Let’s Talk About Microbes

I know that a lot of you have expressed interest in the upcoming flu shot discussion, but I feel the need to do a little background work before launching into that particular discussion. As many of you know, I don’t generally decide that something so pervasive as flu shots is goofy without giving it some real thought first. And it’s hard to put down in a paragraph or two all of the thinking I’ve done about flu shots. Besides, microbes have become really interesting. So, a little background first.

I mentioned Ed Yong’s book “I Contain Multitudes” just a little bit ago. I can’t overemphasize how important and fascinating this book is to me. Here’s why: it isn’t often that a book makes you reconsider your fundamental understanding of how the world works. Honestly, it usually seems to happen with really good science fiction. I’m thinking in particular of “Altered Carbon” by Richard K. Morgan, but I think a couple of the Neal Stephenson books work that way too (“Snow Crash”, “Diamond Age”, “Seven Eves”). So to find that truly paradigm shifting experience in a book of non-fiction is extraordinary made even more so because it’s true.

Let me paraphrase a bit from the beginning of Ed Yong’s book. The concept of the entire history of planet earth expressed as a 12 month time line. It’s a way to illustrate the enormity of geologic time as opposed to our puny concept of time, where time spent on hold with Comcast can seem like an epoch. A couple of highlights from the year:

  • January 1 @ midnight: the earth coalesces from matter in space
  • March 4: the oldest rocks we know of form
  • March 20: algae arrive on the scene
  • July 17: the first cells with nuclei arrive (this would be microbes)
  • November 18: the first basic organisms start to form, including plants
  • December 1: the first insects
  • December 2: the first amphibians
  • December 5: the first reptiles
  • December 13: the first dinosaurs
  • December 14: the first mammals
  • December 22: the first flowering plants
  • December 31 @11:02 pm, just 58 minutes to midnight and the first direct human ancestor makes an appearance.
  • December 31 @11:59 pm: the Revolutionary War

As you can see from this simple illustration, not much seems to have happened in the first 11 months. But, don’t miss that July 17 entry of the first microbes. In this way of looking at the evolution of all animal life on earth, we came on the scene almost 6 months after the microbes. Or, to put it differently, we evolved in an environment that had been completely occupied by microbes for a very, very long time. As mammals, we are Johnny come latelys. As hominids, we are the late coming party crashers, arriving, literally, in the last hour. More to the point, we evolved in the world of microbes.

When I did my medical training (medical school in the late 1980s, surgery training 89–97) I was inducted into the entrenched belief system that the only good “bug” is a dead “bug”. Microbes cause pestilence and disease and are to be eradicated. Almost all of the significant medical advances had involved conquering diseases caused by microbes and this was all the proof anyone needed to know that microbes were nothing but trouble. We didn’t even call them microbes, we called them “germs” in a classic example of demonization. Our medical distrust of microbes spread to the general public and germophobia ran rampant as hand sanitizers and antimicrobial soaps popped up like unwanted mushrooms in a damp field. This may have reached it pinnacle when I saw a dispenser for antimicrobial wipes at a gas pump. I’m not sure I can imagine a much more inhospitable environment for microbes than a gasoline pump handle, but there they were. (As a complete aside, it has always bothered me that we talked about “normal flora” when we talked about microbes that lived in & on our bodies, but we microbes that are pathogens are generically called “germs” and most doctors call them bugs. I should have know this internal inconsistency hid a lot of misinformation!)

Fortunately, not everyone was buying the hype. There were intrepid researchers out there who took a more broad look at microbes and have slowly begun to put together a much more nuanced picture of how we interact with them and the important roles microbes play in everything from planetary health to our day to day health. Not just in disease states, but the ways we co-exist with these partners that have been present long long before multicellular organisms ever existed on planet Earth.

As some of you know, I’ve prattled on a bit about the “gut micro biome” in several posts. Worry not, I will be writing about this for years to come as new and fascinating things come to light. But for those who are wondering if there’s really any practical use to all of this ridiculous micro biome thing, let me close with a little talk about Clostridium difficile colitis. Known as C. diff. colitis in the medical world, this is a disease that is a significant problem that is occasionally fatal and costs us untold millions of dollars to diagnose and poorly treat. And it’s a micro biome problem through and through.

Most people who get C. diff. colitis get it after exposure to antibiotics. That is, they are given antibiotics to treat some problem (whether the antibiotics were a good idea or not in the first place is not the point of this particular discussion, but, as you’ll see, it’s an increasingly germane discussion) and, as a result of the antibiotics, they develop abdominal pain, cramping and diarrhea. Particular to C. diff colitis is a smell, which is hard to forget once you’ve experienced it and is virtually diagnostic. Severe cases can develop breakdown of the lining of the colon (large intestine) which allows bacteria access to the blood stream and can be fatal. Suffice to say, it’s not a problem to be taken lightly. So what happens? How does a dose or two of antibiotic cause such havoc? The answer is that we have trillions of bacteria living in our intestines. All mammals do. These bacteria live in a fairly balanced relationship with our body and immune system and play some pretty important roles. One of the many species residing there is C. diff. But C. diff is resistant to most of the antibiotics you might receive. So as you take antibiotic tablets for that sinus infection, upper respiratory infection, urinary tract infection, etc. the antibiotic can also kill off a large number of the bacteria in your large intestine. As the other bacteria disappear, C. diff has an opportunity to reproduce and take over a bigger role in the gut and, if conditions are right, it will do so. Doctors call this an “opportunistic infection”.

So what’s the treatment for C. diff colitis, a disease caused by the use of antibiotics? Why, more antibiotics, of course! This time specific (and expensive) antibiotics that are generally active in killing off the C. diff as well as the rest of your gut bacteria with the hope that, if you clear everything out, what grows back *should* be more or less normal. It’s like treating your house fire with a couple of cans of gasoline. No wonder some physicians describe this sort of therapy as “flaming the landscape”. In retrospect, probably the most remarkable thing of all is that it has worked more often than not. But it doesn’t always work and some very unfortunate people are left with a chronic C. diff infection that is very hard to shake.

Enter new thinking and a miracle cure. If you take a big step back from the germs as enemies way of thinking and instead think about the colon as an ecology, interesting things start to happen. In the setting of C. diff, the fundamental problem is not that C. diff is there, it has always  been there. The problem is that the other bacteria, that usually keep C. diff in check, are gone. So, can anyone think of a way you might replace the other bacteria that people with C. diff colitis are missing? Or, to reframe the problem in a different language, how could you restore the normal micro biome of the gut? The pretty cheap answer to this conundrum is to transplant a normal micro biome back into the disease colon. Where could you find normal micro biome to transplant? Sorry to say, if you hadn’t already seen this coming, but that’s pretty much what the feces from a healthy person is. So the answer, it turns out, is fecal transplantation. It works, it’s cheap, and it treats the problem in a way that those mired in old “germs are our enemy” thinking have a hard time accepting. Imagine the thought of transplanting trillions of active microbes into a diseased colon and hoping it will cure the problem.

It turns out that it works so well that there is now a preparation for instilling into the colon of people with C. diff colitis. It is a mixture of the bacteria found in a normal, healthy colon grown in the lab and capsulized for easy delivery. The best part? It’s called RePOOPulate. I shit you not. Read about it here.


Zone 2 Training – part 2

In the last post, I talked about what the various heart rate zones are, how they are most simply calculated, and then talked about why it is important. I want to recap the last point because it is so critical. When endurance athletes talk about Zone 3 and Zone 4, they often refer to them as the grey zones. This is not to say that there isn’t a time or place for work in Zone 3 or Zone 4, but if you’re going to venture there you should have a really good reason for doing so, otherwise the time you are spending exercising will burn calories, but will not do a lot for improving your fitness or, in technical terms, your aerobic threshold. I know this seems ridiculous, but if you’re a runner, ask yourself, when was the last time you made a significant gain in your running times? If the answer is “a long time” or “I don’t remember” I’m sorry to tell you that all those hours and miles you’ve put in haven’t been as beneficial as they might have been. On the other hand, they were not for naught and they have taught you excellent habits of discipline. Now let’s make them really pay off.

Step One: find your zone

I showed you the super simplistic calculation for HR Zones in the last post. If you don’t want to delve further, use that calculation. There are several other ways to calculate your Zone 2, including the Karvonen Formula, the Maffetone formula and the Friel formula. If you’re interested, drop me a note and I’ll gladly explain further. Or, if you’re so inclined, I put together an Excel spreadsheet that calculates them for you. This is a link to the spreadsheet. Personally, I like the Karvonen Formula, which uses your age to calculate your maximum heart rate, as before, but then also takes into account your resting heart rate. I like it because it seems to be a way of taking your existing fitness into account (assuming your existing fitness is loosely marked by your resting heart rate, but I’m OK with making that assumption). The Friel formula is probably the most precise as it is a percentage of your actually Lactate Threshold (the point where you go from exercising aerobically to anaerobically) but unless you have access to a physiology lab you’re going to have to guess your Lactate Threshold. Using the various methods, the upper limit of my Zone 2 is somewhere between 126 and 144 beats per minute. For simplicity sake, I’ve chosen 135 as my number. Could I do better? Maybe, but it is’t the lowest or the highest and it seems to correlate pretty closely to my rating of perceived effort (RPE). For those on a beta blocker medication, which keeps the heat rate artificially slowed, all of the Zone 2 calculations in the world won’t really work. In that case, learn the RPE scale and use it!

Step Two: get a heart rate monitor

None of this really works without a heart rate monitor of some sort, unless you’re just going to go with the RPE scale. If you’re a data nerd like me, you’ll need a heart rate monitor. Most of new Garmins, including the smaller ones, have heart rate monitors built in. The newer Fitbits have HRM (heart rate monitors), the Apple Watch has HRM, and you can even go “old school” and get a chest HRM. If you’re going that route, look at Tickr! a newer chest strap HRM that links by both ANT+ and Bluetooth technology, so it links to most anything (including most newer treadmills) and, oddly, is on sale at Amazon today.

Step Three: slow down!

Go ahead, go do a work out. Go for a run. But as soon as you reach your Zone 2 maximum heart rate, you have to slow down. In fact, you’ll probably have to slow down to a walk until your heart rate comes down. Eventually, you’ll find a pace you can keep for a while, but your heart rate is going to go up again, virtually guaranteed and you’ll have to slow down and walk.

Personal Experience: I was just starting up running after a lengthy time off (infectious mononucleosis) so I know that my aerobic conditioning was off. But, when I started Zone 2 I was back running 4 miles or so at a 9:30–10:00 minute/mile pace and feeling pretty good about it. My first run with Zone 2 I knew would be slow, so I slowed the treadmill down to 5.5 (about 11 minutes/mile). I made it about 10 minutes before I hit my Zone 2 threshold and had to slow down and walk. I spent an hour on the treadmill and managed to just get over 4 miles in, so I averaged about 4.0 for the hour, which is a brisk walking pace. But I’ve varied my workout between running, rowing, stationary cycling and elliptical, all keeping at Zone 2 threshold and within 3 weeks I’m covering 5 miles in the hour. More importantly, I’m running for an hour and feeling really good after. No terrible muscle aches, no cramps and no feelings like I’m physically spent. I anticipate being able to run for the entire 60 minutes soon and then starting the get the pace back up to at least 10 minutes a mile if not better.

OK, you are probably thinking, what a slug. But consider this in a different light. If you could run a 10 minute mile pace in Zone 2 and do a marathon, you’d run the entire race in about 4 and half hours and walk away ready to run the next day. I don’t know many runners who can do that.  Imagine, then, what might happen if you did this Zone 2 training not for a couple of months, but a year. Imagine getting to the point that your current “race pace” could be done in Zone 2, so that come race day you could run the first half in Zone 2 and then push yourself a little for the second half. You might walk away with a significant improvement in both your time and your ability to run the next day!

Give up your preconceived notions!

I’ll admit that committing to Zone 2 training is a bit of a leap of faith. But after reading Rich Roll’s account, doing a good bit of research on it and now trying it in my own training, I’m a full fledged convert. So if you think it might be interesting, but know in your heart that you have to run to exhaustion to improve your running capacity, I will ask you to reconsider sometime next year. Because I’m a complete Zone 2 convert and I’m going to run a half-marathon next spring and my firm belief is that: 1) I’ll break my previous PR by at least 5 minutes while 2) feeling better during and after the race than I’ve felt for any previous race. And if I’m right and I’m making serious improvements in my running at age 54 and at least 5 years since I made any other gains, I defy you to come up with a better explanation that just better training through science and understanding.


Zone 2 Training – Part 1

heart-rate-zonesI picked up this concept in Rich Roll’s book “Finding Ultra”. The concept was not completely new to me, but Rich Roll had a way of describing it that made it seem new, which is kind of magical. For those of you who are unfamiliar with the concept, I’ll spend a little time going through the background and basics, then explain why you should care. Finally, a little practical advice that I’ve come up with while trying to use Zone 2 training.

What are Zones?

Zones are heart rate zones. This is a range of heart rates that are a rough indicator of how strenuous the physical activity you are doing is at any given time. Most people talk about 5 heart rate zones:

Zone 1: Very Light, at the end of a work out you feel guilty that you haven’t worked hard enough – walking on a treadmill at a speed that seems easy.

Zone 2: Light, you should be able to converse with someone while working out. Converse, as in speak in sentences, not one or two word grunts – walking or running at a speed that seems easy at first, but over time requires more effort.

Zone 3: Moderate, your heart rate is getting a bit higher, your breath a little faster, you can talk a little, but definitely not hold a conversation – probably where you now spend a lot of time in your work out life

Zone 4: Hard, heart rate higher, breathing faster, this is a sustainable pace, but just. You’re pushing yourself now

Zone 5: Maximm, you’ve pushed your pace to it’s limit and can’t sustain this for very long at all.  For me, I have always thought of this as the place where I “lose my breathing” and have to walk for a moment to get things back on track. A big hill at the end of a workout where you’ve already pushed yourself a bit.

Each of these zones has a heart rate range associated with it and these ranges change with both your age and physical fitness. The most simplistic calculations go something like this: 220 – your age = your maximum heart rate (MHR). Zone 1 is 50–60% of MHR, Zone 2 60–70%, Zone 3 70–80%, Zone 4 80–90% and Zone 5 90–100%. This is pretty much what a LifeFitness machine at a gym will do if you tell it you want to do a “fat burning” workout (Zone 2) or an “aerobic” workout (Zone 3). For me, at age 54, my MHR is 220-54 or 166. Zone 1 is then up to 100, Zone 2 is up to 116, Zone 3 up to 133, etc.

Why do Zones matter?

Unfortunately, most of us grew up with the ridiculous “no pain, no gain” mantra of working out and we just can’t shake it. When it comes to cardiovascular fitness, however, nothing could be further from the truth. I get it that most of us are not looking to do marathons, ironman triathlons, ultra marathons, or more. But it seems like we are looking to “get fit”. So take a moment and ask yourself (because I’m guessing you have never really done it before) what does that mean to you? Is getting fit having bigger muscles, less weight, just feeling better in your skin, or actually increasing your capacity for exercise? Obviously, if you’re into weight lifting, it’s bigger muscles, but I would argue that for everyone else the answer should be increasing your capacity for exercise. This is what would let you exercise more efficiently, for your body to improve it’s ability to use energy to do physical work and would, as a consequence, likely result in some body reshaping and weight loss as well as improving your times. So, for almost everyone who is interested in fitness, I think you should seriously consider thinking about how you go about increasing your capacity for exercise or, in more technical terms, increasing your aerobic capacity.

Chances are that you, like me, have been doing it wrong.

This was my revelation from Rich Roll. I, like almost everyone, have been doing it completely wrong. I’ve been running seriously for 8 or 9 years. I’ve run 9 half-marathons (13.1 miles), so I’m not completely new to the running scene. I have an MD degree and am interested in exercise and physiology (how the body works) and I thought I had a good handle on what I was doing. And yet, despite my efforts over the last years, I had a miserable year in 2016 with running and haven’t really made any significant improvements in my times over the last several years. Why? Because I was doing it all wrong.

When you are exercising and you let your heart rate wander up into Zone 3 and Zone 4, you lose the benefit of actually improving your aerobic capacity. Yes, you work your body harder, but you don’t actually make your body more fit. The only way to do that is to exercise in Zone 2. Exercising at this reduced effort forces your body to adapt to the stress the exercise puts on your body. The adaptation is the thing you’re doing all that work for in the first place. It makes your body add blood vessels to deliver more oxygen and fuel to muscle cells and the muscle cells add a lot of mitochondria, the little power plants that convert oxygen and fuel into work. By adding mitochondria to the cells and growing a richer network of blood vessels to support the muscles, you get more work out of the same effort. It turns out that elite athletes, like Rich Roll, spend 80–90% of their exercise time working out in Zone 2. So why aren’t you?

I’m guessing that you, like me, haven’t been doing it because 1) you had no idea (this is relatively newish exercise physiology stuff), 2) you don’t know how to make it work and 3) you still kind of believe that your exercise has to be really hard to make any serious pay off. But, now you know and I’m going to tell you how to make it work and I’ll try and talk you down off the ledge for number 3, all in the next post….  🙂


Changing direction, a little

This morning I had a shower thought. You know, those little epiphanies that occur when you’re taking a shower. I admit, I also get them running sometimes, which is somewhere in the top 10 reasons I like to run, but that’s beside the point. I came across a little article here that explains that the non-linear thinking that leads to shower thoughts is a result of a mindless-repetitive task that allows your brain to go into idle mode, relaxation, and likely the time of day.

So, my shower thought was this. I have a lot to say. I think a lot about getting a post out, but don’t do it very much because I’ve made it a lot of work. I didn’t mean to make it a lot of work, I just did because that’s how I roll. When I put something out there, I want you to know that it’s something I’ve thought about, researched, and vetted. I want you to know that I’m not just making things up or passing along some quackery. So every post is extensively footnoted with links to the source article and this takes a lot of time. And, I’m guessing, that those few of you out there who read these posts either never noticed the links or, if you did, rarely followed them to read the source material. And this was my epiphany. To make this process much easier and fluid on my end, I’m not going to do that anymore.

Here’s my solemn promise to you, reader. If you ever want to know the source material for something I say (as long as it’s not blatantly opinion) please just ask in the comments. That way I can post the relevant links for you (and the world) to see, keeping my promise to only bring you fact and not fancy. But there’s so much cool stuff out there and I’m dying to share it with you. For just a glimpse of the things rattling around in my head here’s what I’ve been reading lately:

How Not to Die” by Michael Greger, MD & Gene Stone. Dr. Greger is the “host” of and I’m a huge fan. This is fact based nutrition at it’s best. The book is not an easy read, but it’s so jammed full of fun stuff that I need to share.

Finding Ultra” by Rich Roll. Rich is an interesting character and many of you know him from his very popular podcast. He’s an alcoholic (in remission) ultra man athlete. No, not the old TV show, the crazy double Iron Man race in Hawaii. 6.2 mile open ocean swim, 261.4 mile bike followed by a 52.4 mile run. I, personally, think Rich totally missed the mark on his comments on soy in the book (and I emailed him and told him so), but it’s an interesting read. If you want to skip the book, check out the podcast. He did a show with Melanie Joy a couple of months ago that was very nice.

I Contain Multitudes” by Ed Yong. I have written in the past about the amazing science and discoveries being made regarding the human gut microbiome, the ecosystem of bacteria that live within our guts. Ed Yong’s book is a grand tour of all the amazing and cool things that are happening in the science of microbes and microbiomes. I don’t say this lightly, but this is literally paradigm shifting stuff. Really, our entire understanding of we live with bacteria is changing.

Finally, it’s cold and flu season coming up (as I look at the lovely fall colors from my window as I write) and that means the insane pressure for flu shots is just ramping up. I will have a post early next week and will show you why you don’t really need one.