I sh*t, therefore I am

I shit therefore I am


This blog is dedicated by the gut to the rest of the body.

This blog is written in first person, by your gut, giving an explanation of its origins and purpose. Its form and its function. Its symptoms and symphonies. Why it matters, why the digestive tract matters, and what you can do about it…queue the gut.

Dear offal you are invited,
Please bring the blood and bone,
In this story we’re united,
Toilet’s metamorphosis to throne.

Our cells and our bacteria,
Entwined since we began,
Overlapping magisteria,
Each woman, bug, and man.

Journey down this rabbit hole,
From lips to anal verge,
Peristalsis speeds us to our goal,
As me and we converge.


This autobowelography blog is ever-evolving, but begins here and now with an all-important introduction…


Section I: Know thyself.

Blog 1: Introduction

Quote: “Me, we.” Muhammad Ali.

Why Hippocrates, smart chap, suggested that all disease begins in the gut, begins in me, and thus, by extension, all health must also be my purview. This blog, I confess, is somewhat self-serving, but, if you’re reading this then you already probably suspect that what I speak of is at least partly true, that the gut is enormously important.

I hope that this blog surprises you, in the way that dirt-common things, things that you thought were intuitive, may be rendered anew when you dig just a little deeper. So please, stay with me and let’s explain your gut, let’s examine me, and ourselves, together. After all, I contain over 100 million neurons, in my small intestine alone. This is about the same number of neurons that we have in our spinal cord (and I suspect that this is considerably more than some people have in their brains!!), so why shouldn’t I write my own memoir? A memoir of the bowel, the gut, the digestive tract, the gastrointestinal tract, me, moi, myself and I.

Understanding me better, understanding your bowels better, whilst nourishing in itself, can teach us to live healthier, happier and longer lives. Digestion is the process by which food gets broken down into absorbable nutrients with the remainder packaged and disposed of as waste. Biographies are histories of individuals, this autobowelography is a history of me and of my partnerships, ourselves and our luminal environment, the friends and enemies within. We have been, and we are, co-evolving with our microbiome, neither master nor servant, symbiotic, dynamic, and variably balanced since the beginning. This is not so much a biography of “me”, but “we”. This blog may even nudge you to re-examine your very notion of what “I”, of what “self”, even means.

To make sense of my story we first need my prehistory, to give the origin, to give a reason. To understand me, the bowel, we need to provide context, and because form follows function, we need to know why I was necessary, what function do I fill, why did I develop in the first place?

I, your modern digestive tract, begins at the mouth and consists of a muscular tube, engorged and narrowed in sections, with distinct regional roles and responsibilities. I am continuous but my regions are discrete, in anatomy (structure) and physiology (function), all beginning with the mouth. From the mouth, then the oesophagus and stomach, then our bowels, or intestines, divided into the small intestine, colon and rectum, and finally the anus. It is the colon and rectum that house the greatest number of microbes, but the entire gastrointestinal tract has a rich microbial community even within the once believed sterile stomach.

In evolutionary terms, before there was this modern arrangement, my ancestors were just a simple tube, before a simple tube a hole and before a hole a dimple and before that…? So why and how did the gastrointestinal tract evolve, and why and how was I essential for the complex evolution of multicellular life?

Life must satisfy two biological needs: separation and exchange. Separation is essential to life, the packet of “order amidst chaos”. Life must be discrete, integrated and organised to allow the articulation of the biochemical cogs and gears that drive cellular machinery. If life was amorphous, continuous and oozing, flowing and intermingling like a gas, like an ocean or the universe, life, as we know it, would fail, being too dispersed, too removed. Life needs an embrace, not a distant wave of the hand. Indeed, many philosophical and religious debates around when life begins are so vexed, in part, because of the biological difficulty in defining when an embryonic life is “separate” from that of its mother’s, and thus is life at all. The cell membrane is the defining feature of unicellular separation, of isolation. The cell, the irreducible unit of life, was named by Robert Hooke in 1662, upon squinting through his microscope at a piece of cork, taken from a cork tree. He saw, for the first time, these tiny spaces, like a monk’s room or cell. Hooke’s cells were an outline of the cork cells, the caste of the cork cell membrane. Hooke had unknowingly discovered the essence of all life, not the atom, not the nerve, not the nucleic acid, not the spirit but the membrane – life needs separation.

On the other hand, however, life cannot exist of itself, we are all a part of the main. Life must interact with its environment, a continuous transaction, both deposit and withdrawal, at times partnership at others parasitism. Life needs to absorb from its environment the supplies for its cellular factory: water, amino acids, carbohydrates, fatty acids, minerals, and other chemicals to fuel and grease (catalyse) the biochemical machinery within.

But then, like any factory, it also needs to excrete its waste, to clean the floors, remove expended fuel and detritus that, if left uncleared, would clog and paralyse the factory’s future productivity. The cell membrane thus needs to separate, but also allow exchange. The magic of the cell membrane is that it serves as a permeable fence with tightly regulated openings, channels, microscopic mouths and lips, gates and doors to receive nutrients and to expel waste. Each delivery and consignment well vetted and organised.

Extraordinarily, in some Protozoa (larger unicellular organisms) we find actual oral grooves within the cellular membrane, an anatomical mouth-like opening. These organisms, first discovered and named animalcules by Hooke’s Dutch contemporary Antonie Van Leeuwenhoek, use cilia to sweep food into their unicellular “mouths” and use subsequent stomach-like food vacuoles for digestion. In incredible microscopic mimicry of our own digestive tract, the protozoal waste is ultimately excreted via a cytoproct, literally “cell bum”, that opens onto the cell surface and the metaphorical extracellular lavatory beyond. Thus, for unicellular organisms the cell membrane, through passive diffusion or active transport, with both featureless or in larger Protozoa folded membranes, achieve a regulated interface between order and chaos, life and lifelessness.

But, then one cell became two and multicellular communities developed – life existed on both sides of the membrane. Some multicellular organisms were rewarded with greater fitness and proliferated and radiated at the expense of others. Different cells and organised cellular communities (tissues) were permitted to change their nature, differentiating to satisfy new and specialised functions: the gonad, the nerve, the eye, the jaw, where once there as indistinguishable cells.

Sexual reproduction was a new tool for evolution, to develop powerful new ways to better interact with our environment and drive selection. Again, with much time, dizzying complexity followed. This complexity led to greater mastery of our environment and greater likelihood of propagating one’s genes. It was for the want of optimising environmental exchange, including ultimately sex, that propelled adaptation, and it was the modes of exchange, of interaction, that helped drive the diversity of our evolutionary tree, both the successes and, when unsuccessful, the extinctions of genes and their survival machines.

But life, no matter how complex, how grand, how beautiful, is still bound by that fundamental tension found in the single cell, the tension between separation and exchange. Whereas once we needed but one surface, the cell membrane, with complexity, there needed to be two. The first was the natural successor to the cell membrane, the ectoderm, the skin, the master of separation. The skin encapsulates our silhouette as the cell membrane encapsulated the silhouette that Hooke found in his sections of cork. The new surface that was needed, however, was the surface for exchange, an internal surface, the unseen silhouette. These internal surfaces evolved into the mature mucous membranes. The mucous membranes, in their various forms, became the masters of exchange, developing into our lungs for respiration, our urinary tract for blood filtration, our genital tract for reproduction, and our gastrointestinal tract for digestion.

The need for a membrane of exchange, the forerunner to all mucous membranes, is ancient. One of the first recognisable digestive tubes was found in the fossilised remains of an extinct, relative of modern-day urchins, called Blastoidea. This was dated from the Carboniferous period (approximately 323 million years ago).

Granted, this was a primitive template, a U-shaped, internal tubular structure. Initially one membrane, one oral groove and cytoproct, then one more specialised, polarised tube. At the top (cranial) end this tube, this second membrane ultimately evolves into a more sophisticated mature respiratory and upper digestive tract, specific and relevant to the species. At the bottom (caudal) end, the mature genital, urinary, and digestive tracts develop.

One need only look to Australia’s wonderful and unique monotremes, the echidna and platypus, to see that the separation of these mucous membranes, at the top and bottom ends, are relatively recent. The echidna and platypus, egg-laying mammals, have external vents that conceal a combined exit for their genitourinary and digestive tracts and, of course, the very beginning of our own digestive and respiratory tracts are still joined.

Echoes of these common ancient openings are also found in developmental human disorders, such as tracheoesophageal fistula cranially, and cloacal defects caudally. It has been said that ontogeny recapitulates phylogeny, that is, development mirrors our evolution, and our developmental and evolutionary tics, literally, can be heard if one only knows how to listen.

But it is the digestive tract, in my current incarnation, that holds many of you and us, in its thrall. I am the external environment within. I begin with the lips, the teeth, and the tongue. The mouth is ancient, instinctual, and expressive. The mouth is the ultimate interface with our environment, as we coo and cry, sing and swear, laugh and lift people with our words. Our teeth and saliva begin digestion, through mechanical and chemical breakdown and wetting of the solid food into a parcel, a bolus ready to swallow.

From there we take a trip down the palate to the common opening, the pharynx, the entrance to the respiratory and digestive tracts. The pharynx is joined by the sinuses from above (superiorly), and below (inferiorly) into the trachea and lungs at the front (anterior) and behind (posteriorly) emerges our gullet, the oesophagus, en route to the stomach.

The stomach, when empty, is roughly the size of a fist. It is a hollow, muscular bag, full of hydrochloric acid, ever compliant, ever ready to receive the next meal. It churns and breaks down protein. It serves as a reservoir for what we have eaten and helps to prepare the intestine to extract all the consumed nutrients.

The stomach propels the food into the first part of the small bowel, the duodenum, named for its length of 12 Roman fingers. The bolus is turned into chyme as it is met with a blast of digestive juices and detergents from the pancreas and biliary system, enhanced by a kick from the gallbladder.

The internal surface of the small intestine is massively undulating, folded and folded, with tiny villi that stand and wave in the fluid, massively expanding the surface area of the small intestine for absorption.

From the duodenum the food is slowly propelled to the second part of the small intestine, the jejunum, so named for its empty lumen when opened at early autopsies, jejune nature. Then on further to the ileum, (from the Gk eilos, twisted) the last third of the small intestine that meets the large bowel in the right, lower part of our abdomen.

The digesting food, still termed chyme, has had many of its nutrients extracted and absorbed into our bodies, into the blood to be transported through the liver and then to the rest of our body. Some resistant molecules including specific proteins and carbohydrates, however, make their way into the first part of the large intestine or colon, which is called the caecum (Gk for blind end), a short cul-de-sac of the large bowel.

From the caecum emerges the vermiform appendix, or just appendix, (Ln: worm-like appendage), a beautifully apt name. The first part of the colon is large and slow moving and is the bioreactor of the bowel, like a brewery or a bakery, the vat of microbial activity producing something better and worthwhile. Here, the residual carbohydrates and proteins are fermented by immense colonies of microbes. Fermentation is a fabulous way to extract final nutrients out of macromolecules and is an essential feature of the mammalian colon.

But, as with beer or Champagne, fermentation produces bubbles and gases. These gases include carbon monoxide (farts are a greenhouse gas), hydrogen sulphide (providing flatulence with its characteristic, rotten-egg base notes) and hydrogen and methane (giving teenage boys their amazing combustibility). It is this first part of the colon that is responsible for so much health but, on occasion, can cause significant abdominal bloating and other symptoms within our community.

From the caecum to the ascending colon (passing up, under your right ribs), across (transverse colon) to the left and down (descending colon), and then the s-bend of the sigmoid, from the shape of the Greek letter for S, sigma, and the last section of the large bowel called, for its straightness, the rectum. The rectum is an “intelligent” organ, of great importance and of value in social evolution.

The final region, perhaps the bookends to our lips, although of a different nature, is the skin covered, circular muscles of the anus, that aid continence. That was the quick fly through, with details to follow in subsequent blogs.

I, the bowel, have captured the imagination of patients and the population at large. I am listened to, worried about, felt, examined, tested, and studied. I am, admittedly, susceptible to common and serious pathology, I am influenced intimately by the brain, and I must contend with a fabulously filthy environment.

I exist, cheek by jowl with an armada of organisms, sometimes allies but occasionally hostiles. I am the topic of much speculation and gossip, fortunately, there is only one thing in the world worse than being talked about. In modern times, we marvel at our intestinal intelligence and ingenuity, as we identify infections, and inflammation, we send cameras into our innermost recesses to take movies of me, we sequence the genetic communities and manipulate the microorganisms housed within, and we are proud of the molecular, endoscopic, surgical, medical and radiotherapeutic approaches to investigate, treat, and understand my inner workings.

Fundamentally, however, I know that the clinicians and scientists that study me, that seriously study me, are humbled by what is still to learn about the digestive diseases that can best their clinical skills and plague their patients. From irritable bowel syndrome to inflammatory bowel disease, from cancer to constipation, I serve as a bowel-shaped barometer for both health and disease.

In this autobowelography blog, every month we shall, in an orderly fashion travel together north to south, mouth to anus, nutrient to waste, cranial to caudal, plate to toilet bowl. We will examine and explain what is normal, we shall deal with nutrition, the microbiome, health and well-being. We will address important bowel symptoms and discuss important digestive diseases, including irritable bowel syndrome, infection, inflammatory bowel disease and, of course, digestive cancers.

I will, where possible, draw on the knowledge from other experts in colorectal surgery, microbiology, genetics, dietetics, endocrinology and digestive science. There is also much that will not be covered at all in my memoir and there is even more that is covered only with regretful superficiality. But please contact us at Colonoscopy Clinic if there is something that you wish for us to address.

When describing the indivisible nature of society, John Donne used our bowels as a metaphor for shared suffering, “this affliction may lie in his bowels, as gold in a mine…but this bell, that tells me of his affliction, digs out and applies that gold to me”.

In the next blogs I hope that we may mine this gold together with, I trust, little shared suffering, to render natural and normal that which seems strange and stercoraceous, to reveal the inherent brilliance of me, your bowel, and how we might better understand ourselves, our friends, avoid suffering and live healthier lives together.

Please help us to refine our planned list of future blog topics by contacting us 

In the series...

Section I: Know thyself

Blog 1. Introduction
Blog 2. Mouth, oesophagus, and stomach
Blog 3. Small intestine (coming soon)
Blog 4. Colon and appendix(coming soon)
Blog 5. Rectum and anus(coming soon)

Section II: Nothing to excess

Blog 6. Microbiome(coming soon)
Blog 7. Gut health(coming soon)

Section III: Surety brings ruin

Blog 8. Diseases of the upper me (gastrointestinal tract)(coming soon)
Blog 9. Colorectal cancer(coming soon)
Blog 10. Irritable bowel syndrome (IBS)(coming soon)
Blog 11. Inflammation: infections, coeliac disease and inflammatory bowel disease (IBD)(coming soon)

Section IV: Entrails

Blog 12. The future(coming soon)

Section V: Poo-st scriptum

Blog Poo & A. Questions, complaints, answers, and solutions(coming soon)

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