J.D. Moyer

sci-fi writer, beat maker, self-experimenter

Brain Renewal Protocol

Winston Churchill’s nicknamed depression “his black dog.”

A week ago I woke up in a black mood. Instead of feeling excited about my day, I saw a series of dreary tasks ahead of me. Looking into the future, I felt despair instead of hopefulness. Things that usually bring me great pleasure (making music, time with my family and friends, drinking coffee) seemed a little less bright.

I know the signs. Sometimes I get a little depressed. Life stresses add up and darken my outlook.

A few events conspired to bring me to this dark place. A family member had emergency surgery. It went well — everyone is fine — but the episode was unexpected, expensive, and involved an all-nighter in the emergency room on my part. Major stress.

I had a cold that turned into a cough that lingered for a couple weeks. I hate being sick. Reduced energy and concentration cramps my style.

I’ve taken on a difficult consulting project that is progressing slowly, with a steep learning curve in several areas (I’m working with someone else’s code). Usually my freelance database work is fun and progresses quickly, but so far this project has just been grinding along.

I switched dentists, which might not be stressful for most people, but occupied a surprising amount of my mind-space until I finally had my appointment with my new dentist (she’s great — here’s her site if you’re in Oakland and looking for a dentist).

I was dealing OK with all of these events, but then I gave blood. I give blood on a regular basis and usually feel fine the next day, but it hit me like a load of bricks this time. I felt tired and spacey for a couple days, and my mood worsened.

When my mood goes dark, I feel less resilient dealing with everyday stresses, like my four year old’s mood swings. I worry about everything, including neighborhood crime, music sales (or lack thereof), the mental health of various family members, the soaring national debt, the corporate hijacking of our political process, the possibility of Iran and Israel going to war, and so on. Even though most things in my life are going well, I feel irrationally hopeless.

From my own casual observations, I think about 95% of adults experience a “black mood” for at least a few days at a time, at least once a year. And some people grind through life in a constant state of mild depression and never do anything about it.

What’s Going in the Stressed-Out Brain?

The brain reacts to stress by signaling the adrenals to release more cortisol (a steroid hormone that raises blood sugar, increases metabolism, and suppresses the immune system). In the short-term, in conjunction with a nerve growth factor called BDNF, cortisol protects the brain, acting as a kind of lubricant that enables brain cells to make changes.

But long-term exposure to elevated cortisol is bad news for the body and brain, especially when inflammation exists. It is associated with increased belly fat, which is bad for health in many ways. This study found that otherwise lean women with abdominal fat secreted more cortisol in response to stress.

Normally, cortisol has an anti-inflammatory effect. However, people under constant stress (like long-term caregivers) can become resistant to the anti-inflammatory effects of cortisol, and more sensitive to inflammatory factors like NF-κB (NF-kappaB).

Constant stress, especially when combined with poor coping strategies and/or poor nutrition, may also lead to adrenal depletion and crashing cortisol levels, and well as low levels of BDNF in the brain. Low BDNF in the hippocampus essentially means that the brain is atrophying, and is associated with Alzheimer’s Disease.

So what’s a stressed-out person to do? My own action plan is based on the following goals:

  • reduce external stressors
  • spiritual practice to reduce reactivity (“stress spiraling”)
  • reduce systemic inflammation
  • support healthful levels and rhythms of cortisol
  • increase BDNF

There’s no reason to stoically endure depressive feelings. There are things we can do to immediately change our brains and renew our spirits.

Brain Renewal Protocol

When I find myself stressed out by life events, I implement my Brain Renewal Protocol. The goal is to quickly improve my mood, life outlook, and sense of well-being via improved brain chemistry, reduced inflammation, and hippocampal neurogenesis. Here’s what I do, and why:

1. Talk about it

I don’t hide my feelings, but let my family and friends know what I’m going through. A little sympathy and slack go a long way. I try not to be a complaining sad sack — but I don’t stoically pretend I’m feeling great when I’m not.

Taking “talk about it” to the next level would be cognitive behavioral therapy (like psychotherapy, but more goal-oriented, with less sexual Freudian stuff). I did some of this in college when my parents were breaking up and another family member had some psychotic episodes. This was an incredibly stressful period of my life, and  the various on-campus psychological counseling services at UC Davis helped me through it.

2. Take a partial fast day

Intermittent fasting increases BDNF levels in the brain, and offers protection against inflammation and oxidation. Here’s a full post on my intermittent fasting practices. I only do IF once a week, but I notice the positive mood effect after just half a day without food.

3. Go for long fast walks

Long walks at a brisk pace are an ideal form of exercise for boosting BDNF levels while still being easy enough on the body to avoid any risk of over-training (and associated free radical release and increased cortisol secretion). It might be tempting to exercise yourself into oblivion (to get the endorphin rush), but it’s really important to not overdo it physically if you are under a great deal of stress.

4. Increase DHA and curcumin intake

DHA (from fish oil or oily fish) and curcumin (from turmeric — the spice that makes curry yellow) are both associated with higher BDNF levels. Lately I’ve been using Juliet Mae spice mixes for curries — the spices are super fresh and have “no bad stuff” (like MSG). Curcumin is also a good long-term brain investment — it protects against Alzheimer’s disease.

I take up to 4g of refrigerated fish oil a day when I’m under increased stress. One Harvard University study showed such a positive effect on depression and bipolar disorder that the study was stopped after four months so that the placebo group could also be treated with fish oil (the researchers considered it unethical to continue to deny the placebo group the benefits of treatment).

5. Reduce sugar and increase insulin sensitivity

Some researchers have begun to refer to Alzheimer’s as “Type III diabetes” (insulin resistance in the brain). This animal study found that a diet high in both fat and sugar reduced BDNF levels in the brain (though a follow-up study by the same researchers found that exercise mitigated the effect).

There’s a great deal of evidence that a high sugar diet is related to insulin resistance in humans. Saturated fat is also implicated as a possible culprit, but since most studies just have a “bad” diet (high in fat and sugar) and a “good” diet (low in fat and sugar), it’s hard to determine if fat is a culprit or not (ice-cream leads to diabetes, but is it the cream, the sugar, or both?).

Mark Sisson has dedicated many posts to unraveling some of these studies, such as this one.

For myself, I notice that eating lots of high carb foods like bread, beer, and even too much sweet fruit can lead to bad moods. These are generally “cheat” foods for me, so if I’m feeling stressed I tighten up my diet (especially carbs), and eat more fish, vegetables, pastured eggs, grass-fed meats, and so on (“more paleo“).

I’ll also add some supplemental chromium (as chromium polynicotinate) which has been shown to increase insulin sensitivity.

6. Moderate caffeine and alcohol intake

Too much caffeine, especially in the afternoon, can lead to constantly elevated cortisol levels. Coffee is generally healthful, and is protective against many diseases, including Type-2 diabetes. (caffeic acid, found even in decaf, is especially effective at clearing out toxic accumulation of hIAPP [human islet amyloid polypeptide], an amyloid protein implicated in both diabetes and  Alzheimer’s disease).

But it’s good to give your body a break and let cortisol dip (giving your adrenals a break, among other things).

I’m a fast caffeine metabolizer (I know this from my 23andMe.com test results), but I can still overdo it. Here’s a good post from a coffee drinker who benefited from cutting out afternoon coffee. That’s what I’ve been doing lately, and I’ve noticed on overall energy boost (and a tendency towards more evening productivity).

I’m also tempted to drink more (booze) when I’m feeling more stressed (anxiety can reduce BDNF levels, and alcohol can mitigate this effect and temporarily increase BDNF). For me, one or two glasses of wine or beer takes the edge off and makes socializing more enjoyable, but any more than that makes the next day miserable, and accentuates any depressive feelings.

7. Other nutritional factors

Vitamin D has a protective effect in the brain, especially against dopamine toxicity related to Parkinson’s disease and neurodegeneration related to Alzheimer’s. I currently take about 3000IU of vitamin D on most days.

Alpha-lipoic acid can cross the blood-brain barrier and is neuroprotective. I take 10-20mg of r-ALA on most days when I’m experiencing increased stress.

Both vitamin C and vitamin B5 support adrenal function. I take 250-500mg of C on most days, and very small doses of Thorne multi-vitamin supplements to offset increased stress (large doses of B-multis trigger asthma symptoms for some reason, so I can’t do  high doses of B vitamins). Most of the B-vitamins have some role in neurotransmitter production and/or regulation, and niacinamide (a form of B3) is protective against Alzheimer’s disease. I find that small doses (up to double the RDA level) of the B vitamins boost my energy and cognition, but higher doses lead to feeling “wound up” and restless sleep, and asthma symptoms).

I find that magnesium has a calming, anti-anxiety effect, and I take 100-200mg of magnesium glycinate on most days.

8. Boost testosterone, increase sex and healing touch

Higher testosterone is associated with improved mood in men, and is also neuroprotective. I’ve written a complete post about healthy testosterone management here. If I’m feeling stressed out, anxious, and/or depressed, I err on the side of high T. I’ll increase cod liver oil to about 1t daily for vitamin A (I only use brands with no added synthetic vitamin A, like Nordic Naturals Arctic or Carlson Norwegian cod liver oil), and also supplement with a very low dose of tongkat ali.

Estrogen is neuroprotective for both sexes (high T in men may be neuroprotective only because some of that testosterone converts to estrogen).

Sexual activity boosts sex hormones and is good for the brain. If more sex isn’t an option, touch of all forms can reduce stress and inflammation. Massage feels good because it changes your gene expression.

9. No blue light — early to bed

While pulling an all-nighter can bring temporary euphoria (via mesolimbic dysregulation), long-term sleep deprivation is terrible for the mind and body. On the other hand, balanced circadian rhythms can contribute to mental health.

Two times in my life I’ve done a one month experiment during which our household didn’t use artificial light. We read by candlelight and went to bed much earlier than usual (especially when we did the experiment during a winter month). As I wrote about in this post, my wife and I experienced strange episodes of unexplained joy at random times during the experiment. Somehow the combination of being fully caught up on sleep, as well as long periods of quiet wakefulness, tilted our moods towards happiness.

Because of this experience, if I’m under additional stress, I turn off the lights earlier in the evening and go to bed earlier as a result (I find that I can’t go to bed earlier unless I turn the lights down earlier — blue spectrum light disrupts melatonin production and therefore prevents sleepiness). If I use my computer during the evening, I have f.lux installed, which cuts back on the blue light after sunset.

10. Spiritual and religious practice

Are depressive symptoms inversely related to religiosity? Maybe, maybe not. I’m an atheist, though not an anti-religious one. There are some religions (including Reformed Judaism and Secular Humanism) that tolerate or even encourage a non-supernatural interpretation of God (love, star-matter, what have you). I practice personal prayer (I know that sounds strange for an atheist, but here’s why), I say Jewish prayers with my family, and I sometimes go to religious services. I would put all these practices in the “mood improving” column, and I engage in them more when I’m feeling bad.

More important for my own mental health is meditation, and the general set of practices I call “metaprogramming.” In short, programming my own brain, choosing helpful thoughts over unhelpful ones, and tuning my attitude towards gratitude, forgiveness, compassion, a sense of possibility and hope, taking complete responsibility for every aspect of my life, and trying to make the world a better place.

11. Enhance tribal connections, think “we” instead of “me”

We’ve evolved as social, tribal animals. If I spend too much time alone working in a room, I can trick myself into thinking I’m “fine,” whereas the reality is I’m gradually becoming isolated and depressed. Much of my work is solitary by nature (producing music, coding, writing), but even as an introvert I know I need daily social interaction to feel right. Though I can’t find the source at the moment, I’ve read that generally people underestimate how much social time they need to feel happy.

People with “computer addiction” (most of us?) have increased neural activity in areas of the brain having to do with fast visual processing, but reduced activity and brain shrinkage in areas related to processing of speech, memory, motor control, emotion, sensory, and other information. This article on Chinese computer addicts cites “abnormal white matter integrity in brain regions involving emotional generation and processing, executive attention, decision making and cognitive control.” (Here’s the original study.)

I call this issue “overstim/understim.” The web and video games can give us quick dopamine fixes, but large swaths of our brains remain underutilized if we spend too much time staring at screens and clicking on stuff.

I think the cure for overstim/understim is engaging social interaction. Collaborative work, real conversations, team sports, and the like. Here’s a great talk from Nancy Etcoff on this subject.

12. Life priority reevaluation

If I’m feeling down for more than a few days, I’ll take some time to reevaluate my core values, life priorities, and current goals. Am I living in accordance with my deepest principles? Am I using my gifts for the greatest good?

Or have I lost my course? If I’m reacting to the world (putting too much energy into meeting other people’s expectations), or avoiding the world (avoiding my problems, engaging with distractions, not engaging my calling), then I need to reevaluate and reprioritize.

I don’t execute major life decisions if I feel stressed-out and/or depressed, because my whacked-out state of mind is unreliable and untrustworthy. But I do consider big life decisions, and then decide to act or not later (when I’m feeling better).

13. Reduce external stressors

Reality is subjective — we create the world via our sensory impressions, and we turn those impressions into experiences and feelings with our brains.

This doesn’t mean that every problem has an internal solution. We can’t always adjust ourselves to feel better. Sometimes we have to change the world, or remove ourselves from a situation.

A tyrant boss, a dead-end job, a nightmare client, an abusive relationship, a neighborhood with a high rate of kidnappings and/or murder, an environmental or natural disaster, social collapse, war, etc. — you’re not going to feel better by taking fish oil, eating curry, getting enough sleep. You need to get out.

For me, this week, reducing external stressors meant taking a few days off from my consulting/programming work. I’m on schedule with my projects, so this wasn’t a big deal. Generally my life is good and I feel lucky, I don’t want or need to make any major life changes right now.

I do hope that if things ever got bad (some kind of social collapse scenario) I would have the sense to get out with my family (if we could). I’ll take cybernetic discombobulation over being the frog in hot water. On some level this seems unthinkable, but people experienced social collapse during the Great Depression — not that long ago, and much more recently in New Orleans following Katrina. Here’s a long essay from an architect who lived through social collapse in Argentina.

14. Inoculate myself with mood-boosting bacteria

I’ve saved the weirdest one for last.

This episode of RadioLab blew my mind. Mice fed large amounts of a specific probiotic strain were more resistant to anxiety (via influencing GABA levels in the brain, mediated through the vagus nerve). Here’s the original study, and here’s an interview with the scientist.

So what was the bacteria strain, and can you get it at the grocery store? The strain was Lactobacillus rhamnonsus, and it’s in several types of kefir. Does it work the same in humans as in mice? Who knows, but it probably can’t hurt.

Mycobacterium vaccae, found in soil, is another mood boosting bacteria. It works via neurogenesis. Maybe that explains why pulling stubborn thorny weeds out of your front yard is actually fun sometimes.

What About Drugs?

I believe in better living through chemistry. While I prefer to achieve better chemistry with good food, exercise, a good night’s sleep, curry, and vitamins, I acknowledge that stronger measures are sometimes necessary. A quick look at the options …


What about marijuana? Some of my friends “self-medicate” on a daily or near-daily basis, and seem none the worse for wear. And it’s not hard (at least in Oakland) to do this legally, with a note from your doctor. So should you?

I’ve tried a bunch of times, but I always skip the “fun part” and go right to slurry and paranoid. So I abstain totally from this particular drug.

What does science say about marijuana use? Lots of things. For example, marijuana stimulates adult hippocampal neurogenesis and has an anti-depressive effect. That sounds great!

On the other hand, chronic marijuana use through young adulthood impairs IQ. And chronic use at any age impairs working memory. Interestingly, the negative effect on memory is from increased neuroplasticity (weakened neural connections).

So teen marijuana use is probably a terrible idea. But adult use might improve quality of life in many cases, especially during periods of prolonged stress. Here’s an article in the New York Times regarding one such case.


Ecstasy should be legal for the clincial treatment of PTSD. Here’s why.

SSRI’s (Selective Serotonin Reuptake Inhibitors)

As this blog post explains, depression is not caused by a “serotonin-deficiency.” SSRI’s like Prozac raise serotonin levels in the brain within hours, but the anti-depressive effects of SSRI’s typically take weeks or even months to kick in. Also, serotonin reuptake enhancers (like Tianeptine) which reduce serotonin levels in the brain also work as antidepressants.

Anti-depressive drugs work (when they do work) because they encourage hippocampal neurogenesis. They’re helpful for about three quarters of people who use them, and worsen the condition of about 20% (and are especially dangerous for teens and children — associated with higher suicide rates in these groups).

I’m not opposed to the use of SSRI’s, and I’ve never felt depressed for long enough to want to try them. I would be reluctant to try them because the side effects, the expense, and because the “alternative” treatments that I’ve discussed in this post seem to work just as well, and are much safer.

Big Picture

Happiness researchers know, more or less, what makes people happy in general.

Money can make you happier, but the effect caps out at about $75K a year (depending on your local economy). There are ways to spend your money that will bring you more happiness (like spending it on other people, eating out, concerts and movies), and other ways to blow money that don’t help happiness at all (fancy watches and sports cars — large expensive purchases for oneself where the novelty wears off quickly). And according to research cited by David Brooks, joining a group that meets at least once a month will boost your happiness more than doubling your income.

Income equality in a society can make everyone happier and healthier (and income inequality in the U.S. is currently making everyone less healthy and less happy).

Happiness psychologist Martin Seligman asserts that the “meaningful life” comes from finding your highest strengths and using them in service of something larger than yourself.

Dan Gilbert explains why what we think will make us happy is mostly wrong.

As you can tell from the links, most of what I’ve learned about happiness is from TED talks. Here’s another one — Stefan Sagmeister looks at various studies and concludes that race, climate, age, being rich, and even health have little impact on overall happiness. But being married does generally make us happier, as does being more sociable and having meaningful friendships. Once again, we not me.

“We cure people from neurosis to return them to the ordinary misery of life.” -Sigismund Schlomo Freud

Or maybe we should we give up the doomed pursuit of happiness and settle for Freud’s “ordinary misery”? There’s something to U.G. Krishnamurti‘s criticism of all spiritual pursuits as an infantile “wanting to feel good all the time” (and Freud might agree). Feeling good all the time isn’t possible. Life is sometimes miserable, often boring or frustrating, and only occasionally euphoric.

All that is true, but there’s no reason to suffer through long periods of depression and anxiety. We can change our life situation. We can stimulate hippocampal neurogenesis.

And a personal update …

So how am I feeling, a week later? Much better, thank you. My brain renewal protocol works, and it works quickly. I feel refocused, hopeful, and more dedicated to my core principles. And I’ve got my joie de vivre back.

When I’m feeling down I don’t just write it off as “the blues.” I try to make immediate changes. I don’t want my brain to atrophy, ever, and I don’t want my life to end in dementia. So I take brain health (and my own mental state) seriously.

So what works for you? Are you permanently stressed out? If you’re not feeling excited about life, and that your life has meaning, what are you going to change?


If You Want Something More …


Why Going Paleo Is Easier Than You Might Think


  1. Scottish Sue

    Thank you, JD. I know much of what you reference, but seeing it all pulled together with further indepth reading if necessary is wonderful. Tonight is the monthly meeting of the San Diego Brain Club, which I co-founded, and I plan to share some of your thoughts!

  2. Nice one JD, very informative and helpful, thoughtful and thought provoking.

  3. emily ann osler

    hello j.d. !!!! I have just found your blog….yesterday, by chance !!! a lucky day !! your constant research for ways to improve our life is moving and inspirational !! I am very interested in nutrition, and as many others have noted, your curious, non-judgemental approach is a breath of fresh air….I’m an Anglo-Italian 39 year old vegetarian (ah ah!), mum of two adorable bambini….just wanted to thank you from the heart, keep sharing !! ciao !!!

  4. Your article is full of insightful tidbits. I think a lot of us who blog are prone to swings. One of the ways we deal with crashes is to write, take beautiful photographs of nature, and reach out the the community of bloggers. There is always something new to learn.

  5. Thank you very much for this. This is the best “one” page summary I have come across. I have been putting together my own “self manual” for a while and this helps a great deal in getting it to a reasonable workable state. At 55 I am finding sleep, natural dark, fasting and being careful about what I eat when I do, have a significant influence on ability to get the most out of a day. Thanks again.

  6. Marcin

    I don’t know if you have mentioned it before, but I noticed that the paleo lifestyle is broadly speaking the lifestyle of kids (well, at least kids which we were, not some cyber-obese kids of today), whith lots of their diverse movement including running, jumping, climbing trees, squatting, etc. intense social activity, being “in-time” (being occupied with the current activity, not thinking about the future or past too much). Of course, I don’t mean that adults should behave all the time like that, but if you want to know how to act in a natural way just look at kids in the playground.

  7. Thank you…so much! I just stumbled upon your blog while balancing my sleeping three-month-old on my lap and was fascinated to find, in your writing, bits and pieces of that which currently occupies more than 99% of my waking thoughts.

    My family’s health is pretty much constantly fascinating and frustrating and fantastically amazing (sometimes)–we have an eight-year-old whom we are recovering from autism using a gut-healing protocol that has impacted us all. After 2.5 years on this diet (very strict GAPS-type protocol), It Is Working!! Now I’d like to find ways to further help my husband’s autoimmune conditions (multiple, including asthma). I’d like to help myself deal better with the stress of healing our high-needs son, which negatively impacts my sometimes disordered mood. Our third child was born with a tongue-tie (a midline defect which, unfortunately, we did not discover for five weeks, but that can cause intense pain during breastfeeding for me and nutritional deficits (for her, due to impaired sucking), and that is potentially associated with methylation problems as well as autism.

    Anyway, I have to make dinner, but want to read more soon. And I’m ready to turn off our lights at night for the next month. 🙂

    Thanks for your writing! And I would love to hear more of your thoughts (probably I just need to search your archives) concerning inflammation and diet and how to bump things up a notch when 2.5 years of super clean eating isn’t quite “fixing” everything…(although of course it’s the foundation).


  8. Moderate drinking associated with fewer hippocampal new nerve cells

  9. Hi. Great blog post. I like a lot of what you’ve got to say, but I have a bit of a personal crusade against the widespread and completely unjustified aversion to MSG. Seriously – Google it. According to the resources that I’ve surveyed, there’s apparently been no legitimate research demonstrating any negative effect whatsoever. Still, if you don’t like it then that’s fair enough. Personally, I adore it! 😀

    • Thanks Ben!

      You’re right — the research is weak. This article summarizes nicely.

      So why do I avoid it? It may be a minority of people who react to MSG, but I get an instant headache if I eat substantial amounts. It could be that certain combination of glutamate receptor genes (like GRIN1, GRIN2A, GRIN2B and GRIK3) are related to MSG sensitivity. I suppose there is also a chance it is psychosomatic, but my reaction is fairly consistent (and it has sometimes taken me by surprise … so I wasn’t always “expecting” to react). I’m also sensitive to l-glutamine (I briefly tried it as a supplement but it disrupted my sleep cycle).

  10. susan

    really great post!! awesome how you pulled this all together

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