According to a new study,
Fewer than 20% of cancer trial results are published in peer-review journals. . . Industry-sponsored trials only achieve publication one time in 20.
A new website hopes to increase visibility of clinical trials. Publication bias is one reason a method that allows you to see for yourself — self-experimentation — has value.
I just googled “ morning banana diet” and got only a thousand hits. Surely that will change. It is the most popular diet in Japan right now, so popular, Mark Schrimsher of CalorieLab told me, that “You can’t buy bananas in Japan now. It’s crazy. We found some little green ones and some really expensive ones, but the rest are sold out.” Fytte, a woman’s health magazine, has covered it three months in a row. Three books have been written about it.
Like the Shangri-La Diet, it derives from (a) self-experimentation by (b) someone who was not a weight-control expert and (c) was spread by the Internet.
A cartoon.
You probably know that plastics were first used for toys. You probably don’t know that the first metals were used by artists, as far as archeologists can determine. That’s material science, what about non-material science? Here’s Tyler Cowen:
I’ve been thinking of all those old puzzles where a bunch of guys enter the room and only so many of them have smudges on their foreheads and you have to find the algorithm to reveal that information.
The problem is to separate good banks from bad banks, so that good banks can continue business. A big reason I started self-experimentation was Martin Gardner’s Mathematical Games column in Scientific American. I could sometimes solve Gardner’s made-up puzzles, which gave me confidence when a non-made-up puzzle — waking up too early — came along.
More When I pointed this post out to Tyler, he replied, “Exactly what I was thinking in fact, when I wrote that…I even almost mentioned Martin Gardner.”
If you look up vegetarianism in Wikipedia, you’ll find references to several health “concerns”. You won’t find anything about trouble at high altitudes. However, a friend of mine went on a high-altitude camping trip and found himself feeling terrible, with symptoms of altitude sickness. He later learned, when everyone reconvened, that two others in the group of 30 had had similar troubles. All three were vegetarians. They’d done fine on hikes at lower altitudes. None of the other 27 were vegetarians. The correlation makes sense because vegetarians are often much lower in iron — a component of hemoglobin, which transports oxygen — than non-vegetarians.
The interesting question for me is: What can we do with such data? It’s obviously useful, but where does it go? Not in a scientific paper, obviously. In a letter to the editor? Of what journal?
I guess this is from a press release:
John M. Pawelek, Ph.D., a senior research scientist in the department of dermatology at the Yale School of Medicine, recently was awarded a U.S. patent entitled Cosmetic Melanins for producing and composing synthetic melanins that may be used in cosmetic products.
Through its Office of Cooperative Research, Yale licensed the Melasyn technology originating in a medical school laboratory to Vion Pharmaceuticals, Inc. of New Haven. This month, Vion announced an exclusive world-wide licensing agreement with San-Mar Laboratories of Elmsford, NY., to manufacture and market products containing Melasyn.
Throughout nature, melanin is used in such diverse areas as protection from ultraviolet radiation, camouflage and species recognition. It is insoluble and difficult to work with, making it impractical for inclusion in creams and lotions. “But we have invented simple methods for creating melanin substitutes that dissolve readily in water and, when incorporated into cosmetic creams, can be spread evenly on the skin to instantly produce a tan,” Dr. Pawelek states.
In inventing this unique product, Dr. Pawelek employed one of scientists’ historical approaches to research: self-experimentation. “For nearly four years, I have been applying the material daily to my own face, and it produces such a natural-looking tan that it even surprises my dermatologist colleagues at Yale,” he quips. “Scarcely a day goes by when someone on an elevator or in a hallway doesn’t ask me where I was on vacation.”. . .
The Yale laboratory work behind the patenting and licensing offers interesting insight into the process of research and development of potential new products. “It started several years ago with our basic research on skin enzymes that produce melanin,” Dr. Pawelek explains. “Melanin usually is insoluble in water and forms a gummy solid in test tubes. One day, however, we noticed that the melanin in one enzyme assay remained dissolved in water,” he recalls.
Dr. Pawelek credits his colleague, Jean Bolognia, M.D., who conducts her research in his laboratory, with the idea for cosmetic use of melanin. If the melanin were really soluble, she surmised, it should be useful as a cosmetic. “From that point on,” he says, “we began a search for the right combination of ingredients and methods to produce cosmetic melanin.
“We were motivated by the thought that melanin naturally protects our skin from cancer induced by ultraviolet light. Perhaps, we reasoned, synthetic melanin would do the same,” he says. “If we could design a melanin that produced a natural-appearing tan, we believed that people might be attracted to the product through its cosmetic qualities and simultaneously apply a sun-protectant, affording them added sun protection and potentially reducing the incidence of sun-induced skin cancer,” hopes Dr. Pawelek, a cancer biologist who studies melanoma.
I often do something similar: Use an activity I want to do to motivate something I don’t want to do. Drink wine to take vitamin pills, for example.
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.
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.
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.
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?
Norway leads the world in frozen pizza consumption. “Why?” I asked the Norwegian who told me this. “We’re lazy,” she said.