An Independent Race of Thinkers: How Microbes Defend and Define Us

Microbiology Lab

NEUROSCIENTISTS  have been busy for years attempting to establish and finalize the proposed “neuronal correlates of consciousness” originating in the brain.

Modern science seems determined to prove that consciousness, our thoughts and awareness, must somehow originate in the gray matter between our ears.

This mechanistic view was assumed as fact by the Human Genome Project, established to catalog the complete human DNA and identify specific cures for all diseases, yet has failed to do so.

It is held that genes carry information about how we look, how well our bodies metabolize food or fight infection, and can determine even how we behave.

It was thought, therefore, that researchers would easily be able to identify specific genes underlying specific diseases, and then all diseases could be eliminated by manipulating the related genes.

But it was discovered that the seemingly simple concept was much more complex than expected.


Just as the origin of consciousness cannot be tagged to specific neurons in the brain, genes are not easily pigeonholed to one disorder. It was found that they function in complex, and frequently changing teams.

Now science is edging nearer to Theosophy, looking closer at a long-neglected area called the microbiome — researching how hundreds of different species of living microbes, inhabiting the human body and outside, are responsible for our health and behaviors. They even discovered a second brain, in our gut, known as the enteric nervous system!

The Wonder of You

Scientists discovered cognitive (aware) neuronal components, what can be called an “instinctive brain” in our digestive system, and a “feeling brain” in our heart. Who can say where consciousness will show up next? Theosophy maintains that every cell in the body has a brain and memory. (H. P. Blavastsky, Psychic and Noetic Action)

The Locus of Memory

“Memory has no seat, no special organ of its own in the human brain,” Blavatsky wrote in Psychic & Noetic Action — it has, in fact, seats in every organ of the body. The seat of memory, then, is assuredly neither here nor there, but everywhere throughout the human body.”

“To locate its organ in the brain is to limit and dwarf the Universal Mind and its countless Rays…which informs every rational mortal.”


 The “second brain” in our digestive tract, explains Professor W. Prinz of the Max Planck Institute for Psychological Research in Munich, “consists of about 100 billion nerve cells …. a greater number than those in the spinal cord.” Researchers have discovered that we actually have as many brain cells in our gut, as we do in our skull!

Mind of Its Own

The web page on the Enteric Nervous System – “The Brain in the Gut” reports on the work of neurobiologist Michael Gershon, author of “The Second Brain,” who is with New York’s Columbia-Presbyterian Medical Center.

When asked if the brain in our heads influences our second brain, Gershon replied that it does, and that we get butterflies in the stomach when the brain sends a message of anxiety to the gut. This, in turn, sends messages back to the brain that it is not happy!

“However – and this is perhaps the most riveting part of it – the brain in the gut can also work in isolation.”

The Happy Gut

Dr. Mark Hyman shares groundbreaking information about our two brains, and offers a simple, step-by-step plan for feeling better about it.

Conscious Cells

The acknowledged Mother of the New Age, H. P. Blavatsky, taught that “consciousness is universal,” and that every cell and organ in our body has a consciousness of its own.

” Occultism, unlike modern Science, maintains that every atom of matter,” Blavatsky argues, “when once differentiated, becomes endowed with its own kind of Consciousness. Every cell in the human body (as in every animal) is endowed with its own peculiar discrimination, instinct, and, speaking relatively, with intelligence.” (Transactions, P. 24)

There are “well authenticated cases, such as those of clairvoyants, who can perceive by the pit of the stomach.”


“The threshold of consciousness is capable of a very wide extension,” Blavatsky concludes, “far wider than we are accustomed to give to it, both upwards and downwards.”

Not the Genes

The Heart Brain

A human’s brain is larger and more complex than that of any other creature, and his intellect is therefore more pronounced. But, intellect alone “serves humans only for material concerns” Blavatsky writes. “Mentality alone is not capable of leading us to any useful understanding of nature.”

Or to any useful appreciation of either the universal implicate order, or the spiritual intelligence displayed by nature.


A so-called “third brain” was discovered in the heart, Gabriella Kortsch, Ph.D on the Psychology Transformation website reports.

With his revolutionary research the University of Montreal’s pioneer neurocardiologist, Dr. J. Andrew Armour, was the first to introduce the concept of a functional heart brain in the 1990′s.

The Science of the Heart

The brain in the heart – just as the brain in the digestive tract – may act independently of the brain in the head. “The size of this heart brain, according to the Institute of Heart Math:

“is as great as a number of the principle areas of the brain in the head.”

A Mind of Its Own

Many of ancients believed the heart was the seat of the mind. Modern science says the heart is merely a “pump.” Medicine on the cutting edge explained this video clip about California’s Heart Math Institute, says the heart is much more than that. “Your heart emits an electromagnetic field that changes according to your emotions. Others can pick up the quality of your emotions through the electromagnetic energy radiating from your heart.”

The Cognition Network

“The brain is such a complex thing, both physically and metaphysically,” Blavatsky wrote, that it is like a tree whose bark you can uncover layer by layer,

“…each layer being different from all the others, each having its own special work, function and properties.”

Microbe Speaking

“We’re going to have to start changing the way we think about microbes,” writes Hayley Birch in a NewScientist article – Bugging bugs: Learning to speak microbe. “Microbes like P. aeruginosa were once thought of as disorganised renegades, each cell working alone,” Microbiologist Thomas Bjarnsholt says. Bjarnsholt who is battling to understand how P. aeruginosa causes chronic infection in people with cystic fibrosis, now knows otherwise. “They are up against a highly organised army, using a sophisticated communication system to coordinate its behaviour.”

“Bacteria aren’t just isolated cells, or even isolated populations, but multi-species communities that communicate with each other and, crucially, us.”

Microbes in Mud

Birch concludes that “we are, almost certainly, more intimately connected with the bacteria that inhabit us than we ever would have believed,” and quotes microbiologist Steve Atkinson at the University of Nottingham in the UK:

“We’d be naive to believe that we exist in splendid isolation from all other organisms — we’ve thought that way for too long.”


It’s Personal

Eastern religions are accused of crude ignorant superstition because they personified and even deified the chief organs of the human body. “’Foolish’ Hindus speak of the small-pox as a goddess,” Blavatsky comments sarcastically in her article Kosmic Mind, “personifying the microbes of the variolic virus.”

Microbe Cities

Also in the same article Kosmic Mind, she refers to the “Tantrikas,” who are “a sect of mystics, giving proper names to nerves, cells and arteries:

“…connecting and identifying various parts of the body with deities, endowing functions and physiological processes with intelligence.”


“The vertebrae, fibers, ganglia, the cord, etc., of the spinal column — the heart, its four chambers, auricle and ventricle, valves and the rest — stomach, liver, lungs and spleen,” she wrote, “everything has its special deific name, is believed to act consciously.”

Surrounded from Within

Millena ahead of today’s biological discoveries, Blavatsky concluded: “the whole body of man is composed of cells, and these cells ae not being recognized as individual organisms and—quien sabe—

“…will come perhaps to be recognized some day as an independent race of thinkers inhabiting the globe, called man! It really looks like it.”


Gaia’s Village

Microorganisms are essential members of Earth’s closely knit family, actively promoting the balance of health and disease throughout nature.

Ecologically, they are being used in the production of biofuels, and eating excess methane, just two of many important areas of current research.

This is Dr. Marie-Laure Sauer, a post-doc at NC State University, inspecting the growing Dunaliella algae cultures. – North Carolina State University

Many Thinkers

The brains in our head are indeed not unique. Our gut acting as a brain, thinks independently, as does the heart, says Harriet Brown in The New York Times: “A brain in the head, and one in the gut.”

Different Strokes for Different Folks

Another study reported at (“That gut feeling may actually reflect a reliable memory”) suggests that we shouldn’t rely only on conscious memory:

“… we also need to develop our intuitive nature and creativity. Intuition may have an important role in finding answers to all sorts of problems in everyday life …”


“That gut feeling may actually reflect a reliable memory. You know the feeling. You make a decision you’re certain is merely a ‘lucky guess.’

“A new study from Northwestern University offers precise electrophysiological evidence that such decisions may sometimes not be guesswork after all.”


Colon Health Book


More Links

My Excrement, Myself:
The Unique Genetics of a Person’s Gut Viruses

New York Times: A Universe of Us – The Virome


How Microbes Defend
and Define Us


The New York Times, Published July 12, 2010

Allen Brisson-Smith for The New York Times – Dr. Alexander Khoruts, a gastroenterologist at the University Minnesota, used bacteriotherapy to help cure a patient suffering from a gut infection.


Dr. Alexander Khoruts had run out of options.

In 2008, Dr. Khoruts, a gastroenterologist at the University of Minnesota, took on a patient suffering from a vicious gut infection of Clostridium difficile. She was crippled by constant diarrhea, which had left her in a wheelchair wearing diapers. Dr. Khoruts treated her with an assortment of antibiotics, but nothing could stop the bacteria.

His patient was wasting away, losing 60 pounds over the course of eight months. “She was just dwindling down the drain, and she probably would have died,” Dr. Khoruts said.

Muscular atrophy

Dr. Khoruts decided his patient needed a transplant. But he didn’t give her a piece of someone else’s intestines, or a stomach, or any other organ. Instead, he gave her some of her husband’s bacteria.

Dr. Khoruts mixed a small sample of her husband’s stool with saline solution and delivered it into her colon. Writing in the Journal of Clinical Gastroenterology last month, Dr. Khoruts and his colleagues reported that her diarrhea vanished in a day. Her Clostridium difficile infection disappeared as well and has not returned since.

The procedure — known as bacteriotherapy or fecal transplantation — had been carried out a few times over the past few decades. But Dr. Khoruts and his colleagues were able to do something previous doctors could not: they took a genetic survey of the bacteria in her intestines before and after the transplant.

Before the transplant, they found, her gut flora was in a desperate state. “The normal bacteria just didn’t exist in her,” said Dr. Khoruts. “She was colonized by all sorts of misfits.”

Various Intestinal Problems

Two weeks after the transplant, the scientists analyzed the microbes again. Her husband’s microbes had taken over. “That community was able to function and cure her disease in a matter of days,” said Janet Jansson, a microbial ecologist at Lawrence Berkeley National Laboratory and a co-author of the paper. “I didn’t expect it to work. The project blew me away.”

Scientists are regularly blown away by the complexity, power, and sheer number of microbes that live in our bodies.

“We have over 10 times more microbes than human cells in our bodies,” said George Weinstock of Washington University in St. Louis. But the microbiome, as it’s known, remains mostly a mystery. “It’s as if we have these other organs, and yet these are parts of our bodies we know nothing about.”

The bacterium, Enterococcus faecalis, which lives in the human gut, is just one type of microbe that will be studied as part of NIH’s Human Microbiome Project.

Dr. Weinstock is part of an international effort to shed light on those puzzling organs. He and his colleagues are cataloging thousands of new microbe species by gathering their DNA sequences. Meanwhile, other scientists are running experiments to figure out what those microbes are actually doing. They’re finding that the microbiome does a lot to keep us in good health. Ultimately, researchers hope, they will learn enough about the microbiome to enlist it in the fight against diseases.

“In just the last year, it really went from a small cottage industry to the big time,” said David Relman of Stanford University.

The microbiome first came to light in the mid-1600s, when the Dutch lens-grinder Antonie van Leeuwenhoek scraped the scum off his teeth, placed it under a microscope and discovered that it contained swimming creatures. Later generations of microbiologists continued to study microbes from our bodies, but they could only study the ones that could survive in a laboratory. For many species, this exile meant death.


In recent years, scientists have started to survey the microbiome in a new way: by gathering DNA. They scrape the skin or take a cheek swab and pull out the genetic material. Getting the DNA is fairly easy. Sequencing and making sense of it is hard, however, because a single sample may yield millions of fragments of DNA from hundreds of different species.

A number of teams are working together to tackle this problem in a systematic way. Dr. Weinstock is part of the biggest of these initiatives, known as the Human Microbiome Project. The $150 million initiative was started in 2007 by the National Institutes of Health. The project team is gathering samples from 18 different sites on the bodies of 300 volunteers.

To make sense of the genes that they’re gathering, they are sequencing the entire genomes of some 900 species that have been cultivated in the lab.

Before the project, scientists had only sequenced about 20 species in the microbiome. In May, the scientists published details on the first 178 genomes. They discovered 29,693 genes that are unlike any known genes. (The entire human genome contains only around 20,000 protein-coding genes.)

Primary Microbial Centers

“This was quite surprising to us, because these are organisms that have been studied for a long time,” said Karen E. Nelson of the J. Craig Venter Institute in Rockville, Md.

The new surveys are helping scientists understand the many ecosystems our bodies offer microbes. In the mouth alone, Dr. Relman estimates, there are between 500 and 1,000 species.


“It hasn’t reached a plateau yet: the more people you look at, the more species you get,” he said. The mouth in turn is divided up into smaller ecosystems, like the tongue, the gums, the teeth. Each tooth—and even each side of each tooth—has a different combination of species.

Scientists are even discovering ecosystems in our bodies where they weren’t supposed to exist. Lungs have traditionally been considered to be sterile because microbiologists have never been able to rear microbes from them. A team of scientists at Imperial College London recently went hunting for DNA instead. Analyzing lung samples from healthy volunteers,

… they discovered 128 species of bacteria. Every square centimeter of our lungs is home to 2,000 microbes.


Some microbes can only survive in one part of the body, while others are more cosmopolitan. And the species found in one person’s body may be missing from another’s. Out of the 500 to 1,000 species of microbes identified in people’s mouths, for example, only about 100 to 200 live in any one person’s mouth at any given moment.


Only 13 percent of the species on two people’s hands are the same. Only 17 percent of the species living on one person’s left hand also live on the right one.

This variation means that the total number of genes in the human microbiome must be colossal.

European and Chinese researchers recently cataloged all the microbial genes in stool samples they collected from 124 individuals. In March, they published a list of 3.3 million genes.

The variation in our microbiome emerges the moment we are born.

“You have a sterile baby coming from a germ-free environment into the world,” said Maria Dominguez-Bello, a microbiologist at the University of Puerto Rico.

Recently, she and her colleagues studied how sterile babies get colonized in a hospital in the Venezuelan city of Puerto Ayacucho.


They took samples from the bodies of newborns within minutes of birth. They found that babies born vaginally were coated with microbes from their mothers’ birth canals. But babies born by Caesarean section were covered in microbes typically found on the skin of adults.

“Our bet was that the Caesarean section babies were sterile, but it’s like they’re magnets,” said Dr. Dominguez-Bello.

We continue to be colonized every day of our lives. “Surrounding us and infusing us is this cloud of microbes,” said Jeffrey Gordon of Washington University. We end up with different species, but those species generally carry out the same essential chemistry that we need to survive. One of those tasks is breaking down complex plant molecules.

“We have a pathetic number of enzymes encoded in the human genome, whereas microbes have a large arsenal,” said Dr. Gordon.


In addition to helping us digest, the microbiome helps us in many other ways. The microbes in our nose, for example, make antibiotics that can kill the dangerous pathogens we sniff. Our bodies wait for signals from microbes in order to fully develop. When scientists rear mice without any germ in their bodies, the mice end up with stunted intestines.

In order to co-exist with our microbiome, our immune system has to be able to tolerate thousands of harmless species, while attacking pathogens. Scientists are finding that the microbiome itself guides the immune system to the proper balance.


One way the immune system fights pathogens is with inflammation. Too much inflammation can be harmful, so we have immune cells that produce inflammation-reducing signals. Last month, Sarkis Mazmanian and June L. Round at Caltech reported that mice reared without a microbiome can’t produce an inflammation-reducing molecule called IL-10.

The scientists then inoculated the mice with a single species of gut bacteria, known as Bacteroides fragilis.

Nanowired Bacteria

Once the bacteria began to breed in the guts of the mice, they produced a signal that was taken up by certain immune cells. In response to the signal, the cells developed the ability to produce IL-10.

Scientists are not just finding new links between the microbiome and our health. They’re also finding that many diseases are accompanied by dramatic changes in the makeup of our inner ecosystems.


The Imperial College team that discovered microbes in the lungs, for example, also discovered that people with asthma have a different collection of microbes than healthy people. Obese people also have a different set of species in their guts than people of normal weight.

Research Team

In some cases, new microbes may simply move into our bodies when disease alters the landscape. In other cases, however, the microbes may help give rise to the disease. Some surveys suggest that babies delivered by Caesarian section are more likely to get skin infections from multiply-resistant Staphylococcus aureus. It’s possible that they lack the defensive shield of microbes from their mother’s birth canal.

Caesarean sections have also been linked to an increase in asthma and allergies in children. So have the increased use of antibiotics in the United States and other developed countries.

Farm Family

Children who live on farms — where they can get a healthy dose of microbes from the soil — are less prone to getting autoimmune disorders than children who grow up in cities.

Some scientists argue that these studies all point to the same conclusion:

“when children are deprived of their normal supply of microbes, their immune systems get a poor education.”

In some people, untutored immune cells become too eager to unleash a storm of inflammation. Instead of killing off invaders, they only damage the host’s own body.

Microbiome Microsopy

A better understanding of the microbiome might give doctors a new way to fight some of these diseases. For more than a century, scientists have been investigating how to treat patients with beneficial bacteria. But probiotics, as they’re sometimes called, have only had limited success.

The problem may lie in our ignorance of precisely how most microbes in our bodies affect our health.

Probiotic Research

Dr. Khoruts and his colleagues have carried out 15 more fecal transplants, 13 of which cured their patients. They’re now analyzing the microbiome of their patients to figure out precisely which species are wiping out the Clostridium difficile infections.

Instead of a crude transplant, Dr. Khoruts hopes that eventually he can give his patients what he jokingly calls “God’s probiotic” — a pill containing microbes whose ability to fight infections has been scientifically validated.

Dr. Weinstock, however, warns that a deep understanding of the microbiome is a long way off.

Petri Dishes

“In terms of hard-boiled science, we’re falling short of the mark,” he said. A better picture of the microbiome will only emerge once scientists can use the genetic information Dr. Weinstock and his colleagues are gathering to run many more experiments.

“It’s just old-time science. There are no short-cuts around that,” he said.


The Emperor

“The heart is the emperor of the human body. Its subordinate officers are in charge of the nine orifices and their related functions. As long as the heart remains on its rightful path, the nine orifices will follow along and function properly.

“If the heart’s desires become abundant, however, the eyes will lose their sense of color, and the ears will lose their sense of sound.”


“Thus it is said: ‘Keep your heart empty — this is the art of the heart through which the orifices can be mastered.'”

(From the Daoist classic,
Guanzi, prior to 200 B.C.

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4 responses to “An Independent Race of Thinkers: How Microbes Defend and Define Us

  1. Pingback: An Independent Race of Thinkers: How Microbes Defend and Define Us — Theosophy Watch – SHOWERS OF BLESSINGS COVENANT HOUSE

  2. Cool. The GI tract “Dark Matter”.
    DNA is very cool. We are just starting to understand how it works.

    Liked by 1 person

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