Week 8. Gut Physiology, Nutrient Malabsorption, Cognitive Decline, and More

by | Teacher's Copy

Transition from Week 7:

This recent article in Wise Traditions provided a vehicle for linking week 7’s content to Week 8 and 9 – coherently. Ben Greenfield’s story in the Weston A. Price Quarterly Journal provides insight into the connection between:

(Overtraining – Overfeeding – Stress) <–AND –> (Gut problems – Performance – Hormonal imbalance)

Thus, we transition from exploring overall dietary structure and excessive carb intake to understanding gut problems induced by:

  • exercise, heat, stress in general.
  • intake of certain carbs
  • problems linked with incomplete breakdown of nutrients and/or failure to absorb nutrients properly – in each stage of the digestive tract.
  • the conditional state of gut bacteria in the digestive tract, malabsorption of certain nutrients, and problems from eating the incorrect foods based on conditions of digestive ‘power’.
  • prescription drugs – specifically PPI’s. (Proton Pump Inhibitors, which reduce H+ ion release to make stomach acid:

STOMACH ACID IS: (H+ bonded with Cl-)  –> HCl = Hydrochloric Acid)


Week 8 Overview:

Each student illustrates – by hand – a schematic, which begins as a guided and interactive project using the ‘Blank Template’ provided below. The finished product is the stage by stage progression of focusing on one thing:

– food itself – transforming along the way from into your mouth until it exits as poop.

Just below the blank template section I explain the value of teaching though ‘active engagement from scratch’ under the heading: Why focus only on food – chronologically? (as it transforms stage by stage). 

For those who are curious about what such a thing would look like, here’s a finished schematic somewhat related to the one created in this presentation.

Week 9 Overview:

Connects the dots to create a functional and integrative understanding of the big picture, comprised of these elements:

  • current condition of the entire gut – including bacteria and the cellular ‘physical surface condition’ of the intestines
  • digestive power
  • nutrient malabsorption
  • stress
  • anemia – bone loss – structural cognitive decline
  • other common diseases of the gut.
The Blank Template

If you are in my class you will receive this virtually blank template of the digestive tract below – where your hand fills in a timeline of ‘transformation of food’ – which I already possess in its completed form. The notes you take become an ‘integratively dense’ schematic.


On integratively dense content:

I strategically avoid instructing people using a finished schematic because the density of information often overwhelms peoples’ senses. A ‘too-busy’ page interferes seeing where things start, finish, or proceed as ‘many things’ disperse and branch off within the illustration – and thus, the same goes for within the body.

Why focus only on food – chronologically?

(as it transforms stage by stage)

Rather than classically explain each part of the digestive system’s anatomy and physiology, I am presenting the stage by stage progression of one thing: food itself – transforming along the way from into your mouth until it exits as poop.

While I present each stage – you fill in the template and details of each stage – while we interact along the way to clarify things.

When your hand illustrates the flow of food into your mouth and its transformation through the digestive system from start to finish – you see unfold, the chronological order of food breaking down, transforming, and assimilating into your body through specific pathways of the intestinal tract – synchronized perfectly ‘in order’ – resulting in a finished product filled out by yourself.

Another valuable thing happens by doing it this way. Namely, you’ll see how each how each part of the digestive tract, e.g. stomach, pancreas, gall bladder, etcetera, specifically contributes to transforming food. Focusing primarily food transforming creates a contextual-functional relationship between food and each part – framed through the actual chronological order of food moving through the system. In turn, this approach reveals the role of each part without having to numb your mind reading unnecessary details of each part in separate writings.

Moreover, you develop a concrete visual-spatial sense of the system and it parts – along with an enhanced ability to recall through the increased parallel processing occurring when using your hand and brain creating art.

The Whole Picture: Functionallly and Anatomically Speaking - Relative to all Food Eaten and Routes of Dissemination after 'Total' Proper Breakdown

What happens where and why it must happen*:

*not including salivary amylase breakdown of starch

1. HCL (acid) in stomach is stimulated to in turn stimulate pepsin and intrinsic factor. 

  • Pepsin breaks down protein – not the acid (HCL)
  • HCL kills bacteria. Acid is the first line of immunity in the digestive tract, not ‘good bacteria’ downline in the colon and latter part of the small intestine. You eat bacteria on food regularly, e.g. fresh fruit, salads, fresh vegetables, etc.  When you swallow phlegm – say during the buildup of mucus and destroyed/encased infectious material in the phlegm – acid kills the microbes.
  • Intrinsic factor is responsible for absorbing B vitamins – especially B12 – and also:
  1. Calcium
  2. Magnesium
  3. Iron
  4. Zinc
  5. Boron
  6. Copper

CONSIDER NOW – Food stuff, now called chyme is liquified and acidic – around a pH of 1-2 if you are young/healthy.

  • Chyme must be made more basic (less acidic) before entering the small intestine.
  • Protein is not broken down yet to where it needs to be before absorption and neither is fat.
  • Carbohydrate – if glucose can be absorbed through the stomach and get to the brain quickly and directly via dedicated veins from the stomach. (WHY IS THIS SO?)



1. Lack of HCL –


Transition - stomach to small intestine
Small Intestine

Prop: The Blank Gut Template

The graphics in the capsules below the blank gut template correspond to the order in which food moves through your mouth and exits as poop.

The Blank Gut Template

Blank-Gut-Template-Week-8If you are in my class you will receive this virtually blank template of the digestive tract below – where your hand fills in a timeline of ‘transformation of food’ – which I already possess in its completed form.

1. Picturing nutrient absorption

3 portal-tree-roots 4 portal-tree-roots-2 2A Portal-Vein


Talking points:

1. Carbs and protein breakdown primarily into glucose and amino acids respectively.

2. Glucose and amino acids go to the liver via the portal vein, then to the heart.

3. Most fat (long chain fatty acids) do not absorb with glucose and aminos. They absorb through the lacteals into the largest vessel of the lymphatic system – called the thoracic duct.


4. Most fat (long chain fatty acids) do NOT breakdown into smaller units from their original form in the plant or animal.

5. S & M (short and medium) chain fatty acids absorb with glucose and aminos.

Below, top picture: The milky white stuff is chyle (fat) absorbing and channeling to the thoracic duct. Below the chyle pic: Fat is later transported as a chylomicron, which is a big sphere of long chain fatty acids packed together.



Below: Link to a time lapse video I created to demonstrate absorption speed of water through a dehydrated plant’s roots to its leaves.

Turgidity 4Xfaster


Genius Observation from a Past Master



Gastric-BypassGastric-Bypass-2GutGastric pH Bacterial Count

Note: Stomach acid declines precipitously in many people over time. In the next lecture, I present the how problems originating within the  stomach and intestines issue a ‘domino effect’ of degenerative and life threatening conditions. I’ll use heat stroke and bariatric surgery as vehicles for explaining the mechanisms – from gut to blood to cells – which lead to anemia, bone loss, cognitive decline, blood coagulation in vessels, septic shock, and other problems.


Just occurred to me, key word search: bariatric surgey, heat tolerance, heat exhaustion risk elevated?

Transition: stomach to small intestine

Micelle Make-micelle1. Breakdown enzymes from pancreas

note: ‘ase’ is the suffix which indicates the breakdown of something – like salivary amylase breaks starch down in your mouth.

Amylase: Breaksdown carbs into glucose (primarily)

Protease: Protein –> Amino acids

Lipase: Lipids (fats) breaks fatty acids of the triglyceride backbone, glycerol.

Small intestine
Transition: Small intestine into cecum and colon.

CecumRefer to Biofilms in the large bowel suggest an apparent function of the human appendix.

Essentially, the appendix is a reservoir for commensal/beneficial bacteria. In times of a ‘shortage’ or a ‘wipeout’ the appendix provides bacteria to reinnoculate the colon. Its location avoids the stream of food and harmful pathogens in order to remain free of harm. Perhaps appendicitis results from pathogens that get to the appendix that otherwise ‘normally’ should not reach it.


pie chart ferment products Gut Pie ChartThe three primary ferments in the colon are:

1. Acetic acid (acetate or vinegar)

2. Butyrate (butyric acid or butter)

3. Propionic acid. Makes the distinct scent and taste of Swiss cheese.