Month: September 2008

Science in Action: Why Did I Sleep So Well? (part 15)

Seth Roberts6 Comments

Yesterday I went to San Francisco early in the morning. Because of my discovery about standing and sleep, I had slept very well. In Berkeley, it looked like morning: empty streets, angle of light. I felt jet-lagged: I should have been tired but I wasn’t. On BART, the same mismatch: Everyone looked tired but I was wide awake.

It is taking longer and longer to get enough one-legged standing to generate great sleep. Here’s a graph of how long I’ve been standing: Each point is a different bout of one-legged standing. Most of the points are from bouts where the standing leg was straight or bent (usually straight) but a few of them (“bent leg”) are from bouts where the standing leg was bent the whole time. Most days have two bouts: 1. On the left leg until I get tired. 2. On the right leg until i get tired. I’m pretty sure there’s no effect until it becomes difficult — until the muscles are so stressed that they send out a grow signal. The whole thing is pleasant because I watch TV or a movie at the same time but, as the graph shows, it has become seriously time-consuming.

So I have tested keeping the standing leg always bent. I get tired much sooner (2 minutes versus 20 minutes) but the effect is not quite as strong. Probably because fewer muscles are involved — you use more muscles when you stand on one leg in any possible way than if you stand on one leg in only one way.

I assume there’s a steady-state solution. The more muscle you have the more you lose each day. (Just as the theory behind the Shangri-La Diet assumes that the higher your set point, the fast it falls.) Eventually I should have enough muscle and will lose enough in one day so the exercise needed to merely replenish it will be enough to produce great sleep.

How Could Epidemiologists Write Better Papers?

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Inspired by Andrew Gelman’s posting of his discussion of a paper, here is a review I recently wrote of a omega-3 epidemiology paper. The shortcomings — or opportunities for improvement — I point out are so common that I hope this will be of interest to others besides the authors and the editor.

This is an important paper that should be published when the analysis is improved. The data set analyzed was gathered at great cost. The question of the relationship between omega-3 and *** [*** = a health measure] is very important and everyone would like to know what this data set has to say about it.
That said, the data analysis has many problems [= opportunities for improvement]. Most of them, perhaps all of them, are very common in epidemiology papers, I realize. Here are the big problems:

1. No figures. The authors should illustrate their main points with figures. They should use lowess — not straight lines — to summarize scatterplots. The relationships are unlikely to be linear.

2. Failure to transform their measures. Every one of their continuous variables should be transformed to be roughly normal or at least symmetrical before further analysis is done. It’s very likely that this will get rid of the outliers that led them to treat a continuous variable (omega-3 consumption) as a categorical one.

3. What was the distribution of *** scores? How did this distribution vary across subgroups? If the distribution isn’t normal — and it probably is far from normal — then a transformation might greatly improve the sensitivity of the analysis. Since the distribution is not shown the reader has no idea how much sensitivity was lost by failure to transform.

4. Pointless analyses. It is never explained why they separately analyse EPA and DHA; that is, no data are given to suggest that these two forms of omega-3 have different effects. Rather than analyse separately EPA and DHA they should simply analyze the sum. Nor is there any reason to think that fish consumption per se — apart from its omega-3 content — does anything. (At least I don’t know of any reason and this paper doesn’t give any reason.) Doing weak tests (fish, EPA alone, DHA alone) dilutes the power of the strongest test (EPA + DHA).

5. Failure to test the claim of interaction. I don’t mind separate analyses of large subgroups but if you say an effect is present in women but not men — which naive readers will take to mean that men and women respond differently — you should at least do an interaction test and tell readers the result. (You should also provide a graph showing the difference.) Likewise if you are going to claim Caucasians and African-Americans are different, you should do an interaction test. Perhaps the results are different for men and women because *** — and if so there may not be an interaction. Finding the relationship in women but not men has several possible explanations, only one of which is a difference in the function relating omega-3 intake to ***. For example, men might have more noise in their omega-3 measurement, or a smaller range of omega-3 intake, or a smaller range of ***, and so on. The abstract states “the associations were more pronounced in Caucasian women.” The same point: When the authors state that something is “more” than something else, they should provide statistical evidence for that — i.e., that it is reliably more.

6. It is unclear if the p values are one-tailed or two-tailed. They should be one-tailed.

7. It is unclear why the data are broken down by race. Why do the authors think that race is likely to affect the results? Nowhere is this explained. Why not stratify the results by age or education or a dozen other variables?

8. The authors have collected a rich data set — measuring many variables, not just sex and race — but they inexplicably do a very simple analysis. If I were analyzing these data I would ask 2 questions: 1. Is there a relation between EPA+DHA and ***? This is the question of most interest, of course, and should be answered in a simple way. This is a confirmatory analysis. 2. Getting some measure of that relationship, such as a slope, I would ask how that slope or whatever is affected by the many other variables they measured, such as age and so on. This is an exploratory analysis. There are no indications in this paper that the authors understand the value of exploratory analyses (which is to generate new ideas). Yet this is a good data set for such analyses. To fail to do such analyses and report the results, positive or negative, is to throw away a lot of the value in this data set.

9. The single biggest flaw (or to be more positive, opportunity for improvement) is losing most of the info in the *** measurements by dichotimizing them . . . .

It would also be nice if epidemiologists would stop including those “limitations” comments at the end of most papers. They rarely say something that isn’t obvious.

Life Imitates Art School

Seth Roberts4 Comments

I had lunch with Lisa Goldberg, an adjunct professor in the Statistics Department at Berkeley. Her application area is finance. She said that people in finance have at least as much contempt for academics as academics do for people in finance. Thorstein Veblen, of course, wrote about the latter — people looking down on useful work — but not the former. Perhaps his views were skewed by being an academic himself. I blogged earlier about how students in each major at a San Francisco art school look down on the students in some other major.

Lisa also said she sleeps well. I was surprised — hardly anyone says that. It turns out she exercises heavily. She swims or runs seven days a week and when she swims, she swims 2000 meters. As a former swimmer, I know that’s a lot. When I exercised, there was no clear effect on my sleep, apart from falling asleep faster. I still woke up too early in the morning. Maybe I wasn’t exercising enough. Anyway, it’s one little data point supporting my conclusions from standing on one leg.

Chocolate is Good For You (part 3)

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A new study in the Journal of Nutrition:

Dark chocolate contains high concentrations of flavonoids and may have antiinflammatory properties. We evaluated the association of dark chocolate intake with serum C-reactive protein (CRP). The Moli-sani Project is an ongoing cohort study of men and women aged 35 y randomly recruited from the general population. By July 2007, 10,994 subjects had been enrolled. Of 4849 subjects apparently free of any chronic disease, 1317 subjects who declared having eaten any chocolate during the past year (mean age 53 ± 12 y; 51% men) and 824 subjects who ate chocolate regularly in the form of dark chocolate only (50 ± 10 y; 55% men) were selected. . . . The European Prospective Investigation into Cancer and Nutrition FFQ was used to evaluate nutritional intake. After adjustment for age, sex, social status, physical activity, systolic blood pressure, BMI, waist:hip ratio, food groups, and total energy intake, dark chocolate consumption was inversely associated with CRP (P = 0.038). When adjusted for nutrient intake, analyses showed similar results (P = 0.016). Serum CRP concentrations [geometric mean (95% CI)] univariate concentrations were 1.32 (1.26—1.39 mg/L) in nonconsumers and 1.10 (1.03—1.17 mg/L) in consumers (P < 0.0001). A J-shaped relationship between dark chocolate consumption and serum CRP was observed; consumers of up to 1 serving (20 g) of dark chocolate every 3 d had serum CRP concentrations that were significantly lower than nonconsumers or higher consumers. Our findings suggest that regular consumption of small doses of dark chocolate may reduce inflammation.

These findings, like previous epidemiology of chocolate, suggest that ordinary dark chocolate produces these benefits. You don’t have to process the chocolate in special ways or preserve it in special ways. Mars, the company behind Cocoavia, a line of chocolate products that emphasizes health benefits, makes the opposite claim:

Like green tea and red wine, cocoa beans contain naturally occurring compounds called flavanols that scientists believe help promote blood flow, circulation and a healthy heart. But traditional cocoa processing often [emphasis added] destroys these natural compounds. After years of research, the makers of Dove® Brand Chocolates have perfected a breakthrough Cocoapro® process, the only patented process that retains high levels of the flavanols found naturally in cocoa.

Well, how often is “often”? And what fraction of the flavanols are destroyed by ordinary processing?

More on the benefits of chocolate: Part 1. Part 2.

Food versus Nutrients

Seth Roberts4 Comments

A few years ago, I learned that persons who apply to the Chez Panisse Foundation for funding are warned by staffers not to use the word nutrition in their applications — Alice Waters hates that word. A more nuanced version of this attitude was expressed in Michael Pollan’s In Defense of Food. Supposedly we should eat food (= choose our food using food names and categories) rather than nutrients (= choose our food according to nutrient content). Here is Marian Nestle, the prolific and influential NYU professor, on the subject:

Q: How do nutritionists feel about Michael Pollan’s idea in “In Defense of Food” that we should be eating food, not nutrients?

A: I can’t speak for all nutritionists, but my guess is that we are all jealous of how well he writes. But look around you. Except for people in hospitals who are fed intravenously, I don’t know anyone who eats nutrients. Everybody I know eats food.

When I give lectures in Australia or India, as I did last year, I see people eating food – all kinds of food. In Australia, I went to a Chinese restaurant one night and sampled kung pao kangaroo. In India, I ate dosas every chance I got. I never gave the nutrient content of those foods a single thought.

“Everybody I know” indeed. Our understanding of vitamins comes from nutrition research that, contra Waters, Pollan and Nestle, focused on nutrients rather than food. This research has been enormously beneficial, mainly among the poor and institutionalized. From a review article about Vitamin A:

By 1992, most large-scale mortality prevention trials and at least 3 measles treatment trials [in poor countries] were completed. A meeting convened at the Rockefeller retreat in Bellagio reached consensus that vitamin A deficiency increased overall mortality, particularly from measles; improving vitamin A status would reduce overall mortality; and treating children already ill with measles with high-dose vitamin A was an effective means of reducing their risk of complications and death. This “Bellagio Brief,”published widely, helped draw attention to the importance of vitamin A. . . . National programs of varying effectiveness have been launched in over 70 countries and vitamin A “coverage” is now one of the core health indicators published annually in the State of the World’s Children. By UNICEF’s estimate, over one-half a billion vitamin A capsules are distributed every year, preventing 350,000 childhood deaths annually. . . . The World Bank lists vitamin A supplementation as one of the most cost-effective of all medical interventions.

This isn’t esoteric knowledge.

Science in Action: Why Did I Sleep So Well? (part 14)

Seth Roberts10 Comments

Two more people have gotten results similar to mine. From a comment on an earlier post:

I’ve been doing these exercises – standing on one leg – and it’s helped my sleep immensely. About a year ago, I went through a pretty traumatic experience that disrupted my sleep patterns. The end result was that I couldn’t sleep for longer than 3 or 4 hours at night without waking up. For several months, the lack of sleep was like living in a nightmare, and prescription drugs just made the problem worse. I finally decided to go off medication all together and change my attitude, which worked wonders – I could get back to sleep after I woke up – but I’d still only sleep in 4 hour chunks.

About a month ago, I began doing these exercises, and now I’m sleeping 6 to 7 hours at a time. It’s amazing; and on the days I don’t do them, I don’t sleep well at all.

It’s amazing how easy they are to do – if I find myself standing in line, meeting friends for a happy hour, or even watching tv, I’ll do them.

Last night I told a friend to do them while he was at a happy hour, and this morning, he said he slept “like a log.”

As Pale Fire says:

If on some nameless island Captain Schmidt
Sees a new animal and captures it,
And if, a little later, Captain Smith
Brings back a skin, that island is no myth.

I have started to measure my sleep with a SleepTracker so I will have another way to measure the effects, in addition to (a) how rested I feel when I awake and (b) how long I sleep.

More The SleepTracker — my second, the first didn’t work — worked correctly for the first three nights but failed on the fourth.

Park(ing) Day in Berkeley

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Park(ing) Day was today. The first Park(ing) Day was in 2005. You celebrate it by turning a parking place into a park — as in the verb to park. In North Berkeley, around lunchtime, I came across a dozen Landscape Architecture grad students sitting around a long table full of food that filled up two parking places on Shattuck Avenue (a busy street). My big question was where the tables came from — that seemed like the hard part. From Wurster Hall (where the Landscape Architecture Department is). They invited me to join them and the whole thing was so interesting I couldn’t resist.

The food was very good. One person brought tomatoes, broccoli, cucumbers, and purslane picked that morning from his garden. Someone else brought homemade salsa.

You might think you could lay claim to a parking spot by putting money in the meter. Not in Berkeley. A parking cop came by and wondered what was going on. Someone had reported “a picnic,” the cop said. The cop left. Twenty minutes later he returned. Apparently there had been discussion about how to handle this. The ruling was you need a permit. Parking places are for cars, said the cop. Feeding the meters wasn’t enough. The cop gave the students 15 minutes to leave. At that point I left.

Do Genes Matter for Health?

Seth Roberts6 Comments

How much disease do genes cause? Sure, they cause some rare diseases that affect very few people but what about major health problems, such as depression, that affect everyone? The notion that genes make a big difference to human health — that some people are healthy and others sick because of genetic differences — was much of the rationale for funding the human genome sequencing project, which cost billions. The founders of the company 23andme (23 = 23 human chromosomes) often say genes matter, most recently in The New Yorker:

“It’s very useful if you know that you’re at increased risk for deep-vein thrombosis and you’re on a plane,” she continued. “You might want to stay vigilant about moving around.” Instead of finding out the hard way that their children are allergic to peanuts, parents may someday be able to test their DNA. Even small inherited traits, Avey added, can serve as health clues: “There is some correlation between your ability to metabolize caffeine and your risk for a heart attack.”

There is something breathtaking in the fact that someone who believes you can learn about allergies by studying DNA is taken seriously in The New Yorker.

Some rare non-hype on this issue has recently come from Dr. David Goldstein:

But David B. Goldstein of Duke University, a leading young population geneticist known partly for his research into the genetic roots of Jewish ancestry, says the effort to nail down the genetics of most common diseases is not working. “There is absolutely no question,” he said, “that for the whole hope of personalized medicine [where people with different genes are treated differently], the news has been just about as bleak as it could be.”

The researchers have been unable to find genes that make much difference.

If they had found such genes, I would have been stunned. My self-experimentation has led me to believe that our environments are far from ideal — in non-obvious ways. I believe that people don’t get sick because of their genes, or gene-by-environment interactions, they get sick because of their environments, which lack something essential or include something bad. Animal experiments have given us a decent understanding of nutrition; maybe we know half or more than half of the basic requirements. When it comes to subjects that don’t lend themselves to animal experiments, little is known — about what causes depression, for example. My self-experimentation took over where animal experiments left off; it provided a way to do experiments that generate ideas. (Which is crucial for knowledge advancement, as opposed to career advancement.) I have been able to find one big self-experimental effect after another (most recently, about omega-3s and sleep) related to common health problems only because (a) so little was known and (b) I accidentally picked up an effective tool (self-experimentation) that no one else had used this way (to find new experimental effects).

More More from the other side of the debate: 1. Elderly genetics. 2. Google co-founder has Parkinson’s gene. It is hard to find support for my side of the debate in print. It isn’t easy to notice when you don’t get sick (because of advances in the study of nutrition, for example) so it isn’t easy to notice how study of the environment has paid off in concrete ways. I’m in an unusual position: I can easily notice how my life has improved via self-experimentation.

Even more Dean Ornish agrees with me. Thanks to Carl Willat.

Treadmill Desks

Seth Roberts11 Comments

As far as I know, I was the first person to have a treadmill desk. I wanted to be able to stand more easily. I had found that if I stand a lot I sleep better. I reasoned it might be easier to stand a long time if you are walking than if you are standing still.

Treadmill desks are now becoming mildly popular, the New York Times reports. I had nothing to do with this. They were popularized by James Levine, a Mayo Clinic endocrinologist, who believes that calorie burning is a good way to lose weight. I used my treadmill desk for a few years. There were two big problems: 1. The noise bothered my neighbors. The Times article says these desks tend to be placed in common areas, where that would be less of a problem. 2. It was tiring. After one or two years I mainly stood on it and rarely walked on it. Finally I replaced it with a standing-height desk.

The article describes non-weight-loss benefits: Walking makes it easier to concentrate.

“I thought it was ridiculous until I tried it,” said Ms. Krivosha, 49, a partner in the law firm of Maslon Edelman Borman & Brand.

Ms. Krivosha said it is tempting to become distracted during conference calls, but when she is exercising, she listens more intently.

“Walking just takes care of the A.D.D. part,” she said.

Allen Neuringer, a professor of mine at Reed College, found that movement helped him learn. I think an urge to be active builds up during inactivity just as thirst builds up when we don’t drink. Being able to be active while you work gets rid of that distraction — and no doubt is healthier in other ways than sitting all day. I would like to be able to use a computer while I am free to move around the room (or larger spaces) and move my arms, not just walk forward with my hands on the keyboard. I’d like to be able to write this blog post while strolling through my neighborhood, for example.

Thanks to Marian Lizzi.