2014: Year of the Microbiome

There’s nothing worse than a “why my blog is stagnant” post, so I’ll spare you. Suffice to say I blog when I have fresh ideas, and don’t blog when I have nothing original to add. I’m not interested in rewriting what’s already been written elsewhere. My goal is to make a real contribution to the Paleo-sphere. 

At the beginning of 2014 I resolved to improve my microbiome, inspired by a great series on microbiome research from NPR and the fact that my GI function wasn’t where it used to be. After four years, my Paleo honeymoon was over. Old GI problems had resurfaced and I was getting sick more often, despite no dietary changes. I believed there was likely a gut microbiome component to this, and my long-term GI issues as well. Perhaps an important strain of bacteria was missing, or the balance between gut bugs was off.

It’s hard to know, even today. The science isn’t clear on what the human microbiome should look like, and more and more it appears that there is no single microbial profile that promotes health. Striking differences in the microbiomes of healthy people exist. On top of that, an individual’s microbiome is very dynamic, changing with diet and other factors.

That said, I’m also coming to the realization that one’s microbiome may be the single most important factor in one’s health. Recently, it was shown that after simply transferring the bacteria from an obese person to a slim person, the slim person became obese. The importance of the microbiome will continue to be uncovered as research continues.

So what have I done? I’ve started regularly eating fermented foods, and experimented with supplementing with resistant starch and soil-based organisms (SBO). I’ve also dramatically reduced the amount of soap I use. Few diet and lifestyle changes I’ve made over the years have had as profound and immediate an impact as this has. Some of the things I’ve experienced included improved sleep, vivid dreams, mental clarity, and literally overnight GI function improvement after weeks of problems.

A primer on resistant starch:

I’m also going to go out on a limb and posit that the effects, both positive and negative, of diet are actually the results of how those dietary changes affect the microbiome.

Eat your veggies and a salad everyday? Chances are you are getting a good helping of SBO with that as well. Not to mention the prebiotic fiber that the microbiome needs to thrive.

Eating processed junk food regularly? There are many pathways for that to disrupt the microbiome. The best understood pathway is through refined sugar, which disrupts the balance of bacteria and causes yeast overgrowth that begins a cascade of systemic inflammation. Artificial sweeteners that are promoted as a replacement for sugar for diabetics actually increase glucose intolerance through altering the microbiome. Now scientists are finding that some preservatives in processed foods can hurt the microbiome as well. I could go on.

The most intriguing aspect of all of this is the interaction of the microbiome and epigenome. Remember that DNA is not exactly the blueprint for how one’s physiology will turn out. Most of the genes that affect health and are linked to chronic disease are expressed or not-expressed through interaction with the environment. Recent studies are uncovering ways that microbiome/genetic interaction play a role in Crohn’s Disease, ulcerative colitis, and cancer. I think this is the tip of the iceberg.

I suspect that future research will show that there are few areas of human health that aren’t impacted by the microbiome, and we’ll see increased importance put on maintaining gut health as a means to promote and maintain overall health.

Jogging is Paleo, Deal with It

A couple new papers and stories in the media have me thinking more about running lately. I don’t make a big habit out of it, but I do occasionally do some hill sprints and 5k races just for fun, and to mix up my exercise routine. Sometimes I think there is a bit too much naysaying of running and moderate-intensity endurance exercise in general within the Paleo community, and in light of this new research, I wanted to reexamine running within a Paleo framework.

Jogging has gotten a rather cold reception within the Paleo community, but I’m not sure that’s entirely fair. First of all, it’s a really easy activity to do. You don’t need a home gym or thousand dollar bike to do it. A decent pair of shoes (I prefer minimilist shoes) and a bit of sidewalk or trail will do. Second, by stepping up the intensity occasionally, it’s an easy way to reach those peaks of exertion required for the cascade of positive metabolic effects to occur if one is pursuing a weight-loss/metabolic conditioning program. Brief bursts of high-intensity training can increase insulin sensitivity, leptin sensitivity, reduce blood pressure, and increase one’s resting metabolism, among other benefits.[1,2]

Photo by Mike Baird

There is also no doubt that some amount of running was routinely practiced by the Paleolithic people whose’s genetic heritage we carry. It’s very difficult to imagine living in the wild without occasionally running after prey, running from predators, running from/after competing groups, etc. And let’s not forget about persistence hunting.[3,4]

Now, don’t get me wrong. It’s very easy to overdo it. Running marathons, for example, has been shown to cause subclinical heart damage.[5-7] Running for long periods can also expose the runner to an excess of the stress hormone cortisol and oxidative damage.[8] We just need to know what’s healthy and what probably isn’t.

Jogging, or running at a moderate pace for an extended period, is really what get’s the ire of a lot of people, and mostly for good reasons. This is probably exactly what most people picture when reading Mark Sission’s famous “Chronic Cardio” post. But what about joggers that don’t aspire to run marathons and just go out for a few miles every couple of days?

A new, unpublished study found a U-shaped correlation between jogging time and life expectancy.[9]

Undertaking regular jogging increases the life expectancy of men by 6.2 years and women by 5.6 years, reveals the latest data from the Copenhagen City Heart study presented at the EuroPRevent2012 meeting. Reviewing the evidence of whether jogging is healthy or hazardous, Peter Schnohr told delegates that the study’s most recent analysis (unpublished) shows that between one and two-and-a-half hours of jogging per week at a “slow or average” pace delivers optimum benefits for longevity.

Further analysis exploring the amounts of exercise undertaken by joggers in the study has revealed a U-shaped curve for the relationship between the time spent exercising and mortality. The investigators found that between one hour and two and a half hours a week, undertaken over two to three sessions, delivered the optimum benefits, especially when performed at a slow or average pace. “The relationship appears much like alcohol intakes. Mortality is lower in people reporting moderate jogging, than in non-joggers or those undertaking extreme levels of exercise,” said Schnohr.

Two and half hours of jogging per week is a lot more jogging than a lot of Paleo enthusiast are comfortable with (15 miles at a nice-and-easy 10 minutes/mile), but it appears to be safe.

Now, of course, this type of study cannot show causal relationships–there could be other factors at work. For instance, joggers are less likely to smoke, drink excessively, and probably try to eat a healthier diet than most non-joggers. All of these things affect the difference in life expectancy between joggers and non-joggers, but that doesn’t explain why jogging more than 2.5 hours a week ends up having a negative effect, as one would assume joggers that go out even longer are even more committed to leading a healthy lifestyle.

Another study looked at the neurological effects of running (aka the “runner’s high”). They found that a runner’s body produces cannabinoids, the same type of chemicals found in marijuana.* The researchers wondered if this was an evolutionary adaption for species that enage in distance running, and loe and behold, found the same effect in dogs (distance runners) but not in ferrets (not distance runners). While too much running is clearly damaging, there is still evidence that we were “Born to Run” as it’s been put.[10]

So there you have it. Jogging is a perfectly healthy part of a Paleo lifestyle. Just skip the sugared-up exercise drinks, run as close to barefoot as possible, run on uneven terrain to reduce repetitive stresses on the joints, and keep your overall time low. If you want to be out all day, go for a long hike or low-intensity bike ride instead.

* Tangent: The press has presented this as if running is as addictive as hard drugs, which makes about as much sense as claiming marijuana is as addictive as hard drugs. Why everything that activates the reward centers of the brain is considered addictive, I will never understand. Pleasurable experiences, including the use of hard drugs, do active the brain’s reward centers (big surprise), but clearly there is more to the story than blobs on an fMRI. Some rewards we can manage, some we can’t. Just looking at fMRI’s and ignoring the behavioral aspects of addiction because we now have “hard evidence” is foolish.


1. Babraj JA, Vollaard NB, Keast C, Guppy FM, Cottrell G, Timmons JA. Extremely short duration high intensity interval training substantially improves insulin action in young healthy males. BMC Endocr Disord. 2009 Jan 28;9:3. PubMed PMID: 19175906; PubMed Central PMCID: PMC2640399.

2. Irving BA, Davis CK, Brock DW, Weltman JY, Swift D, Barrett EJ, Gaesser GA, Weltman A. Effect of exercise training intensity on abdominal visceral fat and body composition. Med Sci Sports Exerc. 2008 Nov;40(11):1863-72. PubMed PMID: 18845966; PubMed Central PMCID: PMC2730190.

3. Bramble DM, Lieberman DE. Endurance running and the evolution of Homo. Nature. 2004 Nov 18;432(7015):345-52. PubMed PMID: 15549097.

4. Liebenberg L. The relevance of persistence hunting to human evolution. J Hum Evol. 2008 Dec;55(6):1156-9. Epub 2008 Aug 29. PubMed PMID: 18760825.

5. Möhlenkamp S, Lehmann N, Breuckmann F, Bröcker-Preuss M, Nassenstein K, Halle M, Budde T, Mann K, Barkhausen J, Heusch G, Jöckel KH, Erbel R; Marathon Study Investigators; Heinz Nixdorf Recall Study Investigators. Running: the risk of coronary events : Prevalence and prognostic relevance of coronary atherosclerosis in marathon runners. Eur Heart J. 2008 Aug;29(15):1903-10. Epub 2008 Apr 21. PubMed PMID: 18426850.

6. Wilson M, O’Hanlon R, Prasad S, Deighan A, Macmillan P, Oxborough D, Godfrey R, Smith G, Maceira A, Sharma S, George K, Whyte G. Diverse patterns of myocardial fibrosis in lifelong, veteran endurance athletes. J Appl Physiol. 2011 Jun;110(6):1622-6. Epub 2011 Feb 17. PubMed PMID: 21330616; PubMed Central PMCID: PMC3119133.

7. Neilan TG, Januzzi JL, Lee-Lewandrowski E, Ton-Nu TT, Yoerger DM, Jassal DS, Lewandrowski KB, Siegel AJ, Marshall JE, Douglas PS, Lawlor D, Picard MH, Wood MJ. Myocardial injury and ventricular dysfunction related to training levels among nonelite participants in the Boston marathon. Circulation. 2006 Nov 28;114(22):2325-33. Epub 2006 Nov 13. PubMed PMID: 17101848.

8. Witt EH, Reznick AZ, Viguie CA, Starke-Reed P, Packer L. Exercise, oxidative damage and effects of antioxidant manipulation. J Nutr. 1992 Mar;122(3 Suppl):766-73. Review. PubMed PMID: 1514950.

9. “Assessing prognosis: a glimpse of the future.” Symposium: Saturday May 5, 9.15 am to 10.15 am. Liffey B Lecture Room. P. Schnohr, Jogging-healthy or hazard?

10. Raichlen DA, Foster AD, Gerdeman GL, Seillier A, Giuffrida A. Wired to run: exercise-induced endocannabinoid signaling in humans and cursorial mammals with implications for the ‘runner’s high’. J Exp Biol. 2012 Apr 15;215(Pt 8):1331-6. PubMed PMID: 22442371.

The Dairy Question and The Paleo Diet’s Epistemic Continuum

Dairy has a peculiar status among Paleo eaters. Although it’s a Neolithic food, it’s usually considered healthful if one is not lactose intolerant. Recently, I have been struggling with it’s acceptance, for a couple of reasons, and it’s helped elucidate an interesting difference among members of Paleo community.

The most important concern of mine is the difference between acute effects and chronic effects. That is, something that may show no distinguishable harm in the short-term may end up causing harm after decades of consumption. Discovering an effect like this is very difficult, because it’s impossible to do a well-controlled study of long-term nutritional effects in humans, and if your working theory is that something may be harmful, it may also be unethical to attempt such research. Epidemiological studies are the best science can offer, and we’re all familiar with their weaknesses.

Specifically about dairy, it’s been shown to have unique biochemical effects in humans. Several vegetarian diet advocates claim that dairy is addictive, based on the research that it contains peptides that bind to opioid receptors.[1] Effects like this may be suitable for a calf to help it quickly gain body mass, but we certainly don’t need any extra encouragement to eat. I should note that I can’t find any scientific literature that makes the specific claim that dairy is addictive.

More fundamentally, cow’s milk has evolved to feed rapidly growing cows, not humans. As a result, it carries several hormonal effects that may be unsuitable for humans.

On a different note, it seems that dairy has gotten in through the back door, because it’s a low-carb/high-fat food, and for many Paleo eaters, Paleo is just a cleaned-up low-carb diet. But not all fats are OK, as we’re all aware of the trouble with Linoleic Acid.[2] Dairy doesn’t deserve acceptance for being a low-carb food.

I’m lactose intolerant, so of course that colors my view of dairy. Perhaps there is more to this story that I am missing, but it seems best to avoid dairy altogether and eat mostly ancient foods like meat, organs, vegetables, and fruit, regardless of one’s short-term lactose tolerance.

This choice illustrates where one is on the Paleo diet’s epistemic continuum–a concept that explains the differing food choices we make, all under the umbrella term “Paleo.” On one end of the continuum is nutritional science that lacks theoretical underpinnings, and on the other end is relatively unsupported evolutionary theory (the middle is where science and evolutionary theory agree). How do we decide which direction to head when nutritional science and  evolutionary logic/anthropology seemingly conflict?

Most of the time, we have science on our side; well-controlled, randomized studies can be cited to defend a fair amount of the Paleo platform. But sometimes things get messy. The Dairy Question is a prime example. In a way, the continuum has helped explain the various flavors of Paleo. On one end of the continuum, Dr. Cordain and Robb Wolf tend to favor evolution and anthropology when it conflicts with nutritional science. They want you to exclude dairy and legumes from your diet, although the supporting science is far from conclusive. Closer to the other end is Mark Sisson and Dr. Kurt Harris, who say dairy is fine if you can tolerate it, legumes should be limited only because they crowd out more nutritionally dense foods, and Paleo itself is more of a template. It informs their views, but the supporting science, or lack thereof, is more critical. Dr. Kurt Harris has formalized his approach to the problem as PaNu and his writing about it is fascinating and brilliant.

I think that too much faith in ungrounded nutritional science results in a lack of respect for the limits of human knowledge. This is part of the philosophical foundation of Paleo. It’s a mistake to believe that the current nutritional science has discovered everything necessary to proscribe the perfect diet for everyone. We are far from the final word on human health, and we would do well to ponder the probability that our scientific models are wrong. Within Paleo, evolutionary logic guides our understanding when that probability is high, but what about when that probability is low and it conflicts with evolutionary theory?

Maybe dairy, legumes, and white rice[3] really are perfectly safe foods despite not being present in Paleolithic diets? Just because a food is Neolithic doesn’t mean it must be harmful, but I think that warrants a more careful scrutiny than ancient foods.

On the other end of the continuum, we’ve been wrong about the role saturated fat played in human evolution,[5] and Richard Nikoley just dropped a bomb on the Paleo Diet’s low-carb dogma. How do we know we’re telling the right story now?

How do we know which way of thinking is correct? Or rather, is there a point on this continuum that will likely produce more truth than other points? This is the fundamental distinction that lies at the heart of the differing approaches to Paleo.

How and why one decides where they end up on the nutritional science <–> evolution/anthropology epistemic continuum is a bit of a mystery to me. Where are you on there, and how did you get there?

tAs for dairy, do you give more weight to the nutritional science that has found no smoking gun, or do you defer to evolutionary theory in the face of uncertainty and avoid dairy? There is no easy way to answer that question, but questions like it, and the way we answer them, help explain the diversity of approaches to Paleo we’ve seen in the past decade or so.


1. Schmitz G, Ecker J. The opposing effects of n-3 and n-6 fatty acids. Prog Lipid Res. 2008 Mar;47(2):147-55. Epub 2007 Dec 25. Review. PubMed PMID: 18198131.

2. Meisel H, FitzGerald RJ. Opioid peptides encrypted in intact milk protein sequences. Br J Nutr. 2000 Nov;84 Suppl 1:S27-31. Review. PubMed PMID: 11242443.

3. Zhang L, Hou D, Chen X, Li D, Zhu L, Zhang Y, Li J, Bian Z, Liang X, Cai X, Yin Y, Wang C, Zhang T, Zhu D, Zhang D, Xu J, Chen Q, Ba Y, Liu J, Wang Q, Chen J, Wang J, Wang M, Zhang Q, Zhang J, Zen K, Zhang CY. Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA.Cell Res. 2011 Sep 20. doi: 10.1038/cr.2011.158. [Epub ahead of print] PubMed PMID: 21931358.

4. Lindeberg S, Ahrén B, Nilsson A, Cordain L, Nilsson-Ehle P, Vessby B. Determinants of serum triglycerides and high-density lipoprotein cholesterol in traditional Trobriand Islanders: the Kitava Study. Scand J Clin Lab Invest. 2003;63(3):175-80. PubMed PMID: 12817903.

5. Cordain L, Eaton SB, Sebastian A, Mann N, Lindeberg S, Watkins BA, O’Keefe JH, Brand-Miller J. Origins and evolution of the Western diet: health implications for the 21st century. Am J Clin Nutr. 2005 Feb;81(2):341-54. Review. PubMed PMID: 15699220.

Human Genomics Didn’t Fail, The Paradigm Did

At the turn of the century one of the most exciting areas of medical research was the Human Genome Project, a massive scientific undertaking that successfully mapped the entire human genome in 2003. The hope was that by conducting large association studies, researchers could identify the genes that cause various diseases such as cancer, diabetes, heart disease, etc. Once the troublesome gene was identified, pharmacalogical interventions could be developed to reduce or stop the expression of the disease gene, which would end or reverse the progression of the disease.

Unfortunately, very little came from these association studies. Only a few genes were linked to specific diseases, and these proved to only create a predisposition to the disease, not a definite trigger. So far genes can only explain about 5-10% of cancer risk, 10% for type 2 diabetes,[1] and 5% for parkinson’s disease. The “failure” of these studies has lead to the widespread opinion that the study of human genomics has been fruitless.

I see things differently. The fact that these studies found few associations shows that the causes of these diseases are more than likely environmental, not biologically predetermined. That is, certain lifestyles are the most likely underlying causes. We don’t need to worry about “fixing” a “broken” biology. Human beings are not broken by default. I am more and more convinced that the strongest factors in determining disease risk are an industrial, Neolithic diet and a sedentary lifestyle. We only need to leave behind our bad habits.

We don’t need new “miracle” drugs to come along and save us from ourselves. We need to give up the modern, culturally-reinforced behaviors that underly diseases of civilization. That’s something we can do now, on our own, without the need of decades-long research projects and billion dollar, blockbuster drugs.


1. Herder C, Roden M. Genetics of type 2 diabetes: pathophysiologic and clinical relevance. Eur J Clin Invest. 2011 Jun;41(6):679-92. doi: 10.1111/j.1365-2362.2010.02454.x. Epub 2010 Dec 30. Review. PubMed PMID: 21198561.

How To Argue with a Vegan/Vegetarian

So you’re eating meat for health and want to convince every Vegan around they are wrong? How do you do it?

You don’t. Sorry to burst your self-righteous bubble, but you simply aren’t going to change anyone’s mind by arguing with them. And even if you could, why bother? Live you life the way you want to and allow others to live their lives the way they want to. Leave the evangelizing out of it.

But, say a Vegan honestly wants to hear your perspective on meat. In that case, this story from The Atlantic (one of my favorite media outlets) should probably be your go-to link for interested Vegans. It begins…

Collectively, we have lived 52 years vegetarian or vegan. Yet we no longer think vegetarianism is the answer. Now we firmly believe foods from animals can be both healthful and ethical.

Continue reading

Why We’re Sick in One Picture

Want to see everything that is wrong with conventional diet and exercise regimens and the causes of ever-increasing chronic disease in one photo? Here it is. (Hat tip: Reddit)

It goes like this:

Eat a processed, high carbohydrate, grain-based diet that makes you fat and hungry,[1] and results in chronic disease.[2] Try to remedy the situation by doing “cardio” exercise like jogging which over-stresses your heart[3] and saturates your body with the stress hormone cortisol. Finally, double down on this failed strategy by blaming meat for your declining health and adopt an extremely high carbohydrate, unnatural[4] Vegan diet that requires endless pill-popping and results in malnutrition and heart disease.[5,6]

Thumbs up!

Why do we do this to ourselves? There are much better paths to optimal health.


1. Ludwig DS, Majzoub JA, Al-Zahrani A, Dallal GE, Blanco I, Roberts SB. High glycemic index foods, overeating, and obesity. Pediatrics. 1999 Mar;103(3):E26. PubMed PMID: 10049982.

2. Cordain L, Eaton SB, Sebastian A, Mann N, Lindeberg S, Watkins BA, O’Keefe JH, Brand-Miller J. Origins and evolution of the Western diet: health implications for the 21st century. Am J Clin Nutr. 2005 Feb;81(2):341-54. Review. PubMed PMID: 15699220.

3. Möhlenkamp S, Lehmann N, Breuckmann F, Bröcker-Preuss M, Nassenstein K, Halle M, Budde T, Mann K, Barkhausen J, Heusch G, Jöckel KH, Erbel R; Marathon Study Investigators; Heinz Nixdorf Recall Study Investigators. Running: the risk of coronary events : Prevalence and prognostic relevance of coronary atherosclerosis in marathon runners. Eur Heart J. 2008 Aug;29(15):1903-10. Epub 2008 Apr 21. PubMed PMID: 18426850.

4. Milton K. The critical role played by animal source foods in human (Homo) evolution. J Nutr. 2003 Nov;133(11 Suppl 2):3886S-3892S. Review. PubMed PMID: 14672286.

5. Shinwell ED, Gorodischer R. Totally vegetarian diets and infant nutrition. Pediatrics. 1982 Oct;70(4):582-6. PubMed PMID: 6812012.

6. Ingenbleek Y, McCully KS. Vegetarianism produces subclinical malnutrition, hyperhomocysteinemia and atherogenesis. Nutrition. 2011 Aug 26. [Epub ahead of print] PubMed PMID: 21872435.