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Posts Tagged ‘Autophagy’

What Your Doctor Is Not Thinking About (Dragging Medical Professionals Into the Modern Era)

Wednesday, February 29th, 2012

Today we feature a new article from, JD Moyer of the blog Systems for Living Well:

The other day I came across this alarming video of what it’s like to drive in Poland. My first thought after watching the clip was “What’s the Toxoplasmosis gondii infection rate in Poland?” T. gondii is a brain parasite easily acquired from eating undercooked meat, or contact with cats, and is associated with a six-fold increase in traffic accidents (this association has been replicated a number of times, in different countries). Well, I looked it up, and found that the latent infection rate in 2003 was around 41% (at least among pregnant women). That’s quite high — in the U.S. the infection rate is only about 11%.


Is there anything to my hypothesis that terrible driving in Poland is related to the relatively high T. gondii infection rate? Probably not. The accident fatality rate in Poland is relatively high for a modern industrialized country. But France has a very low accident fatality rate, and a much higher rate of T. gondii infection. So while T. gondii might be a contributing factor, it’s probably not the most important variable.

I’m fascinated by latent/chronic biological infections, and how they affect human health and behavior. T. gondii in particular is linked to changes in personality, and even schizophrenia.

What’s shocking to me, as shocking as the driving in Poland video above, is that so few medical professionals are considering latent infections as part of their diagnostic process. The research is here, and so are the diagnostic tests. So why aren’t medical professionals taking advantage of them?

The Future Is Here, It’s Just Not Evenly Distributed -William Gibson

The above quote definitely applies to the medical profession. How many general practitioners are doing the following?


  • a detailed dietary questionnaire (cost: $0, benefits: insights into common subclinical nutritional deficiencies, including vitamins C, D, B12, K2, magnesium, iron, zinc, copper, and chromium, as well as information re: macronutrients — is the patient eating enough protein and omega-3 fatty acids? or consuming too much fructose/sucrose/alcohol?)
  • a personal genetic profile (cost: $200, benefits: insights into disease risk for common health problems, and precise genotype information re: less common genetic conditions)
  •  antibody testing for a full range of common viral infections (HSV1, HSV2, CMV, HPV, etc.) (cost: a few hundred dollars, benefits: insight into diseases that are linked to multi-decade viral infections, including heart disease, dementia, many types of cancer, etc.)
  • an enterotype panel

I’m hoping that in ten years or so, the above practices will be commonplace. Spit in a tube, piss in a cup, prick your finger, and twenty minutes later get a full genome analysis, a full spectrum nutrient level analysis, a metal and chemical toxicity report (lead, mercury, bisophenol-A, etc.), an extremely wide antibody report (for hundreds or thousand of viruses), a complete bacterial panel (blood, gut, and mouth), testing for protozoan parasites like T. gondii, etc.

Why isn’t this happening already?

Gibson didn’t anticipate cheap genome sequencing.

In some cases cost is prohibitive. While a genome SNP test has come down to $200, micronutrient testing like the kind Spectracell offers is still quite expensive. I suspect that we’re on the cusp of (or in the midst of) a rapid advance in portable diagnostic technology, so testing costs may change quickly. It remains to be seen how quickly HMO’s will take advantage of the new technologies as they come online.

Another reason is that your doctor isn’t necessarily thinking along these lines, because when she was in medical school, you couldn’t get an accurate micronutrient panel, or a genome analysis, or an enterotype panel. These tests just weren’t available.

Educate Yourself, Test Yourself, Take Preventative Measure

It’s irritating to me that the medical profession hasn’t caught up with medical research and diagnostic technology. For most people, it’s probably worth taking the following diagnostic and preventive measures:

  1. If you can afford it, get a full micronutrient profile from Spectracell or another reputable vendor. I’m putting this at the top of my list because I haven’t actually done it yet (but I’m going to). At the very least, get a vitamin D test. If your levels are suboptimal, you’ll probably need to supplement, and also consider vitamin A and K2 levels.
  2. Get your genome analyzed, from 23andMe or a similar service. Find out what your risks are. One way to think about it is that reading your genome is like reading your death sentence. Another way to think about it is that reading your genome will give you possible clues into improving your quality of life, and possibly extending your life for a decade or more if you take the appropriate preventative measures.

What about prevention? Some measures are common sense. Others, like implementing a general viral suppression protocol, perhaps less so.

  1. Diet – get most gluten, casein, fructose, and refined vegetable oil (canola, corn, soy) out of the diet to drastically reduce your risk of IBS, autoimmune diseases, heart problems, and diabetes. Eat nutrient dense whole foods, mostly those available during the paleolithic era (for which we are genetically best-adapted to). This would include seafood, grass-fed meat, eggs from free-roaming birds, vegetables, low-sugar fruits, and nuts/seeds. For the research, please see Mark Sisson’s site.
  2. Reduce your carcinogen/toxin load (lead, mercury, bisphenol-A, air pollution, tobacco, hard alcohol, narcotics) to reduce risk of cancer, reproductive, and neurological problems.
  3. Ramp-up autophagy (clean out cellular debris) with both intense exercise and intermittent fasting. This will help ward off cancer, dementia, and suppress chronic viral and parasitic infections (which we all have after age 2 or so, unless we live in a bubble).
  4. Consume chemicals that kill cancer cells and interfere with viral replication. A short list would include curcumin (turmeric/yellow curry), garlic, resveratrol/grapeseed extract/red wine, and coconut oil. The links all go to research or articles about research.
  5. Reduce artificial light in the evenings to encourage natural sleep patterns. My post about giving up artificial light for a month has seen a spike in traffic since this recent BBC article (I was also on The Doctors about a month ago discussing the experiment).

I think the clinical research is there to back up all these claims. But are you going to get any of this advice from your doctor? Probably not. Your doctor is going to tell you to eat a low fat diet, but won’t distinguish good fats (olive oil, coconut oil, fats from grass-fed meats and wild fish) from bad fats (refined vegetable oil, fats from grain-fed animals). He will probably not mention vitamin D, vitamin K2, or the beneficial effects of polyphenols and flavonols. Your doctor is going to ask about your family history, but he’s not going to recommend that you actually look at your genome. Sugar and carbohydrate consumption won’t be mentioned unless you already have diabetes. Viral infections won’t be identified unless they have very specific symptoms (like chicken pox or cold sores), and no recommendations will be made to suppress chronic viral infection to prevent cancer or dementia twenty or forty years later.

I’m not against going to the doctor, or taking medical advice from someone who is better educated and informed than myself. But we should push our medical professionals. We should drag them (even if they protest, kicking and screaming) into the modern era.

The future is here … please help spread it around.

Death Will Eat Itself (The Enormous Benefits of Autophagy, or Why You Should Stop Eating Once in Awhile)

Wednesday, February 1st, 2012
Today we feature a new article from, JD Moyer of the blog Systems for Living Well:

About a year ago I became interested in the benefits of intermittent fasting after reading a number of articles on Martin Berkhan’s Leangains site. Martin is a Swedish nutritional consultant/personal trainer/writer. His recommendations run contrary to conventional wisdom among personal trainers, but his ideas are well-researched and accompanied by numerous examples (pictures) of his own physique and the physiques of his clients, who are all very muscular and impressively lean. Martin’s writing style is bombastic, confrontational, and entertaining, but also thorough, persuasive, and rich in citations.

Martin’s main idea is that intermittent fasting can assist with fat loss and muscle growth simultaneously. Most weight-lifters would tell you that both “growth phases” (where muscle and fat are added simultaneously) and “cutting phases” (where calories are restricted and fat is lost) are required. Martin calls B.S. on that idea, and provides ample evidence that restricting eating to an 8-hour daily “window” (only eating between 2pm and 10pm, for example), combined with simple, consistent workouts can allow a person to get leaner and stronger at the same time.

My Own Experience

At this point in my life I’m not looking for a radical change in my physique, but Martin’s posts piqued my curiosity enough to give intermittent fasting a try. I decided I would “dip a toe in” and try not eating until 2pm, one day a week.

I found it to be easier than expected. On my partial fast days, I only drink water and black coffee until 2pm. I rarely experience any hunger pangs (though I do look forward to my first meal more than I would otherwise). Here are a few other subjective observations:


  • I feel a bit colder, during the winter I usually wear an extra layer on fasting days.
  • I feel mentally clear; fasting days are great writing and/or music composition days.
  • I usually double my productivity on fasting days. I think this is a combination of having better concentration and being less vulnerable to distractions, and the extra time from not having to prepare food or clean up after meals.
  • I usually eat two meals on partial fast days, one around 2pm, and dinner around 6 or 7. These meals tend to be larger than normal. I don’t count calories, but I suspect my caloric intake is less than on normal eating days, even though I eat until I’m full.

What Is Autophagy, and Why Is It Good For You?

Autophagy — it sounds like some kind of disease from the Star Trek universe. In fact, autophagy is a normal biological process. During autophagy, organelles called lysosomes break down waste products inside the cells. What’s an organelle? An organelle is a tiny part of your cell, usually with its own membrane, that serves a specific function (like a cellular organ). Lysosomes break down other worn-out organelles, digest food particles, and destroy viruses and bacteria (using hydrolase enzymes). You could think of them as the stomach of the cell, and/or part of the cellular immune system.

(Photo caption: Artistic depiction of a lysosome during autophagy).

Autophagy can even extend to include the destruction of the cell itself, a process called autolysis. For this reason, lysosomes are sometimes dubbed “suicide bags.”

Without autophagy, damaged organelles survive, and cells become less efficient. Autophagy may protect against neurodegeneration, viral and bacterial infections, and cancer.

Short-term fasting can induce autophagy. I can’t find any clinical studies in humans showing precisely when autophagy ramps up in response to fasting. Liver glycogen stores are depleted 12-16 hours into a fast, and it follows that autophagy would ramp up soon after (Berkhan recommends a 14-16 hour daily fast as part of the Leangains protocol). If I have my last food of the day around 8pm, then don’t eat until 2pm the next day, that’s an 18 hour fast. So my one-day-a-week half-day fast is probably enough to upregulate this powerful physiological process for at least a couple hours.

My own crude way of thinking about autophagy is that this process “cleans out the gunk.” By inducing autophagy, I allow my body to break down old mitochondria (the “energy producers” of the cell), destroy viruses and bacteria, and suppress chronic infections.

What was that last bit? Chronic infections? How bad is it, J.D.?

We’re All Infected

Well, I have some bad news for you. We all have chronic infections. I’ve been reading The Perfect Health Diet by Paul Jaminet and Shou-Ching Shih Jaminet (thanks Dan Pardi for sending it to me, and thanks Tyler Simmons for recommending it — I’m planning on writing a review post soon). There’s a great section towards the end of the book about chronic infections. Unless you’ve lived in a bubble your whole life, you’ve probably got at least one of the following infections:

  • Cytomegalovirus (CMV) — infection rate among adults in the U.S. is between 50-80%
  • HSV-1 — the virus that causes cold sores is found in about 60% of people in the U.S.
  • Toxoplasmosis — you can pick up this protozoan parasite from handling cat poop or eating undercooked meat. In the U.S. only 10% of the population carries antibodies, but infection rates in other parts of the world are up to 60%

All three of these infections are generally considered “harmless” in the non-immunocompromised, but even people showing no symptoms may suffer long-term effects from these infections. Toxoplasmosis infection may slow reflexes and is associated with a sharply higher rate of car accidents. Long-term HSV-1 infection may be a cause of Alzheimer’s disease. Other extremely common chronic infections include C. pneumoniae (also associated with Alzheimer’s, as well as atherosclerosis, stroke, multiple sclerosis, arthritis, and rosacea) and H. pylori (which causes stomach ulcers). The adenovirus AD-36 is present in about 20% of the population and may contribute to obesity (as well as causing respiratory and eye infections).

(Photo caption: The Perfect Health Diet [includes ice cream])

In most cases we’re not even aware of all of our viral and bacterial infections, as many of them start off giving us vague symptoms when we’re first infected, then become asymptomatic in their latent phase. I only became aware that I had picked up CMV after giving blood and losing my CMV-negative status (before, they could give my blood to newborn babies, now they can’t). With hindsight, I realized that I probably got CMV around the time my daughter started preschool. For a couple months around that time I had a slightly swollen submandibular salivary gland. My doctor examined me, shrugged, and said “doesn’t feel like cancer … probably a virus … check back with me in six months if it hasn’t gone away.” Well, the swelling went down, but I later learned that the salivary glands are a common site for CMV infection.

So, we’re all infected. Should we be freaking out, driving to Vegas, and blowing our life savings on one last wild weekend?

Relax, it’s not that bad.

First of all, some chronic infections actually have protective or even positive side effects. H. pylori can cause stomach ulcers, but it is also be protective against GERD (acid reflux), thus protecting against oesophageal cancer. Hookworm infection may protect against symptoms of celiac disease. In some cases parasites have evolved ways to “tamp down” immune responses, thus preventing autoimmune diseases. The basic idea behind the “hygiene hypothesis” is that when our immune systems are underutilized fighting external pathogens (viruses, bacteria, parasites, etc.), the immune system is more likely to malfunction and turn against our own tissues (resulting in more allergies, asthma, and other autoimmune problems).

Still, these infections often prove to be our undoing in the long-run, either by robbing our bodies of resources, causing chronic low-grade inflammation, or slowing invading and damaging internal organs. It’s in our best interest to keep these chronic infections in check.

The Perfect Health Diet recommends eleven ways to enhance immunity and fight chronic infections, but I think that list is too long. Who’s going to do eleven things? I’ve shortened the list to the four most important/effective/doable, IMO:

  1. Get vitamin D levels to within an optimal range (to boost intracellular immunity and increase production of antimicrobial peptides)
  2. Reduce food toxin load (from grains [esp. wheat and other gluten grains], processed vegetable oils, sugar/fructose, bean lectins, etc.)
  3. Get enough sleep (one way to do this is to reduce artificial light in the evening)
  4. Practice intermittent fasting (weekly 16+ hour fasts, optional monthly 36+ hour fasts) to induce autophagy

Other Benefits of Intermittent Fasting (Motivation, Pleasure, Strength)

Short-term moderate food restriction has significant psychological effects. In this study, mice brains were found to remodel in response to food restriction, creating more dopamine (D2) receptors. Adequate dopamine receptors are necessary to allow us to anticipate and respond to rewards, and reduced numbers of dopamine receptors are associated with both aging and obesity. Moderate food restriction may resensitize us, allowing us to experience the same mental rewards from less food, and less palatable food (and other experiences).

This finding syncs with my own experience of intermittent fasting. After not eating for 18 hours, basically any food seems delicious to me — even a bowl of plain oatmeal or a plate of plain raw vegetables.

In addition, if life is feeling a little flat or dull, a short fast somehow alters my perception. Everything seems more colorful, clearer, more vivid, and more exciting.

Can the brain remodel so quickly? Maybe my subjective observations are related to another mechanism, something other than an increase in D2 receptors. Still, something is happening. The mind and body go into a different mode when food scarcity is perceived. Hunting mode, maybe (or gathering, take your pick).

Another benefit of short-term fasting is an increase in growth hormone (which helps to burn fat and build muscle). No wonder Martin Berkhan and his clients are so lean and strong.

Is Intermittent Fasting a Good Idea for Everyone?

I wouldn’t recommend intermittent fasting for everyone, at least right away. If you eat wheat and/or drink milk every day, you might experience exorphin withdrawal soon after skipping a meal. Wheat and milk both contain proteins that mimic endorphins (the pleasure-inducing, pain-relieving chemicals of the brain), and when you cut off the external supply of the chemical mimic, it takes a few days for the brain to ramp up internal endorphin production. In the meantime, you might experience aches, chills, and general grumpiness from cutting out these foods.

Similarly, if your blood sugar regulation is out of whack, intermittent fasting might be less comfortable. If you drink soda or other sweet drinks, eat candy, white bread, etc., then cut these foods out for awhile before you try intermittent fasting. Some supplements and foods may be helpful in regulating blood sugar and restoring insulin sensitivity, including chromium and cinnamon.

Your genetic makeup may also affect your response to intermittent fasting. Many people of Asian and European ancestry (myself included) have a mutation in the SNP rs2291725 that is associated with higher fasting blood glucose. This mutation probably became widespread in some populations thousands of years ago as a response to the inevitable “lean times” that came with a switch to agricultural food production. Women with this mutation were more likely to maintain their pregnancies during times of food scarcity. These days, the same mutation is associated with a higher risk of developing Type 2 diabetes and/or gestational diabetes. I wonder if having this mutation also makes intermittent fasting more comfortable (due to higher fasting blood glucose levels)?

Berkhan has noted that his female clients generally experience negative symptoms of fasting (low blood sugar, poor mood) after a shorter period, and recommends a 14-hour daily fast instead of 16 hours.

Pregnant women probably shouldn’t fast at all, as fasting during pregnancy has been associated with reduced academic performance in the children.

Some fears about shorts fasts are entirely unfounded, like the idea that short fasts will slow down your metabolism, increase cortisol, and force your body to burn muscle for fuel. Berkhan does a good job of debunking these metabolic myths in this post.

If, for whatever reason, you decide that intermittent fasting isn’t for you, fortunately there are other ways to induce autophagy, including exercise (thanks Dan Pardi for the PubMed research).

A Final Thought

I can’t think of a more effective, easier, cheaper anti-aging protocol than my weekly partial fast. The benefits (immunity enhancement, cellular “housecleaning”, growth hormone release, mental clarity, productivity boost) far outweigh the costs (slightly cooler body temperature on fasting days).

There’s also a satisfying kind of mental freedom in knowing you can miss a meal or two and still function normally.

Additional Resources: