Monday, July 20, 2015

For potato starch, maybe less is more?

A friend who is enthusiastic about the affect potato starch had on his sleep, suggested that maybe my less-than-stellar results were caused by the amount I had been taking. Instead of 3-4 TBS/day, try a much smaller amount, he suggested, maybe only a teaspoon or so.

My results are too preliminary to get excited yet, but at least for my short trial, the smaller amount seems to help. Interestingly, my overall sleep doesn't change much, but I do notice more dreams, and Zeo confirms that my REM sleep is up quite a bit.

Here's the raw data (dumped straight from the R software I use to track everything). The one marked in red below is the most interesting number:

I tried potato starch on 91 days, and I have Zeo sleep data for a total of 45 of those days.

On 19 days I took exactly one tablespoon. On 6 days I took more than 0 but less than 1 tablespoon.

For total sleep (Z):

  • P-value on days when I had any potato starch: 0.3109656
  • P-value on days when I had exactly 1 TBS: 0.2020084
  • P-value on days when I had more than 0 but less than 1 TBS: 0.3041962
For REM Sleep (REM):

  • P-value on days when I had any potato starch: 0.2505854
  • P-value on days when I had exactly 1 TBS: 0.0603005
  • P-value on days when I had more than 0 but less than 1 TBS: 0.0012399
For Deep Sleep (Deep):

  • P-value on days when I had any potato starch: 0.5148044
  • P-value on days when I had exactly 1 TBS: 0.7402774
  • P-value on days when I had more than 0 but less than 1 TBS: 0.3264305


##                   days   Z.Mean REM.Mean Deep.Mean      Z.SD
## 0                  128 6.364245 1.817969  1.048698 0.6971406
## 0.25                 1 7.000000 2.100000  1.133333        NA
## 0.333333333333333    5 6.526667 2.136667  1.096667 0.5198290
## 1                   16 6.609979 1.975000  1.064583 0.7015906
## 1.5                  1 6.283333 1.300000  1.083333        NA
## 2                    7 6.111905 1.676190  1.019048 0.6943365
## 2.5                  1 5.750000 1.983333  1.250000        NA
## 3                    5 6.873333 2.050000  1.036667 0.6796241
## 4                    8 6.402083 1.752083  1.068750 0.7167186
## 8                    1 6.000000 1.433333  1.250000        NA

Saturday, July 18, 2015

A gut bacteria for caffeine metabolism?

 23andme says I’m a slow caffeine metabolizer because I have the AC genotype at SNP rs762551. You’d think that means I’m extra sensitive to caffeine before bedtime, but that’s not the case: I sleep just fine even if I have a cup of high-octane coffee after dinner. My 99-year-old grandmother drinks coffee by the potful, crediting its warmth as a calming effect to make her drowsy.

This week's Economist points to a new study in Nature by Javier A. Ceja-Navarro et al that names Pseudomonas Fulva as a bacterium active in the guts of a coffee bean pest. Caffeine is normally toxic to insects, but P. Fulva neutralizes the caffeine, apparently using the demethylase ndmA gene. 

I wish I knew enough genetics to test a theory that occurs to me: maybe my own caffeine metabolism is also affecting by a similar gut bacteria that I have in abundance but which is missing in other people. I already checked for Pseudomonas Fulva — I don’t have it in any of my uBiome samples.  I do have abundant levels of the genus Pseudomonas, but that is not the same thing.

It should be possible to screen every one of my gut bacteria demethylizing ndMA gene, but I’m not sure how to do that. If I did find the gene in one of the gut bacteria I harbor, then that would be pretty cool: a microbe that helps me drink coffee.

Coffee Beans

 

 

Monday, July 06, 2015

Seth Roberts Rules for Self-Experimenters

Digging through the blog of the late Seth Roberts, I find many gems. Here is his concise summary of how to do self-experimentation. He mentions intending to write a book about this, but as far as I know it was never finished:
if you want to figure something out via data collection:
1. Do something. Don’t give up before starting.
2. Keep doing something. Science is more drudgery than scientists usually say.
3. Be minimal.
4. Use scientific tools (e.g., graphs), but don’t listen to scientists who say don’t do X or Y.
5. Post your results.
 Worth reading the entire four-part blog post.

Sunday, July 05, 2015

[book] The Gluten Lie

Most people will think Alan Levinovitz, a Professor of Religion, an unlikely author of a diet book, particularly one like this that refutes many of the most popular diet fads. But in fact it’s one of the best health books I know. Nobody should read a diet or health book without reading this one first.

In my half-century of life, I can remember science being applied to so many different health claims that I’ve forgotten all the now-discredited ones that were once popular, but Levinovitz provides some reminders. Take MSG, for example, which began its road to public vilification with a letter to the editor of New England Journal of Medicine by a doctor who had a bad experience at a Chinese restaurant. Throughout the 1970s it was implicated as the cause of so many ailments that it became the subject of much serious scientific inquiry that all turned up negative. To this day, many people are convinced MSG causes headaches, yet no well-designed study has ever found any difference between MSG and a placebo.

MSG, like gluten and most of the other substances that have come and gone in the public favor, is a nocebo, an inert substance that causes harm because of the expectation of harm, not from anything real. On and on it goes with many other embattled foods. Wheat gluten is just the latest, most popular example, following in the footsteps of a whole line of defamed foods: salt, cholesterol, red meat, soy, and on and on.

Part of the problem is that, for many substances, there really are some people who are negatively affected. Celiac Disease is real for some people, just as sugar is a problem for diabetics and lactose causes stomach distress for many. But just because something negatively affects some people doesn’t mean it’s bad for the rest of us.

Levinovitz’ religious studies background makes him uniquely qualified to see the parallels between various health claims and religious belief. Claims about food are often couched in terms that, with a slight tweak of terminology, would be entirely appropriate coming from a church pulpit. Here are some examples:

You are what you eat: this idea can be traced to Galen, but it’s still in us. It’s why it’s so easy to sell the American public on the idea that eating fat makes you fat. Similarly, it’s not hard to convince some people that meat-eating, and its association with killing of animals, will make you more likely to be cruel to other humans.

If it tastes good it must be bad. It’s not hard to see the Puritan streak in much of the American discussion of the dangers of processed foods. We like the taste of sugar too much, leaving us at the mercy of Evil Corporations (Satan) who exploit our innocent addictions (The Fall) in order to make Big Profits. The truth, unfortunately, it more complex.

The monotonic mind. Religious people are comfortable with black and white conditions. To an Orthodox Jew, pork is 100% bad. The only optimal amount of coffee to a Mormon is zero. But with health, the rules are more complex. A glass of wine at a meal can be healthy for many people, but any positives go away quickly if you drink too much. Food is rarely if ever a black and white health vs unhealthy situation. The dose makes the poison. 

Levinovitz gives many more interesting examples, including critical comments about Bulletproof’s David Asprey, Chris Kresser, and even Gary Taubes. Few diets or diet gurus are 100% bad, of course, and that’s why many will find the book frustratingly difficult to pin down. There’s a little something critical for everyone.

The most entertaining part of the book was the final two chapters, helpfully printed on darker paper to make it stand out. Levinovitz invents an entirely new diet fad, written uncritically in the first part, and then overwritten with his own comments in the second. At first, you’ll be tempted to think Levinovitz’ book is just like so many other diet books, which go into detail taking down other ways of eating, only to return with the One True Diet. But that’s why the second part is so interesting: as he might do with religious commentary, Levinovitz picks apart each of his own dietary claims to show how deceptive they are, how they fit into well-worn patterns, and why you shouldn’t be fooled.

That said, the book does offer one piece of dietary wisdom, but sadly it’s not the one most people are primed to hear. Moderation.  Period. Don’t eat too much.

Perhaps not a satisfying conclusion to some people, but perhaps that’s to be expected when you take all the religion out of eating.

Wednesday, July 01, 2015

My QS Seattle Talk: Cholesterol and my Microbiome

My presentation at the July meeting of Quantified Self Seattle, with more details about the A/B experiment I wrote about on the uBiome blog.


As always the best part of these presentations is the question and answer period, and the mingling that happens long after the formal talk. I met several people who gave me their own microbiome data right on the spot, and I was able to quickly analyze them with my uBiome tools.

One of the attendees told me about his own potato starch experiments and how it had dramatically improved his sleep, contrary to what I found for myself. The difference, we discovered, is in amounts: he uses only a teaspoon a day, much less than the 2-4 tablespoons I had been trying. I can’t wait to try a smaller dose to see if I can get the same great effect.

Monday, June 29, 2015

My QS15 Slides

Here’s the presentation I made at the Quantified Self Conference in San Francisco last week. It doesn’t include audio, but the full text of the transcript is embedded in the notes.

All presentations at this year's conference were on a strict timer: each slide was displayed for exactly 15 seconds, in PowerPoint's automatic mode, so there was no way to go back if you missed something or rambled too long. Although that helped focus the talks and ensured everyone was well-prepared, in my case somebody's unattended cell phone started blaring about a minute into my presentation. It was very distracting and normally a speaker would need to acknowledge the interruption so the noisemaker could be silenced, but the 15-second rule required that I plod on. Hopefully when the audio is released in a few weeks, the noisy phone won't be audible, though it unfortunately meant the audience probably missed key parts of the presentation.

Anyway, I was honored to be the final Show and Tell talk, featured in the closing plenary, where I was proud to offer a small tribute to my QS mentor Seth Roberts.

Saturday, June 27, 2015

Inside Cell Block 7

Signs all over said leave your cell phone in the car, so I have no photographic evidence, but we spent our morning at the Cell Block 7 Prison Museum near Jackson, Michigan. It’s a working state correctional facility but they operate a museum in an unused wing. You can visit the prison yard, see the cells and the place where they eat, look at an exhibit of confiscated weapons, everything.

It was especially interesting to talk to a former guard, a retired guy who likes to spend his Saturdays volunteering as a docent.  He says that although the guards were outnumbered about 80 to one, they typically walk through the prison and interact one-on-one with prisoners and after working there a while, the inmates and guards become pretty friendly with one another.  The New York prison escape is in the news, so we asked and he says it can only have been possible if there was widespread corruption among the staff. All the other prisoners must have known the details of the escape while it was being planned. It’s just a thing among prisoners that they all get to know one another, there are no secrets, and there are no snitches.

Yes, homosexual activity is extremely common. Especially if you’re a young, white man, he says, you will certainly be a target, and you may as well just get used to it. In the showers, in the laundry room — the guards just can’t watch everyone all the time. The prisoners repeat over and over that they’re not gay, it's just something they all need to do.

You should have see the clever weapons and other confiscated contraband.  Plenty of sharpened screwdrivers, spoons, scissors, etc, but other things too: one guy even made a working set of walkie-talkies. Some of the prisoners had TV sets in their cells, which apparently is completely okay as long as it was purchased in the prison store.

From the upper level of the museum cell block, you could look out over the entire facility and see current inmates walking to and fro. I think Michigan must be fairly progressive in its policies (they banned capital punishment in 1846) because the prisoners are all kept busy, on everything from making license plates to growing trees. They have one big rule, though: no prisoner can earn money or be assigned a non-cleanup job, unless they pass their GED.

It feels good to be tough on crime, to think it’s okay for prisons to be cruel places where they get what they deserve, but you need to remember that many of these inmates are fundamentally good people who just made a mistake.  I imagine what it must be like to have your own son or brother in jail, and how you’d want the place to be fair to him. Sixty percent of those who are released end up coming back to prison, partly because there are so few things they can legally do on the outside. Many of them study for business degrees, intending to start their own businesses, like landscaping or home repair. Many of them end up in food service, as cooks, waiters, dish washers, etc.

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