digestion

 When I first moved into the college dorms, one of my favorite meals was Special K (with those freeze-dried "berries") floating in tan-colored soy milk. It was healthy and I thought it tasted pretty good. Looking back I shudder because it was quite clearly the culprit in many of the stomach issues I had, as it was rich in the dreaded Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols (FODMAPS). 

Once I realized that soymilk was one of the major causes of the bloating and other fun stuff I struggled with, I never bought soy milk again. 

But I've never been anti-soy. In fact, I can't imagine life without the culinary treasures of soy sauce and miso. For me, changing my diet was about shifting staples, not clamping down on the margins. I'm only willing to do that if absolutely necessary. I don't think soy is a problem unless you are getting a large percentage of your calories from it. 

And through my explorations of Asian cuisine I've come to appreciate soy for what it, which is a potent substrate for fermentation. That's why soy milk upset my stomach so much. But luckily, long ago someone figured out how to ferment it outside the body, creating rich salty flavors that characterize miso and soy sauce.  

It's by no means a recent food. There is new evidence that humans were using wild soybeans 9000 years ago and that domestication occurred 5,500 years ago.

American vegetarians embraced Asian soy products a long time ago, but it wasn't until I started actually eating authentic Asian food that it struck me on how much they were missing out on. In Asian cuisine, soy is an extender of animal and seafood products, creating potent health and flavor synergies. 

If you think tempeh is just some bland crappy paste-board-like soy concoction, you need to fly to Amsterdam and have homemade tempeh in a rich briny fermented shrimp and black pepper sauce. I've never ever had tempeh like that in America.

And I've found that even unfermented soy doesn't really bother my stomach. Oh, but only when it's served in a Korean restaurant that makes broth from scratch, boiling animal bones for days to achieve a creaminess, then boiling fresh homemade tofu and chunks of ox blood in the broth. It's digestible and much more delicious than it sounds, particularly when you pour some of the homemade kimchee into the broth.

Another unsung hero in Korean cooking is fermented soybean-red pepper paste, Gochujang, which makes sriracha seem bland. It works so well with beef that it's heresy to put it on some vegetarian brown rice gunk. It almost always contains barley though, so stay away from it if you don't eat wheat, though I'd wonder how much of it could be harmful because fermentation can destroy gluten. 

And really, there is nothing like liver or beef belly marinated in soy sauce. I know some folks use coconut aminos because they think they are reacting to soy sauce, but I don't think there is much in most soy sauce to react to, except for amines, which are present in coconut aminos too. 

But Asian food hasn't been immune for the industrialization of soy products, which leads to general mediocrity and upset stomachs all across the globe. The latest issue of my new favorite magazine, Lucky Peach, has an amazing article about miso. There are a great many types of miso, but the miso that most Asian restaurants serve is a powdered, pasteurized, fortified, bleached concoction that barely deserves to be called shinshu miso. But it's bland, ships easily, stores easily, and requires no skill to make into soup. 

The same thing has happened to broth and many other traditional foods. It's hard to find a restaurant that makes its own broths with bones rather than a powder containing MSG and other assorted non-food additives. Many Koreans now make a Gochujang that isn't fermented at all. 

The only good trend is the post-WWII trend of combining butter with miso or soy sauce. You can create some incredibly rich and wonderful sauces this way. I just now enjoyed some scallops with a soy-sauce browned butter glaze. 

For me the fascinating thing about soy sauce and miso is how deep and rich the flavors are, yet they do not compel me to overeat. I think it's a function of their complexity. They are delicious, but have an underlying funkiness. It's important, like fish sauce is to SE Asian cooking, but you definitely don't want to overdo it. 

 I usually don't like to watch people speak about stuff. Maybe that's why I almost never went to lectures in college. I prefer to read things. As Data from Star Trek might say, I find it to be the most efficient form of assimilating information. So you can watch my talk on Vimeo thanks to AHS, but if you read much faster (or you are hearing impaired), you can read the transcript below, which was donated by Averbach Transcription, which is run by a paleo enthusiast and you should consider hiring him if you need a transcript:

"Clues from the colon: How this organ illuminates our digestive evolution and microniche" by Melissa McEwen from Ancestry on Vimeo.

Dynamic Evolution and The Gut

  [applause] So, hi everyone. I was at Mat Lalonde's talk this morning, and I was thinking, "How am I going to introduce myself, what are my credentials?" And I don’t really have any. I have a degree in agriculture and I study anthropology currently at Columbia University, but I'm not in the Ph.D. program.
But I have had the pleasure to study with Professor Ralph Holloway, who's a really excellent physical anthropologist, and he inspired a lot of this presentation. And I have a website, it's called huntgatherlove.com, and you can visit it, and I have also a lot of the stuff from this presentation is there, and a lot of the references to the papers, if you want to read the original ones.

And yeah, I'm not a core scientist, but my boyfriend Chris is, and I try to study, you know, remind myself that chemistry and biology are really important even in anthropology, and I think a good physical anthropologist tries to really incorporate that into their studies.

What is so special about the human gut? Why do we care about it? Why don't we just eat like this nice ape in this picture on the left and just eat some healthy, high-fiber diet, which is low in fat? Just eat like a salad, because everyone knows that salad is really really healthy.

Well, the problem is we are not like gorillas; we're great apes, we have a shared history with gorillas, but we have our own unique niche. And I think when I'm reading a lot of the literature on evolutionary health, I'm seeing these different viewpoints. One I'm going to call statics, and it has an emphasis on what has been conserved from our evolutionary past from some time period, often which is defined somewhat arbitrarily.

And it also focuses on primate relatives such as gorillas. You know, we're great apes, they're great apes, we should eat like them maybe. And I think of course they have very interesting lessons, but I'm going to emphasize more the dynamic view of evolution, the emphasis on unique adaptations that humans have to their own niche, and our continuing evolution even now.

We're evolving as we speak.

So the static viewpoint is that the ancient human diet of some timespan, you know, Precambrian, Upper Paleolithic, was the optimal human diet. And there was a great deal of emphasis on the fossil record. Professor Holloway always likes to say, "When you look at the fossil record, sample size equals two, because there's not that many fossils from certain periods."

You know, we have part of a cranium and that's it of some periods. So it's pretty hard to abstract from the fossil record. And also emphasize related species that we share a common ancestor with. And a lot of times some of this research comes to the conclusion that a high-fiber diet consisting primarily of plants is optimal, and that everybody, every human being should be able to eat this way and be healthy.

There's a lot of Paleolithic Diet papers, but why not the Cambrian Diet? I mean that was a really long timespan, it was 52 million years versus like two and a half, and these creatures look perfectly healthy to me, and they seem way healthier than I am.

Here's a quote from Stephen Jay Gould that, I was a fan of Stephen Jay Gould for a long time, and I still admire him, but I don't agree with this quote, that, "There's been no biological change in humans for the past 40,000 or 50,000 years. Everything we call culture or civilization we built with the same body and brain."
And I thought Stephen Jay Gould was just this nice guy who talked about dinosaurs, but actually Professor Holloway told me that he has some questionable stuff in his research, and that idea that humans haven't changed for a long time is one of those. Another one is that he denies modern human variation quite strongly.
He has this idea that we're mostly the same, which in some ways is true; in some ways it's not true. And I think it denies the fact that we can gain a lot from looking at continuing evolution. And the dynamic view, which I'm going to talk more about, is humans are unique among the great apes, and recent human evolution has led to important changes, especially in digestion.

And besides our own genetics, we have the bacterial microbiome, and our evolution in that has been even more rapid, because bacteria have many more generations, they reproduce faster than we do. And there's high variation among modern humans, particularly with a growing population and introduction into new environments.

So there's probably high variability in [their optimal diet]. And a book that's been a big influence to me is "10,000-Year Explosion" by Gregory Cochrane and Henry Harpending, and it's, "How Civilization Accelerated Human Evolution." And it has pretty convincing evidence that human evolution not only didn't stop 10,000 years ago at the end of the Paleolithic; it's continued to accelerate greater and greater because of all this new environments and greater populations, and also the changes in culture and technology that have happened since then, which have been very rapid.

And in dynamism we have these four keystones I like to think about. One of them is our unique anatomy. Another one is our unique cultural behaviors. Another is our unique bacterial microbiome, which isn't shared with any other primate, and each person has a unique one. But also just in general a very high variability among humans.

And a lot of this is relatively unexplored because it's very controversial. It's hard to get funding. I've met people who do studies on human variability who can't publish them because they're so controversial.

And especially very important in unique cultural behaviors is a shift towards exogenous food processing. So in humans, in our evolutionary past, we processed food inside of ourselves, but in modern humans and in our evolution towards modern humans we have a shift towards processing food outside the body with cooking and grinding and soaking and all these other processes.

So when we're thinking about human evolution, we have to think of—this is an estimate of cells in the human body, and that there's maybe 10 trillion human cells and 100 trillion bacterial cells. And these bacteria are evolving faster than we are. And they're very very important.

They process nutrients, they produce nutrients, they fight off infections, are an important part of our immune system. They have a role in nearly every disease, even diseases you might not even expect, such as heart disease. There's a new paper that shows that metabolites produced by certain gut bacteria that some people have and some people don't have, in response to certain foods, can produce things that are implicated in heart disease.

And also, behavior. I mean, we can't do many of these studies in humans because they're unethical, but in fruit flies if you change the gut bacteria, you can change their sexual orientation. And you can understand why we can't do that experiment with humans; that wouldn't be good.

So there's several factors with these bacteria, and we have to think about interspecific competition—competition between different species, which is driving a lot of this evolution, intra-specific competition—so within even one species, you have tons of strains that are very different, and they're competing with each other, often in one person.

You can have several strains of one bacteria within you at one time. The host function, our own unique anatomy and genetics; our host fitness, which is quite important nowadays, now that a lot of people aren't as healthy as they once were. Particularly in the gut, there's a lot of people with dysfunctional gut permeability, which really affects the bacterial population.

You have food ingested by the host, and you have the metabolites themselves in microbiota, which is tons of different chemicals and fatty acids. And quite important for humans but not unique to humans is culture and technology. These can affect the gut microbiota too.

And there's a bunch of papers that are quite interesting that have more of a static view, and static's this view that we're going to look at other great apes and see what we should eat today. And I think a lot of this research is very admirable, but I think sometimes they come to conclusions that don't make sense in the light of our own unique anatomy.

One of them is Nutritional characteristics of wild primate foods: do the diets of our closest living relatives have lessons for us by talented primatologist Katharine Milton. Then you have this paper, "The Western Lowland Gorilla Diet, are there implications for health of humans. "

And here's a sample sentence from a paper like this, this paper is called "Case Closed: Diverculitis, Epidemiology and Fiber." It says, "The western lowland gorilla, whose diet may approximate a Paleolithic human diet, has an estimated intake of nearly 60% of its calories through the colon," and the second part of this sentence really puts a question mark on the first part:

You can see that this is quite interesting about gorillas. You know, they eat a diet very high in fiber, and it's all plants, pretty much, and they're getting a lot of carbohydrates in the diet, ingesting in their mouth. But then their colon, the bacteria in the colon is this giant bio-reactor. It's turning this carbohydrate, this fiber, this otherwise indigestible fiber into something called short-chain fatty acids.

And short-chain fatty acids are providing over 60% of calories for the gorilla. So the gorilla is eating a high-fat diet, actually; it's just not eating the fat directly. It's turning the carbohydrates that it's eating into fat, fatty acids.

And humans are quite different from other great apes. Here's a famous paper called "The Expensive-Tissue Hypothesis" by Aiello and Wheeler. You can see they did some linear regressions that looked at, based on other primates that we have data for, what should human organ weights look like?

And here's the expected human organ weights, and here's the observed. And what is different? Look how big our brain is and how small our gut is. But even within our gut, there's reorganization, and the reorganization, the driver of this is this food quality. And when I talk about food quality, I'm not talking about [Hardee's] versus Whole Foods; I'm talking about caloric density.

And with this high caloric density, there's less need for this processing equipment that's internal, these internal organs. And so energy is freed up for other organs, such as the brain, in this expensive-tissue hypothesis.

In this gut-brain tradeoff, you have higher diet quality, increased energy availability, and so larger brain. The small gut with the higher diet quality also frees up energy; larger brain. And more complex foraging behaviors, which keep enable… It's driving like a feedback cycle. You know, the more energy we're getting for our brain, the better—the bigger our brain is and the smaller our gut can get.

And you can see that the organization of the gut too, versus other primates—you have all these great apes here, and you have humans here, and look at the human small intestine; look how much bigger that is compared to the other great apes. And the colon is so much smaller. And you can see this in this chart from the Beyond Veg site, which is a great site.

You can see the chimpanzee has a quite long, well-developed colon. The orangutan does as well. But look at the human colon—it's very under-developed and small compared to these other apes. And we're not sure when this change happened in our evolutionary history. It's not like you can find frozen Paleolithic apes very easily.
But we do have this gut—in the post-cranial anatomy you have some indicators that might correspond to a smaller gut or a larger gut. And here is a chimpanzee here, a modern human here, and Australopithecus afarensis, living around maybe 2-3 million years ago, perhaps one of our ancestors.

And you can see this funnel shape in the ribcage, and a large pelvis, which could accommodate a bigger gut. And humans have this defined waist, which we also find very attractive in humans, and a smaller pelvis. And here's some of these apes stripped down, where you can see this giant gut in the gorilla, and the chimpanzee has a pretty bit gut, and an orangutan does.

Humans and gibbons do not. Gibbons are frugivores, so they eat a higher-quality diet than even the more leafy, kind of sticks and stuff that these other apes eat. And here's a human waist—very small compared to the other great apes, except for the gibbon.

And so in humans, how much do we get from short-chain fatty acids? How much do we get from the colon? The colon's smaller. And the human current maximum estimate is maybe nine percent from short-chain fatty acids. So if we go and eat a gorilla diet, we're not going to get as much out of it as the gorilla does.

We'll probably die if we just eat leaves because we can't turn it into short-chain fatty acids with the efficiency that a gorilla does. We don't have the equipment. But I must add a caveat to that. Most of these studies have been done in Westerners, and there's this new hypothesis floating around in papers, this idea that Westerners are the weirdest people in the world—and we are.

Our culture is totally different from most other cultures, and very unique in the history of the world. And so when we're taking data from Westerners, we have to be cautious, and we need more data from other cultures. Because as I say, humans have high variability. Maybe there are people who can get more short-chain fatty acids from fiber than the average Westerner.

And there's very few papers on this, but I found one from South Africa, and they look at autopsies of humans, and they found that some humans have different-shaped colons than other humans, and divided them up into three different kind of morphological types. Here is a short pelvic sigmoid colon, the so-called "classic type", and the long, narrow type.

And different people had different colons. And certain people, like Africans were more likely to have this colon type, and Indians and whites were more likely to have this smaller colon type. And whether or not this has implications for digestion, I don't know. And I think we really need to explore this, because if this colon is so much bigger, what kind of implications does this have?

Can this person get more energy from short-chain fatty acids? Is this person better adapted to a high-fiber diet? And you can see why this sort of research is controversial, because it also has data about different races. But it's very interesting to me. A lot of papers on this subject are not published in English journals at all; you have to read like Czech or something, so it's hard to track down. But it is out there.

What about the evidence that we see in some papers on the Paleolithic Diet, that Paleolithic humans ate 150 grams of fiber a day? I don't know anyone who eats that much fiber, and there's no known modern human culture that eats that much fiber. And most of those estimates are based on [coprolites], and the method for estimating that is quite questionable to me.

We also have to consider the cultural context. There are some good coprolites from hunter-gatherers in the Pecos Basin. But when you look at those coprolites
and the skulls they're associated with, not all Paleolithic or Stone Age or foraging humans are healthy. The Pecos Basin hunter-gatherers have high amounts of tooth decay.

And some anthropologists who study these skeletons say that these are caused by [tooth wear], but this Ota tribesman, he has extensive tooth wear, which is purposeful in this culture. They wear the teeth down to make them look like that, because it's considered beautiful, and they don't have high rates of tooth decay.

If you look at the Pecos Basin skulls, you'll find that they have really high rates of tooth decay. We need to look at whether or not there's impairment of calcium and vitamin D metabolism, and there's a lot of studies that show that really high-fiber diets can impair these. And unfortunately, some of these studies have come about because in places where the macrobiotic diet is popular—the macrobiotic diet, it idolizes high-fiber, particularly brown rice—and in England, in some communities that eat this macrobiotic diet, they're seeing a return of a disease that is associated with developing countries, which is rickets.

And it's infants on macrobiotic diets that have this. And I think there's an upper limit to fiber consumption that's way below some of these so-called Paleolithic accidents. But there's data you can see in some older papers, in particular data from modern hunter-gatherers, foraging people, like this bushman or the Hanza, and they see that these people eat a very high-fiber diet.

But if you look at the later papers, you really have to look at those because they realized that their method for measuring fiber was incorrect. And you can see, this is a very interesting thing. Here's from one of the papers where they're regretting that it was incorrect. And this is inedible material recovered after these Hanza tribe members were eating wild tubers.

They were sending, when they were doing the original fiber assay, they just sent the wild tubers to the lab and they were like, "Estimate the fiber of this," but as you can see here, these people don't eat all the fiber; they're chewing these tubers and spitting out this part of it. So just like you don't eat the tops of your bell peppers, I hope, or the peels of your bananas—although I did meet a raw vegan who was eating banana peels, [laughs]

So cultural evolution is important, and culture isn't even uniquely human. You can see this primate here, this chimpanzee, it's hard to see, but he's taking a leaf and chewing it, and then putting it in this tree that has a hole filled with water and then pulling it out and chewing on it again, and he's doing that to get water.
Humans have even more elaborate techniques. And one of these, of course, is cooking. And we don't know how old cooking is. I mean, you can ask every different anthropologist and they'll give you a different answer. But here we have sago palm starch processing—sego palm is, you know, they're eating a tree. It's not very edible.

Once you cook it, you pound it, and it's quite delicious. I mean it's bland, but it's good to eat; it provides starch for these people, which is very valuable to them. But we also should think about how is food being changed by cooking? It's increasing the food quality, it's increasing the amount of calories you can get from each amount of food.

But it's also really changing some of the nature, the chemical nature of the fibers. Different types of fiber feed different bacteria different ways. So that's very important. And you can look at markers for this. Here's a different kind of culture that a lot of people don’t think about—literal culture, cultured foods.
Fermented foods are universal in nearly every culture. And fermentation increases the bioavailability of protein and several micronutrients. It preserves food. It is a source of short-chain fatty acids. Perhaps it provides us with essential bacteria. Sadly, some fermented foods are in danger of dying out.

And here's an interesting chart—it's comparing the colonic fermentation, this inner fermentation, with exogenous fermentation in fermented foods. And fermented foods can play many of the same roles as colonic fermentation. And perhaps in our evolution as we're shifting towards eating more fermented foods, this was replacing, this exogenous processing was replacing some of the role of colonic fermentation and cooking provides all kinds of different micro-substrates, short chain fatty acids, bacteria, all kinds of metabolites, which also colonic bacteria provide…

They both modulate the system, actually, and there are studies that show fermented food has all kinds of strange effects that you wouldn't expect if it didn't have all these different weird bacteria in it and stuff—to help people lose weight and the way that non-cultured milk would, yogurt is very interesting.

And in terms of metabolites, here's a really interesting one: Butyric acid. It is produced by fiber. Research has focused on just the bulking properties of the fiber. So a lot of early people who wrote about fiber, they were going to Africa and seeing that a lot of different people who ate a very high-fiber diet didn't have the digestive diseases that Americans have.

And they were saying, "No, because it's because fiber is a bulking agent and it increases transit time, keeps toxins from spending a lot of time in the body." But after they were studying more, they found that there were people in Africa who didn't have these digestive disorders who weren't eating a lot of fiber. But what they were eating were other fermentable carbohydrates.

And so now research has shifted away from just fiber as bulking agent, and into seeing fiber more as food for bacteria, whether bad or good. Unfortunately, a lot of research in this area has focused more on fiber being a universal good, when actually it can also feed pathogenic bacteria.

And butyric acid is an interesting byproduct of some of these bacteria. People with colitis, Crohn's Disease, have low amounts of this butyric acid, and butyric acid is very important for modulating inflammation and all kinds of other processes too. They fed these mice the same diet, and the ones that had butyrate didn't gain weight, and the ones that did, that were fed butyrate gained weight. So, pretty interesting.

But you know, when you're thinking of fiber, often your doctors tell you eat more fiber, but different fiber has different effects. And now that we're thinking of fiber more as food for bacteria, you don't need to just think about fiber. And scientists are looking at more of these like resistant starch, for example, and other different complex polysaccharides and carbohydrates. You can see some types of resistant starch are produced by cooking.

Like if you cook potatoes and you leave them in the fridge, then that's resistant starch, and it's very good at producing butyrate. Some of these other fibers aren't so good at making butyrate. A lot of these fibers, a lot of doctors recommend, for example, wheat bran, and that's not even very good at increasing butyrate.
And I'm very sad that there's not a lot of research that is using a lot of these fibers that traditional foraging or horticultural societies eating. A lot of research uses synthetic fibers that's never been eaten before. And they're interesting, but I'd like to see more research on natural fibers.

But also, as humans have developed culture, we have exogenous butyric acid. A lot of people don't know this, but butyric is in the dairy fats and some of the fat under the skin of some animals, particularly cows, goats, sheep. There's a little in elephants too. And there's some in some fermented foods.

Like this is Ogi, it's a pretty delicious fermented food, although it's an acquired taste a bit. But it has some butyric acid. Most Western fermented foods don't have butyric acid because Westerners don't like the taste. If you have tasted skunked beer, you know the taste and you know why we don't like it.

So, it's incrappy traditional foods, you know, foods we don't really like from around the world. But there is one food that you will eat that has butyric acid, and that is butter. The butter is delicious and it has butyric acid. But we don't know whether or not this butyric acid has the same effect as butyric acid produced by colonic fermentation, there's not a lot of research on it.

This presentation's more about hunting hypotheses than presenting research. I'd love to see research on this; maybe I'll do it when I enroll in a program.
But also, not only do humans have all these differences from primates in terms of anatomy and our culture; we have different microbiomes in the gut. And this is a really great study because it looked at the gut biota of wild primates. Most of the other studies have been primates in labs. And you can see, even among these chimpanzees here, these chimpanzees are, some of them are quite geographically isolated from each other.

They have very different branches in the microbiota. They have different gut bacteria. Humans are here. But you can see, we need more data, especially since a lot of these unique cultures are dying out. We should try to collect gut bacteria from them before that, because, so we can get a real accurate reflection of human biodiversity.

And if you think about gut bacteria, it's very complicated because gut bacteria interact with each other, they interact with the metabolites of each other. You have all kinds of diversity among people. Like some people are methane excreters, and some people are not methane excreters. And scientists aren't sure why that is—if that's something that people acquire at a very young age, or if it's something that can be changed.

Methane excreters are quite unfortunate because when they have this bacteria, when it excretes methane, it smells quite bad. So if you're a smelly person, it's probably because you're a methane excreter. But there's just so many questions about why some people are like this and why some people aren't.

And there's so many different sources of gut variation: Cooking and food prep techniques, microbes in food, types of fiber in food, total fiber consumption. Most of us get most of our gut bacteria actually from our mothers, and when we're born, going through the birth canal, we're colonized.

But a lot of us didn't go through the birth canal. I was born by C-section, and C-section babies have different gut microbiota than non-C-section babies, and what is the impact of this? There's some preliminary evidence that C-section babies are more susceptible to certain digestive disorders.

Antibiotic use:antibiotics, if you take them, they can affect your gut microbiota for years. And there's some interactions with genes too. The real question is how plastic is our gut? How much can we change? As adults right now, if we eat differently now, can we really change our gut? Big question.

Here's a really interesting study. This is children in Burkina Faso; this is children in the EU. You can see, you have all these different species, and they differ between these two populations, in different amounts and different species. There are species here that you don't see here. It's interesting because they followed these children when they were breastfeeding, and they had kind of the same gut bacteria when they were breastfeeding.

But when they started eating solid food, their gut bacteria really differentiated. When does this plasticity end? Is it when a child eats its first food? Is that going to really affect the future of that microbiota? Can an adult do this? We suspect they're already there, but in smaller amounts when the infant was breastfeeding.
And then when the solid food was eaten, did it really differentiate based on the food or because of the population seeds planted at birth? We really need to do these studies while different cultures exist because all our multinational corporations are expanding into the developing world, and soon everybody's going to eat the same crappy diet, pretty much, and we won't have this diversity.

And here's the traditional diet of Burkina Faso, a lot of really high-fiber fermented grains. And the environment is very dry. Also, an interesting thing about gut bacteria: Genetic engineering's very controversial, but bacteria have been genetically engineering stuff for ages; it's called horizontal transfer.
A very interesting study looked at Japanese gut bacteria, and they found that some Japanese gut bacteria had species, they had some genes that the gut bacteria had taken from bacteria that live on seaweed, and these bacteria used to digest carbohydrates in seaweed. So these gut bacteria were able to steal these genes and digest these seaweed carbohydrates.

And only Japanese individuals have them, and even breastfed infants have them. So they've probably been in this population for a while. But it really brings it to highlight that our co-evolution with plants, how long have we been doing this? How many genes do we have that are from plant bacteria, for example?
What about the future? Now that we're genetically engineering plants, are we going to acquire some of that bacteria?

And we can use gut bacteria to track human migraation such as h. pylori. H. pylori's considered a pest in the United States because it's associated with some cancers, but actually in Africa, the African strain is not as pathogenic, it's not associated with these things. So these strains are diverse, and you can use their DNA, changes in the DNA to track h. pylori and human colonization of the world.

H. pylori's been with us for 100,000 years, they think. And right now, and most of us don't have it anymore because we tried to eradicate it. What is that doing to us? Did it have positive effects on us that now we've gotten rid of it? There's a lot of variation with it. And also h. pylori has—there's a lot of epigenetic switches that it turns on and off in response to diet.

And a lot of Westerners who do have h. pylori have two strains: They have the non-pathogenic strain and the pathogenic strain. And it's possible that diet can effect an overgrowth in this pathogenic strain. And perhaps the Western diet is taking this h. pylori and turning it into a monster.
But you know, when I'm looking at these different studies, what I said before about Westerners being weird, you really have to question what is normal. There's a hypothesis in anthropology that humans got their first meat and their first high-quality food from scavenging carcasses. It's controversial, though, because most of us don't have the equipment to process rotten meat, although I have met people in the Paleolithic community that are eating rotten meat, and they say they feel fine.

So, you know, that really begs the question if it's normal. And stomach acid, they is genetic variation in stomach acid, but also it's affected by h. pylori—different kinds of h. pylori can affect stomach acid in different ways. Your diet can affect stomach acid. Inflammation. Actually, we associate gastric cancers with the developed world, but actually there are certain types of cancer that are more common in developing nations, such as squamous cell carcinoma, and this is very common in Africa communities that just adopted corn as a staple crop.

And the theory is that, you know, this corn, this omega-6 excess in the diet increases prostaglandin E-2 and it increases inflammation, and that decreases the acidity of the stomach, and leads to heartburn, which is not treated in these developing nations, and then that leads to cancer. There's also an issue I realized studying carrion scavenging, that humans have high transit time variation.

You can feed two people the exact same diet and it'll go through their stomach in different times. And transit time, if you eat carrion, you want a high transit time, and that just varies between humans. An interesting [disease] that I found out about is called [pig bel], and it's people who are in Papua, New Guinea, many who are cultural foraging people, and they eat mainly a very low-protein diet.

They eat primarily tubers, like sweet potatoes and yams. And occasionally they get a pig, and they're very excited about this pig. So they eat it all really quickly. And they get this thing called clostridial necrotizing enteritis. And if I ate this meat, I wouldn't get this, but because they don't eat meat very much, they have low amounts of protease in their gut, so they can't destroy the toxins made by this and can't digest this meat properly.

And it kills some children in these cultures. So, you know, what you eat can affect the different enzymes in your gut too.
And also, the also case of this in a Western individual was a vegetarian who was living in Samoa, and they ate some fish because they were training for a marathon, and they got this disease.

So the point of my talk is that humans are truly unique, and we're not really sure how we got this way, so I'm hunting hypotheses. And within our population diversity is waiting to be discovered. And I'm really worried about loss of biodiversity in cultural adaptations, and what the implications for this are when we're trying to study and trying to flesh out our human history.

When we don't have very much biodiversity to work with, it'll be harder, I think.

And you know, I think the key is balance. I very much admire some of these models that are looking towards the past, and looking at our primate relatives. But also I'm really excited about plant adaptations, new technology and new mutations in human and microbiota DNA.

I think we have to look at both of these things when we're looking at, you know, looking for the best diet for humans. But it also, you know, we often wonder—I have an uncle who's been a vegan for a long time and he's very healthy, and he says, "I've been a vegan for 30 years," and I was a vegan for only a short time and I felt awful.

And we're related to each other, but there's probably some difference in our microbiota or our genes that make him better adapted to this diet than I was. So it gives a new viewpoint on why do some people do better on one diet or another?

So I'd like to thank Ralph Holloway, Chris Masterjohn, Stephan Guyenet and John Speth. They've really helped out. So thank you.
[applause]
Male Voice: So you would say that your main point is that the diversity of humans is under-appreciated and the difference between people is under-appreciated? Is that fair?
Melissa: Yeah. That people are very different from each other, and will thrive on different diets.

Male Voice: I was struck by a thing you said about most of the gut bacteria comes from your mother when you're born. I was wondering what the implications are for celiac, whether that can spread celiac disease.
Melissa: Yeah. I think a lot of celiac research has focused maybe too much on our own genome, what we share, that there's genes that make us susceptible to celiac. But there's also probably gut bacteria that make us susceptible to celiac, and genes within our gut bacteria. So I think that'll be a future avenue of research in the future.
Male Voice: I was wondering about [unintelligible] research on doctor [unintelligible] work? He looked at the microbiota and found that people have different communities, three communities of microbiota.
Melissa: Oh yeah, I saw that. But they're not sure what the implications of that are. They couldn't connect it with anything, like obesity or any diseases yet. But it's very interesting. They found that some people have very specific—that they divide Westerners, at least, into three specific groups of dominant bacterias. And it was fascinating, but I'm really excited to see what that doctor comes up with.
[applause]
 

 While I was doing research on variations in gastric acidity, I came across an interesting paper: Diet, reflux and the development of squamous cell carcinoma of the esophagus in Africa. It's interesting that a lot of conventional dietary advice on digestion is based on studies done in Africa that found that African agrarian cultures eating low-fat high-fiber diets had low rates of common Western digestive issues like hemorrhoids and colon cancer. Unfortunately they forgot to mention that there are a host of similarly bad digestive issues that are MORE common in such cultures, such as sigmoid volvulus and squamous cell carcinoma (SCC) of the esophagus. The latter they have tried to blame on everything from pickled vegetables to malnutrition to alcohol, with none of those hypotheses holding up very well. 

A promising villain is linoleic acid, AKA omega-6 fatty acids, well known for their harmful effects in the ancestral health/paleo/primal communities. The epidemic of SCC tracks the widespread adoption of linoleic acid-rich corn as a staple, not just in Africa, but in regions of Europe as well. 

I bet you are wondering why Americans don't have SCC. I think there are two factors, one is that higher levels of fat in the diet are protective, but I think another is that it's possible that a precursor to it is heartburn, which is widely treated in the US with proton-pump inhibitors. Those have some seriously bad effects, but they might prevent some types of cancer. I think it's better to remove the cause, but if you are going to continue to eat garbage, a PPI might save your life. 

Linoleic acid may be causing heartburn by increasing levels of prostaglandin E2 (PGE2). In animal models, high levels of linoleic acid, particularly in combination with low levels of other fatty acids, lead to elevated PGE2. Other micronutrient deficiencies, such as riboflavin deficiency, might make it worse. PGE2 then inhibits gastric acid production and reduces the tone of reduces of the pyloric and lower esophageal sphincters, causing heartburn. If you thought heartburn was a Western disease, consider that 60% of people in Transkei, South Africa suffer from it. Untreated heartburn exposes the esophagus to damage from the acid, in the long-term this can lead to the development of abnormal cancerous cells. Trypsin can possibly squelch the growth of such cells, but the paper notes that the South African diet is also rich in vegetables that are trypsin inhibitors, such as beans and pumpkin. They also eat the very very bad for you vegetable known as Black Nightshade, which is a pepsin inhibitor. And a lot of people smoke. A bad combination leading to a cancer epidemic. 

Since I have gotten rid of my GERD, I've wondered and wondered how I did it. I started eating a high-fat nutrient-dense diet, which was low in grains and free of vegetable oils, but not completely gluten or grain free. So that ruled out a gluten allergy as a major culprit. Wheat tracks as a cause of SCC too, but rather than an allergy as work, it seems like a complex inflammatory process is at play. We need to look at omega-6 as one of the true causes of GERD. It's also a possible connection between omega-6 and skin issues via the gut-brain-skin axis.  

 Last year I met a girl who was trying the paleo diet and complaining she "felt weird" and her stomach hurt. I asked her what she was eating and it turns out she was eating 5 tablespoons of coconut oil for breakfast! I told her that wasn't food, that it was an ingredient you can use to make foods or a supplement and that maybe she should try eating food. Later she said she felt better. 

I guess there is some impression among certain people that because I and others don't think fat is *bad* that you should drown yourself in it. As far as I'm concerned it's a far cry from a certain Paleo cookbook that advocates trimming fat off of GRASS FED meat, throwing away the fat that is leftover from cooking grass-fed meat,  and avoiding grass-fed "fatty cuts" like shanks to eating a pound of bacon for breakfast with a side of heavy-cream flavored coconut milk. Let's be honest: I don't eat that way. I cook with tallow that I save from the whole goats and lambs I buy, I certainly don't ever throw away any "fatty" cut, and sometimes I use some ghee, bacon, butter, or coconut milk as ingredients. I go through a pound of bacon a month, mostly because of my boyfriend, and maybe a can of coconut milk every two weeks and a pack of Pasture Butter a month. I never make any "paleo" desserts anymore and I don't eat very much dairy unless it's well-fermented and raw. Heavy cream makes my digestive system into sludge. I do eat some grains: I find my stomach is happiest when I include some rice in my diet every few days or so. 

I suspect someone who is more athletic or who doesn't have IBS might tolerate more fat. But this is my personal "sweet spot." I do have experience doing almost-vegan paleo: starches, veggies, fruits, no added fats, and only shellfish as protein. Perhaps it could be perfected, but I found that my keratosis really was itchy and red. I also felt more depressed and had bloating. If I tried it again I would probably use some coconut milk with carrot juice or something in an attempt to get vitamin A, but maybe my body isn't suited for it because of my genetics and health problems. Maybe it's also different for people in different life-stages. I'm a woman of reproductive age, so it's possible my need for certain vitamins is higher. 

I also would note that food sensitivities don't care about the paleolithic. It's very possible to be allergic or sensitive to a host of "paleo" foods from types of meat, to nuts, to eggs, to shellfish. I am personally quite sensitive to vegetables like broccoli, onions, and cauliflower. Honestly, they do a number on my stomach worse than any grain. I think people get caught up in the "paleo" paradigm thinking that because we evolved with foods like it, it must be good. But modern food sensitivities don't discriminate. I find that interestingly my stomach feels much better if I get starch from regular potatoes rather than sweet potatoes. The latter is considered "more paleo" though that stems from botanical ignorance. 

Either way, I don't really follow an orthodox "paleo" diet either, though I do use what I learn about the paleolithic to think about what I eat. I think there is tons of room for experimentation, particularly as the evidence for starch consumption in the paleolithic becomes stronger and stronger.

I don't think there is much room for combining "paleo" with various religious philosophies and I'm a little dismayed that Chinese medicine has somehow crept in and become tolerated. I think if I blogged about how I use Christianity to tell me what to eat I'd get about a million angry comments. Remember, the mechanisms behind Chinese medicine are scientifically implausible and even if a few tiny studies show that Chinese medicine works, it's not because of supernatural forces like conveniently undetectable "energy fields" operating outside of the forces of biology, chemistry, and physics. I know plenty of people who follow a "paleo" diet that is compatible with their religion, such as kosher or halal folks, but they don't claim that their diet is somehow better because of it or that it explains their diet's success. 

There has got to be a scientific explanation or I'm just not buying it...

Addendum:

It seems that some people were upset with the idea that I was attacking alternative medicine in the last post. No, I was attacking scientifically implausible theories of food being integrated by the ancestral food community. It's because people don't want to believe there are both unverifiable supernatural beliefs AND beliefs worth investigating to find out whether or not they have some natural basis or benefit.

Acupuncture, for example, is a system worth investigating because of the possibility that the ancient literature refers to real physiological processes, as Chris Kessler points out, and not energy fields (scientists have looked for these energy fields and NOT found them).

The idea that some Chinese roommates once told me that going to bed with my hair wet would cause demonic possession leading to pneumonia made me wonder if perhaps people in rural China did get sick from chills, but otherwise it is a supernatural belief.

Likewise, I am a huge fan of traditional Chinese foods, but when my waitress at my favorite restaurant in Flushing tells me I eat too much fatty "Yang" food and will get acne and clog my blood (that would be awesome since I have a mild form of hemophilia) I think it's worth investigating, but most of the time Chinese traditional food beliefs have been investigated, they have found to be incorrect or vast simplifications. I'm impressed at the latter, but I won't be basing my food choices on whether or not foods are "Yin" or "Yang." I suspect these beliefs have very little to do with Taoism anyway, as they were probably added on as Taoism blended with local folk religions.

Some of these folk beliefs lead to some absurdly unhealthy behaviors. I know Thai people who believe it's good to wash down beef, which is a "hot" food, with Coke, which is a "cold" food. And Chinese people who follow their fried chicken with heavily sugared red date tea because it's "Yin" and replenishes their "Qi." Since these beliefs are not based on real concepts, they are particularly vulnerable to industrialization. 

Religions/folk beliefs and food: worth investigating and important tools for believers, but not always scientific.