Why You Don't Want To Promote Colonic Fermentation
#1
As humans, we have the unique ability to decide whether we want to promote colonic fermentation of fiber by bacteria, or to minimize it through the conscious avoidance of foods that are not easily digested in the small intestine. Most of us here are familiar with Ray Peat's ideas to minimize serotonin, endotoxin, and other byproducts of colonic fermentation, including butyrate, through the avoidance of starches and fibers, especially those that are easily fermented by bacteria. I think that Ray Peat's general stance on colonic fermentation can be summarized by the following quote:

“Bacterial endotoxin increases serotonin release from the intestine, and increases its synthesis in the brain (Nolan, et al., 2000) and liver (Endo, 1983). It also stimulates its release from platelets, and reduces the lungs’ ability to destroy it. The formation of serotonin in the intestine is also stimulated by the lactate, propionate and butyrate that are formed by bacteria fermenting fiber and starch, but these bacteria also produce endotoxin. The inflammation-producing effects of lactate, serotonin, and endotoxin are overlapping, additive, and sometimes synergistic, along with histamine, nitric oxide, bradykinin, and the cytokines.” (http://www.functionalps.com/blog/2012/11...endotoxin/)

However, Ray Peat is not all-knowing, and I think it is important to explore what is known about human evolution, as well as the evolution of other animals in order to decide whether we want to promote colonic fermentation by bacteria, or potentially eliminate it altogether. Evolution is ongoing, and while what we choose to eat may only effect our gene expression for our lifetimes, our dietary choices impact future generations along with the direction of our evolution as a species. In just the last 5000 years, while most human populations have been eating a large amount of starch, the size of our brains has declined, indicating that these types of changes can occur quite rapidly in response to our environment. (https://www.livescience.com/7971-humans-...hrink.html)

The chimpanzee and the bonobo are the closest known relatives to humans, sharing a staggering 99% of our DNA. (https://www.scientificamerican.com/artic...he-genome/) For some perspective, the following quote emphasizes how similar we are to these primates, compared with other closely related animals. “The number of genetic differences between humans and chimps is ten times smaller than that between mice and rats.” (http://news.nationalgeographic.com/news/...nes_2.html)

Despite the similarities between humans and chimpanzees, we have significant differences in the sizes of the various parts of our otherwise identical digestive tracts. The area of the digestive tract where fiber can be fermented into fatty acids is known as the colon. In humans, the size of the colon makes up 17-23% of the digestive tract, while the small intestine which is responsible for the digestion of easily digested food, makes up 56-67% of our digestive tracts. In the chimpanzee these ratios are essentially reversed as the chimpanzee's colon makes up around 52% of its digestive tract, while the small intestine only accounts for 23% of its digestive tract. (http://huntgatherlove.com/content/human-...ve-anatomy)

The differences between humans and chimpanzees include a difference in brain size. Ordinarily, the brains of different animals are difficult to compare as bigger brains don't necessarily indicate a greater level of intelligence due to differences in density and structure. However, chimpanzee and human brains are very similar with the exception of the size. As humans, our brains are roughly 3.5 times larger than the brains of our closest relative. (https://www.howitworksdaily.com/how-do-h...ns-differ/)

The diets of chimpanzees reflect their need for a larger colon. Chimpanzees primarily eat figs, seasonal fruits, and other vegetation with a smaller percentage of their diets coming from nuts, insects, and an even smaller percentage from meat. (https://janegoodall.ca/our-stories/10-th...nzees-eat/) As a result, chimpanzees rely on colonic fermentation to fully utilize their relatively high fiber diets. Chimpanzees have been observed collecting honey, but without the use of fire they are typically limited to hives housing stingless bees, which reduces the availability of honey in their environment. For chimpanzees, gaining access to honey without the use of fire is a very energy intensive ordeal, which reduces the net caloric benefit they receive from it:

“Dr Sanz explained: "Nobody knew they would pound over 1,000 times to get to the honey.
"Sometimes it could take several hours - they would start in the morning at around 1000, then take some rests, and then finish up at about 1400 or 1500 in the afternoon.
"It is quite physically challenging - in the videos you can see how large those pounding clubs are - some weigh over a kilogram." (http://news.bbc.co.uk/1/hi/sci/tech/7946614.stm)

Some people point to fire as the catalyst that allowed humans to evolve bigger brains. Chimpanzees, while very similar to humans, have never been observed making fire or cooking their food. Yet, researchers have found that cooking food cannot explain the increase in human brain size:

“Furthermore, we provide direct evidence for the unlikelihood of thermal food processing as an important factor to increase calorie availability to sustain the increased number of brain neurons in the hominin lineage.” (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4842772/)

Fire does more than allow humans to cook and make meat, tubers, and fruit slightly easier to digest. With the discovery of fire, humans gained the ability to easily gather honey. Bees don't like smoke, and some of the earliest discovered human art depicts humans climbing trees with torches in order to gather honey from beehives:

“Rock art depicting honeycombs, swarms of bees and honey collecting date to as many as 40,000 years ago. Such art has been found in Africa, Europe, Asia and Australia.” (http://www.smithsonianmag.com/science-na...s-9760262/)

Observations of modern hunter gatherer societies illustrate that honey, which is basically pure sugar, is an important food for our species:

“In Paraguay, for example, the Ache believe honey is the second most important food in their diet, after game meat; honey can provide an Ache with more than 1,100 calories per day. Honey can constitute 80 percent of the calories consumed by the Efe pygmy people of the Congo and 15 percent of the diet of the Hadza of Tanzania. Furthermore, people go to great lengths to get honey. The Hadza often follow honeyguide birds to hives of stinging bees. The honey hunters then burn brush near the entrance of the beehive to smoke out the bees, who become confused and disarmed by the smoke. In Nepal, honey collectors climb bamboo ladders positioned on cliff faces to access nests tucked away in crevices.“ (http://www.smithsonianmag.com/science-na...s-9760262/)

The Hazda of Tanzania, a hunter gatherer society still living in the general area in which humans are believed to have evolved, happen to rank honey above all other foods. (https://www.ncbi.nlm.nih.gov/pubmed/24746602) Furthermore, Hazda men and women rank fibrous tubers as their least favorite food, behind honey, berries, meat, and baobab fruit. The Hazda have actually been observed chewing tubers and then spitting out the fiber. (http://journals.sagepub.com/doi/full/10....0900700409)

When the Hazda men go hunting, they aren't primarily hunting for meat, but for honey:

“It is interesting that men bring back to camp more calories of honey per hour gone from camp than any other food type, followed by meat, baobab, berries, and finally tubers. This happens to be exactly the same as their preference ranking.” (http://journals.sagepub.com/doi/full/10....0900700409)

Hunting for honey is not a recent phenomenon, but likely extends to the advent of our species. A bird, known as the “Greater Honeyguide”, has co-evolved a relationship with humans, unlike any other bird:

“The bird dines almost entirely on beeswax and bee larvae, but it needs help to crack open hives. So the honeyguide calls to both honey badgers and Hadza hunters. When human hunters whistle back, the bird gradually leads the men by call-and-response song to the nearest colony." (http://www.smithsonianmag.com/science-na...s-9760262/)

"The work, by evolutionary biologist Claire Spottiswoode and her collaborators, “is the first to provide clear and direct evidence that honeyguides respond to specialized human signals … and that the birds associate those signals with potential benefits,” says John Thompson, an evolutionary biologist at the University of California, Santa Cruz. “The honeyguide literally understands what the human is saying,” adds Stuart West, an evolutionary biologist at the University of Oxford in the United Kingdom. “It suggests that the honeyguide and human behavior have coevolved in response to each other.”” (http://www.sciencemag.org/news/2016/07/u...ts-thought)

"While most animals are wired to flee from human presence, the Greater Honeyguide embraces it. But how do the birds learn to work with people? Spottiswoode’s theory is that the behavior is innate. Because the chicks are reared by alternative species (hoopoes, kingfishers, scimitarbills, you name it), they can’t learn this highly unusual behavior from their parents. So, instead, the birds must inherit the knowledge, refining it to match their locale as they mature. In Tanzania, for example, the cue is a whistle; in Zambia, the sound of chopping wood draws them near, she says."

"The human-honeyguide alliance was first documented in the 1500s, but some experts believe it might stretch back to Homo erectus, which would put it at about 1.9 million years old. Today, the Yao villagers are keeping the tradition alive. Though brrr-hm is their preferred trigger, Spottiswoode says that the type of sound may be largely arbitrary. It's the meaning that matters." (http://www.audubon.org/news/meet-greater...nds-humans)

I think that with the discovery of fire, humans were able to evolve bigger brains by gaining access to honey, which is Earth's densest energy source. (https://www.ncbi.nlm.nih.gov/pubmed/24746602) Honey negates the need for bacterial fermentation of fiber into fatty acids for energy, allowing for a reduction in the size of our colons, and a surplus of rapidly digested energy, leaving little work for the digestive tract to do.

The gorilla is another primate slightly different than humans or chimpanzees, sharing roughly 98% of our genes. (http://news.nationalgeographic.com/news/...n-science/) Gorillas are herbivores and rely more on colonic fermentation than other primates. If colonic fermentation is desirable, I would expect Gorilla's to have advantages over humans. Gorillas have a smaller small intestine, and a smaller brain than humans. While the gorilla's brain is larger than a chimpanzees it is much smaller when compared with the body size. Chimpanzees are generally recognized as being more intelligent than gorillas. (http://discovermagazine.com/2006/nov/pri...-hierarchy) The most intelligent primate, aside from humans, is thought to be the orangutan. (https://www.thetimes.co.uk/article/chimps-knocked-off-top-of-the-iq-tree-pm25bc6fqsd) The organgutan has a small intestine double the size of the gorilla, and slightly bigger than the chimpanzees. (http://huntgatherlove.com/content/human-colon-evolution-part-1-comparative-anatomy) I don't think this is a coincidence, but a byproduct of the diets of these primates. The organtgutan's diet is primarily comprised of sugary tropical fruits which make up 90% of its diet. (http://www.orangutan-world.com/orangutan-feeding/) The cow is a more extreme example. Like the gorilla, the cow is a herbivore. The cow has 4 stomachs in which vegetation is fermented into fatty acids for use as energy. The average cow weighs roughly 10 times the average human, yet humans have a brain weighing about 3 times more than that of a cow.

Moving on, there is an argument that bacteria have a symbiotic relationship with their human hosts. Antibiotics are said to be unsafe, or detrimental to human health, because we have evolved with microorganisms living in our digestive tracts. Yet, humans have a long history of utilizing strategies which reduce the amount of bacteria living inside of us. The practice of consuming alcohol, which has antibacterial properties, predates the advent of our species:

“The results suggested there was a single genetic mutation 10 million years ago that endowed human ancestors with an enhanced ability to break down ethanol. "I remember seeing this huge difference in effects with this mutation and being really surprised," Carrigan said.
The scientists noted that the timing of this mutation coincided with a shift to a terrestrial lifestyle. The ability to consume ethanol may have helped human ancestors dine on rotting, fermenting fruit that fell on the forest floor when other food was scarce.” (https://www.livescience.com/48958-human-...ption.html)

“Yeasts produce ethanol as a form of chemical warfare—it’s toxic to other microbes that compete with them for sugar inside a fruit. That antimicrobial effect benefits the drinker. It explains why beer, wine, and other fermented beverages were, at least until the rise of modern sanitation, often healthier to drink than water.” (http://www.nationalgeographic.com/magazi...n-culture/)

One of the oldest cities discovered by modern humans is known as Gobekli Tepe. As a stone structure Gobekli Tepe can't be accurately dated, but based on carbon dating of organic material it is a minimum of 11,000 years old. (http://www.smithsonianmag.com/history/go...-83613665/) In Gobekli Tepe there is evidence that the inhabitants were brewing alcoholic beverages:

“Nestled inside the walls of some smaller enclosures are six barrel- or trough-shaped stone vessels. The largest could hold 40 gallons of liquid. The archaeologists suggest that they were used to brew a basic beer from wild grasses.

Analyzing residues from several of those tubs, Zarnkow found evidence of oxalate, a crusty, whitish chemical left behind when water and grain mix. One vessel contained the shoulder bone of a wild ass, just the right size and shape to stir a foaming, fermenting broth of grain and water.” (http://www.nationalgeographic.com/magazi...n-culture/)

The ancient Nubians are a more intriguing example. Fossils of ancient Nubians have been analyzed, and it has been found that they were consistently using the Ray Peat recommended antibiotic, tetracycline, through the consumption of beer:

"Chemical analysis of the bones of ancient Sudanese Nubians who lived nearly 2000 years ago shows they were ingesting the antibiotic tetracycline on a regular basis, likely from a special brew of beer. The find is the strongest yet that antibiotics were previously discovered by humans before Alexander Fleming discovered penicillin in 1928."

“Nelson found large amounts of tetracycline in the bones tested from the ancient population, which lived in the Nubian kingdom (present day Sudan) between 250 A.D. and 550 A.D. and left no written record.

"The bones of these ancient people were saturated with tetracycline, showing that they had been taking it for a long time," Nelson said in a press release August 30. "I'm convinced that they had the science of fermentation under control and were purposely producing the drug."” (http://www.wired.com/2010/09/antibiotic-beer/)

In conclusion, I think that to promote the evolution of a larger and better functioning brain requires more energy. I think that colonic fermentation is an inefficient form of energy production which results in a smaller brain and necessitates a larger digestive tract in order to maximize the energy derived from low quality foods like vegetables and fiber. I think that bacteria produce toxins that inhibit metabolism and result in the liver expending more of the bodies energy on detoxification, leaving less energy available for higher processes. As humans, we can further reduce our liver's burden of bacterial toxins by manipulating our environments. This includes consuming fruit in a fiber free juice form, choosing foods that are primarily digested in the small intestine, and utilizing techniques to partially sterilize our digestive tracts, and increase the speed at which food is digested and moves through the digestive tract(thyroid, caffeine, salt, and aspirin). I think that when one's metabolism is impaired, fiber that isn't easily digested can aid in the binding and excretion of toxins, but is not necessary in a healthy state. I think that as humans we have the unique capability to avoid colonic fermentation, even in diseased states, by utilizing substances like activated charcoal which can serve the detoxification function of fiber, while being impossible for microorganisms to ferment.
"The true method of knowledge is experiment." -William Blake
#2
I have noticed recently that every guru and even real doctors talk about the gut microbiome as if it is a part of our bodies and not pathenogenic scavangers. This way of thinking will get people in so much trouble, blindly thinking that gut bacteria are essential for digesting food, yet nearly noone mentions that most digestion tales place in a sterile environment by bodily produced enzymes.

The probiotic craze will probably have a disasterous effect on the next generation. All this emphasis on fermented food and drink, all of which is mostly lactic and histamine producing strains.

Sea, what do you think about the idea that a lot of digestive health comes from your oral health? Bacteria in gum disease and cavities basically making its way to the gut.

I have taken to swishing with about 20mg tetracycline mixed with water daily and using a xylitol and charcoal paste for brushing. Well see the effect, i do have some cavities that i have not taken care of because of health insurance.
#3
I've heard gurus that promotes fibers and probiotics using gorilla as an example of their strength and that you don't even need animal protein to build muscle to be strong.

Now that you compare gorillas needing colonic fermentation and the fact chimpanzees are usually smarter than them.
I mean just by these two examples:

[Image: frank_troop.jpg]

Seriously, look at its bloated belly. Isn't that just pure gases? And, nicely, this picture has also a baby gorilla and his belly is completely small. So I think it is indeed gases and not their "natural" appearance.

Now about chimpanzees, you probably know about this behavior of them to eat only the juice and remove the fiber:





I think everything is much more complicated that in seems. Nonetheless, I just wanted to show these examples that are in agreement with your post.
#4
Hah! I have been doing what the monkey ia doing for awhile. Ill basically chew up fruit and spit out the fiber. Cool to see i gots instincts.
#5
Its kinda funny cuz now I think that all the different nutrition subgroups are right in their own way (candida, gut dysfunction, sugar avoiders). But I think there are certain ideas that simply squash others in importance.

One of these is the destruction of pathogens under high vitamin a & k conditions.

Check out pg 436 in Nutrition and Physical Degeneration. Saliva bacteria goes from 325,000 to 15,000.
#6
Also, I like the original post a lot. It brings up a lot of good points about honey.

The thing I can't reconcile is that honey does not appear to work out in real life. I have yet to hear of someone in what I consider excellent health using honey. I'm in just about the best health of my life using provable and repeatable metrics. But last weeks foray into unheated raw avocado honey slowed my peak performing digestive system to zero in 2-3 days.

Perhaps I am making some missteps in usage. Like reducing the viscosity, or only eating with certain other food. But this is probably the 25th type of honey I have tried in 4 years rping.
#7
(09-01-2017, 07:40 PM)sm1693 Wrote: Also, I like the original post a lot. It brings up a lot of good points about honey.

The thing I can't reconcile is that honey does not appear to work out in real life. I have yet to hear of someone in what I consider excellent health using honey. I'm in just about the best health of my life using provable and repeatable metrics. But last weeks foray into unheated raw avocado honey slowed my peak performing digestive system to zero in 2-3 days.

Perhaps I am making some missteps in usage. Like reducing the viscosity, or only eating with certain other food. But this is probably the 25th type of honey I have tried in 4 years rping.
I think honey is a huge allergy trigger.  I feel on the same page as you. I feel like I can never find one that my body fully accepts it. But I react to every single food possible... So I may not be the best example.


I think Joseph Cohen from Selfhacked.com eats honey everyday. I think he had to try several different honeys to finally be able to incorporate one on a daily basis. However, I have to say that I think he takes a bunch of supplements to fill the nutrient gaps. So he might not be a good example for someone who has an excellent health, lol.
#8
Honey does not do me any favors either, i use it only on pork. Maple syrup is my go to sugar.

Really though, when you think about what honey is and where it comes from, no wonder it can be so allergenic. I cant believe people think bee pollen is a superfood.
#9
(09-01-2017, 07:27 PM)sm1693 Wrote: Its kinda funny cuz now I think that all the different nutrition subgroups are right in their own way (candida, gut dysfunction, sugar avoiders). But I think there are certain ideas that simply squash others in importance.

One of these is the destruction of pathogens under high vitamin a & k conditions.

Check out pg 436 in Nutrition and Physical Degeneration. Saliva bacteria goes from 325,000 to 15,000.


Can you quote it? I have the pdf and it only goes up to 307, must be formatted differently. 
#10
(09-01-2017, 11:11 PM)Its in ch22 "a new vitamin-like activator" about 2/3 of the way thru the chapter. Its in one of the graphs. Wrote: Can you recommend a specific brand of maple syrup to save me some time? And have you been using unheated/unboiled sweeteners? Ive been operating under the RP idea of sugar deteriorating under high heat. Ive been using unheated coconut crystals the past few days.


Zachs
(09-01-2017, 07:27 PM)sm1693 Wrote: Its kinda funny cuz now I think that all the different nutrition subgroups are right in their own way (candida, gut dysfunction, sugar avoiders). But I think there are certain ideas that simply squash others in importance.

One of these is the destruction of pathogens under high vitamin a & k conditions.

Check out pg 436 in Nutrition and Physical Degeneration. Saliva bacteria goes from 325,000 to 15,000.


Can you quote it? I have the pdf and it only goes up to 307, must be formatted differently. 
  


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