—Or, “The Alimentary Adventures of Ham & Swiss on Rye”

Ham and Swiss on rye is, well, one of the best things ever.

So we’ll use this sandwich to track the digestive system. In this digestive adventure, the sandwich will be our hero.

In this article, we’ll track a ham and Swiss on rye sandwich through the digestive tract, with a focus on the key macronutrients: carbohydrate, protein, and fat.

Warning: This post is a work-in-progress. I’ll continue to update it weekly, but for now, please excuse the mess.

A 30-second tour of the digestive system (aka the alimentary canal or GI tract)

Before we dive into more advanced stuff like hormones and neurotransmitters, let’s take a quick look at the organs involved in the digestive process.

In order, they are:

  • Mouth
  • Pharynx (throat)
  • Esophagus
  • Small intestine
  • Large intestine (colon)
  • Rectum
  • Anus

Food travels through each of those. However, there are three other organs which play supporting roles in the digestive system:

  • Liver
  • Gallbladder
  • Pancreas

Let’s review each organ, its location, and its function.


When you bite into that delicious sandwich, your body begins to digest the food in two ways.

The first is by chewing, though the technical term for this is mastication. Chewing simply breaks down the food into smaller, more manageable chunks so it can later be absorbed. This process is called mechanical digestion, since there are no chemical processes at play. Chewing is, by far, the most pleasurable part of the digestive process.

The second is through several enzymes—most notably salivary amylase and lipase—which break down different nutrients through chemical digestion. For example, salivary amylase breaks down carbohydrates; if you’ve ever let a piece of bread or cracker sit on your tongue, you’ll have felt the sensation of it being broken down without chewing. That’s salivary amylase at work. But it only works so far: only about 20% of digestion of carbohydrates can be done in your mouth (and that assumes you actually chew slowly instead of wolfing it down). Lipase does the same thing for fat, but to a much lesser degree. We’ll discuss enzymes later as we get deeper into the digestive tract.

Once food has been broken down in your mouth, it is called the bolus—which refers to partially chewed food until it reaches the stomach (more on that in a second).

Key point: Your mouth breaks down food in two ways. Mechanical digestion is done by chewing; chemical digestion is done by enzymes.

Pharynx (throat)

After chewing up that sandwich, you swallow. A funny thing about swallowing—and I promise to keep this PG—is that it is both a voluntary and involuntary act. While you voluntarily pass bolus to your pharynx, the act of swallowing is in fact involuntary. (That’s why we are able to swallow while sleeping.)


Bolus travels down through the esophagus. During this time, a series of wavelike contractions—called peristalsis—moves the bolus into the stomach.


Once the bolus reaches the stomach, gastrin is released. Gastrin is a hormone that does two things.

  1. Increases stomach motility. (This is a fancy term for “get the stomach moving.”)
  2. Releases hydrochloric acid into the stomach.

Hydrochloric acid’s main role is to break down food into smaller, soluble amounts. Once this happens, the bolus is no more; the newly formed semi-gelatinous ooze is now called chyme (pronounced kime).

(In addition to hydrochloric acid, proteins are broken down through a stomach enzyme called pepsin.)

Our stomach acids are no joke. They are highly acidic—roughly the same acidity as battery acid. It’s so strong, in fact, that it can burn your skin. So it’s a good thing our stomach doesn’t (usually) leak!

From the mouth to the stomach, our bodies are focused on breaking down foodstuffs, with minimal absorption of nutrients. (That happens in the small intestine.)

Now the chyme moves on to the small intestine through the pyloric sphincter.

Small intestine

Unlike the stomach—which mainly digests food—the small intestine is mainly responsible for absorbing nutrients, which are then passed on to the liver for processing, and then into the bloodstream (which is also known as systemic, or general circulation).

The small intestine is further broken down into three segments:

  • Duodenum (pronounced “doo – ah – duh -num” or “doo – oh – dee – um”));
  • Jejunum (pronounced “juh – joo – num”); and
  • Ileum (pronounced “il – e – um”)

Most of the digestive hormones live in the duodenum.

Until now, your body has focused on breaking down food; now, it’s time to start absorbing the nutrients.

But first, we need to put out the fire. Remember the hydrochloric acid that was released in the stomach? The stuff that has the same acidity as battery acid? Well, that bubbling cauldron is fine in the stomach—but anywhere else it’s a problem.

So how does the small intestine deal with this fire? Simple. The hormone secretin calls on the pancreas and bile ducts to help. The pancreas—which we’ll cover in a moment—releases a flood of bicarbonate, which neutralizes the hydrochloric acid and allows the small intestine to do its thing. Think of secretin as a firefighter; when there’s a fire (in this case, stomach acid) the firefighter appears and extinguishes the fire using bicarbonate.

Put another way: while a firefighter puts out fires with water; secretin neutralizes acidity with bicarbonate.

In addition to secretin, the small intestine has other several hormones; cholecystokinin, gastric inhibitory polypeptide, and motilin.

Cholecystokinin (CCK) works alongside secretin. It is released in response to fat in the chyme and tells the liver to release bile, which is responsible for emulsification. Bile is like vinegar in a salad dressing: it mixes with oil (or in this case, the fat) to create an emulsification. In doing so, the fat clumps together, which increases the surface area of fat for enzymes (called lipases) to break down.

Gastric inhibitory polypeptide (GIP) tells the stomach to stop producing hydrochloric acid. That’s where it gets its name; however, GIP does a lot more than that. It also increases insulin production (more on insulin later) and inhibits the absorption of water and electrolytes in the small intestine; the water and electrolytes are later absorbed in the large intestine.

Motilin increases gastric (stomach) and intestinal motility which helps chyme moves through the large intestine. Put another way: motilin keeps things moving.

As you can see, the small intestine is vital to digestion. It is the first part of the GI tract that primarily absorbs nutrients into the bloodstream. What is left over—primarily water, electrolytes, acids, and gases—is passed on to the large intestine.

Large intestine

Colon illustration lg

Chyme travels from the small intestine to the large intestine through another ring-like sphincter called the ileocecal valve. (As you’ll recall, there are sphincters throughout the GI tract: the lower-esophageal sphincter connects the esophagus to the stomach, and the pyloric sphincter connects the stomach to the small intestine.)

The large intestine is, unsurprisingly, larger than the small intestine. But it’s much shorter than the small intestine: only about five to seven feet (compared to the small intestine, which can measure more than sixteen feet!).

The large intestine is made up of four parts:

  1. The cecum receives food from the small intestine. It’s primarily responsible for absorbing electrolytes and water.
  2. The colon also absorbs electrolytes and any leftover water. There are four parts to the colon—the ascending colon, transverse colon, descending colon, and sigmoid colon—which form a U-turn from the body’s left side to its right (using the anatomical view; see picture above). As you may have noticed, the colon is a part of the large intestine; they’re not the same. You can use this bit of trivia at your next dinner party—your friends will love you for it.
  3. The rectum stores the leftovers. Unlike the colon, the rectum does not absorb any nutrients; they are strictly a storage facility. Because all nutrients have been absorbed, the chyme becomes stool.
  4. The anus excretes stool. Like all the other organ junctions, there’s a sphincter: the anal sphincter.

And there you have it, folks. The digestive tract from end-to-end.

But wait! We haven’t covered the pancreas, gallbladder, and—perhaps the most important of all—the liver.


The liver is, quite frankly, a badass.

Think of the liver as a bouncer. It reviews all nutrients your body has absorbed and decides whether to let them into your blood (called general circulation) or to further process it.

Not only that, the liver can also build up or break down nutrients as they come in. It can choose to store nutrients like carbs and fats (more on this later), break down them down for energy, or strip certain nutrients like protein for further processing.

In addition to its bouncing duties, the liver also secretes bile, which is stored in the gallbladder. Bile is a wonderful substance: it emulsifies fats so your body can digest them properly, eliminates old red blood cells, and detoxifies toxins before they enter your bloodstream. It’s kinda cool looking, too.

Oh, the liver also synthesizes cholesterol, converts toxic ammonia into urea, regulates blood clotting, makes immune cells, removes pathogens, stores blood, makes ketones when carbs are unavailable… and many, many, more things.

But what makes the liver uniquely badass is its ability to regenerate. (No other organ can do this.) A liver can regrow to a normal size even after up to 90% of it has been removed!




There are three macronutrients, or “macros” for short: protein, carbohydrate, and fat.

  • Ham = protein
  • Rye bread = carbohydrate
  • Swiss cheese = fat

Of course, each of those foods contain a blend of macros—for example, Swiss cheese has both fat and protein—but for the sake of simplicity, we’ll just use each food as one macro.

Each macro is made up of a smaller unit.

  • Proteins are made up of amino acids.
  • Carbohydrates are made up of monosaccharides, with the main one being glucose. (More on this in a second.)
  • Fats are made up of fatty acids.

Let’s take a look at each.

Carbohydrate metabolism

First, we have monosaccharides (Latin for “one sugar”). The three are glucose, fructose, and galactose.

Carbohydrates are made up of saccharides (from the Latin for “sugar”). A complex carbohydrate has more saccharides are called polysaccharides (Latin for “many sugar”).

Oligosaccharides have some saccharides. The most frequent are disaccharides.

So what happens to our rye bread?

  1. In the mouth, salivary amylases break down the polys into smaller units.
  2. In the small intestine, pancreatic amylases break them down into maltose disaccharides.
  3. The maltose is broken down by the enzyme maltase, which yields two units of glucose.
  4. The glucose enters the body to be used for energy now, or to be stored for energy later as glycogen.

In addition, there are three types of polysaccharides:

  • Fiber (indigestible; contains cellulose)
  • Starch (exclusively glucose)
  • Sugar (aka “sucrose”; equal parts glucose and fructose)

Disaccharides are made from a blend of monosaccharides. See below:

  • Maltose = glucose + glucose
  • Sucrose = glucose + fructose
  • Lactose = galactose + glucose

Each disaccharide is hydrolyzed by a familiar-sounding enzyme. Thus, maltose is broken down by maltase, sucrose by sucrase, and lactose by lactase. Pretty simple, right?

Hormones and neurotransmitters in the digestive system—in order of appearance

I couldn’t find an order of which hormones and neurotransmitters occur where and when in the digestive process, so I pieced the following together myself. (This may or may not be correct.)

  • Ghrelin is a hunger hormone that is released when you’re not eating enough. It stimulates appetite and the release of growth hormone.
  • Gastrin (stomach). Produces gastric juice. Protein-rich foods tend to stimulate the most gastrin release.
  • When hydrocholoric acid and pepsinogen are released in the stomach, the lower esophageal sphincter closes, peristalsis increases, the gallbladder contracts (to send bile to the small intestine), and the pancreas releases bicarbonate.
  • Secretin (small intestine). Calls for bile and bicarbonate to neutralize acid. It inhibits gastrin. Released in response to hydrochloric acid.
  • Cholecystokinin (CCK) asks the gallbladder to contract and release bile for emulsification of fats. It is released at the same time as secretin. Released in response to fat.
  • Motilin (small intestine). Released when bicarbonate is dumped into the small intestine to neutralize stomach acid.
  • Vasoactive intestinal peptide (VIP) slows down stomach activity while stimulating intestinal activity.
  • Gastric inhibitory peptide (GIP). Small intestine. Decreases stomach churning to slow the stomach from emptying; stimulates insulin release; reduces gastric and intestinal motility; increases fluid and electrolyte secretion.
  • Serotonin increases small intestinal motility and decreases the production of stomach acid.
  • Once food (primarily fat) hits the end of the small intestine, neurotensin relaxes the lower esophageal sphincter, stops the production of stomach acid and peptin, and regulates motility. In other words, it closes up shop.
  • Somatostatin: a hormone that inhibits the secretion of hormones—including glucagon, insulin, and gastrin.
  • Peptide YY is released hours after eating. It inhibits stomach motility and tells the colon to absorb water and electrolytes (sodium and potassium).
  • Acetylcholine is a “rest and digest” neurotransmitter that uses muscle contractions to move food through the GI.
  • Overall, it takes about 4–8 hours for chyme to travel through the small intestine. It takes 12–25 hours to travel through the colon (large intestine) and out the anus.
  • Useful video:
  • Wikipedia

Below is a table that summarizes the hormones and neurotransmitters.

GastrinStomachRelease acid
GIPDuodenumInhibit gastrin
MotilinBicarbonate enters duodenumMove chyme through intestines
Peptide YY
EpinephrineFasting and/or exerciseInhibit glycogen synthase

Increase glycogen phosphorylase
NorepinephrineFasting and/or exerciseInhibit glycogen synthase

Increase glycogen phosphorylase
Glycogen synthase (enzyme, not a hormone!)Turns glucose to glycogen
Glycogen phosphorylase enzymeBreaks glucose off glycogen chain
InsulinGlucose in bloodstreamStores extra glucose in muscle and liver; also up-regulates glycogen synthase hormone
NeurotensinWhen chyme enters the ileumRelax the lower esophageal sphincter

Stop production of stomach acid and bicarbonate
Neuropeptide Y

Glucagon and epinephrine both break down stored glycogen (a process called glycogenolysis)

A table of hormones (and enzymes) and how they affect each other

Hormones, like people, can turn each other on.

Or off.

For example, insulin down-regulates growth hormone while up-regulating glycogen synthase.

Because of these relationships, I find it useful to think of hormones as “switches” that can be turned on or off. These switches are affected by other hormones.

Below is a table summarizing the relationships between hormones.

Hormone 1Hormone/enzyme 2
Somatostatininhibits glucagon, insulin, and gastrin
Secretininhibits gastrin
CCKinhibits gastrin
Insulinactivates lipoprotein lipase
Glucagonactivates hormone sensitive lipase
Epinephrine and norepinephrine inhibits glycogen synthase

Cellular respiration

The purpose of cellular respiration is to convert glucose—found predominantly in carbohydrates—into ATP.

But it’s not that simple. (Of course it isn’t. Nutrition is fucking hard!)

You see, there are three parts to cellular respiration:

  • Glycolysis (also called the glycolytic pathway)
  • The Krebs Cycle (or Citric Acid Cycle)
  • Oxidative phosphorylation

Let’s start with glycolysis. It literally means “The splitting of glucose.” Glycolysis happens in the cytoplasm and is anaerobic. This process breaks down glucose in three ways: glucose in the bloodstream, stored glycogen, and glycerol (which was broken from a triglyceride).

In a nutshell, glycolysis converts glucose to pyruvate.

Between glycolysis and the Krebs cycle lies the transition reaction. This is where the pyruvate from glycolysis is converted to acetyl-CoA, which is the starting point for the Krebs cycle.

Transition reaction = Pyruvate (3 carbons) → acetyl-CoA (2 carbons) + CO2 + NADH.

Remember that each glucose molecule contains six carbons; therefore, each glucose molecule produces two molecules of pyruvate, which is then converted into two acetyl-CoA, two CO2, and two NADH.

Glucose → 2 pyruvate → 2 acetyl-CoA + 2 CO2 + 2 NADH

Riveting, right?

Now, you may be wondering what NADH is. This is when NAD+—which acts as a hydrogen buffer—gains a hydrogen molecule and becomes NADH. (Hence the “H” in NADH.)

In order for glycolysis to continue, the NADH must give up its hydrogen. This is done in one of two ways: either the hydrogen is passed on to the Krebs cycle, or it is combined with pyruvate to form lactic acid. In either case, the NADH recycles back to NAD+ and glycolysis continues.

Keep in mind, however, that while glycolysis continues, it can only go so fast. It’s like a particular gear on a bicycle: no matter how hard you peddle, you can only go so fast before you need to switch gears. So, glycolysis hums along, producing 2 ATP with each cycle, but at some point, you’re going to need to switch gears.

The next gear is the Krebs cycle.

Now, let’s move on to the Krebs cycle. The pyruvate created during glycolysis turns into acetyl-CoA, which is the starting ingredient for the Krebs cycle.

The Krebs cycle consumes acetate (in the form of acetyl-CoA) and water, reduces NAD+ to NADH, and produces carbon dioxide.

What happens if you don’t eat carbs?

Your body adapts. Here’s how: Your body converts fatty acids into acetyl-CoA via process called beta oxidation. During beta oxidation, two carbons are sliced off the end of a long fatty acid. These carbons become acetyl-CoA.

Beta oxidation is all fine and dandy, mind you, but it creates a problem: the acetyl-CoA begins to build up. (Nerd alert: this is because there isn’t enough oxaloacetate to move the acetyl-CoA to the Krebs cycle.) As the acetyl-CoA builds up, your liver—that glorious superhero of the digestive system—converts the acetyl-CoA into ketone bodies.

Key point: The fatty acid synthase system adds two carbon units to a fatty acid chain. Beta oxidation removes two carbon units.

Oxidative phosphorylation

Takes acetyl-CoA and converts it into ATP. There are two parts of this: the Krebs cycle (also known as the Citric Acid cycle) and the electron transport chain. (Is that not the coolest name?)

This energy pathway uses acetyl-CoA—which was produced either from glycolysis (glucose/glycerol) or beta-oxidation (fatty acids)—to produce ATP.

How much ATP? The Krebs cycle produces two ATP, same as glycolysis.

But the election transport chain? While the exact number differs, but it’s somewhere in the neighborhood of a whopping 32 ATP. That’s huge!

Protein metabolism

First, amino acids have their nitrogen removed (in a process called deamination).

Once the nitrogen has been stripped, amino acids are used for either non-protein products (e.g. glucose via gluconeogenesis, which is Greek for “make new glucose”) or its carbon skeleton (also called α-keto acid, which is pronounced “alpha”) is used in either glucose or fatty acid metabolic pathways.

Resistant starch

  • Resistant starch isn’t digested by humans, but it plays an important role in health. When these starches reach the colon, they provide food for bacteria, who convert the starch into short chain fatty acids (SCFAs). These SCFAs are either absorbed by our bodies or used to feed our bacteria. (This is a good thing!)
  • Speaking of good things, here are the benefits of SCFAs in the colon
    • Benefit
  • Long story short: if you eat enough resistant starch, you have enough SCFAs—which leads to improved health.
  • Bob’s Red Mill Potato Starch is an easy way to get more resistant starch. 1 tablespoon = 8 grams of resistant starch. Remember: you must eat it cold! Resistant starch breaks down when heated (but you can always chill it after cooking). For example, you can cook potatoes or rice, then cool them in the fridge before eating.
  • Green bananas are also a great source of resistant starch. While they taste gummy on their own, you can blend them in a smoothie.
  • If you’re in ketosis, don’t fret: since resistant starch is not raise blood sugar levels, it will not kick you out of ketosis.

Lipolysis (“splitting fat”)

Lipolysis occurs when you break a triglyceride into a glycerol and its fatty acids.

Lipolysis = Triglyceride → Glycerol + Fatty acids

Triglycerides don’t enter our cells very well. Therefore, they are broken down through lipolysis so the glycerol and fatty acids can pass the plasma membranes and enter the cell. Once inside, they are put back together as triglycerides.

Ketosis for smart people

Although the “keto diet” has become popular, it’s not widely understood by most people.

In short, the purpose of a keto “diet”—and I loathe to call it a diet—is to restrict carbohydrate intake below ~50g/day. Once below this level, your body begins to produce ketone bodies and you’re said to be in ketosis.

I certainly enjoy being in ketosis. I began experimenting with it in 2016 while training for a 50-mile ultramarathon. Ketosis’s appeal for long-distance runners is simple: by reducing carbs, you increase ketones, and can run farther without running out of glucose. While training for the ultra, I routinely ran trail marathons in a fasted state.

Ketosis is a metabolic state. It is a not a diet based on particular macros. Why? Because there are many ways to get into ketosis. For example:

  • Fasting
  • Salads
  • Carnivore

Not sure if this is correct (from Gundry/Tom podcast) 30% of calories in goat and sheep cheese is MCT. (Cows do not produce MCT.) This helps uncouple mitochondria—meaning the mitochondria produces heat rather than ATP, which can be a sign of metabolic flexibility and longevity. This may be a contributing factor in the Blue Zones, where many people are sheep and goat herders.

Position stands—a short-cut to find reputable, evidence-based advice from leading experts

Search for “position stands” from reputable organizations. You’ll get a brief summary of their stand on a wide variety of issues. This is really helpful for getting a high-level view of a subject. For example, here’s the International Society of Sports Nutrition position stand on protein intake on exercise. And here’s a list of all the position stands from the ACSM. (You can search online for any organization’s position stands pretty easily.)

How to build muscle

  • You must be in a caloric surplus
  • Eat up to 1g/lb protein bodyweight
  • Train every body part twice a week
  • Get at least 10–20 sets per week per body part
  • 5 reps at heavy will get you as strong as 10–12 reps at moderate and 20 reps with light. This assumes you train close to failure. (1–2 reps shy of failure.) Variety is good, but the bulk of your training should be between 8–15 reps. This is the sweet spot that allows you to get more reps in without too much fatigue.
  • Rest between 90 seconds and three minutes.

A list of foods high in fiber (and relatively low in carbs)

What will will likely kill you—and how to avoid it

Below is a list of what kills the most people in the U.S. (and likely most developed nations):


Aim for 500mL of water 30 minutes before exercising, and 250mL for every 15 minutes of exercise. Sure, this is all well and good, but I used to run trail marathons in a fasted state with no water and felt fine. Then again, I was probably being dumb.

Over-hydration can be a problem. In his book Natural Born Heroes, Chris McDougall points out that while long-distance runners die occasionally from over-hydrating, no one ever died from dehydration.

My take? Drink a bit more than you think you need ahead of time. Then sip occasionally.


  • Protein supplements. Be sure to look for ones that are NSF Certified for Sport. Here’s a link.

A 20-minute walk after eating will reduce your post-prandial glycemia by up to 30%. To put that into perspective, that’s twice as effective as metformin, the most widely prescribed medicine for blood sugar control.