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Dr. Paul Jaminet on Chronic Infections, Depression & More


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In this episode Dr. Paul Jaminet answers reader questions, including:

  • Thoughts on the role of chronic infections in disease?
  • How to distinguish between fungal and bacterial infections?
  • What causes depression and how to treat it?
  • Are essential fatty acids actually essential?
  • How to treat acne when diet isn’t helping?
  • What to do if you don’t tolerate coconut oil?

We loved having Paul on the show and I’m sure you’ll enjoy the interview.

In other exciting news, one of our listeners, Jeff Rothschild, has generously agreed to transcribe the podcast! He has already completed a few, and I’ll be adding them to the show notes soon as PDF files. So make sure to check back every now and then if you’re interested!

Danny: Hello everyone and welcome to the Healthy Skeptic podcast. My name is Danny Roddy of DannyRoddy.com and with me is Chris Kresser, health detective and owner of thehealthyskeptic.org, a blog challenging mainstream myths about nutrition and health. Chris, I’m very excited about this week’s episode.

Chris: Me too, we have Dr. Paul Jaminet here who I’m sure almost all of you are familiar with. Paul has become a colleague and a friend, we’ve corresponded a lot and I’m sure a lot of you have read his excellent blog PerfectHealthDiet and a while back I posted a review of his book The Perfect Health Diet which is pretty much my go-to book now that I recommend for all of my patients and friends and family members. It’s an excellent resource and we’re really excited to have Paul here on the show. How’s it goin’ Paul?

Paul: It’s goin’ great, thank you for having me.

Chris: It’s our pleasure. For those few listeners that might not be familiar with you why don’t you tell us a little bit about your background, how you got interested in health and nutrition and we’ll go from there.

Paul: Yeah, well my wife and I are both scientists by training and I used to be a scientist, went into the business world, became an entrepreneur but the common feature of all those things was I was working 60-70 hour weeks, so was my wife. We weren’t thinking too much about food, we’d eat whatever was handy and that’s mostly industrially processed unhealthy food and in my case I ate a lot of bread and cheese and soda. In my wife’s case she had imbibed the fear of saturated fats and she had a lot of vegan, vegetarian friends, buddhist friends and so they got her eating a lot of soy and those kinds of products. Anyway our health kept decaying and I kept going to doctors and didn’t get any help. And so we developed a variety of chronic health conditions, disorders. In my case some of them were annoying like rosacea, physical weakness, but I had some cognitive and neuropathic issues that started to become disabling and so I’m mostly intellectually oriented in my work. I do a lot of writing, creative work, thinking, research, and so the thought of losing my mind, my ability to do intellectual work was pretty scary. About six years ago I decided I had to just focus on my health and started researching that. I had a consulting business that allowed me to work part time and spend a lot of time on diet and health. And I started with an Art Devany style paleo diet, had some success but ran into some problems on it, mainly from going too low carb. I spent the next four years really figuring out how to refine the diet, optimize it for myself, but also researching the literature trying to figure out what would be the best for everyone and how do you have to tweak it for particular diseases. So my main focus at first was how can I solve my problems, but gradually I realized the things I was learning were more and more applicable to other people and they started helping my wife’s problems too. So in 2008 I wrote up a little manual for relatives, the generation ahead of mine, aunts and uncles, was starting to face life threatening health conditions from cancer, heart disease, things like that, so I wanted to help them especially.

Some of my cousins who are more middle aged were also having some chronic health conditions so I wrote up sort of a mini book for my family. In the process of writing you realize there’s a lot of things I still don’t understand or maybe I don’t understand this as well as I did so I did a lot more research for that. And then after that was finished in 2008 I was still researching more, that was basically steps 1 and 2 of our book. And then I continued on looking into micro-nutrition and looking into more disease pathways and so that became the 2010 version of our book which you read in the summer and you gave us a wonderful endorsement so that really introduced us to a lot of people. So after we had this version that we had distributed to friends and family, we kept working on rounding it out, finishing it off. We looked into micro-nutrition and I was still working on my own diseases, I realized that they were the result of chronic infections and so that got me interested in how diet can help recovery from chronic infections and it also convinced me that a lot of diseases were due to those. By 2010 we thought we had enough interesting material that would make a really good book and might really help a lot of people and we put together the next version of our book. We released that originally as an e-book and started blogging and that’s how Chris got to know us and he introduced us to a lot of people through his website and that was fantastic, just getting to know the healthy skeptic audience and getting to know Chris. We came out with the print version of our book in October of last year and it’s been great fun we’ve really gotten to know a lot of great people and we’ve gotten a lot of great feedback. We’ve probably heard from several hundred people who have reported being helped by our book and really no negative stories so we’re very happy.

Chris: Yeah, I can say that I’m really grateful to both you and Shou-Ching for writing that book because I’ve certainly incorporated a lot of the concepts into my practice and they way I work with patients and I can tell you that a lot of my patients have benefitted from your book and of course your blog as well and I really appreciate your generosity in answering all of the comments and questions that people leave you that’s just amazing that you’re able to do that considering I know you have other work that you do and you’re a pretty busy guy so that’s a really great thing that you offer people Paul.

Paul: Yeah it’s a challenge and I’m not gonna be able to do that forever, I wanna make sure our ideas get a good launch into the world. Enough people try the to prove that they work, so I’m trying to help people out for a while and hopefully he ball can get rolling and sustain itself, and then I can move on to other things.

Chris: Teach a man to fish, right? Alright should we dive in Danny?

Danny: Yeah let’s do it.

Chris: We were overwhelmed with questions for Paul, so many people had so many good questions too, and Paul went through and picked some that he thought would be pretty representative and there were several similar questions and we’re gonna do our best to get to as many of them as we can and don’t worry we definitely plan to have Paul back on the show, have him as a regular guest and if we don’t get to your question this time hopefully we’ll get to it in a future episode.

Danny: Awesome so our first question is from Jamie, I’m interested in Paul’s thoughts on chronic infections and would love to hear him expand on how these would manifest as symptoms and his suggestions as to treatment. How can one distinguish between fungal and a bacterial infection?

Paul: Okay well this is a very big issue, I’ve come to the belief that chronic infections are probably the primary cause of disease and so bad diets with toxins and malnutrition vying to really make you more vulnerable to these infections and so everything works together to give you ill health. But the thing about chronic infections is everyone gets them. We’re surrounded in a sea of pathogens, I did some posts every teaspoon of ocean water has something like a million germs, and every breath we take we’re breathing in a few thousand germs. And then everything we touch has germs so we’re exposed to these constantly. Not all of them flourish in the body but many of them can if we didn’t have an immune system, so once we die these germs manage to consume us pretty quickly. You can see that our immune system has to really be active defending us in order to avoid us getting some kind of pathology. And I think we also have to recognize that these things are evolving and changing, and bacterial generations, viral generations are so short and they don’t have the DNA preserving machinery that we have so they tend to evolve very rapidly and we’ve now created a new kind of host that never existed before. So there’s almost 7 billion people in the world who have regular contact with each other, we touch, we kiss, we do all kinds of things that allow pathogens to move among us and we have a very stable environment it’s always the same temperature, the same biological machinery from person to person, so these pathogens can evolve to exploit us. And we’re now I think a very attractive host, we’ve never had one species that was so abundant and transmitted germs between members of the species as readily as humans do today. And also we’ve developed a lot of things that have sanitized the environment like water treatment, plumbing, and we’ve developed some antibiotics. So we’ve really discouraged the most extreme kinds of diseases so you don’t get as much diarrhea type illnesses anymore. The pathogens have evolved so that they don’t spread rapidly. A lot of diseases that used to be, they would kill you off quickly, they would create a lot of symptoms like diarrhea or coughing or sneezing that would help them spread because they had to tke those measures to get to new hosts. But now it’s relatively easier to get to new hosts gradually because there’s so many more people you come in contact with. And a lot of these pathogens I think have evolved over the last hundred years to produce milder chronic diseases. So they’re learning how to hide from the immune system, how to survive, they’re less active, they create less dramatic symptoms. But they try and reproduce over a period of years, and over decades they gradually produce a lot of the chronic disease that are becoming so common.

Chris: Paul if I can, I just wanna get your thoughts on something before we talk about the next part of this question, you mentioned sanitation and how sanitation has reduced some of the diarrheal illnesses and maybe some of the more severe illnesses. What do you think of this idea of the hygiene hypothesis where even though sanitation has led to some improvements, one of the ways that the immune system becomes sensitized and developed is by exposure to various pathogens when we’re young and that perhaps sanitation in some of the more industrialized countries has prevented that process from happening and our immune systems are not as robust and as well developed as they might be otherwise, what are your thoughts about that?

Paul: Well I’m not a big believer in it. I think it is true that we need exposure to bacteria and good gut flora in order to be entirely healthy and a lot of bacterial species have learned to work symbiotically with us in the gut. So it is very important to have good gut flora and in fact we’ve evolved to support that. So actually the mucus in the gut can feed certain species of beneficial bacteria and if your bacterial population in the gut gets low, like if you’re taking antibiotics, then the immune system will relax and let gut bacteria multiply. So clearly evolutionarily we wanna have some gut bacteria. So that part of the hypothesis I think is sound, what I’m not convinced by is the idea that people today are too sanitary and that they need more exposure to germs. I think the germs are all around us we’re constantly exposed, I think it’s more a matter of the quality of the germs that we’re exposed to may need some improvement. Some things you can do are eating fermented vegetables, taking probiotics can help improve the quality of your gut flora, fermented foods can often be beneficial in improving the quality but I think it’s really a quality problem not a quantity problem. I don’t think we’re exposed to too few pathogens and I think if we were less sanitary our health would get worse not better.

Chris: Right, so how can somebody, the second part of that question is how can someone distinguish between, what are the symptoms of infection first and then how can someone distinguish between the different types of infection fungal, bacterial, parasitic?

Paul: Yeah well this is one place I think diet can really help, is in diagnosis. Medicine is still in a primitive state it’s not very good for diagnosing these infections much less treating them. But a lot of these pathogens respond very differently to different diets. So one of the key differences is in how they respond to a ketogenic diet for instance. So pathogens that have mitochondria like fungi and protozoa can metabolize ketones for energy. Bacteria and viruses can’t, and so if you go on a ketogenic diet you’ll starve bacteria and viruses but you’ll feed fungi and protozoa. And so a simple thing to do is go  on a ketogenic diet for a while, do your symptoms get worse or better. And that can tell you which class of pathogen you have, one with mitochondria or one that doesn’t have mitochondria. And those kinds of tests can be a big help, and I think part of the reason medicine doesn’t succeed against all these diseases is that nobody varies their diet, they’re always eating the same diet. It’s always 50% carbs with lots of wheat and sugar, plenty of vegetable oils, if you tell people to change their diet and eat healthy they look around and find other sources of the same nutrients, certainly never sample a ketogenic diet. So our basic diet, the perfect health diet, aims to be pretty much balanced, it aims to supply in food the amounts of nutrients that your body needs. And we tweak it in various ways so we tend to be very slightly low carb, but for therapeutic purposes and certain diseases we might go to more extreme diets like a ketogenic diet that’s more low carb or there’s a few diseases that may benefit from going higher carb. But also even apart from treatment the diet is a good diagnostic tool. And it’s also helpful for gut infections to vary the types of food you eat, different foods get digested in different places in the digestive tract. Different things are accessible to different kinds of pathogens, the time scales in which things happen have diagnostic value. So fungi tend to do everything slower than bacteria, they multiply a lot slower, so fungal infections tend to be relatively stable whereas bacterial infections can be much more variable. There’s a lot of ways you can manipulate diet and help understand your own disease and that can guide you to good treatments.

Chris: What’s interesting is, as you’re probably aware in the alternative health world there’s a lot of different perceptions about how to deal with fungal infections and the word candida is thrown around a lot, which I think obviously that candida infection is real but I also, in my experience see it kind of slapped on as a diagnosis of exclusion, meaning we can’t figure out what else it is so we’ll just call it candida. But I’m really interested in what you were saying, I read your article when you talked about how fungi can utilize ketones and tend to progress on ketogenic diets because one of the interesting things about how the candida diet is typically administered is people remove fruit, they remove carbohydrates, starchy tubers and grains and I think they end up being on a very low carbohydrate diet in a lot of cases and perhaps not completely ketogenic or not strongly ketogenic but maybe mildly ketogenic and I see a lot of patients who just get worse and worse on those diets so I wonder if it has something to do with this mechanism that you’re talking about.

Paul: Yeah I think it’s very likely. It’s not bad to go low carb by standard American diet standards, I think probably optimal for candida might be 600-800 carb calories a day, the average American gets maybe 1700 so cutting carbs in half for the average American is a good move. But going too low carb definitely risks systemic invasion so the very low carb approach, it’s not bad for a fungal gut infection but it’s not that good either. It doesn’t do that much to promote good bacteria taking over the gut. A lot of plant foods can really help suppress fungi in the gut and promote bacteria. So they can help give you a better gut flora and I think a lot of people who go extremely low carb can end up with a gut dysbiosis of some kind after years on these extreme low carb diets.

Chris: Yeah I agree with that and I’ve definitely seen that to be true in my practice. And what about brain infections Paul, this is something you’ve talked a lot about are the nerves in the brain susceptible to the same pathogens?

Paul: Yeah they are. The brain seems to be more vulnerable to bacteria especially and a little less vulnerable to fungi. There are some protozoa that can live well in the brain, some viruses flourish there. The thing about the brain is it’s pretty rich in glucose which bacteria like. Or glucose products like pyruvate or lactate which they can metabolize. So it’s kind of a paradise for bacteria and so it’s very important to maintain the integrity of the blood-brain barrier and try to help keep them out. But just like people get leaky guts they get a leaky blood-brain barrier. Also it’s not uncommon if people get some kind of trauma to the head, they get some kind of brain injury involving bleeding, that breaches the blood-brain barrier and very commonly people get brain infections that develop after some kind of head trauma. They’re not uncommon and bacteria do well in the brain, and  fortunately ketogenic diets can be very helpful. Bacteria can’t metabolize ketones, when you’re on a ketogenic diet glucose levels decrease, so you’re starving the bacteria. And ketogenic diets also promote autophagy which is part of the immune response. And you can also promote that even more with a low protein diet and so in that process the cell basically has its own self digestion machinery, little digestive vesicles called lysosomes that go around and look for junk that the cell doesn’t need and they destroy it, digest it, and among the things they’ll find when they’re looking for junk are bacteria and viruses. So keeping autophagy going very frequently by occasional fasting or occasional ketogenic dieting or low protein dieting either intermittently or regularly, all of those things will help promote brain health and help keep your brain free of infections. And I think brain infections are responsible for a lot of late life degenerative diseases like Alzheimer’s, Parkinson’s, and probably others too. The brain is kind of a special place, it’s a little sheltered in terms of its nutritional status, it doesn’t vary as much with diet as the rest of the body. It has its own kind of immune functions, it’s own kind of needs, so the symptoms are a little different. So I would say in general the three places to look for different kinds of, classes of symptoms would be the gut, brain, and the body. And each one has it’s own characteristic symptoms and pathologies.

Chris: Right. Great. Danny what’s next?

Danny: This is a perfect next question, this one is from A, what does your typical diet look like Paul?

Paul: Well a typical day for me, I spend most of my day at a desk so I’m not terribly active, I’d like to be more active. And I’m also a little bit older than a lot of people in the paleo community so that also seems to reduce calorie intake, so I don’t eat a huge amount, probably about 2000 calories a day. I generally do intermittent fasting so I usually don’t eat at all in the morning, I’ll have a cup of green tea when I get up. Usually the first thing I eat is a banana and maybe a hard boiled egg. I might take a tablespoon of coconut oil sometimes. That might usually be around noon. But I really don’t eat a meal until mid afternoon usually, maybe 3 o clock. And usually that’s made out of leftovers and it looks like the Korean dish bibimbap if you’ve ever had that. I basically have a bowl, I put some kind of safe starch like rice or potatoes or taro or something, that’s generally a leftover. I’ll usually add 3 egg yolks, I’ll put in some kind of acid like lemon juice, sometimes vinegar, and I’ll add leftover meat and vegetables from the previous night’s dinner, and if it’s not fatty enough then I might add something like butter or coconut milk but usually it’s just fine with the eggs. Mix it, heat it up in the microwave and that’s my lunch. I take various nutritional supplements like a multi-vitamin and a few others, and I’ll do that with my lunch. And then around 7 or 8pm we’ll have dinner, and it’s very similar. We’ll usually put up a food plate, which gives a good idea of our diet.

Danny: It’s really pretty.

Paul: Thanks, dinner typically consists of some kind of meat or fish, with some kind of safe starch, some vegetables, and some kind of sauces for flavoring which will add some fats and flavors. We make up a big batch of bone broth every weekend and we’ll typically have some kind of soup. And we keep some kim-chi around and make that regularly and serve that, we also have some seasoned seaweed and we’ll have a glass of wine with dinner. If we feel like dessert then it will typically be berries, possibly with whipped cream, and the whipped cream we would flavor with rice syrup rather than regular sugar. So that’s basically our meal and so on weekdays we might cook a meat and a vegetable maybe 3-4 nights a week and then the other two we’ll have leftovers and that’s usually like a Japanese sushi buffet where we put out all the things and you pick up a piece of seaweed and wrap it around some rice and some meat and some vegetable and wrap it yourself and eat it. And then on the weekends we’ll make some longer dishes like maybe a stew or something, and a broth that will get us through the week.

Chris: Sounds good! I think it’d be an interesting project to put together a list of all of the paleo/primal bloggers’ typical food day. Because of course everyone is aware of this huge controversy that’s been happening in the paleo blogosphere about macronutrient ratios and is a low carb diet better or low fat diet better, I think it would be pretty cool to see, and I know from talking to various people like Paul and Robb and Mat LaLonde and Stephan that there’s a huge variation in what people eat on a daily basis and it’d probably be helpful for people to see that.

Danny: Chris you should be all over that.

Chris: Somebody do it, I don’t have time! Anyways just a thought, so let’s go on to the next one.

Danny: Okay hopefully Ruth doesn’t hate me for not reading her whole question, but here it goes. If there is a food that bothers you and then you eliminate it for say a year, and then  you re-introduce it will you now a. be able to eat it without getting a bad reaction because you “healed”, or b. react even more because your body is no longer used to it. She goes on to answer her own question and then she has another question which I’ll read, what about FODMAP foods, if you eliminate it and then reintroduce it does the sensitivity increase or decrease?

Chris: Let me say a few things about this too, because I receive questions like this and I have my thoughts but I’d love to hear Paul’s. Basically I think the idea is some people are arguing if you remove a food and then you add it back in and you’re more sensitive to it it’s not because you were sensitive to that food it’s just that you’ve sort of decreased your tolerance to it by removing it. I’m not sure what the basis for that is but that’s the idea. What do you think Paul?

Paul: It’s a great question, and let me say first of all sort of a general background about our diet, we don’t in the book anyway talk an awful lot about gut issues. We do talk about them on the blog a little bit and actually I think that’s what got you interested in us the first time was our series. There’s sort of a distinction here because you can analyze diet in two different ways, one is as foods, what goes in your mouth and passes into your digestive tract, and then the other side of it is in terms of nutrients. So they digestive tract breaks all the food down to nutrients and then delivers the nutrients to your body. Most of our analysis is pretty nutrient based, so we’re looking after the gut. But a lot of things can happen in the gut, and there you get into all these issues of compounds in food, bioactive compounds, how they interact with gut bacteria and so on. One of the functions of the digestive tract with its gut bacterial populations is to transform food, to change its macronutrient ratios in a favorable way. Process fiber into small chain fats that benefit us. So a lot of changes happen and understanding that food diet, how that’s affecting you and what’s happening in the gut, is really a big issue. So there’s some diets like the GAPS diet that are really oriented towards the gut. Our diet, it’s a very important issue, we don’t spend a huge amount of time talking about it in our book but maybe we’ll develop that more in the next version.

Alright so, the issue here is it really gets to the ecology of the gut, the quality of the gut flora. What kind of foods they like to digest, and I usually use the term infection to talk about any kind of dysbiosis where you have pathogens that you really don’t want in the gut have taken over some segment of the gut. Usually they flourish fast in one part of it. So some may like the colon but they don’t do well in the small intestine, some may do well in the small intestine or even the mouth. H pylori does well in the stomach, so you can have different pathogens in different places, and each different species of pathogen and each different location in the gut produces different symptoms. And so when you’re having some food that’s giving you trouble it’s usually because there’s some gut infection or dysbiosis there. And if you take it away, usually the things that are giving you trouble are things that are feeding that pathogen. They can exploit it so it helps them multiply and it causes them to run their metabolism and release toxins, something else, and that’s what gives you the symptoms is usually the immune response to that pathogen’s activities. So usually elimination of a food that gives you trouble will help because it will somewhat starve the pathogen. But it doesn’t guarantee that the pathogen will be eliminated because these pathogens are very versatile, they don’t just metabolize one thing they can metabolize lots of others, so they can survive on other foods. If you go too extreme in elimination diets and eliminate whole classes of foods, like some people go zero carbs, or all meat diet or something. They may still be able to survive metabolizing protein, and it may be that you’re starving the good bacteria even more than the bad bacteria. And it can actually get worse and then when you reintroduce the food you’re even worse off because those bad things are more dominant. So usually the elimination diets help but it’s not guaranteed. What I kind of favor is, first of all eating a very good diet. Make sure all of your carbs are from safe sources. And when you have a troublesome food, my inclination would be to try and eat it but at very low levels. You wanna try and develop the good bacteria that can digest that thing, but you also wanna attack the bad ones. I’d really work hard at trying to put in a lot of good things through fermented vegetables, probiotics. And if you can identify where the problem is, attacking it. So some things, if you have candida growth in the intestine that’s great actually, because you don’t really need any fungi in your intestine so you can just take anti-fungals, you can take probiotics, fermented foods. It’s a little tougher when you have bacteria, because antibiotics may be broad spectrum and kill a lot of the good bacteria so that’s a little trickier.

Alright she asked about FODMAP foods, those are kind of interesting those are sugars, oligosaccharides, disaccharides, monosaccharides. They’re already sort of predigested compared to starch. Often they’re not so much trapped within cell walls or something, they’re kind of available. So these sugars are available to bacteria in the small intestine, unlike a lot of other things like resistant starch which usually get to the colon before it is metabolized by gut bacteria. So the FODMAP foods are a little more relevant to small intestinal bacterial infections. You can experiment with different types of foods and try and get an idea of where your problem is, what kind of pathogen it is, and that can help develop a plan for how do you attack it, how do you fix it. So I think given kind of the primitive state of medicine you have to look for clues and feel your way a little bit in resolving gut problems.

Chris: Right, I definitely agree with that. And I think that one of the things Ruth is referring to is, it’s tricky as you mentioned Paul there’s so many different things to consider here but I think one of the things that Ruth’s talking about is Dr. Ayers. I think it was he who wrote  about a study of Japanese who eat a lot of seaweed, and in doing that this certain type of gut bacteria that can metabolize the seaweed proliferates and so they become very, I guess you could say their gut becomes very skilled at digesting that seaweed whereas somebody who doesn’t have that particular gut bacteria wouldn’t absorb it very well. And so he also writes about, in a similar way, if you eat a certain amount of yogurt daily that in theory you can increase  your ability to digest it and that’s what he recommends doing I think that’s what Ruth was referring to and there is something to that. But that doesn’t mean that that works with every type of food that might be provoking a response. Like for example if someone is gluten intolerant and they’re experiencing symptoms with gluten and they remove it, I’m not so sure that eating small amounts of gluten is going to eventually improve their body’s ability to process it.

Paul: Yeah that’s a great point, so you need to distinguish between toxic foods and safe foods that are problematic because of a particular gut ecology that you have or a leaky gut or whatever it may be. Gluten I would say is unsafe for anyone, and you should just exclude it. Whereas other things like tomatoes or dairy, dairy’s a little more complicated, it really is a very complex food. But if we just take the simple case of lactose intolerance, if you eat lactose you will release more lactase and you’ll develop an ability to digest it. So Ayers is right about lactose. With things like the seaweed, it’s really more hit or miss, can you acquire the bacteria that are able to digest these things. And that can take years or decades. Even in Japan only like 30 or 40% of people have these bacteria that can digest these particular polysaccharides in the seaweed, and seaweed consumption is very common there. In America it’s nearly zero, and your best chance would be to eat some raw seaweed, from the ocean. So these bacteria live on these things in ocean and that would be your best chance to get those genes, and to eat that kind of seaweed regularly. But most people eat pretty well cooked seaweed and so Ayers does recommend eating locally grown organic food without washing it in order to get the bacteria that live on them. And that will help diversify your gut floras and that can definitely be beneficial. But it’s not a guaranteed cure and it might take a very long time to really get all of the bacteria that will help you digest something well.

Chris: Right, I think probably unless the food is really essential and can really contribute to your health, in a lot of cases it might just be easier to avoid it.

Paul: Yeah, if a food is giving you trouble, it depends on what it is. Like, all starches give you trouble then you should fix that.

Chris: Yeah it’s worth doing that.

Paul: And similarly with sugars, if anything with fructose gives you problems I would try to fix that. But if it’s some weird food that you don’t even like very much then it’s easy enough to avoid it as long as you can still eat a diverse, varied, nourishing diet.

Chris: Right.

Danny: Chris are you gonna add in it’s the environment, dummy?

Chris: You beat me to it Danny. Let’s go on to the next one and let’s stick with the yellow ones from here on out Danny.

Danny: Alright cool, this one is from Jerry. Short question, how would you go about treating depression, Paul.

Paul: Alright, well let me say I’m not an expert on depression so this would be probably a better question for Emily Deans or Nora Gedgaudas or someone like that. But I know a little bit about it. It tends to be associated with obesity, it probably has similar causes and it’s very likely caused by the presence of high levels of inflammatory cytokines in certain parts of the brain. And so obesity is probably caused by that too, it’s probably caused by those cytokines getting into the hypothalamus and certain parts of the brain that are involved in food and metabolic regulation. Depression involves reaching other parts of the brain but very similar effects probably. And those cytokines can reproduce elsewhere in the body and imported into the brain. So they can be produced in the gut if you have gut dysbiosis and the immune system is reacting to it. So the gut is definitely a good place to look for addressing depression. You wanna clear chronic infections, if you have a brain infection that can easily produce depression. So there can be a diverse set of causes of depression, and the common feature will be inflammation in parts of the brain that regulate mood. And so you really have to do some detective work and start looking at what other symptoms do I have. And I would say basically our book, our 4 step program in our book is a general program for fixing any disease, unknown diseases and so I would start by following that. And usually when you fix enough things

then the other symptoms clarify and it becomes much easier to make a diagnosis and figure out something you can attack. So that’s the general process I would go through. It could be anything from a brain bacterial infection that you treat with antibiotics to a gut dysbiosis that you treat with probiotics, fermented vegetables, some other gut modulating supplements. It’s not really possible to name one therapy and say this is what you do but I think there’s a general strategy that people can follow. You may find that ketogenic dieting and intermittent fasting help. Any kind of neurological disorder I would recommend giving ketogenic diets a try. You should follow the kind of ketogenic diet described in our book, don’t go too low carb, include some starches. It doesn’t need to get you into extreme ketosis, it just needs to supply enough that neurons have an alternative fuel to glucose. So any kind of brain or neurological disorder it’s worth giving ketogenic diets a try. It’s not guaranteed that they’ll improve things but you’ll definitely get information. People can get protozoal infections of the brain like toxoplasma gondii infection of the brain are very common. And if you try a ketogenic diet and you have that then I would expect you’ll get worse. But that would be a great clue and then you could go and try and get treatment for toxo or for some other protozoal infection. I would say depression, it’s definitely gonna take kind of experimental, exploratory approach before you pin down the cause and are able to fix it. But I think it should be curable.

Chris: Yeah I agree, definitely and certainly in my practice I’ve seen the biggest bang for your buck focusing on the gut-brain axis and following the type of strategies that Paul outlined there with the gut. Making sure that you’ve got enough good gut flora and restoring intestinal barrier integrity and reinvigorating that communication between the gut and the brain. A couple other things that might be helpful is making sure you have good essential fatty acid balance, the omega 6:3 ratio which Paul talks a lot about in the book. And this probably goes without saying but I think nutrition and nutritional status is a huge huge part of depression but it’s not the only factor that goes into it. There are other things to consider like your relationship to your work, to your life, whether you’re getting enough exercise, whether you’re getting enough sun, whether you’re having enough fun in your life, all the things that go into total health. One question Paul, what do you think about micronutrient deficiencies and depression?

Danny: I was just gonna go there except with obesity.

Paul: Yeah, I think they’re contributing factors in just about every disease, so I think it’s very important in general to be well nourished and especially if you have any kind of disease. Any kind of nutrient deficiency or imbalance is probably gonna impact your immune function and is gonna inhibit recovery from any disease. It’s gonna produce odd symptoms, transform the symptoms, make it harder to diagnose. It’s gonna slow down healing, so there’s a constant balance. Your body has to constantly fight off pathogens, it has to constantly rebuild itself. A good part of the immune response is killing infected cells, so many cells when they realize they’re infected they kill themselves and that kills the pathogens at the same time. But then you have to heal all those injuries, and a lot of these brain infections, a lot of the problem is people aren’t healing their brains very effectively. So they have neurons dying or becoming damaged but they’re not healing. You definitely wanna be well nourished. In a lot of these cases the interaction is so complex, the malnutrition isn’t the primary cause, but it’s a secondary contributing factor and that makes it harder to prove that it really has a crucial role. Danny you raised the subject of obesity.

Danny: Yeah your article was fantastic and it brought on a third view of obesity besides the Taubesian view and Stephan’s food reward hypothesis and if you could just speak a little on that I’d be super interested because I thought you did a really great job.

Paul: Yeah, well I think obesity is really multi-factorial and in general the three classes of factors that we think are the big ones causing disease are malnutrition, toxins, which is usually food toxins not so much environmental toxins but actual bioactive compounds in the foods we eat, and then pathogens and infections. And so we’re all exposed to all of these things but if we can minimize them then are chances are we have the best shot. And there’s various evidence linking malnutrition to obesity, so in general undernutrition of micronutrients and over-nutrition of macronutrients both contribute to obesity and there’s a variety of evidence on that. And in famines people are just focused on getting calories they don’t worry too much about food quality, and the cheapest and most available calorie sources are usually things like the grains that have not very much micro-nutrition per calories so low nutrient density. So in famines you find a lot of people that are still getting adequate calories but they’re very poorly nourished with micronutrients. And what you find is that the children who are born during these famines are much more likely to be obese at age 50, that was one of the results of the Dutch famine studies. You also find these people who do yo-yo diets, a lot of weight loss diets where they’re restricting calories severely they end up being very poorly nourished while they’re on the diet and it turns out that the more times you go on one of these weight loss diets, the higher your ultimate weight. So it seems like an episode of being malnourished leads to higher future weight. And there’s some various other sources of evidence there’s a Chinese study recently where just giving people multi-vitamins and multi-mineral supplements helped them to lose a significant amount of weight compared to controls. I think definitely on any weight loss diet you should strive to be very well nourished in terms of micronutrients and also macronutrients, you don’t wanna be extremely low carb and deficient in glucose. You don’t wanna be deficient in protein or in valuable fats, it’s good to eat some salmon to get some omega-3, it’s good to eat some starches to get some glucose. But especially you wanna be well nourished in micronutrients, so eat some vegetables, take a multi-vitamin, take some extra supplements, and I think it becomes much easier to lose weight if you’re well nourished.

Chris: Great, Danny let’s skip down to David’s question, the next one.

Danny: Okay cool, my favorite. David, is Ray Peat correct to assert that unsaturated fatty acids are not essential? And you can find the information about that on Ray Peat’s site.

Paul: Yeah I don’t think he’s correct as a biological matter but as a practical matter he might as well be correct because the amount of polyunsaturated fats that you need is extremely low, if they’re well balanced then .5% of energy is enough. If they’re unbalanced you might need 1% of energy. And so that’s as far as developing any kind of pathology. In our book we discuss how difficult it was to prove that there was any human need for any of these omega-6 or omega-3 fats, and they didn’t actually prove it until they put these infants on skim milk diets which had no fat at all. It turned out that the infants would do okay if they had skim milk and lard, but not okay if they had skim milk only. Ray argues that the symptoms of an omega-6 deficiency are very similar to symptoms of a vitamin B6 deficiency and the diets that were deficient in fat were also B6 deficient and that could be the explanation. I don’t think that’s a likely explanation if the problem was cured by lard which doesn’t have B6 so far as I know. But like I said as a practical matter almost every food you buy in the supermarket is in the neighborhood of, every meat has at least 3% polyunsaturated fats, every oil has about that much. It’s basically if you’re eating real food, actual things that used to be plants and animals then it’s impossible to develop any of these polyunsaturated fat deficiency conditions. So as a practical matter he’s right, you shouldn’t think that the fact that some are called essential and some aren’t is meaningful in any way, it’s not. It doesn’t tell you anything about whether you should try to eat more of them or less of them.

Danny: It’s always felt like a moot point because like you said if you eat food you’re gonna get those fats anyways so it seems like a higher cognitive debate but it doesn’t really play out in the real…

Chris: Well one way it does play out is the recommendation to eat a fair amount of fish for example to get enough omega-3 fatty acids that leads to the question that Chris Masterjohn addressed in his essential fatty acid report is, are the short chain unsaturated fats like alpha linolenic acid and linoleic acid essential or not, or are the long chain DHA and EPA and arachidonic acid essential which Chris believes they are and which you’d certainly get from eating fish and meat.

Paul: Yeah so once you delve down to the individual fatty acids then it gets a little more complicated and for optimal health you do want a balance between the different types. And so that’s why we recommend eating in the vicinity of a pound of cold water marine fish like salmon or sardines per week. So definitely as a practical matter making an effort to get some omega-3s will generally improve health, and the reason for that is you’re getting all these omega-6s from other sources and it is desirable to have a balance and you kind of have to make an effort to get some omega-3s because a lot of foods just don’t have them.

Chris: Right, exactly. So when the rubber hits the road, if they’re essential from a scientific perspective meaning we need them from the diet because the body can’t produce them on their own, that’s at a very low level but from a practical perspective the most important thing is to balance the omega 6:3 ratio because if you’re eating any kind of a normal diet you’re definitely getting some omega-6 so you need some omega-3 to balance that out.

Paul: Right, and let me just say this term essential is about the most useless term. Even the ones that are so called non-essential, you can’t manufacture them from nothing, you  have to manufacture them from something else. Like glucose can be manufactured from protein, saturated fats can be manufactured from glucose, but if you’re not eating any saturated fats there’s no guarantee your body’s gonna make enough of them from glucose to make you healthy.

Chris: So Paul you’re not a big support of the breatharian approach I take it? Alright Danny we got time for one more, let’s go to Marlene.

Danny: Okay Marlene’s question, how do you get rid of adult acne when the diet isn’t helping with that? You tout the benefits of coconut oil, but what can I do or use instead when too much coconut gives me a stomach ache? I can’t eat dairy either. Note, I have problems digesting fats in the first place because they cause her to have soft stools. What do you think Paul?

Paul: Okay well this gets back to what we were discussing earlier, when you have trouble with a whole class of food, like fats, then it suggests you have some kind of gut dysbiosis or something wrong, which it’s desirable to fix. Acne, I think is commonly caused by circulating toxins, call them die off toxins from pathogens, they might be cell wall components from fungi, or potentially lipopolysaccharide from bacteria. You have these circulating toxins and in terms of where your immune system is located, roughly speaking 80% of it is in the gut, 20% of it is in the skin. So if you get inflammatory signals and you have circulating toxins, where the toxins will encounter immune cells that will respond to them is mainly in the gut and the skin and so very often when you have these circulating toxins you have some kind of gut dysbiosis you also get skin manifestations. So the immune cells in the skin will react to these toxins and they’ll give you these inflammatory kinds of skin things like acne. Just with acne one thing you can try, it’s hardly diagnostic but it will help relieve symptoms usually, is to try a supplement like cholestyramine or activated charcoal or bentonite clay. Which basically binds to fats and bile and other things in the gut and helps excrete them with your stool. Otherwise those can be reabsorbed in the colon and recirculate. And some things like some fungal cell wall components are very good at reentering in the colon and they can circulate almost indefinitely and you can never get rid of them. So helping excrete them may significantly reduce your acne and that’s a clue, that tells you the acne isn’t the result of some kind of skin infection it’s the result of some kind of gut infection/dysbiosis that’s producing circulating toxins that are causing the problem. So that guides you toward the gut. In Marlene’s case the issue of fats, there’s various things involved in fat digestion. You need to produce bile, you need to produce pancreatic enzymes, you need to coordinate when the stomach releases food into the small intestine, the gallbladder has to release bile, the pancreas has to release enzymes. So lots of things have to happen together. There’s various ways that can get messed up, if you’re not producing enough bile that can be a problem, there’s various supplements that you can take that will increase bile production like vitamin C, taurine, cholesterol, glycine. You can take supplemental enzymes see if that helps. There’s a variety of other causes, you can even have infections of the nerves that coordinate that area like a viral nerve infection that can dis-coordinate the release so when the stomach releases the fats into the intestine you don’t get the bile released at the right time. You can have gallstones or other things that interfere with functions. There’s a variety of causes and you kind of wanna experiment and work with your doctor to try and figure it out.

Chris: Okay, well thank you so much Paul, this has been fantastic and of course as I suspected we answered about 10% of the questions we received so we’re gonna have to have you on I guess 10 more times. Thanks so much for coming on the show Paul, we really do hope that you’ll join us again.

Paul: Alright, it was a great pleasure thanks for having me.

Chris: Danny, take it away with the closing piece here.

Danny: That’s gonna bring us to the end of this week’s episode. Paul where can we find more of your work on the internet this week?

Paul: Well our website is Perfecthealthdiet.com, and you can also find our book at Amazon and other online booksellers. And we hope to have e-books out soon I know a lot of people asked about that, so it’s just a matter of fitting into my schedule so maybe I should take a break from blogging and maybe I’ll get that done.

Chris: Clone yourself.

Danny: Chris same question to you buddy.

Chris: Okay, there’s a few things happening in my world. This weekend we’re gonna do the merger. Some of you probably saw the posts where I’m retiring the health skeptic nom de guerre. It served me well for the last several years but I’m just gonna call the site now just plain old Chris Kresser. There’s a few reasons for that, you can read about it in the post but if all goes well that transition will happen this weekend so when you type in thehealthyskeptic.org don’t be alarmed when you end up at Chriskresser.com. So from a user perspective nothing’s gonna change, same basic site, same design, all the old healthy skeptic links will still work and they’ll just be automatically forwarded to Chriskresser.com. And the podcast for now will stay the healthy skeptic but that could change as soon as I find out another clever name for it. And there’s one more exciting piece of news, which is one of our listeners Jeff Rothschild has very graciously and generously agreed to do transcripts for the podcast. Thank you Jeff. We’ve had a lot of requests for this and I just certainly didn’t have time to do it myself and Jeff stepped in and he’s already done a few episodes so we’re gonna start posting PDFs with transcripts of each episode. You can go back and look at previous episodes of transcripts as they become available so everybody give a big high five to Jeff, and that’s it for now.

Danny: You can find all my insanity at Dannyroddy.com. Keep sending us your questions at thehealthyskeptic.org using the podcast submission link. If you enjoy listening to this podcast head over to itunes and leave us a review. Thank you for listening and thank you for your support guys.


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Join the conversation

  1. Do you think the suggestion to try something like bentonite for acne (i think I have rosacea) is safe during pregnancy?

    I’ve had bad skin since I started eating WAPF. It then worsened on GAPS. Now I’m eating PHD and no sign of my skin improving. I sed to have clear skin until I started to improve my diet and be healthy. I just can’t figure out what went wrong! Any ideas?

  2. I just wanted to note on the discussion of acne towards the end of the podcast Paul mentions taking Activated Charcoal or Bentonite Clay to get rid of circulating toxins in the bloodstream. I did buy some activated charcoal and starting taking one pill per day, the instructions said you could take 1-2 pills so I started with the lowest dose. I noticed around the same time I was getting some severe nausea daily. I stopped taking the pills and the nausea has ceased. I have since done some research on the internet and found that this is a known side effect.

  3. Hi Chris
    Very interesting podcast!!
    Are the symptoms of a fungal infection different to those of a bacterial infection and if so how would these symptoms differ?
    Many thanks.

  4. Dr Jiamet says to eat a varied diet, Dr Guyenet says to eat the same, bland food everyday. Who’s right?

  5. Hi Chris, great podcast. I cant believe you are still doing all this stuff with your baby around- its amazing. Our little girl is 8 weeks now and I find it hard to do anything productive
    Just wanted to ask you about adaptogens, which you mentioned in a previous podcast can help regulate cortisol if it is high or low. My question is, if someone is in adrenal fatigue (stage 2 or 3) , and you use an adaptogen to increase cortisol production, are you just stimulating the adrenals more and therefore fatiguing them more?
    thanks again

  6. Can Dr. Jaminet please elaborate on the protocol he described at the end of the podcast involving activated charcoal and Bentonite? How long do you take these? In between meals? How much of each? Thank You for your help.

  7. Re: micronutrients and depression, I had two years of manic depression. Took a dozen psychiatric drugs, no luck. Likewise psychotherapy, homeopathy. Then I took a Canadian supplement for bi-polar called EmPower Plus, and the mood swings went away over several months. This was six years ago, and the symptoms haven’t returned, and I stopped the psychiatric medication five and a half years ago. Not sure if it was the supplement that did the trick, or something else, but the timing makes me suspect it was the supplement.

    • Hi Peter,
      I know you made your comment some years before I found it today.. but if you get my message, perhaps you would not mind responding :).. I have not met anyone else that takes EmPower for their bipolar diagnosis, and would like to know how you are doing these 4 years later.. I agree that those micronutrients worked where the scads of psychomeds did not– not to mention the adverse med side effects etc!.. I started in 2006, yet still suffer to quite a degree, so I’m wondering if I could get some info/suggestions from you.. for example > Are you still on EmPower/micronutriets for mental illness diagnosis? What further treatment have you sought out, or needed? ETC

      I am considering rTMS treament (repetitive Transcranial Magnetic Stimulation) as well as other alternative treatments..

      I started on Empower Plus, but now on Daily Essential Nutrients from company called Nutratek (an offshoot of EmPower’s Truehope).

      I hope to hear back from you, and thank you for your time in advance 🙂


  8. Hi Chris, loved the podcast. Thought I’d share some interesting articles I found on the connecting between modern disease and the changes and “losses” of the human microbes. Specifically I’d suggest taking a look at some of the work by Martin Blaser, a researcher out of nyu: http://www.med.nyu.edu/medicine/labs/blaserlab/

    One article that really caught my attention and I thought very pertinent to the question you asked Paul about the “hygiene hypothesis”. This is the response of Blaser and a colleague in the article “Losses in Ancestral Microbes Pose Health Risks to Humans”,

    “Blaser and Falkow hold that the major factor for modern allergic and metabolic disease is not our decreased exposure to immune-stimulating microbes in food, air, water, or soil as postulated by the “hygiene hypothesis.” Rather, they attribute the recent trends to the loss of our ancestral microbiota.”

    Here’s the link to the article: http://www.microbemagazine.org/index.php/03-2010-current-topics/1423-losses-in-ancestral-microbes-pose-health-risks-to-humans

    Anyway, just thought this was very interesting and wanted to share the find!

    Jenny K

  9. Hi Chris,

    Great podcast!

    Can you advise what podcasts have transcripts available and where and how to access them as well as future ones?

    Thanks for all you do!


  10. Great podcast, gents. Paul Jaminet is wonderfully clear and insightful. Glad to hear he may return.

  11. Chris,
    I have really enjoyed listening to your podcasts and reading your updates, definitely eyeopening. I have a question related to the latest podcast. Jeff mentioned that he takes a multivitamin at lunch time. If his diet is gear towards ‘perfect health’ should it not include all the nutrients needed without supplementation. Many of the other diet based books, podcasts, etc pretty much eschew supplementation by eating a complete diet. What is your view on this?


  12. hooray! Thank you Jeff Rothschild for the hours of labour you’ve put into the transcriptions! What a treat!