Pitiable, abused, misunderstood.

We suffer from the illusion that we are its master.  Yet, it is a marvelous synchrony of thousands, if not billions of moving parts, most of which have never been under our conscious control.  We need it to survive, but treat it with recklessness and neglect.

Hold on to your seats.  We’re going on a little journey.  My hope is that when we reach the end, you’ll give digestion the reverence it so deserves.


We’ll begin in an unlikely place.  A place that can be dark and dreary, chaotic and mercurial.  Ideally, however, when we’re embarking on our digestive safari, it’s gentle and still.  This place, our launching pad, is the brain.  It is the Central Command of our autonomic nervous system {ANS}, a part of our peripheral nervous system comprised of sections of the brain stem, the limbic system, and a complex network of nerves and endocrine glands.  It controls our “fight or flight” response via regulation of respiratory and heart rates, digestion, salivation, perspiration, pupillary dilation, urination, and sexual arousal.  The two divisions of the ANS are the sympathetic and parasympathetic systems.  The parasympathetic system allows us to “rest and repose”, giving us the chance to eat and make babies.  The sympathetic system gets you the h-e-double L out of Dodge.  It shuts down or minimizes all functions that it sees as superfluous, not essential to life at that very moment {READ: DIGESTION}.

The bottom line- If we want to be able to digest our food, we need to get the message across to our brains that we’re not fleeing from a saber-toothed tiger or a week past that project deadline {because to your brain, there is no difference}.  Sit down, take a load off.  Breathe deeply.  Transition from whatever that really important thing was that you were just doing to, um, NOT DOING IT.


Now that we’ve settled into our lovely, pro-digestive parasympathetic state, it’s into the mouth and down the hatch.  This is a fairly simple step, but mustn’t be overlooked or underemployed.  The key here is in the C-H-E-W.  Food is broken down mechanically by a process called mastication.  This also allows for proper mixing with saliva, a digestive elixir containing amylase {to begin the breakdown of more complex carbohydrates into simpler ones} and lipase {to begin the breakdown of fats}.  It also contains antimicrobial agents, such as secretory IgA, and a pain-killing substance known as opiorphin.  From the point that this bite of our lunch has been broken down by the efforts of our teeth and jaws, and doused appropriately with saliva, we will refer to it as a bolus.  Let’s grab our bolus and it’s down the rabbit hole we go.


A gentle, rhythmic push from the muscles in your esophagus {called a peristaltic wave} pushes the bolus down the tube and through the sphincter controlling entry of materials into the stomach.  This is called the cardiac or lower esophageal sphincter.


Now we’re talkin’, Macaulay Culkin.  Let’s get down to brass tacks.  The stomach continues peristaltic movements, churning, grinding, and mixing our unsuspecting bolus.  Oh, but it’s so much more complex than that.  Stay with me here… Stretching of muscle fibers of the stomach {as well as the presence of partially digested proteins, or polypeptides- this is important.  I’ll tell you why in a minute} stimulate G cells of the stomach to secrete a hormone called gastrin, which in turn signals parietal cells to begin pumping out hydrochloric acid {HCL}.  After the bolus has been sufficiently “acidized” by HCL, G cells will cease gastrin release, effectively shutting down HCL production via negative feedback loop.

Here’s where the polypeptides come into play- Contrary to popular belief, HCL itself doesn’t do much in the way of breaking down food.  Rather, it serves as a disinfectant, killing any microorganisms that may have piggybacked in on our cheeseburger, and provides a specific pH and temperature, optimal for the function of particular enzymes.  Each macro nutrient that we may ingest requires specific enzymes to be digested, therefore a specific pH.  Carbohydrates require a fairly neutral pH.  Proteins require the lowest {or most acidic} pH.  Gastrin production will be “turned on” for longer when polypeptides are sensed in order to get that pH nice and low {I told you those polypeptides would be important, didn’t I?}.  Ever wonder why your dog can eat a piece of raw meat without batting an eyelash?  Read: Car. Niv. Ore.  SUPER acidic stomach.

Gastrin also stimulates the release of histamine from enterochromaffin-like cells.  Histamine and gastrin production are the major factors that increase HCL production.  Gastrin also kicks the stomach’s chief cells into action, to release pepsinogen.  This is the “storage” form of pepsin, an enzyme that breaks food proteins down into polypeptides {long chains of amino acids} and peptides {short chains of amino acids}.  If our bodies hadn’t possessed the innate wisdom to store this enzyme in its more innocent form, we would have all digested ourselves long ago.  Yum.  As pepsinogen comes into contact with HCL , or more specifically, that ever-important low pH {pH 1.5-3.0} it is able to transform itself into its active form- that workhorse, pepsin.  Let’s sit back and enjoy the fireworks as those proteins go kuh-bloo-ey.

The one crucial substance that we haven’t yet mentioned, which is produced {by parietal cells, along with HCL} is termed intrinsic factor.  It is a glycoprotein {a molecule made of amino acids and carbohydrates} that binds with vitamin B12 in the less acidic environment of the small intestines.  This happy couple can then travel the circuitous path of the small intestines to be absorbed in the ileum, its final portion.

Some very small molecules, such as alcohol are absorbed right here in the stomach, but everything else has now been rendered a mass of highly acidic, half-digested glop.  In science, we love to name things like this.  This particular pile of glop is called chyme and it’s ready for some action in the small intestines.  The “gateway” from the stomach into the first part of the small intestines {called the duodenum} is a tight band of muscle known as the pyloric sphincter.  Relaxing of this tight ring of muscle is triggered by distention in the stomach and that all-star gastrin, now pulsing through our veins.  The pyloric sphincter, or pylorus, doesn’t simply open like a dump truck, however, discarding all of its contents into the intestines.  This would overwhelm the capabilities of our digestive system.  Instead the far end of the stomach, adjacent to the pylorus {called the pyloric region. duh.} is used as a kind of antechamber.  It holds roughly 3 mL of chyme and uses those handy peristaltic-type muscle contractions to mini-squirt its contents into the duodenum.

I’d like to take a commercial break here to note that the body, has an order to the exodus that is occurring from the stomach.  It goes in order from the “lightest” nutrients to the “heaviest”, starting with carbohydrates, proteins exiting midway through the process, fats bringing up the rear.



The presence of this corrosive chyme in the duodenum sets another chain of events into action.  First, it causes the pylorus to tighten, essentially telling it and the stomach to “Hold the phone.  I’m a tiddly bit busy at the moment.”  It puts down that phone and immediately places a call to the local fire station,which happens to be the pancreas.  The hormone it uses to place this call is secretin.  In response, the pancreas sends its best men {and women} for the job, pancreatic juices, in through the duodenum’s VIP entrance, otherwise known as the common bile duct.  We’ll talk about those pancreatic juices in a second, but first let me throw a few more morsels about secretin out there… Since it’s sent through the blood stream, it’s tentacles can reach further throughout the body.  It slows down the production of gastrin in the stomach, turning down the production of HCL, allowing the pH level of the stomach to begin to climb {becoming less acidic}.  It also ramps up the production of pepsin, so while the “heavier” nutrients {fats and proteins} hang out in the waiting room of the stomach, they can make themselves useful by being digested.  This segmented release of nutrients highlights why it is best to combine all 3 at mealtimes.  Carbohydrates provide your muscles and brain with immediate energy, while proteins and fats provide a sense of satiety and longer-burning fuel.

Now, back to those pancreatic juices.  First things first… Someone needs to put the stinking fire out.  Chyme, meet pancreatic bicarbonate.  Acidic chyme + alkaline bicarbonate = Relief to duodenum {a pH of 6.0-7.0}.  With the pH now closer to neutral, the other pancreatic superheroes can get to work.  Pancreatic Superheroes?  Who are these masked avengers?  They are a series of heavy-hitting digestive enzymes- proteases {protein digestors}, lipases {fat digestors}, and amylase {a carbohydrate digestor}.  The amylase, however is only capable of breaking carbohydrates down into di- and trisaccharides, not the monosaccharide form required for absorption.  Hang in there.  You’ll see what happens to the rest of the carbohydrates in a minute.

Another duodenal event that will keep us on the edge of our seats is is the secretion of a hormone called cholecystokinin {CCK}.  This is triggered when the presence of fatty and/or amino acids are detected in the area.  It stimulates the pancreas to keep on keepin’ on with it’s juicing and makes the gallbladder aware that the time to release all of that delicious yellow-green bile is NOW.  Bile is produced in the liver and is a witches brew of water, bile salts, mucus, pigments, fats, and other inorganic salts.   Bile salts are concocted in a complex process that involves conjugation of cholesterol that is produced in the body, amino acids, and a cation {an ion with a positive charge}- usually sodium.  Bile helps to emulsify the fats hanging around in the chyme, like grabbing a big bottle of Dawn dish soap.  This breaks up the crowds that fats like to hang around in, so that they can be worked on more efficiently by pancreatic lipase.

In order for fats to be absorbed into our bodies so that we can make use of fat soluble vitamins and beneficial fatty acids, they must be broken down into very small components {fatty acids and glycerol} and then reassembled after absorption into the blood or lymphatic system {Short and medium chain fatty acids into capillaries, long chain fatty acids into the lymphatic system}.  Undigested or partially digested fats are excreted down the road, in the south end of the process, without absorption of any of the good stuff.  When chyme leaves the duodenum, it is almost completely digested.

The Yellow Brick Road of the small intestines is paved with small, finger-like projections called villi, which are in turn covered with more even SMALLER finger-like projections.  Think: Sea anemone covered in tiny sea anemones.  These tiny anemones are called micro-villi {three cheers for originality, scientists}, also referred to as the brush border, and they are where the magic happens.  Their unique configuration is meant to maximize surface area, giving those final stages of digestion and the bulk of absorption the most bang for it’s limited spatial buck.

The brush border is covered with numerous digestive enzymes, such as sucrase, lactase, and maltase.  This is the answer to the question on everyone’s minds, “What happens to the carbohydrates that salivary and pancreatic amylase couldn’t deal with?”.  Remember that pancreatic enzyme action that got us to the di- and trisaccharide stage?  These brush border enzymes will take most of those loafers and put them in their place, as useful, absorbable monosaccharides.  I say most because there’s this: We can’t digest cellulose.  It is the carbohydrate chain within plant materials that give them their structure, otherwise known as fiber, or things that make you go poo.


The anatomical configuration of the small intestines goes something like this- duodenum, jejunum, ileum.  Those trusty old peristaltic waves {or peristalsis} move the chyme from section to section.  The duodenum, which we’ve just spent the past hour discussing, is the first segment, 10-15 inches in length.  It is the primary site of iron absorption.  Next in line is the jejunum.  This is the bulk of the small intestines, about 8 feet long, and is where most nutrients find their way into our system.  Last, but certainly not least, is the ileum.  It is generally a tad shorter than the jejunum and, like the jejunum, has a neutral to slightly alkaline pH {pH 7.0-8.0, though the jejunum can be slightly more alkaline}.  Regarding absorption, the ileum slurps up whatever is available and hasn’t already been grabbed- but its real claim to fame is that its terminal portion is ground zero for vitamin B12 and bile salt absorption.  Each bile salt molecule is reused about 20 times.

The ileum’s other claim to fame is Peyer’s patches {You know know Peyer’s patches, right?  RIGHT?}  There are collections of lymphatic tissue strewn throughout the regular intestinal tissue, but these regions are especially dense in the ileum, containing loads of lymphocytes and other immune system cells.  Ever hear someone say that 80% of your immune system is located in your gut?  If not, it’s true, and this is what they’re referring to.

Now that we’ve made it through the labyrinth of the small intestines, whatever food remains undigested {or only partially digested} or unabsorbed, plus water, sloughed off cells, and leftover bile is passed along to the large intestines, through the guarded portal known as the ileocecal valve.  This sphincter controls forward flow of substances, but more importantly inhibits reverse flow of substances.  Having the contents of your large intestines hanging out in your small intestines does more than just sound disgusting.  That’ll become all too clear in a few seconds.


If the large intestines had to be reduced to one most meaningful feature, that feature would likely be bacteria.  Although bacteria can be found throughout our entire gastrointestinal tract, they exist in varying strains and amounts in different areas.  Whereas the small intestines contain somewhere in the ballpark of 10,000 bacteria per ml of fluid, the large intestines match that with a number in the 1,000,000,000 range.  Small intestinal chump change.  Actually, if bacteria is to be found in the small intestines, it is usually in the duodenum and beginning portion of the jejunum, and is usually aerobic {require oxygen for survival} or at least tolerant of an aerobic environment- usually lactobacilli and enterococci.  Bacterial populations throughout the majority of the jejunum are relatively sparse, if not absent.  In the latter portions of the ileum, we begin to transition to a more bacteria rich environment, specifically rich with anaerobic bacteria {requiring no or very little oxygen}.  Prevention of bacterial growth in the “wrong” areas of the digestive tract is controlled by stomach acid, pH, pancreatic enzymes, intestinal motility, the ileocecal valve, and intestinal immunoglobulins {remember those Peyer’s patches?}.

The names of the game in the large intestines are fermentation, fluid reabsorption, and, to a lesser degree, nutrient absorption.   The bacteria present in the small intestines {known as gut flora} are essential to cashing in on the full nutritional potential of the foods we ingest.  Something that needs to be stressed is that due to one reason or another, even in the most pristinely functioning systems, some food particles will escape complete meltdown by the army of digestive enzymes.  When the bacteria in our large intestines see this coming down the pipeline, they recognize it as an all-you-can-eat-buffet.  While this is an obvious boon for our little hitchhikers, it is actually extremely beneficial to us as well in multiple ways.  I’ll give you a brief list and then explain each in a little more detail.

1.  They keep our intestinal tissue growing and functioning normally.

2.  They break down foods that our bodies are not capable of breaking down.

3.  They provide us with beneficial nutrients.

4.  They crowd out the bad guys.

5.  They metabolize toxins, aiding the detoxification functions of our own bodies.

Let’s open this first point up…  We know that in all animals, the absence {or a deficit of} good bacteria causes those cute little villi to become abnormal, the number  and size of Peyer’s patches and amount of immune cell action decreases, and the mucosal lining of the intestines does not replace itself as rapidly as it should {it usually replaces itself every 3 days}.  In addition to this, without good bacteria, peristaltic waves aren’t quite as spunky, especially those that happen when we’re not actually digesting our food {known as the migrating motor complex}.  These waves help the ileocecal valve to keep large intestinal bacteria where they belong- in the large intestines. Restoring proper bacteria levels brings all of these sad situations back to normal.

Next, the breaking down of nutrients.  When this is done by bacteria rather than enzymes, it is known as fermentation.  Mostly, these little buggers love sugar.  They’ll grab up any of the less complex sugars that you a} overate b} couldn’t digest c} overate and couldn’t digest.  They’ll also metabolize the the more complex sugars that our bodies lack the ability to break down {the ones classified as starches, as well as some found in fruits and vegetables}.  As they digest these substances, they’ll keep some of the good stuff for themselves and pass some along to us- kind of like a rent check.

What they pass along to us gets complicated, as it varies by type of bacteria and nutrients digested, but this is where the third point above comes in.  Complex sugars are broken down into short-chain fatty acids.  These acids affect the pH of our large intestines, provide nutrition for the poorly vascularized cells of our colons, or are absorbed into our bodies for any number of other functions.  Bacteria also produce vitamins, specifically certain B’s and vitamin K.  Byproducts of these processes are gases- things like hydrogen, methane, and hydrogen sulphide.  I don’t think I need to tell you what happens to shady characters.

Point number 4 above speaks for itself.  When the right guys are in abundance, they attach themselves to the walls of our intestines good and hard {called colonization}.  When some not-so-nice fella comes waltzing along, he can’t so easily make himself comfortable.

Number 5 is another complicated one that deserves a future post all of its own, because sometimes it’s a complete lie.  As I’ve pointed out, different bacteria do different things.  Certain bacteria create more toxins for our body to figure out what in the heck to do with, but certain ones {along with yeasts and fungi} actually help to rid our bodies of many of the heavy metals commonly found as environmental pollutants.

Now, let’s keep our eyes on the road… on to the actual structure of the large intestines.  Simply put, it’s the cecum, colon, rectum, and anus.  The cecum cozies up next to the ileocecal valve {and is, incidentally, where the appendix is attached- acting as a sort of nursery for intestinal bacteria}, while the colon is subdivided into segments.  In order, the segments are the ascending, transverse, descending, and sigmoid colon.  The rectum and anus bring up the rear.  It total, it is roughly 5 feet long.

Bacteria act on the remaining chyme, water and remaining minerals are reabsorbed, leaving cellulose and other undigested {or undigestable} materials to collect.  Bilirubin, an unusable component of bile, is metabolized by gut flora to give the material its characteristic brown color.  In this way, feces is formed and stored in the rectum.  When the time is right, the anal sphincter relaxes, and the kids are dropped off at the pool.

Your lunch has just spent between 19 and 24 hours in your digestive tract, has provided you with all of the nutrients you need to flourish, and has neutralized any potential harmful invaders.


Every time I go over this process in my mind, I am blown away by the beautiful and harmonious complexity.  And this is the simplified version.  For every step I just mentioned, there are probably 100 more steps in between on a molecular, cellular, vascular, and neurohormonal level.

The next time you’re about to gulp down that chicken caesar salad while you’re checking your email, or snarf down that sandwich while you’re actually dropping your kids off at the pool… take a moment to think about what your body is about to do.  I think it deserves a few moments of you sitting down, being in just that moment, and savoring that salad.

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