FOOD AS INFORMATION: Living Water, Epigenetic Pathways, and the Wisdom of the Ancestral Diet

Views 9066

Food delivers powerful healing properties that scientists have spent decades analyzing in detail.

Take an apple, for example. This amazing fruit is brimming with pharmacologically (or better yet, nutrigenomically) active compounds, most notably ascorbic acid, also known as vitamin C. Another compound it contains is phlorizin, over a dozen polyphenols, potent antioxidants concentrated in the skin of the apple and known to elicit multitargeted effects that reduce the impact of high blood sugar in animal models.1 But this strictly material layer of nutritional analysis barely touches the surface when it comes to appreciating the informational complexity of food.

Apples contain structured water molecules with a hexagonal crystalline configuration (H302) that's halfway between liquid and crystal. Named "the fourth phase of water" by Washington University professor Dr. Gerald Pollack, the micro-clustering pattern of structured water is capable of holding and transmitting both energy and information.2 In fact, all raw plant, animal, fungal, and bacterial cells contain this structured water, each with a configuration as unique as a snowflake, assuming it has not been desiccated and denatured through cooking, processing, or the gamma irradiation-based food preservation process known as "cold pasteurization." "Raw" is a key word here. Raw fruit juice has a high concentration of naturally structured water, which accounts for a good portion of the anecdotal and scientific evidence regarding its healing benefits. Processed juice, on the other hand, is said to contain dys-information (dys- is a word-forming element meaning "bad, ill; hard, difficult; abnormal, imperfect,") that may misdirect the expression of our genes and harm our physiology.3

Virtually all water in uncooked and unprocessed plant food possesses beneficial genetic-expression-modifying information. This is a profound departure from looking at water as a fundamentally material, inert bystander in biological systems, as has been the case for centuries. Additionally, within the biological tissue of which they are composed, all foods contain the noncoding RNA molecules known as microRNAs, which affect the expression of the majority of genes in our bodies and stimulate biological pathways conducive to our species's health and wellness. Packaged in exosomes, which are roughly the size of a virus (~65 nanometers), microRNAs survive digestion, whereupon they penetrate systemic circulation in the body and affect the structure and function of all our tissues.

One example of the healing potential of microRNAs comes from a study of Chinese honeysuckle (Lonicera japonica), a traditional remedy for colds and flus. An animal study demonstrated that a microRNA isolated from this honeysuckle is delivered straight to the lungs, the area of active influenza infection, via the bloodstream. Once there, it targets and inhibits the replication of influenza A virus.4 The authors of the study additionally proposed that ingestion of the Chinese honeysuckle decoction confers medicinal benefits by enhancing the dietary uptake of other microRNAs.

With every bite of food you take, you are deliberately choosing which messages you want to send to your genome. By simply being thoughtful and intentional with the foods you eat, you can remove interference in the moment-to-moment cellular regeneration that should and will naturally occur.

In this chapter you'll learn how regenerative foods communicate on the smallest levels, through micromolecules and via your microbiome. To understand the major role of these tiny players, let's go back to DNA and reexamine its role as the code at the center of life.

Rethinking the Role DNA Plays in Our Health

Since the 19th century, when Charles Darwin revolutionized humanity's perception of its evolutionary past, present, and future, we've been taught that all organisms are separate from one another and locked into a ruthless system of survival of the fittest. This competitive arms race for resources, territory, and self-preservation yields two distinct groups: winners and losers. In this model, our genes are independent players, hermetically sealed within the chromosomes and concerned only with the solitary task of propagating themselves to the next generation. DNA (deoxyribonucleic acid) is the conductor of this abstract symphony of life, in which our place--and our fate--has been predetermined.

Not unlike the Copernican Revolution, which, in the 16th century, dislodged Earth from the center of the universe and threatened rigid social and political conventions, the New Biology dethrones DNA as the center of life, heralding an alternative vision. In this vision, human molecules, cells, tissues, and organs are absorbed in dynamic flux, communication, and feedback. They are capable of constant change, working harmoniously within a networked biosphere that unifies each individual with the whole. Most importantly, the New Biology inaugurates the radical notion that the body can directly access biologically useful energy from the quantum vacuum. In this reenvisioning, biological structures have access to an all-pervading vacuum energy, once described as an ether, and this quantum energy field is operative at subatomic, atomic, molecular, and supramolecular levels.

A particular groundbreaking facet of the New Biology is food's importance as a source of indispensable information, its function reaching far beyond its nutritional composition of varying macronutrients and micronutrients to help epigenetically modify the expression of the majority of our genome.

Master Molecule of Heredity vs. the Interdependent Model of Systems

Which human organ do you view as most imperative to life? Some instinctively feel that the brain is the most important organ, because without it cognition would not be possible. Some say it is the heart, which keeps our circulation flowing, or the liver, which stands vigil, filtering the blood. But the answer is none of the above. They're all requisite for the intelligent design and operations of our somatic form. These organs are interdependent parts of overlapping systems, superimposed and interwoven into the intricate tapestry of our physiology. Like the notes in a musical composition by Bach, their beauty results from the composite and synergistic way in which they interact.

Consider this: for other domains of science, such as the study of aquatic, marine, and land-based ecosystems, we acknowledge a sophisticated interconnectedness among animal and plant species. Yet this awareness dissipates when we venture more deeply into the human body, down to the level of macromolecules. When it comes to DNA, biologists have abandoned the idea of an interdependent model of systems, embracing instead a hierarchical, linear process to create an origin story of life. In this "central dogma of biology," DNA makes RNA, which makes proteins. DNA, as the supreme biomolecule of life, oversees the genesis of all other biological constituents in a top-down, authoritative fashion. This model traces a one-way trajectory from DNA to RNA to proteins.

However, in truth, a more accurate model would be a bidirectional loop within a web. The New Biology shows us that DNA is not actually at the center of life but is instead one isolated facet of a complex biological economy composed of subsystems, none of which can be ascribed primacy or recognized to exert a privileged level of causation. The New Biology goes even further than that, demonstrating that there is no center. Science overwhelmingly shows that life is self-organized, emerging from a network of interpenetrating and interdependent relationships, each with its own niche, specialized in purpose and fundamental to the larger whole. This exquisitely calibrated organization has long been recognized by traditional Eastern philosophies that envisioned all phenomena, from the infinitesimal goings-on of the human body to the macro-level oscillations of the climate, the rhythms of the seasons, and the movements of the planets as a holofractal unity. No one dimension supersedes or holds dominion over another; life operates in an oscillating dance of give-and-take, expansion and contraction, and ebb and flow.

If we utilize a simple linguistic shift from "DNA controls the production of proteins" to "cells use DNA to make proteins," a different narrative emerges.

There is a better way for our bodies to tap into the energy all around us. We need to seek to understand all parts of the system in which we live--not just DNA. These include our miraculous microbiome, a sophisticated, life-sustaining microbial reservoir that we are only beginning to learn about.

MicroRNAs for Regeneration

The New Biology contends that what you consume profoundly impacts you in real time via the machinery of microRNAs. In fact, noncoding RNAs make up more than 80 percent of transcripts from our genome.5 RNA is the only biomolecule present in all of life, making it a better candidate for being a universal biomolecule than DNA itself.

RNA can be difficult to study because it can't be extracted easily from cells, being so crucial to their function. Structurally, RNA is similar to DNA. However, it is single- rather than double-stranded, and is therefore much more chemically reactive and unstable. More importantly, it can assume an expanded repertoire of three-dimensional molecular shapes relative to DNA, giving it versatility in structure and function.6

RNA and DNA nucleotides are composed of different sugars, ribose in the case of the former and deoxyribose in the case of the latter, and carry slightly different base pairs, with the pyrimidine base uracil (U) found in RNA where thymine (T) occurs in DNA. In most cells, only two chemical modifications to DNA are possible, acetylation and methylation, which are the underlying mechanisms behind epigenetics, which you will remember is the activation or silencing of genes by environmental inputs such as diet and lifestyle. On the other hand, at least 66 chemical modifications can be made to RNA;7 the roles of these modifications remain largely a mystery.

The explanation underlying these molecular differences between DNA and RNA is that the latter was the first to arrive on the scene, which means that life effectively began with RNA, likely predating the emergence of the first cells. In a transposition of conventional wisdom, then, DNA might have evolved as a specialized form of RNA--adopting chemical inertness and structural rigidity in order to serve as a more reliable warehouse for the safekeeping of heritable information.

For the purposes of this discussion, we will focus in on microRNAs, which are the premier regulators of gene expression and the conduits for free information exchange among the plant, animal, and microbial kingdoms, not unlike cellular phone towers bouncing signals from one seemingly disparate region to the next. MicroRNA, as described by University of Gothenburg professor Jan Lötvall, can zip around from cell to cell inside the bubble-like exosomes--nanoparticle-sized vesicles that are produced when the membranes of cell-sorting compartments bud or pinch off.8 Exosomes, which contain a mix of proteins, bioactive lipids, and noncoding RNA, may have originally developed as a way for plant cells to talk to one another and to deploy a concerted first-line immune defense when under threat.9 The exosomes liberated from edible plants when we ingest them may also serve as a portal through which our own digestive tracts can sense and communicate directly with the external environment.

Conventional wisdom holds that cells exchange messages through the secretion of hormones, cytokines, and neurotransmitters, which come from one cell and bind to receptors on neighboring receiving cells to produce physiological effects. But a newly discovered form of exosome-mediated communication suggests that the cargo transported by exosomes can be transferred directly to recipient cells without any intermediaries.10

The concept that microRNAs influence the expression of the majority of the human genome11 and may also serve as a channel for cross-species communication12 is highly biologically plausible since trillions of digested, plant-derived exosome nanoparticles navigate through our digestive systems on a day-to-day basis, interfacing with the mucosal lining of our gastrointestinal tracts.13 Previous studies have also highlighted that food-derived microRNAs that piggyback on exosomes have been found to reside in the blood and tissues of animals.14 MicroRNAs within plants share "molecular homology" with human RNAs, meaning that they look like and can mimic the effects of human RNAs. The significance of these diminutive, noncoding RNAs should not be underestimated. Because they can silence or activate mammalian gene expression, they may influence the course of development, aging, and various disease states.15

The animal model brought validity to the concept that exosomes and the microRNAs they contain are instruments of cross-species communication.16 When administered to mice, exosome-like nanoparticles from grapes penetrated the intestines and triggered enhanced production of intestinal stem cells.17 This is meaningful because stem cells are a one-way ticket to regeneration. Known as "multipotent progenitor cells," stem cells can differentiate into and replace specialized cell types through a process called mitosis, or cell division, as part of an internal repair system. This ability stands in sharp juxtaposition to terminally differentiated cells of the heart, blood cells of the circulatory system, and neurons of the nervous system, which do not normally proliferate, or multiply--and they also differ from stem cells in that only the latter are capable of long-term self-renewal.

In a study published in the American Society of Gene and Cell Therapy journal, researchers issued mice a toxic agent known to cause ulcerative colitis, an autoimmune disease of the colon. They then gave the mice exosome-like particles from grapes. Under ordinary conditions, mice given the toxic substance would have quickly developed colitis. But these mice did not. The mice lived twice as long as the mice that didn't receive the grape substance, suggesting that administration of the grape-derived particles protected them from development of chemically induced ulcerative colitis due to activation of these stem cells. The particles preserved normal histology, or microanatomy of the intestines, in the face of these toxic chemical agents, and they "promoted dramatic proliferation of intestinal stem cells and led to an intense acceleration of mucosal epithelium regeneration and a rapid restoration of the intestinal architecture throughout the entire length of the intestine."18 The grape particles were also completely safe for the mice, with zero side effects.

The shining gem uncovered by this study is that exosomes, which are present in a variety of plant foods we consume, may exert additive or synergistic effects in course-correcting our own biology, nudging it gently back to the mean or boldly stimulating tissue regeneration by activating our body's own reserve of stem cells. Conversely, one could argue that many acute and chronic diseases could be caused by a lack of dietary exosomes from ancestral foods. Exosomes have been isolated and characterized from an assortment of edible plants, including carrots, grapefruit, and ginger root, all of which have the power to lightly prod deviant biochemical pathways back to the straight and narrow.19

For instance, a microRNA derived from broccoli was found to be present in human sera and to inhibit growth of breast cancer through its effect on the gene TCF7.20 Exosome-like nanoparticles from ginger, on the other hand, were found to increase levels of a potent anti-inflammatory signaling molecule, interleukin 10 (IL-10), which tamps down excess immune system reactivity.21 Flavonoid compounds from berries, known as anthocyanidins, delivered via milk-derived exosomes significantly suppressed both the growth and proliferation of chemotherapy-resistant ovarian cancer cells, suggesting that phytonutrients, or plant chemicals with health benefits, are more effective when carried by exosomes.22

While berry anthocyanidins have anticancer properties on their own, their bioavailability, or the proportion ingested that enters systemic circulation and elicits an active effect, is poor, and they are inherently unstable in the absence of attachment to exosomes.23 Exosomes may therefore be mother nature's delivery service that safeguards healing noncoding RNAs and bioactive plant compounds until they arrive at their final destination.

Exosomes and the microRNAs that they shuttle are some of the reasons why fruits, vegetables, herbs, and spices that come directly from the earth into your kitchen or medicine cabinet set the stage for healing. Because microRNAs can travel horizontally across species--from fruit to mouse, or vegetable to human--they can send messages that tell genes when to express themselves and when to remain quiet. It doesn't take eons to make these changes; they can alter your genes in real time, and these changes can be passed down to your progeny, and from them to their progeny and so forth.

MicroRNAs shuttled about in their environmentally protected extracellular vesicles provide a viable scientific explanation for interspecies cross talk and for the interconnectedness between all the domains of life. Their discovery shows that the systems of the body, like the kingdoms of life and the ecosystems of the planet, all operate on the principles of harmony, symbiosis, balance, and holism. Rather than existential islands unto ourselves, we are united in a grand and awe-inspiring wholeness.

Meet Your Miraculous Microbiome

Since the late 1800s, when Robert Koch and Louis Pasteur tackled the challenge of foodborne infections, microorganisms have been uniformly demonized by the scientific community and pigeonholed as the singular causative agents behind diseases. Up until recently, the enduring legacy of germ theory, which promulgates the idea that specific germs are the sole cause of specific diseases, is that we have envisioned ourselves to be in a perpetual war against these microorganisms' hostile intrusion. Our conditioning has led us to perceive the microscopic world as the culpable party behind the plagues and pandemics that have snuffed out so much of humanity in singular episodes. Within this conceptual framework, the immune system has been fashioned as the militant armed force against the invasion, and vaccines and antibiotics our only true defense against certain destruction.

The relatively recent discovery of the microbiome, however, is completely redefining the role of microbes in our bodies and shifting the entire frame of reference for our species's self-definition. It turns out that some microbes are hardly the adversary; in fact, they are crucial to protecting us from disease and dysfunction.

A deceptively diminutive term, the microbiome refers to our unfathomably complex array of microscopic microbial inhabitants that together weigh only three or four pounds. Yet the microbiome's power is immense, as it contains 99.9 percent of our genetic material. Comprising bacteria, viruses, fungi, and archaea that reside in their respective niches on and inside our bodies, our microbiome is instrumental to digestion and assimilation of nutrients, detoxification of cells and organs, control of the immune system, competitive inhibition of pathogens, reinforcement of the gastrointestinal mucosal barrier, and production of neurotransmitters.24 Indeed, we relegate life-sustaining functions to these friendly bacteria, including the breakdown of extremely toxic chemicals.25

The discovery of the microbiome has radical implications because it undercuts the theory that microbes are a leading cause of disease and death. In fact, mortality from infectious disease--measles, scarlet fever, whooping cough, diphtheria, and polio--had declined precipitously due to improved living conditions, nutrition, hygiene, and sanitation infrastructure even before the use of antibiotics and vaccinations became widespread in the mid-20th century. Magic bullet medical interventions designed to combat germs were credited as being the primary factor in extending the human life-span and putting a discernible dent in the burden of human suffering from communicable disease. These medical interventions conceived from germ theory became the foundation of the allopathic medical paradigm that continues to be exalted as the be-all, end-all of human health.

Yet billions of years have primed our physiology to interface with virtually endless microbial challenges and prepared our body tissues for intimate contact with bacterial, fungal, protozaol, helminth, and viral co-inhabitants. Through our evolutionary past of hunting, foraging, and subsisting off the land, our bodies have undergone millions of years of immunologic evolution with the elements, soil, and fermentation, all of which have attuned us to countless interactions with the microbial world that have served to guide the trajectory of future immune responses, thereby fostering our dependence on microbes as some of our greatest allies.

Our bodies resemble plants in that our susceptibility to pests, or opportunistic infections, escalates when we aren't provided with the proper inputs, such as when our ecosystems are in a state of disharmony, when our microbial soil is depleted, and when our micronutrient status is compromised. The modern pressures of a sedentary lifestyle; pharmaceutical drugs; occupational stress; ultra-processed, nutrient-poor foods; electromagnetic pollution; man-made toxicants; and circadian rhythm-disrupting blue light cause our microbial diversity to suffer, in turn opening the door to sickness.

The ways in which we deviate from our evolutionarily encoded template are the ways in which our microbiomes suffer. When we unnecessarily forgo the fundamental inoculation of microbes that comes with vaginal birth in favor of Cesarean section, for instance, we are sacrificing the postnatal transmission of maternal flora that seeds the baby's microbiome--one of the most critical exposures in molding the composition of the infant's microbial ecosystem. When we opt for bottle-feeding our babies instead of providing them with the gut-mammary transfer of mom-derived bacteria, gene-regulatory microRNAs, and prebiotic sugars designed to encourage bacterial growth in the infant, we set the stage for the bacterial imbalance known as dysbiosis, the precursor to a dysfunctional immune system, which is a breeding ground for infectious challenges. Breast milk contains special sugars known as oligosaccharides, including lactose and 1,000 other distinct nondigestible molecules that provide a substrate for bacterial fermentation26--in other words, one of the explicit purposes of breast milk is to allow our microbiomes to flourish. Babies with microbiota underdevelopment are at an increased risk of autoimmunity, allergies, asthma, allergic rhinitis, late-onset sepsis, coronary artery disease,27 and obesity. The pattern of early seeding of the microbiome can even predispose babies to vaccine injury, with certain signatures of dysbiosis--absence of bifidobacteria in particular--leading to systemic inflammation and a greater likelihood that vaccines will cause adverse effects.28

 Although how we are born and our initial feeding methods are not under the realm of our control--in some cases, Cesarean birth is the only option and breast milk is unavailable--other variables that either impede or cultivate microbial diversity fall well within our purview. These include avoiding gut-disrupting antibiotics, eating organic fruits and vegetables, managing stress, and minimizing exposure to toxicants in our home environment.

When we malign all bacteria as microorganisms to be feared and eradicated, we indiscriminately target commensal and virulent microbes alike. We do so with antibiotics, hand sanitizers, chemical cleaning agents, triclosan-laden antibacterial soaps, and gut-disrupting pharmaceuticals like acid-blocking drugs and over-the-counter pain relievers. While they are purportedly designed to heal, these prescriptions inevitably destroy the system that has evolved to protect us.

Being stalwart guardians of our microbiomes is of utmost importance if we are making the health of our future generations, which is perhaps the most fundamental evolutionary imperative we have, a priority. Because our microflora consists of a selective array of commensal microorganisms that ultimately originated from the environment--the air we breathe, the soil we interact with, and the water and food that we ingest--our mission must encompass a wider breadth and a more far-reaching scope if we are to save our microbiomes from certain demise.

The Microbiome as a Key to Evolutionary Survival

A growing body of microbiome research is challenging the prevailing genome-centric story of human evolution, namely that extremely gradual changes in the protein-coding nucleotide sequences of our DNA are primarily responsible for the survival of our species over the ages. This is exemplified by a study published in the journal Nature that found that Japanese subjects had a strain of bacteria in their gut that were loaded with both the genes and enzymes required to digest the polysaccharides found in sea vegetation, which are normally indigestible to humans.29 Absent from the human genome, these genes were found to originate from a strain of the marine bacteria Bacteroidetes, Zobellia galactanivorans, which naturally lives on the red marine algae commonly consumed in East Asia as nori--the dried and roasted sea vegetable that is formed into a sheet and used as the green wrapper of a sushi roll. These bacterium-derived genes fall outside the bounds of the human genome and are not found in the gut bacteria of North Americans.

The human genome contains an informational blueprint capable of producing a mere 17 carbohydrate-active enzymes (CAzymes),30 a small armament developed over millions of years to help us digest terrestrial plants. The average human microbiome far outpaces our own carbohydrate-digesting ability, containing as many as 16,000 different CAzymes. In other words, our microbiome is a treasure trove of carbohydrate-digesting enzymes, allowing us additional biosynthetic pathways to process new food supplies.

The astounding diversity of CAzymes found within strains like the human gut symbiont Bacteroides thetaiotaomicron, which alone contains 261 carbohydrate-digesting enzymes known as glycoside hydrolases and polysaccharide lyases, begs the question of how this immense diversity evolved. The Nature study provides a novel explanation: human gut flora acquiring new genes from microbes living outside the gut, presumably through the phenomenon of horizontal gene transfer. In particular, the researchers showed that genes coding for porphyranases, agarases, and associated proteins needed to degrade marine vegetation were transferred to the gut bacterium isolated from Japanese individuals.

The implication is that when a population eats a food like nori for long enough, the useful genes from marine bacteria residing on nori can be shunted into already-existing bacterial strains in their guts. Bacteria in our guts can therefore enlarge, elaborate upon, and compensate for deficits in our "hardwired" genetic capabilities. Through shifts in our microbiome, our entire physiology can adapt to changes and challenges in our environment and nutritional milieu. The immense plasticity of our microbiome, therefore, improves our ability to survive and remain in harmony with our natural environment.

Another example centers around the ability of our commensal flora to mitigate some of the ill effects of consuming gluten-containing grains. One reason these popular Western foods are so problematic is that they contain what is colloquially referred to as "gluten," a mixture of addictive, hard-to-digest, and immunologically problematic proteins rich in proline also found in rye, spelt, and barley.31 The primary issue with them is implicit in the word gluten, which means "glue" in Latin. The words pastry and pasta, in fact, derive from "wheat paste," the original concoction of wheat flour and water that made such good plaster in ancient times. Gluten's adhesive and difficult-to-digest qualities come from the high levels of disulfide bonds it contains. These sturdy sulfur-based bonds, also found in human hair and vulcanized rubber, resist digestion and decomposition and give off a sulfurous odor when burned.

Wheat is a hexaploid species, the by-product of three ancestral plants becoming one, containing no less than six sets of chromosomes and 6.5 times the number of genes found in the human genome. Thus, it is capable of producing no less than 23,788 different proteins.32 Clearly the monolithic term "gluten" is misleading, as any one of these proteins is capable of inciting an antigenic response, wherein the immune system identifies the protein as other and launches an innate or adaptive immune response, sometimes attacking self-structures in a case of friendly fire.

One saving grace that has ameliorated some of the effects of wheat consumption is our gut bacteria. Research reveals that a wide range of bacteria in the guts of Westerners are capable of degrading thousands of difficult, if not impossible to digest, proteins in modern wheat.33 Indeed, without the help of these gluten peptide-degrading microbes, the sudden Neolithic introduction of gluten-containing grains into the human diet may have had even more catastrophic health consequences.

When considered as a whole, microbiome research peels back the layers of our very essence and lays bare one gleaming, iridescent fact: we must make a conscious effort to get out of our own way to preserve and leverage our relationship with the natural world. We are not separate or superior to the environment, nor are we detached from the ecology of it. Our genetic potential is optimized in the presence of biologically appropriate nutriment that supports our mutualistic and indivisible interdependence with all the plants, animals, and microbes on Earth.

The seemingly supra-human genetic capabilities of our gut microbiome may have been the primary determinant in our species's survivability because they allowed our species to adapt quickly to changing environments and available diets. Research is only just beginning to bring to light how profoundly the microbiome can and does extend our genetic capabilities.

The Connection Between Mother and Newborn

The latest research into the role of the microbiome in sustaining physiological resilience undermines germ theory and presents a challenge to traditional gender dynamics.

We've long known that both men and women pass on nuclear DNA in the form of chromosomes. Yet only women can pass on the DNA that is found within mitochondria, the organelles traditionally considered the energy factories of the cells.

Because we are all designed to gestate in the womb and enter the world through the birth canal, from which the neonate's microbiome is derived and established, it follows that most of our genetic information is maternal in origin. Even when the original colonization eventually changes and is superseded by environmentally acquired microbial strains in infancy, childhood, adolescence, and adulthood, the original composition and subsequent trajectory of microbial changes is a direct by-product of the mother's terrain. Like a gardener planting the seeds, tending to her plot, and provisioning the conditions for growth, the mother is the guiding force for which foliage and greenery will flourish and thrive within the baby. As such, the microbiome of the mother is the bedrock of the baby's microbiome.

The conditions surrounding gestation, therefore, are important because the maternal-to-fetal microbiome trafficking in utero, maternal diet, and mode of birth take on vastly greater importance than previously imagined.

Honey, Please Pass the Genome

With scientific advances, we have reached a critical juncture where certain long-buried pearls about our physiology are being revealed, unfolding in shimmering opalescence before our eyes. The central tenet--and the one that may be most shocking--is that we are more microbe than human. Not only are we meta-organisms, with the vast majority of our genetic information being microbial in nature, but when we peel back the curtain on the "private" genetic contribution of our own cells, we find that the human genome itself is almost one-tenth retroviral in origin.37

Even our mitochondria, popularized in high school classes everywhere as the "energy powerhouses" of the cell, are alien in origin. According to the endosymbiotic theory, mitochondria were once ancient, free-floating proteobacteria that surrendered their independence by becoming subcellular organelles, leading to the evolution of eukaryotic cells that presently make up our bodies.

The distant past, therefore, is embedded within the present; our cells are enriched with billions of years of biological information, and depending on what we eat or do not eat, the information either remains latent or is activated in an expertly executed schematic. Each cell in our bodies, along with all the cells in all living creatures on the planet today, derives from a last universal common ancestor (LUCA) estimated to have lived some 3.5 to 3.8 billion years ago in the primordial ocean. This was echoed by Charles Darwin, the father of evolution, who said that "probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed." Thích Nhất Hạnh, a Vietnamese Buddhist monk, peace activist, and global spiritual leader, articulated the same insight when he wrote these words: "If you look deeply into the palm of your hand, you will see your parents and all generations of your ancestors. All of them are alive in this moment. Each is present in your body. You are the continuation of each of these people."38

Our degree of reconciliation with our evolutionary past--and hence our level of alignment with the molecular and energetic fabric that is the essence of who we really are--will determine our ability to cultivate health and resist illness. One of the pillars of stepping back into alliance with our authentic selves is eating the food our body expects to encounter, the sustenance it has been conditioned over the millennia to use as fuel. Hippocrates's proclamation that "we are what we eat" was true not only in physical terms--the food we eat produces molecular building blocks from which our bodies are constructed--but also in microbial terms.

The billion-dollar question, of course, is this: What did our ancestors eat? The stereotype of the caveman revolves around a meat-heavy dietary template. Animal products were indeed important in our evolutionary past, but not in the way that you might think. A turning point in evolution for our hominid predecessors was the inclusion of high-quality, easily digestible nutrition from coastal and inland freshwater seafood, which dovetailed with the rapid expansion of gray matter in the cerebral cortex of the brain. A staple of the mid-Upper Paleolithic period, freshwater or marine sources of protein made up between 10 and 50 percent of the diet early modern humans consumed. The inclusion of this protein and fat was concurrent with the development of many hallmarks of abstract thought, such as pottery figurines, knotted textiles, burial decorations, and personal ornamentation.39 Our large human brains, especially their frontal lobes, expressed capacity for executive thought, critical thinking, problem-solving, memory retention, toolmaking, language, and learning. All this may be directly attributable to the easily assimilated long-chain fatty acid in seafood known as docosahexaenoic acid (DHA), which is important for membrane-rich brain tissue.

But Paleolithic humans ate a variety of other forageable foods, too, including honey. According to Alyssa Crittenden, a behavioral ecologist and nutritional anthropologist at the University of Nevada, Las Vegas, honey was a central food for early humans. Excavated rock wall art from around the world displays likenesses of early humans climbing ladders to smoke out and collect honey from honeycomb-filled hives. Crittenden also notes that traditional hunter-gatherer populations in Africa, Australia, Asia, and Latin America incorporate honey and bee larvae as integral parts of their diets.

The idea that honey may be a cornerstone for our species's microbial health is substantiated by a study published in the journal PLOS ONE, which discovered the presence of lactobacillus species in honeybees, suggesting an 80-million-year or older history of association.40 In our fostering of an ancient co-evolutionary relationship with honey, it has become an integral facet of our microbial identity, where our own immune systems and microbial populations may share dependency on honey-based microbes.

Honey contains a range of beneficial microbial life-forms contributed by bees and the plants they forage, including the lactic acid-producing bacteria lactobacilli, which support the immune systems and behavioral patterns of individual bees and the hive as a whole. When eaten raw, honey may contribute health-promoting bacterial strains to our bodies. Strains of lactic acid bacteria, for instance, can improve chronic constipation,41 reduce childhood dental caries42 and eczema,43 reduce nosocomial (hospital-acquired) infections,44 reduce infectious complications in elective liver donors,45 decrease the duration of respiratory infections in the elderly,46 alleviate symptoms of irritable bowel syndrome,47 and reduce the incidence and severity of the life-threatening condition necrotizing enterocolitis in very low-birth-weight infants.48

Honey has also been shown to heal wounds49 and burns,50 reduce radiation-associated pain in cancer patients, improve cholesterol profiles,51 and enhance DNA repair in residential populations chronically exposed to pesticides.52 One of nature's ultimate medicinal substances, it is as effective as the mouthwash chlorhexidine in reducing plaque formation,53 treats nocturnal cough better than the over-the-counter cough suppressant dextromethorphan,54 has superior efficacy to standard hydrogel therapy in the treatment of venous ulcers,55 and has efficacy against urinary tract infections.56 It can even help address the antibiotic-resistant infection known as methicillin-
resistant Staphylococcus aureus (MRSA).57

 Since Paleolithic times, the topography of our inner microbial soil has become completely ravaged. Most recently, the daily barrage of synthetic dietary inputs and battery of antimicrobial toxicants has plunged us into a post-industrial chemical soup. It is plausible, however, that honey could help heal these wounds and that ancestral foods infused with equally ancient symbiotic bacteria could help us recover and "travel back" in biological time to a far more stable state of health. Consuming honey and other real, microbiota-impregnated foods may be absolutely necessary for the continued healthy expression of our DNA, establishing vital anchors for the informational integrity of our species identity.

When we allow our evolutionary compass to guide us home to ourselves, we naturally gravitate toward certain foods and avoid others. In the next chapter, we will explore some of the frontiers in the science of food and energy and learn how to assess new inventions, sidestep those that make us sick, and navigate toward the inputs that best align with what our bodies need and crave at a cellular level.

This was an excerpt from chatper 2 of 'Regenerate: Unlocking Your Body's Radical Resilience with the New Biology' an international best-seller published by Hay House, available in 8 languages.


1. Mahmood Najafian et al., "Phloridzin Reduces Blood Glucose Levels and Improves Lipids Metabolism in Streptozotocin-Induced Diabetic Rats," Molecular Biology Reports. 39, no. 5 (May 2012): 5299-306,

2. Shu-Kun Lin, "The Fourth Phase of Water: Beyond Solid, Liquid, and Vapor. By Gerald H. Pollack (Ebner & Sons Publishers, 2013)," Water 5, no. 2: 638-639.

3. "80 Adverse Effects Associated with Isolated Fructose," GreenMedInfo, accessed December 12, 2019,

4. Zhen Zhou et al., "Honeysuckle-Encoded Atypical MicroRNA2911 Directly Targets Influenza A Viruses," Cell Research 25, no. 1 (2015): 39-49,

5. Mihaela Pertea, "The Human Transcriptome: An Unfinished Story," Genes 3, no. 3 (2012): 344-60,

6. Mark G. Caprara and Timothey W. Nilsen, "RNA: Versatility in Form and Function," Nature Structural & Molecular Biology 7, no. 10 (2000): 831-33,

7. Laure Jobert and Hilde Nilsen, "Regulatory Mechanisms of RNA Function: Emerging Roles of DNA Repair Enzymes," Cellular and Molecular Life Sciences 71, no. 13 (July 2014): 2451-65,

8. Zomer et al., "Exosomes: Fit to Deliver," 447-50.

9. Songwen Ju et al., "Grape Exosome-Like Nanoparticles Induce Intestinal Stem Cells and Protect Mice from DSS-Induced Colitis," Molecular Therapy 21, no. 7 (2013): 1345-57,

10. Ju et al., "Grape Exosome-Like Nanoparticles," 1345-57.

11. Dominique L. Ouellet et al., "MicroRNAs in Gene Regulation: When the Smallest Governs It All," Journal of Biomedicine and Biotechnology 2006, no. 4 (2006): 69616,

12. Ju et al., "Grape Exosome-Like Nanoparticles," 1345-57.

13. Ju et al., "Grape Exosome-Like Nanoparticles," 1345-57.

14. Zhang, "Exogenous Plant MIR168a," 107-26.

15. Yu-Chen Liu et al., "Plant MiRNAs Found in Human Circulating System Provide Evidences of Cross Kingdom RNAi," BMC Genomics 18, suppl. 2 (2017): 112,

16. Ju et al., "Grape Exosome-Like Nanoparticles," 1345-57.

17. Ju et al., "Grape Exosome-Like Nanoparticles," 1345-57.

18. Ju et al., "Grape Exosome-Like Nanoparticles," 1345-57.

19. Hervé Groux and Françoise Cottrez, "The Complex Role of Interleukin-10 in Autoimmunity," Journal of Autoimmunity 20, no. 4 (June 2003): 281-85,

20. Andrew R. Chin et al., "Cross-Kingdom Inhibition of Breast Cancer Growth by Plant MiR159," Cell Research 26, no. 2 (2016): 217-28,

21. Groux and Cottrez, "Complex Role of Interleukin-10," 281-85.

22. Farrukh Aqil et al., "Exosomal Delivery of Berry Anthocyanidins for the Management of Ovarian Cancer," Food & Function 8, no. 11 (2017): 4100-7,

23. Farrukh Aqil et al., "Exosomal Delivery of Berry Anthocyanidins," 4100-7.

24. Sai Manasa Jandhyala et al., "Role of the Normal Gut Microbiota," World Journal of Gastroenterology 21, no. 29 (2015): 8787-803,

25. Kenji Oishi et al., "Effect of Probiotics, Bifidobacterium Breve and Lactobacillus Casei, on Bisphenol A Exposure in Rats." Bioscience, Biotechnology, and Biochemistry 72, no. 6 (June 23, 2008): 1409-15.; and Hayato Yamanaka et al., "Degradation of Bisphenol A by Bacillus Pumilus Isolated from Kimchi, a Traditionally Fermented Food." Applied Biochemistry and Biotechnology 136 (February 1, 2007): 39-51.

26. Raish Oozeer et al., "Intestinal Microbiology in Early Life: Specific Prebiotics Can Have Similar Functionalities as Human-Milk Oligosaccharides," The American Journal of Clinical Nutrition 98, no. 2 (August 2013): 561S-71S,

27. Megan Clapp et al., "Gut Microbiota's Effect on Mental Health: The Gut-Brain Axis," Clinics and Practice 7, no. 4 (2017): 987,

28. M. Nazmul Huda et al., "Stool Microbiota and Vaccine Responses of Infants," Pediatrics 134, no. 2 (2014): e362-72,

29. Jan-Hendrik Hehemann et al., "Transfer of Carbohydrate-Active Enzymes from Marine Bacteria to Japanese Gut Microbiota," Nature 464 (2010): 908-12,

30. Tanudeep Bhattacharya, Tarini Shankar Ghosh, and Sharmila S. Mande, "Global Profiling of Carbohydrate Active Enzymes in Human Gut Microbiome," PLoS ONE 10, no. 11 (2015): e0142038,

31. Anastasia Balakireva and Andrey Zamyatnin Jr., "Properties of Gluten Intolerance: Gluten Structure, Evolution, Pathogenicity and Detoxification Capabilities," Nutrients 8, no. 10 (2016): 644,

32. Klaas Vandepoele and Yves Van de Peer, "Exploring the Plant Transcriptome through Phylogenetic Profiling," Plant Physiology 137, no. 1 (January 2005): 31-42,

33. Alberto Caminero et al., "Diversity of the Cultivable Human Gut Microbiome Involved in Gluten Metabolism: Isolation of Microorganisms with Potential Interest for Coeliac Disease," FEMS Microbiology Ecology 88, no. 2 (May 2014): 309-19,

34. Elizabeth Thursby and Nathalie Juge, "Introduction to the Human Gut Microbiota," Biochemical Journal 474, no. 11 (June 2017): 1823-36,

35. Liyong Chen et al., "Sources and Intake of Resistant Starch in the Chinese Diet," Asia Pacific Journal of Clinical Nutrition 19, no. 2 (2010): 274-82.

36. Joanne Slavin, "Fiber and Prebiotics: Mechanisms and Health Benefits," Nutrients 5, no. 4 (2013):1417-35,

37. David J. Griffiths, "Endogenous Retroviruses in the Human Genome Sequence," Genome Biology 2, no. 6 (2001): reviews1017.1-17.5,

38. Jennifer Schwamm Willis, A Lifetime of Peace: Essential Writings by and about Thich Nhat Hanh (New York: Marlowe & Company, 2003), 141.

39. Joanne Bradbury, "Docosahexaenoic Acid (DHA): An Ancient Nutrient for the Modern Human Brain," Nutrients 3, no. 5 (2011): 529-54,

40. Alejandra Vásquez et al., "Symbionts as Major Modulators of Insect Health: Lactic Acid Bacteria and Honeybees," PLoS ONE 7, no. 3 (March 2012): e33188,

41. Ling-Nan Bu et al., "Lactobacillus casei rhamnosus Lcr35 in Children with Chronic Constipation," Pediatrics International 49, no. 4 (August 2007): 485-90,

42. Svante Twetman and Christina Stecksén-Blicks, "Probiotics and Oral Health Effects in Children," International Journal of Paediatric Dentistry 18, no. 1 (January 2008): 3-10,

43. Kristin Wickens et al., "A Differential Effect of 2 Probiotics in the Prevention of Eczema and Atopy: A Double-Blind, Randomized, Placebo-Controlled Trial," The Journal of Allergy and Clinical Immunology 122, no. 4 (October 2008): 788-94,

44. E. Bruzzese et al., "Randomised Clinical Trial: A Lactobacillus GG and Micronutrient‐Containing Mixture is Effective in Reducing Nosocomial Infections in Children, vs. Placebo," Alimentary Pharmacology and Therapeutics 44, no. 6 (September 2016): 568-75,

45. Susumu Eguchi et al., "Perioperative Synbiotic Treatment to Prevent Infectious Complications in Patients after Elective Living Donor Liver Transplantation: A Prospective Randomized Study," The American Journal of Surgery 201, no. 4 (April 2011): 498-502,

46. E Guillemard et al., "Consumption of a Fermented Dairy Product Containing the Probiotic Lactobacillus casei DN-114 001 Reduces the Duration of Respiratory Infections in the Elderly in a Randomised Controlled Trial," British Journal of Nutrition 103, no. 1 (2010): 58-68,

47. K. Kajander et al., "Clinical Trial: Multispecies Probiotic Supplementation Alleviates the Symptoms of Irritable Bowel Syndrome and Stabilizes Intestinal Microbiota," Alimentary Pharmacology & Therapeutics 27 (2008): 48-57,

48. Hung-Chih Lin et al., "Oral Probiotics Reduce the Incidence and Severity of Necrotizing Enterocolitis in Very Low Birth Weight Infants," Pediatrics 115, no. 1 (January 2005): 1-4,

49. Fady F. Abd El-Malek, Amany S. Yousef, and Samy A. El-Assar, "Hydrogel Film Loaded with New Formula from Manuka Honey for Treatment of Chronic Wound Infections," Journal of Global Antimicrobial Resistance 11 (2017): 171-76,

50. Kamran Ishaque Malik, M. A. Nasir Malik, and Azhar Aslam, "Honey Compared with Silver Sulphadiazine in the Treatment of Superficial Partial‐Thickness Burns," International Wound Journal 7, no. 5 (October 2010): 413-17,

51. Hamid Rasad et al., "The Effect of Honey Consumption Compared with Sucrose on Lipid Profile in Young Healthy Subjects (Randomized Clinical Trial)," Clinical Nutrition ESPEN 26 (August 2018): 8-12,

52. Renata Alleva et al., "Organic Honey Supplementation Reverses Pesticide-Induced Genotoxicity by Modulating DNA Damage Response," Molecular Nutrition & Food Research 60, no. 10 (October 2016): 2243-55,

53. Prathibha A. Nayak, Ullal A. Nayak, and R. Mythili, "Effect of Manuka Honey, Chlorhexidine Gluconate and Xylitol on the Clinical Levels of Dental Plaque," Contemporary Clinical Dentistry 1, no. 4 (October-December 2010): 214-17,

54. Ian M. Paul et al., "Effect of Honey, Dextromethorphan, and No Treatment on Nocturnal Cough and Sleep Quality for Coughing Children and Their Parents," Archives of Pediatric Adolescent Medicine 161, no. 12 (2007): 1140-46,

55. Georgina Gethin and Seamus Cowman, "Retracted: Manuka Honey vs. Hydrogel--a Prospective, Open Label, Multicentre, Randomised Controlled Trial to Compare Desloughing Efficacy and Healing Outcomes in Venous Ulcers," Journal of Clinical Nursing 18, no. 3 (February 2009): 466-74,

56. Mabrouka Bouacha, Hayette Ayed, and Nedjoud Grara, "Honey Bee as Alternative Medicine to Treat Eleven Multidrug-Resistant Bacteria Causing Urinary Tract Infection during Pregnancy," Scientia Pharmaceutica 86, no. 2 (2018): 14,

57. Georgina Gethin and Seamus Cowman, "Bacteriological Changes in Sloughy Venous Leg Ulcers Treated with Manuka Honey or Hydrogel: An RCT," Journal of Wound Care 17, no. 6 (2008): 241-47,

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of GreenMedInfo or its staff.
Sayer Ji
Founder of

Subscribe to our informative Newsletter & get Nature's Evidence-Based Pharmacy

Our newsletter serves 500,000 with essential news, research & healthy tips, daily.

Download Now

500+ pages of Natural Medicine Alternatives and Information.

This website is for information purposes only. By providing the information contained herein we are not diagnosing, treating, curing, mitigating, or preventing any type of disease or medical condition. Before beginning any type of natural, integrative or conventional treatment regimen, it is advisable to seek the advice of a licensed healthcare professional.

© Copyright 2008-2023, Journal Articles copyright of original owners, MeSH copyright NLM.