The Ecology of Humans – Nutrition Physiology

Nutrition Physiology

Eating healthy foods does not necessarily ensure adequate nutrition. Foodstuff does not directly translate to nutrients. An enormous number of factors are involved in digestion and absorption: how well food is chewed, the proper secretion of enzymes and gastric juices, and the condition of the digestive tract.

Absorption is not even the final step: nutrients must reach the cells that need the energy and provided molecular building blocks. Transport varies in efficiency.

Intake and delivery are only half the story. For nutrition to occur, there must be a continuous and effective elimination process. Cells are unable to absorb and use new nutrients if crowded with the waste products of metabolism.

Just as coordination of inhalation and exhalation in breathing, in both rhythm and rate, are crucial to healthy respiration, the timing of feeding and tuning of the digestive system are important to nutrition.

Unlike breathing, which must be unceasing and continuous, breaks in the cycle of digestion and elimination are good for the system. Properly done, fasting breaks benefit body and mind.


Research on the biochemistry of foodstuffs – the chemical composition of foods – is much easier than studying the physiology of nutrition. It is exceedingly difficult to map the digestive functions of humans and their gut flora. Further, the digestion and nutrition of each person are unique.

A small fraction of the nutritional value of food is absorbed into our bodies, which are essentially fed leftovers. Our gut flora turn the food we eat into bodily nutrition. The health and diversity of these microbial colonies is critical to supplying the body with nutrients.

Some intake is selective. The body takes what it needs. But often what is needed is not absorbed, even though it passes through the digestive system.

Absorption depends on enzymes. If digestive juices are not adequately secreted, foodstuff is not broken down or absorbed, and the nutritional value lost.

The digestive system acts as both a facilitator and a barrier that nutrients must traverse to reach cells of innumerable sorts, all of which are interconnected into a holistic being by energy pathways that are powerfully affected by the mind and emotions.

Biochemical analysis is test-tube science: a reductionist approach that misleads as often as it informs. A biochemist would tell you that milk, with a pH around 6.5, is not particularly acidic; but digestion of milk requires an acidic environment to break down constituent fat and protein, and so acidity is necessary to derive any nutritional value from milk. Biochemistry has much less to say about nutrition than it has already said.

 Eggs & Cholesterol

A long-standing bugaboo of reductionist biochemists was the health hazard of eating chicken eggs. The controversy seems unending.

Eggs provide all the essential amino acids for humans, and copious vitamins and minerals. Which makes perfect sense since an egg is, after all, the food supply for a growing embryonic chick as well as the yolk being the chick-to-be.

Egg yolks contain cholesterol. Via biochemical analysis, high cholesterol levels have been associated with coronary heart disease, heart attack, and stroke. The publicized view from the test tube was that consuming cholesterol-rich foods like eggs was like turning up the voltage to blowing one’s own porch light.

All animal fats contain cholesterol to varying extent. Only 27% of egg fat is the saturated fat that contains the so-called “bad cholesterol”: low-density lipoprotein (LDL).

LDL is 1 of 5 groups of lipoproteins. LDL enables transportation of lipids – such as cholesterol – in extracellular fluid.

Eggs are high in biotin, which is essential to cell growth and the metabolism of fats and amino acids. Biotin helps maintain a steady blood sugar level. That eggs contain biotin, though, is paltry endorsement. With exception, biotin deficiency is rare, as an excess of it is generally available from production by intestinal bacteria.

The exception to ample biotin bioavailability applies to alcoholics. Among its other wondrous effects, steady heavy drinking impairs biotin availability, though the exact mechanism is not known.

Cholesterol is essential to all animals, as it maintains cell membrane permeability and fluidity. If a cell is a motor, cholesterol is its motor oil. So, naturally, the body itself synthesizes cholesterol. And the body regulates its cholesterol level.

Proper diet and exercise help maintain the body, and so help regulate cholesterol levels. High cholesterol levels are a symptom of bodily dysfunction which exacerbates the situation.

There is no direct connection to cholesterol intake from foods and high cholesterol levels. That is not to say that there is no connection.

The major dietary sources of cholesterol include beef, pork, poultry, shrimp, cheese, and egg yolks. Of that crowd, the best nutrition one could eat, by far, is eggs.

Another dietary source of cholesterol, to infants at least, is breast milk. Plant-based foods do not naturally contain cholesterol, though peanuts and flax seeds have phytosterols: cholesterol-like compounds that may help lower blood serum cholesterol level.

The bottom line on dietary cholesterol is to minimize intake of animal fats, especially those that offer little offsetting advantage, which eggs have but which meat and dairy lack.


The mouth is an indispensable step in the digestive process. The sight, smell, and taste of food program the digestive system for the specific sequence of enzymatic secretions suited to the food being eaten. If one eats without appetite, or stressed, digestive juices don’t flow properly, and poor digestion results.

Chewing is crucial. Chunks of food in the stomach are never digested. Only the outer surface is worked on. In a word: indigestion.

Chewing food to a paste allows digestive enzymes to do their job. Adequate chewing prevents discomfort and the sense of heaviness that follows a poorly chewed meal.

Thorough chewing stimulates saliva production, an alkaline secretion. Saliva in the mouth contains the enzyme ptyalin, which aids digestion of starch. In a non-acidic environment, ptyalin begins breaking down starch into shorter chains by attacking certain links in the longer chains of starchy food. This facilitates starch digestion.


There are no starch-digesting enzymes in the stomach. In the small intestine, a pancreatic enzyme is secreted which completes the work that saliva began by breaking starch down into simple sugars.

The stomach has thousands of glands releasing gastric juices during digestion, with 6 different sets of glands in its wall.

At work, the stomach contracts about 3 times per minute, churning food and mixing it with gastric juice which comprises water, hydrochloric acid, the enzyme pepsin, and mucin, the main component of mucus and saliva.

Hydrochloric acid creates the acidic environment which pepsin needs to begin breaking down proteins. The acid also kills microorganisms that may have been ingested. Mucus forms a coating that protects the stomach from the effects of the acid and pepsin.

Eating protein is digestively intense. The sight and taste of chewing a concentrated protein, such as nuts or cheese, signals the stomach to secret hydrochloric acid and pepsin, so digestion can immediately begin.

Protein digestion in the stomach can take several hours. The result – chyme – is partly digested protein which is passed to the small intestine to break down into amino acids through enzymatic action.

By contrast, eating a starchy food, such as a potato, does not stimulate secretion of a high concentration of acid. Starch digestion in the stomach occurs in a more alkaline environment. The salivary enzyme ptyalin acts, and 2/3rds of digestion occurs in the stomach itself. The first part of the small intestine, the duodenum, receives short starch chains and sugars, and digestion is easily completed.

The order in which food is eaten can be significant to digestive processing, though digestion under different scenarios is not well understood. Succeeding portions of a meal are arranged in corresponding layers in the stomach and digested in order.

The stomach-churning during digestion does not disrupt the layering of food. Liquids that are drunk slip by, around digesting food, and enter the duodenum.

Thicker fluids require more digestion. Next to clear fluid, fruits are most quickly digested, within an hour or 2 from the time eaten.

Protein foods are trumped in the digestive work required only by fats. Oils and fats delay emptying the stomach more than any other food type.

Stimulants, such as caffeine (tea or coffee), and spices stimulate gastrointestinal churning, and so hasten emptying the stomach after a meal. Stimulants and food additives such as salt can interfere with gastric digestion by irritating the stomach walls. The Japanese, who historically have low incidence of vascular disease, tend to stomach cancer because of high salt intake.

Large chunks of poorly chewed food are kept longer in the stomach. If a chunk heads to the juncture of the stomach and duodenum it is squirted back for further stomach digestion.

The lining of the stomach comprises protein cells protected from gastric juices by mucus, which is constantly flowing around the stomach lining during digestion. Even so, much of the mucus, along with some cells from the stomach lining, are digested along with protein and lipoprotein food.

Slightly more of the protein digested from a meal comes from the stomach itself rather than from protein-intense food. This is why heavy protein diets accelerate aging: by forcing the body to expend excessive energy maintaining the digestive tract.

Small Intestine

Most digestion and absorption of digested food happens in the small intestine. These processes can take 3 to 6 hours.

The duodenum, which is the 1st section of the small intestines, is the hub of the gastrointestinal system: receiving food from the stomach, enzyme-rich juice from the pancreas, and bile from the liver. Pancreatic juice has enzymes that break down sugars and starches into simple sugars, proteins into amino acids, and fats into fatty acids and glycerol. Bile breaks down fat from globules to tiny droplets which enzymes can then act on. The autonomic nerve complex that services the duodenum is sometimes called the solar plexus.

The small intestine is a twisting tube, ~2.4 cm in diameter and ~6 meters long. As with stomach, food is transported through the small and large intestines by peristalsis: waves of involuntary muscle contractions.

The lining of the intestinal wall is a single layer of elongated cells that encounter food on one side and the bloodstream on the other. The intake side absorbs nutrients while the output side releases them into the blood.

The 2 sides of the cell differ in their composition of genic instructions (messenger RNA (mRNA)), and in the organelles (ribosomes) that make the enzymes needed for digestion. There are twice as many ribosomes on the food-facing side of the cell than on the bloodstream-facing side, making the food-facing side much more efficient in enzyme production.

When food enters the intestine, cells in the intestinal lining ramp production of ribosomes, particularly in the food-facing part of the cell. To accelerate the process a cell dispatches large numbers of mRNAs to provide instructions for ribosome production. This part of the cell becomes an intensive factory: generating ribosomes which then produce the needed enzymes.

For most of the night and day, cells in the lining of the intestines just loll around, but once food appears, they must instantly step into action. Generating new mRNA molecules from DNA to make new proteins would take the cells about half an hour. Instead, they can increase production of certain proteins within minutes by moving the mRNA molecules encoding the relevant proteins into the side of the cell that is rich with ribosomes. This strategy enables them to deal with the arrival of food in a fast and efficient manner. ~ Israeli systems biologist Shalev Itzkovitz

The surface area for nutrient absorption in the small intestine is enormous. The small intestine is lined with millions of fingerlike projections called villi. Each villus is 0.5–1.5 mm long and covered with a layer of cells.

In an application of fractals in Nature, the villi are covered with even tinier microvilli fingers, which vastly increases the surface area, multiplying capacity for digestive absorption ~150 times.

Behind a villus’ single layer of cells are capillaries of the bloodstream and lymphatic systems. These capillaries transport nutrients throughout the body. Simple sugars and amino acids enter the bloodstream, while fatty acids and glycerol are transported by the lymphatic system.

The huge expanse of surface area in the small intestine for absorbing food also constitutes a portal for pollutants and unwanted microbes. Normally the lining of the small intestine functions as a filter: letting nutrients through but not undesirable materials. A weakened system stops being an effective guard, whether from pesticides, herbicides, drugs, irritation from stimulants or harsh spices, or from bad bacteria.

Some absorption is passive. Sugar concentration, for example, may be so high in the intestine as to force infusion across the intestinal wall. In other instances, absorption is active: metabolic systems pull nutrients from the intestinal tract and into the bloodstream or lymphatic system.

The digestive process does not proceed smoothly if food does not remain in contact with the intestinal wall long enough. The speed of digestive processes is governed by the nervous system, and so heavily influenced by the mind and emotional flux.


The journey of food into nutrition does not end in the blood stream. The proper nutrients must be relayed to cells needing nourishment. Timing is significant. Undernourished cells underperform. That accelerates aging.

Nutrients absorbed through the intestinal wall flow into the portal vein, which delivers oxygen-poor but nutrient-rich blood to the liver.

Gut Flora

The composition and activity of the gut microbiota codevelop with the host from birth and are subject to a complex interplay that depends on the host genome, nutrition, and lifestyle. The gut microbiota is involved in the regulation of multiple host metabolic pathways, giving rise to interactive host-microbiota metabolic, signaling, and immune-inflammatory axes that physiologically connect the gut, liver, muscle, and brain. ~ English molecular biologist Jeremy Nicholson et al

Though humans coexist with their gut flora as mutualists, the host body is outnumbered. The number of microbes in a normal human intestinal tract alone exceeds the number of human cells in the body by a wide margin: 10 trillion human cells outnumbered nearly 10 times over by microbes in the intestines alone.

Bacteria are most of the gut flora by a wide margin, but protozoa and fungi also live there, though little is known of their lifestyles or contributions. Over 99% of gut bacteria are anaerobes, as oxygen is scarce within.

While many bacteria found in food are killed by digestive secretions in the upper digestive tract and digested, the mucus coating of the small intestine lining harbors microbe colonies which aid digestion.

The large intestine relies upon copious bacterial colonies – over 400 species – to complete digestion and facilitate elimination.

The appendix acts as a sanctuary for gut flora and is an interface point between the gut microbiome and the immune system. Hence, the appendix helps maintain digestive health.

Colonization by gut microbiota impacts mammalian brain development and subsequent adult behavior. ~ Swedish neurobiologist Rochellys Diaz Heijtz et al

An animal cannot survive without gut microbiota. Digestion and conversion of foodstuff into nutrition rely upon intimate microbial-host interaction.

To facilitate digestion, animals contract their guts at certain times. Gut flora direct the timing of gut contraction. The microbes are, after all, doing the digesting.

The exchange of nutrients is a long-standing tradition among microbes. Metabolic cross-feeding among different microbial populations helps keep a microbial ecosystem as healthy and robust as possible. In a microbiome, this communal comity is extended to include the host. From a microbiotal perspective, feeding the host is analogous to home maintenance.

The only food the human body can absorb are the simplest sugars. The gut microbiome digests all, providing its host with the nutrition available.

Besides fats, proteins, and carbohydrates, minute gobblers metabolize dietary fiber, vitamins, and drugs. Further, microbes synthesize vitamins which human cells cannot, notably B6, B7, B12, and K. Microbially-produced hormones direct host fat storage.

The gut is not jam-packed with food; it is jam-packed with microbes. Half of your stool is not leftover food. It is microbial biomass. ~ American microbial ecologist Lita Proctor

Gut microbes manufacture 90% of serotonin used by their host. This is one way in which diet and the microbiome affect well-being and mood.

Not only do gut flora digest the food, they tell their host when to stop scarfing it down. The satiation signal comes from microbiota who have had enough to eat, thank you. The mini-munchers produce proteins to suppress further food intake.

Bacteria physiologically participate in appetite regulation immediately after nutrient provision by multiplying and stimulating the release of satiety hormones from the gut. ~ Russian physiologist and nutritionist Sergueï Fetissov

The interaction between the microbiota and host indicate an intelligence among the microbiome as to what their host needs nutritionally and biochemically. This must, of course, be communicated to ensure proper supply, especially manufactured compounds. Such interactive savvy is impossible to imagine as merely biochemical – another existence proof of energyism generally, and specifically of minds as intangible organs of intelligence, possessed even by those living entities lacking brains.

Our ability to digest new foods, such as the lactose in dairy products, is the result of bacterial evolution, not human cell adaptation.

The human gut “metagenome” is a complex consortium of trillions of microbes, whose collective genomes contain at least 100 times as many genes as our own eukaryote genome. This essential “organ” – the microbiome – provides the host with enhanced metabolic capabilities, protection against pathogens, education of the immune system, and modulation of gastrointestinal (GI) development. ~ Italian nutritionist and microbiologist Carlotta De Filippo et al

Gut flora train the host immune system, thereby protecting themselves and helping prevent the growth of their pathogenic cousins who would wreck the joint. The first test of immune system training by gut microbes begins with the first meal, as an early step in the development of an infant body.

A trained immune system mediates host-microbial symbiosis by controlling the richness and balance of bacterial communities. ~ Japanese immunologist Shimpei Kawamoto et al

Some gut flora seek exemption by changing their surface receptors to mimic host cells, thus evading any possible immune response.

Gut bacteria produce an enzyme that modifies signaling of epithelial cells lining the gut. The bacterial enzyme is a homolog of a human enzyme. This establishes biochemical communication lines between gut flora and host cells.

Microbes in the gastrointestinal tract are under selective pressure to manipulate host eating behavior to increase their fitness, sometimes at the expense of host fitness. Microbes may do this through two potential strategies: (i) generating cravings for foods that they specialize on or foods that suppress their competitors, or (ii) inducing dysphoria until we eat foods that enhance their fitness. ~ American evolutionary biologist Joe Alcock et al

As gut flora feed first and provide leftovers to their host, they influence food choice through their communication links with host cells. Dietary habits, cravings, and satiation level are all driven by gut flora. The constituency of gut microbes and host diet are entangled.

A positive-feedback loop exists between the preferences of the host for a particular dietary regimen, the composition of the gut microbiota that depends on this regimen, and the preferences of the host as influenced by the gut microbiota. ~ French molecular biologist and biochemist Vic Norris et al

The particular variety of microbial communities in the gut practically define the health of the host. Viruses play a critical role.

In our gut, also known as the human gut virome, is dominated by bacteriophages (phages). Viruses can control the levels of bacteria in the gut, to make sure that no one type gets the upper hand. Viruses could maintain the biodiversity within us. ~ Dutch virologist Bas Dutilh

Bacteriophages – viruses that infect bacteria – regulate bacterial populations in the gut. One phage – crAssphage – resides in nearly 75% of the human population.

Microbes alter the gut environment, selectively engendering and excluding certain species, creating an ecosystem of a specific type: an enterotype.

The inside of our gut is rather like a war zone, with all kinds of microbes battling it out for survival and fighting over territory. ~ English biologist Jonas Schluter

The battle over microbial dominance has a forceful kibitzer. Gut flora undergo selective pressure from the host as well as from microbial competitors.

Epithelia that line the digestive tract are the host cells in direct contact with gut flora. These cells receive information from neighboring microbes and regulate the microbial ecosystem via host secretions that promote favored factions.

Modest amounts of moderately selective epithelial secretions cause a complete shift in the strains growing at the epithelial surface. This occurs because of the physical structure of the epithelium–microbiota interface. Epithelial secretions have effects that permeate upwards through the whole microbial community. ~ English biologists Kevin Foster & Jonas Schluter

The result approaches an ecological homeostasis, with some species abundant, and others living on the margins. This is how an enterotype is defined and maintained.

3 different human enterotypes have been identified, each with distinctive constituencies of gut flora. An enterotype is named after the genus of bacteria which is prevalent.

Bacteroides is associated with meat eating and consumption of saturated fats. As an enterotype, it dominates others.

The 2nd enterotype, laden with Ruminococcus in the intestines, is common among those who regularly drink alcohol and/or eat a lot of polyunsaturated fats.

The healthiest enterotype has a prevalent presence of Prevotella. It is found in vegans who enjoy fruits & vegetables and eat a wholesome carbohydrate-based diet.

The bacteria, fungi, and viruses in our food transiently colonize our gut. Cooking kills most of these, so raw fruit and veg are particularly important sources of gut microbes. Freshly harvested, organic food harbors a significantly more diverse, more even and distinct bacterial community compared to conventionally grown. ~ German biologist Gabriele Berg

While the composition of the microbiome within an individual tends to be somewhat stable given a consistent diet, the dissimilarity of gut flora between individuals, even identical twins, may be huge. Diet affects gut microbiota differently in females versus males.

Enterotype makeup is influenced by several factors, but diet is most significant. A human can alter enterotype with a sustained change in diet. Changing gut flora composition has cascade effects in altering the microbiome throughout (and on) the body.

Considering that gut flora play a major role in metabolizing dietary carcinogens and other potential toxins, as well as helping prevent diseases, including allergies, the importance to one’s health of engendering a healthy enterotype cannot be understated.

People whose guts contain a low diversity of bacteria are found to have higher levels of body fat and inflammation than those with high gut-microbial richness. ~ Korean geneticist Sungsoon Fang & American geneticist Ronald Evans

Obese people have dissimilar gut microbiomes than healthy individuals. (Fat taxes the body. Obesity is obviously a disease. The notion of healthy chubby people is nonsense.) Resident microbial communities play an active role in maintaining one’s way of being for better or worse.

Colitis – inflammation of the colon and related vicinity – is attributable to gut flora composition. Colitis is one of several maladies that have their origination in lifestyle choices that sustain an unfavorable enterotype. Diabetes is another.

Broad-spectrum antibiotics are like a nuclear explosion to gut flora. But consumption of certain foods can also have outsized effect on gut microbiota.

Even modest consumption of artificial sweeteners disrupts gut flora communities. Despite having no calories, these sweeteners are unhealthy.

Non-caloric artificial sweeteners (NAS) are among the most widely used food additives worldwide. NAS consumption is considered safe and beneficial owing to their low caloric content. But consumption of commonly used NAS formulations drives the development of glucose intolerance through induction of compositional and functional alterations to the intestinal microbiota. ~ Israeli nutritionist Jotham Suez et al

Consumption of artificial sweeteners adversely affects gut microbial activity which can cause a wide range of health issues. ~ Israeli microbiologist Ariel Kushmaro

The Liver

Nutrients pass through the liver before entering general circulation throughout the body. The liver is the largest internal organ of the human body, performing more than 500 functions, including digesting fats, synthesizing proteins, filtering poisons and waste products, storing nutrients, and regulating the levels of many chemicals used by the body that flow through the bloodstream. Some ancient civilizations considered the liver to be where the soul resided.

Most organs have a single blood supply. The liver has 2. The hepatic artery delivers oxygen-rich blood from the heart, providing 25% of the liver’s blood supply.

75% of the liver blood supply is oxygen depleted but nutrient rich, delivered by the (hepatic) portal vein. This vein carries blood that has collected the harvest of digestion. These nutrients are delivered to the liver for further processing and become either immediate fuel or energy reserve.

All other veins in the body flow to the heart, where they are pumped throughout the body. The portal vein is the exception, running to the liver and breaking up into a mesh of tiny capillaries.

The liver is the body’s energy factory, providing glucose: the sugar that fuels the body. When glucose levels are high, the liver pulls excess glucose for storage.

The liver stores energy reserves as glycogen: a carbohydrate made from glucose. Long-term energy storage is put into fat, though not entirely by the liver.

Subject to overwork and abuse, the liver readily regenerates cells. The liver is like the brain in having plasticity: if one section is overwhelmed or damaged, another section performs the functions of the incapacitated area until repaired.

The brain too can regenerate cells. But – as garbage man for the body – the liver has especial need for a fresh change of garment. Hence the liver is adapted to regeneration.

A healthy liver can handle processing a large shot of sugar, converting much into glycogen until later, releasing only a fraction into general circulation as fuel.

An overwhelmed liver is not up to the task, and the body is flooded with sugar. The “sugar burn” from eating excessive sweets is exemplary.

When sugar floods into circulation, the pancreas releases a surge of insulin to tamp the blood sugar level down. Insulin facilitates cells absorbing sugar by increasing the permeability of cell membranes to sugar. Some of the sugar is immediately used, giving a feeling of energy and warmth. The portion that goes unused is converted into energy storage: body fat.

Excessive insulin release floods cells with sugar, sinking the blood sugar level, causing the irritability and weakness of low blood sugar.

Sugar converted to fat by cells for storage is not immediately changed back to fuel. Low blood sugar results in an urge to eat again to fix the hypoglycemia. This begets a cycle of overeating, especially sweets, that causes more eating, leading to being overweight.

The liver is a major protein processor: taking digested amino acid units absorbed by the intestines and reassembling them into various proteins. The liver also distributes amino acids, which cells use to produce whatever proteins are needed there.

The liver may store amino acids, awaiting delivery of further components that make for the complete protein needed. Hence, there is no need to worry about eating complete proteins at a meal if one’s diet is well rounded.

Much of the protein released into the blood and employed by cells is albumin, like that in egg whites. Albumin concentrated in the blood pulls fluids from tissues by osmosis. Therefore, heavy protein consumption invites dehydration.

The liver clears toxins from the bloodstream, including drugs and alcohol, by chemically altering them and excreting them in bile.

Failure to chronically consume and absorb sufficient vitamins and minerals, and other necessary nutrients, cripples liver processing. Poor nutrition means that liver cells are shortchanged of essential nutrition, and poisoned by toxins piling up, waiting for detoxification. The cells began to break down. The bloodstream is then flooded with unprocessed sugars and amino acids, as well as awash in undetoxified chemicals.

Sustained abuse can permanently damage the liver beyond its capability to repair itself. A fine way to accomplish this is by drinking alcohol. Heavy alcohol consumption causes fat deposits to accumulate in the liver.

A prolonged habit of pickling oneself with booze leads to cirrhosis, which is the destruction of liver cells and replacement by scar tissue. Cirrhosis is characterized by diminished flow through the liver. Cirrhosis cannot be reversed.

Liver failure is often the last stage of terminal illness.

Completing Digestion

The large intestine is the final passage of undigested food out of the body. The large intestine has a smooth mucosal lining, lubricated by mucus to ease the passage of waste.

The bowels start with the cecum, which has the ileocecal valve: a one-way passage from the small intestine and the appendix. The valve’s critical function is to limit reflux of colonic contents back into the small intestine.

The S-shaped colon follows. At the terminal end is a 15-cm exit pipe: the rectum, which is capped by an instinctually controlled round muscle, the anus.

All the blood coming through the intestinal tract, including the bowels, is filtered through the liver. Disorders or imbalances in the lining of the intestinal tract impact the liver.

Water is suctioned from waste product in the colon, solidifying into stool. But the colon is more than a mere receptacle of waste.

The colon hosts a tremendous thriving variety of microbial colonies: of bacteria, fungi, yeast, and others. There are 1.4 kilos of bacteria in a healthy person’s colon.

Metabolism in the colon is active. Bacteria in the colon further break down the waste there. 1/3rd to 1/2 of the weight of feces is made up of these microbes which are important in creating the texture of stool, and in maintaining the condition of the intestinal wall. Among their many nutritional contributions, colon bacteria produce B vitamins, which are critical to health.

Only certain strains of bacteria are suitable agents of digestion. Exactly which bacteria thrive in the large intestine greatly depends on what is eaten.

If the delicate symbiosis between digestive bacteria and its host is disrupted, or if there is outsized growth of undesirable microorganisms in the intestine, the protective barrier provided by the intestinal lining can break down.

The Gut Brain

The human digestive tract has its own semi-autonomous brain, with 500 million nerve cells: as many as there are in a cat’s brain. (Alas, in their ignorance, neurobiologists don’t count astrocytes.)

The gut brain controls muscular contractions and secretions from glands and cells. (The gut brain is more properly termed gut mind-brain. Whenever there is brain activity there is a mind behind it.) The gut brain gives the head brain frequent status reports: begging when empty and strutting satisfaction with satiety.

Stomach rumbles are a communication ricochet: the gut brain complaining to the head brain of low blood sugar, which then invokes gastric grumbles.

When food enters, the stomach stretches under gut brain control. Digestion is an extremely intricate process, with the gut brain conducting the orchestra of organs involved.

The gut brain knows when there are nutrients available in the digestive tract. The gut brain feeds the body by stimulating the release of digestive outputs into the blood.

The human gut brain reflects hundreds of millions of years of evolution. The mind-brain system of earlier-evolved organisms is more gut brain than head brain, though little research has been done on the different mind-brain systems in other life forms, as it is and exceedingly difficult study.

In evolutionary time, sophistication developed in the head and gut brains along with adjustments in mental processing and digestive choice. Cooking made foods more digestible, improving nutrient absorption. The evolution of the hominin gut brain reflected this lifestyle choice in conducting its digestive affairs, and in its communications with the brain upstairs.

The Fat System

Fat is more than the body’s energy storehouse. Fat is a major player in a body’s functioning, acting as an endocrine organ. Fat cells continuously dispatch dozens of potent chemical signals to myriad tissues throughout the body, including the brain, muscles, liver, reproductive organs, and immune system.

Fat orchestrates a range of bodily activities. Fat tells the brain how much energy the body has. Fat influences blood clotting and blood vessels constriction. Fat kibitzes on reproduction, playing a role in synthesizing sex hormones such as estrogen, and signaling whether conditions are favorable for pregnancy.

Fat unleashes or suppresses the immune system. The immune system and fat have an intertwined relationship because the body needs energy to fight infection. The intimate relationship with the immune system explains why excess fat triggers stress responses and systemic inflammation.

Brown and White Fat

Brown fat plays an active role in metabolism. ~ American biologist Evan Rosen

There are 2 types of body fat: white and brown. Brown fat is an active form of fat, as opposed to passive white fat. Brown fat cells burn energy and generate heat, regulating body temperature. Brown fat cells are activated by signals that the body is cold. White fat stores energy in the form of lipids.

Mammalian babies, including mice and humans, have pads of brown fat on their backs. Humans lose most of the brown fat in their backside as they grow up.

In adult humans, brown fat is found around the spine, in the abdomen, and in the neck, above the collarbone. Brown fat is far more abundant in healthy humans.

Brown fat helps keep weight off. White fat crowds out brown fat as it provides permanent insulation, making brown fat redundant.


Autophagy is a bulk degradation system induced by cellular stresses such as nutrient starvation. Its function relies on the formation of double-membrane vesicles called autophagosomes. Unlike other organelles that appear to stably exist in the cell, autophagosomes are formed on demand, and once their formation is initiated, it proceeds surprisingly rapidly. ~ Japanese cytologists Shusaku Shibutani & Tamotsu Yoshimori

The cytoplasm of a cell is a busy place. Most cellular activities happen within that voluminous, gelatinous space. A vast population of proteins and other macromolecules bustle about. Waste is discarded as work proceeds. Old proteins expire on the spot.

Autophagy is the cleanup process: hauling out cytoplasmic sludge to keep the cell running efficiently. Reusable bits, such as amino acids, are recycled. All eukaryotic cells employ autophagy.

Amino acid starvation or other trigger sends a complex of proteins to form a cup-shaped container in the cytoplasm. This phagophore expands to engulf the targeted trash.

A phagophore’s open end closes to form a double-membraned vesicle. An autophagosome is born.

Yeast autophagosomes are 0.3–0.9 µm. Mammal autophagosomes range from 0.5–1.5 µm: large enough to engulf a worn-out organelle.

An autophagosome fuses with a lysosome (in animals) or a vacuole (in plants, fungi, yeast, and other microbes). Then the contents inside the autophagosome and its inner membrane are degraded by hydrolases: enzymes that catalyze molecular breakdown via hydrolysis. The entire process takes 15 minutes or less.

Autophagy is an essential cellular process. Cells become cesspools if not for autophagy.

Lively autophagy is promoted by a healthy lifestyle, particularly curtailed food consumption. Chronic overeating promotes autophagy breakdown, as the body has a surfeit of material from which to readily draw cellular building blocks.

The vitality of autophagy is a principal cellular mechanism in the aging process. Its dysfunction causes innumerable diseases, including diabetes, heart problems, tumors, and intelligence system degradation.

Cancer cells know how important autophagy is. They sometimes invoke autophagy to save themselves from treatments intended to starve them to death.


Fasting has been shown to slow aging in a number of species. Caloric restriction acts on many different cell types and tissues and, importantly, also on the brain. There, it leads to a slowing down of age-associated pathologies, such as brain atrophy or loss of plasticity. ~ American science writer Peter Stern

Fasting 2 to 4 days at a stretch every 6 months or so rejuvenates the system. Damaged cells are recycled. This improves the immune system by getting rid of dysfunctional and unneeded cells. Stem cells awake from their normal dormant state and start regenerating.

Fasting is a mental discipline. Plan the fast. Set a goal and stick to it. One needs to positively affirm in the mind the benefit of a fasting program to feel its benefits as pleasantly as possible.

Before fasting, cleaning the colon of stubborn fecal waste and toxins is well advised.

Drinking lots of water is essential to fasting. If you feel the need to lick your lips, you are on your way to dehydration.

A juice fast is a judicious start to fasting. Use fresh squeezed fruit. Avoid juices where sugar has been added.

Vegetable juices are also recommended, as are herbal teas, with or without a spoonful of honey. As always, organic produce is highly preferable.

Fasting on water only is strict but brings the quickest results. Start with a 24-hour fast before building up to a few days.

Use the best-quality water available, not tap water. Distilled water is good, as is high-quality spring water. If tap water is to be used, boil it for 15 minutes first.

A fast is a vacation. Rest while fasting.

Slight exercise, such as taking a walk in the park on a pleasant day, is fine, at least on the first day or so. Don’t overexert yourself, especially on a water fast.

Fasting is a rapid detoxification. Elevated body odor, bad breath, and pimples from the skin releasing toxins is to be expected. Fatigue will tell you that you are exerting yourself to much.

Headaches can occur, typically from a drop in blood sugar. To minimize this discomfort, enter a fast after several days of winding down caloric consumption, eating light foods, such as those you want to break a fast with.

An alternative fasting regime is to reduce caloric intake to a minimum for 1 or 2 days a week.

The cells of the brain are put under mild stress that is analogous to the effects of exercise on muscle cells. The overall effect is beneficial. ~ American neurobiologist Mark Mattson

Break a fast with light, healthy foods: vegetable juices, raw fruits and vegetables, steamed vegetables, and light vegan fare, such as soup.

A junk-food meal after a fast will painfully demonstrate why meat, dairy, and fried foods are bad for you.

Fasting and going back to a bad diet is ill-advised. If you lack the discipline to eat a healthy diet, do not bother fasting. Instead, welcome yourself to the Collective in accepting accelerated decrepitude owing to weak will.

Immune system defects are at the center of aging and a range of diseases. Prolonged fasting promotes stress resistance, self-renewal, and lineage-balanced regeneration in cells. ~ Chinese American gerontologist Chia-Wei Cheng et at


A significant element of what is called a person’s constitution comes from the microbial environment of the intestine. The process starts in the womb, where microbes are transferred from mother.

Out in the world, the digestive environment is constantly shaped by food consumption and other intake. This individualizes the biological constituency and intricate microbial ecology of the colon.

Emotions play a role in the quality of digestion: affecting activity in the intestine, including mucus secretion, as well as the amounts and quality of enzymes produced, and the kind of bacteria that grow there.

Emotional complexes affect the body as a feedback system. Disposition, such as chronic anger, shapes the quality of intestinal mucus and alters the bacteria mix in the gut. The intestinal microbial environment of healthy oldsters is radically different than those who are senile.

Genetic heritage has been misidentified as the major factor in one’s biological makeup. A person’s physiologic and immunologic profile is a product of diet, digestion, activity, and attitude.

We are walking food tubes with brains attached. When it comes to fueling a system for performance, what goes on in the mind can be as important as what goes into the mouth.

The term constitution is colloquial for holotype, which is the summation of every influence on an organism. Constitution commonly refers to a person’s physical robustness (“a strong constitution”). It is a good starting point. A person’s constitution is sustained by a good diet. Your health becomes what you eat, and how much.