Watson and Crick’s discovery, scientists had what was thought to be the magic key to humans: an almost complete sequence of the human genome. We would now know everything that was needed about human nature, health, and disease with the publication of a virtually complete sequence of all of our DNA and the genes within it.
Planning for the Human Genome Project began in the late 1980s, and three phases of five-year plans were launched to complete the analysis. The project itself was housed within the US National Institutes of Health (NIH) under the National Human Genome Research Institute funded through congressional appropriations with an estimated cumulative price tag of approximately $3 billion. It involved several US federal agencies and some twenty different major research institutions and organizations in North America, Europe, and Asia. Legions of researchers were involved in the painstaking work. One of the side benefits from the effort was the new technology for molecular analyses that emerged from this massive undertaking. The result changed biology, but not in the way researchers had anticipated.
Ironically, one of the greatest cooperative scientific accomplishments of our lifetime put an end to the old biology. In February 2001 the most significant results of the massive, global human research effort were announced in the journal Nature. This was the pinnacle of the long march of the twentieth century’s genetic revolution in biology. It was a benchmark achievement for the Human Genome Project.
What caused one of the greatest human science projects to end an entire era of biological thinking? Quite simply, the results. The findings of the Human Genome Project were stunningly different than anticipated. Before the project started, our genome had been estimated to contain approximately 50,000 genes. Based on the science of the time, leading scientists believed our genome must drive protein synthesis, metabolism, and cell and tissue development. Control of the genome would be an almost magic elixir for curing disease. There was nothing inherently wrong with the premise except how much it underestimated the role of environment. The short story on the long march to unravel the human genome is that the results were underwhelming.
Instead of 50,000 genes, the human genome has approximately 22,000 genes—less than half of what was expected, and not nearly the numbers estimated to account for the remarkable complexity and diversity of human biological activities. In fact, we barely beat out the roundworm in gene-encoding proteins. The roundworm’s genome has approximately 20,000 genes. Humans as the pinnacle of life on earth? Well, maybe. But if we are special, it is not because the number of our genes significantly exceeds those of other species.
So that 22,000 result isn’t just a number; it has resounding implications. Our mammalian genes were supposed to rule all, in keeping with evolutionary biologist Richard Dawkins’s ideas. And mastering our mammalian genes would surely cure human disease. At least that was the larger end goal for the Human Genome Project. But how can something as complex as a human be controlled, develop, survive, and even thrive with so few genes? The answer is we don’t. We fail to thrive, get sick, and die with only those genes. Those genes are not designed to support humans in leading long, healthy lives. They are only a small portion of our life-support system. That is why the results of the Human Genome Project have ushered in the new biology. The take-home message is that our basic mammalian genome is only a very small part of what makes healthy children grow into healthy adults and produce more healthy children.
The project’s underwhelming results forced us to look for what lies beyond the human genome. We are not self-contained, self-sustaining organisms as pure human mammals. We are intended to be more than that. The human being is a superorganism.
The twentieth century was a time of remarkable scientific accomplishment. In a sense, we became masters of our domain. And our domain was the whole world, plus space travel that took us beyond our world. In the introduction, I described the mid-twentieth-century changes that occurred surrounding infectious diseases. As a child of the ’50s, I was fortunate enough to personally witness part of that transition as innovative science led to the conquering of many deadly infectious diseases. Salk’s and Sabin’s polio vaccines were just becoming widely available, and I got to witness the iron lung (used to keep polio patients alive) gradually disappear from our society’s landscape. Scarlet fever and diphtheria were no longer threats for every child. Many from my baby boomer generation still carry an upper-arm scar from the smallpox vaccination that is missing from most people of more recent generations.
We were pretty sure we knew humans, knew the environment in which we lived, and knew how to control both to our benefit. We thought if antibiotics are good, more must be better. We could embrace our newfound capacities in both chemical manufacturing and industrial development as well as in food production and transport. It was all good. After all, we could now create a new type of artificial environment in which we controlled what chemicals were released into the environment, and we could isolate ourselves from microbes. We could radically change food availability, food types, and diets. We could seal ourselves away and be totally in charge.
While the intentions were well placed, our fundamental misunderstanding of what makes us completely human led us astray. We thought we didn’t need to exist in our environment, but in fact, we can’t live without enmeshing ourselves in that environment.
What we did during the twentieth century under the old biology was simply to trade one set of health challenges for another. We reduced the risk of death from infectious diseases. However, we increased the risk of lifelong disability and premature death due to NCDs.
In 2012, I was invited to contribute to a special issue of the physics journal Entropy. This issue was to address an important and novel subject: the measurement that could be taken that would best predict a healthy life rather than one filled with disease. What could you measure? What would you measure if anything and everything were open? What is the biological sign that foretells our health? I was certain I had the answer—after all, it was my life’s work of the prior thirty-five years. I spent part of a day trying to start the paper. But the more I read over my argument, I had to admit, the more unconvincing it seemed. I was deflated. Was I having a bad writing day, or did I simply have the wrong answer?
I went to bed frustrated. In the middle of the night, I awoke from a dream. Parts of it eluded me. But what was left was a new concept of what constituted a healthy human. It was something that could be measured in a newborn. It was the microbiome.
The human microbiome is simply defined as the collection of microbes that live on and in us. You will see the term used to refer to both the microbial cells and their genes. Another name given to this collection of microbes sharing our body is microbiota. The microbiome is not in just one location in the body but is distributed throughout virtually every body part that has some exposure to the external environment. Some of the locations include our airways (nose, bronchi, lungs), gastrointestinal tract (mouth, throat, small intestine, large intestine, cecum), reproductive tract, and skin. Different locations have different resident microbes that love to live there and sometimes only there. They are a part of you just as they were part of your ancestors.
The idea I awoke with, that we need both the human mammal and a full complement of microbes for a baby to be healthy, became known as the completed self hypothesis, as described in a 2012 paper I wrote. My hypothesis states that, unlike what I learned as a child in school and church, human mammals are not really viable. As mammals devoid of microbial partners, we lack what we need to exist, let alone thrive. In the completed view of humans, we are each a conglomerate of thousands of different species. If we are missing key species, then we are not healthy. We are a hybrid: Each one of us is a superorganism.
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The previous view of humans was the best of biology and theology that existed at the time. But now we know differently. We are a microcosm of earth’s species. They virtually encase us, existing both inside and outside of us. We have organisms in our healthy bodies, such as archaea, that also live in the most extreme places on earth such as deep under the ice in Antarctic lakes. They are in the deepest oceans, the coldest and harshest conditions, and places where no sunlight can reach. We are connected to our environment in ways we never dreamed of.
Let us return for a moment to Richard Dawkins’s selfish gene idea. Here is Dawkins’s basic premise:
We are survival machines—robot vehicles blindly programmed to preserve the selfish molecules known as genes. This is a truth which still fills me with astonishment.
—Richard Dawkins, The Selfish Gene
The basic assumption is that the human mammalian genome largely determines human existence and behavior. In a 1998 interview on the PBS show Faith and Reason, Dawkins also described how human or animal behavior serves the interest of the genes that developed the nervous system. It is a logical idea in Darwinian evolution but assumes that it is human mammalian genes supporting the human mammalian nervous system, which in turn causes behaviors in the interest of those same mammalian genes.
As part of the new biology, we now know that is not the case. Our microbial genes, or what is called our second genome, is now known to drive behavior that supports the bacterial genes and their propagation (e.g., food cravings). If there is a truly significant “selfish gene” in humans, it is probably microbial and not mammalian. That was not predicted by the old biology.
As you will read in later chapters, our microbial partners, the microbiome, significantly impact human behavior. So who is in charge? Exactly who is driving this bus? Did humans acquire microbes to enable them to build a better human, or did microbes design a better human as a new and improved vessel for their subsequent generations?
Maybe that is missing the point. Maybe neither is completely in charge. But we know thousands of species built today’s human superorganism together, so the best conclusion is that there are predominantly cooperative, coordinated genes of our multispecies superorganism—not selfish genes. Humans without microbes are sick. Microbes without humans have no home.
This relationship is, in fact, even more intricate. Research has shown that there is gene sharing between our microbes and our mammalian self. We are intermixed as an organism even at the cellular-molecular level. Many of our present-day genes were not ours to begin with. They were donated by past microbial partners. You are not what you and I were taught. You are more than that. You are a reflective microcosm of the world in which you live.
Does this new biology I am touting actually do anything other than muddy the waters surrounding decades of debate about the nature of humans and the universe? It is my contention that it changes everything and largely in a good way. This change may happen only gradually, but it will inevitably impact how health care is delivered and how both humans and the environment will be protected. It will change our understanding of interpersonal communication. It may even result in changes in cultural and political climates.
But the first step is to embrace the highly useful part of you that you cannot see.