Understanding digestion

There are four things about digestion that I believe to be essential to understand, remember, and always keep in mind. The first is that although the environment of the stomach can be, and is generally at least mildly acidic, the intestines must be alkaline. The second is that the level of acidity inside the stomach depends on what is in it: it is in response to whatever comes into the stomach that specialised cells of its lining secrete hydrochloric acid in greater or lesser amounts. The third is that only protein requires a highly acidic environment to be properly broken down into the amino acids that make up protein before moving on into the small intestine; fats and carbohydrates neither require nor stimulate the secretion of acid in the stomach because they are broken down in the alkaline environment of the intestine. And the fourth is that water is totally crucial to the proper function of all digestive organs, and to the whole process of digestion from start to finish.


Model of the human digestive system with labels

Because proteins are so hard to break down, they must remain in a highly acidic environment in the stomach for about 3 hours before the resulting chyme should be, can be, and is normally transferred to the small intestine. (Obviously, the time depends on the amount.) And the more acidic the environment of the stomach, the better it is for the breakdown of protein, but also to protect the organism by destroying pathogenic bacteria that could have come with the protein, as is presumably often the case in the wild.

In addition to the hydrochloric acid secreted by the stomach, protein-digesting enzymes (proteases) like pepsin are also secreted by the stomach when it contains protein. Moreover, the acid activates the inactive forms of the enzymes prorennin and pepsinogen into their active forms: rennin is necessary for digesting milk protein, and pepsin breaks down the proteins into polypeptides. It is very important to remember that the stomach has cells that sense what nutrients are present, so that it knows what and how much to secrete for their digestion.

Many people suffer simultaneously from amino acid deficiency, and the consequences of putrefaction of undigested protein in the intestine, even though they eat plenty, if not too much protein, because their stomach does not produce the amount of hydrochloric acid that is needed for proper protein breakdown. In fact, this is very common in older people, but it is also a problem in the middle aged and even in young adults. This problem can be partially remedied by taking hydrochloric acid supplements with protein meals, an approach that works very well for the elderly, but addressing the fundamental issues that lead to digestive dysfunction is obviously most important. The digestion of fats and carbohydrates is entirely different.

Simple carbohydrates eaten on an empty stomach will move out of it and into the intestine in a matter of minutes. This is why blood sugar levels go up almost instantly when we eat or drink simple carbs like whole fruit or fruit juice. Starchy carbohydrates begin to be broken down into sugar when they come into contact with those enzymes in the mouth whose purpose it is to do this (primarily amylase), and will be broken down completely over the course of a few hours, not in the stomach, but in the small intestine.

The same goes for fat: fat or oil by itself eaten on an empty stomach will swiftly move to the small intestine as it does not need an acidic environment, and thus simply does not need to stay in the stomach. But unlike carbohydrates, fats need to first be emulsified into droplets that can mix in the watery environment of the small intestine. This is done by the bile produced by the liver, but stored and secreted by the gall bladder into the small intestine. The emulsified triglycerides are then broken apart by pancreatic lipase that separates the glycerol backbone from the three fatty acids. The free fatty acids are absorbed in the small intestine and into the bloodstream by passive diffusion (as is water).

Another important difference between the digestion of carbohydrates and fats is that while it is no problem at all for fat to sit in the stomach for hours, together with the protein being broken down by the acidic chyme, carbohydrates, and especially simple carbs, start to ferment very quickly if they do not move out of the stomach. This is what gives rise to the characteristic bloating that we feel when we eat simple carbs together with other foods, but especially when combined with any kind of protein, the best example of which is having sweet things either with or after a large meal that typically contains plenty of protein, such as the terrible habit of having fruit after the meal, as is done in most western countries, as opposed to the much wiser habit of eating the fruit as a starter, before the meal, as is done in some other cultures. Bloating, burps, gas, stomach aches, etc, as well as really bad digestion followed by really poor absorption all result from the fermentation of the simple carbs that remain in the stomach for longer than a few minutes, as they normally would, before passing to the small intestine, as well as the incompatibility of various digestive enzymes, each with its own specific nutrient to break down, released into the intestine by the pancreas, all trying to do their work, but clashing against one other in the process.

Therefore, to properly digest protein there should be no simple or starchy carbohydrates in the stomach for the entire breakdown process that lasts about 3-4 hours for a normal (smallish) meal. In addition, there should not be any alkalising liquids like alkaline water, sodium bicarbonate water, lemon water, or green juice in the stomach, because they will work to neutralise the acid needed to break down the protein, and thus cause bad digestion and stomach aches. You can try any of the combinations described here if you want evidence through personal experience, but I’m sure you have experienced most of them at various times, although most probably unaware of it. I guarantee that it works in exactly the same way for everyone, even if some are definitely more sensitive than others.

In case you don’t know or don’t remember from other articles, I think no one should consume simple or starchy insulin-stimulating carbohydrates because their consumption in any amount inevitably damages body and health in any one of several very predictable ways. The reason why I am emphasising these points about carbohydrate digestion is not only because the majority of people in the world get most of their calories from insulin-stimulating carbohydrates, but also because these carbohydrates are most disruptive to digestive health in many more ways than we tend to know or consider.

I have written recently in the article Detoxification about the disastrous consequences on the digestive system of a diet consisting mostly of simple or starchy carbohydrates, all of which are caused by chronic acidosis of the intestine. To recover from or avoid these digestive disorders and the diseases that result from them, it is of paramount importance to, on the one hand, eliminate these acid-forming sugars and starches, and on the other, alkalise as much as we can the intestinal tracts on a continual basis, day after day, and year after year.

The natural consequence of these facts and considerations is that the most healing and health-promoting of diets is one that consists primarily of alkalising drinks and foods—alkaline water, green juices, lemon water, and green and leafy vegetables—and in which energy needs are covered by the best fats—coconut oil, raw grass-fed butter, wild fish and meats, and whole, soaked nuts and seeds—with protein consumption kept to the essential minimum based on individual needs.

Water is exceedingly important for digestion, and I have written about this in Why we should drink water before meals. The two most crucial roles of water in the digestive process are: First, to provide the stomach the level of hydration needed to make, maintain and adjust the thickness and consistency of both the layer of mucus that protects the lining of the stomach from the corrosive acidic secretion required for the breakdown of protein, and for of the chyme itself during the initial phases of digestion when it is churned by the stomach. Second, to provide the pancreas the required hydration for it to be able to produce the all-important pancreatic fluid (bicarbonate solution) whose purpose is to neutralise the acidic chyme once it is transferred from the stomach to the small intestine, as well as to carry the enzymes produced by the pancreas to break down those foods that do not themselves carry and provide the enzymes needed for their proper digestion.

As is always the case for everything that relates to health, we can only truly understand by understanding the physiology—how things work. The digestive system is the one around which all other systems are arranged because the health and survival of the organism as a whole depends entirely on it. And the key to optimal digestion and health is the understanding that the stomach only needs to be acidic when there is protein in it, the intestine must always be alkaline, and the digestive system as a whole always requires a good supply of water.

Therefore, we should aim primarily to alkalise and hydrate by drinking lots of alkaline mineral and chlorophyll rich drinks together with liberal but appropriate amounts of unrefined sea salt (see How much salt, how much water, and our amazing kidneys); consume plenty of fat; always consume protein either by itself, with fat or with green vegetables, but never with simple or starchy carbohydrates; if you eat simple carbs such as sweet fruit, make sure you eat it by itself on an empty stomach; and always make sure that when you eat protein, the environment of the stomach is kept acidic, and thus do not have any alkalising liquids for at least 60 minutes before and 3 hours after the protein meal, but also make sure to have at least half a litre of plain water, at least half an hour before eating.

Keeping to these simple principles will ensure optimal digestion, optimal digestive health, and optimal overall health, day and day, and year after year, throughout life, from childhood to old age.

9 thoughts on “Understanding digestion

  1. Excellent article…one of the best I’ve read and it simply lays things out. Thanks for writing this.

    I’m glad u explained food combining principles bc the way Americans eat is to combine everything at one meal for overall “nutritional balance”…. But no wonder why many of us feel icky afterwards. Some people aren’t affected by this and actually feel more” stable by pairing a carb with a protein to stabilize blood sugar…. But i guess that’s a whole other situation based on poor glucose/insulin control?

    Anyways, thanks for the no nonsense and thoroughly written article! Keep up the good work


  2. Guillaume…. have you ever had anyone who is very chemical sensitive get healed from eating like this? After some home remodeling I reacted to something and then pesticides exposure has made me very sensitive. I was Also exposed to some mold. Everyone says your immune system is 80% in your digestive tract. I’m very fog brain now and having a hard time figuring out how to heal my gut. I have never had digestive problems and thought I was eating correct but some testing came back saying I had lots of bacteria in lower intestines. Probiotics and organic and removing all chemicals from makeup/hair/body products have been removed for over 1 year and see no improvement. Can you explain a little more using an example of a meal of bison, kale and blueberries. In what order/time wise too. All i drink is Mountain Valley Spring water. I just don’t know why my body as turned on me like this! Thanks so much!


    • Hi. You have to take probiotics. I take Prescript-Assist, which is excellent. So, I recommend that you start taking that as soon as you can. Take it three times per day: morning, noon and night. You will feel the difference quickly I am sure. Without a balanced flora, nothing works. I also recommend you continue reading through what I have written. You will learn a lot about digestion and how your body works. But, first and foremost, start Prescript-Assist as soon as possible.


  3. Hi Guillame,

    I apologize if you’ve covered this somewhere in an article, I have not yet been through all of them. A few questions. I am wondering what you recommend for constipation, as whenever I cut out fruit I have trouble having daily bowel movements. Will probiotics solve this?
    Also, since you don’t advocate fruit, can you recommend a fruit-free green juice that is still palatable? Until I get a juicer, will powdered greens as you recommend be a viable substitute? I am also wondering why you particularly recommend Food Matters greens powder over others.

    Thank you:)


    • Hi Caitlin: Constipation can have different causes, but usually it is a question of balance of water/salt, magnesium and fibre, and almost always, a lack of these. Have you started drinking as I suggest we should? Have you started magnesium supplementation? And have you started taking psyllium husks? Probiotics are a must, and another super helpful supplement for digestive health is Mercola’s Mushroom Complex. So in addition to the water, salt, magnesium and psyllium husks, you should get Prescript-Assist probiotics and the mushroom complex, and take those first thing in the morning. For the green juice, I’ll write a post about that, and for the powdered greens, it is just important to get the highest quality you can, and Food Matters is very good. But Vitamineral Greens is also very good. Just don’t get something that is powdered dehydrated veggies, because what you’re taking then is just fibre, not the nutrient dense juice of the veggies. This is how Doc Brocs is made, and I don’t recommend that anymore for this reason. And in fact, most powders on the market are made like that. We have to be vigilant about everything :)


  4. Great, thank you for the recommendations! I look forward to your article on the green juice:)
    I do like Vitamineral Greens, but lately I’ve been taking Athletic Greens. When you get a minute, I’d love to hear your opinion on it. I’m not quite sure how to decide if it meets your qualifications.



    • I can only really comment on things I’ve tried, and I’ve taken Vitamineral Greens. Different products have different qualities. Vitamineral and the Athletic Greens are attempting to put as many things as possible into the product: to make a multi-vitamin-mineral-super foods powder. Food Matters has only a few ingredients. Their approach and also purpose is different.

      For enriching my green juices, I use the simpler, fewer ingredients and so I use Food Matters or straight dehydrated barley grass or wheat grass JUICE, not leaf powder. Sometimes I put a superfood green blend, but these things, including Vitamineral greens don’t taste good at all, and makes the juice not very pleasant to drink. Also, I take a whole foods multi and the supplements that I think are important, so I don’t need another multi in my green powder.

      In any case, you really can’t go wrong in taking any of these kinds of products because they are all much better for you than not taking them. So, just read up on things, and choose the stuff you feel most inspired by.


  5. Pingback: Why every undigested protein is an allergen | healthfully


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