Saturday, October 25, 2014

[book] The Rise of Superman

The Rise of Superman: Decoding the Science of Ultimate Human Performance by Steven Kotler is mostly about extreme sports — the people behind really crazy activities like kayaking off a 56.7 meter waterfall or snowboarding off impossibly-high cliffs). If that part interests you, then you’ll hear insider accounts of the various legends you already know about. I’m not an extreme sport-watcher, but I came away with new respect for the people who do that stuff: they’re the modern day equivalents of great explorers past, like Magellan or Pizzaro

But the interesting part to me was the discussion of “flow", the mental state achieved by these people and by anyone working at peak performance.  Flow, also known as “being in the zone” or in religious contexts something like satori or enlightenment, is a place where every ounce of your being is fully alive, where you are “acting on all cylinders” and being the best you can be. Kotler dissects this state with scientists like Keith Sawyer and many others, including neuroscientists who study the phenomenon and divide it into these stages:

  • Struggle: trying to amp up and get a handle on problem, focusing with all your might. Very nerve-wracking here.
  • Release: the ‘aha’ moment
  • Zone: now you’re in pure perfection
  • Recovery: consolidate memories 

And these neurochemicals:

  • dopamine (pleasure producer like cocaine)
  • norepinephrine (like speed)
  • endorphins (opiates more powerful than morphine)
  • anandamide (“bliss”, inhibits ability to feel fear)
  • serotonin (helps cope with distress)
 Flow is about focus and concentration, and it happens in groups too. Here are some of the key characteristics:
  • serious concentration
  • shared, clear goals
  • good communication (immediate feedback)
  • equal participation
  • element of risk
  • familiarity: the group has a common knowledge base
  • blending egos
  • sense of control
  • close listening
  • always say yes
There’s obviously much more to say about Flow, but I found many of the lessons were buried in anecdotes about extreme heroes, who if that’s your thing will be more interesting to you than it was to me. Still, I definitely want to learn more, especially about some of the Quantified Self devices mentioned, like BrainSport from SenseLabs (formerly Neurotopia) and of course the Flow Genome Project.

Interestingly, Kotler is also co-author with Singularity University and X-Prize Peter Diamondis of Abundance: The Future Is Better Than You Think, a book I’ll have to add to my reading list.

Friday, October 17, 2014

Comparing uBiome data through time

Like I said previously, the data (and tools) at the uBiome site are fantastic, and it’s taking me a long time to understand what meaningful conclusions I can make. But first, one basic question I had is how stable the results are. If the microbiota changes all the time, then maybe you can’t really conclude much unless you track long-term trends.

In an excellent study published over the summer, Lawrence David at Duke University followed two subjects, measuring their microbiota and zillions of other variables every day for a year. His team concluded that although illness or travel can dramatically change microbiota composition in a single day, and different foods cause levels to fluctuate by up to 15% per day, generally things stay pretty stable.

So what happens if I send two samples, taken a few weeks apart, to uBiome? That’s what I tried, keeping close track of exactly what I ate and did in the meantime.

Here are the results for the first sample (the one I posted before)


Here’s the newer sample, taken three weeks later:


Hmmm. As you can see, these results seem quite different – far more than the 15% daily fluctuation from the Lawrence study.

No special travel or other unusual activity during those three weeks. Nothing unusual in my diet. I’m still analyzing what I ate, but for example here’s the amount of fiber per day, starting the week before the first test.


Nothing super unusual there. Note that I am a completely healthy male, normal/stable weight, no history of anything. Last antibiotic use was a long time ago.

Incidentally, Tina Saey (@thsaey) sent the same sample to two labs (uBiome plus American Gut Project), and got dramatically different results. uBiome wrote a detailed response – my takeway was that the differences can be mostly explained by how each lab handles the samples but that you can correct for that (mostly).

Still more analysis ahead of me. Meanwhile, I’ve sent them a third sample to compare further.

Thursday, October 16, 2014

[book] Missing Microbes

Another fantastic book, by Martin Blaser, professor of microbiology at NYU: Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues.

Microbes, a word that refers to microscopic lifeforms like bacteria, archaea, and viruses have been around way longer than anything else, and show far more variety than any visible life. If you imagine a circular clock face representing the degrees of microbiological difference between various life forms, humans and corn plants would be separated by only a single degree — the rest of the clock is an unimaginable variety of life, so different from us and inhabiting every nook and cranny on earth, from the radioactive sludge inside a dark nuclear plant to high in the atmosphere. Life is everywhere, and almost all of it is microbial. But as ubiquitous and resilient as these microbes are, many of those that matter most to humans have been under attack for the past century because of antibiotics, and the resulting changes may be the root cause of many modern afflictions, from obesity to autism to diabetes to cancer.

Here are just a few of the facts you’ll learn in this book:

  • Specialized lab mice that are raised germ-free may appear outwardly normal, but their blood contains only 52 out of the 4200 compounds found in normal mice. The implication is that microbes in the gut and skin generate many thousands of chemicals — vitamins, hormones, and more-- that are important for life.
  • Gut microbes produce a native compound similar to valium, normally cleared out by the liver. End-stage cancer patients often slip into a valium-induced coma when their livers fail.
  • Veridans streptococci usually live harmlessly in the mouth and serve to prevent Step A infections by simply crowding out other bacteria. But when they get into the heart, they are the major cause of heart valve infections.
  • The FDA doesn’t require labeling for products (like milk or organic apples) that contain less than 50mg of tetracycline. That seems like a trivial amount, with no possible affect on your health, but the dosages add up: drink milk every day and you have ingested a noticeable amount after a week.
  • Your gut bacteria produce 80% of the serotonin your brain uses to remain calm and promote good sleep. There are certainly many other examples of important hormones produced, not by the body, but by microbes.
Many, many more facts and ideas, well worth reading.  Highly recommended.

Wednesday, October 15, 2014

What's in my microbiome?

Although I was an early customer of 23andme, I found the results unsatisfying because there is so little that is actionable. I mean, you don't need a test to tell you that you have green eyes or that you're lactose intolerant. And if you have some weird disease in your future, the main advice -- eat well, get exercise, buy life insurance -- applies to everyone whether you know you're at risk or not. Although I think it's fun and interesting for its own sake, I frankly understand why normal people wouldn't bother.

That's why I'm now so intrigued with the microbiome, that collection of hundreds of species of bacteria and other microbes that live all over you, inside and out. In total, they weigh about as much as your brain; it's as if your body has a whole other organ that you can't see. Massive improvements in genetic sequencing technology over the past decade have suddenly brought the ability to view and measure this micro-world, and important new discoveries are happening every day.

The best part? you can change your microbes! It can be difficult, because once these things have found a foothold somewhere in your body, they don't want to let go, but at least it's possible, whether through eating different foods or supplements (fermented products, probiotics, fiber) or by avoiding antibiotics (including germ-killing hand sanitizers), your actions have an affect your microbiome. So if you don't like something, you can (at least in theory) change it.

To find out what's in my microbiome now, I bought a $400 kit from the San Francisco company uBiome. For that, I received swabs for my mouth, gut, genitals, nose, and skin. The most interesting one is the gut, which you can buy for $89, and is the one I'd most recommend. After you collect the samples (warning for the squeamish: it involves soiled toilet paper), send them back and they give you results like this:

The microbiome is so complicated -- we're dealing with hundreds of different species, each with its own genome -- that it's hard to summarize in a single, quick takeaway. The web site lets you dive deeper into the various strains of bacteria, looking at the results organized by phylum/class/order/family/genus, digging into more detail at each level. Since each user fills out a detailed questionnaire when returning the sample, you can compare your results to self-described vegans, paleo dieters, and several other categories to see how you stack up to people who have been gaining or losing weight recently, for example.

The tools on the site are fantastic, and they are obviously putting more effort into improving them (they've become noticeably better just in the past few weeks). Better yet, you can download all of your results in XML format to keep forever, or analyze anyway you like.

My only complaint was the amount of time it took to get results: a full three months for this sample. Their customer support staff is very responsive -- I always got a helpful response within a few hours, even on weekends -- but I do wish it didn't take so long.

But frankly that complaint rings hollow when I consider how long it will take me to understand the plethora of fascinating torrent of data I got back. You can see from the chart above that I have more of certain types of bacteria than their average customer. Is that good? bad? neutral? Who knows?

This is not uBiome's fault. Science just hasn't figured out these answers yet. In my case, I'm a healthy, fit, normal-weight omnivore, so I assume that the percentage differences with "Average" are perfectly fine, but I could imagine how somebody with weight or other problems might be concerned if they saw something significantly different from average. The good news is that, in theory, you can change your results, but the bad news is that science really has little clue exactly how to do that, or even what constitutes "good".

Because the technology is so new, you may find that your snapshot looks different each time you take the test. Sometimes people report different results from different locations on the same sample. So it's best not to read much into of any findings yet. Still, it's the ability to change your microbiome that makes all the difference and I expect to learn much more as the science progresses.

Thursday, October 02, 2014

Why review dentists?

Open Ah!
Searching for a new family dentist I checked the normal reviews on Yelp and Google,  searched a bit on the internet, transferred my records from the previous dentist, and finally this morning went in for my first exam. During the two-hour initial appointment, I spent less than 10 minutes with the dentist, who seems as nice and competent as all the reviews suggested.

But most of my time was spent with the hygienist, who talked with me, reviewed my history, gave me advice, and of course spent the better part of an hour chiseling away one on my mouth one tooth at a time. As long as my teeth and gums remain healthy, (which hopefully will be forever), I expect today’s experience to be typical. I will spend far, far more of my time with the hygienist than with the dentist.

So why do I care about the dentist reviews? Wouldn’t I be better off looking for the best hygienist? In fact, this person who cleaned my teeth, I know only her first name. She’s listed on their office web site, but only briefly under a section on “staff” and they don’t even list her last name. How long has she been there? Will she be there next time? Is she the best one in the office? Who knows?

Isn’t it odd that the person who is truly responsible for my experience is so invisible to the review process?