Circadian Retraining 18 months in: Continued gut and sleep improvements

Welp, before the summer called I planned to do a blog article detailing my health progress 1 year in to paying serious attention to my circadian rhythms.  For the most part, I felt like I had pretty much everything down pat at the time.  Then, of course, research did what research do and I found a couple of things that could be added to improve my results and my program.

So I expanded my Circadian Retraining Program and found a few more variables I could measure to assess progress.  I bought a Fitbit Charge 2 HR to measure sleep and began measuring my heart rate variability with the HRV4Training app.  Before we get in to that data we’ll cover how I’ve been feeling, particularly with relevance to my digestion.

I must say, before I begin here, that I’m not anywhere near the chronic disease end of the spectrum anymore.  At this point, I’m putting the finishing touches on optimization for longevity.  My HbA1c has been steady at 4.8% for about 6 months and I sleep and feel great.  Whereas many of you may be looking to string together a week of good sleep or go a day or 2 without constipation or diarrhea, that’s far behind in my rearview mirror.

Digestion and Circadian Synchronization

At this point my digestion is solid, literally, all day every day.  I certainly had issues many years ago on a chronic basis, but at this point I’m mostly looking to prevent the occasional loose stool after a night of drinking or a dairy binge.  I’m happy to say that I haven’t seen anything remotely loose in several months now.

A lot of this comes down to knowing what I need to do to prevent it from happening.  Looking back, a lot of my non-chronic gut issues were about layering things improperly over the last few years.  Particularly in reference to coffee, alcohol, physical activity, and light exposure.  Mis-timing these things would give me what I believe to be bile acid diarrhea after nights of drinking, and correcting these exposures eliminated the problem.

Practicing time-restricted feeding, knowing when the best time to consume alcohol and coffee are, and not grouping several problematic things together while managing my circadian exposures and layering them properly are definitely icing on the cake.  Even in my college years I’d get the “beer shits”.  Not anymore.

I also used to have a very hard time digesting nuts and high doses of greens.  That seems to be a thing of the past as well.  I’m guessing most of this has to do with the objective measures I’m about to discuss, sleep and heart rate variability.

Circadian rhythms and improvements in autonomic function

You may recall in a blog I wrote a few months back that many of the beneficial effects of exposing yourself to the proper circadian environment have to do with optimizing the autonomic nervous system.  The autonomic nervous system manages all automatic processes in your body including heart rate, blood pressure, respiration rate, blood glucose regulation, sensitivity to stress, digestion, and immunity.

Looking specifically at digestion, the autonomic nervous system manages digestive enzyme synthesis and secretion, motility throughout the gut, sensitivity to inflammatory stimuli, bile storage and output, the microbiome, and mucosal defense.  So, pretty much anything and everything to do with digestion.

As such, being able to measure how well the autonomic nervous system functions is a useful way to give context to subjective improvements such as the digestive ones I mentioned above.  Currently, the best and most accessible way to do this is by measuring heart rate variability.

In layman’s terms, heart rate variability(HRV) is a measure of your ability to switch between “rest and digest” mode and “fight or flight”.  A healthy, properly functioning autonomic nervous system has balance between the two, allowing you to respond to stress when it happens, but to re-enter that calm, submissive state effectively and quickly when it subsides.

What HRV actually measures is the difference between beat to beat intervals in your heart rate.  Your heart doesn’t beat at a constant rate, something you can feel by finding your pulse and breathing in and out slowly.  You’ll notice your heart rate speed up when you breathe in and slow down when you breathe out.  A greater heart rate variability is indicative of a properly functioning autonomic nervous system.

Here are some HRV norms based on age groups.  It’s important to point out that you can measure HRV multiple ways, but the only way validated using a 60 second test like the one I use is called the root mean squared of the successive differences(rMSSD).  As such, pay particular attention to that data.

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Image source

Below you’ll see my HRV when I first started measuring it in January after 2 weeks of developing a baseline, after a month of working on sleep in June, and after 4 months of improving sleep in September.

As you can see, I moved from an HRV representative of men age 45-55 years old to one representative of men age 25-35.  This improvement in cardiac autonomic function is confirmed when you look at the change in my average resting heart rate from Fitbit:

These improvements in autonomic function have also yielded some substantial improvements in my sleep.  Based on my Fitbit data, my sleep has also improved, with my average nightly sleep duration over 10 days increasing from 7 hours in May to 7 hours and 24 minutes over the last 10 days.  This increase is driven solely by a 24 minute increase of REM sleep.

So, it’s clear that things are still progressing nicely.

From chronic disease to optimization

One of the things I’ve found while working with people to optimize this stuff is that we are working with a sliding scale.  At this point I can let multiple things slide for a couple of days with no effect while someone working on a chronic issue gets whacked when they have even the slightest deviation.

I chalk this up to a couple things.  First, people with chronic conditions likely have jacked up mitochondria and mitochondria play a huge role in circadian rhythms.  As such, while I have a robust rhythm, people with chronic conditions probably don’t.  So, any sort of confusing time cue leads to mass disruption and a corresponding whack in the head…or colon…or fatigue button.

Since I’ve been doing this a while, I’d venture to guess I have a pretty robust rhythm.  I also have a large number of variables to manipulate to reduce the risk of “circadian confusion”.  Alcohol is a great example.  Not only does alcohol cause circadian disruption, a large portion of it is processed in the mitochondria.  As such, if I know I’m going to drink, I make sure to hit on every other zeitgeber I can to prevent mass disruption.

Another big issue is that, at this point, I have little accumulated damage.  In my estimation, it takes a minimum of 3-4 months of working diligently to develop a robust circadian rhythm before a substantial “mopping up” of the damage caused by a chronic condition happens.

Think of it like cleaning your house.  A person cleaning up after a party has a lot more work to do if their house was dirty before the party started.  So when someone with a chronic disease goes off-script, they have to clean up the mess they just caused before they get back to cleaning up the accumulated damage.  When you’re working on optimization, all you have to clean is mess you just made.


Tinkering around with circadian rhythms has led to some substantial improvements in my gut and overall health.  I’m particularly psyched about the improvements in sleep and cardiovascular function as I have huge family history of cardiovascular disease.

I realize I’m early to the dance on this, but my hope is that people realize how important their circadian rhythms are.  I know it’s easy to dismiss the contribution of circadian rhythms since most people feel it’s too simple of an answer to their complex problems.  And for some, it’s not the only answer.  The problem is, it’s likely an essential part of the answer for anyone over 40 or someone suffering from a chronic disease.

Given that I’m still seeing improvements as I tweak more variables, the search will continue as I work on optimizing my circadian rhythms for longevity.


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