Brain Gut 1: Who Are We, Really?

Brain Gut 1: Who Are We, Really?

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If you are paleoanthropologist or archeologist you think fossils are the Rosetta Stone for discovering the path that human evolution took. If you are proteomic evolutionary biochemist you think molecular arrays are the best way to decipher the tea leaves of Mother Nature ways. If you are a geneticist you think the RNA/DNA is Holy Grail of human evolution. If you are dental specialist, like University of Arkansas professor, Dr. Peter Ungar you think it’s all about the mammalian teeth. Today’s blogosphere likes to define evolutionary thinking by thinking about the Paleolithic epoch and how it might have shaped the hominid tree. The paleolithic shaped the tree to be sure, but had nothing to do with planting the acorn.

The paleolithic diet has been championed best, in my view, by Dr. Loren Cordain’s sustained efforts over the last 30 years. His work is epic and quite important in point out that Paleo man was far superior to modern man today. But I think this diet was not foundational nor optimal for the initial stages of hominid evolution. This also begs the question, was there a diet before the paleolithic that maybe better for us even today? How might we study that?

My opinion is that we need to look back further to the transition from ape to Australopithecus afarensis is far more important for what maybe Optimal for our version of Homo today. Many of these experts believe that evolution has a purpose as it works. I do not believe this. I think Heisenberg had it dead right in 1925 when he said all life was random because of his uncertainity principle he found in quantum mechanics. Einstein was vexed by this question the rest of his life. He was often quoted saying he did not believe life would be left up to just a roll of the dice. This is one time I think Einstein was dead wrong.

Since I am a neurologic surgeon who does a lot of spine surgery I have a decidedly different view point than most of the experts listed above who are interested in human evolution. The main thing that separates ape from man is his brain, his spine and their guts. The clinical significance is the major difference in these body parts, and I believe, is not what you may have been led to believe from many in the blogospshere on this topic. I come from a completely new perspective on this rather controversial and speculative issue. My unique perspective on these problems opens up new worm holes for you to explore. I believe the answer to human evolution is not found in any one single answer or theory. I think parts of theories are spot on and need to be assimilated and reshuffled. into a new line of questioning or new theory formation.

Answers are someone’s terminus’s explanation of an existing mystery. Theories are someone else’s answer, and in my view answers usually lead to dead ends. In this series I am going to focus on questions for you to ponder. Questions open mindful inquiry and may suggest that your mind expands in ways it may never have done before. I am going to take many known facts today and I am going to connect the dots for your own mind to explore. I will not invent any new theory here. I think my theory of life is built into the the Quilt document. Instead, I will innovate on homo evolution to help modern humans regain their health by putting concepts together that may lead us all to some new conclusions about what is Optimal for us today.

The focus of this series is to ask better questions than the answers the experts have given us to solve the puzzle of human evolution.  I am going to share with you the evidence I have amassed in my brain that has allowed me to think about how disease may be the evolutionary building blocks of the homo species. If my instincts are correct, this has huge implications for how we treat modern humans in modern healthcare.

Ironically, I think the embryology and radical transition of the paracellular pathway of our gastroenterology tract holds the key to the transition. This series is called the Brain Gut series so let us begin to explore the mysteries with some questions of our own.

What are the main differences that separate humans and apes?
How did we acquire them?
What were the factors at play?
What might the ramifications be as time moves on?

How humans acquired this paracellular pathway in our guts however may shock you. In this series I am going to kick down some new doors and stir the pot of modern evolutionary dogma as it stands today. It is time to paint a picture of human evolution that incorporates all the problems with all the theories that are out there to offer a new perspective on an age old problem. Many will complain and call me nasty names because I think differently as they have been apt to do this year to be sure as I lay it out. But for those of you who enjoy deep thinking, these ideas will really make you think about who we really are and why did we come from who we did. I expect to take you to places heretofore that few have gone yet.


The transition from chimp to human happened rapidly in the East African Rift Zone based upon the data contained in multiple branches of science we have today. It happened much more quickly than most of the “so called experts” guessed in the last century. We found that out recently because of modern genomic arrays that 7{a7b724a0454d92c70890dedf5ec22a026af4df067c7b55aa6009b4d34d5da3c6} of our genes have been altered just in the last 20,000 years. This amount of action is far more than any expert expected before this was found. In 1996, Boyd Eaton made the case that we should study man through the paleolithic optic because paleolithic man was clearly healthier than their modern descendants. His arguments were good, if you want to compare modern man to paleo man, but the arguments do not take us back to where we really became human from being ape. I’m more interested in how a four legged, small brained herbivore became us, and why it happened. those answers, I believe will give us tremendous insight in how to tackle modern man’s health maladies.  I think focusing in on the paleolithic solely is myopic for healthcare issues.

I want to know what environmental conditions and diet caused that quantum leap, because it maybe the the diet our species may fare best on even today. I believe we need to focus upon what environmental pressures caused us to break millions of years of mammalian spinal and cranial design to cause a massive epigenetic change in such a short period of evolutionary history. The paleoanthropology experts used bones and fossils to tell us about our evolution. They have believed since Darwin’s time that bones and fossils are the best evidence for human or human like life forms. In reality,  when we rely heavily on bone evidence, we are drawing conclusions using massive inferences. Why you ask? For hominids, the fossil record is quite poor in comparison to all other mammals, so why would it be foundational starting point?  Because when humans began to study evolution bones were  all we had.  Today we have a lot more data, and in my view, we are not innovating our thoughts to ask better questions than the bone collectors are today.  I believe the fixation on bones has stopped productive inquiry.  They have wasted the last 30 years because they just can’t lay their bones down in their boxes and find a new perspective.  That is why we remain in the dark about who we really are.

This means we are making large leaps of assumption that are not fully supported even by the fossil record. This is especially problematic for in the study of the only bipedal primate in evolutionary history. Man is the only bipedal mammal that is terrestrial and we have less then 10 good fossils of primate transitional feet to draw these inferences upon how and why we began to walk upright on two legs. For me it seemed that using bones alone was not a good way to study this transition. Many of those bone experts had theories about where we came from and why it happened. We all know about the Savanna theory, the expensive tissue hypothesis, and even Hardy’s the aquatic ape theory but those “expert theories” (insert Conventional wisdom here) all have major gaping holes in them. Why? I am going to examine them as the series rolls on and you will see where I think they went right and where they went very wrong.

Let’s start with the bone collectors.

If you examine the fossil record as it stands today compared to other evolutionary trees, there is paucity of proof for any of them in the fossil record. When one considers that evolution has been speeding up as time elapses, it should be no surprise to the experts why the bones “just ain’t there” and won’t be found either, in my opinion. A sped up epigenetic program formed this new divide in the evolution of hominids, so why would we find more skeletons?  I believe if I am right we will find few.  So far I think that is more correct than speculative. One of the things I realized years ago is that modern man has developed in the paleolithic time, but his most unique attributes formed in the the period before the “paleolithic.” This era is called the Pilocene.

Prior to the 2009 revision of the geologic time scale, which placed the 4 most recent major glaciations entirely within the Pleistocene, the Pliocene also comprised the Gelasian stage, which lasted from 2.588 to 1.805 million years ago. This is precisely were Homo showed up in the fossil record. I think we need to look right there instead. The first change that happened in transition, occurred because certain groups of apes were isolated by a changing environment fostered by some unusual geologic conditions that exist in this area of the planet. Do we know that happened in the East African Rift Zone back then, today? Yes, we believe we have a pretty good idea of what happened to apes when humans evolved in the environment. (The Vatican will not like this blog or series either, but I still go to church.)


The second change was that in the Pilocene we know the climate got cooler and  drier inside away from the coast, but more wet on the coastline due to rising sea levels (anyone feeling that CT feeling) and began to approximate what we modern humans face on earth today. As with other older geologic periods, the geological strata that define the start and end are well identified but the exact dates of the start and end of the epoch are slightly uncertain. The boundaries defining the onset of the Pliocene are not set at an easily identified worldwide event but rather at regional boundaries between the warmer Miocene and the relatively cooler Pleistocene. The upper boundary was set at the start of the Pleistocene glaciations.

Here is what Wikipedia has to say about the 30,000 ft view of the Pilocene and it is not controversial.

“During the Pliocene epoch climate became cooler and drier, and seasonal, similar to modern climate.
The global average temperature in the mid-Pliocene (3.3 mya – 3 mya) was 2-3°C higher than today, global sea level 25 m higher and Northern hemisphere ice sheet ephemeral before the onset of extensive glaciation over Greenland that occurred in the late Pliocene around 3 Ma. The formation of an Arctic ice cap is signaled by an abrupt shift in oxygen isotope ratios and ice-rafted cobbles in the North Atlantic and North Pacific ocean beds. Mid-latitude glaciation was probably underway before the end of the epoch. The global cooling that occurred during the Pliocene may have spurred on the disappearance of forests and the spread of grasslands and savannas.”

This represents a 30,000 foot view of what was going on in the Earth’s environment. The micro climate of the East African Rift is where we found the ideal environment to lead to homo speciation, in my view.

To get why humans ‘randomly’ came from apes we need to look at the cradle of man when the ape spine was radically changed to Australopithecus afarensis (Lucy) who walked on two feet. Up until very recently most bone collectors believed the brain co evolved with the rest of the skeletal data in unison.  That changed once we found Lucy and Ardi.  Ardi destroyed the Savannah hypothesis but you’d never know it by reading the bone collectors literature.  Bipedalism came first and by a substantial time margin too.  Bone collectors have focused on the pelvis evolution a lot in their literature over the past 150 years. I always thought that was a mistake because with Lucy skeleton, we knew we walked before we got a big brain.  So letting go of the pelvis fixation issues would have made more sense to me.  I decided to look at the spine and the feet first because they have done nothing to figure out why we are walking on two feet looking at the pelvis. I think the pelvic changes are all to do with the later development of the brain.  I know a little something about the brain and spine in my business. So I changed my view point to feet, because bipedal creatures walk on them.  I realized that bone collectors have always stayed away from the the mystery of transitional feet because they do not have many to study. You would have thought that would make them go to examine the spine in a new light,  but they did not.  They were fascinated by the pelvis and this got them into trouble in their formation of theories in my view.  This is how you make big errors in assumption. It all started with Raymond Dart, and the skull he found, and has gone down hill from there. So I asked a different question to myself. Why was the spine and then the pelvis transformed first and not the skull? My perspective as a spine surgeon made me look at ‘their problem’ with a new set of glasses from a new mountain range.

To this neurosurgeon, it sounded like the ideal place to grow larger hind limbs compared to arms then proceed to form a massive brain, based upon what we know today about how mammalian body plans forge neural and spinal growth. The hind limb of most mammals is more well developed in quadrapeds. But I felt the answer had to be an environmental one and one that caused and epigenetic change to our feet. There is a highly conserved embryologic plan the dictates these moves in all vertebrates and uses the same genes and is dictated by hormones. Most of this information has been found in the last ten years and is far superior than the bone data we have previously relied upon. We also now definitiely know the climate was radically different in the cradle of human origins in the Rift Zone than it is today or was before that time. It was colder and wetter and the climate changed quickly and this also helped facilitate our speciation from the Great Apes. Why the climate changed is based upon the geology of the region and the effects of precessation and orbital forcing that I mentioned in my Factor X webinar in May 2012 when we spoke about the K-T event that formed our remote eutherian ancestors.  In this blog, I am going to show you how the same factors affected our recent ancestors.  Our ancestors were cut off from their jungles and most of their grass lands, so they did what any species does. They evolved to the new environment. We cover this mystery in Brain Gut 3.

What was the currency that facilitated this change in those animals?  Strap yourself in.

JUNK DNA IS THAT ANSWER:  What is junk DNA you ask?

I spoke about that in CPC #4. The answer is found in what is not in primate DNA and what is found in human DNA. In primates we find a substantial amount of ‘jumping genes” in their ‘junk DNA’ on our Y chromosome.  The reason African apes have this ability is because they assimilated an ancient pathogen called HERV K that allowed for their genomes to carry the extra junk on their chromosomes without any risk of disease.  Barbara McClintock discovered  this junk in 1951 and called them jumping genes in corn,  but most of medicine and researchers ignored her work (surprise) until  30 years later when they gave her the Nobel Prize. What does it do? Junk DNA allows our genome to move the proverbial furniture around to allow for very rapid DNA expression to occur! In essence the more retrotransposons one has,  the more you can shuffle your genomic deck to adapt to anything you might face in the environment.  This is vital information that bone collectors never saw because they are too busy studying skeletons with no feet.  We learned all this stuff since we cloned the human genome and the chimp and gorilla genome.  This is precisely how epigenetics works on a molecular basis in the primate tree.    In scientific parlance, this means using these transposable genes forms the basis of rapid primate and human epigenetic adaptation. This is precisely why humans were able to quickly evolve from apes when the environmental changes in the Rift Zone called for it.  It also suggests we won’t find more transitional apes, because we came to the party quick.

How did we/they do it?

RADICAL IDEA NUMBER ONE IN THE SERIES: I believe the first major mutation we assimilated to accomplish this task was to acquire a leaky gut from a pathogen bacteria from the coastal waters!

I believe we inherited the leaky gut from transitional apes via our gut, by a bacteria very similar to vibrio cholera. The time apes seemed to be isolated in the East African Rift Zone seems to fit the ecology of this area perfectly for a bacterial parasite like Vibrio to infect shellfish that would have filled the meadows and estuaries in this area.  Moreover, the protein that forms modern human enterocyte tight junctions of the paracellular pathway, is derived from a protein that is found in these bacteria as well.  I think this gene was modified by a retroposon (a jumping gene) called Haptoglobin 2 that was recently found by Dr. Alessio Fasano at the University of Maryland.

Once this bacteria’s genetic code was ingested by the ape and assimilated into our gut and our gut associated lymphatic tissues (innate and cell mediated immune system for further adaptability) we likely gained the ability to produce horizontal gene transfers, but more importantly, it set the table for transposable genetic elements to create new genes to solve old problems that our environment presented to us in the Rift Zone.  In essence, the mutation selected for a leaky gut using genetic alterations in the gut microflora to cause rapid adaptations in our own immune system in an isolated group of apes in the East African Rift Zone. This means transitional apes and man have a leaky gut by design. It is not pathological as most believe today.  (Slaying some dogma)

If this idea is correct, this means that we should also see big changes between primate and human immunity genes as well.  Yes, we do see that too!  That comes later in the series.

What would make primates more prone to persistent latent infections that don’t cause them disease to begin with you ask? African primates genomes have been radically altered by one particular genetic parasitethat makes it far easier for it to become infected by many other pathogens like Vibrio.  This is something particular to African primates, from which humans definitely evolved.  This is why African primates can harbor persistent subclinical infections that may facilitate rapid genetic transfers that alter expression of their genome or the genetic material they have assimilated over their own evolution. This ability would have been a huge adaptation advantage for a tree dwelling herbivore, because prior to this they would not have had an immune system able to defend against the new pathogens they faced in a colder wetter Pilocene environment. Today we have evidence that the primate genome contains genetic material that has colonized its host genome to create a very stable genetic library within their DNA to provide the “creative force” that enabled them to allow for hominid evolution. The proof that this molecular footprint, is in fact buried in primate ancestors, is found in the molecular biology of “jumping genes” (retroposons) of the human genetic code. This genetic remnants are far better than the fossil record of recording our history in my opinion, because they tell us precisely what happened to the mammalian body plan during the primate transition over time. The fossil records help nail the time frames down but it is not the holy grail of human evolution. This unique mechanism also correlates with mammalian complexity in the primate tree. The more complex a mammal is the more jumping genes it has in its genetic stable to deal a hand of cards that best matches the environment the species finds itself in. Humans have more of the jumping genes than any mammal on this planet.

Gene transfers are how bacteria and all eukaryotes genetically recombine their chromosomes to adapt to a changing environment. In other words, this is how apes and hominids are able to respond so quickly to changes they have faced in their evolutionary history. We know from modern genomic surveys of primate and human genomes there is great homology. The similarity is so great (98.5{a7b724a0454d92c70890dedf5ec22a026af4df067c7b55aa6009b4d34d5da3c6} in true coding regions) that it would be difficult to distinguish human from chimpanzee genes only via their true coding regions. Recently, it has been reported that those genes that do differ often correspond to those involved in smell or diet. These are both sensory traits that tie directly to epigenetics and to the brain and the gut.

Apes and humans are the only mammals with massive amounts of these ‘jumping genes’ in their genome. Within these jumping genes, there is an even bigger difference between humans and apes. It is the shear amount of this non coding DNA. Humans have 50-60{a7b724a0454d92c70890dedf5ec22a026af4df067c7b55aa6009b4d34d5da3c6} of their DNA that is non coding. Another shocking difference is that most of human non coding DNA origin is from a special type of virus!   In fact, 8-10{a7b724a0454d92c70890dedf5ec22a026af4df067c7b55aa6009b4d34d5da3c6} of the human genome is composed of assimilated viral elements, and most is on the Y chromosome! The Y chromosome only has 20 genes on it.  That makes it our most unique chromosome.  Most of the genes controlling brain growth are molecularly tied to this region as well!  Are you feeling the homology here people?  We know this from modern molecular biology techniques developed in the last ten years. We assimilate these viral particles from our leaky gut by design to create new genes.  This is how you go from a tree dwelling small brained quadraped herbivore to an upright smart ass in a million years.

You might find this fact more amazing. Only 3{a7b724a0454d92c70890dedf5ec22a026af4df067c7b55aa6009b4d34d5da3c6} of human DNA contains the instructions for building cells and tissues in humans. 97{a7b724a0454d92c70890dedf5ec22a026af4df067c7b55aa6009b4d34d5da3c6} of our DNA is is not active in building a thing normally. Ponder that fact for a minute. Then ask yourself why would evolution collect and carry that much DNA if it were really junk? The reason she does this is simple. This ‘junk DNA’ is how evolution works so rapidly to adapt to changes in the environment. Ever since the K-T event, if you match up DNA genomes from these animals there is a simultaneous corresponding increase amount of junk DNA in their genomes. Humans have the most of all the mammals since K-T event. This is just another fact that supports my idea that evolution decided to speed up DNA expression to all the animals who survived this event. Junk DNA is how it accomplished the task in the primate and homo trees of life to an even greater degree. The more junk DNA you have the better able you are to adapt to a changing environment. It also allows evolutionary speed to increase as time elaspses. At first, scientists called this DNA, ‘junk DNA’ when I was medical school. Since then it has been upgraded to non coding DNA, and now it is called retrotransposons. They now are realizing that this “junk” is really important to all mammalian evolution. In fact, it is the key to understanding how we came from Great Apes so fast.

Jumping genes are found in many life forms but they are loaded in the DNA of apes and humans. Humans, however, have a lot more than primates. Stop and ask yourself why, now?  This, to me, was a lot more interesting that bone data.  This DNA has the information that formed those bones so I left bones alone when I realized how the chain of evidence was falling.


Yes, you read that correctly. Today in the blogosphere everyone and their grandmother thinks the leaky gut is ‘bad actor’. We must always understand the context of something when we speak about it. Yesterdays adaptation becomes todays neolithic disease when the environment changes away from the original adaptation. I showed you in CPC #4 how what you believed about hemochromatosis and T1D might be mistaken too when you viewed it from an evolutionary prism. Well, here is the biggest twist on the evolution of hominid story. In my opinion, the formation of a “leaky gut” is precisely how the homo came from the apes. Why? Because some apes were walled off from their populations they began to rapidly evolve in the new environment that they found themselves in randomly in the East African rift zone. This area of Africa is by far the most geologically active part of that continent in the last 5-7 million years because it is a place where three tectonic plates meet and where water has come and gone several times over that span.


We get junk DNA from bacteria, virus’s and fungi that we assimilate from our leaky guts. How do most mammals get them other than humans? They get them from infections over the course of evolution, but not via their leaky guts. A leaky gut is a purely human adaptation. The evolutionary adaptation of zonulin is the “hardware” of human evolution, in my opinion. The “software” in the plan of this evolution is our co-evolving gut microbiota. Our gut flora was sculpted by the diet we found in the East African Rift Zone at the time we evolved. Our leaky gut became our ‘fossilized genomic library for parts‘ that fueled are rapid ascent to homo. This assimilation of RNA and DNA from bacteria found in our environment at that time is what our ancestors called upon when their environment dictate a change. The more dissimilar DNA we could assimilate the more adaptable we became and the faster it happened.  Notice that I did not use any bone collectors data here…….at all.  You do not need it yet, for this puzzle.

We incorporate bacterial, fungal and viral genetic material into our genomes but humans are especially adept at assimilating viral RNA into their DNA using reverse transcriptase enzymes. I mention this enzyme here, not to confuse you, but many people have heard of this enzyme because this is the enzyme HIV uses to enter our T cell genomes today and cause disease.  I mentioned in the Factor X webinar and the blog that followed it, that HIV may hold a great clue to the unfolding story of human evolution. Well, here you are seeing where a virus like HIV has shaped the primate tree of life to become us.

RADICAL RULE TWO: Retrotransposons are jumping genes and human retrotransposons are overwhelmingly from retroviruses! Most retrotransposons come into our system via our leaky guts and get assimilated via our gut associated immune system (GALT). HIV is the most famous retrovirus humans know about, but not the most important. When I was in medical school the rules of genetics said that genetic information flowed in a one way street moving from DNA to RNA and to protein formation. HIV is a retrovirus that uses RNA to incorporate its RNA into our DNA directly. It broke the rules of genetics back in the 1980’s as we knew them to exist. Today, HIV causes a disease called AIDS. I believe that one day HIV eventually will improve our immune system tremendously because of what we know about how retrotransposons work in our genome today.  It might even be the way where may be able to evolve evolutionary cures from the modern neolithic diseases we face today.  Yes HIV, may one day cure some neolithic disease you have now.

Moreover, we now know today that the fastest route to an HIV infection is in the Peyer’s patches of the gut and not from blood or fluids as we thought initially. When I learned this fact about ten years ago I realized that if a large virus like HIV could get through our gut lining so easily I thought there had to be an evolutionary reason for us to have a leaky gut to begin with for some reason. I also found out that we believed HIV came from a simian version of the virus. Humans acquired this simian virus by eating chimps infected with it as bushmeat in Africa. It appears the virus then mutated in us by antigenic drift and caused human immunodeficiency virus and it came from Africa to the United States by a homosexual male airline stewardess in the early 1980’s. Because the vector of transmission was a human gay male, epidemiologists and researchers thought this disease was predominantly a blood and fluid transmitted disease. This only appeared to be true because of the behavior of the person initially infected who brought this to North America. It spread rapidly here in the gay community initially, because they had no innate immunity to this virus, but within 5 years it began to spread to all human groups. The mode of transmission in Africa is very different than it was in the US. Today, HIV is controlled with protease inhibitors and it is rarely a death sentence. The viral RNA of HIV has become part of an estimated two billion humans DNA already since the pandemic began in 1981. The reason AIDS spread so fast is because humans have a system set up to take advantage of RNA viruses to guide their evolutionary development.  How is that for irony?

Subsequently, we found that in primates they could not acquire HIV via their guts, as humans who became infected with SIV after eating infected bushmeat did become infected initially. This unique feature between two closely related primates made me ask why this was the case? It was at this point I found out that humans have zonulin and primates do not. Zonulin is the protein that makes human guts naturally more leaky than a primates gut! It also appears that African primates are colonized with SIV and this infection makes them much more susceptible to other support persistent infections that have driven hominid evolution.

In other words, these two virus stories strongly suggested to me that this difference is the major difference between our species because of a deep evolutionary reason. In my opinion, that reason was to increase the translocation of genetic material from our diets via our gut flora to incorporate into our DNA to allow for a more rapid adaptation to any environment we might face.

The initial purpose for a “leaky gut” became a major advantage to the evolution of the homo species.

How is that for an unexpected twist?

One of my readers, Alex , got the huge implication of this coming monster series when he made a comment on the last blog that said this, ” The evolutionary advantage of zonulin induced gut permeability conferred to a human would be an accelerated nutritional influx and a subsequent acceleration of tissue growth and repair! Primates and other animals without this inherent advantage would not have been able to adapt to the environment as quickly due to the limitation imposed by an impermeable gut.” Alex got the implications, but just wait until I show you how this occurred. The genetic gymnastics of the transitional apes to early homo was nothing short of amazing and fully accounts for most unique human characteristics of bipedalism and encephalization.

Next up: Brain Gut 2 What were the naturally selected for environmental triggers of isolated primates that selected for having a leaky gut?


1. Eaton, S B, Konner, M. J., & Shostak, M. (1996). An evolutionary perspective enhances understanding of human nutritional requirements. The Journal of nutrition, 126(6), 1732-40.

2. Aiello, L. C., Wheeler, P. (1995). The Expensive-Tissue Hypothesis: The Brain and the Digestive System in Human and Primate Evolution. Current Anthropology, 36(2), 199.

3. Survival of the fattest. Steven Cunnane


5.Milton, K. (1989). Primate diets and gut morphology: implications for hominid evolution. In M. Harris and E. B. Ross, Food and Evolution: Toward a Theory of Human Food Habits (p. 93). Temple University Press.


7.Imamichi H, DeGray G, Dewar RL et al. Lack of Compartmentalization of HIV-1 Quasispecies Between the Gut and Peripheral Blood
Compartments. J Infect Dis 2011; 204: 309-14

8. (How HIV destroys the GALT in the gut)


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  1. Jim June 16, 2012 at 1:02 pm - Reply

    …”I think Heisenberg had it dead right in 1925 when he said all life was random because of his uncertainity principle he found in quantum mechanics. Einstein was vexed by this question the rest of his life. He was often quoted saying he did not believe life would be left up to just a roll of the dice. This is one time I think Einstein was dead wrong.” I have often thought this very same thing when I first learned about it many years ago.

    …”Answers are someone’s terminus’s explanation of a mystery. Theories are answer’s and in my view answers lead to dead ends.” Brilliant. I agree totally. Just look in the dust bin of washed out theories for confirmation.

    …”I am going to take many know facts and I am going to connect the dots for your own mind to explore. I will not invent any new theory. I think my theory of life is built into the the Quilt document. Instead I will innovate on homo evolution to help modern humans regain their health by putting concepts together that may lead us all to some new conclusions about what is Optimal for us.” This is why I keep coming back. This is how I like to think also. Are we evolutionary brothers or something? 😉

    • Jack June 16, 2012 at 1:28 pm - Reply

      @Jim I think when you get older you have less tolerance for the dogma of any science field. We need to all think critically and question all assumptions. This series is going to do that.

  2. John Ward June 16, 2012 at 3:02 pm - Reply

    I remember being taught in elementary school that we only use a small percent of our DNA and thinking that really just means we haven’t figured out what it does, YET! Thanks for the dots and connections.

    • Jack June 16, 2012 at 3:24 pm - Reply

      @John When I get to part two and especially part three of this series John you are going to see why Humans really do roll the dice…….and why we dont use much of our hard code of the DNA. We are dealers of chance and we stack the deck compared to our chimp cousins.

  3. Caroline Cooper June 16, 2012 at 3:17 pm - Reply

    Over the last few years, I have become increasingly interested in how our gut flora protects our health. In fact, I have started to believe each individual should do everything in their power to ensure the health of their internal biota.

    I have also heard about how bacteria, parasites and viruses can get into our genetic code. I have never heard about zonulin and its link to leaky gut. I know nothing about the mechanism gene transfer, junk DNA, jumping genes and the like.

    I am sorry to say, you will have to chew my meat for me so I may be able to digest these ideas in the future!

    • Jack June 16, 2012 at 3:25 pm - Reply

      @Caroline……not to fret. We have just begun. By Brain Gut three I bet your perspective is very different.

      • Jack June 16, 2012 at 4:39 pm - Reply

        @Mike Your email about viruses is a fair one but consider this original thought from 62 years ago.

        “The modern definition of a virus, as a molecular genetic parasite, was first clearly put forward by S. E. Luria in an essay published in Science in 1950. Later in that decade, in his book Virus Growth and Variation, when considering the role viruses might play in cellular evolution, he wrote, “. . . may we not feel that [in] the virus, in their merging with the cellular genome and re-emerging from them, we observe the units and process which in the course of evolution, have created the successful genetic patterns that underlie all living cells?” This view, however, did not gain a following, and has been completely overlooked or forgotten by most evolutionary biologists.”

        Still think you’re right now? When we make bad assumptions sometime we go away from where the science led us originally. I think in the case of evolution we did just that.

  4. Sarah Barron June 16, 2012 at 5:31 pm - Reply

    Dr. K, I was an anthropology major in the 1980s and my daughter is now studying anthropology at her university too….we are both enjoying this series so much. I love the way you work without the constraints of any discipline.

    Looking forward to lots more!

    • Jack June 16, 2012 at 6:29 pm - Reply

      @Sarah I promise you by the time I get to part three……you wont be able to get out of your chair. I told people long ago, who laughed at me I had data…….well it’s a coming and its coming from 8 scientific disciplines. This series was the most fun I had writing the blog…….It took to to places I had not visited since I was a little kid. I even went to the zoo to talk to gorilla trainers and zoo keepers and saw some ape surgery.

  5. Lyndra June 16, 2012 at 6:22 pm - Reply

    Can’t wait to hear more about zonulin, leaky gut, and the blood-brain barrier. I have a feeling CT will be a player.

    • Jack June 16, 2012 at 6:30 pm - Reply

      @Lyndra………you have no idea what a player CT will be. Its gonna be fun.

  6. AK Man June 16, 2012 at 8:04 pm - Reply

    Something never discussed in the fossil record is the human’s loss of the baculum ( It seemed to disappear to quickly; I doubt epigenetics played a role in the loss of a bone.

    • Jack June 16, 2012 at 8:43 pm - Reply

      @AkMan… dont need a bone in man hood when you’re going in face to face……because your spine caused your female’s canal to move anterior in the colder and wetter coastal environment and you could no longer go in the back door as you used too when you where in the forest all the time……..its all about the retrovirus re shuffle……..Stay tuned my friend, because epigenetics did get rid of the proverbial boner. All to be revealed.

      • Jack June 16, 2012 at 9:20 pm - Reply

        @Marie My idea has no rules at all. I do not believe Mother Nature does either. The more corrupt the cell/state, the more numerous the laws need to be. Mother Nature job is simple……make sense of randomness with out pretension. This is why evolutionary form meets function on a nanoscopic level

  7. Lee June 16, 2012 at 9:21 pm - Reply

    I’m stuck on Peyer’s patches. I’m thinking this one is tricky.

    • Jack June 16, 2012 at 9:26 pm - Reply

      @Lee no tricks…….this one was like opening the present on Xmas morning. The next two……well have your trick glasses ready

      • Jack June 16, 2012 at 9:27 pm - Reply

        @Melissa Why am I picking on bone collectors? When you’re the market leader on evoltution and you’re dead wrong……you deserve it. Our progress is narrow; it takes a vast world unchallenged and for granted. This is one reason why, however great the novelty or scope of new discovery, we neither can, nor need, rebuild the house of the mind very rapidly. This is one reason why science, for all its revolutions, is conservative. This is why we will have to accept the fact that no one of us really will ever know very much. This is why we shall have to find comfort in the fact that, taken together, we know more and more. -Oppenheimer

  8. Nonchalant June 16, 2012 at 10:45 pm - Reply

    Sounds like we are GMO’s. We have snippets of all kinds of DNA inside us.

    • Jack June 17, 2012 at 8:14 am - Reply

      @Nonchalant…….just wait until you see just how much and why and what it all does.

  9. Andre van Staveren June 17, 2012 at 4:19 am - Reply

    May I call you Captain James T. Kirk? You ‘go boldly where no man has gone before’.

    Please book me a seat on this Enterprise ;-

    • Jack June 17, 2012 at 8:21 am - Reply

      @Andre Anyone who wants to think a bit is allowed to ride the road to Optimal.

  10. Bob Smith June 17, 2012 at 5:18 am - Reply

    Zonulin’s effect in the small intestine is to make the small intestine permeable. When the partially digested contents of the small intestine cross into the bloodstream, zonulin crosses with it. There’s no reason why zonulin in the bloodstream would not perform the same function as it performed in the gut. It makes membranes permeable.

    Microorganism-to-food protein mimicry elicits zonulin in the gut, and causes the food proteins to flow into the bloodstream. This same reaction happens in the bloodstream. Zonulin becomes a vehicle projecting the same proteins through membranes all over the body, including nerve membranes.

    This is apart from zonulin’s roll in haptoglobin 2.

    Incidentally, the HIV transmission rate among men who have sex with men (MSM) is roughly 75 TIMES as high as the general population, a population which includes IV drug users, prostitutes and MSM.

    While talking about the wonderful protective things which evolution does to protect the species it’s important to remember that these changes only occur with massive deaths of species individuals.

    • Jack June 17, 2012 at 8:21 am - Reply

      @Bob Of course people die using this evolutionary shuffling card trick that is built into life. This is why we see epidemics all the time throughout our history. But who survives is the new evolutionary answer. This is how evolution is proceeding today under our noses. My priest asked my why we dont see evolution working today……I told him its hard to see when you are not looking for it! Anytime, we face an epigenetic challenge we change. HIV, celiac, GMO wheat……..all the survivors are already different genetically. People expect morphologic changes because of the perception of the bone collectors…….WRONG! We change on a cellular level first and then the body types alter.

      I mentioned the 25 miilion that died in Europe in CPC 4. This was half the population at the time! But look at what happened since 1347. The survivorship happened and now their is over one billion inhabitants there. So I say Mother Nature rules for survival work pretty well if you make it. Right now you might die. Then the game plan is to live within the rules and avoid the modern damage makers!!! Sound familiar to anyone?

      When we shuffle the genetic deck we are going to lose people because that is how evolution is wired to roll. But the end result of HIV might leave us with a new homo species that can survive modern disease better than our homo has. In fact, I think that is precisely what might have happened until protease inhibitors slowed it down. I still think the effect will happen but I am not sure it will be as fast. Your point on zonulin is well taken and is in line with where I am going. Once you destroy zonulin in the gut it then demolishes the BBB. These two organs are linked by evolution……..and the vagus nerve for a reason.

      The real point here is that when we understand the process of how our part of the tree differs from the rest of the tree it gives you a better sense of who we are and what we should be doing to stay on the road……..and what mother nature has put in us to determine our path and survival………I believe our species comes built in with a major genetic shuffler to find the right winner…….as a consequence until the winning combo is found……people will die if they do not follow the rules of circadian biology to stay on that road to optimal.

  11. Bob Smith June 17, 2012 at 10:06 am - Reply

    This is great. You should go into the roll reversal which the zonulin dump initiates as DPPIV changes from a digestive enzyme to an insulin mopping enzyme. But don’t forget the negative effects of roll reversal on ferroportin.

    • Jack June 17, 2012 at 10:46 am - Reply

      @Bob……we are just cooling down here on this gut issue……blog was just born and this was the first time we hit it……..tsunami alerts are now out for the people who remain interested in my ideas. I will give you a preview since you are gluten/T2D fan clearly by your last post……My belief is that celiac is a circadian/wheat disruptor of endogenous adenosine pathways in brain……its co apts the endo-opioid system to screw the brain up and it the leakiness at the brush border is transmitted to the BBB to gain access to the CNS……here is where ADHD, autism, obesity, and many other disease are all tied to wheat and casein protein……..I also believe it totally screws circadian clocks because adenosine is the window into those human clocks…… explains the cytokine arrays and it explains why wheat also screws Vitamin D and lipids so badly. Complicated stuff but you seem like a cat who can handle that stuff. Most of my readers head already hurts enough……….You just increased it!!!!

      I hope to see more of you

      PS: DPPIV is evolution working to demolish proteins at our brush border……we needed this to work well in hominid evolution to create the building block that would soon become our massive brains. Without it, we could not be us. And people who think Januvia is good…….are nuts. My bet is that it will never cure them of T2D it will actually make them an institutional diabetic and may guarrantee them Alzheimers……or at least horrible cognitive function. Any thing that destroys the gut function has direct impacts on the brain……hence we have the brain gut series. To understand the deeper complexities you asked……you must start at the genesis of why evolution wanted a leaky gut to begin with……modern autoimmunity is that system gone awry because of circadian mismatches…….Wheat is just one of them

  12. BobWayne June 17, 2012 at 11:21 am - Reply

    Power, Sex, Suicide: Mitochondria and the Meaning of Life is a book that I am currently reading, that may be helpful for those that want more details on gene mixing.

    In this fascinating and thought-provoking book, Nick Lane brings together the latest research in this exciting field to show how our growing insight into mitochondria has shed light on how complex life evolved, why sex arose (why don’t we just bud?), and why we age and die. These findings are of fundamental importance, both in understanding life on Earth, but also in controlling our own illnesses, and delaying our degeneration and death. Readers learn that two billion years ago, mitochondria were probably bacteria living independent lives and that their capture within larger cells was a turning point in the evolution of life, enabling the development of complex organisms. Lane describes how mitochondria have their own DNA and that its genes mutate much faster than those in the nucleus. This high mutation rate lies behind our aging and certain congenital diseases. The latest research suggests that mitochondria play a key role in degenerative diseases such as cancer. We also discover that mitochondrial DNA is passed down almost exclusively via the female line. That’s why it has been used by some researchers to trace human ancestry daughter-to-mother, to “Mitochondrial Eve,” giving us vital information about our evolutionary history.
    Written by Nick Lane, a rising star in popular science, Power, Sex, Suicide is the first book for general readers on the nature and function of these tiny, yet fascinating structures.

  13. Paul N June 17, 2012 at 12:27 pm - Reply

    Fascinating stuff, as always.

    So zonulin was the enabler of the permeable gut, and worked fine (mostly) until we started eating wheat, which, unfortunately, contains gluten and other bad stuff, that exploit the permeability and cause brain problems

    The part that I don;t understand, is why casein does the same thing? why would we have a component of mothers milk that can potentially cause ADHD, autism etc?

    I can see why it might be handy for it to have an addictive quality, so the infant will want to keep drinking it, but then, the nutrient density of milk would assure that anyway?

    I should ask, is the casein issue with all casein, or only the A1 type produced by Holstein (bos taurus) cattle? The A2 casein in the milk of human, goat, sheep and certain cows (bos indicus) is more digestible for humans, but does it still have the same potential negative effects?

    Or is it a case where we haven’t had the time, or need for zonulin to adapt to casein since, normally, it is only consumed by infants?

    looking forward to the rest of the series.

    • Jack June 17, 2012 at 12:48 pm - Reply

      @Paul N I promise that is coming……I think that is where Bob smith was heading in his earlier comments. Wheat is the tipping point for many bad things beside celiac. think T1D, T2D, LADA, autism, ADHD, AD, ED, and the list could go on…….this is just blog one of this monster series……After my Factor X webinar people wanted to know what they could do to make it actionable…….well this series is that first and most important step. To know who you are you must first know where you came from and precisely why…….because it tells you where you might be headed if you fall off the path that brought you to life……..That is why humans today are mediocre as a species and in decline morphologically and are becoming more useless as they age because of how broken they are metabolically. It’s why modern medicine needs a new perspective……because they don’t know how and why we evolved……….when you know the why’s…….you get a lot smarter.

      Here is your preview: about dairy

      What exactly is the problem with the casein protein in dairy? ( Paul A1 is far worse than A2 cows……this is why I spend money on French or New Zeland dairy if I want it. this is the main reason why I am not WAP friendly 100% They are dead wrong on american dairy) Short answer BCM-7 or caseomorphin 7. This stuff does bad stuff to DPPIV Bob brought up earlier. DDPIV breaks down BCM7 so we can handle it but it also depletes itself and then it cant not handle gluten because they may not make enough DDPIV when they eat things like dairy. For those autism folks reading this…….the real problem with DPPIV is that heavy metals are the most potent blocker of DPPIV and its found in pesticides. This is why you want to go organic if you can afford it. Heavy metals are the number one destroyer of DPPIV. Once it wears down it cant handle BCM7 or wheat. And they go on to kill you in many ways.

      It wears down the brush border to go from slight leaky to a broken dam. Once the damn breaks the GALT is right behind it and all autoimmunologic hell breaks loose. BCM7 once in the GALT and portal circulation causes massive food allergies. The tyrosine residues in BCM7 molecular formula cause it to be a very oxidizing particle……think low HDL and high sdLDL. DPPIV also goes by the name CD26 and it alters the toning down phase of eicosanoids (omega 6’s) that stop the immune process from progressing. When this happens the immune system stay lit on alert and makes Ab’s and activates innate and cell mediated immunity to cause all kinds of havoc that we see today as modern disease…….even cancer.

  14. Paul N June 17, 2012 at 1:19 pm - Reply

    That link to zonulin (near the end) makes for interesting reading. My interest was piqued when it linked it with cancer – does all this messing with our guts increase cancer? Following the link, and another one, led me to this interesting article;

    Researchers find pathway for origin and growth of the most common form of brain and spinal cord tumor – meningioma

    (I have a friend who has a meningioma around her pituitary.)

    The article makes this interesting comment;

    “In meningioma cells, Baia studied the activation of a protein called YAP1, for Yes-associated protein 1, which is regulated by Hippo. Without it, YAP1 moves into the cell nuclei and activates genes whose products trigger tumorigenesis and cell proliferation.”

    they studied 70 samples of meningioma tissue and all of them had YAP1

    Googling YAP1 turns up all sorts of studies about YAP1 and – colon cancer!

    Of course, people who eat a lot of wheat get colon cancers…

    One of the links connected YAP1 with skin growth, and skin cancer, and a protein alpha- catenin that inhibits YAP1;

    People who eat wheat seem to get more skin cancers too…

    and finally, googling alpha catenin shows there is also a beta-catenin that increases cell growth (including in cancers), and that omega 3 DHA inhibits this, and omega 6 AA increases it!

    So a diet low in DHA and high in n-6 could cause more cancers – which fits with the pattern happening today.

    Googling DHA and brain cancers shows all sorts of links showing that DHA works against brain, colon, breast, pancreatic cancer and so on.

    The more I learn about DHA the more I like this stuff – it is clearly a very essential part of our diet.

    And didn’t a gradual increase in DHA consumption, in early paleolithic times, have something to do with our brains getting larger?

    It is all very interesting…

    • Jack June 17, 2012 at 1:27 pm - Reply

      @Paul I have a former patient who had a disc herniation very early in life who had Crohn’s and I always told him and his Mom that I thought the disc was tied to his diet. They told me the GI doctor said there was no link between diet and Crohn’s. The kid is 28 yrs old today and dying of stage four Colon Cancer. The GI doctor said wheat and dairy were OK………I wish they would have listened to me. I can barely talk about it without getting pissed off.

    • Jack June 17, 2012 at 1:29 pm - Reply

      @Paul…..Januvia is a DPPIV blocker……it also has been linked to melanoma production……how is that for a complication and a tie in to my theory?

      PS: Paul…..DHA has to be in seafood form not supplement form. And that is why it is the base of my Epi Paleo pyramid. People who frequent my forum are hearing it but the people doing educational consults have been hearing it since I began talking about Cold Thermogenesis.

  15. Bob Smith June 17, 2012 at 1:28 pm - Reply

    @Jack – This is just my assessment. There’s no need to reply. As you said, you’re about to tie this all together.

    The advice to “eat more healthy whole grains” has got to be the crime of the century. The second biggest crime of the century is the advice to cut down on “cholesterol” (fat) intake.

    “Healthy” whole grains are responsible for initiating all of the diseases of modern man. Every organ in the body, including the hypothalamus, is controlled by nerve transduction boundaries. Zonulin makes transduction boundaries permeable to gluten and casein opioids. These boundaries are normally protected by the blood brain barrier (BBB).

    The blood brain barrier is not really a barrier at all. It is mostly controlled by the fact that nerves operate in a hydrophobic environment …..a fat amalgam which controls phospholipid-rich nerve membranes. Control and restoration of these transduction boundaries requires replenishment by ingested fats, and proper cholesterol manufacture by the liver. Protection of these transduction boundaries requires ……adenosine. And adenosine is an essential protein. It is mostly a product of complete digestion of proteins in the gut. Eating grassy grains arrests digestion of plant proteins, and dumps them into the blood before digestion can produce adequate adenosine. The zonulin and opioid assault on cholesterol-starved nerve transduction boundaries is aided by a shortage of adenosine and cholesterol.

    Destruction of circadian rhythm is a two-prong assault. Deterioration of hypothalamus transduction boundaries allows compromise of the orexin/hypocretin system. That’s a BIG problem. The body has three states …..exert, rest and eat. The orexin system has tendrils directly into the transduction control nerves of every organ. Orexin control impulses toggle organs like a symphony conductor toggles instrument sections. Once the hypothalamus orexin center has been compromised, organs lose the capability to sleep and wake on demand.

    The wheat-compromised immune system gets confused. It begins, as you said, different patterns of cytokine release. One of the immune system targets becomes ingested polyphenol dyes like lutein. Lutein has an affinity for retinal nerves. Like vitamin A, lutein coats the retina, blocking out blue light. Blue light in the retina is responsible for setting the circadian clocks which control our pineal glands. Our wheat-compromised immune systems attack lutein, and attack the retina. The attack destroys eyesight, and destroys the pineal gland control nerve’s ability to tell day from night.

    • Jack June 17, 2012 at 1:31 pm - Reply

      @Bob I had to reply…….you’re my kinda of reader. We think a lot alike……

  16. Elin Duke Potter June 17, 2012 at 1:39 pm - Reply

    I have known about my own celiac disease for 15 years. When I first began my research, it was postulated that 1:2500 had celiac disease; now it’s thought to be 1:100. In that time I have done reams of research, which led me to believe that many neolithic disease are a result of undiagnosed celiac disease or non-celiac gluten sensitivity. I used to tell anyone who would listen about it, but getting people who are not obviously ill to give up their beloved cereal grains is like beating one’s head against a brick wall. It’s good to finally see someone else, who knows way more about biochemistry than I, come to the same conclusion.

    Thank you again for bending my brain! It hurts so good!

  17. Bob Smith June 17, 2012 at 2:33 pm - Reply

    @Paul- That’s interesting about YAP1. It provides a pathway from mRNA to nuclear DNA. Assessed, it helps answer one of many “how” questions about cancer. Other pathways are better for answering “Why”.

    Recently a massive meta study showed what anyone watching already knew. It showed that people with type 2 diabetes are between 2 and 5 times as likely to have 24 of the 25 studied major types of cancer than the general population, a population which includes a large segment of type 2 diabetics.

    Ballparked, the cancer incidence among type 2 diabetics is roughly 3.5 times as great as the cancer incidence among non-type 2 diabetics. That, my friends, is a smoking gun. If you want to develop cancer you should first try and develop type 2 diabetes. The rest should take care of itself.

    Type 2 diabetes is largely the result of consuming volatile sugars along with proteins, flavonoids and opiates from foods like wheat. The pathways are pretty well nailed down. Sugar grows intestinal microorganisms. Opiates dull the immune system while, at the same time, mimicking the proteins displayed by the microorganisms. The immune system makes the intestinal walls porous. The partially digested opiates, sugars, flavonoids and proteins flow into the bloodstream, and wreck havoc all over the body.

    Type 2 diabetes is characterized by insulin resistance. Opiates from wheat and other plant foods mimic insulin. They clog up insulin receptors, and prevent cells from consuming blood glucose. Cells starve. The blood increasingly fills with glucose, and elicits ever higher levels of insulin.

    Cancer represents portions of the body ceasing their normal toil. Cells cease to consume food for the performance of specialized tasks, and instead consume food for the creation of useless tissue. Human cells perform this transformation when insulin resistance causes them to abandon their normal diet of glucose.

    Cells are protected from assault by tissue transglutaminase (TTG), a protein in the extracellular matrix (ECM). Ingested flavonoids attack and destroy tissue transglutaminase, leaving cells unprotected. Unprotected cells, starved by insulin resistance, start importing and burning flavonoids for fuel. Unfortunately flavonoids do not lend themselves well to being burned for energy.

    Glutamate is the most commonly consumed flavonoid. Glutamate is so essential to cancer transformation that many cancers produce their own glutamate. Wheat is roughly 1/4 glutamate.

    PKM2 is a catalyst which tells cells why to burn fuel …..whether to burn it for energy or for the creation of tissue. As shown above type 2 diabetes fills the blood with glucose and makes cells starve for glucose. The glucose gradient across outer cell walls causes cells to redirect the aggregation of PKM2. The insulin-resistance form of PKM2 causes cells to start creating tissue.

    Cells start creating randomly mutated tissue, combining human DNA with whatever proteins happen to be hanging around in the cytosol. From this point evolution takes over. In order to survive, mutated cells must feed themselves, reproduce, and avoid the body’s immune system. Unsuccessful cancer cells die. Successful cancer cells survive and form tumors.

    In a nutshell …..When human cells use fuel for energy, they use mitochondria to make ATP. Then they burn the ATP. When cancer cells use glucose to create tissue, they ferment it directly. The cancer transformation starts with human cells in a glucose-charged environment. Because of insulin resistance the human cells cannot use the glucose. The cancer transformation replaces human cells with cells which can use the glucose.

    There are very few differences in the “why” pathways from one type of cancer to another. For avoiding cancer our challenge is to end the insulin resistance and the glucose buildup. We do this by eliminating opiates from foods like grassy grains, dairy and legumes, eliminating flavonoids like glutamate and aspartate, eliminating fructose, and boosting our intake of meat and fats.

    • Jack June 17, 2012 at 2:37 pm - Reply

      @Bob You clearly are getting where I am headed……you jumped way ahead in the Quilt but this is where I will be bring folks. Its going to take time to explain it all to them in ways they can tolerate but this is the core of the oncogenesis levee on my Quilt document. What do you do in real life? Are you in healthcare or just a victim of it? By your writing on this topic makes me think you might have a form of diabetes tied to wheat exposure……Are you familiar with Bill Davis?

  18. philippe chouinard June 17, 2012 at 4:06 pm - Reply

    I’m at the airport waiting for my plane to Turkey. Overnight flight , seven hours time differential, not so paleo probably…help me!
    Plan: as soon I’m on the plane 5mg of melatonin (6pm local time), eyes covers and no carbs… We’ll see. I’ll follow from you all from Turkey!

  19. Paul N June 17, 2012 at 4:32 pm - Reply


    Thanks for the thoughtful replies – I am extending the limits of my depth on the biochemistry here, and will wait for the rest of the series to explain it all.

    Clearly, we know many ways that wheat and high glucose cause problems, and there are probably other ways we don’t know about yet.

    The concept of cancer thriving by fermenting glucose is not new, but it does not seem to be acted upon much, if at all, in cancer treatment/prevention these days. I had a college roommate whose two staple foods were bread and Coke (4-5 cans a day). He was an unstable personality, often got headaches, and was diagnosed with massive stomach cancer at age 20, and died four months later. I have never drank Coke since..

    Jack, thanks for the elaboration on dairy – it would seem the A1 casein deserves to be up there with gluten. Too bad there is such a powerful industry depending on it!
    That said, I grew up on (grass fed) milk from Holstein cows that i milked myself and have no health problems – maybe I am just lucky. Still, I’m not going to push my luck these days.

    On the topic of DHA, clearly getting it from food is always better, but is getting it from supplements “bad”? Thinking about my cancer friend, should she go for a very high intake of DHA, even if that means cod liver or fish oils? She is a pescatarian, and does eat reasonable amounts of salmon.

    Do we get the similar benefits from conjugated linoleic acid? – there seems to be very little research on this.

    • Jack June 17, 2012 at 6:44 pm - Reply

      @Paul N that is all in Brain Gut 4. You may have to wait on that one…….but the answer will make you question a lot what you been taught to believe to be true is in fact false. CLA has its place…..but its not big in making a brain.

  20. coldbren June 17, 2012 at 7:28 pm - Reply

    Brain hurts. Does this mean organic heavy whipping cream is out?

    • Jack June 17, 2012 at 7:29 pm - Reply

      @Bren depends upon your particular gut…..If you have an obvious leaky gut due to celiac you might have to really worry. Dairy is not a good option for human guts contrary to what WAPF says.

  21. coldbren June 17, 2012 at 7:28 pm - Reply

    Sorry I am so overwhelmed I forgot to say…this is all amazing!

  22. coldbren June 17, 2012 at 7:38 pm - Reply

    Is there any benefit to putting on the blue light blockers about an hour before the sun goes down? They seem to calm me down and the sun sets so late in the summer. Will this help or will it make my cir. cycle worse?

    • Jack June 17, 2012 at 7:42 pm - Reply

      @Bren I would not do it…….but I doubt it will hurt badly.

  23. Weila Smith June 17, 2012 at 7:59 pm - Reply

    jack said: “@AkMan… dont need a bone in man hood when you’re going in face to face……because your spine caused your female’s canal to move anterior in the colder and wetter coastal environment and you could no longer go in the back door as you used too when you where in the forest all the time……..its all about the retrovirus re shuffle……..Stay tuned my friend, because epigenetics did get rid of the proverbial boner. All to be revealed.”

    do chimps go face to face?

    • Jack June 17, 2012 at 8:30 pm - Reply

      @Weila No chimps dont go face to face, they coitus from behind. Humans go face to face and this is why they have no bone. Most aquatic mammals go face to face, ironically. Also when you go to face to face it calls for a bigger penis and a man has a bigger penis than a chimp or a gorilla for that reason. The biggest penis on the planet for body size is found in the walrus…..another sea dweller.

  24. NittDan June 17, 2012 at 8:06 pm - Reply

    Missing something…what is WAP?

  25. NittDan June 17, 2012 at 8:09 pm - Reply

    Oh, just got it…Weston A Price.

  26. Bob Smith June 17, 2012 at 9:07 pm - Reply

    Jack- “What do you do in real life? Are you in healthcare or just a victim of it? By your writing on this topic makes me think you might have a form of diabetes tied to wheat exposure……Are you familiar with Bill Davis?”

    I love hanging out on both of Dr. Davis’ blogs, trackyourplaque and wheatbellyblog. I can’t say enough good about them or Dr. Davis’s work.

    I’m more a victim of the healthcare system. I am treating celiac disease, Graves disease and a blossoming case of LADA diabetes with diet. It’s working, but it’s very restrictive. I seem to be one of the unlucky people whose zonulin switch is stuck in the “open” position.

    I’m a mix of celt and solutrean (plains Indian). The fact that central European bloodlines have been improved by permeability is very interesting, but it’s little comfort to people like me whose bloodlines have yet to be purged. The hypothesis that zonulin permeability presents new antigens to the human genome for transcription is very interesting. It answers a longstanding question of mine, namely why does the intestinal immune system hand off bad juju to the blood instead of dealing with it. I figured the blood immune system was more capable. Your theory makes more sense, because it’s more basic to survival of the species.

    Recently I was a caregiver for a relative with lung cancer, and I had a close friend with lung cancer. I researched hard and found answers right down my metabolic pathways. I was not a decision maker. The decision makers refused to listen. My relative and my friend both died. Type 2 diabetes is a totally addictive condition, and food opiates are the reason.

    It seems that most people pleasure themselves until it causes problems. The “problem” level varies widely due to how much agricultural and antigen selection our blood lines have been exposed to. We autoimmune types are canaries in the coal mines of people with metabolic conditions.

    I confess to having written my cancer post a week ago. I posted it on a cancer board, but those people are too addicted to even consider it. My cousin was just killed by a driver supposedly having some kind of diabetic seizure. This sucks rocks.

    • Jack June 17, 2012 at 9:27 pm - Reply

      @Bob you asked, “namely why does the intestinal immune system hand off bad juju to the blood instead of dealing with it.” The answer is improving adaptability of the immune system by gaining more genetic material and being able to collect more DHA to assimilate into excitable membranes in the CNS…… also allows for more genetic material to make a brain via epigenetic shuffling. This was the initial benefit…….but today since our environment is not yoked with our genome nor our epigenome…….we get Autoimmunity. It’s all about mismatches.

  27. Bob Smith June 17, 2012 at 9:22 pm - Reply

    @Jack and @Weilla- Three words ….The Naked Ape, by Desmond Morris. It doesn’t answer everything, but it answers a lot.

    We are marine mammals.

    We’ve been discussing tiny evolutionary changes here. Wholesale changes are made when killing environments kill sepcies down to a breeding pair or two. The remaining individuals posess mutations which allow them to thrive and reproduce.

    And reproduction is key. Morris concentrates on the unique characteristics posessed by a female and her infant which would have allowed them to survive where others failed. These traits are still on display today. There are even more intimate questions which I don’t remember in the book …..such as, what adaptations masked mom and baby’s smell from large aquatic predators?

    Think about it. There are anatomical answers.

    • Jack June 17, 2012 at 9:29 pm - Reply

      @Bob When you read my ideas…….the answer has always been in our heads. The bone collectors only looked at the bones……that is why we don’t know where we come from. I think I do. The answer lies in the brain.

  28. JanSz June 17, 2012 at 9:49 pm - Reply

    @Paul N
    “should she go for a very high intake of DHA, even if that means cod liver or fish oils?”

    one opinion is presented here:

    The elevated levels of EPA and DHA predominantly come from
    suggestions by their regular physicians to try fish oil.
    With the encouragement now coming from
    an authority, the over-expression of EPA and DHA has
    reached epidemic proportions. However, the direct effect
    on the body is that fish oil suppresses arachidonic acid
    and other omega 6 fatty acids (Gurr 2002), which further
    cause metabolic disturbances (see case studies).

    • Jack June 18, 2012 at 7:07 am - Reply

      @JanSz with regard to supplementation I agree with you but not with regard to intake of seafood. The biochemistry of seafood ingestion, digestion, and nutrient assimilation in the brain is nothing short of evolutionary magic. That will be coming in the series future. Patricia Kane science is all about the cell membrane. There is a bit more to the story, although her part is quite important.

  29. Jerry Malone June 17, 2012 at 11:29 pm - Reply

    Jack, given that we have gut designed by evolution to be leaky, is this why we cook our food? I have always wondered why we are the only animal that cooks.

    • Jack June 18, 2012 at 7:08 am - Reply

      @Jerry this came after our encephalization quotient improved but the quality of the nutrient density and the hormone activation is gave us were the signals to drive change to the mammalian body plan to sculpt us.

  30. Paul N June 18, 2012 at 12:15 am - Reply

    @jan Sz,

    That is quite a paper, interesting explanation on Arachadonic Acid, which is demonised (especially by vegans, since it is animal sourced) as inflammatory. It says it is mainly inflammatory in the presence of *excess glucose*!

    “An almost untouchable subject is the consumption of excess carbohydrates and the subsequent rise in blood sugar and its potential inflammatory effect. The physiological effect of too many carbs directly implicates AA.”

    However, they go on to say that linoleic and Alpha linolenic are the two EFA’s and then explain how our production of DHA is less than 55 efficient!

    i suspect that elevated concentrations of EPA and DHA are likely not as much of a problem, if at all, when you are fat adapted/metabolically flexible, and especially when you are in ketosis (like Inuit in winter).

    For an alternative, and quite remarkable n=1 human trial of very high doses of DHA and EPA, consider the sixth comment to this story;
    Omega 3 kills solid tumour cells

    A 78 year old man cured himself of two malignant lung cancers by taking 15g of fish oils a day! (and no flax oil).
    A 93% reduction in the tumours in 3 years and eight years later (now 86) tumours 98% gone.
    Full paper here , interesting reading and amazing CAT scan photos;

    DHA is clearly good stuff – wonder how it became “essential” to us?

  31. Dawson June 18, 2012 at 12:18 am - Reply

    I learn so much every time I read Dr. Kruse’s blog. The changes I’ve made in my health and life are dramatic and evolving. I love optimizing my health and quality of life.

  32. Weila Smith June 18, 2012 at 4:40 am - Reply

    i don’t know if this info would modify your theory or not:

    “Bonobos become sexually aroused remarkably easily, and they express this excitement in a variety of mounting positions and genital contacts. Although chimpanzees virtually never adopt face-to-face positions, bonobos do so in one out of three copulations in the wild. Furthermore, the frontal orientation of the bonobo vulva and clitoris strongly suggest that the female genitalia are adapted for this position.”

    • Jack June 18, 2012 at 7:03 am - Reply

      @Weila no it would not. we came from chimps and we know that from molecular biology……

  33. Weila Smith June 18, 2012 at 4:42 am - Reply
  34. Elin Duke Potter June 18, 2012 at 4:56 am - Reply

    @Weila – Humans and Bonobos go face-to-face and are “rigged” for it. Bonobos also have both hetero- & homo- encounters because intercourse is a socialization for them: they use it create & strengthen alliances, as well as to relieve stress.

    • Jack June 18, 2012 at 7:04 am - Reply

      @Elin I think humans need to use it a bit more for the stress reduction as well.

  35. Jerry Malone June 18, 2012 at 9:17 am - Reply

    Wait, do you mean that cooked food activates hormones that raw food does not?

    • Jack June 18, 2012 at 10:25 am - Reply

      @Jerry Cooking makes digestion easier……..this means nutrients can be assimilated easier. There is some evidence that cooking does affect the hormone signaling but we need more data to make that call.

  36. Andre van Staveren June 18, 2012 at 9:36 am - Reply

    I really feel like my insights are exploding. This is so deep. But I want to know it all. I am 51 now – no health problems yet – and I know I might have to save some friends in the future. All this knowledge certainly will help. This is not just reading. Feel like I’m doing an online course in health management.

    • Jack June 18, 2012 at 10:26 am - Reply

      @Andre it is always best to be proactive than reactive when you are facing some health issues.

  37. Andre van Staveren June 18, 2012 at 10:29 am - Reply


    You state : It seems that most people pleasure themselves until it causes problems.

    Let’s not forget that the foodindustry puts monosodiumglutamate (MSG) to make us eat. It could be less of a choise and more of being victime of a criminal food industry. MSG, Asparame, Carrageenan; all poinson to the brain. Read the food labels; it’s very hard to avoid (and I live in Europe).

  38. Andre van Staveren June 18, 2012 at 12:28 pm - Reply

    Dr Kruse,

    Just did and realised I’d seen it before. First time I learned about it was by Dr Russel Blaylock. Been avoiding these chemicals like the plague ever since. You didn’t mention carrageenan (e407). It’s in every pack of cream I see. Is my paranoia justified?

    • Jack June 18, 2012 at 3:13 pm - Reply

      @Andre your paranoia is perfectly placed. Avoid them all like the plague

  39. JanSz June 18, 2012 at 12:55 pm - Reply

    @JanSz with regard to supplementation I agree with you
    not with regard to intake of seafood.

    The biochemistry of seafood ingestion, digestion,
    and nutrient assimilation in the brain is nothing short
    of evolutionary magic.
    That will be coming in the series future.
    Patricia Kane science is all about the cell membrane.
    There is a bit more to the story,
    although her part is quite important.
    Reminder/credit, you have send me to dr Patricia Kane, (thank you).
    Speaking of seafood, is there a way to get a fresh (whole) krill on our menu,
    plus ghee & extra dose of garlic & sea salt?
    When I look now at Krill oil, I see
    EPA & DHA, lots of them, too much DHA relative to EPA
    “ideal” EPA/DHA=3/1
    But the value of EPA & DHA is fortified by
    phosholipids that come with Krill oil, and are missing in Fish Oil.

    Phospholipids are repairing cell membrane.

    Dr Patricia Kane decided to fortify her phoshatidylCholine (complex)
    with wegetable fatty acids
    linoleic, alpha linolenic & oleic acids.
    I am sure she knows about availability of Kril Oil, but decided against it.

    As for EPA & DHA she recomends Kirunal,EPA/DHA=3, but I have found
    GNC Triple Strength Fish Oil, EPA/DHA=647/253=2.56
    Now Foods Krill Oil one softgel contains, EPA/DHA=80/42.5=1.9

    I have summarized my current plan on post #1 here:

    Can’t wait until you have a time to write on this subject, that will be coming in the future series.

    Thank you so much.


    • Jack June 18, 2012 at 3:14 pm - Reply

      @JanSz I will be hitting this subject in the current series in several ways

  40. E June 18, 2012 at 3:14 pm - Reply

    Jack: I find this both sad & fascinating. My father died of T2D. When I think of all the bad medical advice he was given – advice that clearly made his condition worse and caused his death – I could scream. He was told to eat a low fat diet & he used to say he was always hungry. I often saw him prowl the kitchen for food & eat like a starving man within an hour of having a full dinner (a low fat dinner). The phrase being used here “food opiates” really strikes home. His behaviour was not dissimilar to that of an addict.

    • Jack June 18, 2012 at 4:32 pm - Reply

      @Joan We did not know… we do. That makes today’s situation worse in my view. This info needs to get to people so they can make the correct changes to their environment. Sadly when you are sick n tired and addicted making these changes is rarely done. That is the frustrating clinical side of medicine because few people believe cutting wheat/grains and dairy makes any sense. They call you a quack, until they read the data……..and then their faces turn white.

  41. JanSz June 18, 2012 at 4:10 pm - Reply

    @JanSz I will be hitting this subject in the current series in several ways

    Thank you.


  42. Weila Smith June 18, 2012 at 6:16 pm - Reply

    Jack said: “@Weila no it would not. we came from chimps and we know that from molecular biology……”

    “Bonobos and humans share 98.7 percent of the same genetic blueprint, the same percentage shared with chimps, according to a study released Wednesday by the journal Nature. The two apes are much more closely related to each other — sharing 99.6 percent of their genomes — said the study’s lead author, Kay Prufer, a geneticist at the Max Planck Institute in Germany.
    “Humans are a little like a mosaic of bonobo and chimpanzee genomes,” she said.”

    Now does your theory change?

    • Jack June 18, 2012 at 6:19 pm - Reply

      @Weila No, it does not…….its not about the genome and never has been. I guess you missed that point in BG 1, because it was subtle but I take the gloves off soon enough. Its about the HERV’s we have acquired and their expression via the environment transitional ape and homo first saw……. Maybe BG1-4 will explain it better as we roll on. The Bone collectors have made this error for years…….Molecular biology and ERV’s, and McClintock’s work have changed the evolutionary biology arena…….

  43. Weila Smith June 18, 2012 at 7:29 pm - Reply

    i don’t have the scientific background to judge if the genome is irrelevant here. bye bye

    • Jack June 18, 2012 at 7:36 pm - Reply

      @Weila you don’t need one. Look at a chimp or a bonobo. Do they appears we do? How big are their brains? Yet their DNA is basically the same. So what might be the difference then? Ask yourself…… ain’t the genome. It is how it is expressed. That is all epigenetics and HERV’s. Guess what………we got more of it in our genome than any other mammal…… ask yourself why? And how did we get? I just answered that in BG 1.

  44. TheKid June 19, 2012 at 12:26 am - Reply

    @Jack – In the conventional wisdom in the blogosphere, leaky gut is looked upon as a problem. Since I have one, I tend to agree. And conventionally, it is understood that some people are leaky, while others are not. Question 1: Are you saying that ALL humans are leaky? Can we find any cases of humans who DO NOT have any leakiness in their guts whatsoever? Or is it that some people are MORE LEAKY than others?

    Question 2: If some people indeed experience greater intestinal permeability than others, then how does that impact real time human development? Does the least leaky amongst us humans have the “minimum effective leakiness” that allows them to benefit the same way all other humans do? Or does greater leakiness lead to greater benefit over successive generation?

    Question 3: What you are saying seems to be contradicted by the rapid proliferation of Autism spectrum disorders. If it turns out that a leaky gut is causal in the development of autism or at least a strong co-factor, then leakiness will not be of benefit. Autistics are poor candidates for marriage/relationships and the passing on of their genetic material. All that thanks to a leaky gut. Now I do understand that the gut-Autism link is driven by inflammation, but again, the end etiology drives the same problem. Where does that leave us in the future.

    Question 4: If a leaky gut is the jumping off point for solid brain development, then why do those of us with leaky guts have problems with assimilation of ingested nutrients? Shouldn’t that leakiness be a super-highway for the assimilation of nutrients?

    Question 5: Assuming that starting in the Pliocene certain hominids were more leaky than others (with all of them leaky to some degree), were those variations in leakiness passed on to us? And does less leakiness mean less of a chance for optimal brain development? Can leakiness in modern times be correlated to IQ? For instance, mild autism can manifest in someone becoming a savant? And does the savant, with his/her leakiness represent the new optimal brain development?

    • Jack June 19, 2012 at 6:24 am - Reply

      @The Kid.

      1. Yes, all humans are designed to be leaky to absorb specific nutrients and to absorb HERV’s to make more genes. This implies the key to disease is the relative leakiness. Most people with gut issues have a brush border that is like the Hoover dam with a gaping hole in it. We are designed however to have a slow controlled leak of water to make our immune system and brain highly adaptable. Some people are a lot more leaky than others……you got the concept.

      2. That question will be answered many times over in Brain gut 2 and beyond……I promise. Leakiness tremendously speeds up epigenetic adaptation of the genome. This increases our ability to adapt but if we live with mismatches in our environment constantly……we get disease. The last thought in BG 2 will shock you because it is so counter intuitive to how you think.

      3. No, Autism fits it to a T. You will have to trust me on this until the BG series develops. YOu dont have th efull perspective yet, but you will soon. You mentioned to me after the Factor X webinar…..that the implications for humans today were bad if I was correct……that we had to stop evolving it appeared to you to get optimal today………..remember that as you read the last thought in the next blog.

      4. That is coming too…….slow down enjoy Ohio have a Starbucks and I will take you there.

      5. Yes they were……once we assimilated the vibrio strain……the advantage likely selected for rapid adaptation to the new situation in the Rift Zone. I hope when you return home that you learn more about this area because it is in your backyard. Maybe you’ll visit and send me some pictures for later blogs……? Normal leakiness is a pre requisite for formation of a brain. Excessive leakiness makes the brain sick……ever since we evolved it……we have been making ourselves sick. Yes I believe leakiness does correlate with IQ as well. Chimps, have a savant cognitive ability compared to humans that I will show you due to their simple brains. Idiot Savants are possible in us when we lost cognitive complexity. This is an example of exaptation or reversal to a more primitive forms.

  45. E June 19, 2012 at 4:52 am - Reply

    Jack: I agree with you wholeheartedly! With my father’s example, I have always believed there was a lot more to this than what the CW said. Everything you are saying resonates. I was fortunate enough to encounter a forward thinking gynecologist who told me to cut out dairy over 6 years ago. The changes I saw within 3 days were incredible – the first being the aches and swelling in my joints disappeared. I’ve now weaned myself off grains and it’s only after being off them that you realize how bad they make you feel. You know all about it if you fall off the wagon. I tell everyone I know about your blog. Some listen, some don’t. On a happy note a good friend of mine is now doing the leptin reset. She’s lost over 30lbs in a couple of months and is feeling great. After seeing her success, her husband is now doing the reset and has lost 20lbs. What you are doing is so important Jack. It isn’t just a weight issue – it’s life and death. I have to thank you again for having the courage, generosity and knowledge to put the word out there.

    • Jack June 19, 2012 at 6:26 am - Reply

      @E This science is about how we are designed to work…….This series is foundational to my theory in the Quilt document. Thanks for the info on your friends…….tell them to “epi-paleo it forward”.

  46. Inger Larsen June 20, 2012 at 1:34 am - Reply

    If we get HIV easiest through our guts.. might that be why homo sexuals have a higher rate of AIDS because they use anal sex a lot more than heteros I suppose? That’s way the HIV infected sperm ends in the gut.. oral sex might be dangerous too because of this..

    • Jack June 20, 2012 at 6:53 am - Reply

      Inger, there are different reasons and those will be coming soon.

  47. Inger Larsen June 20, 2012 at 1:37 am - Reply

    “Normal leakiness is a pre requisite for formation of a brain. Excessive leakiness makes the brain sick……ever since we evolved it……we have been making ourselves sick. Yes I believe leakiness does correlate with IQ as well. Chimps, have a savant cognitive ability compared to humans that I will show you due to their simple brains. Idiot Savants are possible in us when we lost cognitive complexity. This is an example of exaptation or reversal to a more primitive forms.”

    This just opened my eyes big time today, Doc.
    Thank you!!!!

    • Jack June 20, 2012 at 6:53 am - Reply

      @Inger I think the next one is really going to open lots of eyes.

  48. Nonchalant June 20, 2012 at 10:36 am - Reply

    So we should thank the leaky gut, which turns out to be my biggest problem.

    • Jack June 20, 2012 at 10:41 am - Reply

      @Nonchalant when the gut is super permeable that is where disease begins……when it is as leaky as designed… issues.

  49. Bob Smith June 20, 2012 at 3:21 pm - Reply

    Jack- “The tyrosine residues in BCM7 molecular formula cause it to be a very oxidizing particle……think low HDL and high sdLDL. DPPIV also goes by the name CD26 and it alters the toning down phase of eicosanoids (omega 6’s) that stop the immune process from progressing. When this happens the immune system stay lit on alert and makes Ab’s and activates innate and cell mediated immunity to cause all kinds of havoc that we see today as modern disease…….even cancer.”

    Wow, I didn’t know the casein molecule contains so much tyrosine, or that DPPIV tries to deamidate it. That’s interesting because the body uses tyrosine as a signaling molecule for protein and tissue creation. I guess it makes sense, though. Milk is the preferred food of baby mammals. They use it for creating tissue. Once grown, though?……

    Tyrosine collects everywhere the body creates protein and tissue. Tyrosine concentrates in the reproductive organs, breast, liver, pancreas, thyroid, thymus, etc. Cancer also represents tissue formation, so tyrosine can be used for forming body tissue or for forming cancer. Cancer stays away from places like muscles where food gets burned for energy, and attacks organs where tyrosine initiates the burning of food for protein and tissue creation. I called it “burning”, but tissue creation is more of a hybrid operation incorporating aspects of fermentation. Cancer ferments food, so it’s a short trip from creating tissue to creating cancer.

    Anyone who wants to know if their body is veering dangerously close to cancer metabolism? Non-autoimmune thyroid shortage is an indicator. Thyroid hormone does not deplete rapidly in energy metabolism. It depletes rapidly in tissue-creation metabolism,

    I spent a long time off of gluten, legumes and nightshades. I couldn’t tolerate milk, but could tolerate white cheeses. My problem, like so many celiacs, was lactose intolerance. After a couple years I started getting bad head and neck pain. My immune system was keying on various things which led me up some blind alleys. Finally I eliminated all dairy, and voila! -I’m slowly getting healthier.

    Now every time I accidentally get “dairied” the headache returns. It appears that some predator fish would help.

    • Jack June 20, 2012 at 3:35 pm - Reply

      @Bob I realized this very link in my back and neck pain patients here in Nashville. I try to change this first before I operate…..sadly many of them think giving up wheat or dairy wont matter and they would rather have the quick fix……until it does not work. Go back and look at the patient video again on the CPC#5 blog……..Vickie’s story is precisely what you describe and you see precisely how I fixed her when one of my competitors could not because he did not realize why her gut and adrenal gland were the source of her spine surgery failure.

      Once growth is gone milk should be gone for humans……the irony is that one a brain gut basis the weaning period for humans should be a lot longer based upon other mammalian norms but it appears this is another thing that has been socialized out of our consciousness to create a mismatch. This makes kids guts a mess earlier in their life because they all have the gut altered but a simple sugar diet which selects out for a gut flora that is the perfect storm to create inflammation, obesity, and a very permeable gut that can not absorb the nutrients the brain or body needs to stay optimal.

      Nothing ruins a gut faster than a diet of simple sugars……..because it destroys the natural gut flora fastest.

  50. Bob Smith June 20, 2012 at 4:42 pm - Reply

    @Jack Now you have another anecdotal case linking neck/headache to casein. I forgot to mention that I’ve been off of fructose and sucrose (including fruit) the longest of all foods ….25 years.

    I’m pretty sure I have no acetaldehyde dehydrogenase ….solutrean ancestry.


    • Jack June 20, 2012 at 6:51 pm - Reply

      @Bob you get real red with red wine and booze…..tell tale sign. Or that you get drunk real easy on a glass of red wine?

  51. Lee June 20, 2012 at 6:10 pm - Reply

    @Jack Now you have another anecdotal case linking neck/headache to casein. I forgot to mention that I’ve
    Bob Smith:
    been off of fructose and sucrose (including fruit) the longest of all foods ….25 years.

    I’m pretty sure I have no acetaldehyde dehydrogenase ….solutrean ancestry.


    Are you Powhatan? Or Jamestown area? Do you have an email on here? PLZ msg me

  52. Lauren Porter June 20, 2012 at 9:12 pm - Reply

    If milk should be out of the diet once ‘growth is gone’ does that theoretically mean that dairy (organic? raw?) is better for children than for adults? Is fermented dairy better than non-fermented as WAP suggests. And does length of breastfeeding have any impact on a human’s ability to tolerate dairy? I have eliminated it totally from my diet, but not totally from my children’s (7 and 11, breastfed for 3 years each). But it sounds like it maybe needs to get the boot along with the grains.

    • Jack June 20, 2012 at 9:21 pm - Reply

      @Lauren…….I’ll be c;lear…….if they ain’t on your breast they should not be drinking any milk. Any questions now? WAPF is not optimal. It is suboptimal for the homo species……jut because you can do something does not mean it is OK for you to do……..just like safe starches.

  53. Bob Smith June 20, 2012 at 9:21 pm - Reply

    I get sick and infected for a week after fructose or ethanol.

    I know that half of my Indian heritage is Creek. The other half I’m not sure about. Put my grandfather’s face with his anglicanized Indian name, and it’s obvious. His tribe probably wasn’t as far east as Powhatan. Andy (curse him) put the fear of God in lots of Indians, so they didn’t talk about their heritage much. Lots of American family trees have redskin limbs. Most Indian blood comes from a few generations back, so it gets re-stitched into a mix of tribes. I’m lucky to be able to trace some of mine directly.

    Back on topic …..My grandfather loved ice cream, and died of a burst brain aneurism.

    • Jack June 20, 2012 at 9:23 pm - Reply

      @Bob I have not gotten to neurosurgery much yet in this blog…….but AVM’s nd aneurysms are preventable. If you read the Quilt levee 5. There is not a disease more sudden than these two inflicted on mankind…….when they hit it is fast and brutal. And it is an epigentic disease caused by a serious lack of an epi- paleo solution……dietary wise. That is also coming in this series. I mention vasospasm from both…….When I get there……my profession like it much. Rest assured.

      The next blog in this series is going to be electric…….and I mean that I am going after some really big dogma.

  54. Lauren Porter June 21, 2012 at 1:08 am - Reply

    @Lauren…….I’ll be clear…….if they ain’t on your breast they should not be drinking any milk. Any questions now?
    Nope, no questions 🙂 Thanks, Dr K!

  55. Caroline Cooper June 21, 2012 at 9:02 am - Reply

    What about butter, raw cream or raw colostrum? Do you think seasonal dairy consumption – May to August – could be safe for some?

    • Jack June 21, 2012 at 9:33 am - Reply

      @Caroline It depends upon the gut…..if it is leaky Im OK with colostrum…..and ghee. I’d limit cream though.

  56. Jerry Malone June 21, 2012 at 11:06 pm - Reply

    Jack, how does vitamin D affect leptin levels? How does vitamin D supplementation affect the LR? I have read that it lowers serum leptin levels. If this is true, is a good idea to supplement with vitamin D while doing the LR and CT? Thanks.

    • Jack June 22, 2012 at 6:23 am - Reply

      @Jerry people who ar LR have low vitamin D levels because LR blocks formation of T3. T3 and Vitamin A are the cofactors that convert LDL cholesterol to all steroids including Vitamin D.

  57. Andre van Staveren June 22, 2012 at 2:40 am - Reply

    Dr Kruse,

    Is chickenskin a sign in it’s self? Does that trigger something inside? Or is shivering required.

    • Jack June 22, 2012 at 6:25 am - Reply

      @Andre I am not sure what you are referring too?

  58. pete eddy June 22, 2012 at 8:20 am - Reply

    Jack, how does 3 or 4 – 10 minute 40 degree showers fair up for a CT Protacol?? Thanks, luv those COLD showers!!

    • Jack June 22, 2012 at 8:44 am - Reply

      @Pete they are fine…….but not as good as cold baths.

  59. matt Ford June 22, 2012 at 8:29 am - Reply

    Dr Kruse, What are you eating these days? I love fruit, how can I incoporate some into my diet? Is it ok to eat it alone or should I combine it with protein and fat???

    • Jack June 22, 2012 at 8:59 am - Reply

      @Matt What I eat is in my e cookbook.

  60. […] what Werner Heisenberg predicted in his uncertainity principle in 1925, that I mentioned in Brain Gut 1. If you do not believe this is actually how molecular biology works in life, consider that one gene […]

  61. Nonchalant June 22, 2012 at 9:36 am - Reply

    Andre asked “Is chickenskin a sign in it’s self? Does that trigger something inside? Or is shivering required.”

    He means goosebumps. 🙂

    I personally think when your hair raises up, that is a good sign. Andre, I did not shiver while taking ice baths after the first couple times. But I did have ‘chickenskin’. Now that it is summer I have backed off of the ice baths, because my tap water is so warm. 84F and climbing. But I try to get cool enough for ‘goosebumps’ at every opportunity.

    • Jack June 22, 2012 at 9:47 am - Reply

      @ Andre Goosebumps/chickenskin are a sign of calorie burning to free heat……and not ATP. I dont eat chicken much so I guess its why I did not make that connection?

  62. JanSz June 22, 2012 at 9:59 am - Reply

    I dont eat chicken much
    I vaguely recall statement made (probably) by you,
    meat from chicken or any other bird is least favorable souce of food for humans.
    Eggs & liver ok.

    If true, what is the reason?


    • Jack June 22, 2012 at 10:33 am - Reply

      @JanSz We are what we eat eats…….you ever seen what a chicken eats? It is a vegetarian that does not change its food to omega threes like fish or ruminants……so this is why I say Fowl is foul for human consumption.

  63. Susan Moles June 22, 2012 at 1:28 pm - Reply

    What about chickens that are feed a lot of flax? Would they be a little bit more beneficial than those not eating flax? Our Costco sells a brand of chicken that are feed lots of flax.

    • Jack June 22, 2012 at 1:45 pm - Reply

      @Susan……..Fowl is foul. It is just above soy on my protein list fit for humans. I rarely eat it.

  64. Susan Moles June 22, 2012 at 1:29 pm - Reply

    I meant fed not feed.

  65. Gretchen June 22, 2012 at 1:49 pm - Reply

    The implications here are phenomenal.

    Leaky gut is a double edge sword. It seems that those of us w/leaky gut who are sensitive to gluten or other substances (, virus, bacteria, fungi) might just be the “Canary in the Coal Mine”. Are we the individuals who adopt this “junk” faster and pass it along (Assuming survival)?
    So is the goal to maintain some permeability, but eliminate the holes you can drive a bus through?

    I’m intrigued where you’re going to take us….

    • Jack June 22, 2012 at 1:53 pm - Reply

      @Gretchen Yes…….those who are most leaky likely will have more junk in their DNA… which to collect. It will do them no good, just like it did Lucy no good in the primate clade……..but it just may make Lucy legacy stunning……..(it was……because we are it) It is life rolling the dice…………

  66. JanSz June 22, 2012 at 5:22 pm - Reply

    Fowl is foul. It is just above soy on my protein list fit for humans. I rarely eat it.
    dr Kruse, sorry to beat this topic to death.
    I would divide fowl parts that are consumed by humans into:
    3.-feet (for broth)
    4.-(meat, fat, skin)

    From what you said, I would assume that definitely you are avoiding #4.

    I am not clear on 1, 2 &3.

    eggs, liver, other

    • Jack June 22, 2012 at 5:25 pm - Reply

      @Jansz the best thing about chickens are its eggs… them with impunity……good stuff…….stay away from the chicken. Liver is great…..but below seafood. Feet for broth is fine……..but add ruminant grass fed bone…….meat skin bone of chicken is worthless……….you should be clear now.

  67. Andre van Staveren June 23, 2012 at 5:31 am - Reply


    There was no connection to food when I said chickenskin; it’s a direct translation from dutch. I’ll us Goosebumps next time, although I don’t eat goose that much 😉

    • Jack June 23, 2012 at 10:11 am - Reply

      @andre I did not know what chicken skin meant……I apologize.

  68. Andre van Staveren June 24, 2012 at 1:28 am - Reply

    No harm done. Just a reminder you have an international audience. Couting on CT to improve my mood 🙂

  69. August June 24, 2012 at 2:12 pm - Reply

    What is the significance of the fact that we don’t have the ability to synthesize Vitamin C? . . I assume the ability was lost. (a trait I believe we share with some of the other primates)

    • Jack June 24, 2012 at 4:04 pm - Reply

      @AugustThe answer to that is coming too…….And it may not be what you think either. I just gave it to you on the forum by the way……

  70. Marijke de Jong June 26, 2012 at 7:33 am - Reply

    I asked about a way to gain weight and you told me to eat raw dairy and take BCAA. But I am not a young animal, I am 67. Could that be why it is not working yet? The BCAA gave me diarrea.

    Anyway, I tried out the spring recipes and I like them a lot. Please tell your wife.

    • Jack June 26, 2012 at 7:41 am - Reply

      @Marijke BCAAs are not for everyone….it is very hit or miss…..but it will help you add weight. I have shared the recipe news and she was pleased.

  71. Bob Smith June 27, 2012 at 3:52 am - Reply

    Jack -Januvia is a DPPIV blocker……it also has been linked to melanoma production……how is that for a complication and a tie in to my theory?

    I read a few years ago that the idiots at big pharma were trying to sell a DPPIV blocker. Thank goodness the FDA stopped them.

    Oh wait, they didn’t.

    DPPIV is the enzyme which digests wheat gluten in the small intestine through deamidation. As shown, wheat peptides are responsible for causing insulin resistant type 2 diabetes. Zonulin permeability places partially digested gluten peptides into the bloodstream because it dumps the peptides into the bloodstream before DPPIV has time to finish digesting the gluten. Block DPPIV, and you exponentially increase the quantity of gluten peptides in the bloodstream, and increase patient susceptibility to type 2 diabetes.

    So far scientists have found no animals besides humans who produce DPPIV in the intestines. Evolution knew that grassy grain gluten causes insulin resistance and type 2 diabetes. Up until about 2 million years ago humans were like other mammals. We used DPPIV in the bloodstream for limiting the lifespan of insulin molecules. When humans started eating grassy grains, the gluten started killing us. But some pair of humans happened to release DPPIV in the small intestine, and it happened to break apart the gluten molecules. The gluten killed off this pair’s competition, and left this pair alive. They survived and produced our ancestors.

    The way this works out? DPPIV digests gluten. People with intestinal permeability place partially digested gluten into the bloodstream. They also place the unused DPPIV into the bloodstream. In the bloodstream the gluten peptides plug into cellular insulin receptors. Insulin gets robbed of the ability to transport sugar into cells. The blood fills with sugar, and elicits higher and higher insulin levels from the pancreas. The extra zonulin-facilitated DPPIV in the blood then limits the lifespan and quantity of the insulin so that it doesn’t cause permanent damage.

    These big pharma geniuses sell DPPIV blockers because they discovered that DPPIV breaks up insulin in the bloodstream. They figured since type 2 diabetics need more insulin, then blocking the enzyme which breaks up insulin would naturally supply the blood with more insulin. I’m sure that it does, but it also increases the supply of the gluten peptides which cause type 2 diabetes. Meanwhile, the increased concentration of circulating insulin gets robbed of any controls. The blood gets left with nothing to limit either the concentration or lifespan of insulin.

    The makers of DPPIV blockers totally disregarded this whole scenario. Like most big pharma products, DPPIV blockers don’t cure disease, they cause it.

    • Jack June 27, 2012 at 6:55 am - Reply

      @Bob you have jumped way ahead of the curve but I love it!

  72. Glamazon June 27, 2012 at 8:07 am - Reply

    I know we talk about this in the forum. I wanted to add this to the discussion: You Can Change your DNA.

    “Stem cell biologist and bestselling author Bruce Lipton, Ph.D., says the distinction between genetic determinism and epigenetics is important.

    “The difference between these two is significant because this fundamental belief called genetic determinism literally means that our lives, which are defined as our physical, physiological and emotional behavioral traits, are controlled by the genetic code,” Lipton said in an interview with the online magazine, Superconsciousness. “This kind of belief system provides a visual picture of people being victims: If the genes control our life function, then our lives are being controlled by things outside of our ability to change them. This leads to victimization that the illnesses and diseases that run in families are propagated through the passing of genes associated with those attributes. Laboratory evidence shows this is not true.” ”

    Taking control of our health…

    • Jack June 27, 2012 at 10:06 am - Reply

      @Glamazon if you read levee one of the Quilt……it is all about epigenetics.

  73. Paul N June 28, 2012 at 10:59 am - Reply

    Bob wrote;
    :Like most big pharma products, DPPIV blockers don’t cure disease, they cause it.”

    Never a truer word was written.

    If big pharma was a mechanic working on your car, here’s how they would approach the problems;

    -if the engine is blowing smoke, they would put a filter on the exhaust so you can see/s,eel the smoke. This filter would be expensive and need replacing, and would also reduce fuel efficiency of the car
    -if the engine is running noisy, they will do a soundproofing treatment so you can’t hear the noise. This will add weight, and possibly reduce airflow, so the (still noisy) engine will be prone to overheating, but at least you can drive on in quiet.
    – if the oil is getting metal particles in it, they will develop a better filter, rather than finding where the wear is occurring.

    etc – it is all about masking symptoms, but not curing the disease, so that you need the drugs indefinitely. Often the disease will then get even worse, because of the treatment, so then you need the symptom blocking drugs even more. Anyone who ends up on warfarin is a good example.

    It is a race to the bottom – with your life.

    BTW, do you have a reference for the wheat peptides causing insulin resistance? – I know a pre-diabetic person – bread and pasta lover – who refuses to admit that wheat could be part of the problem. Would love to show them some real facts.

    • Jack June 28, 2012 at 11:45 am - Reply

      @Paul N…..nice. Tell your friend to buy Wheat Belly by William Davis MD. After reading that if they still eat wheat there is no hope for them.

  74. Bob Smith June 29, 2012 at 8:08 am - Reply

    @Paul N Sorry, I put this stuff in my fact bag and forget….

    “Wheat Germ Agglutinin (WGA), the main lectin in wheat, is an insulin mimetic in tissue culture. A very good insulin mimetic.”

    Effects of wheat germ agglutinin on insulin binding and insulin sensitivity of fat cells

    Insulin-mimetic actions of wheat germ agglutinin and concanavalin A on specific mRNA levels.

    Insulin-like activity of concanavalin A and wheat germ agglutinin–direct interactions with insulin receptors.

    Concavalin A is in legumes …….beans, peas and peanuts.

    WGA and Con A are opiates. They come aggregated with very powerful opiates, so don’t expect a warm reception.

  75. Bob Smith June 29, 2012 at 8:59 am - Reply

    Meat and fat digestion follows a totally different pathway from wheat and dairy digestion. The pancreas releases digestive peptides like pepsin into the stomach while the liver and gall bladder insert bile acid. The bile acid activates the digestive peptides. The peptides deaminate (digest) various meat proteins while the bile acid dissolves the fats. This sludge goes down the intestinal tract where both products get absorbed into the blood.

    The next part is very poorly documented. The liver releases choline and cholinesterase. The cholinesterase neutralizes unused bile acid into bile salt which gets stored in the gall bladder. The key part of this process is the juncture when the liver stops producing bile acid, and starts producing choline. The liver decides when to do this by monitoring its own metabolic rate. When bile-related digestion produces sufficient adenosine, liver metabolism rises, and the liver switches from bile production to choline production.

    When we ingest wheat and dairy instead of meat and fat zonulin permeability produces a shortage of digestive adenosine. The liver delays the switchover from bile production to choline production. Bile acid fills the lower intestine. It causes inflammation and damage.

    But this spawns another big problem. Besides its digestive roll, choline sits, along with acetylcholine, at the juncture of nerve neurons. I think I have this order correct. Acetylcholine facilitates nerve signal transmission, then choline stifles the transmission. When digestion of wheat and dairy stifle production of choline, it takes away control of nerve function.

    Place this nerve disorder in an adenosine-starved inflammatory environment, and it’s easy to see how the immune system would kick into high gear.

    By concentrating on any single link in this chain of events it’s easy to see how big pharma gets it totally wrong.

    • Jack June 29, 2012 at 9:40 am - Reply

      @Bob You have it right……and Acetylcholine is the neurotransmitter of the vagus nerve and the parasympathetic system. It is tied to leptin via the area postrema in the fourth ventricle of the brain directly.

  76. Bob Smith June 29, 2012 at 11:35 am - Reply

    Paul N -“I know a pre-diabetic person – bread and pasta lover – who refuses to admit that wheat could be part of the problem. Would love to show them some real facts.”

    Pre-diabetes does not necessarily lie, as the name implies, in the type 2 diabetes causal pathway. Pre-diabetes usually proceeds type 2 diabetes. But the phenomenon usually represents dual effects of a common cause.

    Pre-diabetes is nebulously characterized by reactive hypoglycemia, and/or high, sustained blood sugar spikes. The blood sugar spikes do not represent the menace claimed by many low-carb gurus. They are a natural reaction. Blood sugar spikes when we ingest volatile sugars like fructose, pure glucose and amylopectin A in wheat. Blood glucose rises. It elicits insulin from the pancreas. Cells absorb the glucose. And blood glucose drops. The scenario is bad for people, but it represents how the body is supposed to respond to these unhealthy sugars.

    When glucose and insulin levels stay elevated after sugar ingestion, that’s a big problem. But it is not caused by anything in the sugar-spike pathway. It is caused by insulin-mimetic proteins, and it represents type 2 diabetes.

    Reactive hypoglycemia is caused by, I forget, the milk opioid which Dr. Kruse pointed at earlier, and by gluten A5 and B5 opioids. These opioids can mimic endorphin in people who are both genetically predisposed and have leaky guts. Both are extremely common.

    The pancreas monitors fight-or-flight catabolism by monitoring beta endorphin. The pancreas responds to endorphin by releasing insulin. The insulin stops catabolism before muscles can permanently damage themselves. When we ingest the above opioids the pancreas floods the blood with unsolicited insulin. Fat cells wick up blood glucose, and blood glucose plunges. Such low blood glucose levels are not harmful to fat-adapted people. The glucose plunge itself is harmful to carb-adapted people.

    Endorphin mimetic opioids, the ones which cause reactive hypoglycemia, are highly addictive. They produce the “kill for another fix” reaction seen in so many people with metabolic conditions. People who are susceptible to endorphin mimetic proteins usually become susceptible to insulin mimetic proteins from the same sources. The insulin mimetic opioids produce type 2 diabetes.

    Both “pre-diabetes” body types, the reactive hypoglycemia type and the spiking blood sugar type, overwhelmingly proceed into type 2 diabetes. But type 2 diabetes is not necessarily caused by either condition.

  77. Bob Smith June 29, 2012 at 11:41 am - Reply

    @Jack Wow. So nerve viruses like herpes simplex, cocksackie and varicella zoster don’t have to access nerves throughout the body via the circulatory system. Through adenosine and choline shortage, these viruses can go directly to nerve central.

    • Jack June 29, 2012 at 1:04 pm - Reply

      @Bob Bingo….as choline and adenosine are depleted it creates space in our cells that allow for easier viral DNA Incorporation and expression……get what else cause more room? Inflammation. As inflammation rises it uses up Vitamin D resources too…..and this affects immune response and the ability of the cell to activate its defense pathways. It then becomes a feed forward system. This is precisely how WBCs get out of the circulatory system and into tissues…..when in tissues they are called macrophages. In the blood they are monocytes. Inflammation creates leakiness everywhere. When somebody gets a latent infection like shingles from chicken pox it is a sign that the system has underlying inflammation…….guess what is called to patch the leaks? LDL cholesterol……….The normal repair response of the human body is to raise LDL in inflammatory conditions!!!! And yet modern medicine thinks its universally bad. Irony at every turn.

  78. Bob Smith June 29, 2012 at 3:13 pm - Reply

    I learn new things every time I come here.

    As an aside, I’m not convinced that most shingles cases come from latent zoster infection. Researchers have found increasingly virile, increasingly drug resistant shingles strains showing up randomly in older patients. Some of these strains are traceable directly back to zoster infections among active AIDS patients. This scenario provides an open transmission pathway, as old-people communities have some of the highest STD transmission rates anywhere.

    As with most wet contact pathogen patterns there are lots of ancillary infections. These unique new shingles stains aren’t recurring from dormant chicken pox. This points a finger at other shingles cases. I don’t believe the mainstream medical dogma. I think a very large portion of shingles comes from fresh transmission, and that’s a big reason why it emerges in people who’s immune systems have perfected ways of keeping their old zoster strains dormant.

    …..IMHO. But emergent or transmitted, the infection pathways are the same.

    By the way, one of the best shingles remedies is Ceylon cinnamon …..laurel cinnamon, NOT cassia cinnamon. I’ve seen it work.

    …..poor man’s Valtrex.

    • Jack June 29, 2012 at 3:47 pm - Reply

      @Bob Lots of toxins in Ceylon though……got to be sourced right

  79. Bob Smith June 29, 2012 at 4:56 pm - Reply

    @Jack, Please elaborate. Where should we be getting cinnamon?

  80. Bob Smith July 3, 2012 at 12:43 pm - Reply

    @Jack Point taken. I am generally intolerant of cinnamon. My wife is not.

    My wife and I were exposed to family memembers with shingles. My wife got shingles. I got extremely worsening autoimmunity.

  81. […] suspended from it. In humans, this plan has been strikingly altered rapidly. We must remember that Brain Gut 1 told us that humans, chimps and gorillas are very similar genetically but very different […]

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