Saturday, April 25, 2015

Potato starch doesn't help my sleep

I've been experimenting with the relationship between sleep and resistant starch, taking a few tablespoons of Bob's Red Mill potato starch, which some people think improves sleep by feeding the helpful Bifidobacterium that may play a role in producing up to 80% of the body's serotonin.

There’s no question the potato starch raised my Bifido levels:
Sprague Bifido over time

But it seems not to have changed my sleep, either in overall hours:
Sprague Z vs potato starch
or in a more precise measure, like REM:
Sprague REM vs potato starch
You can see from these charts that I did notice some fantastic nights of sleep after starting potato starch, but there were plenty of other nights when my sleep was back to normal and sometimes worse. If I hadn’t measured so carefully, I’d be tempted to overplay the good and underplay the not-so-good. If there’s a psychosomatic effect, then yeah it may have made me feel better, but in terms of actual sleep time, resistant starch doesn’t seem to have helped.

Thursday, April 23, 2015

Upcoming talk: Your Microbiome, Your Health

If you’re in the Seattle area on April 29th, I hope you’ll come to a talk I’ll be giving for The STEAM Vent, a local science event organizer. I’ll present the latest that I’ve learned about the microbiome, including the results of a bunch of self-experiments I’ve done since last year to understand more and learn how to manipulate my own microbial environment.

I’m super-excited that uBiome has generously offered a bunch of prizes for attendees, including free uBiome gut kits (worth $89) and some t-shirts.

The event will be held at T.S. McHugh’s, an Irish Pub/Restaurant near the Space Needle. They’re offering a special “microbe-friendly” meal beforehand, an entrĂ©e that includes fresh sauerkraut and other healthy bacterial cultures for those who want to feed their microbes.

My talk starts at 7:30, and The STEAM Vent charges an admission fee of $10. But I strongly encourage you to come a little earlier for the meal ($25, including admission).

Find out more at the Meetup page.

Tuesday, April 07, 2015

Yup, statins make me smarter

After a fifteen day test, I’ve concluded that 20mg of simvastatin daily has a major effect on my results on Seth Robert’s Brain Reaction Time (BRT) test.

Statin affect on BRT

Notice the big changes on the days before and after taking the statin (the “treatment”). The two weeks before were “clean” – no fish oil, no other special vitamins, foods, travel, or other changes in daily habits – making the change even more obvious and sudden: just one day makes the difference. (The chart shows BRT measurements roughly 24 hours after treatment).
With n=33, here’s a simple T-Test to show the effect:
## Welch Two Sample t-test ## t = 7.0834, df = 28.313, p-value = 9.835e-08 ## alternative hypothesis: true difference in means is not equal to 0 ## 95 percent confidence interval: ## 15.88029 28.79244 ## sample estimates: ## mean of x mean of y ## 71.20000 48.86364
My fellow Seattle Quantified-Selfer Mark Drangsholt, who studied something similar on himself, says 2-3 weeks of treatment helped him reduce or eliminate brain fog and it appears to help me too. This is consistent with other research that shows that statins seem to benefit the brain.
Incidentally, the statin had no significant effect on my sleep (as measured with Zeo):
Sleep (n=33)Average (hrs)Standard Deviationw/Statin (n=15)
total sleep (Z) 6.418 0.625 6.424 (SD=0.58)
REM 1.796 0.416 1.814 (SD=0.44)
Deep 1.039 0.198 1.006 (SD=0.13)
I’ve already demonstrated that two or three Kirkland fish oil pills taken daily give me a statistically-significant higher score, while other obvious candidates like sleep or alcohol make no difference. Seth’s app clearly is measuring something. In my next experiments, I’ll try to pin down more precisely what that is as I refine the app to make it easier and faster to use.

Saturday, April 04, 2015

Data is not a substitute for strategy

When I was in grad school, my data sciences class assigned us this incredibly complex optimization problem where we were supposed to recommend the best place to locate a series of factories given expected product demand, availability of suppliers, distance to customers, wage and materials costs, etc. It was too complicated to solve on a normal PC with off-the-shelf software, so the other students simply gave up treating this as a data optimization problem and instead made recommendations based on strategic considerations.

Me? No, I used brute force: I rewrote the software to run on the more powerful and expensive campus mainframe, applying every trick I knew until I found the “correct” answer. It was tough, and at the time I was quite proud of my computer skills, thinking somehow I had bettered my fellow students.

But when I saw the other answers, I realized how silly I was to think that data could beat strategy. Sure, with sufficient computation power I was able to identify a mathematically-provable solution given today’s data. But who cares? Data keeps changing. It’ll be months, maybe years before some of those factories are operating, by which time all my data assumptions would have been irrelevant. Good strategic thinking, on the other hand, doesn’t depend on fluctuations in the data.

I’m reminded of that lesson in this post from Aaron Carroll (at the Incidental Economist blog), responding to Mark Cuban’s advice that everyone get their blood tested quarterly. Data, says Carroll, is not the problem. If you think that more data is always better, you will likely miss the forest for the trees. Or as the post says:

“Ordering a lab test is like picking your nose in public. If you find something, you better know what you’re going to do with it.”

Pony

Thursday, April 02, 2015

I’m rich!

The uBiome blog posts the results of a large (n>500) study of their users that shows a fascinating relationship between household income and a large change in a particular bacterium, the non-pathogenic Genus 713, actinobacillus. Their number crunching shows that wealthy people are far less likely to have this organism in their guts. For the statistically-minded, it’s a p-value of 0.00001 – as near to scientific certainty as you can get. If you have it, you’re poor. If not, you’re wealthy.

Obviously upon hearing this my first step was to check my own uBiome results to see if I have any actinobacillus (which, incidentally, was first isolated from the respiratory tracts of pigs).

Answer: no!  My latest sample shows no Genus 713!  I must be rich!

But wait, I did have a smidge (under 0.0008%) in the sample I submitted last May. Fortunately it cleared up by the following month and I’ve been Genus 713-free ever since! Obviously my microbiome is responding in advance to the large jackpot it knows I’ll be receiving any day now.

Now that science has demonstrated my wealth with such certainty, I am feeling extra generous today. Instead of money, I’ll share this comic (from the always excellent XKCD) which explains why they found this unassailable correlation between wealth and the microbiome:

Sunday, March 22, 2015

Will statins make me smarter too?

For the next two weeks, I’ll conduct a new test to measure the effect of simvastatin on my Brain Reaction Time.
Two or three Kirkland fish oil pills taken daily make me score higher on Seth Robert’s Brain Reaction Time test. After six months of self-testing, the effect is pretty robust, as you can see from this simple T-test:
## 
##  Welch Two Sample t-test
## 
## data:  rik$ptile[rik$Fish.Oil == 0] and rik$ptile[rik$Fish.Oil > 0]
## t = -2.7736, df = 90.886, p-value = 0.006728
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -14.489218  -2.396073
## sample estimates:
## mean of x mean of y 
##  45.36170  53.80435
What causes the effect? I have some guesses related to role that Omega-3 fats play in brain nutrition, but are there other ways to get similar effects? I’ve already disproven many of the obvious other candidates (sleep, alcohol, vitamin D), but several fellow quantified-selfers have suggested I look also at statin drugs, which besides lowering cholesterol, also seem to benefit the brain. Mark Drangsholt, who studied this extensively on himself, says 2-3 weeks of treatment helped him reduce or eliminate brain fog.
So I’m going to try the same thing: for the next two weeks, I’ll take 20mg of simvastatin daily while I continue to test my BRT for changes. I’ve taken no fish oil for the past two weeks (and as predicted, my BRT averages have declined), so this should be a “clean test”.
I’m posting my trial and methodology in advance to reduce “reporting bias” that happens when people only post their successes. You can follow along with my (mostly) daily updates here: http://rpubs.com/Sprague/SimvastatinBRT